From 89999ddeb39dd0ae02b3d0380a3b49cdf2817483 Mon Sep 17 00:00:00 2001 From: Eniatorudabo Abomaye Date: Sat, 1 Apr 2023 11:34:44 +0100 Subject: [PATCH] Revert "adding deleted test_align file back" This reverts commit 916ef67dfc1494eb576a457fda99c2645b8bbdf2. --- "an\357\200\272hbond-analysis-update" | 59969 ---------------- .../analysis/encore/clustering/affinityprop.c | 8714 --- package/MDAnalysis/analysis/encore/cutils.c | 6404 -- .../stochasticproxembed.c | 6929 -- package/MDAnalysis/coordinates/timestep.cpp | 19857 ----- package/MDAnalysis/lib/_augment.cpp | 26847 ------- package/MDAnalysis/lib/_cutil.cpp | 28266 -------- package/MDAnalysis/lib/c_distances.c | 32752 --------- package/MDAnalysis/lib/c_distances_openmp.c | 8462 --- package/MDAnalysis/lib/formats/cython_util.c | 23148 ------ package/MDAnalysis/lib/formats/libdcd.c | 33912 --------- package/MDAnalysis/lib/formats/libmdaxdr.c | 33593 --------- package/MDAnalysis/lib/nsgrid.cpp | 29962 -------- package/MDAnalysis/lib/qcprot.c | 10244 --- .../MDAnalysisTests/analysis/test_align.py | 586 - 15 files changed, 329645 deletions(-) delete mode 100644 "an\357\200\272hbond-analysis-update" delete mode 100644 package/MDAnalysis/analysis/encore/clustering/affinityprop.c delete mode 100644 package/MDAnalysis/analysis/encore/cutils.c delete mode 100644 package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c delete mode 100644 package/MDAnalysis/coordinates/timestep.cpp delete mode 100644 package/MDAnalysis/lib/_augment.cpp delete mode 100644 package/MDAnalysis/lib/_cutil.cpp delete mode 100644 package/MDAnalysis/lib/c_distances.c delete mode 100644 package/MDAnalysis/lib/c_distances_openmp.c delete mode 100644 package/MDAnalysis/lib/formats/cython_util.c delete mode 100644 package/MDAnalysis/lib/formats/libdcd.c delete mode 100644 package/MDAnalysis/lib/formats/libmdaxdr.c delete mode 100644 package/MDAnalysis/lib/nsgrid.cpp delete mode 100644 package/MDAnalysis/lib/qcprot.c delete mode 100644 testsuite/MDAnalysisTests/analysis/test_align.py diff --git "a/an\357\200\272hbond-analysis-update" "b/an\357\200\272hbond-analysis-update" deleted file mode 100644 index 49bed797cf1..00000000000 --- "a/an\357\200\272hbond-analysis-update" +++ /dev/null @@ -1,59969 +0,0 @@ -commit 4086defb873b279d9637cfbf79257e7a0f185ec0 (HEAD -> numpy.testing-function-change, origin/numpy.testing-function-change) -Author: yickysan -Date: Sat Mar 25 09:45:11 2023 +0000 - - changed argument from relative tolerance to absolute tolerance in numpy.testing.allclose - -commit 9c116315d946b44a55be972e7ecb0409d6952bbd -Author: yickysan -Date: Sat Mar 25 09:16:37 2023 +0000 - - made changes to the functions that failed the tests - -commit 0d7bfd4b90626c1e43dc39a552493a78b79dc53c -Author: yickysan -Date: Fri Mar 24 19:42:50 2023 +0000 - - changed comparisons of scalars to use pytest.approx function and comparison of arrays to use numpy.testing.assert_allclose function - -commit 09b8b16f9066f715df6f31c0bced67f83662c15d -Author: Ahmed Salah <72524423+AHMED-salah00@users.noreply.github.com> -Date: Thu Mar 23 18:03:31 2023 +0200 - - fudge_factor and lower_bound for AtomGroup.guess_bonds (#4059) - - * Fixes #2395 - * Added fudge_factor and lower_bound args to the AtomGroup.guess_bonds - method and the Universe class constructor - * Added tests for fudge_factor and lower_bond attributes in test_universe.py - -commit 9c84981e1f005dff57de577d2b6532be96a83f23 -Author: Irfan Alibay -Date: Thu Mar 23 14:46:53 2023 +0000 - - Update linters.yaml (#4088) - - * update event trigger type for darker_lint - -commit 72e3cdb26560d3cba074aaf7f675453da32969aa (origin/develop, origin/HEAD, develop) -Author: Domenico Marson -Date: Wed Mar 22 20:55:46 2023 +0100 - - Fix for NetCDF files with no time (#4074) - - * attempt to deal with netcdf without time - - * NetCDF update - - * edited to my real name - - * time is now setted based on frame index - - * added the tests for cpptraj netcdf trajs - - * shrinked the cpptraj traj test files - - * if time is not set, use default time assignment - - * rely just on one traj instead of two - - * made the linter happyer - - * removed unnecessary commented code - - Co-authored-by: Irfan Alibay - - * renamed misnamed method - - Co-authored-by: Irfan Alibay - - * Update testsuite/MDAnalysisTests/coordinates/test_netcdf.py - - Co-authored-by: Irfan Alibay - - * Update package/CHANGELOG - - Co-authored-by: Irfan Alibay - - * Update testsuite/MDAnalysisTests/datafiles.py - - Co-authored-by: Irfan Alibay - - * Update test_netcdf.py - - * fixed and improved dt checking - - * warn the user about missing time - - --------- - - Co-authored-by: Irfan Alibay - -commit cf8d5cecb18625833712d9176eedf2ef5e86f9d5 -Author: Irfan Alibay -Date: Tue Mar 21 00:13:44 2023 +0000 - - fix permissions entries (#4083) - -commit 49ed0d79901f7fb08248540cd410b38d83173ca6 -Author: Irfan Alibay -Date: Mon Mar 20 00:24:59 2023 +0000 - - Try to fix issue with darker lint bot falling over with PRs from forks (#4081) - - * switch to pull_request_target with locked down permissions - -commit c452da746865e2e4104c32e3bcbd29aea215781c -Author: Irfan Alibay -Date: Wed Mar 15 22:45:39 2023 +0000 - - Move darker information to a PR comment instead (#4067) - - Expands the Daker GH action - * Action no longer fails if the linter fails - * Action now creates a PR message which points authors to read the outcomes of the linter - * Message mentions that if flake8 does not fail then this is all purely informative - -commit dd234c101829f79c21ad21a511a9af04d7cc691c -Author: Jennifer A Clark -Date: Wed Mar 15 18:21:31 2023 -0400 - - Gyration_moments method / allow shape parameters to yield per residue quantities (#3905) - - * Added gyration_moments method which allows shapre parameters to yield per residue quantities - - * Update docs for gyration tensor - - * Bugfix in topologyattr - - * Added test for codecov - - * Update added/changed version - - * Update Changelog - - * Response to review - - * Bug fix - -commit ec2f2c010b9659aa090de60d203d83d919744a62 -Author: Irfan Alibay -Date: Wed Mar 15 10:38:58 2023 +0000 - - Add readthedocs preview action (#4069) - -commit c742a4cfb2c2b025214f63a6e8783710c0217947 -Author: xhgchen <110699064+xhgchen@users.noreply.github.com> -Date: Mon Mar 13 14:11:15 2023 -0600 - - Fix doctest for MDAnalysis.core.groups (#3925) (#4062) - - Towards #3925 - * Fix doctest for MDAnalysis.core.groups (#3925) - * Add imports to asunique() examples - * Fix code logic for ag*.ix in unique() and asunique(): change expected array to specify dtype=int64 - * Add imports to unique() examples - -commit f984e8e6052e39103acd805fbadf7211f1a697a8 -Author: Irfan Alibay -Date: Mon Mar 13 20:05:49 2023 +0000 - - Add xfail on randomly failing 32bit-windows h5md test (#4068) - - * add 32bit xfail on commonly failing h5py test - * remove duplicate test_slice method in h5md - -commit ac96a656c10bb298a75b3582f77c45ab8c5c6ae0 -Author: xhgchen <110699064+xhgchen@users.noreply.github.com> -Date: Thu Mar 9 15:00:56 2023 -0700 - - Add tests for exception raise in PSA (closes #4036) (#4037) - - * Add tests for exception raise in PSA (per issue #597) - - * Towards #597 - * Checks that get_num_atoms in PSAnalysis and Path raises a ValueError - and displays "No path data" - - * Fix linting issues and add to AUTHORS - - * Fix comments for clarity - - * Make fixture for Universe and add paths tests - - * Make universe1 = mda.Universe(PSF, DCD) a fixture - * Add similar tests to raise ValueErrors for get_num_paths - and get_paths - * Reorganize tests under class TestPSAExceptions - - * Remove trailing whitespace - - * Collapse tests into one test - - * Add and revise comments for clarity - - * Update CHANGELOG - -commit 55a5abdfd8876c33e795aa3b9aa09de43ba15287 -Author: Jan Domański -Date: Sun Mar 5 13:15:16 2023 +0000 - - fix: get_writer errors if filename is none (#4043) - - * fix: get_writer errors if filename is none - -commit 2cad39e5c784c9c89e6b2c41d186fe1bf1a7f222 -Author: ooprathamm <89736193+ooprathamm@users.noreply.github.com> -Date: Sat Mar 4 00:21:34 2023 +0530 - - Fix doctest for MDAnalysis.analysis.psa (#4035) - - * Updated imports - * Moved to Python 3 compatible code - * Updated reported numerical results - -commit 79e0c860ca560f2b9d2677fcf71593226691a9db -Author: Jonathan Barnoud -Date: Thu Mar 2 14:36:02 2023 +0100 - - Support TPR files produced by gromacs 2023 (#4052) - - * Add test TPR files for gromacs 2023 - - * Allow tpx version 129 - - These files are produced by gromacs 2023. Note that we only allow the - tpx version here. We do not implement any of the changes to the tpr - format. - - * Update changelog to account for TPR 129 - - * Update the documentation to account for tpx 129 - -commit 6fc901f7561215c4f035ab339c4c02ae44cd18e1 -Author: MoSchaeffler <104832726+MoSchaeffler@users.noreply.github.com> -Date: Wed Mar 1 22:40:09 2023 +0100 - - resolved Issue #4026 (PR #4049) - - * fix #4026 - * fixed syntax error in h-bonds example docs - (added missing brackets in the package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py documentation) - * added @MoSchaeffler to contributors - -commit de6d0a896fabb22a7e2815a177bb264ae7222131 -Author: Vishal Parmar -Date: Wed Mar 1 01:33:59 2023 +0530 - - Updated test_encore.py (#4032) - -commit 4e3ea0eb5c177ff8521d2cf3a3ea4a883e226ba4 -Author: Irfan Alibay -Date: Mon Feb 27 18:51:44 2023 +0000 - - Update gh-ci.yaml - -commit c215a8e7ab1a327f61818506c0994decbd1f01ee -Author: Irfan Alibay -Date: Fri Feb 24 16:38:07 2023 -0800 - - [CI] Update main ci components to use py311 at upper limit (#4034) - - * update main ci components to use py311 at upper limit - - * update numpy pins - -commit c8c806d4d0cd97393098aa81f706fee918e8f570 -Author: chrispfae <116820495+chrispfae@users.noreply.github.com> -Date: Fri Feb 24 23:16:15 2023 +0100 - - Fix doctest for MDAnalysis.analysis.encore.similarity (#4021) - - * Fix doctest for MDAnalysis.analysis.encore.similarity - * part of #3925 - -commit 7a7bcdcad58e6e1dbe9166cfc3ccf59c92b5a93a -Author: ooprathamm <89736193+ooprathamm@users.noreply.github.com> -Date: Tue Feb 21 23:43:55 2023 +0530 - - [doc] Resolving doc index issue. (#4011) - - * fix #3998 - * Resolving doc index issue where module members showed up in the sidebar toc - * Updates sphinx conf.py to prevent automodule members from being included in toctree - (Note that sphinx > 5.2.0 changed to automatically including members of automodules sphinx-doc/sphinx#10804; - we disable the behavior globally but one could also disable locally with the toctree `:titlesonly` flag, see - https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html#directive-toctree ) - -commit 508ed968512272238e9de7792a48ffcac59145b6 -Author: BFedder <80363742+BFedder@users.noreply.github.com> -Date: Mon Feb 20 22:51:30 2023 +0000 - - Fix: EDRReader fails when reading only one step (#4030) - - * fix single frame read error - - * new test now only runs with pyedr installed - - * Update package/MDAnalysis/auxiliary/EDR.py - - Co-authored-by: Rocco Meli - - * Apply suggestions from code review - - Co-authored-by: Irfan Alibay - - --------- - - Co-authored-by: Rocco Meli - Co-authored-by: Irfan Alibay - -commit b71fccc7f90db47edb882d7362817b7f48146afc -Merge: d27a32abe 290fcf3b8 -Author: Tyler Reddy -Date: Mon Feb 20 08:36:28 2023 -0700 - - Merge pull request #4033 from MDAnalysis/fix-cirrus - - [CI] Fix cirrus - -commit 290fcf3b88344dc6db4b1ec295cbd940c8b5c82c -Author: Irfan Alibay -Date: Mon Feb 20 15:08:05 2023 +0000 - - Update .cirrus.yml - -commit d27a32abe39cc950a3943f3c1a03340f86c22a4a -Author: Hugo MacDermott-Opeskin -Date: Wed Feb 15 14:31:51 2023 +1100 - - Add distopia! (#3914) - - * add starrt of calc_bonds - - * refactor to use distopia inplace API - - * add in upcast - - * actually return the distances - - * distopia to ci - - * add initial docs - - * move to using _run backend - - * add upcast back in - - * fix yml CI files - - * change test_pairwise_dist to use allclose rather than equals - - * change another test to sue assert allclose - - * improve docs - - * change distance tests to use distopia backend - - * split numpy compliance test - - * changelog - - * fix merge issue in changelog - - * add note on varying precision to docs - - * Update testsuite/MDAnalysisTests/lib/test_distances.py - - Co-authored-by: Irfan Alibay - - * add warning for triclinic boxes - - * darker - - * add second importlib try block - - * return callable or ndarray - - * Revert "return callable or ndarray" - - This reverts commit 56e5091576c42363d4ab08395fd97ca0057f272c. - - * change docs on default - - * start of stub - - * Update package/MDAnalysis/lib/distances.py - - Co-authored-by: Irfan Alibay - - * add align - - * WIP on stub - - * finalise distopia stub - - * change calc_bonds to use distopia stub - - * fix type annotation - - * darker - - * darker distances.py - - * try to make black happier again - - * fix distances.py again - - * finally fix everything - - * fix versionchanged - - * remove try except - - * Update package/MDAnalysis/lib/distances.py - - Co-authored-by: Irfan Alibay - - * finalise merge - - --------- - - Co-authored-by: Hugo Macdermott - Co-authored-by: Irfan Alibay - -commit 94904b5608f4e7ac5b18cad1ccfbfd2e7082fca7 -Author: BFedder <80363742+BFedder@users.noreply.github.com> -Date: Mon Feb 13 22:52:45 2023 +0000 - - Added copy method for AuxReaders (#3887) - - * fix #1785 - * Added a copy method for AuxReaders to make them and Universes that have them copyable. - * Added tests to make sure all currently implemented AuxReaders (XVG, XVG-File, EDR) are copied properly - - Co-authored-by: Irfan Alibay - -commit f5efa422f25caca5d6fe575ff444c9c68ca79520 -Author: MeetB7 -Date: Mon Feb 13 12:02:53 2023 +0530 - - MDAnalysis.analysis.rms.rmsd docs fixed version entries (#4022) - - * fix #4014 - * fix MDAnalysis.analysis.rms.rmsd docs version error - * Updated AUTHORS - * Updated CHANGELOG - -commit e8cebb25fa80209befa47d3e5c0e03f5502c9766 -Author: ooprathamm <89736193+ooprathamm@users.noreply.github.com> -Date: Mon Feb 13 05:35:04 2023 +0530 - - Fix doctest for MDAnalysis.core.topology (#4024) - - * Adds missing imports in docstrings in MDAnalysis.core.topology - * solves failing darker_lint - * Part of #3925 for MDAnalysis.core.topology - - Co-authored-by: Pratham Chauhan - -commit b928ff1dcad8e0733b5385a2cf95a2a3288a7b7c -Author: ooprathamm <89736193+ooprathamm@users.noreply.github.com> -Date: Mon Feb 13 02:14:46 2023 +0530 - - filtering warnings (#4010) - -commit 096f79998f1612f08dcb4b30ba419b0aa90f55b8 -Author: Irfan Alibay -Date: Mon Feb 6 20:16:24 2023 +0000 - - Fix deprecated numpy dec import issue (#4018) - -commit d49b9cbab39effb608f3447d3ab20f148198b6d6 -Author: chrispfae <116820495+chrispfae@users.noreply.github.com> -Date: Wed Feb 1 00:52:10 2023 +0100 - - Fix doctest for MDAnalysis.analysis.rms (#3925) (#4009) - - Towards #3925 - * Fix doctest for MDAnalysis.analysis.rms (#3925) - * Add name to AUTHORS and CHANGELOG - -commit c7c5f0a6850d7f63b14b7697134c4cf7dd860fb9 -Author: Irfan Alibay -Date: Mon Jan 30 19:19:21 2023 +0000 - - Set expected list of elements for Parmed PSF test (#4016) - - Fixes #4015 - * fix expected list of elements for Parmed PSF test - -commit d73523f93c53338d8365dac98ffc1615c097d3be -Author: Jennifer A Clark -Date: Mon Jan 23 23:03:08 2023 -0500 - - Add dipole and quadrupole calculation in AtomGroup (#3842) - - Add dipole and quadrupole calculation in AtomGroup (#3842) - - Co-authored-by: Irfan Alibay - Co-authored-by: Hugo MacDermott - -commit f966ec2a2d3d6c1a53ec0e63f10a0acad6ee51bc -Author: Irfan Alibay -Date: Fri Jan 20 16:27:23 2023 +0100 - - Increase minimum numpy version to 1.21 (#3983) - - * Increase minimum numpy version to 1.21 - * ndarray to npt.NDArray typing for various MDAnalysis.lib modules - -commit 130e86276ab1ef6dca70ee6698f8e42da324e399 -Author: Irfan Alibay -Date: Fri Jan 20 12:56:41 2023 +0100 - - Add doctest step to docs build (#3997) - - * move linters to separate CI file - * don't run darker on merge - * add doctest to docs building step - * CI actions invoke use-mamba not uses-mamba - -commit 0696e11e084177432e0cbfafd12adb2df1e98789 -Author: Manuel Nuno Melo -Date: Fri Jan 20 11:54:51 2023 +0000 - - Fix duplicate test in lib/test_util.py (#4000) - - * Fix duplicated test_check_weights_raises_ValueError in test_utils.py - -commit b36bebac27b4d08ddf08e501e14a0cd83cbae3cc -Author: Irfan Alibay -Date: Fri Jan 13 06:44:43 2023 +0100 - - Switch to miniforge to avoid current failures (#3995) - - * Switch to miniforge to avoid current failures - -commit 363037a31d2eb208540c0f255d4aaf8e1944cf4b -Author: Hugo MacDermott-Opeskin -Date: Mon Jan 9 04:02:05 2023 +1100 - - Fix MSD docs issue in error metric (#3992) - - * fix #3991 - * fix error in msd docs - * update changelog - -commit f1b18e94003337b4994fd322c9dc021c66b9a1e3 -Author: Irfan Alibay -Date: Fri Jan 6 23:25:11 2023 +0100 - - remove deprecated attributes from nucleicacids results classes (#3982) - - * fix #3961 - * Remove deprecated times and direct indexing from the results dictionaries of the nucleicacids classes - * remove deprecated attributes from nucleicacids results classes - * updated docs - * make linter happy - -commit 08cf96f819ede893c810264535defce692903254 -Author: Mikhail Glagolev -Date: Fri Jan 6 11:19:57 2023 +0300 - - Add 'PairIJ Coeffs' section to the list of sections in LAMMPS parser (#3959) - - * Add 'PairIJ Coeffs' section to the list of sections in LAMMPS parser. This ensures correct processing of LAMMPS data files - - * Updating AUTHORS and CHANGELOG - - * Adding a simple test - - * Revert "Adding a simple test" - - This reverts commit 383423f9622196dd49a1fe7535f8e724ce37dbd4. - - The test needs to be integrated into the test_lammpsdata.py - instead of a separate script, and the sample datafile needs - to be placed in the appropriate directory. - - * Adding test for LAMMPS PairIJ Coeffs file to test_lammpsdata - - * Revert "Adding test for LAMMPS PairIJ Coeffs file to test_lammpsdata" - - This reverts commit 8269b2013dfb5a5f03decbd7655a5afe42b0881b. - - * Adding the zipped test datafile and class - - * Implementing requested changes - - * Bugfix to pass the tests; adding whitespace to pass darker lint - - * Bugfix - - * Merging - - * Remove a duplicate record due to a merging mess - - * Fixing the format - - * Fixing the PEP8 violation - -commit 8d430734270bed98faac5a4b2417350dcbf7c5b7 -Author: Irfan Alibay -Date: Wed Jan 4 18:59:41 2023 +0100 - - Fix nightly NumPy cron job, add numpy 1.25-dev0 fixes (#3977) - - * Fix cron jobs against nightly wheels - * Address incompatibilities with NumPy 1.25 changes in streamlines and streamlines_3d - -commit d67b4f1e65bb471e748836c7bb273a896efeccf4 -Author: German P. Barletta -Date: Tue Jan 3 22:56:47 2023 +0100 - - Add pickling of Atom, Residue, Segment and groups. (#3953) - - Add reduce() method to both ResidueGroup and SegmentGroup - Change _unpickle() so it can create any kind of group from its indices. - Add one test for each group in the parallelism section. - -commit 0c4f823a457fd9ca91c25e41b318b3b2d0c582d8 -Author: Irfan Alibay -Date: Fri Dec 23 12:56:33 2022 +0000 - - histogramdd normed argument replaced by density (#3976) - - * histogramdd normed argument replaced by density - * pin numpy for 32bit in azure pipelines - -commit d8526ff96edc2c6dff15b0e09f64dc186dbb3498 -Author: Irfan Alibay -Date: Tue Dec 20 00:08:09 2022 +0000 - - Start 2.5.0-dev0 (#3974) - -commit c815614b5ae8ed86eaa0d68e10451fde7e72242b (tag: release-2.4.1) -Author: Irfan Alibay -Date: Sat Dec 17 16:08:12 2022 +0000 - - Pre-release 2.4.1 + fix pyproject.toml version pins (#3971) - -commit 80619b7652c1a958bd6af2e77b6352d3ebdf8b3d -Merge: c620b141f 80bb3377a -Author: Oliver Beckstein -Date: Fri Dec 16 10:59:32 2022 -0700 - - Merge pull request #3966 from MDAnalysis/start-2.5.0 - - Start 2.5.0-dev0 - -commit c620b141f018628356bb9cdd16eefa640b6080ba (tag: release-2.4.0) -Author: Irfan Alibay -Date: Fri Dec 16 14:26:14 2022 +0000 - - Add pdbx and txt files to packagedata (#3968) - -commit 80bb3377ae7fa4218392bf6e3a4e24043f5239c1 -Author: IAlibay -Date: Fri Dec 16 13:07:31 2022 +0000 - - Start 2.5.0 - -commit 74c6b91d40e26daf5d4f75415939a5250e546c6a -Author: Irfan Alibay -Date: Fri Dec 16 09:36:10 2022 +0000 - - move readme to dynamic (#3963) - -commit 2af50b8f7728e780323cbe5a70d8ff021263137f -Author: Irfan Alibay -Date: Fri Dec 16 01:06:32 2022 +0000 - - Tie off release 2.4.0 (#3960) - -commit 5e4dea3857aeccd2116ca1f30d2c3fb56bcc5175 -Author: Irfan Alibay -Date: Fri Dec 16 01:05:22 2022 +0000 - - Deprecate nucleicacids pair distances results in favour of results.pair_distances [Issue 3744] (#3958) - - Fixes #3744 - * Deprecated `times` and indices based results - * Remove populating of times separately from the main class - * Add comments to remove deprecations in 2.5.0 - -commit 4e544712e3fe3acfa6a303f221ee7390d71dc69a -Author: Hugo MacDermott-Opeskin -Date: Fri Dec 16 11:14:58 2022 +1100 - - Add more detail to DCD timestep deprecation message (#3957) - - * Add link to DCD timestep deprecation issue in warning message - Co-authored-by: Irfan Alibay - -commit b3b907bb2284570496e6e6b6f4022901ca807a3c (upstream/issue-3404) -Author: Irfan Alibay -Date: Thu Dec 15 18:23:46 2022 +0000 - - Towards PEP621 (#3528) - - Fixes #3526 - * Add PEP621 compliance to main MDAnalysis package - * Limitations: tests currently not available due to issues with using `version` as package pin for MDAnalysisTests - -commit 1f48778308816d476654e6cfd578909025f473a6 -Author: Hugo MacDermott-Opeskin -Date: Fri Dec 16 03:33:31 2022 +1100 - - Add a reader for TNG files using pytng (#3765) - - Fixes #3237 and partially addresses #865 (reading TNG) - * Add TNG reader - - Co-authored-by: Oliver Beckstein - Co-authored-by: Irfan Alibay - -commit 8886efafd9cb4f34cd4fc2f3f04b0bcf9ab59ee5 -Author: Irfan Alibay -Date: Sun Dec 11 18:11:53 2022 +0000 - - Add Darken action to check for pep8 violations in diffs (#3954) - - * Adds darken+flake8 action to lint PRs - -commit 526cdd52043713791518c70897bf08f7b7b9ecce -Author: Hakarishirenai <118894598+Hakarishirenai@users.noreply.github.com> -Date: Sun Dec 11 05:49:23 2022 +0530 - - Calc_dihedral docstring updated (#3956) - - * fix #3936 - * Calc_dihedral docstring updated - * Author, Changelog & Docstring Updated - -commit 4c9108b0cc89368fadb613cf77d4f8a021c61858 -Author: Irfan Alibay -Date: Fri Dec 9 19:06:55 2022 +0000 - - Replace deprecated pytest.warns(None) (#3952) - - * Replace deprecated pytest.warns(None) - -commit 10b0a917ad7ab2177b6bcc2e2967fa7e6ad5a06f -Author: Irfan Alibay -Date: Fri Dec 9 12:05:18 2022 +0000 - - bump up azure and gh CI to py3.11 (#3903) - - Towards #3878 - * bump up gh CI to py311 - * Add rdkit to azure pipelines - * Fix cibuildwheels to add py311 - * bump up windows minimum numpy version - * Add 3.11 to testpypi checks - -commit a05a5245042361fd4fa27f03993f34cee2cda901 -Author: Oliver Beckstein -Date: Thu Dec 8 14:45:32 2022 -0700 - - deprecate sequence_alignment() and replace deprecated Bio.pairwise2 with Bio.Align.PairwiseAligner (#3951) - - * deprecate align.sequence_alignment for removal in 3.0 - - add deprecation - - test for deprecation warning - - combined tests for sequence_alignment in a class for easier removal - - update CHANGELOG - * replaced deprecated Bio.pairwise2 with Bio.Align.PairwiseAligner - - fix #3950 - - engineered return tuple as namedtuple to functionally match - the originally returned pairwise2.Alignment; we only documented - a tuple as return type anyway - * use biopython >= 1.80 feature for updated alig.sequence_alignment() - * additional docs for sequence_alignment() - (The docs show how one should write code if/when we deprecated this function.) - * update CHANGELOG - - Co-authored-by: Irfan Alibay - -commit 3712439b418f2910ebac9233c5b5cdc0732bead0 -Author: Jennifer A Clark -Date: Wed Dec 7 06:44:54 2022 -0500 - - Hbond update (#3848) - - Fixes #3847 - - Changes made: - * Added warning when distance or angle cutoffs produce zero hbonds to clarify a returned value of NaN - * Guess_donor uses bonding information when available since it calls hydrogen types anyway - * If resnames or names are not available, atom types are used. This is inclusive to LAMMPS users - * Change min max constraints documentation to use exclusive bound language - - Co-authored-by: Jennifer A Clark - Co-authored-by: Oliver Beckstein - Co-authored-by: Irfan Alibay - -commit dd92db83ac6533c39166c724c5425cbe0315a46d -Author: Irfan Alibay -Date: Fri Dec 2 14:15:53 2022 +0000 - - Attempting to unpin coverage (#3877) - - * Unpin coverage from CI - -commit bd0ab25401e9b30f8dc22e29d693e14f4862547d -Author: Irfan Alibay -Date: Wed Nov 30 15:23:56 2022 +0000 - - Update README.rst - -commit 6bc52ec2f0744cdf3c63a2e43aff232381ec4dd1 -Author: Hugo MacDermott-Opeskin -Date: Wed Nov 30 11:01:58 2022 +1100 - - Improve xdr cython (#3892) - - * incremental improvements to libmdaxdr - - * fix wrong dims - - * add boundscheck=False - - * slight improvement - - * move to module level decls - - * try read_direct - - * fix frame iteration - - * use direct read into array for trr - - * experimental trr read - - * Revert "experimental trr read" - - This reverts commit 943e6991153c92a22fffab81e50727ac54e0c9cd. - - * add pxd for libmdaxdr - - * make timestep fat - - * add explanation - - * change to xvf - - * add some notes - - * test branching on ts.positions in _read_next_timestep - - * add CHANGELOG - - * fix docs - - * add cdef - - * Update package/MDAnalysis/lib/formats/libmdaxdr.pxd - - Co-authored-by: Oliver Beckstein - - * fix inheritance - - * add read failure error - - * fix changelog - - * add to libmdanalysis - - * fix error code checking - - * Consolidate licenses across top directory, testsuite and package (#3939) - - * ensure that the same LICENSE file appears everywhere - * update CHANGELOG - - Co-authored-by: Oliver Beckstein - -commit 9e1953359397e9743770815c5520d712017493cb -Author: Irfan Alibay -Date: Tue Nov 29 21:23:03 2022 +0000 - - Consolidate licenses across top directory, testsuite and package (#3939) - - * ensure that the same LICENSE file appears everywhere - * update CHANGELOG - -commit d63cd6d21db7b56760eaa4ef93a02f3d158d97a3 -Author: Hugo MacDermott-Opeskin -Date: Wed Nov 30 08:04:46 2022 +1100 - - Improve libdcd cython (#3888) - - * Fixes #3882 and #3923 - * Improves the cython in the DCD reader to be more compiled. - * add annotate_cython setup.cfg option - * add types and fix is_periodic - * make int cast explicit - * change whence dict - * move DCD reader to no copy API and update tests accordingly - * add temporary buffer to DCD reader - * add module level directives - * pxdify libdcd: add new lib/formats/libdcd.pxd - * Add deprecation warning for `timestep` copying in DCDReader (Issue #3889) - * add DCD to public libmdanalysis API - * update tests - * update CHANGELOG - -commit 2d98ad54af78757c44d09af30d0ea0eb448f7d1c -Author: Hugo MacDermott-Opeskin -Date: Wed Nov 30 01:40:06 2022 +1100 - - Allow kwargs to be passed through in `universe.transfer_to_memory()` and `in_memory=True`` (#3938) - - Fixes #3684 - * pass kwargs to memoryreader on calling transfer_to_memory() and `in_memory=True` - -commit 5df4a550d5126e36d45f25fe03d5d6082ce4404d -Author: Tyler Reddy -Date: Thu Nov 24 17:27:38 2022 -0700 - - ENH: support pathlib ReaderBase (#3935) - - * allow the handling of `pathlib` objects - in `ReaderBase` - - * `NamedStream` gets special treatment (no string coercion) - in `ReaderBase` - -commit 497f45e23c834780f9ca172b3e4d4ad7602136bc -Author: Hugo MacDermott-Opeskin -Date: Sat Nov 19 11:52:17 2022 +1100 - - Add docs for libmdanalysis (#3922) - - * add docs for libmdanalysis - - * fix spelling error - - * add docs - - * add example - - * Apply suggestions from code review - - Co-authored-by: Oliver Beckstein - -commit fc9dee00b945a56f005b15406d40865f039f1fa6 -Author: Irfan Alibay -Date: Fri Nov 11 23:15:09 2022 +0000 - - Fix implicit optional (#3920) - - * fix implicit optional - * turn off cron CI on PR - -commit 6444031cecc3c5f1af0051227cd381e20d1a92f6 -Author: Hugo MacDermott-Opeskin -Date: Sat Nov 12 09:30:52 2022 +1100 - - Move libmdanalysis to lib (#3913) - - * move libmdanalysis to lib - -commit beb8aa1a3f253502b59ad104968b348be19fadbc -Author: Oliver Beckstein -Date: Fri Nov 11 15:15:34 2022 -0700 - - move changelog entry for #3845 to enhancements section (#3919) - -commit bb63135fada830fae83a0b446245bf4bdf399073 -Author: Hugo MacDermott-Opeskin -Date: Sat Nov 12 08:10:54 2022 +1100 - - Add timeseries for all readers (#3890) - - * Add timeseries for all readers - * Update empty asel to be ValueError rather than NoDataError - * Remove DCD timeseries NoDataError tests - - Co-authored-by: Irfan Alibay - Co-authored-by: Hugo Macdermott - -commit 345d5d2d25a68df8ffac213fc3fe8bba2c9ec374 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Nov 7 09:52:34 2022 +1100 - - Remove `pbc` kwarg from AtomGroup.wrap (#3910) - -commit dbf06bd0c88e699caf065738121a59f16b455eb2 -Author: Irfan Alibay -Date: Sun Nov 6 22:06:40 2022 +0000 - - Enabling pure python py3.11 cron CI and get Cirrus to py3.11 (#3879) - -commit 89d19d55349772be44a3e08eab8e54f586a3fd97 -Author: Rocco Meli -Date: Fri Nov 4 00:51:02 2022 +0100 - - [MAINT] Fix Cython linting issues (#3900) - - Fix the main Cython linting issues described in gh-3838 - -commit 398ac0b6139f3e7cab97253c6098b4a768c934af -Author: Irfan Alibay -Date: Tue Nov 1 19:48:18 2022 +0000 - - Update gh-ci.yaml - -commit db2b5e4929c616b45e57105e3e30cfa29247ac64 -Author: Hugo MacDermott-Opeskin -Date: Wed Nov 2 06:56:11 2022 +1100 - - Add deprecation warning for memoryreader inclusive indexing in timeseries. (#3894) - - * Add deprecation warning for memoryreader inclusive `stop` behaviour. - - Co-authored-by: Irfan Alibay - Co-authored-by: Oliver Beckstein - -commit 45d84612e8145e38d97e332b7e1e1b7c8f4f65a4 -Merge: c9685fb39 31b66c002 -Author: Tyler Reddy -Date: Wed Oct 26 13:07:19 2022 -0600 - - Merge pull request #3886 from MDAnalysis/fix-azure - - Fix 32bit azure - -commit c9685fb394dbca54e74e9c58e0afcf21e4cacccc -Author: Jake Fennick -Date: Wed Oct 26 10:56:29 2022 -0600 - - Fixed lockfile check when using a Docker read-only filesystem (#3832) - - Fixed lockfile check when using a Docker read-only filesystem - * Added OSError in addition to PermissionError - - Co-authored-by: Jake Fennick - -commit 2949af7145b56595540f929b237dc44a109e8dd0 -Author: Irfan Alibay -Date: Wed Oct 26 17:54:04 2022 +0100 - - fix EDR file packaging (#3885) - -commit 31b66c0025c4c9926e4503b9372bda72bfd7be76 -Author: Irfan Alibay -Date: Wed Oct 26 17:16:20 2022 +0100 - - tyler's version - -commit 463e52c0ba16339ddc94cf57714ecad36b7c02b2 -Author: Irfan Alibay -Date: Wed Oct 26 15:50:19 2022 +0100 - - Don't limit pyproject.toml NumPy support to known versions (#3871) - - * Update pyproject.toml to allow for undefined numpy versions for undefined python versions - -commit 5b2f447afc545d2b8b5cb158e1962bbce98b769f -Author: Jennifer A Clark -Date: Wed Oct 26 09:03:43 2022 -0400 - - Improve LAMMPS DUMP parser (#3844) - - * Add check in LAMMPS Dump Reader for velocities and forces - * Translate LAMMPS coordinates to range from zero to box length - * Add unwrap feature to LAMMPSDump - * Added LAMMPS test files reference in datafile.py - * Moved LAMMPSDUMP vel and force check with ATOM card parsing - - Co-authored-by: Hugo MacDermott-Opeskin - -commit 998a0203862b68457df4b49d410f8f523fc09fac -Author: Hugo MacDermott-Opeskin -Date: Wed Oct 26 16:53:25 2022 +1100 - - add annotate_cython setup.cfg option (#3884) - -commit b8911572e6260d260aa6a97b4ef9a3c18b0713e0 -Author: German P. Barletta -Date: Tue Oct 25 12:57:47 2022 -0300 - - Access hbonds results through new results member in count_by_ids() and count_by_type() (#3876) - -commit d67c1afb02023a9645abc3c853fe23875d108c70 -Author: Irfan Alibay -Date: Tue Oct 18 04:42:02 2022 +0100 - - Add missing init file for converters tests (#3867) - - * Add missing init file for converters tests - * fix pylint issues with test_rdkit - -commit a0fbddfd533e4b0d97ba6db551d9af9a6bceb15b -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Oct 18 14:06:00 2022 +1100 - - Add rmsip docs (#3868) - - * add rmsip docs - -commit df0a764e50462390c5a9171c6639d0f3a7599ed6 -Author: Irfan Alibay -Date: Mon Oct 17 22:12:42 2022 +0100 - - Add py311rc2 cron job (#3862) - -commit 512c024e43af40138439c4bebdc3acd68240d734 -Merge: 35248e87e da679b605 -Author: Tyler Reddy -Date: Wed Oct 12 14:44:14 2022 -0600 - - Merge pull request #3859 from MDAnalysis/azur - - Pin 32bit Windows Azure runner to 1.9.1 - -commit da679b605f587e075efd82b37cf6a1795fe1a190 -Author: Irfan Alibay -Date: Wed Oct 12 21:05:04 2022 +0100 - - add missing bracket - -commit ddcf78ab74d6ce42cbb1f5de8c56f22e4053472d -Author: Irfan Alibay -Date: Wed Oct 12 20:59:47 2022 +0100 - - switch to using pre main pip installs - -commit 5b4ac8868b885d133a051fc01a6b9b085f5b0cb1 -Author: Irfan Alibay -Date: Wed Oct 12 20:03:18 2022 +0100 - - Update azure-pipelines.yml - -commit 35248e87ec002c2e4d363680c77eb8a1cca8144a -Author: Jennifer A Clark -Date: Wed Oct 12 05:05:11 2022 -0400 - - Add decorator to check for empty atomgroup (#3839) - - * Added check to center_of_mass calculation that the AtomGroup is not empty - - * Response to PR request. - - * Added check_atomgroup_not_empty decorator and test for AtomGroups - - * Update package/MDAnalysis/lib/util.py - - Co-authored-by: Hugo MacDermott-Opeskin - - * check_atomgroup_decorator - - * Make PEP8 compliant - - * Update CHANGELOG - - Co-authored-by: Hugo MacDermott-Opeskin - -commit 81ed5d0073d5eae032790bb6ced7fc217e994d3a -Author: Irfan Alibay -Date: Sun Oct 2 15:39:51 2022 +0100 - - Fix duplicate authors (#3855) - - Remove duplicate author entry (Xiki Tempula == Zhiyi Wu) - -commit 5f77a54af49396d8007842f78cd32b5a224e6cfa -Author: Jennifer A Clark -Date: Fri Sep 30 23:10:31 2022 -0400 - - Add isolayer selection method (#3846) - - * Add isolayer selection method - - * Added test_isolayer assertion that comparison isn't with empty - - * Added author and docs - - * Isolayer: Fix documentation and removed unused code - - * Update CHANGELOG - - Co-authored-by: Hugo MacDermott-Opeskin - -commit fa8b03b210827e288bcdf5c77898f6a4faca1385 -Author: Aya Alaa -Date: Wed Sep 21 07:42:58 2022 +0200 - - adding element attribute to txyz parser (#3826) - - * adding element attribute to txyz parser - - * adding elements when names is valid only - - * update docstring and change log - - * Update TXYZParser.py - - * Update TXYZParser.py - - * Update TXYZParser.py - - * Update TXYZParser.py - - * Update TXYZParser.py - - * Update TXYZParser.py - - * Update TXYZParser.py - - * Update CHANGELOG - - * Apply suggestions from code review - - Co-authored-by: Jonathan Barnoud - - * Apply suggestions from code review - - Co-authored-by: Jonathan Barnoud - - Co-authored-by: Jonathan Barnoud - -commit 80ff64710c0dd4682bc1068772fca000d05327e0 -Author: Aya Alaa -Date: Tue Sep 20 10:12:09 2022 +0200 - - gussed_attributes and read_attributes methods unexpected behavior (#3779) - - * gussed and read attributes methods unexpected behavior - - the guessed_attributes and read_attributes methods of the Topology class doesn't behave as expected with bonds, dihedrals, angles, Impropers, and any other attribute object that have a list values for its is_guessed attribute. - - * Update topology.py - - * pep8 - - * pep8 - - * pep8 - - * empty is_guessed list errors - - resolving error that happened from an empty is_guessed list - - * Update test_topology.py - - * Update test_topology.py - - * Update test_topology.py - - * Update topology.py - - * Update CHANGELOG - - * fix pep8 styling - - * Apply suggestions from code review - - Co-authored-by: Jonathan Barnoud - - * Update CHANGELOG - - * Update CHANGELOG - - Co-authored-by: Jonathan Barnoud - -commit 22ceb5a61971240c27c33167accfef801f264a3e -Author: BFedder <80363742+BFedder@users.noreply.github.com> -Date: Tue Sep 20 00:14:21 2022 +0100 - - Add an AuxReader for EDR Files (#3749) - - * initial file created, test working on different computers - - * continued work - - * Minimum working system: EDRReader - - * Fixed typos, PEP8 - - * added pyedr to CI setup - - * EDRReader now fully functional in stand-alone use - - * Changed EDR so that base.get_description() works - - * Implemented tests for standalone use - - * Added pyedr to azure-pipelines.yml - - * addressed orbeckst's reviews, fixed test for datafiles.py - - * begin refactoring coordinates/base.py - - * further work on handling energy data - - * EDR Reader functionality complete - - * Added pyedr to maintainer/conda/environment.yml - - * PEP8 stuff - - * PEP 8 - - * improving coverage - - * further coverage improvement - - * added function for returning data from auxreader - - * modified CHANGELOG - - * Added type hinting - - * added documentation - - * Use List, Dict from typing to fix CI - - * Update package/MDAnalysis/auxiliary/EDR.py - - Co-authored-by: Irfan Alibay - - * Fixed Docstring for EDRStep class - - * pep8.... - - * addressing some of IAlibay's comments - - * Moved adding of aux data from coordinates/base to auxiliary/base - - * refined API overhaul and hopefully fixed CI, also now allowing None to add all data - - * Addressing reviewer comments - - * Apply suggestions from code review - - Co-authored-by: Irfan Alibay - - * fixed test for get_data - - * changed get_data docstring - - * added class attribute documentation to EDRReader - - * added memory usage monitoring - - * Memory warning now reports memory usage - - * Warning message changed from KB to GB - - * fixed parentheses escape by using r-string - - * updated CHANGELOG, added test for NotImplemented, pickle, etc. - - * removed asterisk option from attach_auxiliary() - - * Unit handling for EDRReaders - - * added TODO comments for issue 3811 - - * minor change to trigger GH Actions - - * added pyedr to requirements.txt and setup.py for cirrus - - * Added 'convert_units' kwarg to EDRReader __init__ - - * Documentation overhaul - - * went from 4810 warnings to 237 in like 7 lines of code - - * Add test for MDANALYSIS_BASE_UNITS, some doc work - - * revert from ResourceWarning to UserWarning - - * pep8 stuff - - * make pyedr optional and other IAlibay requests - - * PEP8 - - * changed changelog, docstring; used defaultdict - - * fixed CHANGELOG - - * Apply suggestions from code review - - Co-authored-by: Irfan Alibay - Co-authored-by: Hugo MacDermott-Opeskin - Co-authored-by: Oliver Beckstein - -commit dcb909506c6e0a561664881a682c7939a2404111 -Author: Irfan Alibay -Date: Thu Sep 15 14:01:55 2022 +0100 - - Rename wheel_cache_size to build_cache_size in asv.conf.json (#3829) - -commit e7ee5a4a077c2179d6037ba634240ce7ebcb76ef -Author: Uma Kadam <90750049+umak1106@users.noreply.github.com> -Date: Mon Sep 12 13:46:26 2022 +0530 - - Type hints for lib module (#3729) - - * Type hints for mdamath.py - - * fix errors in mdamath.py - - * changed input from NDarray to arraylike - - * Added type annotations to init.py - - Added type annotations to init to avoid mypy from raising errors when other modules are type checked . - - * Allowing mypy to type check lib module - - * Update changes in init.py - - * Update __init__.py - - * type hints for pkdtree - - * Fix all errros in pkdtree.py - - * Chage npt.NDArray to np.ndarray - - * Update pkdtree.py - - * Update pkdtree.py - - * Update pkdtree.py - - * Update NeighborSearch.py - - * Update NeighborSearch.py - - * Update pkdtree.py - - Co-authored-by: Jonathan Barnoud - -commit 0788165b99be47b0d2e05fe62db85351e9ac42ff -Merge: fc0403853 f8b359d5a -Author: Tyler Reddy -Date: Sat Sep 10 16:06:13 2022 -0600 - - Merge pull request #3823 from umak1106/patch-5 - - Annotations for init file - -commit f8b359d5a6d7257997a325a8c8d9960dcc53c22e -Author: Uma Kadam <90750049+umak1106@users.noreply.github.com> -Date: Sat Sep 10 09:52:32 2022 +0530 - - Annotations for init - -commit fc0403853eaf157fadba5a0760e748ee4242be94 -Author: Irfan Alibay -Date: Thu Sep 8 12:58:47 2022 +0100 - - Fix ARM runner issues (#3816) - - * Remove tkinter import - - * temporarily remove arm cron guard - - * Remove python tk install from cirrus file - -commit 93c0aac51c7b2fea8895b128abc42ba80d843348 -Author: Jonathan Barnoud -Date: Tue Sep 6 16:06:33 2022 +0200 - - Reduce warnings from Universe.empty (#3814) - -commit 311b93eee0fba4072fc713756389933f1d213615 -Author: Rafael R. Pappalardo <45312334+rafaelpap@users.noreply.github.com> -Date: Mon Sep 5 16:02:21 2022 +0200 - - Avoid using set operations in distances.between (#3807) - - Avoid using set operations in distances.between and test that an AtomGroup is always returned - - Co-authored-by: Irfan Alibay - Co-authored-by: Hugo MacDermott-Opeskin - Co-authored-by: Oliver Beckstein - -commit 4cdcd3f7b53d44cbe1281e51c80c1c424ca9e777 -Author: Hugo MacDermott-Opeskin -Date: Mon Sep 5 08:35:40 2022 +1000 - - Add a simple benchmark for bonds (#3806) - - * fix #3785 - * add a simple ASV benchmark for bonds, the full slice of bonds from the universe. - * update CHANGELOG for 2.4.0 - - Co-authored-by: Irfan Alibay - -commit 35ad3e85a18d41d6255ee9f1d477d8fc48243a1c -Author: Irfan Alibay -Date: Sun Sep 4 23:28:05 2022 +0100 - - Remove AMBER entry in extra_requires (#3810) - - * Remove AMBER entry in `extra_requires` - -commit cb6e4f50ad93aa7a32db7bc9c6d62c36ffaa1649 -Author: Guillaume Fraux -Date: Thu Sep 1 03:13:29 2022 +0200 - - Update Chemfiles tests for 0.10.3 (#3808) - - * Update chemfiles tests for 0.10.3 - - * Update package/CHANGELOG - - Co-authored-by: Irfan Alibay - - Co-authored-by: Irfan Alibay - -commit ba491be9d3d202b90e15f85450444528c4b24934 -Author: Hugo MacDermott-Opeskin -Date: Wed Aug 31 10:35:47 2022 +1000 - - Fix citation in calc_distances.h (#3805) - -commit 730ecf7b87738d43875672795d58caa13ee293da -Author: Irfan Alibay -Date: Wed Aug 31 00:37:26 2022 +0100 - - Start 2.4.0-dev0 (#3809) - -commit c56e8df543e1aba21959a7c7b3029eacd57d9130 (tag: release-2.3.0, tag: package-2.3.0) -Author: Irfan Alibay -Date: Mon Aug 29 20:02:51 2022 +0100 - - Pre release 2.3.0 (#3802) - - * complete changelog, don't forget lily - * bump up versions - -commit 0c2a8f6aee6cf2c2132ede603437644e1ca0ab1e -Author: Irfan Alibay -Date: Mon Aug 29 17:57:36 2022 +0100 - - Update test_chemfiles.py (#3799) - -commit 578d28be562d141b4148bbde94938af9b9f6669b -Merge: 97ec6df20 4da39dc00 -Author: Tyler Reddy -Date: Tue Aug 23 12:00:50 2022 -0600 - - Merge pull request #3780 from tylerjereddy/treddy_native_m1_ci - - CI: native M1 testing - -commit 97ec6df207fa934095ffb093daadf319ca2bfb38 -Author: Jonathan Barnoud -Date: Tue Aug 23 14:53:17 2022 +0200 - - Fix type annotations in lib.distances (#3787) - - * Fix type annotations in lib.distances - - A couple of type annotation in distances.py caused mypy to complain. - Most importantly, the check_coords decorator does some type wrangling - that is opaque to mypy. - - With this commit, distances.py does not yield any mypy error anymore. - - * Make pep8speaks happier - -commit 4da39dc0001a7802afcfd3f353575bb89925fd32 -Author: Tyler Reddy -Date: Sat Aug 20 10:03:15 2022 -0600 - - CI: native M1 testing - - * add native M1 MacOS testing to CI - with Cirrus CI: - https://cirrus-ci.org/guide/macOS/#macos-virtual-machines - - * there is no concurrency so just a single - job/Python version for now - -commit 6302b4c7d0dc3fbd57c1e85e5d6fd90efddd3fd8 -Author: hsadia538 -Date: Fri Aug 5 00:04:22 2022 -0700 - - Edited overview.rst (#3772) - - -Replaced term "pos" with "position" to reflect the correct example - -commit 7116d5e10d39cda98bc25766297e73933ea85f48 -Author: Irfan Alibay -Date: Wed Aug 3 08:26:01 2022 +0100 - - [CI] Update macos runners (#3771) - - * add macos-12, switch min to macos-11 - - * strings for py310 - - * openmm 7.7 py310 was pulled for macos - -commit cce5291cab0c7902cda6c0dc3a642ea4b417dd5e -Merge: b57b26ed8 65c6e0276 -Author: Richard Gowers -Date: Wed Aug 3 00:53:23 2022 -0500 - - Merge pull request #3751 from hmacdope/AtomGroupNSGrid - -commit b57b26ed874dfae72f79e4fcbec98b4fcfa85c65 -Author: hsadia538 -Date: Tue Aug 2 18:49:30 2022 -0700 - - Removed return of trajectory and universe in fixtures in test_distances.py (#3769) - - * Edited fixtures in test_distances.py - - -Removed trajectory return calls - -Universe fixtures return universe only now - -Edited tests and called trajectory where needed - - * Edited fixtures in test_distances.py - - -Removed trajectory return calls - -Universe fixtures return universe only now - -Edited tests and called trajectory where needed - - * Edited fixtures in test_distances.py - - -Removed trajectory return calls - -Universe fixtures return universe only now - -Edited tests and called trajectory where needed - - * Updated test_distances.py as per PEP8 checks - - * Updated Changelog - - * Updated CHANGELOG - - Added GitHub handle - - * Updated CHANGELOG - - Added username as contributor to release - -commit 86efe83d77209ef7c6c555a2370cd07589b64a50 -Merge: c3b03eaa8 b6c42c657 -Author: Richard Gowers -Date: Mon Jul 25 03:31:15 2022 -0500 - - Merge pull request #3724 from yuxuanzhuang/opt_topology_serialization - -commit c3b03eaa8c740f6a10ee091d9a99661194586b23 -Author: Estefania Barreto-Ojeda -Date: Mon Jul 25 02:28:09 2022 -0600 - - Updated references format to BibTex. (#3663) - - * References formatted in bibtex (uses new markup for citations): enabled BibTeX extension for sphinx - * updated references.bib and added/update references in analysis docs - * Added references and MDA style. - * Added pybtex-docutils, sphinxcontrib-bibtex to deps in CI - * Changed version of Sphinx to 4.5.0 - -commit b6c42c65703b068c1a40a3ec0fcddca193844c2e -Merge: 267dcb6e0 886cb60b3 -Author: Oliver Beckstein -Date: Mon Jul 25 01:22:58 2022 -0700 - - Merge branch 'develop' into opt_topology_serialization - -commit 886cb60b3fbdfe10468fd3853243e874c77608a8 -Author: Irfan Alibay -Date: Sun Jul 24 12:53:26 2022 +0100 - - Remove universal wheel creation from setup.cfg files (#3763) - -commit 91313882db7d12ba2f4de235696dc5096881a5f8 -Author: Yuxuan Zhuang -Date: Sun Jul 24 02:38:04 2022 +0200 - - Fix reading/writing CONECT records in PDB files with many atoms (#3670) - - * disable write conect with more than 100000 atoms - - * raise warning if conect is corrupt - - * add tests for conect - - * changelog - - * doc - - * move doc to parser - - * add new pdb to all - - * check every conect entry - - * changelog - - * move conect check forward - - * mapping instead of raw bug - - * changelog - -commit d5c7cb9a7807b06c169b418dd5c6c072c33580f5 -Author: Irfan Alibay -Date: Sat Jul 23 16:49:46 2022 +0100 - - Add formalcharge attribute and read/write them from PDB (#3755) - - * Add formalcharge attribute and read/write them from PDB - -commit 50b8fdb3b026fd98fe4f588028e24dce0364b013 -Author: Raymond Zhao <7199958+rzhao271@users.noreply.github.com> -Date: Fri Jul 22 01:38:53 2022 -0700 - - Modernize tests under converters and visualization (#3757) - - * Improve float testing for converters and visualization - -commit 65c6e02764d8e39452c2775d09a0f8e4802dc3f2 -Merge: 5483f6e0c dbda8ebe8 -Author: hmacdope -Date: Fri Jul 22 17:46:04 2022 +1000 - - Merge remote-tracking branch 'upstream/develop' into AtomGroupNSGrid - -commit dbda8ebe8bf3789016c1a62fbe0620b36ba1083e -Author: Hugo MacDermott-Opeskin -Date: Fri Jul 22 17:42:22 2022 +1000 - - Allow distance routines to accept an NumPy Array or AtomGroup [Core] (#3730) - - Allow distance routines to accept an NumPy Array or AtomGroup in one or both positions. - @check_distances can now also extract coordinates from an AtomGroup. - - Co-authored-by: Irfan Alibay - -commit 5483f6e0c9b06d7114e53248f83e46038af7c4a7 -Author: Hugo MacDermott-Opeskin -Date: Thu Jul 14 13:37:36 2022 -0500 - - pep8 again again - -commit 2ade0b35e4ffe0b6f5635305681606912f03b429 -Author: Hugo MacDermott-Opeskin -Date: Thu Jul 14 13:35:49 2022 -0500 - - pep8 again - -commit e435fd27705f4d11572c91acf8b1bd3b9758d4e5 -Author: Hugo MacDermott-Opeskin -Date: Thu Jul 14 13:28:12 2022 -0500 - - pep8 - -commit 3440c2d541a45578433bde58d510991dd3f2601a -Author: Hugo MacDermott-Opeskin -Date: Thu Jul 14 11:30:02 2022 -0500 - - pep8 - -commit 2236ccf41dff4e96d3cc70d563f46a7a17b9e231 -Author: Hugo MacDermott-Opeskin -Date: Thu Jul 14 10:21:04 2022 -0500 - - improve tests - -commit ebd9638960f1b34592dc48cc690a44214948d3a3 -Author: Hugo MacDermott-Opeskin -Date: Wed Jul 13 17:52:01 2022 -0500 - - refactor tests - -commit 7521957ac4eeee20c4acc6e51bf86e3091f673ce -Author: Hugo MacDermott-Opeskin -Date: Tue Jul 12 17:01:28 2022 -0500 - - add optional back onto return_distances - -commit 0ddccc20a7b588057b18b241d24f146ea4a80738 -Merge: 1e1e11b48 588f75399 -Author: Hugo MacDermott-Opeskin -Date: Tue Jul 12 16:43:03 2022 -0500 - - Merge branch 'Distances_AtomGroup_Array_v2' into AtomGroupNSGrid - -commit 1e1e11b4812249b7419eb5fd2523a874e53c38be -Author: Hugo MacDermott-Opeskin -Date: Tue Jul 12 16:37:46 2022 -0500 - - remove strange import - -commit d57dcfd5a53fdaecdea458944f4f5913a2f8257e -Author: Hugo MacDermott-Opeskin -Date: Tue Jul 12 16:23:41 2022 -0500 - - add in imports of type hints - -commit e4341000c513104e5154bbadbf37a7b0769f9c89 -Author: Hugo MacDermott-Opeskin -Date: Tue Jul 12 16:06:17 2022 -0500 - - change self_capped distances functions - -commit 42c002022b484c00f81cc9b5b0c37305e1508117 -Author: Hugo MacDermott-Opeskin -Date: Tue Jul 12 15:48:47 2022 -0500 - - type hinting and AtomGroup overloads - -commit 588f75399944558473003e5754e1e19044d93e7c -Author: Hugo MacDermott-Opeskin -Date: Mon Jul 11 14:10:35 2022 -0500 - - add typing future warning - -commit 626b45a41f64310dbb92ba44614076f0e32b78b5 -Author: Hugo MacDermott-Opeskin -Date: Sun Jul 10 10:45:30 2022 +1000 - - roll back to arr: np.ndarray typing - -commit 939aae48d862c6a6ff37c750613cc47eb5f86078 -Merge: 7d75c9b8d 2c32ed11c -Author: Hugo MacDermott-Opeskin -Date: Wed Jul 6 19:11:21 2022 +1000 - - Merge remote-tracking branch 'upstream/develop' into Distances_AtomGroup_Array_v2 - -commit 2c32ed11c1e6b800397f147e4242f7325900b669 -Author: Oliver Beckstein -Date: Wed Jul 6 01:58:40 2022 -0700 - - add h5py to setup.py's extra_requires (#3711) - - * add h5py to setup.py's extra_requires - - fix #3701 - - new 'extra_coordinates' target in extra_requires where we can - add pip-installable packages for additional formats that are not - installed by default - - keep minimum version of h5py at >= 2.1.0 - * minimum h5py >= 2.10 - - GitHub actions - - maintainer/conda/environment.yml for readthedocs - - Azure pipelines - * update extra_deps in setup.py - - include chemfiles>=0.10 in extra_formats - - added comment to remove AMBER in 3.0.0 - * updated CHANGELOG - * updated sklearn --> scikit-learn in setup.py - * deprecate extras_require "AMBER" target for 2.4 - - Co-authored-by: Irfan Alibay - -commit 7d75c9b8d4ab288e66d6e7f54b8b114e5467eddc -Author: Hugo MacDermott-Opeskin -Date: Wed Jul 6 18:24:58 2022 +1000 - - close some unclosed lines - -commit 11e04e57194d94bc3db21914d970f44e7b73a55a -Author: Hugo MacDermott-Opeskin -Date: Wed Jul 6 09:00:46 2022 +1000 - - Apply suggestions from IAlibay code review - - Co-authored-by: Irfan Alibay - -commit cf17d429b4693a39e325149691e4062a5b8a090d -Author: Irfan Alibay -Date: Tue Jul 5 08:42:30 2022 +0100 - - Increase numpy min version to match NEP29 (#3737) - - * Set numpy min version to 1.20 - * Set min numpy version for arm64-osx to 1.21 - * Set min numpy version for py3.10 to 1.21.6 - -commit f088887badcaca0900a66130dd0b14fcc5cc4019 -Author: hmacdope -Date: Thu Jun 30 10:00:16 2022 +1000 - - PEP8 again again - -commit 3b61689237ce27df6c9ce361900f3f12dc81ea0e -Author: hmacdope -Date: Thu Jun 30 09:58:24 2022 +1000 - - PEP8 again - -commit c3d81006cb8481f821670ee1955e2c4dda65d294 -Author: hmacdope -Date: Thu Jun 30 09:53:54 2022 +1000 - - PEP8 - -commit 085963f418cc77b2ef0e2668bef3f3d42afd95fc -Author: hmacdope -Date: Thu Jun 30 09:40:37 2022 +1000 - - line continuation for unreadable fixture - -commit d0e31a393e812227307debe9eb3825590c05980c -Author: hmacdope -Date: Thu Jun 30 09:38:14 2022 +1000 - - add implicit line continuation - -commit 1fa961959717c232425a7bd1bab02a7874dfb34b -Author: hmacdope -Date: Thu Jun 30 09:32:10 2022 +1000 - - change error to fstring - -commit c3e7361885fccb3baa4bd794b89093ebde44eec6 -Author: Hugo MacDermott-Opeskin -Date: Thu Jun 30 09:18:51 2022 +1000 - - Update testsuite/MDAnalysisTests/lib/test_distances.py - - Co-authored-by: Irfan Alibay - -commit 71076654d7ca0952db029e426ae9f5d2ed0b21bb -Author: hmacdope -Date: Wed Jun 29 21:38:31 2022 +1000 - - refactor distance test for 2x atomgroups to use fixture - -commit 9142cd42393ee80330bb333715a33f0144983e40 -Author: hmacdope -Date: Wed Jun 29 21:27:17 2022 +1000 - - remove reraise of TypeError on check_coords - -commit 267dcb6e0df1a0248cfb5ba7a10875cc3efe2ec9 -Merge: cd998c695 c01d82bb8 -Author: Richard Gowers -Date: Wed Jun 29 01:03:07 2022 -0700 - - Merge branch 'develop' into opt_topology_serialization - -commit ec1a1e943392896a1c81d43e6ce8d7cc90857bfe -Author: hmacdope -Date: Wed Jun 29 09:43:20 2022 +1000 - - restructure try-except in _check_coords - -commit 1416fc935d523e75c0a117806edd5d5a7595d17c -Author: hmacdope -Date: Wed Jun 29 09:32:17 2022 +1000 - - remove turtle import (how did it get there?) - -commit ecb81f48a72e2d228bedcc150c3a35dd8f97bd8b -Author: hmacdope -Date: Wed Jun 29 09:24:01 2022 +1000 - - space after comma in docstring of check_coords - -commit 4ba082854f7dacf7f53806c582f646a9c20764ab -Author: hmacdope -Date: Wed Jun 29 09:22:58 2022 +1000 - - add pragma nocover to type checking guard - -commit c01d82bb86b480c8b2ae87f36497e7fc0a726c84 -Author: Hugo MacDermott-Opeskin -Date: Tue Jun 28 17:35:49 2022 +1000 - - Rename libmda to libmdanalysis and clean up __init__.pxd (#3739) - -commit cbacaa15dcc2daec9836806f3d649370cf446835 -Author: hmacdope -Date: Tue Jun 28 17:33:27 2022 +1000 - - clean up formatting in check_coords - -commit f9f42e7ef89174524a14704066bee1da8a466f2b -Author: hmacdope -Date: Tue Jun 28 17:24:40 2022 +1000 - - move to duck typing over isinstance(AtomGroup) - -commit 53f70045aaba182c7c7603d377b08d558a8d13e8 -Author: hmacdope -Date: Tue Jun 28 13:25:35 2022 +1000 - - move to NumPy type hints - -commit 0e36bf32c7efd29a548f82a3344d587b1cd5e9e6 -Author: Irfan Alibay -Date: Tue Jun 28 01:09:07 2022 +0100 - - Pin back pytest-cov (#3736) - - * fix "internal errors" resulting from issues with newer versions of codecov and the - pytest coverage plugin with cython files - * see PR #3736 for comments, also PR #3713 for an example failure - * Pin back pytest-cov to <=2.10.1 and restrict coverage < 5.0 - * Remove extra coveragerc, try to enforce parallel argument - -commit 682f5e867447b0df29e8d08fca8a16cea35bd71f -Author: Tengyu -Date: Sat Jun 25 00:04:42 2022 +0800 - - add 0.5 for correct midpoints (#3713) - - * fix #3715 - * correct midpoints in HOLE plot_mean_profile() - * add and correct tests - * update AUTHORS - * Update package/CHANGELOG - - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - Co-authored-by: Oliver Beckstein - -commit 7124a3f5ea0ac3bfcd52eb62ff75dcd670790e08 -Author: hmacdope -Date: Fri Jun 24 14:11:56 2022 +1000 - - fix final pep8 - -commit df6e53a4d2f5da58132ce3f7ea2c157a8a5e25e4 -Author: hmacdope -Date: Fri Jun 24 14:05:34 2022 +1000 - - pep8 again - -commit b41a5aa17abd50615404003b254c915103d74e81 -Author: hmacdope -Date: Fri Jun 24 13:56:03 2022 +1000 - - PEP8 again - -commit 24129c00f5a680564da7ef9ec0eca3e1e6f755fa -Author: hmacdope -Date: Fri Jun 24 13:39:16 2022 +1000 - - PEP8 - -commit fb248648d8666dba5731c6f5529ab1f82ee7a95f -Author: hmacdope -Date: Fri Jun 24 13:23:18 2022 +1000 - - clean up apply_PBC - -commit abb9d3f83d131a5eb0d25c8ce384cdf4a0145ffa -Author: hmacdope -Date: Fri Jun 24 11:09:36 2022 +1000 - - remove extra test - -commit a694c56cbece0c8fd4cfadb3e1bb335986ce8d50 -Author: hmacdope -Date: Fri Jun 24 10:26:04 2022 +1000 - - remove code duplication in DistanceArray with parametrize - -commit 7b886a2535d8e6b98318bfc56201048b5c3d31d6 -Author: hmacdope -Date: Fri Jun 24 09:48:47 2022 +1000 - - parametrize noPBC - -commit ad2cce25b93332791c41d0c9f507dbdd04bcf862 -Merge: 5e1ec61c6 36bc5a62b -Author: hmacdope -Date: Fri Jun 24 08:37:43 2022 +1000 - - Merge remote-tracking branch 'upstream/develop' into Distances_AtomGroup_Array_v2 - -commit 36bc5a62b9d0da427dd4f21744f4e5dc1e67459d -Author: Rocco Meli -Date: Thu Jun 23 23:27:25 2022 +0100 - - Fix OpenMP backend for self_distance_array for triclinic boxes (#3728) - - Fixes OpenMP backend error for self_distance_array for triclinic boxes caused by #3706 - -commit cd998c695631fa25e1c9775841b2390904b28c11 -Author: Yuxuan Zhuang -Date: Thu Jun 23 21:19:05 2022 +0200 - - pep8 - -commit fe595b2e4f1c38d3b6925e8c867938875f88695f -Author: Yuxuan Zhuang -Date: Thu Jun 23 21:12:52 2022 +0200 - - test - -commit cbb8448d9e37a473f1cf5413f61b268f3399d188 -Author: Yuxuan Zhuang -Date: Thu Jun 23 21:09:43 2022 +0200 - - lazy build RA, SR - -commit c983609f1aa7fedc5417c61c306efba85f180740 -Author: Yuxuan Zhuang -Date: Thu Jun 23 20:00:31 2022 +0200 - - changelog - -commit 5e1ec61c6d0e30696873c93526425167f0643cd1 -Author: hmacdope -Date: Thu Jun 23 17:13:05 2022 +1000 - - fix wrong type hints - -commit 0fc971fdb10d0371191dac15724f7450102effb6 -Author: hmacdope -Date: Thu Jun 23 16:52:02 2022 +1000 - - whoops changelog - -commit 36bc1246d5212790189558e40092ca7e9c11654b -Author: hmacdope -Date: Thu Jun 23 16:50:11 2022 +1000 - - changelog - -commit e14210ebb91cd6fa7f46ece1649d37cb8b7d891c -Author: hmacdope -Date: Thu Jun 23 16:47:38 2022 +1000 - - fix classnames - -commit 57be4042bb200ec000d56fd25e99cde461c46fa5 -Author: hmacdope -Date: Thu Jun 23 16:32:58 2022 +1000 - - changes to test_util - -commit d2bd296ebbcaa453711fc894b3cd55bf3977f195 -Author: hmacdope -Date: Thu Jun 23 16:09:39 2022 +1000 - - add tests for unchanged input - -commit 1684eb7dbd66e3f34b6927273c4790b63bf1e322 -Author: hmacdope -Date: Thu Jun 23 15:34:27 2022 +1000 - - refactor some of distances - -commit bba17c7113081354284cf0ceacf80e43e72592f7 -Author: hmacdope -Date: Thu Jun 23 15:10:35 2022 +1000 - - apply PBC - -commit 6a909e694e69faaaf1426805bc507128d22197e6 -Author: hmacdope -Date: Thu Jun 23 14:44:29 2022 +1000 - - add atomgroup to apply_PBC - -commit 1a7536e3a19632dec3ca156ea6abc63e9669f6c1 -Author: hmacdope -Date: Thu Jun 23 13:59:42 2022 +1000 - - add allow_atomgroup option to @check_coords - -commit a19e23dbc28c64ec96fab0900716e47bc7539b6e -Author: hmacdope -Date: Thu Jun 23 12:07:58 2022 +1000 - - improve docs - -commit 19b6b383dd3206b6162ebef05366207f743a8b7f -Author: hmacdope -Date: Thu Jun 23 11:56:17 2022 +1000 - - improve docs - -commit 3b184d2c64eb5de7694e359ad4426c8bb2b5292a -Author: hmacdope -Date: Thu Jun 23 10:51:01 2022 +1000 - - add docs to dihedrals - -commit e11ef063b29348c6208383ca2a212852d6883393 -Author: hmacdope -Date: Thu Jun 23 10:43:15 2022 +1000 - - improve docs - -commit 74d02f29131a98059abbd671b014ff548554cda3 -Author: hmacdope -Date: Thu Jun 23 10:15:26 2022 +1000 - - add dihedral atomgroup tests - -commit 55da6abc84d7a591b06404c6e6f8da7a370762dd -Author: hmacdope -Date: Thu Jun 23 10:08:51 2022 +1000 - - move to atomgroup fixture - -commit 0fbef153ce4c491e6cbc2f41049d030806bd7abb -Author: hmacdope -Date: Thu Jun 23 10:00:10 2022 +1000 - - add atomgroup tests to calc_bonds - -commit 2d92bd39afdf5d2571ba6666e841c4874530ad2e -Author: hmacdope -Date: Thu Jun 23 09:59:39 2022 +1000 - - add type hints to calc_* - -commit af4bd22e846f39d7b78d46631b91c5a0bfe1335e -Author: hmacdope -Date: Wed Jun 22 17:19:21 2022 +1000 - - add test for mismatched ag sizes - -commit 849720252b8ea71053ac247dfcdeae53fd3b86c4 -Author: hmacdope -Date: Wed Jun 22 17:14:28 2022 +1000 - - add test for @check_coords - -commit c9849a3955c344ef1358836369d7e11dab1deabc -Author: hmacdope -Date: Wed Jun 22 15:09:48 2022 +1000 - - add note for openmp bug - -commit 8a0061c8e5ce230645744c6c1032e14533caf6a1 -Author: hmacdope -Date: Wed Jun 22 13:23:27 2022 +1000 - - identify that problem is with OpenMP backend - -commit 540e74d0c82108bc740a8294045dea58a7d552cf -Author: hmacdope -Date: Wed Jun 22 13:08:11 2022 +1000 - - add triclinic tests - -commit a7c420de3ffda19d282e79f35d6e8a44130b2091 -Author: hmacdope -Date: Wed Jun 22 10:49:31 2022 +1000 - - add tests for different boxes - -commit 5fe36e8024e389f647d5087ef1c449f09abf32af -Author: hmacdope -Date: Wed Jun 22 09:59:07 2022 +1000 - - remove two universes test from atomgroup_matches_numpy - -commit c3bd36257ce7af0d56f2d0467e1c0546846a0d84 -Author: hmacdope -Date: Wed Jun 22 09:43:35 2022 +1000 - - add more tests for AtomGroup distances - -commit 561d6c0fd5dbe5f1ce4adb41c71abe08b12568fc -Author: hmacdope -Date: Wed Jun 22 09:26:16 2022 +1000 - - add noPBC atomgroup test - -commit 03ed438cc5d5884188203129b0a1e1b4797e9ffe -Author: hmacdope -Date: Tue Jun 21 16:04:12 2022 +1000 - - add type hints and change docs for distance_array - -commit c7ff93989b1590086003512bfd4c2c30bf55f0b6 -Author: hmacdope -Date: Tue Jun 21 15:31:18 2022 +1000 - - add type hinting and versionchanged to self_distance_array - -commit 0c7e4de14770caa253b12f544aef890feed1d886 -Author: hmacdope -Date: Tue Jun 21 15:20:49 2022 +1000 - - add tests for atomgroup - -commit 932df2376ed698d1743d54cf3c4d59216ccb371d -Author: hmacdope -Date: Tue Jun 21 15:18:57 2022 +1000 - - add type hinting - -commit 90d35538d5e87448f0150a08596a94318e35a94c -Author: hmacdope -Date: Tue Jun 21 15:14:17 2022 +1000 - - @check_coords can now accept an AtomGroup - -commit d82a356e17fdeec56f6526a2d4623dacc6a62b4e -Author: Yuxuan Zhuang -Date: Mon Jun 20 00:30:27 2022 +0200 - - add missing start value test - -commit 1eb4794e09718784dd5f509759a4dbe27be1a3e9 -Author: Yuxuan Zhuang -Date: Mon Jun 20 00:24:20 2022 +0200 - - fix missing resid is 0 - -commit 71920b1cd9a60171bb2790fcc1ec5ed9abff17d3 -Author: Yuxuan Zhuang -Date: Sun Jun 19 23:51:22 2022 +0200 - - refactor topology serialization - -commit a2f9e9457175ac67185e397adc6c6ad67eb9bce0 -Author: Uma Kadam <90750049+umak1106@users.noreply.github.com> -Date: Wed Jun 15 00:24:21 2022 +0530 - - Type Checking in CI (#3705) - - * add mypy type hinting machinery and CI testing - -commit ec5da1de682322c436970252f03b5a24ea673113 -Author: Irfan Alibay -Date: Mon Jun 13 17:30:58 2022 +0100 - - Unpinning CI dependencies (#3503) - - * unpin coverage and pytest-cov in CI - -commit b302e40ee45831409b5641311ac51fc4db08e07a -Merge: d7e7276ef 2ca43d6ea -Author: Richard Gowers -Date: Mon Jun 13 07:37:37 2022 +0100 - - Merge pull request #3683 from hmacdope/CythonTimestep - - Cythonized Timestep [Core] - -commit 2ca43d6ea8fcbdbdd0fe7995171dd598a4f3dc3b -Merge: 182928160 d7e7276ef -Author: Richard Gowers -Date: Mon Jun 13 07:36:56 2022 +0100 - - Merge branch 'develop' into CythonTimestep - -commit d7e7276ef8583ef0a19268f42746d17bd8e1dbdc -Author: BFedder <80363742+BFedder@users.noreply.github.com> -Date: Fri Jun 10 16:52:05 2022 +0100 - - Fixed typos in Aux module docs (#3716) - -commit 0b3ba59d7a31d461593dfa83ef50b38f171ad9eb -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu Jun 9 15:20:57 2022 +1000 - - Update README.rst (#3712) - - This isn't rendering so well. - -commit 08824a86afc59f974fcd4c4d12ef9abdac7bf8fa -Author: Oliver Beckstein -Date: Wed Jun 8 17:57:35 2022 -0700 - - analysis.base updates (docs and logging) (#3710) - - - fix incorrect versionchanged for new frames argument for base.AnalysisBase.run() - - updated docs to conform to Style Guide - - additional logger.info output in run() when per-frame analysis starts - -commit 56cbf565883a6f654ede36ee23e7e9288c6b18bf -Author: Philip Loche -Date: Tue Jun 7 19:40:01 2022 +0200 - - Added a `norm` attribute to `InterRDF` classes (#3687) - - * Added `norm` attribute to rdf classes - - This PR adds a `norm` attribute to the two rdf classes - `InterRDF` and `InterRDF_s`. It works similar as the density - parameter which was only available for `InterRDF_s`. - - Also, the universe attribute in `InterRDF_s` is - deprecated because the universe can be accessed via - the AtomGroups. - - Finally, I slightly cleaned up the code and moved the - attributes within the classes themselves. - - * linting + fix docs (and use single backticks thoughout to refer to keyword arguments) - * Update CHANGELOG and bump version - * Add u deprecation to docstring - -commit 09957bc114af36bb5d9a00fd4ab8cb40f61d2da0 -Merge: 77d936600 4f7087f99 -Author: Richard Gowers -Date: Tue Jun 7 09:35:22 2022 +0100 - - Merge pull request #3706 from RMeli/openmp - - Remove OpenMP private clauses by narrowing variable scopes - -commit 182928160cc54c0c8cafc71193961026b9d5a2be -Author: hmacdope -Date: Tue Jun 7 09:41:19 2022 +1000 - - CHANGELOG - -commit c691ace115b83567077a972dd0e997957b2ea527 -Author: hmacdope -Date: Tue Jun 7 09:37:12 2022 +1000 - - add __getattr__ dunder back in - -commit 35c47727b7bfce3ce2de1b1ea2c5175ab3b8fd44 -Author: hmacdope -Date: Tue Jun 7 09:30:51 2022 +1000 - - remove __getattr__ special method - -commit 5631c33af26f7411e27e5f7b587b75d7bd5a7208 -Author: hmacdope -Date: Tue Jun 7 09:28:27 2022 +1000 - - remove dtype kwarg - -commit 352512758b5fa1f23d779a64a51c7170c565c845 -Author: hmacdope -Date: Mon Jun 6 12:17:45 2022 +1000 - - add alloc flags - -commit 93d63d6e38c02208ad736fdafb872a3ceb9b18f5 -Merge: 8c735b7a3 77d936600 -Author: hmacdope -Date: Mon Jun 6 10:17:56 2022 +1000 - - Merge remote-tracking branch 'upstream/develop' into CythonTimestep - -commit 8c735b7a3cf55afbb383ece6ab7e2d076ee92b63 -Author: hmacdope -Date: Mon Jun 6 10:10:15 2022 +1000 - - add test for __repr__ with and without a box - -commit 8b862bb9603cbcaf81aa4f8904b97c24431bcca4 -Author: hmacdope -Date: Mon Jun 6 10:09:54 2022 +1000 - - remove try except block for repr - -commit 92cad0ba740a0238ee2581917586a3db5e892c95 -Author: hmacdope -Date: Mon Jun 6 09:54:20 2022 +1000 - - add timestep API test for setting box to None - -commit af3337db17b59ef69be026468cccbe406dde44cf -Author: hmacdope -Date: Mon Jun 6 09:41:11 2022 +1000 - - add dtype tests - -commit 9fbf8d1686821d6adbee5d481a79b4fcb91e7fd8 -Author: hmacdope -Date: Mon Jun 6 09:22:13 2022 +1000 - - change isinstance __eq__ check to return NotImplemented - -commit 32e2a80340ee3ec3a5b5aaeeec96a1317bf39ad4 -Author: hmacdope -Date: Mon Jun 6 09:18:11 2022 +1000 - - remove __ne__ - -commit 95372bf41ff3b732763e2cb0de0e360e62dc1e2c -Author: hmacdope -Date: Mon Jun 6 09:17:58 2022 +1000 - - add header int64_t - -commit e2f18279435b7a343fa230827b818c426441943d -Author: hmacdope -Date: Mon Jun 6 09:06:56 2022 +1000 - - change BUG to NOTE for dtype - -commit 714c97c0c910ac3b899570871af8222bdb987116 -Author: hmacdope -Date: Mon Jun 6 08:51:19 2022 +1000 - - add and improve comments - -commit cee886026b8d069b8f0cd597595c618565332bd6 -Author: hmacdope -Date: Mon Jun 6 08:36:47 2022 +1000 - - remove header junk - -commit 4f7087f99f63b5a8f837be894a1027b051b25ca7 -Author: Rocco Meli -Date: Sun Jun 5 17:30:51 2022 +0200 - - fix openmp code - -commit 33d119cc7e0e534993c7af40537768a1df5de81c -Author: Rocco Meli -Date: Sun Jun 5 12:08:22 2022 +0200 - - remove omp private by reducing variable scope - -commit 77d93660070d846f40a3fcac6ef00d819ae89141 -Author: Irfan Alibay -Date: Fri Jun 3 10:09:18 2022 +0100 - - Fix awk call in deploy.yaml (#3694) - - * switch awk call - * fix erroneous changelog entry - - Co-authored-by: Oliver Beckstein - -commit d0be0e62e9001391fd1efa8a59f53dada5d90cb4 -Author: Irfan Alibay -Date: Thu Jun 2 23:12:04 2022 +0100 - - Start 2.3.0-dev0 (#3697) - -commit 0a1427cb5b13e60d86fc64a395a770e23d033580 -Merge: b89537e85 eab18cb84 -Author: Rocco Meli -Date: Wed Jun 1 21:59:37 2022 +0200 - - Merge branch 'MDAnalysis:develop' into develop - -commit eab18cb8418ddb1dd72b44f474833de4a2999884 (tag: release-2.2.0) -Author: Irfan Alibay -Date: Wed Jun 1 17:23:58 2022 +0100 - - finalize release 2.2.0 (#3690) - -commit 0b5b8ab99c83bce7e6f5c75904c2c11189e8edaf -Author: Orion Cohen <27712051+orioncohen@users.noreply.github.com> -Date: Wed Jun 1 07:39:21 2022 -0700 - - increased the maximum number of matches from an rdkit smarts query (#3470) - - Fixes #3469 - - ## Work done in this PR - * Added ``smarts_kwargs`` for RDKit's GetSubstructMatch - * Increased GetSubstructMatch's ``maxMatch`` to ``max(1000, n_atoms*10) - * Added warning when ``maxMatch`` is reached - * Associated docs fixes - - Co-authored-by: Irfan Alibay - Co-authored-by: IAlibay - -commit 0eb1eefd4dd48d85077c8bd6e264820fdfb409cf -Author: Irfan Alibay -Date: Wed Jun 1 13:52:05 2022 +0100 - - Fix reader copying by storing init arguments (#3685) - - * Fix reader copying by storing init arguments through decorator - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - Co-authored-by: Oliver Beckstein - -commit eea743f462c8054f3547e1ba1aac1f35d9fe9ec1 -Merge: c9105dada 1cf8362bb -Author: Richard Gowers -Date: Wed Jun 1 10:40:29 2022 +0100 - - Merge pull request #3681 from rafaelpap/develop - - add DL_POLY Classic support - -commit 1cf8362bbba817a399e2f37c331d1eca5c215247 -Merge: 96e02968b c9105dada -Author: Richard Gowers -Date: Wed Jun 1 10:37:30 2022 +0100 - - Merge branch 'develop' into develop - -commit c9105dada393a6102a4709b1d159acb4d0b044cb -Merge: 1945878e2 c03ac8d48 -Author: Richard Gowers -Date: Wed Jun 1 10:29:27 2022 +0100 - - Merge pull request #3680 from MDAnalysis/wheels-on-the-bus - - Enable automated wheel and dist uploads on releases - -commit 5f709eb23ac1049f87cd1cb55b5b396173ff5476 -Author: hmacdope -Date: Wed Jun 1 16:05:37 2022 +1000 - - move decls of C level vars to pxd file - -commit daa2c9c5dbc0ed48d662093cb46b5c398f8d8eca -Author: hmacdope -Date: Wed Jun 1 16:01:20 2022 +1000 - - add pxd and libmda imports - -commit 3b15c8d1db606e9216dec5275a7465cccf7a7830 -Author: hmacdope -Date: Wed Jun 1 13:54:05 2022 +1000 - - remove useless imports - -commit e2bfd339331215d96880c6816f008d438a29d70a -Author: hmacdope -Date: Wed Jun 1 13:45:36 2022 +1000 - - iron out _frame attribute hanging around in TRZ reader - -commit 3c89c85e15176a8450cdf13c9489858293f3198c -Author: hmacdope -Date: Wed Jun 1 12:37:39 2022 +1000 - - move to copy api - -commit 90ca2a26821aebb1a7d6216e3110118aff57c2aa -Author: hmacdope -Date: Wed Jun 1 11:04:40 2022 +1000 - - add explicit import for NoDataError - -commit 1df32e0362603b1c1f5f2f5f480353674d20a9d5 -Author: hmacdope -Date: Wed Jun 1 11:04:22 2022 +1000 - - change from attribute error in TRZwriter so that velocities can be correctly detected - -commit b900709231e85bfdecb8f8ac6e1115ec80706a4f -Author: hmacdope -Date: Wed Jun 1 10:49:42 2022 +1000 - - fix imports in readers that specifically import timestep - -commit 405d55b7a114c515bb92bd938e39efe585968f33 -Author: hmacdope -Date: Wed Jun 1 10:33:24 2022 +1000 - - change refs in docs to base.Timestep to timestep.Timestep - -commit 138727ba17b6ef01a435baeeeea7045cfce78d16 -Author: hmacdope -Date: Wed Jun 1 10:20:59 2022 +1000 - - change import - -commit 9bb8eb7c5af2913f1b2659c4ae5d08dc91b222a8 -Author: hmacdope -Date: Wed Jun 1 10:16:47 2022 +1000 - - fix bug on setting pos - -commit 7cab52f0c54f3f2b39178c5edc5aadd7c236b79c -Author: hmacdope -Date: Wed Jun 1 09:26:41 2022 +1000 - - fix docs build - -commit 96e02968b695a337c097cd409242ffd877aa0a01 -Author: rafaelpap -Date: Tue May 31 08:54:38 2022 +0200 - - Add missing blank line to AUTHORS - -commit 80a140795b9fc21753fa5e47f26168f4cb3577de -Author: hmacdope -Date: Tue May 31 14:15:47 2022 +1000 - - add __all__ and change docs in init - -commit e9923b43ef7a7873eecfe879bd2422db5dba0286 -Author: hmacdope -Date: Tue May 31 13:24:26 2022 +1000 - - autopep8 - -commit e606af5f17f12f9571e5898a51e650d246f8e406 -Author: hmacdope -Date: Tue May 31 11:55:12 2022 +1000 - - change to 0 size init - -commit 058e6ea1a3da2c95a285fa518c0d44909873a50d -Author: hmacdope -Date: Tue May 31 11:44:29 2022 +1000 - - tidy docstrings - -commit 12d52b0a5ec43e27a4a4de64b22fc1ae8375896c -Author: hmacdope -Date: Tue May 31 11:27:45 2022 +1000 - - improve for docs - -commit f9a5d2a0a709d906eb22e68a167b6baefd6dbb6f -Merge: 4d393c59a 1945878e2 -Author: hmacdope -Date: Tue May 31 09:53:13 2022 +1000 - - Merge remote-tracking branch 'upstream/develop' into CythonTimestep - -commit 4d393c59ad9e7c3861dfb82a6682936bb57a6144 -Author: hmacdope -Date: Tue May 31 09:40:02 2022 +1000 - - add in some explanatory notes - -commit 548d0ce1be576d4126e6e9a0686c6cde956b75bb -Author: hmacdope -Date: Tue May 31 09:35:31 2022 +1000 - - clean up unsued snippets and make array innit smaller - -commit c03ac8d48c7887f9866af62e358dd54402676f4e -Author: IAlibay -Date: Sun May 29 21:51:34 2022 +0100 - - disable action on develop, keep verbosity at 1 - -commit 731a9ed1e1ad0161f04219432ad0626064090057 -Author: IAlibay -Date: Sun May 29 21:40:45 2022 +0100 - - bump up verbosity - -commit 2290a09446426b7a082dd4182d61cb06f540163a -Author: rafaelpap -Date: Sun May 29 21:42:59 2022 +0200 - - Added to AUTHORS & added versionchanged section - -commit 7ea9700c3459b6d9fe8f4130c19fd06866a3ab2a -Merge: 92306a5ab dff038a28 -Author: IAlibay -Date: Sun May 29 20:06:10 2022 +0100 - - Merge branch 'wheels-on-the-bus' of github.com:MDAnalysis/mdanalysis into wheels-on-the-bus - -commit 92306a5ab7dcb121ba474d8b180b970e053a3873 -Author: IAlibay -Date: Sun May 29 20:05:49 2022 +0100 - - clarify upload to pypi action names - -commit dff038a28a567d913e41df45bea13b651eaf85fe -Merge: 5e9e5cfce 1945878e2 -Author: Irfan Alibay -Date: Sun May 29 19:05:10 2022 +0100 - - Merge branch 'develop' into wheels-on-the-bus - -commit 5e9e5cfce1739cd1d16e07aebdace462301b0b87 -Author: IAlibay -Date: Sun May 29 19:04:02 2022 +0100 - - simplify version getter - -commit 1945878e224beb1076be258432d911d5fda5f54a -Author: Philip Loche -Date: Sun May 29 20:02:59 2022 +0200 - - Addd center_of_charge attribute (#3671) - - * Addd center_ofcharge attribute - * Removed unused imports - * fixed equations for cog and com - -commit d800e945760317fe381895b749112f1052122bfa -Author: IAlibay -Date: Sun May 29 18:55:36 2022 +0100 - - Update changelog - -commit c5d9d55058498759175ac5d562393b0564b3b635 -Author: IAlibay -Date: Sun May 29 18:52:41 2022 +0100 - - Add guards back, make workflow trigger on pr - -commit 6272545cf7941de8407bd746ddeea82fbeac12c7 -Author: IAlibay -Date: Sun May 29 18:12:23 2022 +0100 - - Normalise version numbers for testing - -commit ff2d0b4d45ba9dbf3f7a7ca9711207f6db192587 -Author: IAlibay -Date: Sun May 29 17:42:24 2022 +0100 - - nomralise version on testpypicheck - -commit cda7a185e51b7d6eb037f672b648ad60aee49050 -Author: IAlibay -Date: Sun May 29 17:30:43 2022 +0100 - - try pointing to the right testsuite package dist - -commit 5c6596a15dcfb540b0bfb092e3308c6796fbdd08 -Author: IAlibay -Date: Sun May 29 17:20:41 2022 +0100 - - try to fix testsuite upload - -commit abbf67cfdde58247a329b117ac02b0359c8ab9bc -Author: IAlibay -Date: Sun May 29 17:09:26 2022 +0100 - - corectly point to testpypi for upload - -commit 8d4c317e33931c31ea32f46caa61a966c75f84b4 -Author: IAlibay -Date: Sun May 29 16:57:20 2022 +0100 - - try to fix versioning on action again - -commit 2978f0de7bbc99ba1e440131dd6587313564c8bd -Author: IAlibay -Date: Sun May 29 16:45:47 2022 +0100 - - try to fix pypi upload action - -commit db0cee1f966c491e76dd6d2fe260b858654834a1 -Author: IAlibay -Date: Sun May 29 16:30:55 2022 +0100 - - full testpypi deployment run - -commit 4662f1746933033068caeb0534b7bfc428c8b635 -Author: IAlibay -Date: Sun May 29 15:55:13 2022 +0100 - - add retention limit, fix workflow hiearchy - -commit 07dc4b1b79c2b69519d4183e62a7394554c41145 -Author: IAlibay -Date: Sun May 29 15:45:25 2022 +0100 - - Add guards, allow artifact loading for checking - -commit ecac5a9886d7018020dfc02f14f0f7154d42a83c -Author: IAlibay -Date: Sun May 29 15:32:35 2022 +0100 - - test purely on version - -commit 2042e75735cf2475b0b151e539df20a61d274a74 -Author: IAlibay -Date: Sun May 29 14:37:42 2022 +0100 - - fix exclude matrix - -commit 623a3bc093f78cc93f966dbf4e2fa0eca653a5d7 -Author: IAlibay -Date: Sun May 29 14:25:25 2022 +0100 - - fix py310 for various OS version - -commit f4927300a9913e3fde18bc058f85dc61592e46de -Author: IAlibay -Date: Sun May 29 14:04:55 2022 +0100 - - Need checkout to use custom actions - -commit 14eb0968f03d2d2fb0c6ab6520e1479e95fcd8ee -Author: IAlibay -Date: Sun May 29 14:01:15 2022 +0100 - - Add testpypi testing and make 310 matrix full - -commit 255de91b667e3848d584f0e2d79e242f88d6dbae -Author: Hugo MacDermott-Opeskin -Date: Sun May 29 20:46:48 2022 +1000 - - update forces and vels to use PyArray interface - -commit aa01cb8d18a4fbfb045b6eaf90287e0e9cf503fa -Author: Hugo MacDermott-Opeskin -Date: Sun May 29 20:40:07 2022 +1000 - - move memory reader to Timestep - -commit cec7f85da101b83c6c242bf082d96b84f37e6d69 -Author: Hugo MacDermott-Opeskin -Date: Sat May 28 23:36:03 2022 +1000 - - promising improvememnt - -commit 1800b8bb863b2177473aa1ecc2754b724d1395d0 -Author: Hugo MacDermott-Opeskin -Date: Sat May 28 23:23:09 2022 +1000 - - add options - -commit a478b806fcc80a763bed5aebb43acb49ed30557b -Author: Hugo MacDermott-Opeskin -Date: Sat May 28 19:34:26 2022 +1000 - - okay I know this works - -commit c64143a620c32a8ff4f23aedff0baed9b8a10099 -Author: Hugo MacDermott-Opeskin -Date: Sat May 28 17:48:56 2022 +1000 - - improve casts - -commit be8b156cb4a04625a3cd7d730adb734db5c24e7c -Author: Hugo MacDermott-Opeskin -Date: Sat May 28 16:03:55 2022 +1000 - - add cast - -commit 1f225e00c98b02ca14c7c1519433d5b28d915b5a -Author: Hugo MacDermott-Opeskin -Date: Sat May 28 15:46:31 2022 +1000 - - tidy up a fraction in timestep.pyx - -commit 478e193d6162b56a769ec5cedfeee761311019ec -Author: Hugo MacDermott-Opeskin -Date: Sat May 28 15:19:55 2022 +1000 - - add docs to build - -commit 5c5ae312079c58476f24fd29f573d5646cdfdb75 -Author: Hugo MacDermott-Opeskin -Date: Sat May 28 15:17:24 2022 +1000 - - remove doc subclasses of Timestep in TRJ and memory readers - -commit 00d3ccd94b0810f4d8ddcc8373548572166ffa62 -Author: Hugo MacDermott-Opeskin -Date: Sat May 28 15:04:05 2022 +1000 - - add in docs changes - -commit 197ab49a17e24bcaf4d6b6c3d0c75b703cd5ad57 -Author: rafaelpap -Date: Fri May 27 17:56:06 2022 +0200 - - added blank line - -commit 28bf98be1e32fc427cdd5f2c7e84a51ca5ffbe1d -Author: rafaelpap -Date: Fri May 27 17:51:37 2022 +0200 - - Add support for DL_POLY Classic - -commit c58ed6a30abb8899d0c2c7d99c3292a7459b705f -Author: Hugo MacDermott-Opeskin -Date: Sat May 28 00:27:31 2022 +1000 - - stash - -commit 9695fa185fba56e6df6d496a2a89cca87358a412 -Author: Hugo MacDermott-Opeskin -Date: Fri May 27 23:49:30 2022 +1000 - - improve casting etc, but whole new class of errors - -commit 47e53dc0a5a276c9627413adf25d8f43fe6c73cb -Author: Hugo MacDermott-Opeskin -Date: Fri May 27 22:31:11 2022 +1000 - - move to helper method - -commit 1151da6b28102e395af92d5b22cd65d8a20faf6e -Author: Hugo MacDermott-Opeskin -Date: Fri May 27 22:16:53 2022 +1000 - - work on correct casting and pathing for ndarray creation - -commit da4ba99a7d9c326b5c00f80ae2014f9f30288ddc -Author: rafaelpap -Date: Fri May 27 12:54:31 2022 +0200 - - add DL_POLY Classic support - -commit e8e2305d5bf681a54a583cd22468d93e54df07c2 -Author: hmacdope -Date: Fri May 27 12:26:16 2022 +1000 - - add start of NPY API calls - -commit af953639621b12bae15f90f10c6dec47f5f58ccb -Author: hmacdope -Date: Fri May 27 10:10:23 2022 +1000 - - remove requirement for c-style contiguity - -commit 2a6bc0d4a168c53733fdaef06d0681a330653d39 -Author: hmacdope -Date: Fri May 27 10:06:04 2022 +1000 - - improve setter API - -commit dcc48d9773f8a65e2a85c5b9248d51ce8e4e961a -Author: IAlibay -Date: Fri May 27 00:56:37 2022 +0100 - - Don't need os in the matrix - -commit cdf29fc17c7974489c92223cfefaa86d3912cbf6 -Author: IAlibay -Date: Fri May 27 00:46:40 2022 +0100 - - specify python and platforms - -commit 53dd6043cd14586309ba3b1c0d346bebe6944c8a -Author: IAlibay -Date: Fri May 27 00:34:28 2022 +0100 - - try passing the package-dir input directly - -commit 9b27fac94faaf45cb028290660803501c88cbd41 -Author: IAlibay -Date: Fri May 27 00:20:34 2022 +0100 - - Fix more typos - -commit 7dfb58d5b1526bd3c1b04892e4491b70965b789b -Author: IAlibay -Date: Fri May 27 00:17:42 2022 +0100 - - Set working-directory - -commit a9aba49382b4f92e2d34da133df310a9b796c39c -Author: IAlibay -Date: Fri May 27 00:02:50 2022 +0100 - - fix typo - -commit ad598ee913bc4504fb1ec39a4143681123514a5e -Author: IAlibay -Date: Thu May 26 23:54:26 2022 +0100 - - The wheels on the bus go? - -commit 6f17cb11ed6d9eea13c497e1a866537dc3294303 -Author: rsexton2 <31674930+rsexton2@users.noreply.github.com> -Date: Thu May 26 10:55:11 2022 -0700 - - Added frames processing to AnalysisBase (#3415) - - * Added frames processing to AnalysisBase - * Added rmsd test and 'frames' examples in docs - * Added rewind test, fixed .run example - * improved AnalysisBase documentation - - outline general ideas and features - - show example (RMSD) with different frame selections - - fixed generic example on top analysis page - - Co-authored-by: Oliver Beckstein - -commit b440cc3ea638077b0e815d816d20124dbdf17147 -Author: hmacdope -Date: Thu May 26 18:59:58 2022 +1000 - - fix attributeError - -commit 84222d536d1ee88061ca77d44d931d853ff409d9 -Author: hmacdope -Date: Thu May 26 16:18:02 2022 +1000 - - fix import in TRJ / TRZ - -commit a26f4fc142781ca1a69b04aab0164efcaf4a3d3f -Author: hmacdope -Date: Thu May 26 15:00:08 2022 +1000 - - change dms test to has_velocities rather than hasattr - -commit 2d84a67562137e2c34d3aaaa72fbe05047033af6 -Author: hmacdope -Date: Thu May 26 14:57:35 2022 +1000 - - change dlpoly test to has_ rather than AttributeError - -commit 954aaf3a9936cf9e6746455c1bed6b695d015287 -Author: hmacdope -Date: Thu May 26 14:19:58 2022 +1000 - - move docs around - -commit 5d7d8efe93ac7364ab0bfad1948346ddcd56a356 -Author: hmacdope -Date: Thu May 26 13:47:25 2022 +1000 - - partially fix pickling - -commit 25a6a7bc347dafb87a14698bae13142bb706cac2 -Author: hmacdope -Date: Wed May 25 21:29:21 2022 +1000 - - make changes to base - -commit 64cba3b60e1f98f4713a1055f08bc863453b0faa -Author: hmacdope -Date: Wed May 25 16:42:57 2022 +1000 - - working - -commit 085a7b494464bc28722de1c9f0a4ec0e53fc9ebe -Author: hmacdope -Date: Wed May 25 16:28:02 2022 +1000 - - make sure to cinit numpy arrays - -commit 3db54d632cfc19c4e6d5d3a0fb112cfcef9a931b -Author: hmacdope -Date: Wed May 25 15:31:14 2022 +1000 - - add _frame attr - -commit ddac2efdb91572efb1b6c54a09411ad65a174eb2 -Author: hmacdope -Date: Wed May 25 15:08:58 2022 +1000 - - remove frame get set method - -commit 7919324101b63601707fcf1dc3b34a8b88659fb4 -Author: hmacdope -Date: Wed May 25 14:33:51 2022 +1000 - - imporve error message - -commit 23344838b71947cd45a4c592f9634b2bc771cfbf -Author: hmacdope -Date: Wed May 25 14:31:41 2022 +1000 - - fix hasattr calls - -commit 0238c0b3e29ff8a21da6c9ccbdd92af057deddac -Author: hmacdope -Date: Wed May 25 12:38:29 2022 +1000 - - partially working - -commit a1a5253b30b90a396d42b0d09a15bf416e9e6d47 -Author: hmacdope -Date: Tue May 24 17:20:00 2022 +1000 - - passes api tests - -commit 7c9eb5f257ce4476e0fb04ff7c5d895e797135e2 -Author: hmacdope -Date: Tue May 24 14:44:05 2022 +1000 - - add to init dunder and change tested class - -commit 401201d5db4d8ba635feaaf998b9a414df42c799 -Author: hmacdope -Date: Tue May 24 14:26:21 2022 +1000 - - finalize copy over - -commit 15f6f34fb9c05010ef31f93743cf453754cedb79 -Author: hmacdope -Date: Tue May 24 10:50:04 2022 +1000 - - add start of timestep class - -commit badc7e72e1c4a6f716395ba721478c1b3c73b1bb -Author: manishsaini6421 <57342164+manishsaini6421@users.noreply.github.com> -Date: Tue May 24 05:25:43 2022 +0530 - - Benchmarks for more lib.distances methods required #3205 (#3641) - - * Benchmarks for more lib.distances methods #3205 - -commit 5dc774784ba31ae04f18f9baf59ccfddd617fa74 -Merge: da4312a7e c0bf060c4 -Author: Richard Gowers -Date: Mon May 16 15:42:42 2022 +0100 - - Merge pull request #3669 from MDAnalysis/deprecations - - Fix deprecation warnings from Issue #3535 - -commit da4312a7e500f2265aa3f9fb292e63049ea2357a -Merge: 174080ca6 620774950 -Author: Richard Gowers -Date: Mon May 16 15:42:28 2022 +0100 - - Merge pull request #3668 from aditi2906/issue#3638 - - replaced atoms.coordinates() with atoms.positions in benchmarks - -commit 174080ca61b8947d03add629c966a98f6d962aa4 -Author: Yuxuan Zhuang -Date: Mon May 16 15:20:58 2022 +0200 - - On loading the same XTC offset in parallel (#3375) - - Fixes #3230, #1988 - - ## Work done in this PR - * Add a fasteners.InterProcessLock for loading the offset for XDR files - * Add a ValueError exception for corrupted npz file (fix Error loading XDR files with corrupted offset files #3230) - * Adds fastener as a new core dependency - -commit 82d182785e245a25e7113a3b25d1e29c66be556a -Author: Aditi Tripathi <61978541+aditi2906@users.noreply.github.com> -Date: Mon May 16 17:39:11 2022 +0530 - - public function listed (#3666) - - Fixes #3655 - ## Work done in this PR - * Adds minimized_vectors to docs - * Fixes versionchanged rendering for minimized_vectors - -commit c0bf060c4634b44f05b5d1bb2d16b4c824072a85 -Author: IAlibay -Date: Mon May 16 13:04:47 2022 +0100 - - Fix deprecation warnings from Issue #3535 - -commit d2a9e0b24850bb373d085da07e58dbd2b4583409 -Author: Irfan Alibay -Date: Mon May 16 11:42:47 2022 +0100 - - [MAINT] Update to python>=3.8, numpy>=1.9.0, gsd>=1.9.3, networkx>=2.0, and scipy>=1.5.0 (#3665) - - * python>=3.8, gsd>=1.9.3, scipy>=1.5.0, and various other bumps - - Co-authored-by: Oliver Beckstein - -commit 6207749500f29eb90f58ce896c5e396eecf26a1c -Author: aditi2906 -Date: Mon May 16 02:06:11 2022 +0530 - - replaced atoms.coordinates() with atoms.positions in benchmarks - -commit b53bce01cf5dbc56e4953e6a6b498c0cce270f64 -Author: Irfan Alibay -Date: Fri May 13 15:21:40 2022 +0100 - - Rewind singleframe before on iter call (#3642) - - Fixes #3423 - - ## Work done in this PR - * Rewind singleframe before on iter call - * add documentation on rewinding after iteration - - Trajectory API - - FrameIterators - * fix failing RDF test - - use in-memory trajectory to make local coordinate patches - permanent for tests (after rewind) - - use function-scoped fixtures instead of module-scoped - to safely be able to patch coordinates - * fixed missing copy of convert_units=False in Reader.copy() - - update SingleFrameReaderBase.copy() - - update ReaderBase.copy() - - bug was uncovered after tests for - TestGROReaderNoConversion::test_transformations_copy failed: with - the fix, the original tests pass again TOGETHER with the other - changes in PR #3642 - - Co-authored-by: Oliver Beckstein - -commit 5474cf83fdde57c0905b1f649f427877e310aa9a -Author: Aditi Tripathi <61978541+aditi2906@users.noreply.github.com> -Date: Fri May 13 18:51:52 2022 +0530 - - Adds aditi2906 to changelog (#3661) - -commit 256c731d289c3477303a42872ae0fa08788e3b2d -Author: BFedder <80363742+BFedder@users.noreply.github.com> -Date: Wed May 4 08:28:38 2022 +0100 - - Several improvements for LinearDensity (#3617) - - Fixes #2508 (partially) - - Changes made in this Pull Request: - - * LinearDensity now works with updating AtomGroups. A new test was added to verify this. - * Result variables "pos" and "char" as well as their "std" were renamed to "mass_density", "charge_density" and "stddev", respectively. - * The bin edges of np.histogram are now saved for xyz as "hist_bin_edges" - * This PR addresses points 1, 2, and 3 raised by @lilyminium in #2508. - -commit f494c98dbc1c169854399ff6815f699718d903fe -Author: Aditi Tripathi <61978541+aditi2906@users.noreply.github.com> -Date: Fri Apr 29 17:32:47 2022 +0530 - - replacing usage of np.all with assert_allclose in encore tests (#3631) - - Fixes #3568 - - ## Work done in this PR - * Replace use of np.all with assert_allclose and assert_equal for some tests - * Some pep8 fixes - -commit d22886dbd9e3af7608fe06a5280b0d23a42ec904 -Author: Atharva Kulkarni -Date: Wed Apr 27 02:06:12 2022 +0530 - - Fix OpenMM parser not working when elements is not set (#3511) - - * Fix OpenMM parser not working when elements is not set - - * PEP8 fix - - * fix openmm parser - - * Add tests - - * Review changes - - * More review changes - - * Add one more test - - * Fix failing checks - - * Review Changes - - * Added support for abnormal elements - - * Fix failing checks due to bad import - - * Review - - * Fix openmm import - - * Rearrange tests - - * Make warnings more clear - - * review - - * Update docstring - -commit 3a03af01886977aa53d2a43086cae86c45038738 -Author: Philip Loche -Date: Fri Apr 22 15:20:03 2022 +0200 - - Sort and add PMDA intersphinx_mapping (#3652) - - - The `See Also` entry for pmda.density.DensityAnalysis was not - rendered and linked correctly. The PR also updated the links - to the most recent location. - -commit e586ba9c1be535ce2b008478c3f9f79fb6adc235 -Author: Matthijs Tadema -Date: Fri Apr 22 10:41:06 2022 +0200 - - Remove None from filenames in analysis.hole.HoleAnalysis (#3650) - - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - -commit 3769ee29e5907221527ff0ec88a8c5acf9f86dee -Author: Robot Jelly <36916536+robotjellyzone@users.noreply.github.com> -Date: Wed Apr 20 19:01:45 2022 +0530 - - Improve `HELANAL` docstring for `split_residue_sequences` (#3643) - - Added more details for split_residue_sequences parameter - -commit 97ffb087df2454d7dbf0d427ac941d8b6a503d66 -Author: Uma Kadam <90750049+umak1106@users.noreply.github.com> -Date: Wed Apr 20 17:50:54 2022 +0530 - - Bat cartesian method modifies input data (#3640) - -commit be4b6ee8fa243a0d9e18b936a3d018f2b7418914 -Merge: 32de86f14 374ba4927 -Author: Richard Gowers -Date: Tue Apr 19 09:17:37 2022 +0100 - - Merge pull request #3611 from ALescoulie/wc_pair_perf - - Higher Performance nuclinfo - -commit 374ba4927c34ee0f156e92d039267ecbc538cc63 -Merge: a16c79a0a 32de86f14 -Author: Richard Gowers -Date: Tue Apr 19 09:17:06 2022 +0100 - - Merge branch 'develop' into wc_pair_perf - -commit a16c79a0a9291b943770402c34e0275468ddf7e2 -Author: alescoulie -Date: Mon Apr 18 23:00:11 2022 -0700 - - fix username in CHANGELOG - -commit 211a74fd7b876997bf006c4601c8ce9d1f1b9f0a -Author: alescoulie -Date: Mon Apr 18 22:55:41 2022 -0700 - - update AUTHORS and CHANGELOG - -commit 625d238e43bdbcdb5fcfafb102d3c90180559b18 -Author: alescoulie -Date: Mon Apr 18 22:55:10 2022 -0700 - - fix docs - -commit 32de86f149561b2cea474d098b135c7ffdb5949f -Author: Marcelo D. Polêto -Date: Mon Apr 18 16:18:49 2022 -0400 - - Make CRD EXT format selectable in CRDWriter (#3635) - - * Fixes issue #3605 - * Inclusion of an boolean kwarg extension=False|True for the CRDWriter.write() function to - force use of the EXTENDED output format - * add tests for EXT writing - * update CHANGELOG - * update AUTHORS - -commit c0a4f610656baf08294d01ebff2fafc859887cfc -Author: Aditi Tripathi <61978541+aditi2906@users.noreply.github.com> -Date: Mon Apr 18 18:53:39 2022 +0530 - - spelling errors corrected accross various files (#3646) - - * spelling errors corrected accross various files - - * linting errors fixed - - * fixed errors in previous commit - - * Revert "fixed errors in previous commit" - - This reverts commit 5580846dcee9495a4ac58b7e84fb1cf0475dd4a7. - - * fixed previous commit issues - - * fixing styling errors - -commit a805dda0aa807741e2f4b4b0094f43d2571f534e -Author: Mark Verma <78155861+markvrma@users.noreply.github.com> -Date: Mon Apr 18 16:29:31 2022 +0530 - - MSD example where multiple replicates are combined (#3633) - - Add an example where MSD replicates are combined and correct failing doc example due to reversed order of top and traj. - -commit 13d49243bc66ff72ed19b11e988fe863c7bc7615 -Author: alescoulie -Date: Sun Apr 17 15:57:32 2022 -0700 - - add analysis to tree - -commit b954c97c79744ce08e27ed965c91fe5cd667cfe3 -Author: alescoulie -Date: Sun Apr 17 15:30:33 2022 -0700 - - update docs - -commit d3050e09e3a97cf1cfdeeafa35c7716c0cccba4a -Author: alescoulie -Date: Sun Apr 17 14:53:54 2022 -0700 - - add nuc acid name kwargs - -commit cd193ed7106daf502555885f213b46f5a5678eb0 -Author: alescoulie -Date: Sun Apr 17 14:46:25 2022 -0700 - - remove internal selection and simplify pr - -commit fe9a403dbacde06232ef5f987a45498b97afe952 -Author: SUKEERTI T <98384608+Sukeerti1@users.noreply.github.com> -Date: Fri Apr 15 12:52:02 2022 +0530 - - Updated elementwise comparison (#3619) - - Fixes part of #3535. Fix a numpy deprecation warning about elementwise comparisons. - - * Updated elementwise comparison - - * mend - - * Updated Elementwise Comparison - - * Updated Elementwise comparison - -commit 02a644392eb4a8cc3e1da83df9ba5b8bd97d449f -Author: Robot Jelly <36916536+robotjellyzone@users.noreply.github.com> -Date: Thu Apr 14 18:25:20 2022 +0530 - - formatted unit.py doc (#3634) - - * formatting unit.py doc - - * added authors,changelog & formatting of exponent - - * fixed typo , formatted greek letter & resolved pep8 error - -commit 54d9e4e4425349aa9876d00614a032536d565588 -Author: Irfan Alibay -Date: Thu Apr 14 03:21:30 2022 +0100 - - Update greetings to have right permissions (#3636) - - * Update greentings to have right permissions - -commit 1afbac1f61411a1a7a49242511111cd0f276be1f -Author: Aditi Tripathi <61978541+aditi2906@users.noreply.github.com> -Date: Wed Apr 13 06:28:46 2022 +0530 - - issue#3584 added plots for rama_ref and janin_ref (#3615) - - * fix #3584 - * added plots and text for rama_ref and janin_ref - * fixed code sample for plotting Janin reference - * updated figure links in filenames.py - * updated AUTHORS - -commit 294c710723fb8f63e4e808ffadc1ef927730396f -Author: alescoulie -Date: Tue Apr 12 12:18:05 2022 -0700 - - remove relative imports - -commit ff18452914a918ad6f2b200b43d71e7179740c05 -Author: alescoulie -Date: Tue Apr 12 11:59:03 2022 -0700 - - add nucleicacids.py to analysis imports - -commit c8367bc9698045f57f8d8d6b58c9fe0977d2419c -Author: alescoulie -Date: Tue Apr 12 11:23:37 2022 -0700 - - commit tests - -commit f1dc8899901db8dc9a39e90c2dd8a10322fa6437 -Author: alescoulie -Date: Tue Apr 12 11:19:39 2022 -0700 - - convert results to Results object - -commit 77c8ed1f8aefb3b71d89c180467dc6be2df1db3a -Author: Uma Kadam <90750049+umak1106@users.noreply.github.com> -Date: Tue Apr 12 23:47:07 2022 +0530 - - [DOCS] added id selection in selection commands. (#3607) - - Updated documentation in selection commands. - * Added `id` selection description in selections.rst with note to distinguish between `bynum` and `id` selection. - - Co-authored-by: Estefania Barreto-Ojeda - -commit dd7ce7b2d10a0990b7bac540b6a34bb1734e6bba -Author: manishsaini6421 <57342164+manishsaini6421@users.noreply.github.com> -Date: Tue Apr 12 14:35:32 2022 +0530 - - Shift hole2 docs to module level docstring (#3579) - - Part of #2786 - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - -commit 51661637ee1444a15eec331e8777cbc60c9c9836 -Author: Matteo Tiberti -Date: Tue Apr 12 09:52:05 2022 +0200 - - Replaces outdated method in encore.covariance_matrix (#3621) - - * fixed code path for when using reference structure - - * added explicit tests to test code paths in covariance_matrix - - * updated CHANGELOG - - * removed leftover whitespace - - * removed superseded test draft - - * added PR number to CHANGELOG - - Co-authored-by: Oliver Beckstein - -commit 459c04ea86fc9f885d0c259e831a735111c249ce -Author: rishu235 <64803300+rishu235@users.noreply.github.com> -Date: Mon Apr 11 18:34:25 2022 -0600 - - Fix issue 2703 (On-the-fly transformation for principal component projection) (#3596) - - * fix #2703 - * Added a method for inverse-PCA transform along selected PC components. - * Added a test function to run the added functions in pca.py - * add docs (including docs that show how to use it as a on-the-fly transformation) - * update CHANGELOG and AUTHORS - -commit 9d090e695fae02f40328942648bb06a5e3b6553b -Author: Hugo MacDermott-Opeskin -Date: Mon Apr 11 20:36:15 2022 +1000 - - Create greetings.yml (#3609) - -commit 0eb42ca780fe7f433a9e6ee840e9f464c685141c -Author: Anir G <54763591+AnirG@users.noreply.github.com> -Date: Mon Apr 11 14:28:20 2022 +0530 - - Accept AtomGroup alongwith Universe in the DistanceMatrix (#3541) - - * Accept AtomGroup instead of Universe in the DistanceMatrix - - * Modified Tests - - * Added a test to assert same values of distmatrix - - * Accept both AG and Universe - - * Resolve PEP8 - - * Final changes - - * updated AUTHOR and CHANGELOG - - * corrected and updated docstrings - - * modified and displaced import statement - - * updated changelog and added self to authors - - * updated changelog and authors - - * updated docstrings - - * fixed typo and edited docstrings - - * fixed merge issues with authors and changelog - - * update docstring - - * remove github id from previous release - - * tests on an updating AG - - * upstream changes merged - - * revoked the redundant testcase and user warning if updating atomgroup is parsed - - * minor docstring edit - - * warning test for updating atomgroup - - * modified warning message - - * added test where ag and select string is parsed - -commit 8eda52fe9eff20bcd739a7e2b87397a6eb6639a4 -Author: megosato -Date: Sun Apr 10 17:19:23 2022 -0700 - - Fix FrameIteratorIndices doesn't rewind (#3416) (#3606) - - * Fix FrameIteratorIndices doesn't rewind (Issue #3416) - - - Previously iterating through FrameIteratorIndices did not rewind back to 0 and stayed on the last iterated frame. - - FrameIteratorIndices now rewinds back to 0 and is consistent with FrameIteratorSliced and FrameIteratorAll. - - Co-authored-by: IAlibay - -commit 8cd0a9403a14a1445cab2fad5d3862ea0674606c -Author: Irfan Alibay -Date: Sat Apr 9 08:47:51 2022 +0100 - - Fix docs for lineardensity (#3616) - - * Fix issue with code block for lineardensity docs - * Also various other small changes in wording - -commit 7c166c0686847583b3f90d36e4d35d78ff6c1931 -Author: BFedder <80363742+BFedder@users.noreply.github.com> -Date: Fri Apr 8 22:43:09 2022 +0100 - - LinearDensity now working with residues/segments (#3572) - - Fixes #3571 : LinearDensity does not work on residues or segments - - MDAnalysis/analysis/lineardensity.py: - - in _prepare(self): - - try/except statement replaced by if statements checking the grouping - specified for LinearDensity. - - masses and charges are obtained in a way appropriate for each case. - - - Floating point arithmetic issues could lead to negative radicands. A check - was implemented to set numbers which are close to zero to precisely zero - before the square root (for standard deviation) is calculated. - - - renamed previous test function and added expected masses and charges - - added test functions for the other groupings with their respective expected - masses and charges - - Changed the if/if/if for reading masses and charges - to if/elif/else. - Will now raise an AttributeError if invalid grouping is chosen. - 'residues', 'segments' and 'fragments' now use the same logic - (elem.atoms.total_mass()). - - * Changed test of radicand to only convert negative numbers to 0 - * Now uses CoM rather than CoG for density calculations - * Changed Class docstring to reflect change to CoM - * Now uses parameter for compound instead of list comprehension when - calculating masses, charges, and CoM - * refactored test_lineardensity.py, make use of pytest functionality - better - * Added test for case of invalid grouping selection - - - Co-authored-by: Irfan Alibay - -commit 993770ffacb26a62eacaa64391549da6d46d9b16 -Author: Irfan Alibay -Date: Fri Apr 8 22:25:31 2022 +0100 - - fix pypi check issues: install recent readme-renderer (#3613) - - * fix #3612 - * Add pip install of readme-renderer because conda-forge package is outdated and not maintained. - -commit e940bd1db2a055c866acec914d19d56dee1cb607 -Author: Mingyi Xue <2415309890@qq.com> -Date: Fri Apr 8 15:01:02 2022 -0500 - - Fix optional field handling in MOL2Parser and MOL2 reader (PR #3598) - - - Fixes #3385 : MOL2Parser requires ATOM optional fields can now be properly handled. - - Modified MOL2Parser: when optional fields are not provided: - - subst_id (=resid) defaults to 1 - - subst_name will be used as resname if present for ALL atoms; if no subst_name present - then topology will generated without resname; else ValueError - - charges are handled by looking at NO_CHARGES: - - If "NO_CHARGES" exists in MOLECULE section, and no atoms have charge field, - charges attribute will not be set in the topology - - If "NO_CHARGES" exists in MOLECULE section while some atoms have charge field, - OR charge model exists in MOLECULE section while some atoms don't have "charge" - field, a ValueError will raise. - - Modified coordinate reader MOL2.py to unpack only the first 6 required columns. - - add tests - - update AUTHORS - - modify CHANGELOG - -commit 88628a1ab91d2f8465b56e7824a9a961a96bea6d -Author: Tyler Reddy -Date: Fri Apr 8 09:04:34 2022 -0600 - - BLD: improve M1 build support (#3595) - - Partly addresses #3592 - - * BLD: improve M1 build support - - * the changes here allow me to build MDAnalysis and its - dependencies on an M1 Mac on the gcc compile farm using - `python3 -m pip install --user .` - - * the full test suite passes, except for 1 extra `xfail` - I've added in here--which is also documented by gh-1389 - (it has apparently been failing on "exotic platforms" - for almost 5 years). Issue re-raised as #3599 - -commit 779557bd7dceea4a30100ff46eab6483b5c72576 -Author: alescoulie -Date: Thu Apr 7 14:41:48 2022 -0700 - - add tests - -commit ac04d1482ff630c83a2900477f30a50642ae0161 -Author: alescoulie -Date: Thu Apr 7 14:41:37 2022 -0700 - - commit major and minor dist - -commit 369d29c97d35e2241e5ab847512702262a42bb52 -Author: alescoulie -Date: Thu Apr 7 14:25:45 2022 -0700 - - commit wc_dist test - -commit e1a17e221fc83cce271e2856df7604d14c377f81 -Author: alescoulie -Date: Thu Apr 7 14:25:27 2022 -0700 - - finish WCDist - -commit c5bfde4e6f56795a36a20ad3bbfd70594652f54e -Author: Tyler Reddy -Date: Thu Apr 7 15:14:30 2022 -0600 - - CI: bump actions versions (#3610) - - * follow NumPy in bumping to latest GitHub - `actions` versions - -commit 3e8e0fc00ad622166841ccbfaac22952b27ed34d -Author: alescoulie -Date: Thu Apr 7 13:04:49 2022 -0700 - - commit NucPairDist - -commit 3d8c75c62af1fefb005a02ea748389694b0f317e -Author: Tamandeep Singh <90107053+tamandeeps@users.noreply.github.com> -Date: Wed Apr 6 13:08:01 2022 +0530 - - [DOCS] changes made to more specific imports (#3604) - - * fix #3602 - * use specific imports in examples on overview page - * Added name to Authors and github handle in Changelog - -commit 0d1587796c52db8324d4e4c9a7fa69ab1d375e3f -Author: Uma Kadam <90750049+umak1106@users.noreply.github.com> -Date: Wed Apr 6 05:19:10 2022 +0530 - - [DOCS] Added RMSD plot example in section 4.2.4 (#3591) - - fix #3581 - -commit b27913a32c3780a6c93255d87e0e8c59189d5a91 -Author: Henok Biadglign Ademtew <46082799+HenokB@users.noreply.github.com> -Date: Tue Apr 5 21:38:52 2022 +0300 - - Change code snippets from python 2 to python 3 in the documentation (#3588) - - * Update overview.rst - - * Change code snippets from python 2 to python 3 in the documentation - - * Change code snippets from python 2 to python 3 in the documentation - - * Update selections - - * Update AUTHORS - - * Update package/doc/sphinx/source/documentation_pages/selections.rst - - Co-authored-by: Oliver Beckstein - - Co-authored-by: Oliver Beckstein - -commit dee9f14cb35a5bee4cade3f6108cc00a27c64a00 -Author: Henok Biadglign Ademtew <46082799+HenokB@users.noreply.github.com> -Date: Tue Apr 5 10:53:16 2022 +0300 - - Added a new badge to link it to the benchmark (#3587) - - Co-authored-by: Estefania Barreto-Ojeda - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - -commit 81404f8abb256ddae9c187a6d7c66be4077dcbc1 -Author: Uma Kadam <90750049+umak1106@users.noreply.github.com> -Date: Tue Apr 5 02:21:41 2022 +0530 - - Added link to ordered selections to docs (#3589) - - * Fixed add link to ordered-selections in selections.rst #3583 - -commit 51aa6bba7a9882a214f7a5eff8645a01375f9ed1 -Author: Alia Lescoulie -Date: Mon Apr 4 03:09:32 2022 +0000 - - commit nucleicaid - -commit 5fc4db4544492fb42980dea5eccd3272a53ca506 -Author: Alia Lescoulie -Date: Mon Apr 4 01:55:41 2022 +0000 - - commit nucleicacids tests - -commit a86508d7313d40d6164ce1ba8a620749784e02d7 -Author: Alia Lescoulie -Date: Mon Apr 4 01:42:07 2022 +0000 - - commit WCBase - -commit 009c467511210c442d15e4014f02e62e07dc9e85 -Author: Cédric Bouysset -Date: Sat Apr 2 09:33:10 2022 +0200 - - An "accurate and reliable" RDKitConverter (#3044) - - Improves inferring of bond orders and formal charges to cover 99.1% of the 1.7M compounds in CHEMBL27, up from previous 90% - - - Fixes monatomic ion charges that were always negative - - Fixes more cases of conjugated systems - - Fixes tetravalent phosphorus - - Fixes some edge cases with sulfur and nitrogen - - Modifies the bond inferring tests to try matching with resonance structures - - Adds tests for ions, all standard amino-acids and all standard nucleic-acids - - Adds tests on molecules encountered in the ChEMBL 27 dataset - - Fixes atoms in the RDKit molecule that weren't always in the same order as in the atomgroup - - Fixes atom name formatting when writing a PDB file with RDKit - - Fixes sanitization errors that occurred when using `NoImplicit=False` - - The `names` property is now available through `atom.GetProp("_MDAnalysis_name")`, while `atom.GetMonomerInfo().GetName()` returns the PDB-formatted version (with spaces). - - See https://github.com/MDAnalysis/RDKitConverter-benchmark for a benchmark. - - Co-authored-by: Oliver Beckstein - -commit b89537e851eaa20856de501fca4a48d7e835b9a0 -Merge: 95234d2b7 bf95f9cc1 -Author: Rocco Meli -Date: Wed Mar 30 20:51:43 2022 +0100 - - Merge branch 'MDAnalysis:develop' into develop - -commit bf95f9cc18cafb2f387f90e467c7944b371abeb4 -Author: Shudipto <32040453+shudipto-amin@users.noreply.github.com> -Date: Sun Mar 27 16:53:25 2022 -0600 - - Provide ability to use AtomGroup as selection for Contact (#3565) - - Fixes #2666 - - ## Work done in this PR - * Allow selections in Contacts to be AtomGroups - -commit 800298ad271a00762ba3f51629c1ce41b7bf4172 -Author: Aya Alaa -Date: Wed Mar 23 17:06:12 2022 +0200 - - Test features of Cluster class (#3566) - - * Adds new test for Encore's Cluster class. - -commit 7670dad96a6e827826b009bf81a7cbc79ba6b1ee -Author: Agorfa -Date: Wed Mar 23 04:34:45 2022 +0100 - - Fixes LAMMPS DumpReader to expect orthogonal bounding box format used for triclinic box in lammps. (#3403) - - * Fixes LAMMPS DumpReader to expect orthogonal bounding box format used for triclinic box in lammps. - -commit e0a44cd98e0ca9c4c3130279a7f1a63358088711 -Author: Pratik Gupta <66073063+inomag@users.noreply.github.com> -Date: Sat Mar 19 07:06:03 2022 +0530 - - MDAnalysisTest badge now points to GH Actions CI instead of Travis (#3559) - - * Update MDAnalysisTest README - - Co-authored-by: Irfan Alibay - -commit 9c0ba8c30ab203a6375afab852e81b85eb2dc144 -Author: Oliver Beckstein -Date: Fri Mar 18 16:11:12 2022 -0700 - - updated Code of Conduct (#3567) - -commit 05b3e10c93a2e20069cbec36b08e0b755a09730f -Author: BFedder <80363742+BFedder@users.noreply.github.com> -Date: Thu Mar 17 11:50:12 2022 +0000 - - Issue #2417: ITPParser should not add angles to SETTLEd waters. (#3564) - - * Issue #2417: ITPParser, no angle for SETTLEd water - - ITPParser no longer adds angles for water molecules with SETTLEd - geometry. The tests were modified to reflect this. - Changes: - MDAnalysis/topology/ITPParser.py - * Molecule.parse_settles changed to no longer add angle - - MDAnalysisTests/topology/test_itp.py - * TestITPNoKeywords now expects 0 angles - * TestITPKeywords changed to continue to expect 1 angle - * def test_angles_values moved from TestITPNoKeywords to - TestITPKeywords - * TestNestedIfs now expects 0 angles - * TestReadTop's topology file has 3 SETTLEd water molecules - and now correctly expects three fewer angles than before - - * added changes to AUTHORS and CHANGELOG - - * fixed typo - - * Update ITPParser.py - - * Update test_itp.py - - * Update package/CHANGELOG - - Co-authored-by: Jonathan Barnoud - - * Update ITPParser.py - - Co-authored-by: Jonathan Barnoud - -commit af12ce0a513d9b37f19418f5f129612efe5c6115 -Author: Irfan Alibay -Date: Tue Mar 8 12:28:04 2022 +0000 - - Start 2.2.0-dev0 (#3558) - -commit 392c8ae5391e20f5e496f7ac03dae08c44deca3b (tag: release-2.1.0) -Author: Irfan Alibay -Date: Tue Mar 8 08:24:23 2022 +0000 - - Fix more typos in 3.10 setup.py docs (#3555) - -commit f9dfff3b85a7c65590af79648347578cba08b92f -Author: Irfan Alibay -Date: Mon Mar 7 23:00:41 2022 +0000 - - Fix typo in setup.py documentation (#3554) - -commit 001e6e01582a133d79daeaf33f68399eace1ae85 -Author: Irfan Alibay -Date: Mon Mar 7 21:56:00 2022 +0000 - - Complete release v2.1.0 (#3553) - - Fixes #3446 - * Complete release v2.1.0 - * officially advertise py3.10 support - -commit 8835ab77e411f0a5ee0516583ed6edfe6898a501 -Author: Oliver Beckstein -Date: Sat Mar 5 09:15:08 2022 -0700 - - fixed moment of inertia doc string - -commit c1a68bd47c5e4aa12b0c17e693bf357b32854cd6 -Author: Oliver Beckstein -Date: Fri Mar 4 18:47:20 2022 -0700 - - added docs for tensor moment of inertia - -commit d704b046f6676baed59365f702a9d68793933318 -Author: Oliver Beckstein -Date: Fri Mar 4 18:09:24 2022 -0700 - - updated docs - - - versionchanged for pbc -> wrap everywhere - - fixed format of older versionchanged markup - - added missing docs for moment_of_inertia() - and replaced kwargs with explicit keyword arguments - - removed superfluous kwargs from shape_parameter() - -commit 069d39b492ba528746307b0ac1f52173761ef920 -Author: Jonathan Barnoud -Date: Thu Mar 3 11:47:20 2022 +0100 - - Ignoed expected lint warnings - - Testing deprecated arguments lead to false positives in pylint. This - commit ignores the specific warning on the problematic lines. - -commit 4bbefc75493e747a793e5e9bd6f9e6e7e7239a3e -Author: Jonathan Barnoud -Date: Thu Mar 3 11:00:50 2022 +0100 - - Fix PEP8 - -commit 260817bd6aed082a8bbffe99d669ce86c7b0574b -Author: Jonathan Barnoud -Date: Thu Mar 3 10:56:00 2022 +0100 - - Update deprecation notice about pbc->wrap - -commit d99fb3ee30ee5be4e5c17b14368a2183a09c5e21 -Author: Jonathan Barnoud -Date: Thu Mar 3 10:34:28 2022 +0100 - - Fix tests that used both wrap and unwrap - -commit f6ec13b21c727236b8d593066653e50f19c51963 -Author: Jonathan Barnoud -Date: Wed Feb 16 11:25:36 2022 +0100 - - Fix a broken test - - topologyobjects.Bond.length still has a pdb argument. This commit - reflects this. - -commit ce1f196f56caff09789c555c6230a0c029f786e1 -Author: Jonathan Barnoud -Date: Tue Feb 15 12:55:52 2022 +0100 - - Fix some changes missed during the rebase - - Rename a missed variable and remove calls that use both wrap and unwrap. - This commit does not pass the tests because some of them rely on both - wrap and unwrap in the same call. This will be fixed in a subsequent commit. - -commit 4bb3913c06f1d532a95c59c43538a866596dc544 -Author: richard -Date: Tue Jul 21 08:34:53 2020 +0100 - - added CHANGELOG and deprecation warning for pbc kwarg - -commit c227d0b19d4de17e8d59708556d3df6f60a1251f -Author: richard -Date: Sun Jul 19 14:25:46 2020 +0100 - - renamed 'pbc' kwarg to 'wrap' for Group methods - - issue #1760 - -commit 95234d2b79f4e876a9deb2aa4ca8af79a19f94fa -Merge: eb58ba930 018dcb767 -Author: Rocco Meli -Date: Sat Mar 5 13:02:05 2022 +0000 - - Merge branch 'MDAnalysis:develop' into develop - -commit 018dcb767fc6e4c58eb25c9d69579428cf2b63f7 -Author: Irfan Alibay -Date: Fri Mar 4 13:05:07 2022 +0000 - - Fix leftover simtk import and fix openmm docs (#3552) - - * fix leftover simtk import and fix openmm docs - - * fix parmed docs - - * pragma no cover added - - * Apply suggestions from code review - - Co-authored-by: Jonathan Barnoud - - Co-authored-by: Jonathan Barnoud - -commit 4509856692ca07c3208fd2b19a154f645b886cbc -Author: Irfan Alibay -Date: Thu Mar 3 13:41:19 2022 +0000 - - Add packaging as a core dependency of MDAnalysis (#3549) - - * Related to #3527 - -commit acd929faf60c63ce7e11e3dd8995ff8663061292 -Author: Tyler Reddy -Date: Wed Mar 2 14:59:06 2022 -0700 - - BLD, MAINT: hoist packaging import (#3527) - - * hoist the import of `packaging` outside of a Cython-focused - `try`/`except` block to avoid a deceptive error message when - `packaging` is missing, per discussion at: - https://github.com/MDAnalysis/mdanalysis/pull/3398#issuecomment-1037371853 - -commit eb58ba930d1f9865013448831d930e13ea21a01c -Merge: a0f80160e 4381f44c8 -Author: Rocco Meli -Date: Sat Feb 26 16:32:59 2022 +0000 - - Merge branch 'MDAnalysis:develop' into develop - -commit 4381f44c8ecb5c9170e0c7a0638bc3b754f20fd0 -Author: Hugo MacDermott-Opeskin -Date: Thu Feb 24 10:48:03 2022 +1100 - - Refactor distance header to use wider integer representation (#3513) - - Fixes #3512 - * refactor calc_distances.h to use uint_64 indexing to avoid overflows - -commit a0f80160e31c54cc70116ff36d92adb9fbc4124a -Merge: eb57f95e7 55fa72f34 -Author: Rocco Meli -Date: Sun Feb 20 14:20:27 2022 +0000 - - Merge branch 'MDAnalysis:develop' into develop - -commit 55fa72f34f50294f088fe0a43b75eda792d3d366 -Author: Jonathan Barnoud -Date: Thu Feb 17 14:18:19 2022 +0100 - - Remove deprecated np.object (#3537) - - Switch from deprecated np.object to object. - -commit 26da934bf294a4a32e54b186b3b9b4c9b00e4aba -Author: Irfan Alibay -Date: Wed Feb 16 20:12:11 2022 +0000 - - Fix for leftover simtk imports in openmm tests (#3531) - - * fix imports for openmm tests - - * bit more heavy handed skip of whole module - - * Add missing author info - -commit 16edabd9ff14f9f0d908c8b2411dfa6b691cacbc -Author: Irfan Alibay -Date: Mon Feb 14 23:18:18 2022 +0000 - - switch from deprecated scipy.io.netcdf to scipy.io (#3530) - -commit 6b3a1603b8890ec4f537cc2a26f89430665f656f -Author: Philip Loche -Date: Mon Feb 14 07:49:43 2022 +0100 - - Continued dielectric analysis module (#2118) - - * Added dielectric constant analyse script - - * Update test_units.py - - * Restored Angstrom sign - - * Added option for make_whole + better docu - - * updated changelog - - * Restored accidently changed docu - - * Added more tests and checks - - * Added check for free charges - - * Use new total_charge and grouped tests - - * Updated tests - - * Added dielectric constant analyse script - - * Update test_units.py - - * Restored Angstrom sign - - * Added option for make_whole + better docu - - * Added option for make_whole + better docu - - * updated changelog - - * Restored accidently changed docu - - * Added more tests and checks - - * Added check for free charges - - * Use new total_charge and grouped tests - - * Updated tests - - * Bumped versionadded - - * Updated docs - - * Updated for MDA 2.0 - - * PEP8 - - * Added link to citation - - * Revert some changes in CHANGELOG - - * Cleanup citation - - * Apply suggestions from code review - - Co-authored-by: Irfan Alibay - - Co-authored-by: Richard Gowers - Co-authored-by: Jonathan Barnoud - Co-authored-by: Irfan Alibay - -commit 3b7590e5e9de93371c26572f0d4dc35a31d891cd -Author: Tyler Reddy -Date: Sat Feb 12 16:19:28 2022 -0700 - - BLD: comply with PEP518 (#3398) - - * BLD: comply with PEP518 - - * add a a `pyproject.toml` file to comply - with PEP518, and to allow for wheel builds - that leverage PEP517 - - * in short, in a fresh/naive Python environment - with no dependencies available, it is not currently - possible to use i.e., `pip install .` to install - MDAnalysis (or to use any of the other emerging tools - like poetry and flit that are PEP518 dependent) - - * this will change almost nothing about how we - operate builds in the near-term (still very `setup.py` - focused), but it does begin to bring us into alignment - with the future of the Python packaging ecosystem - - * this solves various "chicken and egg" problems like - "how does pip know your project needs setuptools - if it has to read setup.py, which contains elements - that require setuptools to read them to understand - what dependencies are needed" - - * I verified this works on an aarch64 ThunderX2 node - running RHEL with `python -m pip install .` successfully - building a wheel for MDAnalysis and installing it; many - other pieces of information can be added to this file, though - this `build-system` section is the most fundamental - - * add `packaging` as dependency in `pyproject.toml` - -commit e4ed4ff3886c8e1342b3e8741c9853ad6825defa -Author: Irfan Alibay -Date: Thu Feb 10 16:29:40 2022 +0000 - - Swap equal to allclose for StoR test float comparison (#3525) - -commit db0c3d3b28ffb1861b130d388b8a33f81c178239 -Author: yangtcai <77475012+yangtcai@users.noreply.github.com> -Date: Wed Feb 9 03:41:14 2022 +0800 - - Fix import warning (#3518) - - Fixes #3506 - * Fixes openmm import warning - - Co-authored-by: yylc - -commit 11d1b7feca9726c428d8869d8f77d215e7eba959 -Author: Oliver Beckstein -Date: Tue Feb 8 11:35:01 2022 -0700 - - updated template asv.conf.json to Python 3.8 (#3521) - - Fixes #3430 - - automated benchmarks were updated (see https://github.com/MDAnalysis/benchmarks/issues/11) - -commit 01c9dec4296d58a08f4c6f6effdbb8fd38bdeb95 -Author: Tyler Reddy -Date: Tue Feb 8 10:43:31 2022 -0700 - - DOC: fix SciPy intersphinx link. (#3522) - -commit 3c0875c7b25bf97a5a2d70f8c31bd661072911ec -Author: Irfan Alibay -Date: Thu Feb 3 14:39:47 2022 +0000 - - Prevent flush on closed NamedStream (#3507) - - * Prevent flush on closed NamedStream - - * update changelog and docs - - * revert versionchanged entry - -commit 7fa06a6fc7542a105163d9982ab6ad5cdb67aa26 -Author: Jonathan Barnoud -Date: Thu Feb 3 11:39:14 2022 +0100 - - Remove dead code from the TPR parser (#3516) - - Fixes #3515 - -commit 18bad9db0e803e8c0c37ec62f1cfdb1757979dea -Author: Jonathan Barnoud -Date: Thu Feb 3 11:38:45 2022 +0100 - - Raise TypeError when calling AtomGroup[None] (#3517) - - Fixes #3092 - * Raise TypeError when a group is indexed with None - -commit e482c39c9624259f617da16bae3b9aff3246d958 -Author: Jonathan Barnoud -Date: Wed Feb 2 14:31:25 2022 +0100 - - Update the TPR parser for Gromacs 2022 (#3514) - - ## Work done in this PR - * Update the TPR parser for Gromacs 2022 - - This commit adds the necessery test files. These were built using - gromacs 2022-rc1. The commit also adds the tests corresponding to these - files. - - Finally, this commit updates the TPR parser itself based on the changes - in `src/gromacs/fileio/tpxio.cpp` between gromacs 2021.5 and gromacs - 2022-rc1. - - Gromacs 2022-rc1 is available at https://manual.gromacs.org/documentation/2022-rc1/download.html - The changelog is available at https://manual.gromacs.org/documentation/2022-rc1/release-notes/index.html - - * Update doc and changelog for TPR from gromacs 2022 - -commit eb57f95e7242eed70495f04ecafa89f00501850e -Merge: 483d316b2 d593993eb -Author: Rocco Meli -Date: Tue Feb 1 15:56:54 2022 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit d593993eb5b3ab06ecc3562cb7572605544f77d0 -Author: Tyler Reddy -Date: Fri Jan 21 14:19:19 2022 -0700 - - WIP, CI: add newer msvc to Azure CI (#3399) - - Fixes #3509 - - ## Work done in this PR - * bump to new Azure windows image - more broadly - * `xfail` `test_augment` on Windows - per gh-3248 - -commit 64d67e1f7aec0726bee32ab12aed54107e5eaef6 -Author: Irfan Alibay -Date: Fri Jan 21 21:17:18 2022 +0000 - - Remove skipifs from streamio tests (#3508) - - Fixes #1534 - - * Remove skipifs for test_streamio and fix tests - * Add more global warning filters for expected warnings - -commit 3322ab2b9cb4987306225a574dde6ce1bae51fab (upstream/tpr-no-elem-warn) -Author: Atharva Kulkarni -Date: Sun Jan 16 21:16:32 2022 +0530 - - Fix executable path error handling in HOLE2 (#3496) - - Fixes #3493 - - # Work done in this PR - * Add exe_error imports - * Add OSError tests - * Unhardcode `sph_process` executable name - * Fix name handling for OSError message when missing hole executable - -commit 98dd08ce86928aafa678cb934645ffba122ee4ff -Author: Estefania Barreto-Ojeda -Date: Thu Jan 13 14:59:34 2022 -0700 - - Coverage of density raised to 100% [issue #3207] (#3249) - - Fixes #3207 - - - Add test to increase coverage of density code. - -commit 3488df3cdb0c29ed41c4fb94efe334b541e31b21 -Author: Richard Gowers -Date: Tue Jan 11 13:31:51 2022 +0000 - - Feature minimise vectors (#3472) - - * added minimum vectors function - -commit 4a6aee43515db6b954281efdf6d7092ec58452e2 -Author: Irfan Alibay -Date: Sun Jan 9 02:45:49 2022 +0000 - - Cleanup of CI actions & cron job (#3490) - - Fixes #1727 Towards #3052 #3442 - ## Work done in this PR - - Implement composite actions for similar steps across multiple workflow jobs - - Adds a fully tune-able composite workflow for conda/pip installing - - A variety of cron jobs (running at 3 am UTC on Sunday) - - pip only install - - install with numpy & scipy nightly dev versions - - "march=native mtune=native" cflags build - -commit d1fd7485a45a3ca971041a70636f396ff5a18d1f -Author: Guillaume Fraux -Date: Sat Jan 8 19:17:45 2022 +0100 - - Chemfiles version support update & switch from disutils.version (#3499) - - Fixes #3492 #3498 #3216 - * Use packaging.version.Version instead of deprecated distutils.version.LooseVersion - * Drop support for chemfiles 0.9 - -commit 1f082ec7641172bf40ff160e32e449aef7adb2ab -Author: Atharva Kulkarni -Date: Wed Jan 5 02:27:19 2022 +0530 - - Add support for millisecond and microsecond units (#3491) - - Fixes #3474 - -commit 79104dc14cf8567af9b349e42ea39a051d87d0a3 -Author: Irfan Alibay -Date: Tue Jan 4 03:12:57 2022 +0000 - - Fixes frame indexing in create_vmd_surface (#3489) - - Co-authored-by: Oliver Beckstein - - Changes made in this Pull Request: - - changes the loop over self.frames to index self.results.sphpdbs properly - - swaps internally the use of self.outfiles and self.sphpdbs instead of self.results.outfiles and self.results.sphpdbs - -commit f83c29fa3649860fdf0f23b60b32f5dbd4bae697 -Author: Irfan Alibay -Date: Tue Jan 4 01:01:21 2022 +0000 - - Switch from assert_equal to assert_allclose for float comparison tests (#3495) - - Fixes #3494 - -commit 6ac7dd29ecc348d906cfa9a22cee2fe0a08e3526 -Author: Irfan Alibay -Date: Thu Dec 30 18:42:42 2021 +0000 - - Add minimal deps py3.10 to linux CI matrix (#3458) - - Towards #3457 - - ## Work done in this PR - * Add minimum dependency py3.10 to linux CI matrix - * switch from using the biobuilds channel to bioconda - -commit 062143bef96414043021f243a44971c758057dfe -Author: Irfan Alibay -Date: Wed Dec 29 10:35:27 2021 +0000 - - Defaults TRZReader timestep to 1.0 ps (#3488) - - Fixes #3257 - ## Work done in this PR - * Switch TRZ dt behaviour to return 1.0 when not available - -commit 7df5a6157843d1f2a5c9e9d3ba8347eaf9f345de -Author: edisj <59893899+edisj@users.noreply.github.com> -Date: Tue Dec 28 13:00:34 2021 -0700 - - add parse_n_atoms() to H5MDReader (#3466) - - Fixes #3465 - ## Work done in this PR - * Adds parse_n_atoms method to H5MDReader - -commit ac01c9e3711d39f47cb284f0a33d062b4cf5cc5c -Author: Paul Smith -Date: Tue Dec 28 17:24:19 2021 +0000 - - Make HydrogenBondAnalysis handle empty selection strings (#3454) - - Fixes #3453 - - ## Work done in this PR - * Adds UserWarning to warn when selection string is empty - * Only guess hydrogens and acceptors if selection is `None` - * Add test for empty selection strings for HydrogenBondAnalysis - -commit e2c4f7032be52669e81958391c4f5c3efbe20a28 -Author: Richard Gowers -Date: Mon Dec 27 20:25:40 2021 +0000 - - Rs chirality (#3445) - - # Work done in this PR - * add R/S chirality to the RDKit parser - * added chirality docs to select_atoms - -commit cd7fdce0d0326ce37e2133d93cd71cd67efc693c -Author: Tyler Reddy -Date: Mon Dec 27 13:14:22 2021 -0700 - - CI: add Win 3.10 (#3461) - - Towards #3457 - - * Add py3.10 to Windows CI - * use `h5py` for all Python versions, including `3.10` - * restore the usage of the `gsd` package; it was only meant to be unpinned, not deleted - * restore the `xfail` for `test_write_with_drivers` on Windows for now, as this test seems - problematic once again for newer versions of `h5py` - -commit 02b62c272bd59b867bccf080e4236baf306405f1 -Author: Philip Loche -Date: Mon Dec 27 20:17:33 2021 +0100 - - type-hinting in Dihedral doc (#3482) - - * introduces new doc style with type hints (only in docs, not yet in code) - * more precise Dihedral doc (to help with mdacli) - * PEP8 fixes - -commit 5bf6359a821c085a1039ca414ce51ca2820722fb -Merge: 46c8badd8 9490241dc -Author: Richard Gowers -Date: Tue Nov 30 11:49:29 2021 +0000 - - Merge pull request #3468 from tylerjereddy/treddy_issue_3455 - - MAINT: update Cython imports - -commit 9490241dc08f18d50f65dd69dc551302a508d593 -Author: Tyler Reddy -Date: Sat Nov 27 19:26:23 2021 -0700 - - MAINT: update Cython imports - - * use `np.import_array()` to prevent convoluted issues with - newer versions of Cython when using `cimport numpy ..` in - Cython sources - - * in short, Cython and NumPy try to coordinate to do the right - thing with interwoven header inclusions, but this explicit call - prevents any confusion between the two - -commit 46c8badd8b8967dc25f8125ef87582490ab497e3 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Nov 22 12:28:34 2021 -0800 - - Use Mamba in ReadTheDocs (#3451) - - Fixes #3447 - -commit 735abb8c76d71e1dc8197d73ee6f5d1845634914 -Merge: a33e3031c 6afc2dc0c -Author: Richard Gowers -Date: Tue Nov 9 15:10:34 2021 +0000 - - Merge pull request #3441 from scal444/nsgrid_debug - - Add check for too many grids in NSGrid - -commit 6afc2dc0cda886c709bb83e52874c6a466c215bc -Author: Richard Gowers -Date: Tue Nov 9 15:09:28 2021 +0000 - - Update test_nsgrid.py - -commit 1be6f64c5610d3042f85f26690b700a2f0aeb243 -Author: Kevin Boyd -Date: Sat Nov 6 13:43:19 2021 -0700 - - Address review comments - - Used parentheses for string concatenation and a bool check converter - -commit b58048b2c443b5431ccd3e72a43495ead5c675b5 -Merge: 0c6fd4ad1 a33e3031c -Author: Richard Gowers -Date: Thu Nov 4 11:39:23 2021 +0000 - - Merge branch 'develop' into nsgrid_debug - -commit a33e3031cb6788b0bdb406d678b8178aaa2ecd6d -Merge: 0fd933d4a ab1bdb8a9 -Author: Richard Gowers -Date: Thu Nov 4 11:38:28 2021 +0000 - - Merge pull request #3440 from MDAnalysis/issue-3437-NewSegment_stringinterning - - Issue 3437 new segment stringinterning - -commit ab1bdb8a99515b43251aa05840a1ee600e0dbe34 -Merge: c88137d75 0fd933d4a -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Wed Nov 3 10:58:14 2021 -0700 - - Merge branch 'develop' into issue-3437-NewSegment_stringinterning - -commit 0fd933d4af2e9408a841bfd3ce4a375948b50406 -Author: Irfan Alibay -Date: Wed Nov 3 15:03:25 2021 +0000 - - Towards sphinx >= 3 (#3438) - - Fixes #3224 - Fixes #2667 - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - Co-authored-by: Oliver Beckstein - Co-authored-by: richard - -commit 0c6fd4ad1b78784fa865fa35d9a4df0726bcbe1e -Author: Kevin Boyd -Date: Tue Nov 2 16:46:48 2021 -0700 - - Fix more accidental autoformatting - -commit c440f0dcecc290fb20fe66faa975f906a1f0199a -Author: Kevin Boyd -Date: Tue Nov 2 16:44:44 2021 -0700 - - Add versionchanged - -commit f67b46c9e921072a895bc6f128b517510b4911c4 -Author: Kevin Boyd -Date: Tue Nov 2 16:39:17 2021 -0700 - - Undo some accidental autoformatting - -commit 6479298d090750070b138844aa882d02faa6c9af -Author: Hugo MacDermott-Opeskin -Date: Mon Nov 1 21:39:19 2021 +1100 - - Fix arch option in setup.py to work properly + not trigger on MSVC (#3429) - - Fixes #3428 - - ## Work done in this PR - - Replaces `march` keyword in setup with `extra_cflags` allowing user defined c/c++ flags to be passed at compile time - - Fixes the code paths so that the optimisation flags are parsed properly & not applied to the encore compile flags - -commit 685a6a05b0c450419430fe2cabea8c349c258785 -Author: Kevin Boyd -Date: Sun Oct 31 12:39:11 2021 -0700 - - Extract high-grid test to own fixture and add skip criterion. - - Enable test in macos runners which have sufficient memory - -commit 650620125a4c182eaeaa4c168dcd74ece552a480 -Author: Kevin Boyd -Date: Sun Oct 24 16:19:59 2021 -0700 - - Pep8 fixes - -commit 736f4cfeed8c1bed83fb3f6d2840bc43376fdcff -Author: Kevin Boyd -Date: Sun Oct 24 16:11:02 2021 -0700 - - Add Kevin Boyd to authors and changelog - -commit dff262b6a633b5a62340cd4e088fe54d141d8318 -Author: Kevin Boyd -Date: Sun Oct 24 16:08:39 2021 -0700 - - Automatically resize grids to avoid int overflow - - Rather than throwing an exception, the number of grids is capped, - not affecting the algorithm output - -commit 9e6daa805f1d398ae7f23589eac3f7043d3cc183 -Author: Kevin Boyd -Date: Sat Oct 16 11:25:33 2021 -0700 - - Add check for too many grids in NSGrid - - The NSGrid cython code uses integer indexing, which is typically - 32 bit. 3D grids with small cutoffs or giant box sizes can have - grids > 1000 per dimension, which leads to integer overflow when - trying to index the grids. - - Fixes #3183 - -commit c88137d75c1a5064c9d5877dd12396c45b851829 -Author: Richard -Date: Wed Oct 20 16:05:48 2021 +0100 - - I got potatoed - -commit 49f575074395624afa5adf83ce54a49a4220969c -Author: Richard -Date: Wed Oct 20 14:18:49 2021 +0100 - - remove redundant property - -commit e9c239e4e43d5abb83c46178b7472445d8bbf3e7 -Author: Richard -Date: Wed Oct 20 14:15:26 2021 +0100 - - better tests for issue #3437 - -commit ef8b20f3be268213b8d51250992fc091b5903701 -Author: Richard -Date: Wed Oct 20 13:48:27 2021 +0100 - - make AtomStringAttr et al public classes - -commit d674b361d675f9182e6aafb4f1c260ec100ae1db -Author: Richard -Date: Wed Oct 20 13:45:43 2021 +0100 - - derp - - last minute optimisations never pay off - -commit bc6c39a927dbbab63cfeaaf19fcd25d4b39678a0 -Author: Richard -Date: Fri Oct 15 16:37:30 2021 +0100 - - more docs - -commit 890ec088afe9951ea478e26fc7a28d85487af830 -Author: Richard -Date: Fri Oct 15 16:33:07 2021 +0100 - - docs for fix - -commit 60c61ab8ca48449ac02841ba512402853a32e265 -Author: Richard -Date: Fri Oct 15 16:22:24 2021 +0100 - - fixes issue #3437 - -commit 01661751303cb928878f1c8f0c87d6acad1866cc -Author: Richard -Date: Fri Oct 15 16:21:34 2021 +0100 - - tests for issue #3437 - -commit 9b37cd676f22bea14e715ade32b0714f1057a553 -Author: Richard Gowers -Date: Mon Oct 25 21:56:29 2021 +0200 - - Issue 3443 coordinateless objects (#3444) - -commit 483d316b2718d8e7843a4529255e6fd4da3c52db -Merge: ec71a6d9e 149eb504e -Author: Rocco Meli -Date: Tue Oct 12 17:17:02 2021 +0100 - - Merge branch 'MDAnalysis:develop' into develop - -commit 149eb504e35670568201af28306fa04462f6c100 -Author: Oliver Beckstein -Date: Tue Oct 5 09:05:32 2021 -0700 - - [MAINT] removed --py3k argument for pylint (#3424) - - * [MAINT] removed --py3k argument for pylint - - fix #3422 - - py3k checker was removed in pylint 2.11 - https://pylint.pycqa.org/en/latest/whatsnew/2.11.html#removed-checkers - * fix all pylint warnings - - ignore warning for justified global use in RDKit.py - - fix pylint W0233 warning - - removed deprecated "import imp" (not needed for Py > 3.3) - - disable pylint E1133 (not-an-iterable) on one line - * _ConnectionTopologyAttrMeta: removed superfluous type() and call super() earlier - connectionmeta is just adding more stuff onto the existing meta, and - this way round expresses that - - Co-authored-by: IAlibay - Co-authored-by: Richard - -commit e1c90ae4e3151423bc25ac9a6e111232c6022491 -Author: Ian Kenney -Date: Mon Oct 4 15:58:02 2021 -0700 - - TRRWriter, use ts.data['step'] if it exists (#3432) - - * Fixes #3350 - * use ts.data.get('step', ts.frame) instead of ts.frame for the step variable - * When writing TRR, see if ts.data['step'] exists - * If ts.data['step'] exists, use this for the output step value. Otherwise, use ts.frame, - consistent with previous behavior. - * Added ts.data test for TRRWriter - * Fixed typos in TRRReader and TRRWriter docstrings - * Updated CHANGELOG - * Added verionchanged entry to TRRWriter docstring - -commit 56027b1485ad45fb2d4c1b3d009121b633a867f2 -Author: Ian Kenney -Date: Mon Oct 4 14:57:10 2021 -0700 - - [DOCS] Updated RMS-fitting tutorial (#3421) - - - Fixes #3420 - - mobile0 should be the mobile CA positions less the mobile CA center of mass - - ref0 should be the ref CA positions less the ref CA center of mass - - Output values of rmsd() were different in previous versions - - subtracted AtomGroup center of mass now matches the alignment AtomGroup for both mobile and ref - - Rerunning the tutorial commands as outlined gave different print results, these have been updated - -commit 95791dde54851f1cb42aee89babcf1c01db23e93 -Merge: 39850215e 9d95f68ea -Author: Richard Gowers -Date: Sun Sep 26 18:07:28 2021 +0100 - - Merge pull request #3425 from mdd31/itpparserchargefix - - Itpparserchargefix - -commit 9d95f68eae8e6a950c7c95a61f9b5405d4323e88 -Author: Richard Gowers -Date: Sun Sep 26 18:07:08 2021 +0100 - - Update CHANGELOG - -commit 007ede65f432b70fe605118cab7c3e178e83f0de -Author: M. Driver -Date: Sun Sep 26 13:20:41 2021 +0200 - - update to add name of variable to __all__. - -commit 8e876bda568a278a277f08d295376d114cbfb14d -Author: M. Driver -Date: Sat Sep 25 10:24:10 2021 +0200 - - update to use assert_allclose instead of assert_almost_equal. - -commit a69cd8cd3695aea4309a5b800fac384ee301d605 -Author: M. Driver -Date: Fri Sep 24 12:12:36 2021 +0200 - - update location of update. - -commit 8a276cd8e8bd6a91b5de1639d627200f9b72f7a1 -Author: M. Driver -Date: Fri Sep 24 12:03:11 2021 +0200 - - resolve pylint issue. - -commit cadc658bca7a83c9c9ef47f8d0021af65cbb5ca8 -Author: M. Driver -Date: Fri Sep 24 12:01:13 2021 +0200 - - inclusion of simple test case to check resolution of issue #3419. - -commit 8b1de8ec1fcc2f19a486c3d5fb7f60c2ccfb66b1 -Author: M. Driver -Date: Fri Sep 24 11:02:56 2021 +0200 - - update Authors and changelog. - -commit f53da283c4fc0b271a61e4880f7cdb850ea48cff -Author: M. Driver -Date: Fri Sep 24 09:40:16 2021 +0200 - - Explicitly set dtype of charge and mass arrays in ITPParser- designed to solve issue #3419. - - Update to test as extra decimal place is now picked up from file. - -commit 39850215eae5a3e2c9d28a24dbc670646e305f79 -Author: Tyler Reddy -Date: Mon Sep 6 17:47:52 2021 -0600 - - MAINT: use github labeler (#3414) - - ## Work done in this PR - * for simple PR labels, leverage the GitHub Actions bot - to apply labels based on filepaths that are adjusted - * docs are here: - https://github.com/marketplace/actions/labeler - * based on example upstream: - https://github.com/scipy/scipy/pull/14677 - -commit 943da486c0947ce5f92b17b1b229a51a03a5dbda -Author: Marcelo C. R. Melo -Date: Fri Sep 3 21:00:56 2021 -0400 - - Update docs for in-memory trajectory to match new AnalysisFromFunction API (#3413) - - Fixes #3412 - - ## Work - * Update docs for in-memory trajectory to match new AnalysisFromFunction API of using results.timeseries - -commit 5c3fc1c15a0afe5dc90ba91ec234639e474b330f -Merge: 13265bc89 bae4d87e2 -Author: Tyler Reddy -Date: Wed Sep 1 09:24:43 2021 -0600 - - Merge pull request #3411 from MDAnalysis/setup-numpy-1.18 - - change error message numpy version 1.16 -> 1.18 - -commit bae4d87e29e621828cae982c5100f62c9bd4d61b -Author: Irfan Alibay -Date: Wed Sep 1 13:37:19 2021 +0100 - - change error message numpy versino 1.16 -> 1.18 - -commit 13265bc89523a8f28161ea42cdc55e75616c99b3 -Author: Oliver Beckstein -Date: Fri Aug 27 10:29:34 2021 -0700 - - added GitHub citations for main library (#3405) - - Fixes #3402 - ## Work done in this PR - - Add .bib file which currently cites the 2011 and 2016 papers - -commit a801482a45681cea0de1fcf9e476fc205114b226 -Author: Irfan Alibay -Date: Fri Aug 27 16:35:26 2021 +0100 - - xfail on h5md write nt test, more py3.6->3.7 changes (#3407) - - ## Work done in this PR - * Remove extra py3.6 things - * pin h5py to <3.4 for windows - -commit cb05695ca422c216406a0eae4040c782a2a03812 -Merge: b43f0bbc0 993ee16ba -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Aug 24 09:21:08 2021 -0700 - - Merge pull request #3400 from MDAnalysis/start_2.1.0 - - * Fixes #3254 - * Raises minimum python version to 3.7 and numpy to 1.18 in accordance to current NEP29 support. If we have an idea of when the release is going to be we can provide a more accurate minimum version here. Ideally I'd like 2.1.0 to be out faster than normal so we can add the RDKit fixes. - -commit 993ee16ba3e2b9ace07eaa4e178e0cd67b24e2b3 -Author: IAlibay -Date: Sun Aug 22 02:46:54 2021 +0100 - - Update universe to match new 3.7 lower limit - -commit e2a643464b8bcb1d8e0cc15578646ae34434ff84 -Author: IAlibay -Date: Sun Aug 22 02:01:29 2021 +0100 - - numpy 1.18.0 not on conda - -commit 41614eb9e2d57aa98dbaafc9635927d1c8fcd2c1 -Author: IAlibay -Date: Sun Aug 22 01:54:46 2021 +0100 - - Start off version 2.1.0, also set current NEP29 minimum - -commit 1cd2b3b4f4d70c24c8de234d35ba1a7f900212c0 (tag: release-2.0.0, upstream/master) -Author: Irfan Alibay -Date: Sat Aug 21 18:02:12 2021 +0100 - - release changes for 2.0.0 (#3397) - -commit b43f0bbc0b463e3a1659ef71817bb2ca042f0367 -Author: Hugo MacDermott-Opeskin -Date: Sun Aug 22 02:22:19 2021 +1000 - - Fix reading of lammpsdump ATOM card. (#3360) - - Fixes #3358 - Supersedes #2333 - - ## Changes made in this PR - - Allow coordinates in different conventions to be read by LAMMPSDumpReader - - Unhardcode LAMMPSDumpReader to expect a set number of columns - - S->R transform with distances.transform_StoR is no longer applied by default, only if the coordinates are in the scaled (xs,ys,zs) or scaled_unwrapped (xsu, ysu, zsu) convention - -commit ddb1d95f218e1645a708023d0bd00fae6a5afcd0 -Author: edisj <59893899+edisj@users.noreply.github.com> -Date: Sat Aug 21 08:09:24 2021 -0700 - - adding H5MDWriter to H5MD.py (#3189) - - Fixes #2866 - - ## Work done in this PR - - Adds H5MDWriter - - Adds entry on ts.data to Timestep documentation - - Adds duecredit entries to H5MD reader & writer - -commit bd0ed5dca76880282c0c6bdccbae79d320b37231 -Author: Irfan Alibay -Date: Fri Aug 20 22:35:50 2021 +0100 - - Add scale_factor write support for NetCDF writer (#3294) - - - Fixes #2327 - - Completes #3185 - - Adds `scale_factor` writing support to NCDFWriter. - - Changes the default `scale_factor` value for velocity writing to 20.455 in order to match the AMBER default - - - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - Co-authored-by: Oliver Beckstein - -commit 00c4c3c989168a5fce0f4cdb857f10ac61a318ed -Author: Oliver Beckstein -Date: Fri Aug 20 12:55:21 2021 -0700 - - Fix writer apidocs (#3393) - - Fixes #3392 - - * change Coordinate Writer API - - writers are not required to process start, stop, step, which is what - all our code does anyway - - clarified that writer needs to ignore kwargs that they cannot process - - clarified that __init__ can delay actual I/O until Write - - * doc cleanup in coordinates and converters - - fix links to Trajectory API - - link coordinates.ConverterBase to MDAnalysis.converters - - minor reST fixes - -commit 45ad91a210802fe2aa3f5ddd44217a7356df49bb -Author: Irfan Alibay -Date: Thu Aug 19 19:25:37 2021 +0100 - - Add userguide information to docs (#3391) - - * Add userguide information to docs - * minor text changes in top level doc - - show conda installation instructions before pip - - capitalize User Guide and Quick Start Guide - - Co-authored-by: Oliver Beckstein - -commit a40c23bddc52a306254e963646aa881ce9a5de0b -Author: Irfan Alibay -Date: Thu Aug 19 18:02:03 2021 +0100 - - Adds temporary warning on accuracy of RDKit converter (#3390) - - * Adds temporary warning on accuracy of RDKit converter - see https://github.com/MDAnalysis/mdanalysis/pull/3044#issuecomment-900521290 - -commit 55ffd255013dac427be3a8f4cf7962a4a886b712 -Author: Cédric Bouysset -Date: Wed Aug 18 17:57:13 2021 +0200 - - Passing arguments to the RDKitConverter from `select_atoms` (#3324) - - Fixes #3319 - - ## Changes made in this PR - * Adds the rdkit_kwargs parameter to the select_atoms method for passing arguments to the RDKitConverter. - -commit f5e9603f35b1e1587c1a1583793374fbfa0f80c5 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Aug 17 13:41:20 2021 -0700 - - Add asunique, change unique, change atom selection behaviour (#3368) - - Fixes #3364 #2977 - - ## Work done in this PR - - Add .asunique. This function (through ._asunique) now does all the grunt work in making unique groups and caching - - Change .unique to always return a copy of the sorted unique group - - Add .issorted - - .unique is no longer cached. _cache['unique'] no longer exists - - .sorted_unique and .unsorted_unique are now cached - - .unsorted_unique and .sorted_unique can be the same group, which can be self - - Added .cache_properties - - uniqueness and sorted properties now propagate to children. They did not use to, the new function is called `_set_unique_caches_from` - - Add ability to selectively sort `select_atoms` calls through `sorted` argument - -commit 7ce532e2992b730db6bf4ff93978112d29b13cae -Merge: f8bb8ecf6 902416750 -Author: Richard Gowers -Date: Mon Aug 16 15:25:13 2021 +0100 - - Merge pull request #3388 from MDAnalysis/issue-3329 - - Adds missing timestep equality tests - -commit 902416750d26cfe251e2a959ab0465369ffcbc4f -Author: IAlibay -Date: Mon Aug 16 02:55:47 2021 +0100 - - Actually use parametrize - -commit 03ef1ed7eb945438c2da1bb6b5fca002573723f2 -Author: IAlibay -Date: Mon Aug 16 01:59:04 2021 +0100 - - Adds missing timestep equality tests - -commit f8bb8ecf615fdf1760965de35ab9d50796275c47 -Author: Rocco Meli -Date: Fri Aug 13 16:59:30 2021 +0200 - - MOL2 parser populates elements attribute (#3063) - - Fixes #3062 - - ## Work done in this PR - - Adds the ability to read elements from MOL2 files when using SYBYL atom types - -commit aba8b7d2604777ab0e1750ed4c21428a5559590b -Author: Irfan Alibay -Date: Fri Aug 13 14:01:54 2021 +0100 - - Ensure that GRO reader treats lack of unit cells consistently (#3380) - - Fixes #3305 - - ## Work done in this PR - * Ensure that GRO reader treats lack of unit cells consistently - -commit 09f50ecc0c4425f089059b53d1f11edee9bbecb6 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu Aug 12 12:28:14 2021 -0700 - - Alias bfactor to tempfactor (#3345) - - Fixes #1901 - - ## Work done in this PR - - Aliases bfactor to tempfactor - - Adds deprecation warnings for bfactor - -commit 6bf99632f7bc8498a18a66fdd620e59b0fcc0999 -Author: Irfan Alibay -Date: Thu Aug 12 19:17:25 2021 +0100 - - Adds warning for writing DCD files with no dimensions (#3379) - - * fix #3303 - * Adds warning for writing DCD files with no dimensions - * Update DCD.py (code and add note to docs) - * Add test for warning - -commit 586ae3dc82098328429bf74545259a3fcc50d720 -Merge: 1e3118021 38f703297 -Author: Tyler Reddy -Date: Wed Aug 11 19:23:01 2021 -0600 - - Merge pull request #3384 from MDAnalysis/codecov-action-v2 - - Increase codecov action version to v2 - -commit 38f7032972c570285b5c828347dbe6f5420b0329 -Author: Irfan Alibay -Date: Sun Aug 8 13:10:15 2021 +0100 - - increase codecov action version - - change ahead of deprecation - -commit ec71a6d9e0670b745bb742fca6a645fdf71df588 -Merge: a4e9f155c 1e3118021 -Author: Rocco Meli -Date: Tue Aug 3 10:37:43 2021 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 1e31180217e4b42b6b7b68553dbd6b4045b207d4 -Merge: 65319046c 2f5fb15b9 -Author: Richard Gowers -Date: Sat Jul 31 21:39:32 2021 +0100 - - Merge pull request #3378 from MDAnalysis/issue-3327 - -commit 2f5fb15b949d14ffb3b44aa05ab7d49380f7fad8 -Author: IAlibay -Date: Sat Jul 31 20:28:36 2021 +0100 - - Fix pep8 - -commit a40460e37f81a7243dc1746cfbba116e83691f3b -Author: IAlibay -Date: Sat Jul 31 20:22:59 2021 +0100 - - Add simple test - -commit 754f90b8af3b37ddb401c15f572b50870465eb70 -Author: IAlibay -Date: Sat Jul 31 20:20:45 2021 +0100 - - Remove unused unitcell lines - -commit 65319046c49f4bce5e49949b7ab451039adcbd67 -Merge: 591da9499 ecf5f29db -Author: Tyler Reddy -Date: Thu Jul 29 20:14:32 2021 -0600 - - Merge pull request #3376 from MDAnalysis/fix-3374 - - Increase minimum numpy version for aarch64 CI. - -commit ecf5f29db255cbc83d44bd6afaa09dcdc956c914 -Merge: e955e388e 591da9499 -Author: IAlibay -Date: Thu Jul 29 17:01:27 2021 +0100 - - Merge branch 'develop' into fix-3374 - -commit 591da9499f9844ec43a2b6b5c35a37bb01037739 -Author: Irfan Alibay -Date: Thu Jul 29 16:53:35 2021 +0100 - - Pin pytest-cov, remove coveralls (#3369) - - Co-authored-by: Guillaume Fraux - -commit e955e388e04d32cd2f3adee0898d9cbcddd852cf -Author: IAlibay -Date: Thu Jul 29 16:30:17 2021 +0100 - - Remove unused travis yaml file - -commit fc0ec63054f490cf8879a27d5f653c7146301f23 -Author: Irfan Alibay -Date: Thu Jul 29 16:20:27 2021 +0100 - - Increase minimum numpy version for aarch64 CI. - -commit 8f9f402fe65d6a90e88b60b6da735c130425f00e -Author: Hugo MacDermott-Opeskin -Date: Mon Jul 5 16:32:13 2021 +1000 - - Add warning for unwrapped coordinates in MSD module (#3357) - - Fixes #3074 - - ## Work done in this PR - * Adds warning for unwrapped coordinates in MSD module - -commit 64840d5df32ecb73ceadcc022dc4b71738537404 -Merge: e4c7673f8 68c2509df -Author: Richard Gowers -Date: Mon Jun 28 18:25:53 2021 +0100 - - Merge pull request #3353 from MDAnalysis/issue-3353-unwrapsort - - Fixed wrong atom sorting in _split_by_compound_indices - -commit e4c7673f87db4708e2a2a83ce52c7154cefcc64d -Merge: 4154e6304 9fef9a6a6 -Author: Richard Gowers -Date: Fri Jun 25 08:59:38 2021 +0100 - - Merge pull request #3356 from MDAnalysis/TRZ_fixes - -commit 9fef9a6a668ed8049b1de0cb1cd8ce781e709895 -Author: richard -Date: Mon Jun 21 10:45:14 2021 +0100 - - test for trz zero box - -commit 4154e6304a38c076ef008907ed393d36ba5958a8 -Merge: a6d4ffc26 6eacb88ff -Author: Richard Gowers -Date: Mon Jun 21 10:34:51 2021 +0100 - - Merge pull request #3354 from IAlibay/macOS-11 - - Adds macos-11 runner - -commit 1e61beeb4315982c8e98b980459dfa57515f38a7 -Author: richard -Date: Mon Jun 21 10:30:52 2021 +0100 - - fixes #3307 - - writing a trz file with dimensions=None issues a warning - -commit 6eacb88ffcab99d29e3e5990e667c2b889650865 -Author: IAlibay -Date: Sat Jun 19 15:17:14 2021 +0100 - - Set min to 10.9 given that is the py3.9 minimum - -commit 064ef473c1a3a02ec2faa1e956cfdffa41e3f4af -Author: IAlibay -Date: Sat Jun 19 14:47:09 2021 +0100 - - Raise deployment target to 10.14 - -commit 3762b90c159db9a89018ed78ba06ace083db7bd4 -Author: IAlibay -Date: Sat Jun 19 13:25:02 2021 +0100 - - 10.15 not 10.5 - -commit c2ca2902530e67e9efd6ff1a5ca89093e62cc4a6 -Author: IAlibay -Date: Sat Jun 19 13:15:58 2021 +0100 - - remove psutil fully, add HOLE to macOS-10.5 py3.6 CI - -commit 9ad009dbbc461e3c115429d8991bd576f1f48bf0 -Author: IAlibay -Date: Sat Jun 19 12:58:09 2021 +0100 - - Do we even need psutil? - -commit 8602305e4370503e6c5d068148dcff7208b8393b -Author: IAlibay -Date: Sat Jun 19 12:45:31 2021 +0100 - - try activating macos-11 runner - -commit a4e9f155c375684e84f4d557e660f687499f8c76 -Merge: b6bcd3c1b 8618b7df9 -Author: Rocco Meli -Date: Thu Jun 17 17:05:43 2021 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 68c2509df869f6b60def5039467c326b09c918be -Author: Manuel Nuno Melo -Date: Thu Jun 10 12:58:53 2021 +0100 - - Fixed wrong atom sorting in _split_by_compound_indices - - Closes #3353 - -commit a6d4ffc26375a44d4aaa53de88d193b9e1e645e9 -Author: Cédric Bouysset -Date: Fri Jun 4 22:15:28 2021 +0200 - - Raise error if partial ResidueInfo in RDKit mol (#3325) - - * raise error if partial metadata - - * add test - - * update docs and changelog - - Co-authored-by: Jonathan Barnoud - -commit bf1370e3462e0c4c96f2b2f3c2eaa1410fb181fb -Author: Irfan Alibay -Date: Thu May 27 23:28:03 2021 +0100 - - Clarifies the way MDAnalysis deals with MOL2 dimensions (#3340) - - Fixes #3331 - - # Work done in this PR - - Asserts dimensions is None for MOL2 file writing/reading - - Clarifies that MDA does not currently deal with @CRYSIN records. - -commit 497f74e798bb79da73873aeb550a85d524aa2abc -Author: Irfan Alibay -Date: Thu May 27 23:26:30 2021 +0100 - - Adds python_requires >= 3.6 to develop (#3338) - - Fixes #3333 - # Work done in this PR - * Adds python_requires > 3.6 - * Remove deprecated requires entry from setup.py - -commit 13e1a0f6cec8a234e780e0a95dc2a91741b031dc -Author: Philip Loche -Date: Thu May 27 23:04:39 2021 +0200 - - Use Results class for PCA Analysis (#3285) - - Fixes #3275 - - # Work done in this PR - * Make PCA use the Results class - * Added relevant tests - * Updates and fixes to docs - * cross-referenced rmsip <-> cumulative_overlap - - Co-authored-by: Oliver Beckstein - -commit 560feed11603dc40c913040620dab5d5af8c54ac -Author: Fiona Naughton -Date: Wed May 26 15:34:43 2021 -0700 - - Allow PCA to run with given reference mean values (#3296) - - * Fixes #2728 - * Changes made in this Pull Request: - * Fix shape of positions array from provided reference atomgroup so the PCA will actually run - * change means from atomgroup to array - * Update the corresponding test to actually run with given mean values - * Removed mean_atoms from PCA - * update CHANGELOG - * update docs - - Co-authored-by: Oliver Beckstein - Co-authored-by: Irfan Alibay - -commit 3500131284b2d91846fda9696f569bc1f6bfe741 -Merge: 401798c0e c4b021d36 -Author: Richard Gowers -Date: Sat May 22 22:01:22 2021 +0100 - - Merge pull request #3332 from MDAnalysis/prep-2.0.0b - - Update pypi-description.rst based on README.rst - -commit c4b021d36ec97b434dd9a30aa037d2ac0e641e7b -Author: IAlibay -Date: Sat May 22 21:49:13 2021 +0100 - - Update pypi-description.rst based on README.rst - -commit 401798c0e2f26ca65253fd61645b997b8ef54545 -Author: Richard Gowers -Date: Sat May 22 21:34:27 2021 +0100 - - WIP: Issue 1738 (#3132) - - Fixes #1738 - Fixes #2698 - Fixes #2210 - - Changes made in this Pull Request: - - `ts.dimensions` gives a **view** of the box info - - `atomgroup.dimensions` gives a **copy** of the box info - - no longer use `ts._unitcell` any more (use `ts.dimensions`) - - `ts.dimensions` can be `None` for no box info, was previously often all zeros, but not consistently. This means blindly calling e.g. `distance_array(..., box=ag.dimensions)` will just work - - Removes reader specific `Timestep` objects, now everything works from `base.Timestep` - -commit ff60cbc5b52ce7d5fe08b5bae82c212fabb8ffaf -Author: Irfan Alibay -Date: Sat May 22 20:03:42 2021 +0100 - - Switch openmm from MIN to EXTRA CI dep (#3323) - - * Fixes location of OpenMM as an non-minimum dependency for CI - * Checks that CI works without OpenMM - -commit 3b7755ba80184ed670a19b7aafacdb38e3e30c6d -Merge: acc713c27 abe62d746 -Author: Richard Gowers -Date: Sat May 22 17:56:23 2021 +0100 - - Merge pull request #3312 from fiszczyp/fs_dlpoly_history - - DL_POLY HISTORY may contain cells even for non-periodic simulations - -commit abe62d746f7b045ba79408b219d570f05bd7604c -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Sat May 22 16:55:06 2021 +0100 - - Added to authors - -commit acc713c272bcb33d9047fc30d6d0c2d578767366 -Merge: b1c438ffa 04d9a10c1 -Author: Richard Gowers -Date: Fri May 21 18:55:52 2021 +0100 - - Merge pull request #3316 from MDAnalysis/hotfix/openmm-segment - -commit b1c438ffaaebd797fec3d4290c9ffb40f0d89a83 -Author: Yuxuan Zhuang -Date: Fri May 21 18:30:33 2021 +0200 - - Add pickling to Results Class (#3311) - - Fixes #3309 - -commit 04d9a10c1804b0804735c9f0b61356bb33171763 -Author: Jonathan Barnoud -Date: Fri May 21 17:08:33 2021 +0100 - - Fix broken test - -commit 1f956d3c7cdad94e3cbd38986d2878c433acd1aa -Author: Jonathan Barnoud -Date: Fri May 21 16:31:39 2021 +0100 - - Set the segids as str in the OpenMM parser - -commit 656848c0435965dae9f2f4b152258c8a48a2ecd8 -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Fri May 21 12:46:33 2021 +0100 - - EOFError if wrong files passed to HistoryParser - -commit 69c08cf93c692ccb32c7e56d3a2d441ff83e94c5 -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Fri May 21 12:28:41 2021 +0100 - - Cache n_frames - -commit e4b2a4570d2ba33c2d121974d8eb7bb35a805c1d -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Fri May 21 11:07:40 2021 +0100 - - Cache n_frames. - -commit d9bb45434e90d766e18bebe901d5e3b2d2b09f70 -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Fri May 21 10:49:52 2021 +0100 - - Added DL_POLY4 minimal cell HISTORY to datafiles - -commit f9dccaf9bcc38ad00b415d5146e34cf536e19675 -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Thu May 20 17:32:33 2021 +0100 - - Tests for HISTORY with cell dimensions and imcom 0 - -commit 9889101a8ad5335a1bc4726f04390d2725efb089 -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Thu May 20 16:52:49 2021 +0100 - - Added CHANGELOG (Issue 3314). - -commit 833e9ab6bfa848656ea029e0c2c5291ccc79805b -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Thu May 20 16:21:05 2021 +0100 - - Added CHANGELOG. - -commit b07d6c161143b7b40cff6418bffaba97a017298c -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Thu May 20 15:54:28 2021 +0100 - - Cleanup - -commit 82b1ba4b6d5a739c8db93fc8943690668e0e7278 -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Thu May 20 15:53:38 2021 +0100 - - Cleanup - -commit 6c212175285ce2deba924ffdf449658ca6ae1c67 -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Thu May 20 15:28:08 2021 +0100 - - Rollback _reopen - -commit d1f3d1d1ab20396159e634f49cc7faaeaee20be2 -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Thu May 20 15:22:27 2021 +0100 - - HISTORY may contain cell if imcom=0 - -commit e6b3c2fe208c506b6f61b9f9d58f46be9d09e22d -Author: Philip Loche -Date: Thu May 20 12:00:32 2021 +0200 - - Consistent ` : ` in Analysis modules (#3308) - - * Consistent formatting of `:` in Analysis modules documentation. - -commit a24317099e455c711fd3187cb0471f4a21753cd9 -Author: edisj <59893899+edisj@users.noreply.github.com> -Date: Thu May 20 02:58:36 2021 -0700 - - Use read_direct() in H5MDReader (#3293) - - * using read_direct() for H5MDReader - -commit 92f12d828e3def2ebc0f6d2cc9b14bd77eef27a9 -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Wed May 19 18:06:36 2021 +0100 - - DL_POLY HISTORY can contain cell if nonperiodic - -commit dc378158d2c289f9c829004673a58d077546ac16 -Author: Filip Szczypiński <47000594+fiszczyp@users.noreply.github.com> -Date: Wed May 19 17:51:52 2021 +0100 - - Cell is now also possible for non-periodic systems - -commit 6b4eea02081bec633ed90f44416b350d7d7ab629 -Merge: 122b88466 1cc193917 -Author: Richard Gowers -Date: Fri May 14 15:41:13 2021 +0100 - - Merge pull request #3299 from MDAnalysis/master_merge - - WIP: Master merge - -commit 122b884662a285aa74e8476af2fbe945327ad285 -Author: Irfan Alibay -Date: Fri May 14 15:00:07 2021 +0100 - - [CI] Change concurrency group naming (Issue #3301) (#3302) - - * change group naming - - * cycle CI - - * Cycle back - -commit 1cc193917affdaf25382f4cbf5e540c174d32265 -Author: IAlibay -Date: Fri May 14 09:26:10 2021 +0100 - - fix invalid escape sequence match - -commit 66acbdf4a42cf32ada4fad6b1e0d5a43a5e95037 -Author: Irfan Alibay -Date: Fri May 14 14:44:07 2021 +0100 - - Update testsuite/MDAnalysisTests/core/test_universe.py - - remove as_Universe test - -commit 4dc31dcb311cb2b6315cd8bd70d8cfbbe83495ec -Author: IAlibay -Date: Fri May 14 08:57:36 2021 +0100 - - revert wrap changes, fix references, remove unused import - -commit 0f730939e1cb42148e2bae6168a2d8789500d5c3 -Author: Irfan Alibay -Date: Fri May 14 12:15:31 2021 +0100 - - Apply suggestions from code review - -commit 80ce50d6af6e8f2836681300f728f5a5dc6bcda9 -Author: Irfan Alibay -Date: Thu May 13 23:11:54 2021 +0100 - - Add concurrency group (#3300) - - Adds a concurrency group based on github.head_ref to cancel previously running workflows for a given pull request. - -commit b027575c299251fe8f39ed3bc55d209f5afa13b4 -Author: Irfan Alibay -Date: Thu May 13 21:48:23 2021 +0100 - - remove deprecate import - -commit 80467a77361dc630b83226781f0cbbff6cdf7393 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu May 13 13:35:44 2021 -0700 - - Update package/MDAnalysis/core/selection.py - - Remove redundant selections classes - - Co-authored-by: Irfan Alibay - -commit 22122b45760896a0fbac004d0457088c56814ca6 -Author: Irfan Alibay -Date: Thu May 13 20:20:22 2021 +0100 - - remove chainID warning - -commit db2a6d8dee41535f98449b5bfea8549dd5026d38 -Author: Irfan Alibay -Date: Thu May 13 20:15:54 2021 +0100 - - Update testsuite/MDAnalysisTests/converters/test_parmed.py - -commit c3b776bf782d0b358b8ff4fcfadcd1bd7359419d -Author: Richard Gowers -Date: Thu May 13 20:08:24 2021 +0100 - - Update test_groups.py - -commit 01ee954bb0e17a9251c340170aec5f1fa22366ea -Author: IAlibay -Date: Thu May 13 20:02:05 2021 +0100 - - chainID warning - -commit 947f497db7757bdf2dbd50b120aceedc5403a8c7 -Author: Irfan Alibay -Date: Thu May 13 14:52:31 2021 +0100 - - Apply suggestions from code review - -commit 3938f92574259a38952984657987910e614325ab -Author: IAlibay -Date: Thu May 13 14:49:30 2021 +0100 - - Review suggestions - -commit 9c6e751e19a2d19e6c2eaecb8b8838730b5cf61b -Author: IAlibay -Date: Thu May 13 14:39:33 2021 +0100 - - Add travis cron job back - -commit 03a9a0b8b8b6be74f4fd7c169c80abdfee27bbdd -Author: Irfan Alibay -Date: Thu May 13 13:54:44 2021 +0100 - - Apply suggestions from code review - -commit d25edd04eaf574bc9a3c710f4a4e004ca2703367 -Author: Irfan Alibay -Date: Thu May 13 13:43:03 2021 +0100 - - Apply suggestions from code review - -commit a4f5438ceb280001033450ff02b179d213a2ea65 -Author: Richard Gowers -Date: Thu May 13 12:07:26 2021 +0100 - - Update utils.py - -commit 6e1815e6ee1bc2dcb5d099f6805252f7ebc02ce0 -Author: Richard Gowers -Date: Thu May 13 11:19:44 2021 +0100 - - Update setup.py - -commit aa5825290c15c0a93cb55fd8aaead4ed7c1aa64a -Author: Richard Gowers -Date: Thu May 13 11:18:29 2021 +0100 - - Update hbond_autocorrel.py - -commit f570784474b703669c6bee22eb863efc9157e0d4 -Merge: 53b4baef5 8618b7df9 -Author: richard -Date: Thu May 13 11:13:41 2021 +0100 - - Merge remote-tracking branch 'origin/develop' into develop - -commit 53b4baef5b1ca4697a9239237fd8c5caa8bdcc99 -Merge: d734a8964 1e456e85b -Author: richard -Date: Thu May 13 11:11:45 2021 +0100 - - Merge remote-tracking branch 'origin/master' into develop - -commit 8618b7df97987969a634cfa6d583779dc36118ac -Author: Shujie Fan -Date: Tue May 11 10:24:34 2021 -0700 - - Make classes in rdf use the Results class (#3284) - - Fixes #3284 - - ## Work done in this PR - * make rdf AnalysisBase classes use Results class for storing data - -commit 6d5ef34292899958ea2a0148388ecc47cf499da1 -Author: Cédric Bouysset -Date: Tue May 11 12:45:23 2021 +0200 - - Improving the RDKitConverter caching system (#2942) - - Fixes #2958 - - ## Work done in this PR - * use lru_cache for the RDKit converter - * add force parameter to allow for the conversion of systems with no hydrogens - -commit d0fc581fe36c56352a8668a6f782a2e5ccd3f01e -Author: Rocco Meli -Date: Tue May 11 00:35:20 2021 +0200 - - Use Results class for WaterBridge analysis (#3287) - - * Fixes #3270 - * update WaterBridge analysis to use results (but keep deprecated original attributes) - - results.network - - results.table - - results.timeseries - * update docs - * add tests for deprecations - * update CHANGELOG - -commit ca1bd9cb4e12cf7c63e882d9ae6097b7977ff0c0 -Author: Irfan Alibay -Date: Mon May 10 22:57:17 2021 +0100 - - Remove flags section from core docs (#3298) - -commit cef7d3fc566ec313a639a92506f81420da7c9358 -Author: Cédric Bouysset -Date: Mon May 10 21:11:36 2021 +0200 - - Converters API (#2882) - - Fixes #2790 - - ## Work done in this PR - * Creates a new converters API - * Makes u.atoms.convert_to("PACKAGE") case insensitive - * Allows passing kwargs to converters: u.atoms.convert_to("rdkit", NoImplicit=False) - * Adds u.atoms.convert_to.package() methods automatically from the metaclass magic, with TAB completion support, and docstring from the converter - * Moves RDKit, Parmed, and OpenMM to MDAnalysis.converters - - Authored-by: Cédric Bouysset - -commit 1a11ac8c747435415f54a74bfec77affb3015622 -Author: Irfan Alibay -Date: Sun May 9 22:39:09 2021 +0100 - - Unpin pytest (#3297) - -commit d734a8964d4fbdf7686cbdac2017d90c3ee67031 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sat May 8 18:51:50 2021 -0700 - - remove np.int and np.float (#3295) - - Fixes #3113 - - np.int and np.float is deprecated and will not work for numpy 1.20+ - - Changed np.int in RDKit tests to np.int32 and np.int64 - -commit a9eafab2e29c62319f817bcc7842792bf61ec03f -Author: Guillaume Fraux -Date: Sat May 8 18:49:51 2021 +0200 - - Update to chemfiles 0.10 (#3126) - - * Update to chemfiles 0.10 - - * Pin chemfiles to a version >=0.9 - - * Put conda-forge first in the list of channels - - Otherwise conda picks outdated version of libssh2 from biobuilds, which links to - non-existing libopenssl.so.1.0.0 - - * Add a test for chemfiles version check - - * Refactor ChemfilesWriter to follow the same code as the XYZ writer - - * Update condition checking for missing cell data - - * Update package/MDAnalysis/coordinates/chemfiles.py - - Co-authored-by: Oliver Beckstein - -commit f5c9159325f19b3203e54801b1a7eb5d3b8fe9ed -Author: Philip Loche -Date: Sat May 8 11:27:14 2021 +0200 - - Switch PersistenceLength to Results class (#3289) - - Fixes #3291 - - ## Work done in this PR - * Switch PersistenceLength to Results class - -commit 0986c7362a1c9fe946a4aafd025dea1e0bf6416b -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Fri May 7 18:51:38 2021 -0700 - - Use Results in Hole2 (#3292) - - * Fixes #3269 - * hole2 analysis class uses Results - * Tidies some code (e.g. self.frames is now part of AnalysisBase) - * added versionchanged and deprecation - * add tests - * update CHANGELOG - -commit 51fa4e4fdad411ed3e24701b44bb9340f1bdec18 -Author: Philip Loche -Date: Sat May 8 02:16:28 2021 +0200 - - Switch DistanceMatrix to Results class (#3288) - - * Fixes #3290 - * Switch DistanceMatrix to Results class - * add tests for deprecations - * Updated CHANGELOG - -commit 0e7d2f9f71a1796a470551232a8a93666f08d644 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Fri May 7 15:47:38 2021 -0700 - - Move results attributes of helix_analysis to Results (#3279) - - * Fixes #3268 - * Fixes #3267 - * Changes made in this Pull Request: - - Moved attributes to results - - changed versionchanged to the right number - * note: no need for deprecation notes as helix_analysis is new in 2.0.0 - -commit be3ec1b837de4da92c524356caa97e2ac5fb0c4f -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Fri May 7 15:00:57 2021 -0700 - - alias __setattr__ to __setitem__ in Results (#3281) - -commit f8b20fb769e90ff583894b50e4a8f69f0298dc40 -Author: Irfan Alibay -Date: Fri May 7 21:31:06 2021 +0100 - - Make align AnalysisBase classes use the Results class (#3280) - - Fixes #3278 - Towards #3261 - - ## Work done in this PR - * Switch align AnalysisBase classes to use Results class - - Co-authored-by: Oliver Beckstein - -commit 8deaa1e6f825b5acdec12dfe965efd878f64eb86 -Author: Irfan Alibay -Date: Fri May 7 19:25:23 2021 +0100 - - Switch hbonds to results.hbonds for HydrogenBondAnalysis (#3283) - - - Fixes #3271 - - Towards #3261 - - Switch hbonds to results.hbonds for HydrogenBondAnalysis - - Some docstring changes - - add tests for deprecated features - - update CHANGELOG - -commit b6bcd3c1b40d2e78ef44bcd66f84af8b13bda6b7 -Merge: d7bbd32f8 d7b3c2481 -Author: Rocco Meli -Date: Fri May 7 15:13:23 2021 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit d7b3c2481f43a5a1e39065058c52b1d0eb6672a0 -Author: Zhiyi Wu -Date: Fri May 7 12:18:33 2021 +0100 - - bug fix: double counting water in Water bridge analysis (#3120) - - Fixes #3119 - - * Fixes bug linked with double counting of waters in WaterBridgeAnalysis - -commit da46e8406b863503004daa06686ba86da0428f39 -Author: Irfan Alibay -Date: Fri May 7 01:18:55 2021 +0100 - - Switch rms.RMSD and rms.RMSF to using the Results class (#3277) - - * Fixes #3274 - * Towards #3261 - * Switch rms.RMSD and rms.RMSF to using the Results class - -commit a43c0a0deeb21c346d7683102fe1ebdb563afbbd -Author: Irfan Alibay -Date: Fri May 7 00:30:57 2021 +0100 - - Move angles to results.angles for dihedral classes (#3266) - - Towards #3261 - - ## Work done in this PR - * Move angles to results.angles for dihedral classes - - Co-authored-by: Oliver Beckstein - -commit b6ae72fc303c88707a8b382ee9145739ec1c1187 -Author: Irfan Alibay -Date: Thu May 6 23:36:16 2021 +0100 - - Moves msd results to use the Results class (#3265) - - Towards #3261 - - ## Work done in this PR - * Moves msd results to use the Results class - - Co-authored-by: Oliver Beckstein - -commit 503cf1ec68c26d05565d1ac442eb4f799c72da10 -Author: Irfan Alibay -Date: Thu May 6 22:50:02 2021 +0100 - - Switch BAT to use Results (#3273) - - Fixes #3272 - - ## Work done in this PR - * Switch BAT to use Results - -commit d7bbd32f818d8fb325a175fb6bd1cbeac741776e -Merge: c57697e9e 2c714fccd -Author: Rocco Meli -Date: Thu May 6 23:18:34 2021 +0200 - - Merge branch 'MDAnalysis:develop' into develop - -commit 2c714fccd95d8b05f807e38175557e398199b1d6 -Author: Irfan Alibay -Date: Thu May 6 19:24:01 2021 +0100 - - Make contacts.Contacts use the Results class (#3264) - - Towards #3261 - - ## Work in this PR - * Use analysis.base.Results to store timeseries data for contacts.Contacts. - * Deprecate `timeseries` in favour of `results.timeseries`. - -commit 44506be90c64599e78e3e3bc84d970affc78a0a3 -Author: Irfan Alibay -Date: Thu May 6 18:24:24 2021 +0100 - - Make DensityAnalysis use the Results class (#3263) - - * Towards #3261 : - deprecate .density in favour of .results.density. - * Update DensityAnalysis to use new Results class - * Update changelog and docstring - * Remove unused import - * add test for deprecation warning - -commit b5bff33098fd9c8d4a2adb6e48e432fdc03af67c -Author: Irfan Alibay -Date: Thu May 6 17:04:51 2021 +0100 - - Moves hbond_autocorrel and removes old hbond code (#3258) - - Fixes #2739 #3259 - - ## Work done in this PR - * Moves hbond_autocorrel from hbonds to hydrogenbonds, stub - will be removed in 3.0.0. - * Removes deprecated hbonds.hbond_analysis code. - * tests (note: tests were copied and we run full tests on the deprecated - and the moved code, mainly to make sure that they can be called as - expected; deprecation warnings are also tested) - * make hydrogenbonds.hbond_autocorrel primary entry for docs - * add entry for deprecated module at bottom of Hydrogen bonding docs - * fixed doc in hydrogenbonds.wbridge_analysis - * include the Gregoret 1991 reference (that was removed with the - deprecated hbonds.hbond_analysis module) - - Co-authored-by: Oliver Beckstein - -commit 1e456e85be62fc1d7d97140b60ab2983310af386 -Author: Oliver Beckstein -Date: Thu May 6 07:54:40 2021 -0700 - - retroactive CHANGELOG 1.0.0 fixes (#3260) - - Entry for 1.0.0 had incorrect entry (on PDBWriter and chainID writing) and a missing issue reference for GRO reader/parser. - -commit 903ae4cdad390938a0e356dc0ce59b090c2b1085 -Author: Philip Loche -Date: Thu May 6 08:47:48 2021 +0200 - - Add results class for storing analysis results (#3233) - - * API change for AnalysisBase derived classes: results are stored in new .results attribute - that holds an instance of analysis.base.Results - * fix #3115 - * Add results class for storing analysis results - * Added frames and results to AnalysisFromFunction - * breaking change: update to using new Results: GNMAnalysis, LinearDensity, polymer.PersistenceLength - * add docs - * add tests - * update CHANGELOG - - Co-authored-by: Manuel Nuno Melo - Co-authored-by: Oliver Beckstein - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - Co-authored-by: cbouy - -commit 7f2ce3de73f5a9cab86e3873ed397d33fc5ea793 -Author: Alex Yang -Date: Wed May 5 14:21:26 2021 -0400 - - Converter for OpenMM (#2917) - - * Topology from omm topology and simulation objects. Coordinates from omm simulation - - * Remove debug lines - - * Move omm topology parsing code outside class for re-use in multiple omm reader objects - - * Change openmm trajectory reader into single frame reader - - * Add coordinates conversions for openmm modeller and pdbfile classes - - * Add topology parsing for openmm pdbfile and modeller objects - - * Tests for openmmtopology parser - - * Revert init - - * Test openmm topology parsing on pdb file with connections, add atomtypes - - * Use guesser for guessing atomtypes from atomnames - - * Off by one errors for 1-indexed resids - - * Set frame to 0 for first timestep - - * Unwrap simtk quantity for time - - * Coordinates tests for openmm pdbfile, modeller, simulation objects - - * update error messsage - - * Update documentation - - * Try updating some yaml files - - * Include datafiles and tests for pdbx files - - * More documentation for pdbx - - * Typo in format - - * Blacken code - - * Refactor so generic application objects share the same readers and functions - - * Adjust line length - - * Revert datafiles without black formatting - - * Add pdbx file to datafiles, update changelog - - * Update docstring with proper versionadded tag - - * Missing comma in list - - * Add pytest importorskip for testing openmm topology c onversion - - * Merge conflict - - * Remove unnecessary imports, more documentation for openmm application layer objects, additional openmm test from a basic openmm simulation made from scratch - - * Example usage in documentation - - * Convert simtk quanitties into default internal units - - * Update travis with extra variables for openmm, installing only on py37 tests - - * Revert back to atomtype guessing - - * Use proper openmm atom naming conventions for unit test - - * Modify appveyor config to specify openmm on py36 vs py38 - - * Correct syntax for appveyor env vars - - * Change appveyor var syntax - - * Empty string for conda openmm var - - * Merge conflict - - * Update GHA conda min dependencies for openmm on conda-forge - - * Remove inplace flag for converting energies, not used anywhere in openmm conversions - - * Update appveyor to pull openmm from conda-forge - - * Use simtk syntax for unit conversions - - * - Sanitize box angles when converting from OpenMM unitcell to MDA unitcell - - Add xfail to pickle single frame reader for openmm tests - - Use elements to specify atomtypes from OpenMM topology - - * Make sure OpenMM appears in the documentation - - * Add the stubs to trigger the build and link to the documentation of - the new modules - * Fix issues with references in the docstrings - - * PEP8 fixes for OpenMM reader and parser - - Co-authored-by: Oliver Beckstein - Co-authored-by: Jonathan Barnoud - -commit 79183bfca165a4a51c90f2bb918e0d61ae20aa09 -Author: Irfan Alibay -Date: Tue May 4 22:24:08 2021 +0100 - - Fixes issues 3166 and 3255 (#3256) - - * Fixes issues 3166 and 3255 - - * Add tests - - * Changelog and docs - - * fix pep8 issue - -commit a82113bcccb7b66c292720f549e9f603825446ff -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon May 3 11:57:31 2021 -0700 - - Add intra_connections (intra_bonds, intra_angles, etc) (#3200) - - * added get_connections - - * modified tests for atoms.bonds/angles/dihedrals etc - - * modified parsers and things to use get_connections or bonds - - * updated CHANGELOG - - * pep8 - - * undo half of PR 3160 - - * add intra stuff - - * Update package/MDAnalysis/core/groups.py - - Co-authored-by: Jonathan Barnoud - - * tighten up base class checking - - * update docstring - - * suppres warnings - - * Use absolute file paths in ITPParser (#3108) - - Fixes #3037 - - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - - * Adds aromaticity and Gasteiger charges guessers (#2926) - - Towards #2468 - - ## Work done in this PR - * Add aromaticity and Gasteiger charges guessers which work via the RDKIT converter. - - * BLD: handle gcc on MacOS (#3234) - - Fixes #3109 - - ## Work done in this PR - * gracefully handle the case where `gcc` toolchain - in use on MacOS has been built from source using `clang` - by `spack` (so it really is `gcc` in use, not `clang`) - - ## Notes - * we could try to add regression testing, but a few problems: - - `using_clang()` is inside `setup.py`, which probably - can't be safely imported because it has unguarded statements/ - code blocks that run right away - - testing build issues is typically tricky with mocking, etc. - (though in this case, probably just need to move `using_clang()` - somewhere else and then test it against a variety of compiler - metadata strings - - * Remove ParmEd Timestep writing "support" (#3240) - - Fixes #3031 - - * Adding py3.9 to gh actions CI matrix (#3245) - - * Fixes #2974 - * Python 3.9 officially supported - * Add Python 3.9 to testing matrix - * Adds macOS CI entry, formalises 3.9 support - - * fix changelog - - * special metaclass - - * move function down - - * tidy code - - Co-authored-by: Jonathan Barnoud - Co-authored-by: Aditya Kamath <48089312+aditya-kamath@users.noreply.github.com> - Co-authored-by: Cédric Bouysset - Co-authored-by: Tyler Reddy - Co-authored-by: Irfan Alibay - -commit fe22dc3794f1f5d466f9128e4c7050fa0d58e62f -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun May 2 06:31:28 2021 -0700 - - Streamline angles(), bonds(), dihedrals() (#3203) - - * use underlying function - - * rm slow() versions - -commit 43842bfd38bc1dc0af95bbfee8fb6be87c595456 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun May 2 06:00:38 2021 -0700 - - Add del_TopologyAttr (#3069) - - * add del_TopologyAttr - - * pep8 - - * use contextlib and add tests - - * add error - - * add more tests - -commit e4cb6bab0ad8b2e64d77aaaf5f6525dc762396e7 -Author: Richard Gowers -Date: Sun May 2 13:57:40 2021 +0100 - - removed autogenerated C/CPP files from version control (#3250) - - * removed autogenerated C/CPP files from version control - - * setup: changed default cython usage - - by default, if cython is there, use it - -commit 740cae26820eba538f9990ec904adc9f39a65b2e (tag: release-1.1.1) -Author: Irfan Alibay -Date: Sat May 1 15:58:10 2021 +0100 - - Update to 1.1.1 (#3251) - -commit c510aca1310f8658c66cc23d1735b6c12159d0b1 -Author: Oliver Beckstein -Date: Thu Apr 29 15:44:40 2021 -0700 - - updated email addresses, authors, metadata in setup.py files (#3239) - - * close #3174 - * updated email address and author in setup.py files - - use mdanalysis@numfocus.org as official address - - use MDAnalysis Development Team as author - * setup metadata update - - make MDAnalysis Core Developers the maintainer - - updated links for Google groups - - updated link to testing instructions (userguide instead of wiki) - - add new PyPi links for docs - - User Guide - - Blog - - Twitter - - Discord - -commit 4753a8c12fc1f911b4feec0766883c5294fc341d -Author: Philip Loche -Date: Thu Apr 29 01:21:08 2021 +0200 - - Switch GNMAnalysis to AnalysisBase (#3244) - - * Fixes #3243 - * Switch GNMAnalysis to AnalysisBase - * replaced print with warning (when SVD fails on a frame) - * Added testcase for SVD failure - * update CHANGELOG - - Co-authored-by: Irfan Alibay - Co-authored-by: Oliver Beckstein - -commit 8bc6ca32b7865fe8a52570cdf658e00e7965ef3d -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Wed Apr 28 14:29:10 2021 -0700 - - Patch chi1_sel to match all gamma atoms (#3241) - - * Fixes #2044 - * chi1 selection now follows IUPAC 1970 convention for the gamma heavy atom (IUPAC-IUB Commission 1969 Draft (doi: 10.1021/bi00820a001)) for standard protein amino acids - * added tests - * add warning to chi1_selection() docs (Janin analysis class uses stricter convention from the Janin 1978 paper) - * update CHANGELOG - -commit c70504d99e8b6ff7f61778cff1f5956da708ddad (tag: release-1.1.0) -Author: Irfan Alibay -Date: Wed Apr 28 17:49:07 2021 +0100 - - Prep for release 1.1.0 (#3246) - - * Sets version for 1.1.0. - -commit 76c9dc0f2c125d37e0eced4b927f2fb2899090cb -Author: Richard Gowers -Date: Wed Apr 28 12:17:07 2021 +0100 - - hbond_autocorrel exclusion fix (#3242) - - Fixes #2987 - - ## Work done in this PR - * Fixes the hbond_autocorrel exclusion code path - * removed deprecated numpy usage in hbond autocorrel - * added _in2d - * correct distances docs - * added C sources for updated _cutil - -commit a23b1e9d82691dbdaead559e05e4e7356ceac915 -Author: Irfan Alibay -Date: Tue Apr 27 19:29:05 2021 +0100 - - Adding py3.9 to gh actions CI matrix (#3245) - - * Fixes #2974 - * Python 3.9 officially supported - * Add Python 3.9 to testing matrix - * Adds macOS CI entry, formalises 3.9 support - -commit 44f5f25ba2ea795fa5afbc541c45eef59eceefd7 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Apr 26 16:44:10 2021 -0700 - - Remove ParmEd Timestep writing "support" (#3240) - - Fixes #3031 - -commit fa074966bfe21c85bde8e4b61cd29ef8aecd692a -Author: Tyler Reddy -Date: Sat Apr 24 09:18:20 2021 -0600 - - BLD: handle gcc on MacOS (#3234) - - Fixes #3109 - - ## Work done in this PR - * gracefully handle the case where `gcc` toolchain - in use on MacOS has been built from source using `clang` - by `spack` (so it really is `gcc` in use, not `clang`) - - ## Notes - * we could try to add regression testing, but a few problems: - - `using_clang()` is inside `setup.py`, which probably - can't be safely imported because it has unguarded statements/ - code blocks that run right away - - testing build issues is typically tricky with mocking, etc. - (though in this case, probably just need to move `using_clang()` - somewhere else and then test it against a variety of compiler - metadata strings - -commit 32e3254b1d78376346b2c1e6f6bb9a7675b3a912 -Author: Cédric Bouysset -Date: Fri Apr 23 23:40:44 2021 +0200 - - Adds aromaticity and Gasteiger charges guessers (#2926) - - Towards #2468 - - ## Work done in this PR - * Add aromaticity and Gasteiger charges guessers which work via the RDKIT converter. - -commit b82635a5bb873e913840fa98d897da26daff6633 -Author: Aditya Kamath <48089312+aditya-kamath@users.noreply.github.com> -Date: Fri Apr 23 07:29:28 2021 -0400 - - Use absolute file paths in ITPParser (#3108) - - Fixes #3037 - - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - -commit ec7d636509aa2b905ce5f2f2ac1d77ff0a0d666b -Author: Irfan Alibay -Date: Wed Apr 21 22:11:16 2021 +0100 - - Re-enable mamba in CI (#3177) - - Fixes #3048 - -commit b8911ec2bac006896cfce258c61b9f3a809abc3f -Author: Irfan Alibay -Date: Wed Apr 21 18:39:21 2021 +0100 - - Fix permission error test to not be language centric (#3236) - - * Fixes #3221 - * Fix permission error test to not be Language centric: Changes check to be on PermissionError (which reflects what we are testing) and the error number [13]. - * Use errno value - -commit f2745a9dd484fa1dc87b416bb6a5fc107dabcb9c -Author: Manuel Nuno Melo -Date: Tue Apr 13 17:15:27 2021 +0100 - - Adds badge description to the README (#3229) - - * Added badge description to the README - * Update CHANGELOG - * Add link to markup eamples in the website - -commit 8a5ef48e235d595cbe913db199d1e25603b84a11 -Author: Sulay Shah -Date: Sat Apr 10 04:00:44 2021 -0700 - - Fixes error GAP assignment error in fasta2select (#3156) - - Fixes #3124 - - ## Work done in this PR - - Moves the assignment of the GAP variable in fasta2select in order to avoid cases where it is referred to but not assigned. - -commit 13a5df0fcbf13852da5613cefd84708e1fd506c6 -Author: Yuxuan Zhuang -Date: Sat Apr 10 12:37:07 2021 +0200 - - New TransformationBase class (#2950) - - Fixes #2996 - - ## Work done in this PR - - Adds a TransformationBase class - - TransformationBase uses threadpoolctl to allow the number of threads used to be limited in order to improve performance. - - TransformationBase also includes a check for whether a transformation is parallelizable. - - Refactors existing transformation classes to use TransformationBase. - -commit b1d8bccb1a977df9c595155877296cbb5419edb6 -Author: 1ut <69892398+1ut@users.noreply.github.com> -Date: Fri Apr 9 22:26:50 2021 +0900 - - Add sort method to AtomGroup (#3188) - - Co-authored-by: Irfan Alibay - -commit d59f71f17b3757ed8a0a9b0949f3df5115e174b3 -Author: Estefania Barreto-Ojeda -Date: Fri Apr 9 01:52:59 2021 -0600 - - Improve test coverage for diffusionmap (#3223) - - Fixes issue #3208 - - ## Work done in this PR - - Adds tests to increase the coverage of the diffusionmap code. - -commit e5935b5e24e8c166e5810738e9c1e950df3cab65 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu Apr 8 11:45:05 2021 -0700 - - Moved test_altloc (#3226) - - Fixes #3222 - -commit fe26097b7c4b6b00883172293c5eaf6f9baf62e7 -Author: Henry Kobin -Date: Wed Apr 7 22:13:32 2021 -0700 - - Write out chainID to PDB instead of segID (#3157) - - Fixes #3144 - - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - -commit 3aebcb5726f75eac0b433640414de0b899f7e1fb -Author: Paarth Thadani -Date: Wed Apr 7 20:06:14 2021 +0530 - - Removes deprecated sklearn arguments from encore (#3178) - - Fixes #2986 - - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - -commit 9fde9d1ef85190d7a2210d0a12e4126b477b35e4 -Author: Henrik Jaeger -Date: Wed Apr 7 08:35:22 2021 +0200 - - Parse atomtypes section of itp files (#3220) - - Fixes #3199 - -commit 12bebfd7ef3fdfec50cf14496a3cd749c5403d96 -Author: Estefania Barreto-Ojeda -Date: Tue Apr 6 16:40:36 2021 -0600 - - Raise helix_analysis coverage to 100% (#3219) - - Fixes #3209 - - ## Work done in this PR - - Removes no longer needed __future__ imports. - - Adds tests for helix_analysis warnings/errors. - -commit 8740a22241d7eae7d76cbe720a4d7a7d6161d0c2 -Merge: 10fede2c3 5160dfe1f -Author: Tyler Reddy -Date: Tue Apr 6 15:00:13 2021 -0600 - - Merge pull request #3027 from tylerjereddy/treddy_azure_py39_ci - - MAINT, CI: Azure add Python 3.9 Win - -commit 5160dfe1fd528e695af09eb5b7df673140e406a1 -Merge: 08c804ca2 10fede2c3 -Author: IAlibay -Date: Tue Apr 6 20:47:50 2021 +0100 - - Merge branch 'develop' into treddy_azure_py39_ci - -commit 10fede2c3ad815c0ccef0565bd532f867fbde2ce -Author: Yuxuan Zhuang -Date: Tue Apr 6 20:02:24 2021 +0200 - - Fix for h5py 3.0 (#3025) - - * Fixes #3023 - * fix h5py format failure after version 3.0 (now supports 2.0 and 3.0) - * unpin h5py version on conda (use latest available) - * pin h5py only binary on Azure - -commit 7618445eb9068cc02fa2193fd9951c326565dbcb -Author: hp115 <77673542+hp115@users.noreply.github.com> -Date: Tue Apr 6 16:05:56 2021 +0100 - - Add Transformation to set box dimensions (#3175) - - Fixes #2691 - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - Co-authored-by: Irfan Alibay - -commit aa37b8cea224f673d48feea5498bf30d98c063c6 -Author: Dimitrios Papageorgiou -Date: Tue Apr 6 18:02:40 2021 +0300 - - Fixes RMSD weights_groupselections docstring (#3134) - - Fixes Issue #2796 - -commit 62089a5e40643e05c4effa76a3b357f2c52411d5 -Author: Orion Cohen <27712051+orioncohen@users.noreply.github.com> -Date: Mon Apr 5 12:54:14 2021 -0700 - - Fixes sphzone, sphlayer, cyzone, cylayer empty selections (#3202) - - Fixes issue #2915 - -commit 361ca7e13786de42a4b4a62a449db3a2b64d193d -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Apr 5 12:39:29 2021 -0700 - - Undo half of PR 3160 (#3212) - - Undo deprecating AtomGroup.bonds to return bonds outside the group (and angles, etc.) - Co-authored-by: Irfan Alibay - -commit de8933ad6cdb01ec13f328e80c7589cd0c968c0c -Author: Philip Loche -Date: Mon Apr 5 18:44:31 2021 +0200 - - Deprecation warning for results attribute (#3194) - - Deprecate structure of `results` attribute for LinearDensity, PersistenceLength, GNMAnalysis, AnalysisFromFunction (Issue #3115) - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - Co-authored-by: Irfan Alibay - Co-authored-by: IAlibay - Co-authored-by: Richard Gowers - -commit 375b3f6c41419e08ad9b67bb92cd65c7dcd74ed2 -Author: Irfan Alibay -Date: Mon Apr 5 17:18:29 2021 +0100 - - Deletes empty analysis.utils (#3214) - -commit b5ab73d53a2c3fde3f0acc67d029660b0e18b45e -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Apr 4 06:46:21 2021 -0700 - - Added get_connections (#3160) - - * added get_connections - - * pep8 - - Co-authored-by: Richard Gowers - -commit 0880dc18c211a6508240a43ff6fe618c9be7f568 -Author: Johannes Zeman -Date: Sat Apr 3 23:59:51 2021 +0200 - - use branching instead of bool multipliers (#3210) - -commit 15226534fbf64424e99ebc83e59ef7f44bbf2457 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sat Apr 3 12:29:57 2021 -0700 - - Remove Timestep code path for ParmedConverter (#3172) - - Towards #3031 - - # Work done in this PR - * Removes the non-working code path for timestep handling in the ParmedConverter - -commit 3e249fe7173e68bb61d4ad7a2dfd316014760410 -Author: Jan Stevens <49684318+biogen98@users.noreply.github.com> -Date: Thu Apr 1 17:17:35 2021 +0200 - - Fixed issue -3148 (#3154) Warn user grid ignored DensityAnalysis - - Fix silent ignore on user defined grid coordinates in DensityAnalysis - -commit bb5d2912d67308839fb2d30130fed3f6317043c9 -Author: Henrik Jaeger -Date: Wed Mar 31 15:32:05 2021 +0200 - - Fixed the parsing of tpr files created by the 2021 version of gromacs (Issue #3810) (#3196) - - * Fixed the parsing of tpr files created by the 2021 version of gromacs (Issue #3810) - - * Added the virtual_site1 definition to the TPRParser. - - * Some tests for gromacs-2021 tpr files added. - - * Changelog appended. - - * * Added missing tests gromacs-2021 tpr files. - -commit 4c1390ea29aed32c210b42e8e8f2114865402cb4 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Mar 29 06:34:32 2021 -0700 - - Add LeonardoBarneschi to changelog (#3193) - -commit c6f1a5a5663913f00cc5f727ad0e662bbf23f18f -Author: Johannes Zeman -Date: Mon Mar 29 11:27:17 2021 +0200 - - improved FastNS performance for orthorhombic boxes (#3186) - -commit 04e8af4786a82a0cab388b552d2df3051716bbc0 -Author: Irfan Alibay -Date: Sat Mar 27 17:18:53 2021 +0000 - - Issue 2327 - Warn of upcoming scale_factor changes (#3185) - - Towards #2327 - - # Work done in this PR - * Adds warning for upcoming changes to scale_factor writing in NCDFWriter - -commit e32ce97f7b7f3cafe8d18d3d2027010ed3a8eaec -Author: LeonardoBarneschi <48569856+LeonardoBarneschi@users.noreply.github.com> -Date: Sat Mar 27 18:08:53 2021 +0100 - - Create Universe from empty RDKit ROMol (#3184) - - Fixes #3142 - -commit 9a03aecf8b89b1b8a4e8bd0349fab4f5af19a2d4 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Mar 22 14:13:30 2021 -0700 - - Deprecates using segid for chainid (#3173) - - Towards #3144 - - # Work done in this PR - - Deprecates the use of segid as the input for chain ID in the PDB writer. - -commit eb734681a39be244bea7e3e07e646c5b602fc2ac -Author: Johannes Zeman -Date: Sun Mar 21 09:38:31 2021 +0100 - - fixed NSGrid bug #2345 (#3182) - -commit 5c61de4ecf31b3a7ee117eb4a89a4438b107e3d9 -Author: Richard Gowers -Date: Mon Mar 15 10:00:50 2021 +0000 - - Fixed issue -3129 (#3130) - - * Fixed issue -3129 - - * Update changelog - - Co-authored-by: IAlibay - -commit 6282385644d672cf7023584347e35048935ab429 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Mar 15 02:08:20 2021 -0700 - - Add kwarg to index TPRParser from 0 or 1 (#3152) - - * add kwarg - - * change default to True for 2.0 - - * fix tests to index resids from 0 again - - * Update package/CHANGELOG - - Co-authored-by: Oliver Beckstein - - * change default arg for TPR utilities and remove warnings - - * updated to 1.1.0 - - Co-authored-by: Oliver Beckstein - -commit 347a3318f7e927ecdf765714b5e0fd2b94179913 -Author: Irfan Alibay -Date: Mon Mar 15 00:46:40 2021 +0000 - - Increase coverage with test for failed tests datafiles import - -commit 473c44cafa3c8c2349e8ad7a5a16e2c6fe606f3c -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Mar 14 16:42:38 2021 -0700 - - Use match to check hole2 warnings (#3164) - - ## Work done in this PR - - Change HOLE2's `test_output_level` test to check for a specific warning message rather than counting the number of warnings being emitted. - -commit 2c9be4e823bab0fdb036aafb752288924d6b466a -Author: Irfan Alibay -Date: Sun Mar 14 23:24:56 2021 +0000 - - Adds test to make sure small box issue is now fixed #2670 (#3163) - - Fixes issue #2670 - - ## Work done in this PR - * Adds test to check we no longer get the small box failures seen in issue 2670 - -commit e4659fb3d0a212e40238cfae90ab6ffc302e397b -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Mar 14 16:09:20 2021 -0700 - - Use match to check hole2 warnings (#3162) - - ## Work done in this PR - - Change HOLE2's `test_output_level` test to check for a specific warning message rather than counting the number of warnings being emitted. - -commit 03c631705e63a5aeba26698567161259f5446f50 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Mar 14 15:20:56 2021 -0700 - - Add tpr_resid_from_one keyword to TPRParser (#3153) - - - Fixes #2364 - - Master version of #3152. - - Changes made in this Pull Request: - - Add `tpr_resid_from_one` keyword to TPRParser - - Set default to `False`, keeping current status quo - - Emits a warning for `tpr_resid_from_one=False` indicating that default behaviour will change in 2.0 - - add tests - - update CHANGELOG - -commit 1eede18101cedf2be9ba686cc41429719d8bb3da -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Mar 14 14:51:08 2021 -0700 - - Adds deprecation warning when trying to add_TopAttr bfactors or tempfactors (#3161) - - Towards #1901 - - ## Work done in this PR - - Adds a warning when trying to add_TopologyAttr for bfactors or tempfactors when the other already exists. - -commit cadf5b992ad176fbb5d2b52b8287705087e8fda6 -Author: Irfan Alibay -Date: Sun Mar 14 08:52:38 2021 +0000 - - Add Travis CI shield.io badge (#3158) - - Badge for weekly Travis CI cron job for aarch64 and ppc64le - -commit 3f589e375434fd6a9b16c7da2cb1342cc3088b0e -Author: Irfan Alibay -Date: Sat Mar 13 19:46:16 2021 +0000 - - [MAINT] (re)-enabling CI for non-x86 archs and ppc64le support (#3149) - - Partially fixes #1389 and #3127 - - # Work done in this PR - - Adds basic support for ppc64le - - Adds encore specific C compiler args to reduce optimisations in non-x86 systems - - Enables travis cron CI for aarch64 and ppc64le - -commit 7ed893d787a4afe55085a9f036836e7c419a89d1 -Author: Zhiyi Wu -Date: Sat Mar 13 19:28:18 2021 +0000 - - Move and deprecate old waterbridge analysis code location (#3111) - - Related to #2913, #2739 and #2746 - - ## Work done in this PR - - Moves hbonds.WaterBridgeAnalysis code to hydrogenbonds.WaterBridgeAnalysis - - Add a temporary stub which links hbonds.WaterBridgeAnalysis to hydrogenbonds.WaterBridgeAnalysis - - Some docstring changes - -commit 6e38aa4f355a6356ea3f0f1d432e79740da28d7f -Author: Oliver Beckstein -Date: Fri Mar 12 19:45:06 2021 -0700 - - Updated the CHEMFILES docs (#3128) - - ## Work done in this PR - - Fixes broken link to the chemfiles format - - Adds chemfiles to list of supported file formats - - Adds examples for reading and writing files using chemfiles - -commit 232b4dc0322a206c60fb898d43ba214005f4acff -Author: Irfan Alibay -Date: Fri Mar 12 23:10:57 2021 +0000 - - Unpin dependencies for py3.6+ in setup files (#3139) - - Fixes #3103 and backports #2845 and #2834 - - # Work done in this PR - - Backports fixes to deprecation warnings with numpy 1.20 - - Unpin the maximum dependency versions for py3.6+ (except for matplotlib) - -commit a35608f0ff0b85193f0187e360e0b34878b1da77 -Author: Irfan Alibay -Date: Thu Mar 11 06:37:52 2021 +0000 - - Change CI to use matplotlib-base (#3147) - - Fixes #2540 - - - Changes CI conda install from matplotlib to matplotlib-base to match how we release on conda-forge now. - -commit ec9ec23fb6551add83b6cbb6a9523ffa7705c36b -Author: Aditya Kamath <48089312+aditya-kamath@users.noreply.github.com> -Date: Wed Mar 10 20:30:24 2021 -0500 - - Emit warnings for empty Ag and user grid in DensityAnalysis (#3091) - - - Adds ValueError if AtomGroup is empty and no user defined grid is provided - - Adds UserWarning if AtomGroup is empty and a user defined grid is provided - -commit d3b38cdfaca6713e7d346a98126910355890f5f3 -Author: Irfan Alibay -Date: Mon Mar 8 23:45:24 2021 +0000 - - Implement legacy CI for py2.7 and 3.5 (#3143) - -commit d9dcdcd79845bdfbdcea0528ceb127159e694783 -Author: Richard Gowers -Date: Sun Mar 7 19:15:31 2021 +0000 - - Fixed NSGrid (#3133) - - * Fixed NSGrid - - Rewrote lib.nsgrid module - - Issues #2919 #2345 #2229 - - * enabled nsgrid again - - * bumped version to 1.0.2-dev - - * remove nsgrid warnings - - * regenerated nsgrid C files - - * Revert removal of nsgrid from test_distances - - Co-authored-by: IAlibay - -commit ff7ffa10901e2df2be12c3d3dd78e4e0a262e90e -Author: Manuel Nuno Melo -Date: Thu Mar 4 00:11:37 2021 +0000 - - Implements cache validation at the Universe level (#3135) - - * Implements cache validation at the Universe level - - Objects keep their own caches, but those can now be set to be validated against - a centralized registry under object.universe. This simplifies the - centralized invalidation of object caches. - - Applied to fragment caching and added asv benchmark. Already large speedup in - fragment accession (Fixes #2376). Tests include cache invalidation when - bonds are added/removed. - - Added asv's benchmarks/results subdir to .gitignore - -commit 92038aa9dbd6d6f13c50be3aba73d50532533d8c -Author: Irfan Alibay -Date: Wed Mar 3 05:11:46 2021 +0000 - - Switch CI build badges from Travis to GH actions (#3137) - - And rename GH actions workflow - -commit f542aa485983f8d3dd250b36a886061f696c3e97 -Author: Oliver Beckstein -Date: Wed Feb 17 11:13:40 2021 -0700 - - Logo fixup (#3122) - - Fixes #3121 - - ## Work done in this PR - - * fixed up square logo - - transparent version was buggy: still had white patches: fixed - - regenerated SVG, PDF, and PNG versions - - * fixed wide logos - - cleaned up wide logos (PDF and PNG for docs) - -commit 42c541771ab7aee318783d296caa3e10b33f53eb -Author: mnmelo -Date: Sat Feb 13 14:12:32 2021 +0000 - - Optimized and refactored common compound code. (#3005) - - * Optimized and refactored common compound code. - - Performance increased and code duplication reduced. - - * Added compound-splitting performance benchmarks - -commit 258a73e0d9a67a41f10f9027ecd017085d0c7608 -Merge: cbda8a669 7932e2949 -Author: Tyler Reddy -Date: Fri Feb 5 17:58:36 2021 -0700 - - Merge pull request #3117 from IAlibay/issue-3116 - - Fix import tests failure (issue 3116) - -commit cbda8a669b02fe7e4c3ebd2ff1b40ce817640907 -Author: Zhiyi Wu -Date: Fri Feb 5 17:08:06 2021 +0000 - - Move water bridge analysis from hbonds to hydrogenbonds (PR #2913) - - * Move water bridge analysis from hbonds to hydrogenbonds (PR #2913) - * part of #2739 - * deprecate hydrogen bond analysis in water bridge in PR #3111 - * Update CHANGELOG - - Co-authored-by: Irfan Alibay - -commit 7932e294947868bff64a9f3e6fba9a8f1f17d919 -Author: IAlibay -Date: Fri Feb 5 03:54:23 2021 +0000 - - Fix import tests failure (issue 3116) - -commit 7d614857cec0071f2088bea675377efabc9ec1fd -Author: Philip Loche -Date: Thu Feb 4 10:57:15 2021 +0100 - - Fixed import of several `__all__` lists (#3013) - - * Removed missing rdf_s package from analysis `__all__` list - - * Fixed more __all__ lists and added a test - - * Removed unused import - - * Raise warning if sklearn is missing - - * Added generator for testcase - - * Fixed more __all__ lists - -commit 76b746353107a1da3cf420d8ba9673a881634255 -Author: Irfan Alibay -Date: Tue Feb 2 12:57:12 2021 +0000 - - [maint] numpy 1.20 type deprecations (#3114) - - Fixes #3113 - - ## Work done in this PR - - switches np.int/float builtin type aliases to more specific versions (as per numpy 1.20 deprecations). - -commit bc95e31af1bd1a583161318ab381d005452d48ea (tag: release-1.0.1) -Author: Rocco Meli -Date: Wed Aug 12 02:57:03 2020 +0200 - - Fix rotateby documentation (#2903) - - * Fixes #2901 - * Changes made in this Pull Request: - - Added call to rotateby (instead of rotate) - - Removed () from atom group - -commit 6eb715a6883db91621618deccb692c946406ca74 -Author: Irfan Alibay -Date: Sun Jan 24 02:21:43 2021 +0000 - - Fix python_requires (#3104) - - Fixes #3103 - - ## Work done in this PR - - Fixes `python_requires` syntax - - Re-enables py3.5 support for 1.0.x releases - - Pins max python version at 3.8 - -commit 658a73d127716c6e1f5d4bcfd6dd5b12ecf71cef -Author: Irfan Alibay -Date: Sat Jan 23 00:40:11 2021 +0000 - - Copy README into package (#3094) - - To fix Pypi uploading issues - -commit f64e5a52234b9bb4c039a789be100944ac3060bf -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Fri Jan 22 11:16:02 2021 +1100 - - Change tmpdir fixture to tmpdir_factory (#3095) (#3097) - - - Changes function-scoped `tmpdir` to session-scoped `tmpdir_factory` - - Turns deadlines off to ignore unreliable test timings - -commit c69be8f2f70955e7aa94c8ae35adc25a4a210103 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Jan 19 10:01:59 2021 +1100 - - Turn off mamba for Travis CI (#3099) - - Fixes issue #3098 - - # Work done in this PR - - Disables mamba from the Travis py2.7 runs, which seem to be causing stalls. - -commit 76d9ca1bd0b48cf692b6b3d720fa3a85dc13ef98 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Jan 18 11:53:16 2021 +1100 - - Change tmpdir fixture to tmpdir_factory (#3095) - - - Changes function-scoped `tmpdir` to session-scoped `tmpdir_factory` - - Turns deadlines off to ignore unreliable test timings - -commit c1bef0f47ae113946b19700a19efcacb33047880 -Author: Richard Gowers -Date: Sun Jan 17 11:48:45 2021 +0000 - - Rel 1.0.1b (#3093) - - ## Work done in this PR - - Admin changes for the 1.0.1 release! - -commit c57697e9e5d283adbc8f90e29078bd75146aae5f -Merge: 3f8c5a6b7 c4c121ed7 -Author: Rocco Meli -Date: Wed Jan 13 14:36:41 2021 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 0de538ea70a88f4107d3101b029d48d1e100b1ff -Merge: 87e71bb2f a758a7afd -Author: Tyler Reddy -Date: Tue Jan 5 09:45:58 2021 -0700 - - Merge pull request #3072 from tirkarthi/fix-warnings - - Fix syntax warning over comparison of literals using is. - -commit a758a7afd51e42db5d9966334ff4851a2ad39cfc -Merge: 92bdd968e 87e71bb2f -Author: Oliver Beckstein -Date: Mon Jan 4 16:40:37 2021 -0700 - - Merge branch 'develop' into fix-warnings - -commit 92bdd968e23daf536db11f65b7d6a30f1d67b9f3 -Author: Karthikeyan Singaravelan -Date: Mon Jan 4 13:32:22 2021 +0000 - - Add to authors list. - -commit 87e71bb2fccfbf8ff3127130d1716c86f6682ccb -Author: Aditya Kamath <48089312+aditya-kamath@users.noreply.github.com> -Date: Sun Jan 3 23:38:37 2021 -0500 - - Quick fix for atommethods to return empty residue group (#3089) - - Returns empty residue group for _get_prev_residues_by_resid and _get_next_residues_by_resid - -commit d496bdaaea89be44d18b5da4ea7b3a52b689eb88 -Author: Karthikeyan Singaravelan -Date: Thu Dec 10 15:21:00 2020 +0000 - - Fix syntax warning over comparison of literals using is. - -commit 8f7e338c0999dea5feb1d7895c3d4620c1f52ffe -Merge: 1ed6e681a 22f511fc2 -Author: Oliver Beckstein -Date: Wed Dec 30 16:58:39 2020 -0700 - - Merge pull request #3088 from tylerjereddy/treddy_char_class_overhead - - MAINT: char class regex improve - -commit 22f511fc296e62e24b97642fca88a427afd35414 -Author: Tyler Reddy -Date: Wed Dec 30 08:31:57 2020 -0700 - - MAINT: char class regex improve - - * avoid the overhead of a regex character class - when that character class has only a single character - (i.e., serves no purpose) - - * there is only one instance of this in MDA codebase - discovered by my [scraping - code](https://github.com/tylerjereddy/regex-improve) - - * for a longer explanation see my similar changes in - NumPy codebase: - https://github.com/numpy/numpy/pull/18083 - -commit 1ed6e681a6c27c3c5a038ea1065a64bcd1816fd2 -Author: Tyler Reddy -Date: Fri Dec 25 21:20:39 2020 -0700 - - MAINT: simplify guessers regex (#3085) - - * the `SYMBOLS` regex in `guessers.py` does not require - any escape sequences because the metacharacters are inactive - in the character class (this includes the range metacharacter - when placed at the start or end of the character class) - -commit 12a92fc4319b0a689b30946618dd56aa3e00c46e -Author: Irfan Alibay -Date: Fri Dec 25 08:26:40 2020 +0000 - - Fixes RMSF docstring (Issue #2806) (#3033) - - Fixes the RMSF docstring's align command and adds transformation to make the results accurate - -commit 6e2d8e7f94c0559be9c66970574433d87b29ccb7 (upstream/rel-1.0.1) -Author: Irfan Alibay -Date: Tue Dec 22 22:12:42 2020 +0000 - - Temporarily disable nsgrid (Issue #2930) (#3004) - - Fixes #2930 - - Temporarily replaces nsgrid with pkdtree - - Adds note on the use of nsgrid - -commit ebd9c02d1dc2f29e113a4a4def7a55c946ee40d9 -Merge: c3c424044 8c1fbd67b -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Dec 22 14:28:33 2020 +1100 - - Merge pull request #3078 from lilyminium/rtd-master - - Add ReadTheDocs configuration for master - -commit 8c1fbd67b1e3c5db5b0dd8ce869eca3aef358b4d -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Wed Dec 16 07:50:41 2020 +1100 - - Install MDAnalysis on ReadTheDocs via pip (#3071) - - Install via `pip install package/` to build current docs on ReadTheDocs - -commit fe6cb348373958258f31f1730fce530053f40321 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu Dec 10 12:46:15 2020 +1100 - - Add ReadTheDocs configuration for PR builds (#3060) - - - Adds RTD configuration - - Add `environment.yml` for package installation - -commit c3c42404465b0d5792184409e1e184aeae2567f9 -Merge: 2ef90f2e8 09bdc9ac5 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Dec 22 10:35:36 2020 +1100 - - Merge pull request #3067 from lilyminium/gh-actions-py3 - - Fixes #3079 - - * ports fixes from develop to master - * Keeps GH actions for pythons 3.6-3.8 - * Keeps Travis for pythons 2.7 and 3.5 - * removes Appveyor - * pins packages for Python 2.7 - -commit c4c121ed7ce57afa269819941f39b927fb24422f -Merge: d4f8e94a3 7a7885fb1 -Author: Tyler Reddy -Date: Sat Dec 19 17:38:21 2020 -0700 - - Merge pull request #3081 from lilyminium/pdb-metals - - Try StringIO in test_PDB_metals - -commit 7a7885fb17e667b9550d35fd39510fe48ba43dbe -Author: Lily Wang -Date: Sun Dec 20 09:41:10 2020 +1100 - - pin pytest on gh actions - -commit 8e121584949e5e2c818b41ac18b9fe6a8009d798 -Author: Lily Wang -Date: Sat Dec 19 15:21:29 2020 +1100 - - pin pytest - -commit 67e04456589533635c75a1fbb9b74d7ec9244947 -Author: Lily Wang -Date: Fri Dec 18 20:56:11 2020 +1100 - - rm metals file - -commit f75bd1ff4d20806adac98627d733c79cbfabcec6 -Author: Lily Wang -Date: Fri Dec 18 19:07:11 2020 +1100 - - try stringio - -commit 09bdc9ac5e2728a525eb1680f607b9254025cd59 -Author: Lily Wang -Date: Wed Dec 16 11:23:27 2020 +1100 - - try pinning - -commit d4f8e94a3ef4f3e87f87956ad518cf0a4b1e6ae2 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Wed Dec 16 07:50:41 2020 +1100 - - Install MDAnalysis on ReadTheDocs via pip (#3071) - - Install via `pip install package/` to build current docs on ReadTheDocs - -commit 6a99f57bab43897370cd2e755f6dd3676596c77c -Author: Lily Wang -Date: Tue Dec 15 09:22:31 2020 +1100 - - rm appveyor - -commit c88698dd8121c2c2139652b227e26a5a32d61674 -Merge: 60ea0bbfe 74f229c60 -Author: Lily Wang -Date: Tue Dec 15 09:22:21 2020 +1100 - - Merge branch 'gh-actions-py3' of github.com:lilyminium/mdanalysis into gh-actions-py3 - -commit 60ea0bbfe1ccd01845378e11ba827bb32a3de414 -Author: Lily Wang -Date: Wed Dec 9 14:43:17 2020 +1100 - - move py3.5 job - -commit 454bd4d85217e7accd5d103debf2f17161cc6e1c -Author: Lily Wang -Date: Wed Dec 9 12:56:46 2020 +1100 - - mv travis back and only keep 3.5 and 2.7 - -commit a64eed98b38307e4699b59eef9f265cbead37ad6 -Author: Summersnow -Date: Thu Nov 19 10:57:47 2020 +0800 - - Improve the performance of ParmEd converter. (Fix #3028) (#3029) - - Fixes #3028 - - * Improves the performance of the ParmEd converter by using a dictionary lookup for the atomgroup to universe index mapping. - -commit 7f83f4a7c9c8abbc2df411a60ffe80dbcfe3fd44 -Author: Cédric Bouysset -Date: Fri Oct 30 20:50:21 2020 +0100 - - ParmEdConverter: fix NameError when catching NoDataError (#2953) - - * fix NameError when catching NoDataError - * add test + missing imports - -commit 0f9a6e558a5798880c7b5604346a8a15826d0187 -Author: Tyler Reddy -Date: Mon Oct 19 08:57:47 2020 -0600 - - TST, CI: add ARM64 Graviton 2 to CI (#2956) - - * TST, CI: add ARM64 Graviton 2 to CI - - * start testing MDAnalysis on ARM64 using - new AWS Graviton 2 architecture available - in Travis CI - - * testing on my fork shows only two failures - in the MDAnalysis test suite using a fairly - minimal set of dependencies; we can probably - either fix those or skip them and open an issue - - * the test failures are: - `test_written_remarks_property` - `TestEncoreClustering.test_clustering_three_ensembles_two_identical` - - * run time for this CI entry is about - 23 minutes, which is solid for ARM; we save a lot - of time using experimental upstream wheels in some - cases and excluding (source builds of) dependencies - where possible until the ARM64 binary wheel ecosystem - matures a bit more - - * MAINT: ARM64 shims - - * adjust `CAffinityPropagation()` C-level function to use `double` - instead of `float` in some strategic locations that allow the - `test_clustering_three_ensembles_two_identical()` test to pass - on gcc115 ARM64 machine - - * mark `test_written_remarks_property()` as a known failure on - ARM64; it fails in Travis CI on that platform, but not on gcc115 - ARM64 machine; that said, this test is already known to be flaky - on Windows 32-bit (may depend on character settings on machine?) - - * MAINT: MR 2956 revisions - - * reduce optimization level of MDAnalysis builds on - ARM64 to avoid problems with `ap.c` causing test failures - on that architecture - - * revert any source changes to `ap.c` - -commit 86eb383b6efaf2b14543679766b5e90ea264faa9 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Dec 6 11:54:35 2020 +1100 - - Deploy docs via GitHub Actions CI (#3053) - - Fixes #3046. Deploys docs in gh-ci.yaml script and removes Travis - -commit 383d15e0a673350fd33070448a6d3470498d9e3b -Author: Irfan Alibay -Date: Wed Dec 2 18:56:39 2020 +0000 - - Adds basic GH Actions CI workflow (#3040) - - Fixes #3036 - - ## Work done in this PR - - Adds a continuous integration workflow based on github actions. - - Disables previous continuous integration workflow based on TravisCI. - - Fixes minor Visibledeprecation warnings with the hole2 tests. - -commit 08c804ca27d9e01ef21190c4ef83f177a4214bfc -Author: Tyler Reddy -Date: Tue Nov 10 20:30:47 2020 -0700 - - MAINT, CI: Azure add Python 3.9 Win - - * the upstream ecosystem has had a bit of time - to release binaries for Python 3.9; let's see - what happens if we turn on Python 3.9 Windows testing - in Azure CI - -commit 9b115906a05f4a2311dc8f4ac1caf73f500fa10f -Merge: 222336396 4ef25c3ad -Author: Tyler Reddy -Date: Sat Dec 12 17:44:51 2020 -0700 - - Merge pull request #3073 from IAlibay/issue-3065 - - Remove appveyor - -commit 4ef25c3ad2823fcc30a24ea4d87ab764f4a5bb5b -Author: IAlibay -Date: Thu Dec 10 15:52:36 2020 +0000 - - Remove appveyor - -commit 222336396417c5d0ded2b461448bfbe856b4b99d -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu Dec 10 12:46:15 2020 +1100 - - Add ReadTheDocs configuration for PR builds (#3060) - - - Adds RTD configuration - - Add `environment.yml` for package installation - -commit 7746207a148367edf01697d5543022315d855bf9 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu Dec 10 12:02:15 2020 +1100 - - Add arbitrary TopologyAttr selection (#2927) - - Fixes #2925 - Fixes #2875 - Fixes #3054 - - Changes made in this Pull Request: - - added a class factory to subclass `core.selection.Selection` for each TopologyAttr - - added tokens to `core.selection.SameSelection` - - added `FloatRangeSelection` and `BoolSelection` - - added negatives, scientific notation and "to" delimiter for ranges - -commit 74f229c60ec236911cf4c0e460d4de1ea0cc99a7 -Author: Lily Wang -Date: Wed Dec 9 14:43:17 2020 +1100 - - move py3.5 job - -commit 7a92b3c1301fadaca736d531badd6691fcab7316 -Merge: 082b087bd 2ef90f2e8 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Wed Dec 9 13:04:00 2020 +1100 - - Merge branch 'master' into gh-actions-py3 - -commit 082b087bd3af8346befd36448d257134a21063db -Author: Lily Wang -Date: Wed Dec 9 12:56:46 2020 +1100 - - mv travis back and only keep 3.5 and 2.7 - -commit c07b5c8897688d778e57e1ef34be86f58c969fe7 -Author: Summersnow -Date: Thu Nov 19 10:57:47 2020 +0800 - - Improve the performance of ParmEd converter. (Fix #3028) (#3029) - - Fixes #3028 - - * Improves the performance of the ParmEd converter by using a dictionary lookup for the atomgroup to universe index mapping. - -commit 3b941da27393fc97d2b19c62b49685985e8eac90 -Author: Cédric Bouysset -Date: Fri Oct 30 20:50:21 2020 +0100 - - ParmEdConverter: fix NameError when catching NoDataError (#2953) - - * fix NameError when catching NoDataError - * add test + missing imports - -commit 0030b3864eb77a90a9442904e7d64d1619c6add5 -Author: Tyler Reddy -Date: Mon Oct 19 08:57:47 2020 -0600 - - TST, CI: add ARM64 Graviton 2 to CI (#2956) - - * TST, CI: add ARM64 Graviton 2 to CI - - * start testing MDAnalysis on ARM64 using - new AWS Graviton 2 architecture available - in Travis CI - - * testing on my fork shows only two failures - in the MDAnalysis test suite using a fairly - minimal set of dependencies; we can probably - either fix those or skip them and open an issue - - * the test failures are: - `test_written_remarks_property` - `TestEncoreClustering.test_clustering_three_ensembles_two_identical` - - * run time for this CI entry is about - 23 minutes, which is solid for ARM; we save a lot - of time using experimental upstream wheels in some - cases and excluding (source builds of) dependencies - where possible until the ARM64 binary wheel ecosystem - matures a bit more - - * MAINT: ARM64 shims - - * adjust `CAffinityPropagation()` C-level function to use `double` - instead of `float` in some strategic locations that allow the - `test_clustering_three_ensembles_two_identical()` test to pass - on gcc115 ARM64 machine - - * mark `test_written_remarks_property()` as a known failure on - ARM64; it fails in Travis CI on that platform, but not on gcc115 - ARM64 machine; that said, this test is already known to be flaky - on Windows 32-bit (may depend on character settings on machine?) - - * MAINT: MR 2956 revisions - - * reduce optimization level of MDAnalysis builds on - ARM64 to avoid problems with `ap.c` causing test failures - on that architecture - - * revert any source changes to `ap.c` - -commit 63444aad24fe31627499a0879ae63c8343250aa3 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Dec 6 11:54:35 2020 +1100 - - Deploy docs via GitHub Actions CI (#3053) - - Fixes #3046. Deploys docs in gh-ci.yaml script and removes Travis - -commit 0e3c1083ea16467c194479491fe556cc68d94296 -Author: Irfan Alibay -Date: Wed Dec 2 18:56:39 2020 +0000 - - Adds basic GH Actions CI workflow (#3040) - - Fixes #3036 - - ## Work done in this PR - - Adds a continuous integration workflow based on github actions. - - Disables previous continuous integration workflow based on TravisCI. - - Fixes minor Visibledeprecation warnings with the hole2 tests. - -commit 9da444233c22f1a5403b7c61679bd5448183000c -Author: Oliver Beckstein -Date: Sat Oct 24 09:29:27 2020 -0700 - - increase default Python to 3.7 on Travis CI (#3011) - - * increase default Python to 3.7 on Travis CI - - set PYTHON_VERSION=3.7 - - set MAMBA=false for Python 3.5 (no mamba package available, fall backto conda) - * ensure conda package is available for numpy 1.13 - NumPy 13.3.3 packages are available for Python 2.7 and 3.6 only so for the tests with the - minimal numpy version we set Python to 3.6. - -commit b37f51870b088099bde09e808c90b927b3baae95 -Author: mnmelo -Date: Sun Oct 18 10:35:15 2020 +0100 - - Fixed AtomGroup.center's behavior when using compounds in conjugation with unwrapping (PR #2992) - - fixes #2984 - - (cherry picked from commit beb5232dc7501e6bc0138036f697aa14da2a4162) - -commit 0b6b372fdfcdef15aacbe1c2b82d728f4f1c0401 -Author: Jonathan Barnoud -Date: Thu Oct 15 14:55:52 2020 +0100 - - Have CI use mamba (#2983) - - Not an issue targetted fix. - Improve CI (no user facing changes) - - - Overview - - mamba is a dropin replacement for the conda CLI but faster - - - Work done in this PR - - Enabled the `MAMBA` environment variable keyword for the CI helper. - - (cherry picked from commit 2ee4e9da5aa3a2c1b21fc3d1897bd70e0ab2064d) - -commit e8403c77d2fda81c936d76554307e326166bf182 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sat Oct 24 11:22:20 2020 +1100 - - Add dev and stable versions once (#3009) - - * fix #3006 - * fixed the for/else loop that accidentally added too many versions of dev/ and stable/ - - (cherry picked from commit 2d14dbd71b58c534a6bf710fc6a063b4eaf33cdf) - -commit 25ec58dbe1aa7988271f67c88a7499c5e0a39328 -Author: Cédric Bouysset -Date: Tue Dec 8 18:13:42 2020 +0100 - - Fix mol2 with no bonds (#3059) - - - Fixes #3057 - - MOL2 files without bonds can now be read and written - -commit 3f8c5a6b77898f7cf3154b5720ccf25db79a17d3 -Author: Irfan Alibay -Date: Wed Dec 2 18:56:39 2020 +0000 - - Adds basic GH Actions CI workflow (#3040) - - Fixes #3036 - - ## Work done in this PR - - Adds a continuous integration workflow based on github actions. - - Disables previous continuous integration workflow based on TravisCI. - - Fixes minor Visibledeprecation warnings with the hole2 tests. - -commit b8067f531c2c63c370814248f189b75d74a0d284 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Dec 6 11:54:35 2020 +1100 - - Deploy docs via GitHub Actions CI (#3053) - - Fixes #3046. Deploys docs in gh-ci.yaml script and removes Travis - -commit 1ec8b20db888504aee2afc69cdb3f9b91fab9990 -Merge: 751d4416e 6803cf6c5 -Author: Rocco Meli -Date: Thu Dec 3 14:49:58 2020 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit cf75dd6fe20e935c95fef57b0029382883ab0283 -Author: Irfan Alibay -Date: Wed Dec 2 18:56:39 2020 +0000 - - Adds basic GH Actions CI workflow (#3040) - - Fixes #3036 - - ## Work done in this PR - - Adds a continuous integration workflow based on github actions. - - Disables previous continuous integration workflow based on TravisCI. - - Fixes minor Visibledeprecation warnings with the hole2 tests. - -commit 6803cf6c5aa62744099803145f3ac9398389244c -Author: Rocco Meli -Date: Fri Nov 20 19:05:05 2020 +0100 - - Write CONECT record only once in multi-MODEL PDB files (#3020) - - Fixes #3018 - - ## Work done in this PR - * The writing of CONECT records is now done once in multi-model PDB files, improving adherence with the PDBv3 standard. - * Note: CONECT records, like END entries will be written once `close()` is called. - -commit 456807dd5052df616fe2857eb4d5ac9dc0371f27 -Author: Irfan Alibay -Date: Thu Nov 19 20:03:45 2020 +0000 - - Adds NC file extension to NCDFWriter (#3032) - - * fix #3030 - * Adds NC file extension to NCDFWriter (matching docs now) - * update changelog - -commit 404040598f78db05882fa5b2bba1d35fc6a30510 -Author: Summersnow -Date: Thu Nov 19 10:57:47 2020 +0800 - - Improve the performance of ParmEd converter. (Fix #3028) (#3029) - - Fixes #3028 - - ## Work done in this PR - * Improves the performance of the ParmEd converter by using a dictionary lookup for the atomgroup to universe index mapping. - -commit e9d0e88ed40a810273af4cf1c742058b1a761b66 -Author: Irfan Alibay -Date: Mon Nov 16 06:38:45 2020 +0000 - - Adds PDB element writing and fixes reading (#3001) - - - Fixes #2423 and #2422 - - PDB parser now allows for partial element parsing, setting an empty record if the element is not recognised. - - PDB writer now uses the elements attribute instead of guessing. - -commit 751d4416e707efa206e9ae1f3345d4ea77eedcc8 -Merge: 0359fec12 51014e435 -Author: Rocco Meli -Date: Mon Nov 9 22:10:21 2020 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 51014e435cc6188d2ebaec49cfcfd73f78eee96a -Author: Tyler Reddy -Date: Mon Nov 9 10:30:25 2020 -0700 - - MAINT, CI: pin Azure h5py (#3021) - - Partially fixes #3019 - - * pin the version of `h5py` used in Azure Windows CI testing - because of gh-3019; CI failures were observed to start/coincide - with a recent release of `h5py` - -commit 934a5bed13e1f38a33fb22629c6c61e671bf0a87 -Author: Tyler Reddy -Date: Mon Nov 9 10:27:02 2020 -0700 - - MAINT: Travis/Appveyor pin h5py (#3022) - - Partially fixes #3019 - - * pin the version of `h5py` used in Travis and Appveyor CI runs - because CI failures related to recent versions of this dependency - were observed in gh-3021 (where the same pinning was applied to Azure - CI) - - * original issue was described in gh-3019 - -commit dca4fa882621f3841c169ed7fb0567b5d2c127bb -Author: Cédric Bouysset -Date: Fri Oct 30 20:50:21 2020 +0100 - - ParmEdConverter: fix NameError when catching NoDataError (#2953) - - * fix NameError when catching NoDataError - * add test + missing imports - -commit 9511192a67ae163339a44ffcbba4df637a52a3f1 -Author: mnmelo -Date: Fri Oct 30 09:22:28 2020 +0000 - - Cleanup and better parametrization of test_atomgroup.py (#3012) - - * Cleanup and better parametrization of test_atomgroup.py - - Fixes #2995 - - * Further PEP8 compliance - - * Fixed duplicated and wrongly-parametrized pbc tests - - * Cleaned trajectory rewinds and stabilized RNG use - - * Reverted to numpy.random.RandomState for v1.16 compatibility - - * Further tweaking for numpy v1.16 compatibility - - * Adjusted the unlucky RNG seed so we actually get an unordered ResidueGroup - -commit db2e830646cb836b9cc2f73aafb27ed0fd60b349 -Author: Philip Loche -Date: Tue Oct 27 00:40:13 2020 +0100 - - consolidated analysis class docstrings (#2998) - - * consolidated analysis class docstrings (improves interaction with MDACLI) - - Changed `: ` -> ` : ` - - removed default values from docstrings - - removed trailing spaces and empty lines - * Updated CHANGELOG - -commit 2ef90f2e88d62d1109cae94b2fc10216be813853 -Author: Oliver Beckstein -Date: Sat Oct 24 09:29:27 2020 -0700 - - increase default Python to 3.7 on Travis CI (#3011) - - * increase default Python to 3.7 on Travis CI - - set PYTHON_VERSION=3.7 - - set MAMBA=false for Python 3.5 (no mamba package available, fall backto conda) - * ensure conda package is available for numpy 1.13 - NumPy 13.3.3 packages are available for Python 2.7 and 3.6 only so for the tests with the - minimal numpy version we set Python to 3.6. - -commit 49cb0a8b3fa7d3dd30c4480e5adb992b61c1e218 -Author: mnmelo -Date: Sun Oct 18 10:35:15 2020 +0100 - - Fixed AtomGroup.center's behavior when using compounds in conjugation with unwrapping (PR #2992) - - fixes #2984 - - (cherry picked from commit beb5232dc7501e6bc0138036f697aa14da2a4162) - -commit 73cd1e69be88f1b47b1327c1918c0ad326bec302 -Author: Jonathan Barnoud -Date: Thu Oct 15 14:55:52 2020 +0100 - - Have CI use mamba (#2983) - - Not an issue targetted fix. - Improve CI (no user facing changes) - - - Overview - - mamba is a dropin replacement for the conda CLI but faster - - - Work done in this PR - - Enabled the `MAMBA` environment variable keyword for the CI helper. - - (cherry picked from commit 2ee4e9da5aa3a2c1b21fc3d1897bd70e0ab2064d) - -commit 5ac87b6e0cd731b328bd0e80d2442462c18a3145 -Author: Oliver Beckstein -Date: Fri Oct 23 13:40:51 2020 -0700 - - removed funcsigs (not needed for Py >= 3.6) - -commit 088a6661f4d645c914b8ee2aefa7a2ed096a9af5 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sat Oct 24 11:22:20 2020 +1100 - - Add dev and stable versions once (#3009) - - * fix #3006 - * fixed the for/else loop that accidentally added too many versions of dev/ and stable/ - - (cherry picked from commit 2d14dbd71b58c534a6bf710fc6a063b4eaf33cdf) - -commit 2d14dbd71b58c534a6bf710fc6a063b4eaf33cdf -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sat Oct 24 11:22:20 2020 +1100 - - Add dev and stable versions once (#3009) - - * fix #3006 - * fixed the for/else loop that accidentally added too many versions of dev/ and stable/ - -commit 3640cd8af5254bd48582e63187667ae92aa267aa -Merge: c4fa754c7 e12bd3f07 -Author: Oliver Beckstein -Date: Fri Oct 23 15:47:43 2020 -0700 - - Merge pull request #3007 from MDAnalysis/backport-PR2427 - - backport of stub transplants of AtomGroup (PR #2427) - -commit e12bd3f078ec6be7a560caa39d48d782f2a0e072 -Author: Oliver Beckstein -Date: Fri Oct 23 13:12:07 2020 -0700 - - update CI files for Py2/Py3 packages - -commit 5a259b7be9b0d5b5d9f8a94b754af54d40e1233b -Author: Jonathan Barnoud -Date: Thu Oct 22 09:24:42 2020 +0100 - - Always transplant a stub for transplanted methods (#2427) - - - Fixes #1845 - - Adds dummy method with documentation of original method - - Dummy method gets replaced by actual method on instantiation - - (cherry picked from commit 799100b33633ff7729b29c1f6943abe873b4a112) - -commit 799100b33633ff7729b29c1f6943abe873b4a112 -Author: Jonathan Barnoud -Date: Thu Oct 22 09:24:42 2020 +0100 - - Always transplant a stub for transplanted methods (#2427) - - - Fixes #1845 - - Adds dummy method with documentation of original method - - Dummy method gets replaced by actual method on instantiation - -commit 0aace31e5ab5999e3567ce87c053168ee0d5a2e9 -Author: Jonathan Barnoud -Date: Wed Oct 21 16:22:21 2020 +0100 - - Add a reindex argument to the PDBWritter (#2886) - - * Add a reindex argument to the PDBWritter - - * Tests for PDB reindex - - * Remove extra print - - * Test PDB CONECT with reindex=False - - * Update CHANGELOG - - * More precise version change for PDB reindex - - * Fix long lines - - * Increase test coverage for #2886 - - Also silence some warnings for the tests in the PR. - - * Remove useless branch in PDB.py - - There was a test in PDBWriter._write_pdb_bonds about writing the bonds - for an atomgroup that does not have AG.ids but asking to not reindex. - The test was silencing the problem and would lead to the bonds not being - written. However, that part of the code would never be reached because - writing the atoms would have raised an exception before that method is - called. - - This commit removes this test. Now, if that part of the code is called - (which should not happen), an exception is raised when the method tries - to access AG.ids. - -commit c4fa754c7f79955a575d3d6a445a34e7513f2a4d -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Oct 20 20:48:06 2020 +1100 - - Stable sitemap master (#2999) - - Fixes #2993 - - Master version of #2994 - -commit 6b0cbd6d8057906df2cf7621e926f5c8b113e798 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Oct 20 14:45:29 2020 +1100 - - Re-write URLs in sitemap.xml (#2994) - - Fixes #2993 - - Redirect URLs in stable/sitemap.xml and dev/sitemap.xml to correct locations - -commit 75efc315aaa118bd5f78aa20c11253f9b785f7bc -Author: Tyler Reddy -Date: Mon Oct 19 12:34:59 2020 -0600 - - MAINT: ARM64 CI cleanup (#2997) - - Fixes issue #1989, completes PR #2956 - - ## Work done in this PR - - * Switches CI to using recently released SciPy `1.5.3` with "official" Linux ARM64 wheels - over the weekend, instead of the previous "special"/unreleased wheels - * Add a `CHANGELOG` entry to reflect preliminary MDAnalysis support - for the Linux ARM64 platform (minimal dependencies) - -commit daee516f23ead8e42c2e42b7636f9ec243ab306e -Author: Tyler Reddy -Date: Mon Oct 19 08:57:47 2020 -0600 - - TST, CI: add ARM64 Graviton 2 to CI (#2956) - - * TST, CI: add ARM64 Graviton 2 to CI - - * start testing MDAnalysis on ARM64 using - new AWS Graviton 2 architecture available - in Travis CI - - * testing on my fork shows only two failures - in the MDAnalysis test suite using a fairly - minimal set of dependencies; we can probably - either fix those or skip them and open an issue - - * the test failures are: - `test_written_remarks_property` - `TestEncoreClustering.test_clustering_three_ensembles_two_identical` - - * run time for this CI entry is about - 23 minutes, which is solid for ARM; we save a lot - of time using experimental upstream wheels in some - cases and excluding (source builds of) dependencies - where possible until the ARM64 binary wheel ecosystem - matures a bit more - - * MAINT: ARM64 shims - - * adjust `CAffinityPropagation()` C-level function to use `double` - instead of `float` in some strategic locations that allow the - `test_clustering_three_ensembles_two_identical()` test to pass - on gcc115 ARM64 machine - - * mark `test_written_remarks_property()` as a known failure on - ARM64; it fails in Travis CI on that platform, but not on gcc115 - ARM64 machine; that said, this test is already known to be flaky - on Windows 32-bit (may depend on character settings on machine?) - - * MAINT: MR 2956 revisions - - * reduce optimization level of MDAnalysis builds on - ARM64 to avoid problems with `ap.c` causing test failures - on that architecture - - * revert any source changes to `ap.c` - -commit beb5232dc7501e6bc0138036f697aa14da2a4162 -Author: mnmelo -Date: Sun Oct 18 10:35:15 2020 +0100 - - Fixed AtomGroup.center's behavior when using compounds in conjugation with (#2992) - - unwrapping (closes #2984). - -commit 26880f0f0a4bb831fca9668650400858c34f442b -Author: Jonathan Barnoud -Date: Sat Oct 17 00:06:46 2020 +0100 - - Update indexing in Charges and Masses get_residues (#2991) - - * Fixes #2990 - * Update indexing in Charges and Masses get_residues: - Avoid indexing a numpy array with a list of arrays, use a tuple of array - instead. Multidimensional indexing of arrays with a non-tuple argument - is deprecated. - * Turn warnings into errors to avoid regression over #2990 - * Update CHANGELOG - -commit 2ee4e9da5aa3a2c1b21fc3d1897bd70e0ab2064d -Author: Jonathan Barnoud -Date: Thu Oct 15 14:55:52 2020 +0100 - - Have CI use mamba (#2983) - - Not an issue targetted fix. - - ## Overview - - mamba is a dropin replacement for the conda CLI but faster - - ## Work done in this PR - - Enabled the `MAMBA` environment variable keyword for the CI helper. - -commit 64a7c051f1a51ff2a89b9da9257a21cea0ef00fa -Author: Jonathan Barnoud -Date: Wed Oct 14 13:39:56 2020 +0100 - - Use a fixture for npz files in test_bat (#2981) - - Fixes #2979 - - ## Work done in this PR - - The file test_bat_IO.npy was created in one test and used in - another one. This leads to the second test possibly failing - when the tests are run in parallel. This commit moves creating - the file into a fixture that the two tests depends. - - The new fixture also uses the tmpdir fixture to avoid the file - created during the tests to remain in the test directory. - -commit 0359fec1200c84dd2652c2395c2e29fefcdd750f -Merge: 488484cb1 a9543ba29 -Author: Rocco Meli -Date: Tue Oct 13 11:20:32 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit a9543ba29083449944b34d0b77429cab12f2409a -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Oct 11 03:50:31 2020 +1100 - - restores parmed intersphinx (#2978, Issue #2951) - - Fixes issue #2951 - - ## Work done in this PR - - - Restores the parmed intersphinx link. - -commit 488484cb1add69de25c6a794108610ba558fbb72 -Merge: 54c2af95d 5e8caf089 -Author: Rocco Meli -Date: Wed Oct 7 19:10:51 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 54c2af95dda6e30d25a7983a42dd934644fa819b -Merge: 58e79d2be 3df458123 -Author: Rocco Meli -Date: Wed Oct 7 18:13:46 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 1116b7efe399d64bdbd3953205e9f3f83bf13cff -Author: Irfan Alibay -Date: Tue Oct 6 19:32:54 2020 +0100 - - change CHARMM selection syntax page (#2973) - -commit 5e8caf0894570f9c37dda2d226033fa1514eb319 -Author: Irfan Alibay -Date: Tue Oct 6 19:32:24 2020 +0100 - - Change CHARMM selection syntax page (#2972) - -commit efb9137a18611722451fcc06dbafee08f10b8a24 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Oct 6 12:54:27 2020 +1100 - - Have copies of docs at stable/ and dev/ (#2970) - - - Copies the latest release to https://docs.mdanalysis.org/stable/ - - Copies latest dev docs to https://docs.mdanalysis.org/dev - - Allows docs to be intersphinxed at above URLs - -commit ecaec3fe4dff7523b6edad3072458e010ef558fc -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Oct 6 11:01:50 2020 +1100 - - Have copies of docs at stable/ and dev/ (#2968) - - - Copies the latest release to https://docs.mdanalysis.org/stable/ - - Copies latest dev docs to https://docs.mdanalysis.org/dev - - Allows docs to be intersphinxed at above URLs - -commit 542daa9035a7e8fe3354bcb1ed13f506a87f8ef2 -Merge: be9380b6c d83c78214 -Author: Oliver Beckstein -Date: Fri Oct 2 16:14:23 2020 -0700 - - Merge pull request #2885 from tylerjereddy/treddy_invalid_escape_fix - - MAINT: fix invalid escape seqs - -commit d83c78214c90f258ee200151f4b3a90b86114be3 -Author: Oliver Beckstein -Date: Mon Aug 10 15:08:48 2020 -0700 - - MAINT: cleaned up escape strings and fixed reST - - - mostly convert strings to raw strings - - removed a number of embedded newlines from raw strings - (because they do not work in raw strins as expected) - - fixed heading of MDAnalysis/core/topologyattrs.py - - fixed reST in Janin - -commit 33379426b0e7121970b6afe3d103c9c26a220413 -Author: Tyler Reddy -Date: Sun Aug 9 17:43:13 2020 -0600 - - MAINT: PR 2885 revisions - - * invalid escape sequence usage is now treated - as an error in our full test suite to prevent - regressions - - * CHANGELOG update - -commit 5c70cf0814091955af706c300636d0ade8183b5b -Author: Tyler Reddy -Date: Wed Aug 5 20:41:13 2020 -0600 - - MAINT: fix invalid escape seqs - - * invalid escape sequences in `str/bytes` are deprecated - in newer versions of Python: https://bugs.python.org/issue27364 - - * fix the various `DeprecationWarning: invalid escape sequence \..` - warnings emitted by our full test suite, mostly by using raw strings - `r'...'` to allow use of internal `\` - - * full test suite warning count drops slightly from 30,298 to - 30,276 - -commit be9380b6c1a0227433cf5a144b03043d6702691e -Author: Lily Wang -Date: Fri Oct 2 17:09:31 2020 +1000 - - revert version - -commit 43032886e9d77dd3437a2ecacd3b3c71db230053 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Fri Oct 2 17:55:58 2020 +1000 - - Add doc script changes but revert VERSION variable (#2964) - -commit 08491ccbe04c503683b4e14251a1409548ef2e63 -Author: Lily Wang -Date: Thu Oct 1 18:19:38 2020 +1000 - - added error messages and progress printing - -commit 11f343ad9959926b1e0032338e75759a7f0007a1 -Author: Lily Wang -Date: Thu Oct 1 18:12:01 2020 +1000 - - fix 2.0.0-dev0 and sort versions so dev is 2.0.0-dev not 1.0.1-dev - -commit 60d3d1844a8c45a81e4497b5750f1940bae26e3a -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu Oct 1 13:38:35 2020 +1000 - - Write more redirect stubs (#2955) - - * Redirect URLs like https://docs.mdanalysis.org/documentation_pages/converters.html to https://docs.mdanalysis.org/1.0.0/documentation_pages/converters.html - -commit 3619b5311faf68b5d97468501b10daf08dbe880a -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu Oct 1 12:51:02 2020 +1000 - - Add more docs redirects (#2960) - - * Redirect URLs like docs.mdanalysis.org/documentation_pages/converters.html to docs.mdanalysis.org/1.0.0/documentation_pages/converters.html - -commit 108f1c25a0473d0bff6a6c2944033b9d57b6a905 -Author: Irfan Alibay -Date: Wed Sep 30 23:01:02 2020 +0100 - - Fix readme tutorial link (#2961) - - * Update README.rst - * Remove bolding from tutorials (does not work as a reST link) - -commit 9b88b8358c12c9c8e185d8c17e44f575dbfc7407 -Author: Irfan Alibay -Date: Wed Sep 30 13:34:30 2020 +0100 - - Removes element guessing from ParmedParser (Issue #2933) (#2959) - - * assigns empty string for missing elements - * PEP8 fixes - -commit 9c496f64a6e04ebf4523964724217ef60796400d -Author: Lily Wang -Date: Mon Sep 28 12:03:24 2020 +1000 - - comment out parmed intersphinx - - fix #2951 (temporarily) - - (cherry picked from commit 2687c401742ef081684b93cc5c493dc0805a1686) - -commit 2687c401742ef081684b93cc5c493dc0805a1686 -Author: Lily Wang -Date: Mon Sep 28 12:03:24 2020 +1000 - - comment out parmed intersphinx - -commit 3df45812391c585fbc233fb3de7b5135d5a13200 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Wed Sep 23 19:58:56 2020 +1000 - - Remove helanal (#2929) - - Towards #2739 - - ## Work done in this PR - Removes the old helanal code in favour of helix_analysis - -commit ecbbc4e2148d2a08f2dd0d65f7df2655af954078 -Author: Oliver Beckstein -Date: Fri Sep 18 16:59:01 2020 -0700 - - ensure that unistd.h is included for spe.c with recent clang - - - fix #2934 - - use unistd.h in ENCORE's spe.c when not WIN32 (e.g. __unix__ or __APPLE__ but to be consistent - with other uses in the code base we do not specifically test for __unix__ || - __APPLE__) - - update CHANGELOG - - (cherry picked from commit 56c5ea9cdda14b18cf925dfec00dca31b7dba740) - -commit a321fa757affd24c512db1cb1db4298290a3c57f -Merge: c4478d3fa 56c5ea9cd -Author: Oliver Beckstein -Date: Tue Sep 22 17:42:38 2020 -0700 - - Merge pull request #2949 from MDAnalysis/issue-2934-unistd-apple - - ensure that unistd.h is included on recent clang - -commit 58e79d2be7bce962de5cfd141fb5f5fa43be7e07 -Merge: 206b547d3 f0899e44a -Author: Rocco Meli -Date: Sat Sep 19 23:23:28 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 56c5ea9cdda14b18cf925dfec00dca31b7dba740 -Author: Oliver Beckstein -Date: Fri Sep 18 16:59:01 2020 -0700 - - ensure that unistd.h is included for spe.c with recent clang - - - fix #2934 - - use unistd.h in ENCORE's spe.c when not WIN32 (e.g. __unix__ or __APPLE__ but to be consistent - with other uses in the code base we do not specifically test for __unix__ || - __APPLE__) - - update CHANGELOG - -commit c4478d3faec44913921a947eadd571ee856864f8 -Author: Cédric Bouysset -Date: Fri Sep 18 02:36:59 2020 +0200 - - RDKitConverter bugfix on HIP residue (#2941) - - * fix hip with reaction - -commit ddb354e3bb4dd7cd0be4d84c0eb89d0e4abcb2ef -Author: Oliver Beckstein -Date: Tue Sep 15 09:16:43 2020 -0700 - - add docs for analysis.align.AverageStructure - - fix #2943 - -commit 992d0e36a4784c150d63da75ade1adffa27a9b1e -Author: Oliver Beckstein -Date: Tue Sep 15 09:16:43 2020 -0700 - - add docs for analysis.align.AverageStructure - - fix #2943 - - (cherry picked from commit 7cae0345af729c9dccba1e3043d4cc4004dad6a2) - -commit 2ebb052904829c068742144d17eb38a950ed057c -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu Sep 10 09:31:44 2020 +1000 - - Add test files (#2940) - - * Fixes issue #2939 - - * Work done in this PR - - Adds missing file types of testsuite/setup.py - (*top, *in, *sdf, and the contents of data/gromacs/gromos54a7_edited.ff/*). - - (cherry picked from commit 3148207b81fc11de0c1ffa901ba455ef31ceadd0) - -commit 132758373d56da021a1276e8e9f13c190288c538 -Author: Lily Wang -Date: Sun Sep 6 23:17:36 2020 +1000 - - oops - -commit f0899e44a4fcb150752bba93f5443df4218be7ba -Author: Lily Wang -Date: Sun Sep 6 23:14:47 2020 +1000 - - oops - -commit 3148207b81fc11de0c1ffa901ba455ef31ceadd0 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu Sep 10 09:31:44 2020 +1000 - - Add test files (#2940) - - Fixes issue #2939 - - ## Work done in this PR - - Adds missing file types of testsuite/setup.py - (*top, *in, *sdf, and the contents of data/gromacs/gromos54a7_edited.ff/*). - -commit 2c5e3859b9ecaa618b634b74307579f38af472c6 -Author: Yuxuan Zhuang -Date: Tue Sep 8 02:55:51 2020 +0200 - - Refactor Transformations from closure into class (#2859) - - * Fixes #2860 - * refactor transformations from closure into class (necessary so that a Universe - with transformations can be pickled). - * change universe pickling to `__reduce__` (instead of `__setstate__`/`__getstate__`, which - did not work with transformations) - * add test for pickling a Universe with transformations - * update docs for transformations - - examples (written as class) - - deprecate transformations as closures (still works but cannot be pickled due - to limitations in Python's pickle module) - * update changelog - -commit 52679c7742c314398cc13c74a0ac4089aa29c8f4 -Merge: 7313cf1ce d91e5e86b -Author: Oliver Beckstein -Date: Fri Sep 4 14:51:05 2020 -0700 - - Merge pull request #2798 from MDAnalysis/backport-1.0.1 - - - Fixes #2768 - - backport fixes from 2.0.0 development version to the 1.0.x branch (master) - - includes backports of all fixes tagged with Milestone 1.0.x (currently 1.0.1) via cherry-picked commits - -commit d91e5e86b83087035773c14fab0f871aa8e3477b -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sat Sep 5 03:37:49 2020 +1000 - - Deprecate helanal (PR #2928) - - * deprecate helanal, to be removed in 2.0.0 (use analysis.helix_analysis in 2.0 from PR #2622) - * add deprecation warnings to analysis.helanal - * update CHANGELOG - -commit 206b547d33d6d5b8f3a4e15fba9f05fecc6c5df0 -Merge: 919260466 ca745a31d -Author: Rocco Meli -Date: Wed Sep 2 23:40:17 2020 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit ca745a31da72cc9dcd539848de3afbd6cfb0c5d8 -Merge: b2b7bcbdf 919260466 -Author: Rocco Meli -Date: Wed Sep 2 23:40:06 2020 +0100 - - Merge branch 'develop' into upstream/develop - -commit 919260466f73cd3829de788fd84bef3dc13ffffb -Merge: 698b2b1b6 b2b7bcbdf -Author: Rocco Meli -Date: Wed Sep 2 23:05:48 2020 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 698b2b1b63947059f3d69356d60221abcf5a7b58 -Merge: da33ac60a 45e56e831 -Author: Rocco Meli -Date: Wed Sep 2 23:05:07 2020 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit f6cf5954ea75fd94682c413dada9c7b7f5462859 -Author: Oliver Beckstein -Date: Wed Sep 2 10:58:53 2020 -0700 - - fix minor inconsistencies in backport - - Co-authored-by: Irfan Alibay - Co-authored-by: Lily Wang - -commit 41730281ba2e218082eb2d67a7646832f185d9d6 -Author: Oliver Beckstein -Date: Tue Sep 1 15:29:36 2020 -0700 - - install chemfiles via pip for Python 2.7 - - Work around conda-weirdness which just fails to properly resolve the pinned chemfiles-lib - that would be compatible with the last working Py 2.7 version of netcdf4. - -commit b2b7bcbdf4e2fe4e221d5e67842c90cf317375e5 -Author: Cédric Bouysset -Date: Sat Aug 29 04:36:08 2020 +0200 - - Add SMARTS selection (#2883) - - Towards #2468 - - ## Work done in this PR - Adds a new SMARTS based selection which uses the RDKit converter. - -commit a8227f03300bb787118563ef94809c30e5f1e0f9 -Merge: 3e6b38cb1 84d227583 -Author: Oliver Beckstein -Date: Fri Aug 28 09:24:21 2020 -0700 - - Merge pull request #2923 from lilyminium/fix-2921 - - Update function signatures in core.Universe - -commit 3e6b38cb14c7deca7201b48b3a054404a0e1def8 -Author: Irfan Alibay -Date: Thu Aug 27 18:30:57 2020 +0100 - - Remove as_Universe (Issue #2920) (#2922) - - - Removes `as_Universe` from MDAnalysis.core.universe - - LeafletFinder no longer accepts paths to files as Universes - -commit 84d2275836e03ac648a8b70b36361ab8066d9120 -Author: Lily Wang -Date: Fri Aug 28 03:26:10 2020 +1000 - - updated function signatures - -commit 27dae7cdbd006729095c04755bbae8535a8b963e -Author: Ramon Crehuet -Date: Wed Jun 10 18:33:36 2020 +0200 - - Added space to separate field in helanal output files - - - fixes The output files had all the the floating point numbers joined in a single string. - - see PR #2733 - - update AUTHORS - - update CHANGELOG - -commit b27a59fc5b6fd030b9ba05be39f77e29e9c79e69 -Author: Oliver Beckstein -Date: Wed Aug 26 17:54:27 2020 -0700 - - deprecate core.universe.as_Universe - - - see #2920 - - add deprecation note to as_Universe - - add deprecation notice to LeafletFinder: filename instead of Universe will be removed - (uses as_Universe so users will see the DeprecationWarning from as_Universe) - - add test - - update CHANGELOG for 1.0.1 - -commit 4ed8f41704b6e89bc3e36d68092c5c8635a386d2 -Author: Oliver Beckstein -Date: Tue Jun 30 16:46:40 2020 -0700 - - consolidate package info files - - - generate LONG_DESCRIPTION from README.rst - - remove SUMMARY.txt (out of date) - - read top-level repository README.rst for LONG_DESCRIPTION - - changed README.rst - - add installation instruction (link) - - add links to Quickstart Guide, User Guide, and API docs - - add links to issue tracker and mailing list in text (Contributing) - - replaced links to wiki with links to User Guide - - remove raw html from README (raw html not allowed on PyPi) - - replace NumFOCUS logo image with reduced size version (200 x 61 px) and standard reST - image syntax (logo added to web site in commit - https://github.com/MDAnalysis/MDAnalysis.github.io/commit/ec4fe2c72a7238581adf6475c0555ed57db29cf6 ) - - fix broken link - - tutorials direct to Examples in User Guide - - add link to video section of "Learning MDAnalysis" - - passes `twine check` - - cleaned up MANIFEST.in (for pypi packages) - - fixed links in Py files - - Make sure that we always use the SSL url of the home page - - git grep -l 'http://www\.mdanalysis\.org' | xargs perl -wpi~ -e 's(https://www\.mdanalysis\.org)(https://www.mdanalysis.org)' - - - fixed link to issue tracker in files - - git grep -l 'issues.mdanalysis.org' | xargs perl -wpi~ -e 's(https?://issues\.mdanalysis\.org)(https://github.com/MDAnalysis/mdanalysis/issues) - - - fixed PEP8 issues in files - - - various updates in testsuite/README (link to userguide, update badges) - - use User Guide as style reference - - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - (cherry picked from commit d0b03e6e61fc36438d960ba01d2cb3a7f07d0229) - -commit 82ff196074b4e41c60d87ee7f36924cb8844a120 -Author: Oliver Beckstein -Date: Tue Jun 30 23:22:00 2020 -0700 - - add travis job to test pypi packaging - - - explicit PYPI_CHECK in script section - - switch travis to beta for config validation - - https://docs.travis-ci.com/user/build-config-validation - - get feedback on problems with the config yml file - - Note: Use ci-helper's algorithm for installing numpy and don't pin a numpy version, - not even for the simple PYPI_CHECK section - (cherry picked from commit bbc3dcb46ebc21c09d7ac3c7fa14d663ced5c7e7) - -commit c6e27a383c0172b949ad440ba0489d03d1615f56 -Author: Oliver Beckstein -Date: Wed Aug 26 17:16:46 2020 -0700 - - pin chemfiles-lib for Python 2.7 - - - pinning ensures that chemfiles conda package pulls the last working - netcdf4 package in; otherwise we get failures such as - - OSError: libnetcdf.so.18: cannot open shared object file: No such file or directory - - - https://github.com/MDAnalysis/mdanalysis/pull/2798#issuecomment-679991785 - - Co-authored-by: Guillaume Fraux - -commit b672b595b57f6862d486391d646cf30c31fd8501 -Author: Richard Gowers -Date: Tue Aug 25 14:35:33 2020 +0100 - - Faster name selections (#2755) - - * fix #2751 - * Python 2.7/3 backport of PR #2755 (use six.string_types, update CHANGELOG and versionchanged as 1.0.1) - * modified AtomNames topologyattr to include lookup table index - * rework atom name selection to use lookup tables - * fixed test supplying integer as atom name - * Update test_topologyattrs.py - * use dict-lookup string attrs EVERYWHERERE - * made protein selection faster, 48ms -> 0.5ms on GRO testfile - * improved nucleic/backbone selections - * Added explicit tests for Resnames topologyattr - tests now provide str types for resnames/icodes - * use fnmatchcase to be case sensitive (this was a small unreported bug in 1.0.0: the matching - was done case-insensitive) - - Co-authored-by: Irfan Alibay - Co-authored-by: Oliver Beckstein - - (cherry picked from commit 45e56e8314c278e3eb98ed7a6029b74e7435e8be) - -commit 45e56e8314c278e3eb98ed7a6029b74e7435e8be -Author: Richard Gowers -Date: Tue Aug 25 14:35:33 2020 +0100 - - Faster name selections (#2755) - - * modified AtomNames topologyattr to include lookup table index - - * cheeky little optimisation - - * rework atom name selection to use lookup tables - - * Update topologyattrs.py - - * fixed test supplying integer as atom name - - really topologyattrs need to be statically typed and protective about this - - * Update test_topologyattrs.py - - * use dict-lookup string attrs EVERYWHERERE - - * removed some code duplication - - made protein selection faster, 48ms -> 0.5ms on GRO testfile - - * improved nucleic/backbone selections - - * Added explicit tests for Resnames topologyattr - - tests now provide str types for resnames/icodes - - * use fnmatchcase to be case sensitive - - * Update package/MDAnalysis/core/selection.py - - @jbarnoud's fix - - * apply suggestions from code review - - Co-authored-by: Irfan Alibay - - * added test for setting multiple segids at once - - Co-authored-by: Oliver Beckstein - Co-authored-by: Irfan Alibay - -commit ca2cbe4088f0a4f7740fa3c824f05a0abeeefe2d -Merge: 2f0381e58 9ebc1b23e -Author: Irfan Alibay -Date: Sun Aug 23 13:31:38 2020 +0100 - - Merge PR #2916 (originally PR #2775): RDKitConverter (Issue #2468) - - Towards #2468 (RDKit interoperability GSOC project) - - PR #2916 -> Originally PR #2775 - - ##Overview of work done in PR - - This PR adds the RDKitConverter class which converts MDAnalysis - Universe/Atomgroup objects to RDKit rdchem.Mol objects. - - ##Limitations - - - Bonds and elements must be present (the former will be inferred if not - present). - - This converter mainly aims at supporting cases where explicit hydrogens - are present. - - ##Extra implementation details - - - Bond order and formal charges are inferred via atomic valencies & the - number of unpaired electrons (see _infer_bo_and_charges). - - In part due to the influence of atom read order on inferring, bond - conjugation and functional groups are standardized using SMARTS - reactions (see _standardize_patterns). - - ##Other changes - - Also includes some PEP8 changes and some cleaning up of the tests for the - RDKITReader. - - ##References - - For more information on the development process for this PR, see: - https://cbouy.github.io/blog/2020/07/01/rdkit-converter - https://cbouy.github.io/blog/2020/07/22/rdkit-converter-part2 - -commit 9ebc1b23e83eaa270a3241fe2ede21afacbdb17a -Author: Cédric Bouysset -Date: Fri Aug 21 17:14:30 2020 -0700 - - Towards #2468 (RDKit interoperability GSOC project) - - * Overview of work done in PR - - This PR adds the `RDKitConverter` class which converts MDAnalysis - `Universe`/`Atomgroup` objects to `RDKit rdchem.Mol` objects. - - * Limitations - - Bonds and elements must be present (the former will be inferred if not - present). - - This converter mainly aims at supporting cases where explicit hydrogens - are present. - - * Extra implementation details - - Bond order and formal charges are inferred via atomic valencies & the - number of unpaired electrons (see `_infer_bo_and_charges`). - - In part due to the influence of atom read order on inferring, bond - conjugation and functional groups are standardized using SMARTS - reactions (see `_standardize_patterns`). - - * Other changes - - Also includes some PEP8 changes and some cleaning up of the tests for the - `RDKITReader`. - - * References - For more information on the development process for this PR, see: - 1) https://cbouy.github.io/blog/2020/07/01/rdkit-converter - 2) https://cbouy.github.io/blog/2020/07/22/rdkit-converter-part2 - -commit 2f0381e58328e4b2d684315fa5721a6de9945512 -Author: Yuxuan Zhuang -Date: Fri Aug 21 20:31:42 2020 +0200 - - Serialization of AtomGroup and remove core.universe._ANCHOR_UNIVERSES (PR #2893) - - * AtomGroup now are pickled/unpickled without looking for its anchored Universe - * removed core.universe._ANCHOR_UNIVERSES (originally introduced with #293) and related machinery to keep global state. No global state is kept any more. - * update docs for atomgroup pickle - * update CHANGELOG - * update tests - -commit da33ac60ad0a3e0f356c9b9a517a57b6255015e1 -Merge: 7330ca399 23074c64f -Author: Rocco Meli -Date: Fri Aug 21 13:45:46 2020 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 23074c64f5de2795756c44eb16e488d4f1d253f0 -Author: Yuxuan Zhuang -Date: Mon Aug 17 11:20:38 2020 +0200 - - fix DCD/XDR pickling on last frame (#2911) - - - Fixes #2878 - - Changes made in this Pull Request: - - add more comprehensive tests for pickling low-level dcd and xdr files - - fix a bug that was introduced in #2723 (wrong seeking in DCD and XDR, note: this bug was only in develop, never in released code, see discussion in PR #2908) - - update CHANGELOG - - maybe backport in #2908 - -commit 91007202dca5f5445f4802a868e6242238cf21e2 -Author: Oliver Beckstein -Date: Fri Aug 14 02:04:31 2020 -0700 - - cleaned up lib.log (#2902) - - - fix #2734 - (docs now build with sphinx 2.3) - - formally deprecated lib.log.echo() (CHANGELOG, @deprecate, and test) - - explicitly added docs to ProgressMeter - - avoids sphinx failure due to wrong formatting in tqdm.auto.tqdm - - add specific example for MDA - - document our own verbose kwarg - - improved markup - - not documented: gui kwarg (discouraged in original docs) - - (cherry picked from commit 5e686178c94eca11cf7bff9143489eaffb53ef13) - -commit 22612de473319f40e028f64257fa0b297d89255b -Author: Mieczyslaw Torchala -Date: Fri Aug 14 23:42:00 2020 +0100 - - Write HETATM record types (#2880) - - Fixes #1753 and #2906 - - ## Overview of work done in this PR - 1) PDBWriter will now write out either `ATOM` or `HETATM` entries based on the contents of the atomgroup `record_types` attribute. If the `record_types` attribute is missing, writing will default to `ATOM` entries. - 2) Updates the PDB documentation to refer to PDBv3.3 instead of PDBv3.2. - -commit 5e686178c94eca11cf7bff9143489eaffb53ef13 -Author: Oliver Beckstein -Date: Fri Aug 14 02:04:31 2020 -0700 - - cleaned up lib.log (#2902) - - - fix #2734 - (docs now build with sphinx 2.3) - - removed unused code from lib.log (left over from ProgressMeter removal) - - explicitly added docs to ProgressMeter - - avoids sphinx failure due to wrong formatting in tqdm.auto.tqdm - - add specific example for MDA - - document our own verbose kwarg - - improved markup - - not documented: gui kwarg (discouraged in original docs) - -commit a3d10b001d891a0b789ce5a3ff27596f4470d6dd -Author: Zhiyi Wu -Date: Fri Aug 14 09:54:13 2020 +0100 - - Clean the NeighborSearch and allow uniformed output (#2907) - - * test edit - - * fix AttributeError - - * Update test and docs - - * fix test - - * Update package/MDAnalysis/lib/NeighborSearch.py - - Co-authored-by: Oliver Beckstein - - * make it compile PEP8 - - Co-authored-by: zhiyiwu - Co-authored-by: Oliver Beckstein - -commit e0916339b4b8239a9ac6036e9a0ab2c88bd206cb -Author: Oliver Beckstein -Date: Thu Aug 13 06:50:24 2020 -0700 - - Add keywords to filter residues in Janin analysis (#2899) - - Fixes #2898 - - - add select_protein and select_remove keywords to Janin analysis - - filter CYS* by default - - updated docs and plots - - made plots prettier (degree symbol on ticks) - -commit 89cf0a3f8f0fcee079fa2000026ba802421f1981 -Author: Ian Kenney -Date: Tue Jul 28 18:05:37 2020 -0700 - - Implemented extraction of chains from DMS formats (#2872) - - * partially addresses #1387 for the DMS parser - * Changes made in this Pull Request: - * Repeated residues are not squashed - * Multiple segids are created when multiple chains are present - * Implemented extraction of chains from DMS formats - * Properly split repeating segids: ["A", "B", "A"] -> ["A", "B"] - * tests: New DMS file that includes multiple segids - Derived from adk_closed.dms and edited in sqlite3 - ```sql - UPDATE particle SET segid = "CORE"; - - UPDATE particle - SET segid = "NMP" - WHERE resid BETWEEN 30 AND 59; - - UPDATE particle - SET segid = "LID" - WHERE resid BETWEEN 122 AND 159; - ``` - where the domain definitions can be found in: - - Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path Similarity Analysis: A Method for Quantifying - Macromolecular Pathways. PLoS Comput Biol 11(10): e1004568. https://doi.org/10.1371/journal.pcbi.1004568 - * tests: - - Modified atom selections in test_dms.py - - added new selections in test_dms.py and relabeled previous selections - - Added DMS with no segid - * Updated CHANGELOG - - (cherry picked from commit 2f16a16aa3b9484ba37c9281e32bc80a18e5878e) - -commit 7c1c426a4d104999376718665b2ab625473f4da0 -Author: CalCraven <54594941+CalCraven@users.noreply.github.com> -Date: Wed Aug 12 18:10:10 2020 -0500 - - fix masses and charge bug in HOOMD-XML parser (#2889) - - * Fixes #2888 - * Fix the HoomdXMLParser.py so that it properly reads in masses and charges instead of overriding all of those values with 0.0. - * add tests - * update CHANGELOG - * update AUTHORS - - Cherry-picked from 01bbf3c8fa7ecc9c523e6299aadec83104adcd03 - -commit 01bbf3c8fa7ecc9c523e6299aadec83104adcd03 -Author: CalCraven <54594941+CalCraven@users.noreply.github.com> -Date: Wed Aug 12 18:10:10 2020 -0500 - - fix masses and charge bug in HOOMD-XML parser (#2889) - - * Fixes #2888 - * Fix the HoomdXMLParser.py so that it properly reads in masses and charges instead of overriding all of those values with 0.0. - * add tests - * update CHANGELOG - * update AUTHORS - -commit 3a31ef60693e09cc69c14999585b36d81d293b93 -Author: Yuxuan Zhuang -Date: Wed Aug 12 13:45:34 2020 +0200 - - imp deprecated - -commit a9e749c1b29bb3c278153692585f2b6a90b6a923 -Author: edisj <59893899+edisj@users.noreply.github.com> -Date: Wed Aug 12 00:44:58 2020 -0700 - - Make H5MD serialize with pickle (#2894) - - * fix #2890 - * added H5PYPicklable class (works in serial but not with driver="mpio" and MPI comm) - * mock h5py so that the docs build even in the absence of h5py - * tests (anything related to mpi is excluded from coverage) - * update CHANGELOG - -commit 5c0eb207d2141bb4166112fe3af4fe61d0fad2fc -Author: Rocco Meli -Date: Wed Aug 12 02:57:03 2020 +0200 - - Fix rotateby documentation (#2903) - - * Fixes #2901 - * Changes made in this Pull Request: - - Added call to rotateby (instead of rotate) - - Removed () from atom group - -commit 7330ca399c0d12ff1b879c248bbdff5d44420b4e -Merge: fe8420e88 3ea6e430b -Author: Rocco Meli -Date: Tue Aug 11 19:03:23 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 3ea6e430b2820fd9d367f800d036a9c3ee87721a -Author: IAlibay -Date: Mon Aug 10 15:18:12 2020 +0100 - - MSD typo - -commit 563995c78c30a59404b37e4832f5c2a774ebba19 -Author: Yuxuan Zhuang -Date: Sat Aug 8 02:40:41 2020 +0200 - - Serialize FileIO and TextIOWrapper and Universe (#2723) - - * Fixes #2878 - * basic approach: composition instead of inheritance for pickling Universe (which was - tested in PR #2704 (which was derived from PR #2140)) - * Changes made in this Pull Request: - - add new classes and pickle_open function to picklable_file_io.py - - add new picklable `BufferedReader`, `FileIO`, and `TextIOWrapper` classes. - - implement `__getstate__`, `__setstate__` to `Universe` and `BaseReader` - - fix DCD, XDR pickle issue - - modified gsd and ncdf to be picklabel - - modified ChainReader to be picklabel - - ensure chemfiles is picklable - * add tests (MultiFrameReader will test for serializability) - * update CHANGELOG - * update docs - - Note: This merge squashed 120 commits. See PR #2723 for the full history with 420 comments. - -commit 27278bbd02d4aa54d2c9bc5e21d36541e681c195 -Author: edisj <59893899+edisj@users.noreply.github.com> -Date: Fri Aug 7 15:18:59 2020 -0700 - - add h5md format (#2787) - - * Fixes #762 - * add H5MD coordinate reader (supports parallel MPI in principle but is not well tested at the moment, see #2865) - * added test h5md datafiles: real example (derived from cobrotoxin.trr) and synthetic example for MultiframeReaderTest reader tests - * add tests (MultiframeReaderTest and custom) - * add documentation (example and parallel MPI) - * added h5py into conda dependencies and pyh5md into pip dependencies - * update CHANGELOG - * update AUTHORS - -commit 2f16a16aa3b9484ba37c9281e32bc80a18e5878e -Author: Ian Kenney -Date: Tue Jul 28 18:05:37 2020 -0700 - - Implemented extraction of chains from DMS formats (#2872) - - * partially addresses #1387 for the DMS parser - * Changes made in this Pull Request: - * Repeated residues are not squashed - * Multiple segids are created when multiple chains are present - * Implemented extraction of chains from DMS formats - * Properly split repeating segids: ["A", "B", "A"] -> ["A", "B"] - * tests: New DMS file that includes multiple segids - Derived from adk_closed.dms and edited in sqlite3 - ```sql - UPDATE particle SET segid = "CORE"; - - UPDATE particle - SET segid = "NMP" - WHERE resid BETWEEN 30 AND 59; - - UPDATE particle - SET segid = "LID" - WHERE resid BETWEEN 122 AND 159; - ``` - where the domain definitions can be found in: - - Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path Similarity Analysis: A Method for Quantifying - Macromolecular Pathways. PLoS Comput Biol 11(10): e1004568. https://doi.org/10.1371/journal.pcbi.1004568 - * tests: - - Modified atom selections in test_dms.py - - added new selections in test_dms.py and relabeled previous selections - - Added DMS with no segid - * Updated CHANGELOG - -commit 2550d061a3134e0002fc8ec4eb31eb3c63bcfa5b -Author: Jonathan Barnoud -Date: Tue Jul 21 13:02:51 2020 +0100 - - Add elements attribute to TPR parser (#2858) - - Fixes part of #2553 - -commit 2e6b9608bfdbbf02133d5d1f0cd29db0cd43473b -Author: Tyler Reddy -Date: Sun Jul 19 11:38:57 2020 -0600 - - MAINT: explicit ragged arrays (#2845) - - * adjust our `pytest` config to turn NEP 34 warnings - into errors with NumPy `1.20.0` (current NumPy `master`) - - * fix the errors picked up by the test suite with above - adjustment - - Co-authored-by: Jonathan Barnoud - -commit 784ccc717dba2ceff7fa5233bc3cc9d4640c2464 -Author: Jonathan Barnoud -Date: Sun Jul 19 15:46:32 2020 +0100 - - Remove compatibility aliases in mda.lib.util (#2856) - - Some functions were aliassed so we could provide an alternative for - python < 3.6. These aliasses are not necessary anymore. - -commit c7a6b62d78fbf1f59e3369ed43152e8a8cc98310 -Author: Irfan Alibay -Date: Sun Jul 19 11:10:01 2020 +0100 - - Remove assignment of bond attribute when PDB file contains no CONECT records (#2855) - - * Fixes issue 2832 - no PDB bond attribute whene empty - - * Update changelog - - * Fix test and simplifies bond envaluation - -commit d084bd67a11f835fe121c2c23956fb78aa731984 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Jul 19 11:28:51 2020 +1000 - - Refactored HELANAL to use AnalysisBase (#2622) - - Fixes #2452 - - * added new helanal using AnalysisBase - * deprecated old helanal - * added universe_from_origin - * updated to use np clip - * added new local_screw algorithm - * changed screw angles to projection onto cross-axis - -commit 40a8c95572799e58976a51ad18f086e9498ed413 -Author: Irfan Alibay -Date: Sat Jul 18 07:49:24 2020 +0100 - - changes cython language_level to 3 (#2854) - - * changes cython language_level to 3 - - * fix pep8 issues - -commit 90c2c8135b57d6a2fb2133e27ef3290127d3c7ae -Author: Jonathan Barnoud -Date: Fri Jul 17 07:06:48 2020 +0100 - - Spring cleaning for the TPR parser (#2840) - - * Remove python 2 compatibility hacks in TPR parser - - The TPXUnpacker class and its children had hacks to work on python 2. - This commit removes these hacks has support for that version of python - is now dropped. - - * Use f-strings throughout the TPR parser - - * Remove useless alias - - * Remove redundant version test in TPR perser - - The TPR parser supports file generated from gromacs 4.0 (tpx version 58) - and newer. There were checks about older version that were either always - true or always false. Because some of these checks were hidding - erroneous code, this commit factor them out. - - * Remove useless alias - - * Use f-strings in TPR parser - - * Fix a spelling error - - * Use f-strings - - * Remove unused iparams from TPR parser - - The do_iparams function in the TPR parser reads the parameters of the - various interactions in the TPR file. As we do not use these parameters, - he function does not return anything. We use to store this absence of - return value (None). This commit removes this. - - * Remove redundant version check - - * Add forgotten TPR tests - - * Improve test coverage - - * Add tests for gromacs 2020 in double precision - - * Add comment - - * Cover virtual site code in TPR parser - - * Improve TPR virtual sites tests - - * Test more interactions in TPR parser - - * Rename TPR_VS_2020 to account for its content - - The TPR containing he virtual sites example does now contain all the - possible interactions. It is now called EXTRA rather than VS to account - for that change. - - * Increase test coverage in TPR parser - - * Increase TPR test coverage - - * Remove more dead code in TPR parser - - * Update changelog for #2840 - -commit ecb863851c5fe4217059918bb8a4bc511efaae64 -Author: Cédric Bouysset -Date: Thu Jul 16 12:24:33 2020 +0200 - - RDKitParser with table of attributes and icodes (#2852) - - * add table of attributes - - * add icodes attribute - - * pep8 - -commit d6df1a74c26ef455d31b19ece56af58d34340a89 -Author: Hugo MacDermott-Opeskin -Date: Thu Jul 16 18:18:40 2020 +1000 - - Fix MSD docstring and accept AtomGroups (#2841) - - * fixes #2784 - * MSD now accepts AtomGroups - -commit 8e1c4adbbee72eb8c570fe2f690ef9b1ae30c1ca -Author: Tyler Reddy -Date: Thu Jul 16 00:01:19 2020 -0600 - - CI: migrate to Azure for Win (#2850) - - * fixes #2846 - * CI: migrate to Azure for Win - * the majority of Windows CI testing previously provided by Appveyor - is now avaiable in the Azure CI Windows test matrix; 64-bit Python - 3.6, 3.7 and 3.8 have been added to Azure CI Windows testing - * however, Azure CI has been kept PyPI/`pip`-only, to avoid - mixing `conda` and `pip`, which has meant the exclusion of the - `RDKit` dependency - * as a result, it may be advisable to keep the Appveyor testing - in our CI for the moment to test Windows + `RDKit` until - they provide a wheel; possibly, we could consider slimming - down the tests executed in Appveyor CI to only exercise `RDKit` - and other `conda`-only code paths - * move `tdqm` to the "core dependencies" installed for both 32-bit and - 64-bit Azure builds - -commit 5608bb8ab324ec39dd486228944a7d04e209db4d -Author: Paul Smith -Date: Wed Jul 15 16:03:02 2020 +0100 - - Fixes AttributeError in HydrogenBondAnalysis (#2849) - - * Fix Issue #2848 - * An attribute error is thrown when finding D-H pairs via the topology if hydrogens is an - empty AtomGroup. This has been fixed so that an empty donors group is created, rather - than assigning donors = 0. - * Added a test case that raises the attribute without the fix. - * Updated CHANGELOG - * add @bieniekmateusz and @p-j-smith to CHANGELOG 1.0.1 author section - (was forgotten in PR #2849) - - Co-authored-by: bieniekmateusz - (cherry picked from commit 575c027d4fd564254fa7dcca3032cff1b072a7a0) - -commit 575c027d4fd564254fa7dcca3032cff1b072a7a0 -Author: Paul Smith -Date: Wed Jul 15 16:03:02 2020 +0100 - - Fixes AttributeError in HydrogenBondAnalysis (#2849) - - * Fix Issue #2848 - * An attribute error is thrown when finding D-H pairs via the topology if hydrogens is an - empty AtomGroup. This has been fixed so that an empty donors group is created, rather - than assigning donors = 0. - * Added a test case that raises the attribute without the fix. - * Updated CHANGELOG - - Co-authored-by: bieniekmateusz - -commit d1c55751a8850986401e0db7cdc3e177839d4331 -Author: Mateusz Bieniek -Date: Tue Jul 14 21:39:13 2020 +0100 - - Remove the deprecated waterdynamics.HydrogenBondLifetimes class (#2842) - - * remove the deprecated waterdynamics.HydrogenBondLifetimes class, see PR #2791 for more info. - * update waterdynamics docs and link to the replacement, - hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.liftetime - * corrected doc formatting in hydrogenbonds.hbond_analysis - * update CHANGELOG - - co-authored-by: p-j-smith - -commit 83f21dca671e67da525aa1c2043afffb633318a6 -Author: Irfan Alibay -Date: Tue Jul 14 17:11:49 2020 +0100 - - Switches leftover cStringIO call & docs to StringIO (#2847) - -commit 75706b44a6988748d063b6f7a9d86faf04498893 -Merge: d266b0ba2 bbc3dcb46 -Author: Oliver Beckstein -Date: Mon Jul 13 23:30:11 2020 -0700 - - Merge pull request #2808 from MDAnalysis/update-pypi-SUMMARY - - consolidate package info files - -commit bbc3dcb46ebc21c09d7ac3c7fa14d663ced5c7e7 -Author: Oliver Beckstein -Date: Tue Jun 30 23:22:00 2020 -0700 - - add travis job to test pypi packaging - - - explicit PYPI_CHECK in script section - - switch travis to beta for config validation - - https://docs.travis-ci.com/user/build-config-validation - - get feedback on problems with the config yml file - - Note: Use ci-helper's algorithm for installing numpy and don't pin a numpy version, - not even for the simple PYPI_CHECK section - -commit d0b03e6e61fc36438d960ba01d2cb3a7f07d0229 -Author: Oliver Beckstein -Date: Tue Jun 30 16:46:40 2020 -0700 - - consolidate package info files - - - generate LONG_DESCRIPTION from README.rst - - remove SUMMARY.txt (out of date) - - read top-level repository README.rst for LONG_DESCRIPTION - - changed README.rst - - add installation instruction (link) - - add links to Quickstart Guide, User Guide, and API docs - - add links to issue tracker and mailing list in text (Contributing) - - replaced links to wiki with links to User Guide - - remove raw html from README (raw html not allowed on PyPi) - - replace NumFOCUS logo image with reduced size version (200 x 61 px) and standard reST - image syntax (logo added to web site in commit - https://github.com/MDAnalysis/MDAnalysis.github.io/commit/ec4fe2c72a7238581adf6475c0555ed57db29cf6 ) - - fix broken link - - tutorials direct to Examples in User Guide - - add link to video section of "Learning MDAnalysis" - - passes `twine check` - - cleaned up MANIFEST.in (for pypi packages) - - fixed links in Py files - - Make sure that we always use the SSL url of the home page - - git grep -l 'http://www\.mdanalysis\.org' | xargs perl -wpi~ -e 's(https://www\.mdanalysis\.org)(https://www.mdanalysis.org)' - - - fixed link to issue tracker in files - - git grep -l 'issues.mdanalysis.org' | xargs perl -wpi~ -e 's(https?://issues\.mdanalysis\.org)(https://github.com/MDAnalysis/mdanalysis/issues) - - - fixed PEP8 issues in files - - - various updates in testsuite/README (link to userguide, update badges) - - use User Guide as style reference - - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - -commit 721c800c8dfb3f79d19e7b77cafeb474e8eaa53b -Author: Oliver Beckstein -Date: Sun Jul 12 01:56:45 2020 -0700 - - deprecation of waterdynamics.HydrogenBondLifetimes - - - see #2547 and PR #2791 - - will be replaced by MDAnalysis.analysis.hydrogenbonds.HydrogenBondAnalysis.lifetime (in 2.0.0) - - add test for deprecation warning - - update CHANGELOG - -commit d266b0ba29cc9db062c4d05fddcbefc244011d2f -Author: Mateusz Bieniek -Date: Sun Jul 12 09:27:07 2020 +0100 - - Hydrogen Bond Lifetime in waterdynamics.hydrogenbonds (#2791) - - * Fixes #2547 - * The standalone autocorrelation function is now used to calculate the hydrogen bond lifetime in the new - implementation of the hydrogen bond analysis class. - * Added ability to select groups between which to find hydrogen bonds.: - new parameter "between" for hydrogen binding (backwards compatible): The `between` keyword can - be used to specify pairs of groups between which hydrogen bonds will be calculated. - Hydrogen bonds found other pairs of atom groups will be discarded. - * We deprecate the waterdynamics.HydrogenBondLifetime class because of #2247. - * Basic unit tests added to check the integration of the separate components - * add docs with example - * update CHANGELOG - - co-authored-by: p-j-smith - -commit de8813ea96061308316a1c4733228bea4d1cd864 -Author: Yuxuan Zhuang -Date: Tue Jul 7 18:46:36 2020 +0200 - - TRZReader check for n_atoms (#2820) - - * fix #2817 - * TRZReader checks that TRZ file contains the same number of atoms as the topology or n_atoms and fails otherwise - * TRZWriter correctly writes n_atoms to file (previously wrote 0!) - * add test - * add docs - * update CHANGELOG - - (cherry picked from commit c8abbee6d8dc9d80bb798cd9a49b0b0b7b8c6ab7) - -commit 720ab7aef2cf0a75e3460960799af619088ead20 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sat Jun 20 17:12:36 2020 +1000 - - decorate Selection.apply to ignore empty atomgroups (#2767) - - * decorate Selection.apply to ignore empty atomgroups - * added test for global selection off empty AG - * fix for global selections and empty AG - * decorate functions instead - * update CHANGELOG - - Co-authored-by: richard - (cherry picked from commit 016f2c6e2642a68d41b68aac4545366189da25dd) - -commit fa6bc1fec8a2ff2d76c7b286b16059c37a7748d0 -Author: Yuxuan Zhuang -Date: Sat Jul 4 01:42:35 2020 +0200 - - ChainReader Refactoring (#2815) - - * Fixes #2814 - * changes in ChainReader: - * new `_read_frame` and `__iter__` are now properly connected - (previously, they moved independently, which could lead to the ChainReader - being in an inconsistent state) - * remove `_chained_iterator`. - * add `__next__` - * add an extra attribute `__current_frame` to internally monitor absolute current frame - * add tests - * update CHANGELOG - -commit e8fbd529fc55cb187d38bdef141d74757f22bdc5 -Author: Jonathan Barnoud -Date: Thu Jul 2 18:16:43 2020 +0100 - - Make the TPR parser a bit faster (#2804) - - * Make the TPR parser a bit faster - - A function in the TPR parser calls list.pop thousands of times, which is - slow. This commit avoids that exansive call. - - Taking the TPR from - https://github.com/bioexcel/covid_modelling_simulation_data/tree/master/spike_protein/full_spike/trimer - the parsing time on my computer goes from 25.6s to 9.39s. On a more - pathological TPR file, it goes from 3 minutes to about 6s. - - * Update changelog for #2804 - - Co-authored-by: Richard Gowers - -commit 1e107ed3fc79090485d37f1d137cb8d143ee27b5 -Author: Oliver Beckstein -Date: Wed Jul 1 00:22:29 2020 -0700 - - bumped release to 1.0.1-dev (so that docs are properly labeled) - -commit dd0bbe4e75715147735ad201ef8fb37ee69edd9d -Author: Oliver Beckstein -Date: Wed Jul 1 00:22:02 2020 -0700 - - fixed maintainer/change_release.sh - -commit 656e7240b0bf679f9fdf82143f2dd63819b3c94d -Author: Irfan Alibay -Date: Thu Jun 18 13:45:12 2020 +0100 - - fixes google badges (#2772) - -commit 28f043f2c50e07426672d5308c2ceac3d3dd610e -Author: Oliver Beckstein -Date: Tue Jun 30 15:18:45 2020 -0700 - - file clean-ups - - - removed superfluous coordinates/dcdtimeseries.c - - removed execute permissions from module NAMDBI.py - -commit bbafbbe21c4e7b5f36d9d841c006b3ec08fc637a -Author: Oliver Beckstein -Date: Fri Jun 26 11:30:47 2020 -0700 - - fixed 1.0.1 contributor list based on git log - - (List was messed up in a previous cherry-pick and not fully correct then.) - -commit dd4490a09c00cbb7f8e6f9029ef78a3d7b6e09f1 -Author: Tyler Reddy -Date: Fri Jun 26 06:38:25 2020 -0600 - - CI: add codecov to Azure CI (#2720) - - * CI: add codecov to Azure CI - - * add a codecov upload to Azure CI (32-bit - Windows) - - Co-authored-by: Thomas Hu - -commit dbaf95716c36eb9d9d996e64bb43513d654b0462 -Author: Oliver Beckstein -Date: Mon Jun 15 17:31:16 2020 -0700 - - removed matplotlib.use('agg') from tests - - - fix #2191 - - use MPLBACKEND=agg in the CI environments - - Travis - - appveyor - - Azure pipelines - - update CHANGELOG - -commit 7313cf1cec3921b793e8753aa48f60fe4a23a0f3 -Author: Lily Wang -Date: Wed Jul 1 10:24:06 2020 +1000 - - build docs for master as well - - - backported CI code to build versioned docs - (see https://github.com/MDAnalysis/mdanalysis/pull/2798#issuecomment-655938572) - - added outside PR #2798 - -commit 8af09d7fce48686e220f297af7ab0b4a3e0405f9 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Jun 15 21:49:21 2020 +1000 - - Add scripts for doc versioning (#2749) - - - Scripts move docs into a version subfolder - - Write versions.json at root directory - - Write sitemap_index.xml at root directory - - Write html stubs for redirection - - Change URL to CNAME one of docs.mdanalysis.org/ - -commit dbd39c2900d8b84184d61ff1adfd5250616994e8 -Author: Oliver Beckstein -Date: Fri Jul 10 14:28:03 2020 -0700 - - changed InterRDF_s density keyword semantics - - - fix (because it was not documented before) - - density=True now means "calculate the single site density"; - default is still "calculate RDF" (now meaning density=False) - - update docs - - update tests (add test for default behavior) - - update CHANGELOG - - backported issue #2811 fix (directly rebased onto master - instead of added to PR #2798 - -commit a2a9a5cacbb3399b6516a7ac2e735b0903c627fb -Author: VOD555 -Date: Wed Jul 1 13:56:09 2020 -0700 - - fix InterRDF_s(..., density) normalization - - - fix #2811 - (see also https://github.com/MDAnalysis/pmda/issues/120) - - add test to compare InterRDF and InterRDF_s - - add description for density option (was not documented since 0.19.0) - - updated docs for rdf - - updated docs with equationi - - attributes for InterRDF and InterRDF_s - - reference equations - - minor grammar/style fixes - - remove ill-advised usage of InterRDF_s from docs - - update CHANGELOG - -commit 87045111fdc2110ce1df7bdac40bacc27725020e -Merge: 3c97ae0d1 9046bf583 -Author: Oliver Beckstein -Date: Sat Jul 11 18:18:28 2020 -0700 - - Merge pull request #2812 from VOD555/fix_rdf_density - - * Fixes #2811 - * enable hitherto undocumented kwarg density for InterRDF_s (but changed - meaning of True/False): - If you used density=False since 0.19.0 to calculate a single particle density then you - now have to use density=True. The default remains the same: calculate the RDF and not - the density. - * Fix normalization for InterRDF_s(..., density=True) - * add test to compare InterRDF and InterRDF_s - * add description for density option - * update CHANGELOG - -commit 3c97ae0d1babed8573d17f807b36ec3fdf94b765 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Jul 12 01:43:18 2020 +1000 - - make Atom target class of ResidueAttr by default (#2805) - - * make Atom target class by default - - * make molnums apply to segmentgroup - -commit 3c087bb759de2e5a962b4068d0b6439e29a2600b -Author: Tyler Reddy -Date: Sat Jul 11 09:42:11 2020 -0600 - - MAINT: use modern ConfigParser (#2838) - - * when MDAnalysis is built from source with Python 3.8 there's - a deprecation warning: - - ```setup.py:129: DeprecationWarning: The SafeConfigParser class has been - renamed to ConfigParser in Python 3.2. This alias will be removed in - future versions. Use ConfigParser directly instead.``` - - * fix it by doing what is says, since we are `Python >= 3.6` now - -commit 02e276fb1a52906c84d66b7b4c9b57682ddd8ffd -Author: Cédric Bouysset -Date: Sat Jul 11 01:57:04 2020 +0200 - - Set numpy and rdkit min version (#2831) - - * Fixes #2827 - * raise numpy minimum version from 1.13.3 to 1.16.0 - * set the minimum RDKit version to 2020.03.1 for tests (CI only), - RDKit is not listed in setup.py because it is not available from PyPi - -commit 9046bf583d9c9ece70a673d0c083c2a21a2654eb -Author: Oliver Beckstein -Date: Fri Jul 10 14:28:03 2020 -0700 - - changed InterRDF_s density keyword semantics - - - fix (because it was not documented before) - - density=True now means "calculate the single site density"; - default is still "calculate RDF" (now meaning density=False) - - update docs - - update tests (add test for default behavior) - - update CHANGELOG - -commit de8b47ed850f25a048cfe8e71dc577f1d649b8be -Author: VOD555 -Date: Wed Jul 1 13:56:09 2020 -0700 - - fix InterRDF_s(..., density) normalization - - - fix #2811 - (see also https://github.com/MDAnalysis/pmda/issues/120) - - add test to compare InterRDF and InterRDF_s - - add description for density option (was not documented since 0.19.0) - - updated docs for rdf - - updated docs with equationi - - attributes for InterRDF and InterRDF_s - - reference equations - - minor grammar/style fixes - - remove ill-advised usage of InterRDF_s from docs - - update CHANGELOG - -commit 3e56b70da3b48a523924308e1149d46fadddbb5d -Author: Tyler Reddy -Date: Thu Jul 9 21:45:54 2020 -0600 - - MAINT: master -> main where possible (#2836) - - * MAINT: master -> main where possible - - * replace `master` with `main` in locations where - it does not appear to cause burden for the development - team - - * none of the cases replaced here appear to be related - to `master` branch on GitHub (indeed, we might leave - that transition to the GitHub team) - - * this is similar in spirit to GitHub's indication that - they will do the same for branch renaming: - https://twitter.com/natfriedman/status/1271253144442253312 - - * this is not fully comprehensive, but catches the low-hanging - cases I think; I saw a few others, but they were more functional - like parts of test files I didn't want to mess with, at least - initially - - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - -commit 155ae40325426025826603f221dd29dc2252d4a2 -Merge: 56cb47c93 a19204081 -Author: Oliver Beckstein -Date: Thu Jul 9 18:51:29 2020 -0700 - - Merge pull request #2834 from tylerjereddy/treddy_npy_type_alias_comprehensive - - MAINT: comprehensive type alias cleanup - -commit a19204081f6a556773afc866299bb4de14cc7d44 -Author: Tyler Reddy -Date: Wed Jul 8 20:27:02 2020 -0600 - - MAINT: comprehensive type alias cleanup - - * the NumPy type aliasing `DeprecationWarning`s are now - converted to errors for the `pytest` suite to enforce - future-proofed `dtype` specifications and prevent regression - (see NumPy PR 14882), though this will not take effect - in our CI until the next NumPy release, or until we adopt - a pre-release wheel test with NumPy - - * NOTE: in the future we should switch to `pytest.ini` or - `pyproject.toml` for `pytest` config because of this complication: - https://docs.pytest.org/en/latest/customize.html#setup-cfg - - * fix all cases detected by the full test suite via warnings - converted to errors when running with latest NumPy checkout - -commit 56cb47c93eda3574c84788ad374e0723068fcbf2 -Author: Oliver Beckstein -Date: Tue Jul 7 17:45:28 2020 -0700 - - add GoatCounter and link tor Privacy Policy - - - close #2813 - - add link to our privacy policy in footer - (see https://github.com/MDAnalysis/MDAnalysis.github.io/issues/129) - -commit 332fb83e5fc238ac3f8197b2990f90ec8b5201b6 -Author: Oliver Beckstein -Date: Tue Jul 7 17:35:29 2020 -0700 - - removed unused CSS - -commit fe8420e88dd567bf2da54e1dbdabc886cc5d4a60 -Merge: d7902cf28 bce3967f6 -Author: Rocco Meli -Date: Wed Jul 8 22:37:34 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit bce3967f672b3d75ebeb621e3bdfd2705d9c903b -Merge: c8abbee6d f112a92f7 -Author: Tyler Reddy -Date: Wed Jul 8 08:32:52 2020 -0600 - - Merge pull request #2829 from tylerjereddy/treddy_numpy_master_adjust - - MAINT: fixes for NumPy master - -commit f112a92f7175a09a0b72f12b19e2a8cd76428c12 -Author: Tyler Reddy -Date: Tue Jul 7 20:00:06 2020 -0600 - - MAINT: fixes for NumPy master - - * fixes needed to get full MDA test suite passing - with NumPy `master` branch - - * remove usage of pertinent deprecated NumPy type aliases - like `np.int`; see https://github.com/numpy/numpy/pull/14882 - - * this only removes the deprecated type aliases that cause - MDAnalysis test suite failures; there are still deprecated uses - that do not cause failures, however the volume of warnings - emitted by the MDAnalysis test suite is so large that only - actual test failures are addressed at this time (I will try - to follow-up for the remainder later) - - * it may be worthwhile to consider addition of a CI matrix - entry using a NumPy pre-release wheel, although that addition - is not made here - -commit c8abbee6d8dc9d80bb798cd9a49b0b0b7b8c6ab7 -Author: Yuxuan Zhuang -Date: Tue Jul 7 18:46:36 2020 +0200 - - TRZReader check for n_atoms (#2820) - - * fix #2817 - * TRZReader checks that TRZ file contains the same number of atoms as the topology or n_atoms and fails otherwise - * TRZWriter correctly writes n_atoms to file (previously wrote 0!) - * add test - * add docs - * update CHANGELOG - -commit 17969df7bad2fe2a9e58c744f64a8d8fefa7083d -Author: Irfan Alibay -Date: Sun Jul 5 11:12:05 2020 +0100 - - Removes profraw file and adds ignore (#2824) - -commit e878e5de312ed8da0ffb36ff0e9e7e4a084556c8 -Author: Yuxuan Zhuang -Date: Sat Jul 4 01:42:35 2020 +0200 - - ChainReader Refactoring (#2815) - - * Fixes #2814 - * changes in ChainReader: - * new `_read_frame` and `__iter__` are now properly connected - (previously, they moved independently, which could lead to the ChainReader - being in an inconsistent state) - * remove `_chained_iterator`. - * add `__next__` - * add an extra attribute `__current_frame` to internally monitor absolute current frame - * add tests - * update CHANGELOG - -commit 61e236d45c52030d74ba6277c0a59e8a43a13ea9 -Author: Jonathan Barnoud -Date: Thu Jul 2 18:16:43 2020 +0100 - - Make the TPR parser a bit faster (#2804) - - * Make the TPR parser a bit faster - - A function in the TPR parser calls list.pop thousands of times, which is - slow. This commit avoids that exansive call. - - Taking the TPR from - https://github.com/bioexcel/covid_modelling_simulation_data/tree/master/spike_protein/full_spike/trimer - the parsing time on my computer goes from 25.6s to 9.39s. On a more - pathological TPR file, it goes from 3 minutes to about 6s. - - * Update changelog for #2804 - - Co-authored-by: Richard Gowers - -commit 8314f7d33b08bd467f1974fdc886f60b02f226c3 -Author: David Minh -Date: Wed Jul 1 13:04:33 2020 -0400 - - Bond-Angle-Torsions coordinate module (#2668) - - * new MDAnalysis.analysis.bat module: convert between internal bond-angle-torsion and - Cartesian coordinates (based on published research) - * standard analysis class - * can load and save results (numpy format) - * references with duecredit - * tests - * docs with example - * update CHANGELOG and AUTHORS - -commit 3d952829949a5e67682fa387f9945e0b1ed6319e -Author: Lily Wang -Date: Wed Jul 1 10:24:06 2020 +1000 - - build docs for master as well - -commit 343e10a257690e4312673f2a0fa4703b31b2e223 -Author: Lily Wang -Date: Sat Jun 27 09:07:15 2020 +1000 - - blank line - -commit dddb7847f8cae8ad060901268927e0b735b53b03 -Author: Tyler Reddy -Date: Fri Jun 26 06:38:25 2020 -0600 - - CI: add codecov to Azure CI (#2720) - - * CI: add codecov to Azure CI - - * add a codecov upload to Azure CI (32-bit - Windows) - - Co-authored-by: Thomas Hu - -commit 31929685389638232b8f22a2ee9cc63bd659f8d5 -Author: Irfan Alibay -Date: Thu Jun 25 00:17:50 2020 +0100 - - Makes tidynamics a non required install (#2783) - - * Fixes #2782 - * Removes tidynamics from `install_requires` lists - * Refactors MSD tests to allow for partial testing when tidynamics is not available. - * Make MSD FFT tests skip if no tidynamics - * refactors test_msd to simple and fft cases - * Test for bad msdtypes - * move import test to util - -commit 333bb04e3a730278aa49ff4c6db372e800f05cd6 -Author: Irfan Alibay -Date: Mon Jun 22 16:50:20 2020 +0100 - - Remove deprecated hole, and completes py2 removal (#2778) - -commit d7902cf28a204e418e356e83622bf10f562c3787 -Merge: a5d7d684f 2fb1adebb -Author: Rocco Meli -Date: Sun Jun 21 22:56:24 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 2fb1adebba30f3ec7789c4bf15f6fdf59559af80 -Author: Irfan Alibay -Date: Sun Jun 21 14:13:48 2020 +0100 - - Use unittest.mock instead of mock (#2779) - -commit bf16435099b8c3298bd2f55cc2ab526471c9b88a -Author: Irfan Alibay -Date: Sat Jun 20 16:12:16 2020 +0100 - - change status from beta to mature - -commit 016f2c6e2642a68d41b68aac4545366189da25dd -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sat Jun 20 17:12:36 2020 +1000 - - decorate Selection.apply to ignore empty atomgroups (#2767) - - * decorate Selection.apply to ignore empty atomgroups - - * added test for global selection off empty AG - - * fix for global selections and empty AG - - * decorate functions instead - - Co-authored-by: richard - -commit 50cd6e756336e7e0e41048e7a0d09a6af06bb841 -Author: Cédric Bouysset -Date: Fri Jun 19 17:11:40 2020 +0200 - - RDKitReader and RDKitParser (#2707) - -commit 788f294e53ca19fdfba8cc7e2f86d0de7be82bbf -Author: Irfan Alibay -Date: Thu Jun 18 13:45:12 2020 +0100 - - fixes google badges (#2772) - -commit 329c3fc2f9376f1ec040addf3cc69fc969f00bca -Author: Irfan Alibay -Date: Wed Jun 17 06:11:24 2020 +0100 - - Remove py2 things from lib (#2752) - - - remove six and __future__ imports - -commit e9e47c3853bb769b03eb9cebbb28bffc1e9e57b2 -Author: Irfan Alibay -Date: Tue Jun 16 06:52:48 2020 +0100 - - Remove py2 things from aux, vis, transform, and others (#2762) - - * Remove py2 things from aux - - * rm py2 for selections, tests, transformations - - * Remove py2 from visualization - - * Remove misc py2 things - - * errsmg typo - -commit 0d951a2e726a25c59cc2550a852eb35726dd3226 -Author: Irfan Alibay -Date: Tue Jun 16 06:51:29 2020 +0100 - - Remove py2 things from coordinates & topology (#2759) - - * Removes py2 things from coordinates - - * Removes py2 things from coordinate tests - - * Removes py2 things from topology - -commit 34288cced239a35c9250daf72151e486fc18bc56 -Author: Oliver Beckstein -Date: Mon Jun 15 22:45:36 2020 -0700 - - removed matplotlib.use('agg') from tests (#2763) - - - fix #2191 - - use MPLBACKEND=agg in the CI environments - - Travis - - appveyor - - Azure pipelines - - update CHANGELOG - -commit c761ba3538fefe5df96f28f4c0b33990a72196f0 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Jun 15 21:49:21 2020 +1000 - - Add scripts for doc versioning (#2749) - - - Scripts move docs into a version subfolder - - Write versions.json at root directory - - Write sitemap_index.xml at root directory - - Write html stubs for redirection - - Change URL to CNAME one of docs.mdanalysis.org/ - -commit 46e505c0805e6a6f3f0933c62731be95edd1c59f -Author: Hugo MacDermott-Opeskin -Date: Mon Jun 15 21:16:15 2020 +1000 - - Add in analysis function to calculate MSDs (#2619) - - - Add in experimental code for calculation of MSD - - both simple "windowed" calculation (N^2) - - more sophisticated FFT based calculation (Nlog(N)) - -commit da72d551133a8723be5a25fa52e2c0b9e3ae2125 -Author: Irfan Alibay -Date: Mon Jun 15 08:13:38 2020 +0100 - - Remove py2 things from analysis (#2753) - -commit 74c2c15afb21c9cc5fa35f0249d569d2648b2211 -Author: Irfan Alibay -Date: Mon Jun 15 08:12:12 2020 +0100 - - Remove py2 things from core (#2756) - -commit 734d32adde6e228875447f1b2aabec3fcbd81113 -Author: Irfan Alibay -Date: Mon Jun 15 08:10:13 2020 +0100 - - Remove ts from writers (#2754) - - * Removes deprecated timestep input to writers - -commit 085ac0f686ef202fae303ca1e36a038c263efbcc -Author: Irfan Alibay -Date: Sun Jun 14 00:06:41 2020 +0100 - - Removes deprecated density code (#2740) - - * removes deprecated density code (part of #2739) - * Removes density_from_Universe, density_from_PDB, Bfactor2RMSF, BfactorDensityCreator, and notwithin_coordinates_factory - * Moves _set_user_grid to be a staticmethod of DensityAnalysis - * Unused tests removed - * Removal of six - * some PEP8 string formatting changes - * Adds a versionchanged for the removal - * Adds changelog entry for deprecated density removal - * Adds _set_user_grid to docs - * Adds return entry - -commit bf74d6531c74904dcd1fafca20bb88cc1b89617d -Author: Irfan Alibay -Date: Sat Jun 13 10:12:38 2020 +0100 - - Remove ProgressMeter (#2743) - - * removes PM from package - - * Remove PM tests - - * updates CHANGELOG - - * Remove tests - - * Adds docstring versionchange - -commit 105e47a4c60de71c6602d4837cc1b12cb57d3518 -Author: Lily Wang -Date: Fri Jun 12 18:53:01 2020 +1000 - - clean up align to have something to die on - -commit cb4d19594465060f118c6f7d6356ba9e178084ea -Author: Lily Wang -Date: Fri Jun 12 18:47:17 2020 +1000 - - does the easy way work - -commit 9ac7f7c2ca257c7bae96bde9d8cd3e3b87a61084 -Author: IAlibay -Date: Thu Jun 11 12:28:40 2020 +0100 - - ASV py3.6 - -commit 8710b5c9b9569cbcc5ed52b8ac026c4719ba9887 -Author: Irfan Alibay -Date: Fri Jun 12 12:13:22 2020 +0100 - - Removes element guessing for TOPParser (#2714) - - - Removes the element guessing default behaviour of the TOPParser - - Cleans up the test_top.py to remove duplicate code - -commit a5d7d684f0846600e1db30347d98f2018acf5859 -Merge: 264b5647a 3da643f37 -Author: Rocco Meli -Date: Thu Jun 11 12:16:10 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 3da643f37bec7ca28a8807f0948e2de3fce79014 -Author: IAlibay -Date: Wed Jun 10 23:26:07 2020 +0100 - - Changelog entry swap - -commit dc0905f62a8888cd4f073402fe53343fc3293278 -Author: IAlibay -Date: Wed Jun 10 23:04:29 2020 +0100 - - Fix broken docs - -commit ccefc034f18cd4e164e80f2c04d5462c67226c21 -Author: IAlibay -Date: Wed Jun 10 22:56:10 2020 +0100 - - Update changelog - -commit 82ca06bf38cb166db29fbc5cfbde4f368dda2b24 -Author: IAlibay -Date: Wed Jun 10 22:50:44 2020 +0100 - - Removes deprecated MDAnalysis.units.N_Avogadro - -commit 4db8130ffbe6e863018c9129712f5b5980fe558f -Author: Oliver Beckstein -Date: Wed Jun 10 15:10:49 2020 -0700 - - update CHANGELOG - -commit efe48c4063c4fbd891efae6810c60278da9215c8 -Author: Oliver Beckstein -Date: Wed Jun 10 15:04:53 2020 -0700 - - restrict pip package versions to Python 2.7 compatible ones - - - fix #2736 - - restrict numpy, biopython, joblib to versions that support - python 2.7 - - removed deprecated 'requires' in setup.py (see - https://setuptools.readthedocs.io/en/latest/setuptools.html#developer-s-guide) - - added python_requires (2.7 and >= 3.6) - -commit 264b5647a241f07904877dfa72610f6bbc682980 -Merge: b11c51712 6a188e421 -Author: Rocco Meli -Date: Wed Jun 10 23:26:45 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 6a188e4219e87d7188007d5fc2669717a28c5a61 -Author: richard -Date: Wed Jun 10 11:11:19 2020 +0100 - - start v2.0 instead - - 1.0.x will be backports of serious bugs - -commit ab30bb802d24e82f7b6404e110e4c66848cdc97f -Author: richard -Date: Wed Jun 10 10:38:41 2020 +0100 - - derp I'm the best release manager - -commit 9e562cd9728d32a96ea9fe3aa14d3827c9e56544 -Author: Richard Gowers -Date: Wed Jun 10 10:32:18 2020 +0100 - - Update .travis.yml - -commit d97c3cbe23cc598559332b3558d6f4e666a24035 -Author: richard -Date: Wed Jun 10 10:11:40 2020 +0100 - - really increment the version this time - -commit 57e753e24d4aa8abea683ea35b9d9c663014e046 -Author: richard -Date: Wed Jun 10 10:10:19 2020 +0100 - - remove python 2.7 from travis CI - -commit 7dc147880511389aba4149066e715290e9fafe0a -Author: richard -Date: Wed Jun 10 10:08:41 2020 +0100 - - bumped version to 1.0.1 - -commit 4f50ba73aa33d9bf052358bc41f6b21f19cbb48b -Author: richard -Date: Wed Jun 10 09:05:59 2020 +0100 - - bumped version number to 1.0.0 - -commit b468e574146f139f798b685db19740f5c3f58e95 -Author: richard -Date: Tue Jun 9 07:50:20 2020 +0100 - - finalised 1.0.0 changelog - - renamed 0.21.0 references to 1.0 - -commit b11c51712a5cef864d7a1b89c7f3022f7f3d8d30 -Merge: 200257054 6eb8f6812 -Author: Rocco Meli -Date: Wed Jun 10 13:24:17 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 4365f3b07c1bf2ebcf16424b26162102954c5b90 (tag: release-1.0.0) -Author: richard -Date: Wed Jun 10 09:20:05 2020 +0100 - - update c/cpp files for 1.0.0 release - -commit 7d03843c2261807ef6f19377f8b5e07967e59c0c -Merge: 169db04f4 85ebe4355 -Author: richard -Date: Wed Jun 10 09:06:49 2020 +0100 - - Merge branch 'develop' - -commit 85ebe4355c419bf5c477f05ca87318e03af6800c -Author: richard -Date: Wed Jun 10 09:05:59 2020 +0100 - - bumped version number to 1.0.0 - -commit 169db04f4eb3742ebd5b8eeebe968893fc237376 -Merge: ee4759293 1a8759cfd -Author: richard -Date: Tue Jun 9 21:49:42 2020 +0100 - - Merge branch 'develop' - -commit 1a8759cfd9931edb895381227d7b0d14d7054890 -Author: richard -Date: Tue Jun 9 07:50:20 2020 +0100 - - finalised 1.0.0 changelog - - renamed 0.21.0 references to 1.0 - -commit 6eb8f6812883db30f200ae9b2f73fe96f2227a3b -Author: Richard Gowers -Date: Tue Jun 9 21:45:04 2020 +0100 - - fix for gcc 9 (post 7 really) (#2726) - - fixes failing triclinic image test - -commit 200257054a5a8533c3faf09a8b2dea8d1a15525a -Merge: c454e4f7d 3f7f5d345 -Author: Rocco Meli -Date: Tue Jun 9 10:47:53 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 3f7f5d345eb0f650bdb38d46db1091637061cf0c -Author: Richard Gowers -Date: Mon Jun 8 21:20:31 2020 +0100 - - WIP Issue 2043 deprecate ts write (#2110) - - * deprecate Timestep argument to Writers (issue #2043) - - Co-authored-by: Irfan Alibay - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - -commit c454e4f7d599995121d04e3244bc5cf6e97215e2 -Merge: dbe775073 ae6193e3e -Author: Rocco Meli -Date: Mon Jun 8 21:00:20 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit ae6193e3e93093500a2253d1a82e9b286d2852a6 -Author: Irfan Alibay -Date: Mon Jun 8 11:48:51 2020 +0100 - - Mol2 universe (#2718) - - * Fixes issue 2717 - - * Adds tests - - * Switched ag safeguard to encode_block - -commit dbe775073138fdbe411bd7790517bdd50d45d725 -Merge: d1ff4c466 e835b5bef -Author: Rocco Meli -Date: Mon Jun 8 10:31:19 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit e835b5beff00bb6a5870e6b71435290408f0bc57 -Author: Rocco Meli -Date: Sun Jun 7 04:04:30 2020 +0200 - - Fix #2692 (#2694) - - - Use user-provided remark in XYZWriter and add MDAnalysis version if not - -commit d1ff4c46632480a58ce11ce741dfa25e5dc29bfe -Merge: 9581ee471 8c06037ec -Author: Rocco Meli -Date: Sun Jun 7 01:36:40 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 8c06037ec8298e729eb7e93c82c514c54c00bcd0 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sun Jun 7 00:56:58 2020 +1000 - - Make NoDataError subclass of AttributeError and add informative error messages (#2636) - - * made NoDataError subclass of AttributeError - - * getattr checks for topologyattr-related info in raising errors - - * special-cased timestep properties - -commit 736a12c35e9688a5b113d5ca0c54be8d1617d36b (upstream/faster_atomname_sels) -Author: Tyler Reddy -Date: Sat Jun 6 06:53:48 2020 -0600 - - CI: enable more win32 Azure tests (#2713) - - * add `pip` install of `scikit-learn` for Azure - 32-bit Windows testing, so that a few more - tests are probed there (+11 more tests pass - instead of skip; approx. 45 seconds added - to test suite in testing on my fork) - - * clean up the `pip install` line in Azure CI - to span several alphabetically-sorted lines - for readability (achieved using yaml multiline - folding: https://yaml-multiline.info/ ); this - is similar to the approach suggested for i.e., - `Dockerfile`s that have long `apt-get` dependency - install lines - - * use `rsx` pytest flag to report some details - on the test skips (etc.) in Azure CI Windows - 32-bit - -commit abfd74814ceb7b98ef66f9351e861463b74cf845 -Author: Richard Gowers -Date: Sat Jun 6 13:48:31 2020 +0100 - - Issue 2656 nsgrid segfault (#2665) - - segfaulting on zero box size - - Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> - -commit 9581ee471a3e585072bf0293ababa2b044f14185 -Merge: 13d6c5ee6 8d7d77f45 -Author: Rocco Meli -Date: Fri Jun 5 12:58:13 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 8d7d77f45e3de293b27217f75cf5990c1582d9ce -Author: Irfan Alibay -Date: Fri Jun 5 11:33:13 2020 +0100 - - Remove lib.mdamath._angle (#2712) - - Removes unused lib.mdamath._angle() (Issue #2650) - -commit 3a0ccb89c67b193dba3a860a77fd2952f8d2f8a9 -Merge: ea2e8c43b 7b7e1d322 -Author: Oliver Beckstein -Date: Fri Jun 5 03:18:28 2020 -0700 - - Merge pull request #2705 from Marcello-Sega/fhiaims - - FHI-AIMS format added - -commit 13d6c5ee60ae0fc97d0a4269258463e2c6281f43 -Merge: 888b1f9e5 ea2e8c43b -Author: Rocco Meli -Date: Fri Jun 5 10:58:46 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 7b7e1d32239983078d926c14195debc5a1ab61c4 -Author: Oliver Beckstein -Date: Fri Jun 5 01:00:01 2020 -0700 - - topology format table and docs update - - - add links to codes in table - - fixed MMTF formatting (can only have one line in first cell in the simple - reST layout) - - FHI-AIMS formatted - - added page for GSD format (had been previously forgotten) - -commit 2ef87ba2ebaa56ef49a48c56eb9a121c33e4d024 -Author: Marcello Sega -Date: Sat May 30 11:07:44 2020 +0200 - - FHI-AIMS coordinate format and topology - - - Parser - - read atoms - - Reader - - read atoms and fractional atom positions - - read 0 or 3 lattice vectors - - read velocities - - Writer - - writes atom positions and lattice - - writes velocities - - documentation - - tests for all functionality (Reader, Writer, Parser) - - CHANGELOG and AUTHORS updated - - Co-authored-by: Oliver Beckstein - -commit ea2e8c43b8023f07a7583878051bef41a1514550 -Author: Rocco Meli -Date: Fri Jun 5 10:09:02 2020 +0200 - - Fix #2679 (#2685) - -commit 888b1f9e5d3680a16381b7a4a56ee970fffb7e0a -Merge: a6a197636 8c3577f5a -Author: Rocco Meli -Date: Wed Jun 3 14:51:43 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 8c3577f5a72bee654d94367e4bef51791ffa5d0b -Merge: 0911ff3a0 c1827e780 -Author: Richard Gowers -Date: Wed Jun 3 10:42:08 2020 +0100 - - Merge pull request #2706 from lilyminium/faster-dih - - Select dihedrals faster - -commit c1827e780a60de797bd63b9e281a0b0964abd7f7 -Author: Lily Wang -Date: Tue Jun 2 02:31:11 2020 +1000 - - moved docstring to class, added example, updated CHANGELOG - -commit fb29974183ffd91360c3e6f123012d51f622c574 -Author: Lily Wang -Date: Tue Jun 2 01:57:05 2020 +1000 - - updated Rama and added function to get previous residues - -commit 56fa4e84bcaae36b414d5c473e45bd56a2000416 -Author: Lily Wang -Date: Tue Jun 2 00:58:35 2020 +1000 - - added residuegroup dihedrals and refactored residue dihedrals - -commit 9b5d8d06a759136a79278f4549cd4522baceb715 -Author: Lily Wang -Date: Mon Jun 1 21:16:01 2020 +1000 - - select dihedrals faster - -commit 0911ff3a0379356ee603ff4aa21eec3b990f9958 -Merge: 41ebfdf5b 63680fe65 -Author: Richard Gowers -Date: Mon Jun 1 09:34:50 2020 +0100 - - Merge pull request #2525 from IAlibay/waterdynamics-sp-startstop - - Waterdynamics.SurvivalProbability start/stop/step/tau_max - -commit 63680fe656aaa3a0732c3c67772524396135e2a6 -Author: Irfan Alibay -Date: Sat May 30 08:43:15 2020 +0100 - - Adds documentation of exclusive behaviour - - Adds more documentation to detail that :class:`SurvivalProbability` now has an exclusive behaviour unike the other :mod:`MDAnalysis.analysis.waterdynamics` classes. - -commit 31f1ea7475e80671aaa86e944d1cbd2721271081 -Merge: 3bd4fe96c 41ebfdf5b -Author: Irfan Alibay -Date: Sat May 30 08:17:28 2020 +0100 - - Merge branch 'develop' into waterdynamics-sp-startstop - -commit 41ebfdf5b12dc1753b99c177e4e7404b6e1288f2 -Author: Irfan Alibay -Date: Sat May 30 00:01:23 2020 +0100 - - Change `align.fasta2select` default file behaviour (#2702) - - * Fixes #2701 - * Change the behaviour of default alnfilename and treefilename in fasta2select to write to the current working directory, rather than where fastafilename or alnfilename were located respectively. - * Adds tmpdir use to test_fasta2select_file to prevent persistent temporary files. - * Some PEP8 changes (> 79 chars) around test_fasta2select_file. - -commit a6a1976369b85778167a2949b5ba79bf9cc4b5cd -Merge: d263d1ff3 57e7bd47d -Author: Rocco Meli -Date: Fri May 29 11:07:53 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 3bd4fe96c5afdc8c19b3f0c51c3e5ae51997f9d4 -Merge: 6cb1f6cc7 57e7bd47d -Author: Oliver Beckstein -Date: Fri May 29 01:05:30 2020 -0700 - - Merge branch 'develop' into waterdynamics-sp-startstop - -commit 57e7bd47da5d27750dbcf1a53c9014ece5d445e7 -Merge: 186cebf0a 401901133 -Author: Oliver Beckstein -Date: Thu May 28 09:55:46 2020 -0700 - - Merge pull request #2700 from IAlibay/remove-numtoelem - - - Fixes #2699 - - Changes made in this Pull Request: - - Removes MDAnalysis.topology._elements.py (Remove `NUMBER_TO_ELEMENTS`) - - Switches `NUMBER_TO_ELEMENTS` to `Z2SYMB` in TOPParser - - Adds a more thorough elements test and starts cleaning up tests in anticipation of #2651 - -commit 186cebf0aa273d60c86f35d09c99ae8883cba67f -Merge: 55afb4c36 0b560f547 -Author: Tyler Reddy -Date: Thu May 28 08:52:35 2020 -0600 - - Merge pull request #2696 from MDAnalysis/add_win32_ci - - CI: add 32-bit Win to CI - -commit 401901133b3d95e355278092b9e440542ef2921f -Author: Irfan Alibay -Date: Thu May 28 03:18:23 2020 +0100 - - More CHANGELOG details - -commit 0b560f54713447e6b45b980361b3f845906be493 -Author: Tyler Reddy -Date: Wed May 27 19:45:38 2020 -0600 - - DOC: relnote for gh-2696. - -commit 6cb1f6cc7a7f26313ef150477a8bb08befd8982c -Merge: 828152281 55afb4c36 -Author: IAlibay -Date: Wed May 27 13:39:08 2020 +0100 - - Merge branch 'develop' into waterdynamics-sp-startstop - -commit 791e5a71e1a1d9c2abcbaa31c15edcc68931f724 -Author: Irfan Alibay -Date: Wed May 27 13:02:16 2020 +0100 - - Update CHANGELOG - -commit 52e10774c3ae56aec979ef4c835f666f2cfb4e5f -Author: IAlibay -Date: Wed May 27 10:37:50 2020 +0100 - - Remove extra .aln and .dnd files - -commit e064c2baed234f84bcb7ff1fefee88d451217091 -Author: Irfan Alibay -Date: Wed May 27 10:27:33 2020 +0100 - - PEP/FLAKE8 fixes - -commit 2f632c1089b9d04c5950a93cf68fb925f540ed99 -Author: IAlibay -Date: Wed May 27 10:13:27 2020 +0100 - - Fixes tests - -commit aacae3da34420a1f5b717e9ac4d8bb9223629111 -Author: Irfan Alibay -Date: Wed May 27 09:52:59 2020 +0100 - - improve element testing - -commit 701c0afa6dee63b6f468bea264aa6f4fe1690f32 -Author: IAlibay -Date: Wed May 27 06:12:10 2020 +0100 - - Removes NUMBER_TO_ELEMENTS - -commit 55afb4c36328e79c1390c0f4364b2cf5c1aff481 -Author: Rocco Meli -Date: Tue May 26 23:24:33 2020 +0200 - - ignore duecredit output (#2697) - - updated .gitignore - -commit d6ea367725f7b61fe8d91f9b6866388583824df2 -Author: Tyler Reddy -Date: Mon May 25 20:12:39 2020 -0600 - - MAINT: PR 2696 revisions - - * remove an extraneous type coercion in `selection.py` - based on reviewer feedback - -commit 2392c35c8eb5699e7dcdb91117c1fbcea12444da -Author: Tyler Reddy -Date: Mon May 25 11:46:46 2020 -0600 - - MAINT: PR 2696 revisions - - * we now conditionally `xfail` a test that is problematic - on 32-bit Windows: - `MDAnalysisTests/formats/test_libdcd.py::test_written_remarks_property` - - * `hypothesis` only occasionally produces a failure for this test - on 32-bit Windows - -commit d263d1ff385af15c4428f1818e401966f9cdb83f -Merge: 833aff33b a0bd19ce0 -Author: Rocco Meli -Date: Mon May 25 15:42:13 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 522f9aeaec6b535a566c62da6528a6fc2d1f5e2c -Author: Tyler Reddy -Date: Sun May 24 11:00:12 2020 -0600 - - MAINT: 32-bit windows support - - * changes needed to pass full test suite - on 32-bit Windows - - * primarily, use `np.intp` indexing types in - appropriate locations instead of forcing - `np.int64` - -commit 336d3ff65abd12693d3b781b397a56a8eb027ef5 -Author: Tyler Reddy -Date: Sun May 24 11:45:27 2020 -0600 - - CI: add 32-bit Win to CI. - -commit a0bd19ce036a38fd91fed8b594604b5d8ee04e36 -Author: William Glass -Date: Sat May 23 01:50:19 2020 +0100 - - Ensure principal axes follow right hand convention (PR #2686) - - * Fixes #2637 - * Added a check when calculating the principal axes to ensure that they follow the - right handed convention. - * Added a test with PDB code 6msm that returned a triple product of -1.0. Now returns 1.0 - * update doc string - * update CHANGELOG - * update AUTHORS - -commit 833aff33b6d2b860bc14812c68a55da8422294c4 -Merge: a0b2a79bd b341090aa -Author: Rocco Meli -Date: Tue May 19 16:07:45 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit b341090aaa0bace9b946316ebf1e5bf965b026da -Author: Rocco Meli -Date: Tue May 19 15:02:04 2020 +0200 - - Resize NumFOCUS Logo (#2684) - - * resize image in readme - - * add raw tag - - * fix spacing - - * resize - - * try center - - * try rst center - - * try html center class - - * remove centering - - * use numfocus template - - * fix link - - * add line break manually - - * alt text - -commit a0b2a79bde8c132eddc3e85c64e4b489f4822587 -Merge: 9009c8253 6df837e9d -Author: Rocco Meli -Date: Tue May 19 11:45:48 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 6df837e9dddcf43e27b983b9e66e3083cc71e9c7 -Author: Andrea Rizzi -Date: Mon May 18 22:45:51 2020 +0200 - - Fix reading new ts after reading last one (#2674) (#2683) - - Fixes Issue #2674 - - ## Work done in this PR - - Fixes bug which did not allow for further reading of aux data after the final frame had been read. - - Some PEP8 fixes. - -commit 39b6385b358a7b38d52693b2345620292a2b4297 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon May 18 15:16:07 2020 +1000 - - Added PCA subspace comparison methods and fixed n_components selection (#2613) - - - fixes #2623 and now correctly computes cumulated variance - - adds root mean square inner product and cumulative overlap method as ways to compare subspaces - -commit 375245c10bdc922efb4e3eab5cf86c03aa0919e2 -Author: Tyler Reddy -Date: Fri May 15 15:29:25 2020 -0600 - - MAINT, TST: remove tempdir (#2682) - - * Fixes #2681 - * use the upstream `pytest` temporary file/path handling instead of using/maintaining our own - * no residual test artifacts were observed when the full test suite passed locally for this feature branch - - Co-authored-by: Oliver Beckstein - -commit 2d866385b6cd7906c0ab964b31f92f8f96d8ce09 -Author: Rocco Meli -Date: Fri May 15 19:29:37 2020 +0200 - - Fix 'same residue|segment' selections (#2669 and #2672 (PR #2673)) - - * fixes #2669 - * fixes #2672 - * fixes "same residue" and "same segment" selections - * Use resindices of resids for same residue selection - * Use segindices of segids for same segment selection - * Use resindices for byres selection - * add failing test - * failing tests with correct number of atoms - * fix same selection - * add failing byres test - * fix byres test - * add comments - * updated changelog - -commit 9009c82534925c910d656cdf81f9ca5015b329ed -Merge: 2e248fb82 89db3b122 -Author: Rocco Meli -Date: Fri May 15 10:42:30 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 89db3b122fa0b8278b1811f8d20bcbaf8e0a41e0 -Author: Tyler Reddy -Date: Fri May 15 01:12:31 2020 -0600 - - BUG: allow repeated mol2 writes (#2680) - - Fixes #2678 - -commit 111224c3a13590075c16bbda46057d4f7f0f3425 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu May 14 20:20:33 2020 +1000 - - Added frames and times to AnalysisBase (#2662) - - * fixes #2661 - * added frames and times - * changed hole test - * added deprecation warning, docs, pep8 fixes - * added test and doc change - * removed timesteps attribute from hydrogenbonds.hbond_analysis and all 1.0 versionchanged notes - * updated CHANGELOG - -commit d692fcd9e35ff3e7aca1e727f14bb99fe60c365b -Author: Mateusz Bieniek -Date: Tue May 12 15:13:20 2020 +0100 - - Consistent Autocorrelation and Intermittency across Different Analysis (#2256) - - * Summary of changes - - The main issue with HydrogenBondLifetimes (besides the bug #2247) is that it defined - its own definition of a hydrogen bond, without allowing the user to change it. - It should be clear that the hydrogen bonds first have to be computed by the user, - and then the autocorrelation for the bonds can be found. - This is achieved with the autocorrelation() function, which is now made available in a - separate module, `MDAnalysis.lib.correlations` so that it can be used by any code. - - * Provides well defined autocorrelation which can be used for both, SurvivalProbability and HydrogenLifetimes (and more?) in new module MDAnalysis/lib/correlations.py - * Autocorrelation function and intermittency function are now independant with their own test cases - * Removed the class HydrogenBondLifetimes and moved the autocorrelation functionality into the hbond_analysis class as a .autocorrelation method. This method should replace also hbond_autocorrel.py file in the future. - * New test cases for the method .autocorrelation (HydrogenBondAnalysis) were added - * Added a test cases that, with our definition of intermittency, would fail in the case of the hbond_autocorrel.py. - * Fixes the issue #2247 - - * Detailed code comments - * new module MDAnalysis/lib/correlations.py - * Extracting the autocorrelation and intermittency from SP into their own functions with their own test cases. - * A more general documentation in the autocorrelation. - * The documentation updated with the code. The HydrogenBondAnalysis - should ideally be extracted from the HydrogenBondLifetime and fed into - it in the constructor. - * Removed the class HydrogenBondLifetimes and moved the autocorrelation - functionality into the hbond_analysis class as a .autocorrelation - method. This method should replace also hbond_autocorrel.py file. Test - cases for the new method .autocorrelation are added. - * Updated logging. - * Added __future__ imports. - * Remove deprecation warning for HydrogenBondLifetime. - This function will be removed in a future PR once a replacement that uses the - new hydrogen bond class is in place. - * Added checks for parameters types and dimensions. - * reST citations - * Detailed test comments - * Updated test cases to illuminate the bug in #2247. - * Correction for the test to make it consistent with the previous author's test. - Our end index is inclusive (5th frame, giving 6 frames). But the other author's - analysis was done on 0-4 frames (5 frames). - * Exhaustive testing for autocorrelation. It will now return 1 at tau=0. - Now the function can be embedded into HydrogenBondLifetime. - * Exceptions marked as not covered - - Co-authored-by: Paul Smith - Co-authored-by: Oliver Beckstein - -commit 1d4444f75abe283f62311130302e58c243840d1d -Author: Rocco Meli -Date: Wed May 6 07:08:31 2020 +0200 - - Remove spurious icode variable from PDBParser and fix other PEP8 complaints (#2677) - -commit 2e248fb824cb330c12c020a9367eca50a543b4a0 -Merge: 591bf39ae 400f93cd9 -Author: Rocco Meli -Date: Fri Apr 24 17:39:04 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 400f93cd94626ae94de0fa5ab283beac5aa3ad40 -Author: SHUBHAM SHARMA -Date: Wed Apr 22 11:36:10 2020 +0530 - - Add pbc kwarg to Contacts (#2646) - -commit 8deea98a999e20d7458f62dcd55f89e83ec9f234 -Merge: c35a6bffa 9ec36338c -Author: Tyler Reddy -Date: Tue Apr 21 18:07:55 2020 -0600 - - Merge pull request #2660 from ss62171/module - - print message if C extension not installed - -commit 9ec36338c2dedfde8ea93af8121ff337ba4193f4 -Author: ss62171 -Date: Tue Apr 21 20:45:47 2020 +0530 - - removed print statement - -commit e0a90751e08f1f080c6e7c4adee226bc3a7dfd73 -Author: ss62171 -Date: Mon Apr 20 21:23:27 2020 +0530 - - changed checking version using sys.hexversion - -commit 197b7a8c35b04e123ec2667f49c0b46c4ccc1ec0 -Author: ss62171 -Date: Sat Apr 18 00:02:06 2020 +0530 - - Added import error - -commit c35a6bffaad6834ffaa0e601364ac28a1fb4c00c -Merge: e01176f58 bca46843d -Author: Richard Gowers -Date: Thu Apr 16 00:26:03 2020 -0700 - - Merge pull request #2645 from Oscuro-Phoenix/EM_cryst_fix - - Added warning for 1 A^3 CRYST1 Record - -commit bca46843d63baa23f633f94f6e8ac48a0e5348f9 -Merge: 2bff8b116 e01176f58 -Author: Irfan Alibay -Date: Wed Apr 15 10:35:26 2020 +0100 - - Merge branch 'develop' into EM_cryst_fix - -commit 2bff8b116c9cdb8cb40b24976efd32266ec9b26d -Author: Shakul Pathak -Date: Wed Apr 15 14:57:12 2020 +0530 - - CHANGELOG Update 3 - -commit 7cb91797f50b025887dc8b78754e9ee20f8eda97 -Author: Shakul Pathak -Date: Tue Apr 14 20:20:51 2020 +0530 - - CHANGELOG Update - -commit 579be07227222eae49a14e82cd812343e5e0ef1a -Author: Oscuro-Phoenix -Date: Tue Apr 14 22:07:20 2020 +0530 - - CHANGELOG and AUTHOR - -commit 591bf39ae96a8b9b23a1c4193580432d431d8b98 -Merge: 8023811c1 e01176f58 -Author: Rocco Meli -Date: Mon Apr 13 10:54:48 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 62eeb9ce7de2a75eed574b3c5f237a6ebe5efe84 -Author: ss62171 -Date: Mon Apr 13 05:30:10 2020 +0530 - - improved test - -commit 94484bc4518e7a34a9e3f0b9df34f4cc2260e48b -Author: ss62171 -Date: Sat Apr 11 07:14:13 2020 +0530 - - print message if C extension not installed - -commit e01176f5849426c9ee24a0b4a9aa8b4d6a811b29 -Merge: e0e3462e5 888ec3385 -Author: Tyler Reddy -Date: Fri Apr 10 07:06:59 2020 -0600 - - Merge pull request #2659 from ss62171/dead_code - - remove dead code - -commit 8023811c1fde07ece7206a3a424f9380ba9fbffd -Merge: 51d134733 e0e3462e5 -Author: Rocco Meli -Date: Fri Apr 10 09:47:16 2020 +0200 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 888ec3385cc4bfa8a0ff0036f7417bf1e6686df9 -Author: ss62171 -Date: Fri Apr 10 05:48:06 2020 +0530 - - remove dead code - -commit e0e3462e51714f0115cf009a506a0bd352d7329a -Merge: faebd3ed7 2d59fb722 -Author: Tyler Reddy -Date: Wed Apr 8 22:10:50 2020 -0600 - - Merge pull request #2652 from ss62171/align - - added test for alignto and fasta2select - -commit 2d59fb722dcf59e4b928c0a2930e4e00a52d94c8 -Merge: 6780115ca faebd3ed7 -Author: SHUBHAM SHARMA -Date: Wed Apr 8 03:25:32 2020 +0530 - - Merge branch 'develop' into align - -commit 6780115ca157fb82aedaa144002ae51dc54463ba -Author: ss62171 -Date: Wed Apr 8 03:24:01 2020 +0530 - - Exit Stack removed - -commit 56f2fb293439e6dfe1d0830a2835442da9cf274a -Author: ss62171 -Date: Tue Apr 7 01:57:40 2020 +0530 - - nullcontext error correct - -commit 89cf90f9b26440128d2ab94e3257701df0738ed5 -Author: ss62171 -Date: Tue Apr 7 00:14:28 2020 +0530 - - parametrized conditional raising - -commit 41ad5783ab44219a9e78ad4954f11ad9d3fd8f99 -Author: ss62171 -Date: Mon Apr 6 06:10:44 2020 +0530 - - parametrized test - -commit 755224c6b0d3edba6269a7b959cfbcf36b6c08c3 -Author: ss62171 -Date: Sun Apr 5 18:45:45 2020 +0530 - - new_rmsd equals old_rmsd for same universe - -commit 158f507ab4822d6f477f05552612dc07f1b756a1 -Author: Oscuro-Phoenix -Date: Mon Mar 30 16:47:29 2020 +0530 - - PEP8 Fix - -commit faebd3ed76af1194385a79500a1726f7bf119cb8 -Author: Ameya Harmalkar -Date: Mon Mar 30 02:54:17 2020 -0400 - - Providing Elements attribute to PDB parser (Issues #2553 & #2467) (#2627) - - Fixes #2647, towards #2553 - - ## Work done in this PR - Elements are now read from PDB files and added to the elements attribute of the universe. - This is currently only done in cases where all elements in the PDB file are valid (i.e. match IUPAC naming). In all other cases a user warning is thrown and the elements are not assigned. - - ## Files changed - - MDAnalysis/topology/PDBParser.py - - MDAnalysisTests/topology/test_pdb.py - - CHANGELOG and AUTHORS (new contributor) - -commit 9a5467db55584eebbbe068bac0ba273f33713a6c -Author: shfrz <39633713+shfrz@users.noreply.github.com> -Date: Mon Mar 30 04:14:36 2020 +0530 - - Updated mdamath (#2634) - - FIxes issue #2632 - - ## Changes made in this PR - - When lowerbound roundoff errors occur in `mdamath.angle` (i.e. the internal value of `x` becomes < -1.0), the returned angle is now `np.pi` rather than `-np.pi`. - - The `if`/`else` construct for roundoff errors has now been switched to an `np.clip()` call. - - ## Files changed - - MDAnalysis/lib/mdamath.py - - MDAnalysisTests/lib/test_util.py - - CHANGELOG - -commit 722a9b2f114d610ff3440bd53a7a41d9cc3de94c -Author: ss62171 -Date: Mon Mar 30 01:49:13 2020 +0530 - - added test for alignto and fasta2select - -commit febb2279dc89188bbe18718477975860447beae1 -Author: Oscuro-Phoenix -Date: Mon Mar 30 01:46:30 2020 +0530 - - Added docstring - -commit a0fdd2b509457704190ebc3e7ac7f2bcc6dac548 -Author: Oscuro-Phoenix -Date: Mon Mar 30 01:40:39 2020 +0530 - - Revised PEP8 - -commit 828152281e8b367042017a122d78eeb72b6c9208 -Merge: 9c9e453f0 60eb9d828 -Author: Irfan Alibay -Date: Sun Mar 29 17:15:19 2020 +0100 - - Merge branch 'develop' into waterdynamics-sp-startstop - -commit 6b7b5723435f033e1e21f9d914c4c1bed2c1f1b4 -Author: Oscuro-Phoenix -Date: Sun Mar 29 04:59:11 2020 +0530 - - PEP8 - -commit 0ddd0dcc8afd3ba712aa0071cd02dd53fce2fe5d -Author: Oscuro-Phoenix -Date: Sun Mar 29 04:57:40 2020 +0530 - - Resolve dtype - -commit 24647aceec707ef83327525308f50f631f02d41f -Author: Oscuro-Phoenix -Date: Sun Mar 29 04:54:54 2020 +0530 - - Revised test 2 - -commit 60eb9d8289f79a3e5a38b788c5e25999bbe185e4 -Author: Siddharth Jain -Date: Sun Mar 29 03:15:54 2020 +0530 - - Add warning for matching atoms without masses (#2614) - - * Fixes issue #2469 - * raise SelectionWarning if AlignTraj is called with match_atoms=True and masses are not present - * fit_translation and fit_trans_rot now raise TypeErrors (originally ValueErrors) for getting weights from atoms without masses - * get_weights now raises ValueError if weights is given as incorrect value (originally TypeError) - - Co-authored-by: Philip Loche - Co-authored-by: Oliver Beckstein - -commit 5be247bcaebc685c230edfee33dfad410990473c -Author: Oscuro-Phoenix -Date: Sat Mar 28 17:58:08 2020 +0530 - - Resolved try - -commit ee2124b3a39443e57c5a0bf398f3865b4d39c8c4 -Author: Oscuro-Phoenix -Date: Sat Mar 28 01:03:31 2020 +0530 - - Revised test for CRYST1 - -commit db0e933565fa8378eacbfcf7ddb91ad696d62bca -Author: Oscuro-Phoenix -Date: Thu Mar 26 16:36:35 2020 +0530 - - Revised Warning CRYST1 and added test - -commit 5a88586493bb933e0413db2463e6fdeafb074873 -Author: Oscuro-Phoenix -Date: Wed Mar 25 17:09:09 2020 +0530 - - Added Warning for 1A^3 CRYST1 Record - -commit 24776e4c9fbce2577a0bf1070a54fc3bf5bace32 -Author: Oscuro-Phoenix -Date: Wed Mar 25 17:06:01 2020 +0530 - - Revert "Fixed mdamath" - - This reverts commit c45f1ecb34f8d23af005f445ec149e29eb23a8d8. - -commit 5f513831301492ffcf054c7b57ee6092bf153c41 -Author: Cédric Bouysset -Date: Sun Mar 22 18:44:27 2020 +0100 - - tqdm ProgressBar replaces deprecated ProgressMeter (PR #2617) - - * Fixes #928 - * Fixes #2504 - * Added the ProgressBar class which inherits the tqdm.auto.tqdm object. - - For now, the disable keyword takes precedence over verbose, i.e. if both are set to - True the progress bar won't show. Setting disable=True will disable the progress bar - as expected. Setting verbose=False will disable the progress bar. - - Automatically detect which version of tqdm to use (console or notebook): - If run from a jupyter notebook or jupyter lab, will use the - tqdm.notebook.tqdm class, else (ipython, shell, or anything else) - will use the default tqdm.tqdm class - * add tqdm to dependencies - * Deprecate ProgressMeter through warning and text - * Replace ProgressMeter with ProgressBar everywhere in MDAnalysis - * add tests (for #928 and #2504) - * update CHANGELOG and AUTHORS - -commit 865f5c14199a62198c858609aeb16c086a07be89 -Author: Oscuro-Phoenix -Date: Sun Mar 22 18:00:36 2020 +0530 - - Revert "Added n_initial_contacts" - - This reverts commit 959d904a9e1714f954332876e444c69366aec0fc. - -commit 8bbdf55942831f975e4dd5fadf4124b8a5c86ee6 -Merge: e2fabab73 ee93e2eb7 -Author: Oscuro-Phoenix -Date: Sun Mar 22 17:58:07 2020 +0530 - - Merge branch 'develop' of https://github.com/Oscuro-Phoenix/mdanalysis into develop - -commit e2fabab73812e420e709fde1d36626583dd92519 -Author: Oscuro-Phoenix -Date: Sun Mar 22 17:56:28 2020 +0530 - - Revert "Added n_initial_contacts attribute" - - This reverts commit ee93e2eb7e66e65bd6ba4cebd3b2d6490295affe. - -commit 959d904a9e1714f954332876e444c69366aec0fc -Author: Oscuro-Phoenix -Date: Sun Mar 22 17:45:52 2020 +0530 - - Added n_initial_contacts - -commit ee93e2eb7e66e65bd6ba4cebd3b2d6490295affe -Author: Oscuro-Phoenix -Date: Sun Mar 22 17:04:42 2020 +0530 - - Added n_initial_contacts attribute - -commit 9a0a6573caaa0b5471f35a1304c13d4450c5cd47 -Author: SHUBHAM SHARMA -Date: Sun Mar 22 04:54:15 2020 +0530 - - Fix #2590: Created new axes for plot of persistence_length. (#2591) - - * Fixes #2590 - * Created new axes for plot of persistence_length if ax is not passed in as an argument (analysis/polymer.py) - * Added test (analysis/test_persistencelength.py) - -commit c45f1ecb34f8d23af005f445ec149e29eb23a8d8 -Author: Oscuro-Phoenix -Date: Sun Mar 22 03:41:47 2020 +0530 - - Fixed mdamath - -commit 4102481643dd59cf40db382a190f8b35ece9b831 -Author: Yuxuan Zhuang -Date: Fri Mar 20 11:18:04 2020 +0100 - - Weights rework for #2429 (#2610) - - Fixes #2429 - - ## Work done in this PR - weight_groupselections option added to allow selection of weights (*mass*, *None* or 1D float array) for each groupselection in RMSD. Weights for select now gets masses from mobile atoms. - - ## Files changed - - rms.py - - test_rms.py - - CHANGELOG - -commit 89646b4ee29c4b99396da743e52f49910aa53161 -Author: Abhishek Shandilya -Date: Thu Mar 19 13:56:48 2020 -0400 - - Fix #2606: moving local function to the top (#2615) - - * Fixes #2606 - Pytest and/or multiprocessing fails to pickle local functions. Found a workaround here: - https://bugs.python.org/issue33884 (Basically, moving the local function to the top level.) - * the function which is being evaluated in parallel is global now - * make parallel test xfail for windows (because even this workaround does not help under windows) - -commit e0883c88834584b307e0ab34f4d3b7f9f724ddda -Merge: a78307f0d 1c2e94334 -Author: Irfan Alibay -Date: Thu Mar 19 17:48:36 2020 +0000 - - Merge pull request #2537 from MDAnalysis/densityanalysis-2502 - - Fixes #2502 - - ## PR overview: - Adds the new AnalysisBase DensityAnalysis class. - - ## PR details - - A new Density class based on AnalysisBase was created. - - The old density_from_Universe, density_from_PDB and associated code was deprecated, with removal set for v2.0. - - Tests were added to cover some of the untested parts of the code. - -commit 1c2e943340434ec35a853c3f9a5d4123359f80d1 -Merge: 1bfb9a822 a78307f0d -Author: Irfan Alibay -Date: Thu Mar 19 14:10:40 2020 +0000 - - Merge branch 'develop' into densityanalysis-2502 - -commit 51d134733b4dc1e295157d621e686f796ca6ada5 -Merge: a2951ee22 a78307f0d -Author: Rocco Meli -Date: Thu Mar 19 12:14:39 2020 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit a78307f0d99b7310707ef015cab2908ce4770a4e -Author: shfrz <39633713+shfrz@users.noreply.github.com> -Date: Thu Mar 19 14:56:59 2020 +0530 - - Remove details from ClusterMethods [Fixes #2575] (#2620) - - Fixes issue #2575 - - ## Work done in this PR: - - Here the always-empty `details` dictionary which used to be returned by ClusterMethods has been removed. - - ## Files changed - - - ClusterMethods.py (removed details). - - test_encore.py (removed details). - - cluster.py (removed details). - - AUTHORS and CHANGELOG updated accordingly. - -commit 1bfb9a8228b9fd8efdbf492d95ad0fbd164e0bae -Author: wvandertoorn <31660235+wvandertoorn@users.noreply.github.com> -Date: Tue Mar 17 19:14:28 2020 +0100 - - Wrap up loose ends from PR review (#2633) - -commit 7cb41846a8eebe1d2f46764ee5cb3a708fbeb20d -Merge: e7dfc961a 2801f2d4b -Author: Johannes Zeman -Date: Mon Mar 16 22:43:04 2020 +0100 - - Merge pull request #2572 from bieniekmateusz/hbondtests - - Fixed the run() method of analysis.hydrogenbonds.hbond_analysis method to use atom indices instead of ids - -commit e7dfc961ae8fd74778eca0daeb11e5ee55e96f35 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Mar 16 21:23:39 2020 +1100 - - updated tests (#2621) - - Fixes #2618 - - ## PR details - - In light of recently pytest changes (5.4.0), this PR switches some tests over to explicitly declared fixtures. Also included are some typo and PEP8 corrections. - -commit 4cfdec6d76751364c7794b585639b254553ee7e4 -Author: wvandertoorn <31660235+wvandertoorn@users.noreply.github.com> -Date: Mon Mar 16 11:11:50 2020 +0100 - - Indentation and import fix (#2629) - -commit 422370f36948ebf1eb92251e6e871074bf1afbba -Merge: 837c2dea0 95d19093a -Author: Irfan Alibay -Date: Sun Mar 15 14:22:11 2020 +0000 - - Merge branch 'develop' into densityanalysis-2502 - -commit 837c2dea0ca8e0365b2be39574c3133910bb8d99 -Author: wvandertoorn <31660235+wvandertoorn@users.noreply.github.com> -Date: Sun Mar 15 15:15:44 2020 +0100 - - Finalizing #2537 (#2616) - - Partially fixes #2502 (completes PR #2537) - - ## PR contents: - - This PR by @wvandertoorn finalises the work done as part of #2537 - Key commits: - - Fixes docstring (adds .. deprecated information). - - Adds back :class:`TestGridImport`. - - Reduces precision matching of `test_density_from_PDB`. - - CHANGELOG and AUTHORS updated accordingly. - -commit a2951ee2273c978cb5b08f2e47615c3ae6d989de -Merge: 30effbda0 95d19093a -Author: Rocco Meli -Date: Sun Mar 15 10:58:27 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 95d19093a7ae69459eede951366a8f85f6104d76 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sat Mar 14 20:50:54 2020 +1100 - - added pyd to gitignore (#2626) - -commit 30effbda0721aef83e5a72f323e9e2ff24731792 -Merge: 4d639f963 da677897f -Author: Rocco Meli -Date: Fri Mar 13 11:23:35 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 2801f2d4b93bed4fbac2aa20d5d42d8e2ea736cd -Merge: 6efffec9d da677897f -Author: Mateusz Bieniek -Date: Fri Mar 13 11:11:54 2020 +0000 - - Merge branch 'develop' into hbondtests - -commit 6efffec9d045233bfbe31efbc241a67b5a3b77bb -Author: bieniekmat -Date: Fri Mar 13 11:09:16 2020 +0000 - - Minor refactorting (#2572) - -commit da677897f2c4be3f0d0f0a54add678528d52ce4e -Author: Morgan Nance -Date: Fri Mar 13 06:09:19 2020 -0400 - - Read XDR offsets from trajectory if file read-in fails (#2611) - - * use try:except to wrap 'read_numpy_offsets' to catch if offsets file fails to load. provide warning to user and read offsets from trajectory instead - - Co-authored-by: Oliver Beckstein - -commit 9740d80abd6bc3927a925c621d1ba03cade8b457 -Author: Abhishek Shandilya -Date: Thu Mar 12 15:07:55 2020 -0400 - - avoid importing ABCs from `collections.abc` to remove deprecation warning (#2607) - - * Fixes #2605 - * test for `dict` instead of deprecated top level ABC `collections.MutableMapping` (compatible with Python 2.7 and 3.x) - * updated AUTHORS and CHANGELOG - -commit 53ccf6def40ca0e1342179269b1dfeef0e4877b4 -Author: Yuxuan Zhuang -Date: Thu Mar 12 11:26:13 2020 +0100 - - Increase coverage of leaflet.py (#2603) - - Commit title: Increase coverage of leaflet.py (#2603) - - Contents of commit: - ============= - - 1) This commit adds a series of tests to `analysis/leaflet.py` which cover parts of the code which did not use to be tested (Issue #2600). As of this commit, coverage is now at over 95% for this module. - - 2) This commit also fixes a missing import for the selection module (#2612). - - Unaltered commit history: - ================= - - * _get_graph without self.pbc for leaflet.py - - * using update - - * add test for leaflet write_selection and fix one missing module in leaflet.py - - * tyop - - * check expected lipids contact are returned when pbc on - - * check leaflet write_selection output - - * remove unused codes - - * add more tests on update function - - * cover three options for sparse - - * add test on components index in group & add name CHANGELOG - - * add test on update without cutoff - - * PEP8 formatting - - * exclude valueerror in matrix cal from coverage - - * add author - -commit e416aa7d9adb9a9c14adb0774e65162da89a0d1c -Author: Guillaume Fraux -Date: Tue Mar 10 12:47:15 2020 +0100 - - Add Chemfiles as a coordinate reader/writer (#1862) - - * Implement CHEMFILES reader and writer - - Co-authored-by: richardjgowers - Co-authored-by: Max Linke - -commit d9a78a4eb1c3add937b34524b071e5ed185d924c -Author: Irfan Alibay -Date: Tue Mar 10 01:45:15 2020 +0000 - - Removed PersistenceLength.perform_fit (#2597) - - - Fixes #2596 - - Removes deprecated :meth:`PersistenceLength.perform_fit` (was deprecated in 0.19.2 but no removal date give: in #2596 it was determined that it will be removed in 1.0) - -commit ca1f5a80f6f2a5b77530123a15334f0e8d7fdebf -Author: Irfan Alibay -Date: Tue Mar 10 01:40:03 2020 +0000 - - PSAnalysis generate_paths defaults and fixes load tests (#2594) - - * fix #2593 - * Changes the :meth:PSAnalysis.generate_paths defaults for store and filename defaults to those originally documented in the docstring. - * Updates the test for :meth:PSAnalysis.save_paths and :meth:PSAnalysis.load so it no longer fails. - * Also some blank line PEP8 changes, because I got carried away - * Update CHANGELOG - -commit 9389ecfa7cf481ef03bb7504a749587fb0ab59ff -Author: Paul Smith -Date: Mon Mar 9 20:56:51 2020 +0000 - - Using u._topology.bonds rather than u.bonds. - - It is a million times faster to access. - See https://github.com/MDAnalysis/mdanalysis/issues/2396#issuecomment-596251787 - -commit 9581bc41d8887085d4fb2c3cf9f74db11d5d3546 -Author: Irfan Alibay -Date: Mon Mar 9 11:27:10 2020 +0000 - - Fixes TRJReader random frame access docs (#2595) - - * Fixes #2398 - - * Update CHANGELOG - -commit 920e8dc98bc1ba11aaa7ce42d656b7bb890ec880 -Merge: 9be38c919 82e0d6da2 -Author: p-j-smith -Date: Sun Mar 8 09:34:14 2020 +0000 - - Merge branch 'develop' into hbondtests - -commit 9be38c919a026ce7067ef49c3576003ab0f80b14 -Author: Mateusz Bieniek -Date: Sat Mar 7 19:07:01 2020 +0000 - - Fixed the test case for the NoDataError when bond info is missing. - - Co-authored-by: p-j-smith - -commit 82e0d6da244b3bfa91b31dfd619ef12298910ab1 -Author: SHUBHAM SHARMA -Date: Sat Mar 7 23:01:50 2020 +0530 - - Fix #2582: polymer persistence length example fix (#2589) - - * Fix #2582 - * fix polymer persistence length example fix - * Added name to AUTHOR file - * Update CHANGELOG - - Co-authored-by: Richard Gowers - -commit 00d0db1c7e11c313b6fac523ff4ab335d08808e4 -Author: Paul Smith -Date: Fri Mar 6 11:27:55 2020 +0000 - - Updated the CHANGELOG. - -commit 06f9fa2fae98ae1947a71a266709daa930ea6061 -Author: Paul Smith -Date: Fri Mar 6 11:22:38 2020 +0000 - - Added a test for _get_dh_pairs(). - - Tidied up the mock universe in TestHydrogenBondAnalysisMock. - - Using numpy asserts rather than bare asserts. - -commit 3a8e187027848852b9c549784108b16b6cb7f736 -Author: Paul Smith -Date: Fri Mar 6 10:29:57 2020 +0000 - - Replaced bare Exception with NoDataError. - -commit 1f4e492662955e483fc98982728404149f7a1deb -Author: Richard Gowers -Date: Thu Mar 5 18:17:30 2020 +0000 - - Merge universes without coordinates Fixes 2470 (#2580) - -commit aeef04b388432fe0958baa5c0ee25a325f14e0ee -Author: Richard Gowers -Date: Thu Mar 5 10:55:53 2020 +0000 - - fixed PCA align=True problems (#2561) - - * fixed PCA align=True problems - -commit fd8b8fae015e9a493231898b23411b58d9cf430c -Author: Richard Gowers -Date: Thu Mar 5 10:53:16 2020 +0000 - - update GitHub templates (#2581) - - * update bug report template - - - fix typo - - use subheading levels - - * updated CONTRIBUTING - - - link to Code of Conduct - - link to Contributing in User Guide - - * removed outdated ISSUE template - - * updated questions template - - Made clear that this issue will be closed. - - * hide instructions in html tags - - * update feature requests - - - use md headings - - hide instructions in html comments - -commit 0b20ae8b0518ff06466a622fa9155944ae1f19eb -Author: Oliver Beckstein -Date: Wed Mar 4 17:19:23 2020 -0700 - - Bump up auxiliary coverage (#2570) - - * contributes to #597 - * bump auxreader core coverage - * add more test on failures - * test XVGStep failures - * remove unused module - -commit 9d602ec01f4b7fd28d951011c86a0ee424096a30 -Merge: eb18a3389 fc938b6c2 -Author: Oliver Beckstein -Date: Tue Mar 3 21:22:23 2020 -0700 - - Merge pull request #2523 from lilyminium/hole - - Created hole2 module - -commit fc938b6c2ce475d745f55d228fd56d59bbd9f76e -Author: Lily Wang -Date: Thu Feb 20 01:10:10 2020 +1100 - - added binning and plotting functions, and tests - -commit c54990def772a757bff2399d5546ae9878f7fc9e -Author: Lily Wang -Date: Mon Feb 17 17:46:37 2020 +1100 - - updated HoleAnalysis docs - -commit 259ec80ed3e070e56229d67fd76bc27b9e73498c -Author: Lily Wang -Date: Mon Feb 17 14:46:48 2020 +1100 - - moved run arguments to __init__ - -commit ade85145ebc9963ddf1fc48592e608cc4189a195 -Author: Lily Wang -Date: Sun Feb 16 22:36:32 2020 +1100 - - deprecated original hole module - -commit 0cafbafd97065208ef3896cb5b553983c996eb7c -Author: Lily Wang -Date: Sun Feb 16 14:41:47 2020 +1100 - - added tests - -commit e1e28619b73ba091fde1035488a45d6c4ada3132 -Author: Lily Wang -Date: Sun Feb 16 07:09:07 2020 +1100 - - added docs - -commit d91dbe71fcb295172b6ab93512ee82911457abad -Author: Lily Wang -Date: Sun Feb 16 00:05:37 2020 +1100 - - created new hole2 module - -commit eb18a338936207692bbae5df71d7ddc3ed5bcc96 -Author: Iv-Hristov <61376106+Iv-Hristov@users.noreply.github.com> -Date: Wed Mar 4 00:36:56 2020 +0000 - - More flexibility with wildcards in selection (#2551) - - * Fixes #2436 - * Selection strings changed to use fnmatch. This now allows for more flexible wildcard usage as well as for using multiple wildcards at once. - * Added two new tests to match the new functionality - * New doc section on wildcards - * Remove test for multiple wildcards - * Update in AUTHORS - * Update CHANGELOG - -commit 4d639f9639fcec982ef8bd94c207fcae98bfd56d -Merge: 640ce81b5 bc2f1a546 -Author: Rocco Meli -Date: Tue Mar 3 14:22:49 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit bc2f1a54695b4fc9256a2b8d500fd65028e34110 -Author: shfrz <39633713+shfrz@users.noreply.github.com> -Date: Tue Mar 3 06:42:02 2020 +0530 - - Updated Readme (#2552) - - Fixed typos in README.rst. - -commit 62c92e11727e8770003aacf2cf7621659d66e92f -Author: Hao Tian -Date: Mon Mar 2 18:47:17 2020 -0600 - - test AnalysisFromFunction args order (#2549) - - * Fixes #2503 - * Correct argument order inspired by @lilyminium - * More compact coding for AnalysisFromFunction function - * Add new testing on AnalysisFromFunction. - * Update AUTHORS and CHANGELOG - -commit ee38518fb1cfffbaba10c4a7707d16041ade4f7d -Author: Mateusz Bieniek -Date: Sun Mar 1 15:42:08 2020 +0000 - - Fixed the run() method to use atom indices instead of ids. - - Fixed the attribute error (#2396). - - Added test cases that check the ids and indices of atoms in a hydrogen bond. - - Co-authored-by: p-j-smith - -commit 9bcf6f4c118e1ea137e8514bd60cbd1cd1972062 -Author: Irfan Alibay -Date: Sat Feb 29 22:27:26 2020 +0000 - - Remove deprecated format from MemoryReader.timeseries (#2567) - - * Completes #1453 for MemoryReader (and towards v1.0 #2443) - * Removes support for the deprecated format keyword in MemoryReader.timeseries. - * Removes deprecation test - * Update CHANGELOG - -commit 7efc83d5af52b0fc80032fed9016dcf6f13c4ef8 -Author: Irfan Alibay -Date: Sat Feb 29 22:11:42 2020 +0000 - - Removes LAMMPSDataConverter (#2569) - - * Fixes #2564 - * Removes deprecated LAMMPSDataConverter class - * Fixes docstring order. - -commit 964d40e33d2ca18e0ca713a0d79bc9ee99bf85e3 -Author: Irfan Alibay -Date: Sat Feb 29 22:06:51 2020 +0000 - - Atomgroup removal (#2562) - - * Completes #1070 and moves us towards v1.0 #2443 - * Removed AtomGroup stubs. - * Removed unnecessary import from groups.py - * Removes deprecation test - * Update CHANGELOG - -commit 4933830aec0182926088c7df78b461e1b8a47d8d -Author: Rocco Meli -Date: Sat Feb 29 21:48:31 2020 +0000 - - ignore html coverage report (#2568) - -commit 640ce81b5dffc611959db06a7341d4ff7647f924 -Merge: 5944b83ec 977fb79c5 -Author: Rocco Meli -Date: Sat Feb 29 11:29:06 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 977fb79c51b6a2fbdfa1c419a7bad0a97aa8d117 -Author: Michael Quevillon -Date: Fri Feb 28 20:17:29 2020 -0500 - - Update links to wiki pages (#2559) - - * Update links to wiki pages - * Add Michael Quevillon to author list - -commit 71c7f576444940b2f29d95a799f69e719c6ac736 -Merge: aa95e39b5 a97fe346e -Author: Oliver Beckstein -Date: Fri Feb 28 15:29:14 2020 -0700 - - Merge pull request #2546 from tylerjereddy/treddy_issue_2545_asv_check - - TST, BENCH: add asv check to Travis CI - -commit a97fe346e2cc43bf091d6feb448711e21655eaf2 -Author: Tyler -Date: Thu Feb 27 21:46:07 2020 -0700 - - MAINT: PR 2546 revisions - - * the `asv check` in Travis CI is now its own - separate matrix entry that runs in Python 2.7 - & avoids running the full test suite (MDA - build only) - -commit 93fe3d46f9aaeb3c7b8c96a1b7629eb12e49e78a -Author: Tyler Reddy -Date: Sat Feb 22 14:39:24 2020 -0700 - - TST, BENCH: add asv check to Travis CI - - * add `asv check` to Travis CI to help - catch issues in the benchmark suite without - running the full suite - -commit 5944b83ec9d8a91ed6d8b38e58af50d3e36a2288 -Merge: af65b1786 aa95e39b5 -Author: Rocco Meli -Date: Thu Feb 27 09:55:22 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit aa95e39b519e0d8476c2cc1d39eb62c2bd146387 -Author: Rocco Meli -Date: Wed Feb 26 20:47:13 2020 +0000 - - import full seaborn package (#2556) - -commit af65b1786b6f358085d88b7d7a924d678dac3a28 -Merge: 7546c3e6b 18b50cd9c -Author: Rocco Meli -Date: Wed Feb 26 16:10:02 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 18b50cd9c8427e6097e24c60050d712dac6ba61d -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Wed Feb 26 21:24:09 2020 +1100 - - Move parmed to optional dependency (#2477) - - * moved parmed to optional dependency - - make minimal build really minimal (ie no duecredit or parmed) - - Co-authored-by: Richard Gowers - -commit 3621b27123ed6226a8a92bebf387d83d4bb18c9f -Author: Tyler Reddy -Date: Wed Feb 26 03:21:19 2020 -0700 - - BENCH: fix benchmark suite (#2544) - - * there were two basic errors in the `asv` - benchmark suite; the errors were first - reproduced then confirmed fixed using - `asv check`, which does a sort of - syntax/lint check on the benchmarks - -commit 115453270f08087a834922de10e4785b4faa639a -Author: Oliver Beckstein -Date: Tue Feb 18 18:47:45 2020 -0800 - - density_from_PDB: deprecated, test, and bugfix - - - density_from_PDB is terrible code (I wrote it) and not used: deprecated and to be - removed for 2.0.0 - - added test so that it is covered - - fixed bug that was uncovered by test (us ag.tempfactors) - - added test for Bfactors2RMSF - - test for deprecation warnings - - organized in classes - - shortened test names for density_from_universe() - -commit 9764455cb61a80bb751bb794ce16fb28d76814b2 -Author: Oliver Beckstein -Date: Tue Feb 18 18:30:00 2020 -0800 - - Bfactor2RMSF:simple test - -commit 548c43f0ddd16288e6fc3c94e1749274e70a5e55 -Author: Oliver Beckstein -Date: Tue Feb 18 00:29:42 2020 -0800 - - deprecate density.notwithin_coordinates_factory - - When density_from_universe() is gone we will not need the function factory either. - -commit 2714988acb5dee5924a814968354f9eb1aa1998c -Author: Oliver Beckstein -Date: Mon Feb 17 23:35:12 2020 -0800 - - add new density.DensityAnalysis - - - close #2502 - - DensityAnalysis is based on @nawtrey's pmda.density.DensityAnalysis - but replace _reduce with accumulation in _single_frame - - added tests (based on the Test_density_from_universe): both give the same - answer as they pass the same tests; - test specific exceptions in DensityAnalysis - - update docs (also write ångström consistently throughout) - - update CHANGELOG - -commit 72654fa3c3a880de5de3f9efd4d8371f7a4350b6 -Author: Oliver Beckstein -Date: Mon Feb 17 22:03:01 2020 -0800 - - removed tests for missing gridDataFormats - - These tests are not necessary because gridDataFormats is a dependency. - -commit c04d2118c9ec0df53aad1192b1c81994419db0c4 -Author: Oliver Beckstein -Date: Mon Feb 17 17:29:08 2020 -0800 - - deprecated density.density_from_Universe() - - - deprecate in 1.0.0 - - remove in 2.0.0 - - adjusted tests that test for warnings: only test for UserWarning and match the - message with regex in pytest.warns() instead manually looking through the WarningReport - object: the problem is that the deprecation warning changes the number of entries - -commit bed3523d611da995c9f552e3f7f2ba00ee93d63e -Author: Oliver Beckstein -Date: Tue Feb 18 19:23:57 2020 -0800 - - fixed reST in AnalysisBase - - (need two lines before ..versionchanged) - -commit 3e8ea8e0744f3163ddbf7b4f5f66874dd26796a7 -Author: Philip Loche -Date: Tue Feb 18 14:56:38 2020 +0100 - - Fixed a typo and removed unused import (#2538) - -commit 1e3f3627990353cf0d5ee00a567e563f012de624 -Author: Richard Gowers -Date: Tue Feb 18 07:58:48 2020 +0000 - - added READER_HINTS (#2533) - - * added _READER_HINTS - - allows Reader to interrogate object and return suitability - - * added _TOPOLOGY_HINTS - - Co-authored-by: Oliver Beckstein - -commit 156ca53f465242168b0923d7d0a06eda4dd2a236 -Author: Matteo Tiberti -Date: Tue Feb 18 08:33:40 2020 +0100 - - Changes encore.hes() details output (#2484) - - * Fixes #2465 - * Removed arrayfication of `encore.hes` details. - * changed hes so it always returns details (instead of needing to use `details=True` - This is more consistent with the behaviour of `ces` and `dres`. Previously, `None` - was returned instead if the details flag was `False`. - * removed `details` kwarg from `hes()` - * updated docstrings; - * updated `encore.similarity` docs to Python 3 syntax - * added changes to CHANGELOG - -commit 7b87dc3a6c28fe066596490d5f2c3b25c012b128 -Author: Richard Gowers -Date: Mon Feb 17 19:35:51 2020 +0000 - - Removed instant selectors (Fixes Issue #1377) (#2535) - - * Removed instant selectors (Fixes Issue #1377) - -commit 7546c3e6b1851f73fde3aebccd0199047b4170ad -Merge: ccd77e927 ae4b51697 -Author: Rocco Meli -Date: Sun Feb 16 14:30:22 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit ae4b51697134d35728f29717ba145672f828003b -Author: Rocco Meli -Date: Sun Feb 16 14:17:39 2020 +0000 - - Use tempdir when testing align.AlignTraj (#2534) - -commit aca26d254a8c1f6920b74a9c1e4047389b3f894c -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Mon Feb 17 01:07:58 2020 +1100 - - Tidying Universe.__init__ (#2322) - - * added error to Universe.__init__ - - * butchered function signatures for py2 - - * update changelog - - Co-authored-by: Richard Gowers - -commit 6f51a2610308a9788a6c9bd97d3df7f31e49dfcc -Author: Richard Gowers -Date: Sat Feb 15 23:51:17 2020 +0000 - - Issue 782 removeflags (#2515) - - * removed flags - - added parameter docs to AtomGroup.select_atoms - to highlight periodic (and other) kwargs - -commit f430a00eed6363774a5d537c8be4268a9b24decf -Author: Rocco Meli -Date: Sat Feb 15 23:50:28 2020 +0000 - - Select keyword everywhere (#2531) - -commit ccd77e927e1209e6550bd4c9dcf638f73b976225 -Merge: d7eda7867 be41c708d -Author: Rocco Meli -Date: Sat Feb 15 11:10:27 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit be41c708d85f011015e13d6e535b652d9f01c995 -Author: Irfan Alibay -Date: Sat Feb 15 09:16:02 2020 +0000 - - Remove start/stop/step from AnalysisBase kwargs (#2505) - - - Co-authored-by: Oliver Beckstein - Co-authored-by: Richard Gowers - -commit 41ff944352c1b32a75c558e0c4a93a2687e4e13c -Author: Zhiyi Wu -Date: Sat Feb 15 08:40:46 2020 +0000 - - Replace the distance search of finding hydrogens with a dictionary lookup (#2519) - -commit 4b18243de93423fb7b950d995fba9f8d4a3a8cc5 -Author: Matteo Tiberti -Date: Sat Feb 15 09:40:02 2020 +0100 - - Fix return of encore.dres details (#2529) - - * corrected details assignment - - * added fix to changelog - -commit c434620547d2c7715f224a505a8d527b3b68f5a2 -Author: Rocco Meli -Date: Sat Feb 15 08:39:12 2020 +0000 - - Standardise select keyword (#2528) - -commit d7eda7867bc393c1d33ae85a0922ad6146822679 -Merge: 4d5f7de23 6fa3b6d68 -Author: Rocco Meli -Date: Thu Feb 13 12:09:03 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 6fa3b6d68b3c03d2ac7c50e4a94ea26992fbc1cd -Author: Irfan Alibay -Date: Thu Feb 13 08:13:33 2020 +0000 - - Changes holetraj start/stop/step keywords (Issue #2513) (#2514) - - * Fixes #2513 - * contributes towards #2443 - * Removes support for start/stop/step in :meth:HOLEtraj.__init__. - * Adds a check_slice_indices to the values passed to :meth:HOLEtraj.run. - * changes holetraj start/stop/step keywords - * update CHANGELOG - -commit ea98a62626f6eabee9b6714ec44d80856e6a0e0f -Author: Irfan Alibay -Date: Thu Feb 13 07:43:00 2020 +0000 - - Removing multiprocessing portion of waterdynamics.hydrogenbondlifetimes (#2520) - - * Fixes #2511 - * removes the multiprocessing portion of the Waterdynamics.HydrogenBondLifetimes code, which could fail - * removes nproc argument - * update docs - * Update CHANGELOG - -commit d873d367fcada2441cbad7b2f5060c8dc59772bd -Author: Rocco Meli -Date: Wed Feb 12 10:42:21 2020 +0000 - - Minimum mass for hydrogen guess in HydrogenBondAnalysis (#2516) - - * added minimum hydrogen mass - -commit abc90493f27ad160e311405f78d4377ac7a357ef -Author: Rocco Meli -Date: Tue Feb 11 12:49:17 2020 +0000 - - Fix PDBWriter with StringIO for invalid coordinates (#2518) - - * failing test - - * check if file is StringIO - - * changelog - - * small change - - * fix typos - - * actually check exception message - - * fix problem with exception catch - - * use pytest match - -commit 9c9e453f072f050beda390d6abaf9caefe3333ec -Author: Irfan Alibay -Date: Mon Feb 10 18:14:20 2020 +0000 - - Update CHANGELOG - -commit dd16e4b7e9e436b7f6afdb2f17da7807bb7e1f96 -Author: Irfan Alibay -Date: Mon Feb 10 18:03:01 2020 +0000 - - keyword removal - -commit 5efc8cbb4625145d09ac33d193ef35f19c13a6d9 -Author: IAlibay -Date: Mon Feb 10 17:55:10 2020 +0000 - - Aligns traj control to AnalysisBase methods - -commit d3a052b9bed351ed585e8aa50b81f4f35f454a8c -Author: Irfan Alibay -Date: Mon Feb 10 17:23:03 2020 +0000 - - removes deprecated keywords - -commit 4d5f7de234eff21938f2f10e239a8dfa8ef927af -Merge: f527e621b 121ec06c6 -Author: Rocco Meli -Date: Sun Feb 9 15:09:21 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 121ec06c6a873ff545307d1c70bae07c3bb5ee23 -Author: Zhiyi Wu -Date: Sun Feb 9 14:21:24 2020 +0000 - - Replace distance search with capped_distance in water bridge analysis (#2480) - - * Replace distance search with capped_distance - - * Add heavy test - -commit f527e621b370f55bf7d85a0846bb2190fe44c109 -Merge: 549c1a259 e1d13e2d3 -Author: Rocco Meli -Date: Sun Feb 9 13:58:35 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit e1d13e2d346c5f24bad35d5bf499280b43c5d5ec -Author: YuanYu -Date: Sun Feb 9 12:28:54 2020 +0800 - - I/O for namd binary coordinate format (#2485) - - * I/O for namd binary coordinate format - - * replace unpack to numpy.fromfile - - * change default extension to 'coor' - - * add more test - - * clean codes - - * updated CHANGELOG - - * addressed comments that reviewer suggested - - * fix typo for versionchanged - - * Update CHANGELOG - - * fixed versionadded in NAMDBIN coordinate reader/writer - - * made CHANGELOG entry more precise - - * [DOC] sort coordinate reader/write entries alphabetically - - * include *.coor files in tests via setup.py - - Co-authored-by: Richard Gowers - Co-authored-by: Oliver Beckstein - -commit 0dede258ce40c7b07f30b289b2d1e21698a27d9c -Author: Irfan Alibay -Date: Fri Feb 7 10:44:58 2020 +0000 - - Remove save() methods for v1.0 - Part 1 (#2487) - -commit 02f35b58f8d2d9f43b6821c7f6110f7137db73f3 -Author: Oliver Beckstein -Date: Thu Feb 6 12:04:27 2020 -0700 - - README.rst: changed NumFOCUS donation link - - - use the recommended numfocus.org based link - - fixed link to governance - -commit e1f11970482f6f9ddc02c564a12dd8eea07066e1 -Author: Irfan Alibay -Date: Thu Feb 6 17:39:05 2020 +0000 - - Remove save part2 (#2494) - - * Partly addresses #1745 (completes save() removal with PR #2487 and PR #2486 ) - * removes save methods - - removes save method from psa.py - - also minor change to test_hbonds.py - * deprecates hbond_analysis - - close #2492 - * updates changelog - -commit 549c1a2595df0db0955dea00250dee79bf6ce13d -Merge: 65e4d66ed 009ec225f -Author: Rocco Meli -Date: Thu Feb 6 11:31:44 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 009ec225f0408f4e4f1366bec2c5576b61c88160 -Author: Richard Gowers -Date: Wed Feb 5 23:58:29 2020 +0000 - - add NumFOCUS sponsorship (issue #2460) (#2467) - - * close #2460 - * close #2506 - * Add NumFOCUS sponsorship text with affiliation and donation links (donation link from #2506) - * use rst syntax (based on official template https://github.com/numfocus/templates/blob/master/fiscal-sponsor-readme-attribution.md) - * add link to Code of Conduct (as in template) - * updated high level description - * add NumFOCUS audit anchor as a reST link target as suggested by @jbarnoud - * create GOVERNANCE.md (This file is required as a NumFOCUS sponsored project. Our primary governance document is https://www.mdanalysis.org/about/#governance) - - Co-authored-by: Max Linke - Co-authored-by: Oliver Beckstein - -commit 8ad702c79d1da478f53675a3bf8d9d03e727c0e2 -Author: Irfan Alibay -Date: Wed Feb 5 09:51:24 2020 +0000 - - Removes skip and format from DCD reader (#2501) - - * removes skip and format - -commit 1d5ec0210633f1bdbe7bae4c2b7014d6a3187211 -Author: Irfan Alibay -Date: Wed Feb 5 09:50:31 2020 +0000 - - FullGroup selection keyword removal (#2500) - - * removes fullgroup - -commit 9d5520c611cb8ccfe7a35b1741b948e92475acb5 -Author: Irfan Alibay -Date: Tue Feb 4 17:47:54 2020 +0000 - - Density docs + padding warning (Issue 2372) (#2474) - - * Fixes #2372 - * Adds tests to check for the new padding userwarning - * Standardise units - * Don't assume uniform delta - * adds tests - * Update CHANGELOG - -commit 65e4d66edcaf7e0d16888836ac4c17f1800593c8 -Merge: ad1766e2e 4c03a2f5b -Author: Rocco Meli -Date: Tue Feb 4 13:24:09 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 4c03a2f5b6b49abeb8826832d9c05f58ba320748 -Author: Irfan Alibay -Date: Tue Feb 4 12:42:52 2020 +0000 - - Remove save() and changes filename in AlignTraj (#2486) - - * Update align.py - - * fixes save and filename - -commit 041f02f2f431c6c1ed08735637c565aed8e18775 -Author: Rocco Meli -Date: Tue Feb 4 12:41:13 2020 +0000 - - Issues/#2493 matplotlib (#2498) - - * Set the Tick attributes visibility on the underlying artists - -commit cd72f8b831a9b9d69204d071f3a279ce99089f67 -Author: Rocco Meli -Date: Tue Feb 4 12:40:35 2020 +0000 - - Issues/#2490 migration (#2496) - - * remove migration module - - obsolete, was used to migrate from 0.10 to 0.11 - - * changelog - -commit ad1766e2e5c8ec21eb5f517433a147703ca454c0 -Merge: 8c5dc00bd f1a2048b3 -Author: Rocco Meli -Date: Tue Feb 4 09:36:53 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit f1a2048b30918e3c81a069ba5f0c5d2d2a398ab8 -Author: Rocco Meli -Date: Tue Feb 4 00:47:05 2020 +0000 - - Issues/#2495 seaborn (#2499) - - * fix #2495 - * Cap seaborn version to 0.9 (note: need 0.9 because version 0.10 drops Python 2 support) on Travis CI - * do NOT cap in setup.py - * reference issue in comment - -commit 8c5dc00bd505e5737f2ab372763ffa60fa5d7d75 -Merge: 93413dc15 6d6b86202 -Author: Rocco Meli -Date: Sat Feb 1 14:52:21 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 6d6b86202a16bff69fad3d8017aca19eed76578c -Author: Rocco Meli -Date: Sat Feb 1 00:57:45 2020 +0000 - - auxreader fix #2410 (PR #2411) - - * fix #2410 - * Changed `time_frame_0` with `time_frame` so that auxreader behaves according to documentation and returns correct time differences - * added tests - -commit 24023716b2a804d8268fda16d8ab659594663ba0 -Merge: c9eb47e2a c9731e172 -Author: Tyler Reddy -Date: Thu Jan 30 21:39:48 2020 -0700 - - Merge pull request #2483 from lilyminium/install-parmed - - added parmed to setup.py - -commit c9eb47e2a18891007418a0cce7c9047711e59d18 -Author: CCook96 <56447505+CCook96@users.noreply.github.com> -Date: Thu Jan 30 22:56:20 2020 +0000 - - PDBWriter ChainID now from last character of segid - Issue #2224 (#2478) - - * fix #2224 - * PDBWriter ChainID now from last character of segid - * Added docstrings, streamlined test code and updated CHANGELOG and AUTHORS - * Update AUTHORS - * Update CHANGELOG - -commit c9731e17286e1e0ca0315f2279459659e12dca89 -Author: Lily Wang -Date: Fri Jan 31 02:36:46 2020 +1100 - - added parmed to setup.py - -commit 4aeaffbb707fbd5c01c737e11ff908f2418494a9 -Author: Irfan Alibay -Date: Thu Jan 30 10:26:07 2020 +0000 - - Chamber-style TOP files user warning (Issue #2475) (#2476) - - * Adds CTITLE check - -commit 2e05ca780a42304ee4ed1e4c969aaa6c651ef6a5 -Author: Matteo Tiberti -Date: Thu Jan 30 11:22:48 2020 +0100 - - Fixes to ENCORE's ClusterCollection and Cluster output (#2473) - - * fixed return of ClusterCollection.get_ids() - - * changed repr of Cluster and ClusterCollection classes - -commit 53f0b0f94baa91a4ec49b8661f5037e7156c2367 -Author: Irfan Alibay -Date: Thu Jan 30 10:21:13 2020 +0000 - - Removes stubs files for v1.0 (#2481) - - * Core removal - - * Remove old import test - - * Removes deprecation tests - - * removed x3dna.py - - * Update CHANGELOG - -commit 59ea579e89c0831e647ba4a1c80c294724ee2070 -Author: Irfan Alibay -Date: Thu Jan 30 10:20:09 2020 +0000 - - Removes degrees support (#2482) - -commit b567168da6cddb342fba53e475753d34438ef248 -Author: Irfan Alibay -Date: Wed Jan 29 09:56:02 2020 +0000 - - GNM MassWeight removal (#2479) - - * remove MassWeight from gnm - -commit 3be5c98271c67ed05bf7f63cfc0cf7d2adef2495 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Jan 28 01:32:42 2020 +1100 - - Modifications to ITPParser (#2408) - - * fixed itp impropers, type parsing - - * added if/else to itpparser - - * generalised ITPParser to ITP and TOP files, so it now reads #include, #define, and stacks #if - -commit 45c967c4b98a6b9e12eb30cd2955603f29ea6406 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Jan 28 01:29:09 2020 +1100 - - ParmEd i/o (#2404) - - * added parmed i/o - - * added parmed dependency - - * added AtomGroup ureybradley and cmap properties - - * added get_converter_for - -commit 93413dc15ff353eb690d5b351a42078ba456e781 -Merge: 22def6adb b5cb49fc0 -Author: Rocco Meli -Date: Fri Jan 24 16:59:09 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit b5cb49fc06c05d4038f75ba98c66dc30f856d303 -Author: Oliver Beckstein -Date: Thu Jan 23 04:59:52 2020 -0700 - - add logo in SVG format (#2459) - - - exported from the PDF in AdobeIllustrator (SVG 1.1.) - -commit 22def6adbc167710db05027672584118a16ba187 -Merge: 3c35af0d4 66f3ac891 -Author: Rocco Meli -Date: Thu Jan 23 11:35:29 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 66f3ac891352badc5e69b5327d2bdb5fd3a7a734 -Author: Lily Wang -Date: Thu Jan 23 12:59:09 2020 +1100 - - changed menu navigation level - -commit 5eaa922e7a5f23506485fd671c03b6299f45e5c1 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Thu Jan 23 18:32:35 2020 +1100 - - Add radius_cut_q as a method to contacts.Contacts (#2458) - - * added radius_cut_q to contacts.Contacts - * used functools.partial for radius_cut - * cleaned q1q2 - * updated changelog - -commit 972a8b1893b5e353b9d796b15d6fcdd022a93f00 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Jan 21 22:11:52 2020 +1100 - - added TopologyObject API (#2382) - - * added add_TopologyObjects - - * added delete_TopologyObject/s - - Co-authored-by: Richard Gowers - -commit 3c35af0d451f9a143dd627f234e9654b49a7703a -Merge: 7d2713803 72ce35ad2 -Author: Rocco Meli -Date: Tue Jan 21 10:16:21 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 72ce35ad213e9266e0a15de1067fa56ab6c5c031 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Jan 21 03:37:22 2020 +1100 - - align.AverageStructure for out-of-memory average structures (#2430) - - * added align.AverageStructure - * added more tests and example - * related to #2039 - -commit 3b7e86e6f3268d1f8596b4015e37d9a4b5991ad1 -Author: Rocco Meli -Date: Sun Jan 19 19:39:04 2020 +0000 - - XYZ elements (#2456) - - - Fixes #2420 - - FIxes #2421 - - Changes made in this Pull Request: - * XYZParser adds elements attribute - * XYZWriter tries to use the atoms.elements attribute (fallback to atoms.names) - - detailed changes - * add element attributes (naive) - * guess mass from names: assumes a standard-conforming XYZ file - * try to get element before atom name - * name change - * add test for elements attribute - * update docstrings - * test XYZ writer using elements if present - * add versionchanged tag - * update changelog - -commit 563bf3dacb66357fbe378529e1412f6176bb71cb -Author: Rocco Meli -Date: Sun Jan 19 19:30:20 2020 +0000 - - Removes explicit use of Bio.Alphabet (deprecation pending) (#2457) - - * remove Bio.Alphabet from align.py: This assumes the standard gap char - - * remove Bio.Alphabet from topologyattrs: use default alphabet - * update changelog - * fix #2448 - -commit 733b6171735cee35dcf667b92f2a692f1229c1ef -Author: Rocco Meli -Date: Sat Jan 18 22:55:57 2020 +0000 - - Typo (#2409) - - * fixed small typo - * add test - * Update base.py - - Co-authored-by: Richard Gowers - -commit 7d2713803f9459d07cb491b45298511acc809080 -Merge: c515e8968 96ba46c8b -Author: Rocco Meli -Date: Sat Jan 18 15:13:46 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 96ba46c8be7e0602a6e20a527b899d8afe6c540a -Author: Rocco Meli -Date: Fri Jan 17 17:08:23 2020 +0000 - - fix indentation (#2454) - - E11? - -commit c515e896878e14dddb41500a57b1e04ffce75e00 -Merge: ff4ed8dc5 7e6e18b6f -Author: Rocco Meli -Date: Fri Jan 17 15:32:17 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 7e6e18b6ff60f59228dc800ea68b4ca512ae8a5d -Author: Rocco Meli -Date: Fri Jan 17 15:23:31 2020 +0000 - - Ignore Emacs backup files and VSCode folder (#2455) - - * move editors to end of gitignore - - * ignore emacs backup files - - * ignore vscode folder - -commit ff4ed8dc5dc50c4750312961e76672a2b750acff -Merge: de7afcc44 509c5b46d -Author: Rocco Meli -Date: Fri Jan 17 11:28:46 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 509c5b46da45560109749d56cfe8fee9c801989a -Author: Rocco Meli -Date: Fri Jan 17 10:38:12 2020 +0000 - - Fixes #2426 (#2451) - - * Added 2016 citation on docstring - -commit de7afcc442216aec7c88a905f849f85ffe3fae57 -Merge: 2184e2bfa d319080ca -Author: Rocco Meli -Date: Thu Jan 16 13:19:24 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit d319080ca3a6d15b165e17d9b6662e044b3487a4 -Author: Tyler Reddy -Date: Tue Jan 14 17:51:55 2020 -0700 - - TST: pin setuptools in Python 2.7 CI - - * pin setuptools to a version < `45.0.0` - in Travis CI Python 2.7 matrix entry to - prevent pulling in newer/unsupported versions - -commit 2184e2bfac5c8bc90148e90fbcf554c6f2d2bb7b -Merge: 2e2561e94 8f384c2ee -Author: Rocco Meli -Date: Tue Jan 14 21:35:05 2020 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 8f384c2eeada398b69cd44b6dc9fa4037c35fb9f -Author: Jonathan Barnoud -Date: Fri Jan 3 14:22:11 2020 +0000 - - Adapt how strings are read in TPR for gmx 2020 - - Addresses a review comment: https://github.com/MDAnalysis/mdanalysis/pull/2431#discussion_r362761479 - -commit 24186c4d31052acd701c34c07c311419624bcf76 -Author: Jonathan Barnoud -Date: Fri Jan 3 13:04:52 2020 +0000 - - Fix python 2 compatibility - -commit 1eeabc2645f2aa723526275db22b02c2041e2111 -Author: Jonathan Barnoud -Date: Thu Jan 2 21:40:30 2020 +0000 - - Remove support for TPR files from gmx 2020-beta - -commit 233441786ba0dcedfb14809f5a54d68aa6864c09 -Author: Jonathan Barnoud -Date: Thu Jan 2 19:12:21 2020 +0000 - - Fix documentation - -commit 797240b9d5e9e76f49173ab517bd76fd4cb55020 -Author: Jonathan Barnoud -Date: Thu Jan 2 18:24:22 2020 +0000 - - Fix compatibility with TPR files from gromacs 2020 - -commit 2a739bb156044b41b5d7e47d01eb846896361e3e -Author: Jonathan Barnoud -Date: Thu Jan 2 10:24:27 2020 +0000 - - Tests for TPR files produced with the first release of gms2020 - - See #2428 - -commit d0d435a8dbdb63ef33d4caa6fdced83a48c48b67 -Author: Tyler Reddy -Date: Wed Jan 8 17:02:12 2020 -0700 - - TST: pin NumPy version for Travis MacOS - - * try pinning the NumPy version used for - the Travis CI MacOS matrix entry, which - is currently failing on master branch - - * at the time of writing, the most - recent NumPy version available from - conda-forge in 1.17.3 - -commit 8990c16b3ad848f1cf98052f9a200e2cccec7124 -Author: Jonathan Barnoud -Date: Sat Jan 4 12:09:50 2020 +0000 - - Remove useless cast - -commit fd4db0ba6a85ffdc2c657e1d91d2b437da30ad6a -Author: Jonathan Barnoud -Date: Sat Jan 4 11:12:00 2020 +0000 - - Update changelog - -commit 4e0c1028c197c3576dfb6d7a82368601da5b009e -Author: Jonathan Barnoud -Date: Sat Jan 4 10:50:09 2020 +0000 - - Convert atom types to string in TXYZ - - Fixes #2435 - -commit cdb21550a902d4cc286e276ed7da8410f53af0a5 -Author: Jonathan Barnoud -Date: Sat Jan 4 09:47:13 2020 +0000 - - Add tests to reproduce #2435 - -commit 74548f25dc4550d86c6a6d0095883a6950175c93 -Author: Jonathan Barnoud -Date: Fri Jan 3 15:59:56 2020 +0000 - - Fix identity comparisons for strings - - Fixes #2432 - -commit d79a2d2365bb5965e5b52cbf8a85668b1bce4a42 -Merge: 4adbd6c01 0cfaf4243 -Author: Tyler Reddy -Date: Wed Dec 25 12:07:35 2019 -0700 - - Merge pull request #2419 from MDAnalysis/bugfix/issue-2413-traj-stride - - Bugfix/issue 2413 traj stride - -commit 2e2561e948a159acebdc167984cd56af7c43d6a6 -Merge: 64bcae5bd 4adbd6c01 -Author: Rocco Meli -Date: Tue Dec 24 00:35:48 2019 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 0cfaf4243199c42eef7e7c476704a67ceb21d4a6 -Author: Jonathan Barnoud -Date: Sat Dec 21 18:11:23 2019 +0000 - - Update CHANGELOG - -commit 629b1dfb68109e05e080205ac71f20516eba9959 -Author: Jonathan Barnoud -Date: Sat Dec 21 18:03:55 2019 +0000 - - Fix issue with trajectory slice sliced with None - - Fixes #2413 - -commit 95f68c25e5f0b88e8a879c9d64a4cde403382ac0 -Author: Jonathan Barnoud -Date: Sun Dec 15 19:15:14 2019 +0000 - - Add a test to reproduce #2413 - -commit 4adbd6c01673fcc9d13d4cd5c9089c1139257a57 -Author: Jonathan Barnoud -Date: Sun Dec 15 10:35:27 2019 +0000 - - Ignore a pylint error in TPR parser - - Pylint does not recognize the mangled attribute and thinks they are not - defined. - -commit 592b41399506beaa013004510ca2a19f68ad8f85 -Author: Jonathan Barnoud -Date: Sun Dec 15 09:34:25 2019 +0000 - - More python2 fix for the TPR parser - -commit 8aa177427243ddd4d860268b2354913d5564d58f -Author: Jonathan Barnoud -Date: Thu Dec 12 07:58:20 2019 +0000 - - Fix compatibility issue with python 2 - -commit 542e1419fbe7229d5b423b189c3646572f71721e -Author: Jonathan Barnoud -Date: Thu Dec 12 07:55:07 2019 +0000 - - Add referende to new virtual site from gmx 2020 - -commit 3e6dfaa1e86c20e9c3a3386ae152a3e2b34020da -Author: Jonathan Barnoud -Date: Wed Dec 11 22:16:05 2019 +0000 - - Update documentation table - -commit 379041560e9343400e3384d1a3fce7eb068fc5d7 -Author: Jonathan Barnoud -Date: Wed Dec 11 22:13:04 2019 +0000 - - Update changelog for TPR from gromacs 2020 - -commit ef051adbfbd4701323c7a564ee88519e5fb2f534 -Author: Jonathan Barnoud -Date: Wed Dec 11 22:08:59 2019 +0000 - - Some cleaning and doc for TPX 119 (gmx 2020) - -commit e0c4d0c3a631104342df3de1ff3b15407ae90bbb -Author: Jonathan Barnoud -Date: Wed Dec 11 21:33:14 2019 +0000 - - Fix compatibility with TPR from gromacs 2020 - -commit 532842e93c5bc4206d9d7f7fb03c2f1b767b4a68 -Author: Jonathan Barnoud -Date: Tue Dec 10 07:58:40 2019 +0000 - - Introduce a new unpacker for TPR files - - Starting with gromacs 2020, the body of TPR files is not encoded in XDR - format. While the API to read the file remains the same, the underlying - encoding is different: instead of using file-byte per data-byte, the new - format uses 4 file-bytes per data-byte, the new format is also - little-endian rather than big-endian like before. - -commit f8a748cccd7722529a4c807fb6ea856218bf1c52 -Author: Jonathan Barnoud -Date: Mon Dec 9 18:42:08 2019 +0000 - - Update the reading of the header for TPR from gmx 2020 - -commit d7b569a898f9805a32803055cfb34209c0746d9e -Author: Jonathan Barnoud -Date: Mon Dec 9 18:10:19 2019 +0000 - - Update settings for TPR produced by gromacs2020 - -commit 491f6c9c4c8787093f6e306d37c429167188a210 -Author: Jonathan Barnoud -Date: Sun Dec 1 17:07:07 2019 +0000 - - Add tests for the TPR parser using files from gromacs 2020 - -commit ab55bb6d2cca323fb71af84521771628515ba636 -Merge: 3bf810062 ffde740b0 -Author: Tyler Reddy -Date: Sat Dec 14 13:40:30 2019 -0700 - - Merge pull request #2416 from tylerjereddy/treddy_py38_windows_ci - - TST: add Windows Python 3.8 to CI - -commit ffde740b008eced30d7c8c9d14c36c45eda19989 -Author: Tyler Reddy -Date: Sat Dec 14 10:56:51 2019 -0700 - - TST: add Windows Python 3.8 to CI - - * update Appveyor configuration to test - Windows/Python 3.8; also remove some - extraneous Appveyor config code related to - Python 2.7 and left-over code from duplicating - an upstream configuration file - -commit 3bf81006284a4996a151a2ea2d3143513eaee275 -Merge: 5a38ee64d 2c409ce48 -Author: Tyler Reddy -Date: Sat Dec 14 04:06:24 2019 -0700 - - Merge pull request #2415 from tylerjereddy/treddy_py38_linux_ci - - TST: add Python 3.8 Linux to CI - -commit 2c409ce488fc265c348b6345d175610a15510bf8 -Author: Tyler Reddy -Date: Thu Dec 12 22:17:14 2019 -0700 - - TST: add Python 3.8 Linux to CI - -commit 64bcae5bde18b2a2cbfc0cfedb92b3150e7c789f -Merge: f7d5bc6ff 5a38ee64d -Author: Rocco Meli -Date: Thu Nov 28 16:36:22 2019 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 5a38ee64d5684e5cfc69f63a70b4af439efae89f -Author: João M.C. Teixeira -Date: Fri Nov 22 18:54:35 2019 -0500 - - Improved exception message for traj file without extension. (#2406) - - * improves exception message for no extension paths and if format is given as empty string - * updates changelog - * add tests - -commit f7d5bc6ff1d6ad1e381eec065aa737576d2a279c -Merge: 2d693e3f6 9834b09f4 -Author: Rocco Meli -Date: Thu Nov 21 22:25:25 2019 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 9834b09f4fb86ad12652cf0d562d7da90c4ee1f2 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Nov 19 07:32:30 2019 +1100 - - Empty TopologyAttrs for missing entries and tests (#2390) - - * fix #2387 - * fix #2389 - * added empty topologyattrs for missing entries - * removed unused code - * more comprehensive test - * updated CHANGELOG - -commit 3b0bdcebd9f087d8b8497815616e53003de6ab2a -Merge: 61eacf7be 05ef9d114 -Author: Oliver Beckstein -Date: Mon Nov 18 13:11:30 2019 -0700 - - Merge pull request #2038 from davidercruz/wrap-unwrap - - Added unwrap/wrap transformations - -commit 61eacf7beaacf842f1b8536fd3b39cf81e9c6201 -Author: Lily Wang -Date: Sat Nov 16 10:42:58 2019 +1100 - - added docs - -commit 66c60be3f6342e280612857cc55f9b5c2bf69558 -Author: Lily Wang -Date: Sat Nov 16 10:39:43 2019 +1100 - - unreshape topologygroup attributes - -commit 615b86b6fb3bf591289ededb8408ecbcf7059309 -Merge: 4b82988b4 8c4af0c54 -Author: Oliver Beckstein -Date: Fri Nov 15 17:49:01 2019 -0700 - - Merge pull request #2399 from lilyminium/api-rtd-theme - - - fixes #2397 - - switched docs theme to user guide theme - -commit 4b82988b4dd2a033003cf247c7c8e55a71797965 -Author: Oliver Beckstein -Date: Thu Nov 14 09:44:20 2019 -0700 - - fixed benchmark for fragment timing - - (useful for #2376) - -commit 05ef9d114f0dd09a9f9cce9a14d31c6471dd4fcf -Merge: 86a90a115 e1101089f -Author: Oliver Beckstein -Date: Thu Nov 14 10:41:41 2019 -0700 - - Merge branch 'develop' into wrap-unwrap - -commit 8c4af0c54a0f7c4e1dfabb9c5c373096ca2d7914 -Author: Lily Wang -Date: Thu Nov 14 14:47:52 2019 +1100 - - orange notes, grey seealso - -commit 7792a39d25313f7bfbb26b48bfbf68f1a4efc4de -Author: Lily Wang -Date: Thu Nov 14 09:00:12 2019 +1100 - - color re-orangement - -commit bf03567209822416538e7d144ad40c963605f749 -Author: Lily Wang -Date: Wed Nov 13 10:01:46 2019 +1100 - - added new colours - -commit 90bb98df26010bd64b19ab5e89ad7dff57eb0278 -Author: Lily Wang -Date: Mon Nov 11 21:19:20 2019 +1100 - - added rtd theme to travis - -commit 232c5a7e0e4d9aac7053a0e5c01866d2065f5430 -Author: Lily Wang -Date: Mon Nov 11 15:03:30 2019 +1100 - - only modify field-lists at top body level - -commit 474508c36bd338b4fbd1ea600d9c130595c59548 -Author: Lily Wang -Date: Mon Nov 11 14:20:19 2019 +1100 - - switched to RTD theme - -commit e1101089ffc7aa58be654f7d0a82840a9d5a7175 -Merge: e12958ca0 fa17fd930 -Author: Richard Gowers -Date: Fri Nov 8 10:33:13 2019 +0000 - - Merge pull request #2391 from PicoCentauri/huge_boxes - - Added correct parsing for huge GRO boxes - -commit fa17fd930ee2dc8190b5d04ae2d5d491e0a823c8 -Merge: 7b97fa1c7 e12958ca0 -Author: Richard Gowers -Date: Fri Nov 8 10:32:22 2019 +0000 - - Merge branch 'develop' into huge_boxes - -commit e12958ca0e6c5700563e236e21023c2b696489b7 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Fri Nov 8 04:01:33 2019 +1100 - - added match_atoms keyword to analysis.align (#2380) - - * Fixes #2285 - * added match_atoms keyword to analysis.align - * added issue - * added test - * removed redundant test - * logged error - * split tests - * moved match_atoms to 0.21.0 - -commit 240586ebcf6e0136384406bb3d10d9def00bff9e -Author: Lily Wang -Date: Thu Nov 7 02:03:53 2019 +1100 - - add CA test - -commit bbe0d26f810647863c61ac5ea03cc2f055861b58 -Author: Lily Wang -Date: Thu Nov 7 01:59:44 2019 +1100 - - guess zinc properly - -commit 971248a1cf099f26db899b899a8e10d4e96ac3cd -Author: Lily Wang -Date: Thu Oct 31 09:26:42 2019 +1100 - - added doc stub - -commit 139de3f352dddaa82becd68e1cb0968aa6b4220b -Author: Lily Wang -Date: Wed Oct 30 09:38:06 2019 +1100 - - added files to testsuite - -commit 290730eec6d919682231cbf2669325b3ceae90ec -Author: Lily Wang -Date: Tue Oct 29 11:48:19 2019 +1100 - - added connectivity types - -commit e5c913f68fd34ddf750f87f7a880f10e1bdb1ab0 -Author: Lily Wang -Date: Tue Oct 29 09:52:28 2019 +1100 - - updated links - -commit 2acd2b632b172b0bc5779974887f8c1837ebaa08 -Author: Lily Wang -Date: Tue Oct 29 09:12:09 2019 +1100 - - updated docs - -commit af8931ffdef5e841cc39b980e3abb1b7d9ee0e9b -Author: Lily Wang -Date: Tue Oct 29 09:04:59 2019 +1100 - - wrote ITPParser - -commit 7b97fa1c769cba819d888ea4b0a87690bd19c5b8 -Merge: f14622a1d 7f82b88f7 -Author: Richard Gowers -Date: Wed Nov 6 14:41:59 2019 +0000 - - Merge branch 'develop' into huge_boxes - -commit 7f82b88f769f3882e44b5121463c93b899ef5b55 -Author: João M.C. Teixeira -Date: Tue Nov 5 17:18:44 2019 -0500 - - Improved Exception handling (#2357) - - * implemented uniform exception reporting between Python 2.7 and Python 3: - re-raised exceptions do not show the original exception - * from None in custom exceptions - * use six.raise_from() for compatibility - * updated CHANGELOG - * added to AUTHORS - -commit f14622a1d52632f55f1731f135f696f8e9a74064 -Author: Philip Loche -Date: Tue Nov 5 21:51:16 2019 +0100 - - Be less strict on precision - -commit 594c0288c7802d14243f760f88d7e0ccb1bb3852 -Author: Philip Loche -Date: Wed Oct 23 20:25:27 2019 +0200 - - Added correct parsing for huge GRO boxes - -commit 5b477f6f1724d060c063f4ebacacc206240dca93 -Author: Richard Gowers -Date: Fri Nov 1 18:00:19 2019 +0000 - - Update universe.py - -commit e811ab9678e2ad2b7fc5f43765470152e580f1b3 -Author: Lily Wang -Date: Fri Nov 1 13:54:22 2019 +1100 - - check len array - -commit 09490b3eed0c8f4f0072fa035372bd72659c21de -Author: Lily Wang -Date: Thu Oct 31 10:23:47 2019 +1100 - - updated CHANGELOG - -commit 250a674bb6db702a88dfbbeabce3da7b5f4aedaf -Author: Lily Wang -Date: Thu Oct 31 10:21:28 2019 +1100 - - added test - -commit 13c7e65a3b3c4bde078fcff965e6124bd0275feb -Author: Lily Wang -Date: Wed Oct 30 18:39:16 2019 +1100 - - added empty universe - -commit 2d693e3f63d0df298b0923bd13f3e475aeeba1f6 -Merge: def7c14ca 2501d3e01 -Author: Rocco Meli -Date: Wed Oct 30 11:04:35 2019 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 2501d3e014943286dcb123139e3028988c61718f -Author: Bradley Dice -Date: Wed Oct 30 00:38:57 2019 -0400 - - Update CHANGELOG. - -commit 964f8df54be0f719468f3ecda2f24c4d6a77656f -Author: Bradley Dice -Date: Wed Oct 30 00:23:56 2019 -0400 - - Update GSD tests to run on Windows. - -commit 4f6edbaabc6e34436c3836c8fd971e9f86897103 -Author: Bradley Dice -Date: Wed Oct 30 00:23:27 2019 -0400 - - Require gsd>=1.9.3 on Windows (previous versions lacked proper Windows support when installed via pip). - -commit 0a99d38eddd7533ef471f7013c154ed55d7f105f -Author: Bradley Dice -Date: Wed Oct 30 00:22:41 2019 -0400 - - Remove conditional Windows errors from GSD topology reader. - -commit 68a252afd70f9f532eb9e0fa0392cd014bcbec7a -Author: Bradley Dice -Date: Wed Oct 30 00:21:55 2019 -0400 - - Remove conditional Windows errors from GSD coordinate reader. - -commit 1a3cefd5843e681e3dd995abaeef94b236acf454 -Author: Bradley Dice -Date: Wed Oct 30 00:21:21 2019 -0400 - - Update gsd version in Appveyor. - -commit dc67acfcd6eebdf8550b5cc05f745b3e6e1998c9 -Merge: 54a7addd3 bdfdf159f -Author: Oliver Beckstein -Date: Tue Oct 29 13:25:32 2019 -0700 - - Merge pull request #2237 from p-j-smith/hbond_analysis - - new Hbond analysis - -commit bdfdf159f255feb8105588da5eec10e4a5b8eb4e -Merge: 21c256358 54a7addd3 -Author: Oliver Beckstein -Date: Mon Oct 28 16:08:09 2019 -0700 - - Version update to 0.21.0 - -commit 54a7addd3630566364b6f59c1f9c12f613b45c14 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Sat Oct 26 00:36:32 2019 +1100 - - removed unintended changes - -commit a77ce8d7bb9ecb36cd610591764f23550723c257 -Author: Lily Wang -Date: Fri Oct 25 23:01:34 2019 +1100 - - added icodes to pdbqtparser - -commit f044278edbe2b2c8ff092dd60b633308cbcc06a0 -Author: Lily Wang -Date: Mon Oct 28 12:08:47 2019 +1100 - - added type checking to Connections - -commit 530bb513bed018ce2f8b9ff08712dae596bb6329 -Author: Lily Wang -Date: Mon Oct 28 11:58:45 2019 +1100 - - expanded tests - -commit 1cddc1226d70abd52da2b8904bb2a18a8e6aae7e -Author: Lily Wang -Date: Mon Oct 28 11:49:13 2019 +1100 - - added type check to connections - -commit 6f88517f92e22d39206f815e8106b529699d8f2e -Author: Lily Wang -Date: Sun Oct 27 14:16:47 2019 +1100 - - commented test - -commit 30fc5c0136501397d890614fc248f13d8a46f487 -Author: Lily Wang -Date: Sun Oct 27 14:13:20 2019 +1100 - - expanded wildcard selections - -commit 21c256358a86f3e856ab677f8e2edce9eda927dd -Author: Paul Smith -Date: Sat Oct 26 15:04:48 2019 +0100 - - Updated the CHANGELOG - -commit c77382364be576edba92ab48b0d7c08657d031d0 -Author: Paul Smith -Date: Sat Oct 26 15:04:37 2019 +0100 - - Updated the documentation - -commit f50305c690c18961048183d474c26575ad84dfde -Author: Paul Smith -Date: Sat Oct 26 15:03:22 2019 +0100 - - Added deprecation warnings for the original implementation. - - Added warnings to :mod:`MDAnalysis.analysis.hbonds.hbond_analysis` and - :class:`MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis` - -commit d21ae194ab8848be726b32cb92c83ef10e401664 -Author: Paul Smith -Date: Sat Oct 26 15:03:00 2019 +0100 - - Added for the original implementation of the hbond analysis. - - New regression test added to directly compare the behaviour of the - original implementation with the new one. - -commit 54872daa3017c1aba1d732567bd2f86fad40fed8 -Author: Paul Smith -Date: Sat Oct 26 15:02:28 2019 +0100 - - Added tests for the new HydrogenBondAnalysis class. - - The tests are based on those for the original implementation of the - hydrogen bond analysis, which allows for direct comparison of the - results to ensure the behaviour of the new class is correct. - -commit eb2dfea54c6832c8906926d6a294aad16882e8b2 -Author: Paul Smith -Date: Sat Oct 26 15:01:23 2019 +0100 - - New implementation of the HydrogenBondAnalysis class. - - The class itself and the run() method have both been simplified in - comparison to the original implementation. - The detection of hydrogen bonds has been optimised using the - MDAnalysis.lib.distances.capped_distance() method. - For loops have been replaced by vectorised numpy code. - The data from run() is stored in a numpy.ndarray in the 'tidy data' - format suggested in Issue MDAnalysis#2177. - -commit 86a90a115964f4bf234b5a4f9549ebb05622f7f6 -Author: Davide Cruz -Date: Thu Aug 9 22:32:23 2018 +0100 - - added wrap/unwrap transformations - - - simple wrap/unwrap transformations (needs fragments) - - compound tests are now done on multiple segment universes - - added docs - - updated changelog - new feature wrap transformation in 0.21.0. - -commit 9372d093acebb78bc5b1a2b4dba815a4e3281b04 -Merge: 0cc020c89 5e546107f -Author: Oliver Beckstein -Date: Thu Oct 17 09:25:11 2019 -0700 - - Merge pull request #2365 from kain88-de/fix-2353 - - FIX 2353: Chainreader not reporting correct errors - -commit def7c14cad13f3bf2b980b521ff8a7966461d5ef -Merge: ad0c14951 0cc020c89 -Author: Rocco Meli -Date: Wed Oct 16 11:55:49 2019 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 5e546107ffdc8bbe74b3416662e75b171f13b9fe -Author: Max Linke -Date: Sun Oct 13 22:05:56 2019 +0200 - - FIX 2353: - - If using a chainreader with continuous=True and a reader like the PDB - reader report a correct error for usage to the reader. - -commit 0cc020c89c8dea89ff8934b79cbbeb429ee780b9 -Merge: 5ff1c2455 eeb567ae8 -Author: Oliver Beckstein -Date: Mon Oct 14 20:09:04 2019 -0700 - - Merge pull request #2366 from kain88-de/fix-numpy-fault - - fix numpy for python 2.7 builds - -commit eeb567ae87551a8d0208ce573b13491dcf6e58a6 -Author: Oliver Beckstein -Date: Mon Oct 14 16:05:03 2019 -0700 - - disable macOS Python 2.7 (times out) - -commit 08b0deeed1a8617beb79628abf19296681e55cd0 -Author: Max Linke -Date: Mon Oct 14 19:59:43 2019 +0200 - - fix numpy for python 2.7 builds - -commit 5ff1c24550d5b717d72d695fee70314bac608e3f -Author: Oliver Beckstein -Date: Thu Oct 3 10:02:46 2019 -0700 - - disable pylint warning for some E1136(unsubscriptable-object) - - Recent updates of pylint now flag some constructs with E1136 which - in fact are perfectably subscriptable. Apparently, some numpy - constructs are not recognized as producing arrays. The additions - in this PR disable the warning for the relevant code blocks. - -commit ad0c14951fd9feb2a81794f07714414c10224e3c -Merge: 51111031c 663776c4e -Author: Rocco Meli -Date: Thu Oct 3 09:26:22 2019 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 663776c4e21060505b24efd7788ffe4ad54412ed -Merge: a114b6b5d e33a0889b -Author: Matteo Tiberti -Date: Thu Oct 3 09:10:30 2019 +0200 - - Merge pull request #2301 from mjtadema/develop - - Added argument to get_distance_matrix to change the 'max_nbytes' parameter of joblib.Parallel - -commit 51111031cdd42d6f80a1604cc38bf9421fe585de -Merge: 36fa2eac7 a114b6b5d -Author: Rocco Meli -Date: Wed Oct 2 20:17:33 2019 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit a114b6b5d5f062bf1c3cedac96f026e187c54ccd -Merge: bb239f94c c83442426 -Author: Oliver Beckstein -Date: Mon Sep 30 23:38:18 2019 -0700 - - Merge pull request #2351 from MDAnalysis/issue-2350-guess_bonds_periodic - - fixes Issue #2350 - -commit bb239f94c4f4313a66746ac5d76cf43c7e27c7a7 -Author: Michael Gecht -Date: Thu Sep 26 14:31:38 2019 +0200 - - fix: docstring typo and indent - -commit e8df31e7ebf84ad2bdacd58530ee76903f594145 -Merge: d1b0e6593 5db11b6af -Author: Oliver Beckstein -Date: Wed Sep 25 15:02:50 2019 -0700 - - Merge pull request #2335 from lilyminium/format-chainreader - - Allow ChainReader to accept format keyword - -commit 5db11b6af4676f447d284833ef6d06d3fe8f27f9 -Author: Lily Wang -Date: Sun Sep 22 15:46:44 2019 +1000 - - added tests and typeerror - -commit c83442426a16f60744d046f99fda1fc9ecc0f08e -Author: richardjgowers -Date: Tue Sep 17 16:50:00 2019 +0100 - - fixes Issue #2350 - - AtomGroup.guess_bonds now uses periodic boundary information where available - -commit 36fa2eac7f33129a5773a574c55dc643d98ce1f0 -Merge: 80370af95 d1b0e6593 -Author: Rocco Meli -Date: Tue Sep 10 16:37:13 2019 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit d1b0e659329b1d98fc2422c88614a196976f3497 -Author: richardjgowers -Date: Thu Sep 5 18:20:36 2019 +0100 - - started version 0.20.2 - -commit df914698c560e7c62d46803abfe8aa23f02ab823 -Author: richardjgowers -Date: Thu Sep 5 18:02:05 2019 +0100 - - finalised v0.20.1 release - -commit ee4759293e1a4a5109c6b66e133acb1af7d24b0d (tag: release-0.20.1) -Merge: 7c468a463 e5e4f5e32 -Author: richardjgowers -Date: Thu Sep 5 18:04:03 2019 +0100 - - Merge branch 'develop' - -commit e5e4f5e323e79c49a4a840909c0ef6fe8935236d -Author: richardjgowers -Date: Thu Sep 5 18:02:05 2019 +0100 - - finalised v0.20.1 release - -commit e9ac561c9ff61ae914830ac5a9c6792a87add0ff -Author: richardjgowers -Date: Wed Sep 4 19:05:25 2019 +0100 - - fixes Issue #2337 - - Release builds without cython should now work - -commit 80370af95453a1acc107c9bb0afd944418b78316 -Merge: 94ac6cc0d 1e8167c6d -Author: Rocco Meli -Date: Thu Sep 5 17:51:41 2019 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 1e8167c6d292fef062dc5e5f98ceda4d7fabe3ca -Author: Irfan -Date: Wed Sep 4 19:42:51 2019 +0100 - - Switches units test to DLP_CONFIG and removes duplicate test - -commit 6bb195924919e7ad56e68b5ee84f6dca70fe9657 -Author: Irfan -Date: Wed Sep 4 17:51:20 2019 +0100 - - Changes cell_angle units to degree - -commit e33a0889b0b638ce49b43a1eff16ab7e7db4ec53 -Author: Matteo Tiberti -Date: Mon Sep 2 16:43:59 2019 +0200 - - bumped minimum version of joblib to 0.12 in Travis - -commit f1253ba0076d45f414fa6347c1ee744f7801a319 -Author: richardjgowers -Date: Wed Aug 28 22:49:36 2019 +0100 - - started version 0.20.1 - -commit 80605265e9cf265ad69fbe588cf4b1740ef27e15 -Author: richardjgowers -Date: Wed Aug 28 21:55:37 2019 +0100 - - updated version to 0.20.0 release - -commit e524f192b68a94043df7ac3aff566b70426a3ea1 -Author: richardjgowers -Date: Wed Aug 28 21:53:38 2019 +0100 - - finalised release date of v0.20.0 - -commit 7c468a46344d17f91d44059332fcc533dad01cde (tag: release-0.20.0) -Author: richardjgowers -Date: Wed Aug 28 22:01:57 2019 +0100 - - updated C/Cpp sources for v0.20.0 - -commit cdb96fff744c79aca1830e685a4a4d8d1e644ce1 -Merge: 5c19974c4 4f469462f -Author: richardjgowers -Date: Wed Aug 28 21:57:51 2019 +0100 - - Merge branch 'develop' - -commit 4f469462f1f85a5845d63aab69cd8d372301104d -Author: richardjgowers -Date: Wed Aug 28 21:55:37 2019 +0100 - - updated version to 0.20.0 release - -commit 074a4e1154e3aa83c5b78b8aee07a505652ae7d1 -Author: richardjgowers -Date: Wed Aug 28 21:53:38 2019 +0100 - - finalised release date of v0.20.0 - -commit e059c92fb678c821f4928e8a667cbda86690e363 -Author: Rocco Meli -Date: Wed Aug 28 21:47:02 2019 +0100 - - Try uppercase atom names when guessing the mass (#2331) - -commit aa25af1ad6975e528e30d473813f870914a2ef4a -Author: Matthijs Tadema -Date: Fri Aug 23 15:57:59 2019 +0200 - - Added back max_nbytes as a user-selectable parameter. Defaults to None - -commit 5cb42a7114bf9eaef6205efb9f4aa1be6dd81680 -Author: Matthijs Tadema -Date: Fri Aug 23 15:48:01 2019 +0200 - - Changed prefer=threads to require=sharedmem. Require sharedmem will limit the backend to a thread based one anyway so prefer threads is not required anymore. - -commit 440f086a6e9ddffa9fdf995d2fa4103dc2b3ef62 -Author: Matthijs Tadema -Date: Fri Aug 23 15:43:24 2019 +0200 - - Bumped up minimum joblib version to 0.12 - -commit 057c156d67486ec550d4bf158d1c4eb8eb5fd522 -Merge: 3a5d9f5e4 57bc1838c -Author: Oliver Beckstein -Date: Thu Aug 22 11:05:43 2019 -0700 - - Merge branch 'develop' into develop - -commit 36834a2be937d8e1927661d1e1fabe3503df100c -Author: Lily Wang -Date: Thu Aug 22 18:36:35 2019 +1000 - - added general error - -commit e64e8f159e7113d0f66ee1cb60f7e5cb69c30b9b -Author: Lily Wang -Date: Thu Aug 22 18:08:07 2019 +1000 - - added explicit format to ChainReader - -commit 94ac6cc0d4637d86ef3eafa5436489c7016112a6 -Merge: fa7777e63 57bc1838c -Author: Rocco Meli -Date: Tue Aug 20 14:48:30 2019 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 57bc1838c3bbe043860573a3df11dda1d490d424 -Author: Lily Wang <31115101+lilyminium@users.noreply.github.com> -Date: Tue Aug 20 19:43:30 2019 +1000 - - Guess element (#2314) - - * updated guessing elements - -commit b7a8590dcf77eac4e4381e19ac4edba4251aad31 -Author: Irfan Alibay -Date: Tue Aug 20 00:50:55 2019 +0100 - - Fixes velocity units and adds support for scale_factors in NCDFReader (#2326) - - * Fixes #2323 - * Now checks for presence of scale_factor in all AMBER NetCDF convention variables - * Adds support for scale_factor values, set in NCDFReader __init__ and multiplied through in _read_frame. - * assumes/uses AKMA velocity scaling by default (as produced by AMBER) - * Implements several new exception checks, mainly revolving around ensuring that units are properly adhered to. - * Also included in this PR is part framework for the introduction of an NCRST file reader (singleframe version of the NCDFReader for .ncrst files). These can be seen in the _NCDFGenerator class of test_netcdf.py - * Update changelog - * DeprecationWarning (1.0) if NCDF file uses units "degrees" instead of correct "degree" for attribute "cell_angle" (MDA < 0.20.0 would write degrees (see #2327), we will now correct these units and from 1.0 onwards raise an error if we encounter degrees instead of degree) - -commit 9b227a8d3b59486cc0315663a598e6c014e5af59 -Author: Irfan Alibay -Date: Mon Aug 19 12:36:22 2019 +0100 - - Swap match_expr for match, raise pytest minimum version (#2330) - -commit fa7777e632540d90448eaaa4ed52c99af83f7e18 -Merge: 51624f3b0 e910a12b6 -Author: Rocco Meli -Date: Tue Aug 13 12:37:32 2019 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit e910a12b67ffe298cf03721bb3d41d7e8a380be4 -Author: Zhiyi Wu -Date: Tue Aug 13 06:10:58 2019 +0100 - - Move the water bridge analysis to the new analysis class (PR #2087) - - * Move the water bridge analysis to the new analysis class as defined in #719 - * add high Order water bridge support – see PR #2087 - * Add a brief theory session to the docs - * Add additional tests for water bridges - * Add hydrogen bond testing to the water bridge test cases - * Update CHANGELOG - -commit b39796e941a6ff566c95298075a61fc220df95a3 -Author: Rocco Meli -Date: Mon Aug 12 14:43:50 2019 +0100 - - Fixes PDBWriter and PDBReader newlines for PDB header (#2325) - - * strip trajectory header of spaces and newlines - -commit 51624f3b00d0077fb9f4ce5911646e2ee35f1561 -Merge: 7af33520e 78540119b -Author: Rocco Meli -Date: Fri Aug 9 14:09:08 2019 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 78540119b3137f8407a31a95dd1cca0c79ceef19 -Author: Irfan Alibay -Date: Fri Aug 9 11:03:44 2019 +0100 - - Unpin GSD from version 1.7.0 (#2321) - - * Unpin GSD 1.7.0 - - * Revert "Pin gsd to v1.7.0" - -commit e071ef437a303d2c3310e96810970d257dd7dbd2 -Author: Rocco Meli -Date: Thu Aug 8 01:14:02 2019 +0100 - - mol2 bugfix for #2318 (#2319) - - * fix #2318 - * Ignore MOL2 status bit strings if present - * add breaking test - * update datafiles.py - * updated authors and changelog - -commit 8cd80d14ac0298251325636363c0e65d47224897 -Merge: 165d2e485 8551c4793 -Author: Oliver Beckstein -Date: Wed Aug 7 17:08:02 2019 -0700 - - Merge pull request #2320 from IAlibay/GSD1.7.0 - - Temporarily pin GSD to 1.7.0 (py2.7 failures) - -commit 8551c479340f5156a6e16bab6d7dee5ff81316a4 -Author: Irfan -Date: Wed Aug 7 18:49:31 2019 +0100 - - Temporary pin comments - -commit 7af33520e071c9684b2d9cf98c2d76b8f8d2ade1 -Merge: 67aa3b720 165d2e485 -Author: Rocco Meli -Date: Wed Aug 7 18:41:05 2019 +0100 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 165d2e485d91db2672762ef0f753c164d0b56e75 -Merge: 16aaad181 74a4426f5 -Author: Oliver Beckstein -Date: Wed Aug 7 10:24:15 2019 -0700 - - Merge pull request #2310 from IAlibay/PMFix - - Fixes PM issues (jlab and non-AnalysisBase) - -commit bced247e1964586b36248ab81afd2469ff86a9b5 -Author: Irfan -Date: Wed Aug 7 18:05:43 2019 +0100 - - Pin gsd to v1.7.0 - -commit 16aaad181b65baf0fc8d6a4dcffe66f28131b456 -Author: Irfan Alibay -Date: Wed Aug 7 13:42:26 2019 +0100 - - Index selection (#2316) - - * Adds index selection keywords - -commit 67aa3b7208056039672bde8ef23c5b9be9d0f452 -Merge: 7449a38eb f89f76170 -Author: Tyler Reddy -Date: Fri Aug 2 19:41:57 2019 -0600 - - Merge pull request #2312 from MDAnalysis/appveyor-old-miniconda-2311 - - use older miniconda for appveyor - -commit f89f76170a3784a376e66acbabb77e18901382a9 -Author: Oliver Beckstein -Date: Fri Aug 2 16:13:20 2019 -0700 - - removed outdated image from appveyor config - - See https://github.com/astropy/ci-helpers/issues/369 and PR https://github.com/astropy/ci-helpers/pull/377 - -commit bd1c1748eead12310a062c2e373c74f4889c5521 -Author: Oliver Beckstein -Date: Fri Aug 2 16:09:47 2019 -0700 - - use older miniconda for appveyor - - - fix #2311 - - temporary fix (until https://github.com/astropy/ci-helpers/issues/406 properly addresses the issue) - -commit 74a4426f50c7ef5749f0143ba4984aff1f6829af -Merge: 05849eba4 7449a38eb -Author: IAlibay -Date: Fri Aug 2 23:11:01 2019 +0100 - - Merge branch 'develop' into PMFix - -commit 05849eba41e9e6e7a2f16f4811cc0a5bd8eef1ab -Author: IAlibay -Date: Fri Aug 2 23:08:22 2019 +0100 - - Replace FinishTimeException with ValueError - -commit 7449a38ebdaa80f7bf4df400df7855d83a5a7037 -Author: Irfan Alibay -Date: Fri Aug 2 20:38:33 2019 +0100 - - Parsing negative values in ATOMIC_NUMBER records of AMBER topologies (#2307) - - * Negative values in the ATOMIC_NUMBER records are now read by guessing the atom element using `guessers.guess_atom_element`. - * Switch for dummy atoms ("DUMMY" as element) - * DUMMY atm guess + tests - * Changelog update - * Tests for new TOPParser warnings - * fixes #2306 - * element guesses in the Amber parser now output user warnings (for #2222) - -commit 44bf4bd2743ecc4f94a700ac59b114b2dbdfdda8 -Author: IAlibay -Date: Fri Aug 2 20:04:48 2019 +0100 - - Changelog update - -commit 152f6ac783bde4ac6de6313628762afadf0c66c0 -Author: IAlibay -Date: Fri Aug 2 18:59:04 2019 +0100 - - Fixes PM issues for non-base class analysis methods - -commit 89a9514e901ff4e16b93b4244d52379f667b7cf8 -Author: Abhishek Kognole -Date: Tue Jul 23 17:58:06 2019 -0400 - - fixed nucleic acid analysis for Chi torsion calculation (#2304) - - * fixed nucleic acid analysis for Chi dihedral calculation - * Updated tests, authors and changelog - -commit 3a5d9f5e42b1f398ee8de9a6bbeb0106a1ae689c -Author: Matthijs Tadema -Date: Wed Jul 17 17:27:14 2019 +0200 - - Update confdistmatrix.py - - Removed `max_nbytes` parameter - Added `prefer='threads'` to call to joblist.Parallel - The treading backend gets rid of the memory sharing problem and seems to have less overhead. - -commit 0c86533c1be76e0baf6980759a40a0b7e438dbf5 -Author: Matthijs Tadema -Date: Wed Jul 17 14:15:38 2019 +0200 - - Update CHANGELOG - -commit 281177f9d94afacb58834585c84aeda51c97e42b -Author: Matthijs Tadema -Date: Wed Jul 17 14:12:10 2019 +0200 - - Update documentation - -commit af8e0183f3a310ed35193efa52edf494cb2604c2 -Author: Matthijs Tadema -Date: Wed Jul 17 13:34:28 2019 +0200 - - Update AUTHORS - -commit fccfc24d0704aad774111f93111774eb5632a10d -Author: Oliver Beckstein -Date: Wed Jul 17 03:40:23 2019 -0700 - - updated docs for transformations (#2302) - - - made clear that MDAnalysis.transformations needs to be imported - - define what a "transformation" and a "workflow" is - - more structure - - removed docs from transformations/__init__.py: they are not used - and text was repeated in trajectory_transformation.rst; only minimal - docs are left so that help() shows something - - close #2246 - -commit b387296c8110c62c397155b2e49b99c38d8d14a3 -Author: Matthijs Tadema -Date: Tue Jul 16 14:56:55 2019 +0200 - - Added argument to get_distance_matrix to change the 'max_nbytes' parameter of joblib.Parallel. By default this is set to '1M', but raises a 'destination is read-only' exception in some cases. I am not sure why, but increasing the max_nbytes seems to fix the problem - -commit b1c68e4bfcdfaa2230121e28783e1c67469ac040 -Merge: 6185a57ca df3684c92 -Author: Tyler Reddy -Date: Wed Jul 10 10:10:14 2019 -0600 - - Merge pull request #1991 from davidercruz/fitting-transforms - - Added fitting transformations - -commit 6185a57cac4d17eb1d98fe5b7114665fe7ad8a2b -Author: Ninad -Date: Wed Jul 10 16:28:09 2019 +0530 - - Adds unwrap keyword to Asphericity method (#2290) - -commit df3684c921c538e5c4df3bb42fda3ea9780f3f44 -Author: Tyler Reddy -Date: Tue Jun 11 19:35:38 2019 -0700 - - MAINT: final reviewer adjustments in PR 1991 - - * just minor DOC adjustments noticed in a final - review - -commit cdc1205cf779bf095bfef71b36efde182b0b1219 -Author: Tyler Reddy -Date: Sun Apr 28 16:01:12 2019 -0700 - - MAINT: reviewer adjusts PR 1991 - - * test_fit.py now uses proper __future__ imports, - which should alleviate code style / linting issues - for old style division - - * test_fit.py adjusted to bump coverage of fit.py to - 100 % - -commit e5fef8e56da92605cca9516ff85735b23454f3cc -Author: Davide Cruz -Date: Sat Jul 28 17:57:27 2018 +0100 - - improved docs - -commit 408243a27274f80667af85fb49b4d8a7ed0ec880 -Author: Davide Cruz -Date: Thu Jul 26 18:06:45 2018 +0100 - - added plane tests - -commit 9f7791e6a1809e9b5f8f8059cab4482a4d723be2 -Author: Davide Cruz -Date: Tue Jul 24 22:55:58 2018 +0100 - - corrected plane rot+trans fitting; removed alignto - -commit a0390ac89149aa87cb8529b55cb0f8545189660b -Author: Davide Cruz -Date: Wed Jul 18 20:23:24 2018 +0100 - - corrected some errors in fit_rot_trans ; added more tests - -commit 5a702d3caaa83ada1e5b6baee5d3628bf083387a -Author: Davide Cruz -Date: Tue Jul 17 23:14:37 2018 +0100 - - updated __init__ - -commit ce3ac2ba55c741c3130a11b20ff2436718725621 -Author: Davide Cruz -Date: Tue Jul 17 23:12:35 2018 +0100 - - added rotation+translation fitting with plane support - -commit 09c8aaefc2a132358d4dc4db3e3c035d5acab07c -Author: Davide Cruz -Date: Tue Jul 17 13:03:01 2018 +0100 - - added transformations based on alignto ; added translations fitting transformation - -commit 2f878525fab9873df02bf9ef891dbbb395432e35 -Author: Ninad -Date: Tue Jul 9 15:28:06 2019 +0530 - - Adds unwrap keyword to moment of inertia (#2288) - -commit 8dd88cc7ab32da226aae4c1dee44829f6bc7f62f -Author: Richard Gowers -Date: Mon Jul 8 15:34:52 2019 +0100 - - fixed GRO file reading (#2277) - - - * added docs clarifying single-frame-ness of GROReader - -commit 90232931b4327ae5041520aee9aec78befc5caf4 -Author: Ninad -Date: Sat Jul 6 17:13:54 2019 +0530 - - Adds unwrap keyword to center_of_mass (#2286) - -commit 8212fc76ef321dc3798aabfd432b861fa679b3b7 -Author: Ninad -Date: Thu Jul 4 14:06:37 2019 +0530 - - Add unwrap to Group.COG (#2279) - -commit f3e45692a1b55260721654e8b6a47db26d63d9ef -Author: Ninad -Date: Wed Jul 3 21:18:29 2019 +0530 - - Adds Unwrap keyword to center (#2275) - - - * Adds check_pbc_and_unwrap Decorator - -commit 66038c772c1c045d690d2b0ab32e073e01f6ee14 -Merge: b0c70cd71 3e84e818e -Author: Oliver Beckstein -Date: Wed Jul 3 11:22:03 2019 -0400 - - Merge pull request #2284 from MDAnalysis/issue-2232-psf_bz2 - - Issue 2232 psf bz2 - -commit 3e84e818e9e9449687108ac9f46ed56c698e8739 -Author: richardjgowers -Date: Wed Jul 3 11:59:28 2019 +0100 - - fixed py2.7 not liking Path objects - -commit f94d35fb75dd7a2f2b2140f9bf61ddf819f54b64 -Author: richardjgowers -Date: Wed Jul 3 10:49:55 2019 +0100 - - fixes issue 2232 - - can now read bz2 compressed psf files - -commit fbd87d03b8d670b5253da5dd1a20ddc5dc579d59 -Author: richardjgowers -Date: Wed Jul 3 10:45:26 2019 +0100 - - tests for issue 2232 - -commit b0c70cd713d7139534230043dba150edbad1039f -Author: Tyler Reddy -Date: Mon Jul 1 02:24:41 2019 -0600 - - MAINT: bumpy minimum NumPy required to 1.13.3 (#2283) - -commit c820cc5143c504d06680b5e3fa42a3eb495c7be7 -Author: Richard Gowers -Date: Thu Jun 20 14:19:31 2019 +0100 - - fixed example of group.intersection (#2281) - - issue #2280 - -commit f83498ec6b5cc546a0d75598a4d1d6ede6fe2782 -Author: Irfan Alibay -Date: Fri May 10 09:44:29 2019 +0100 - - Allow for comments in mol2 file headers (#2262) - -commit 75078ec1aa97ba09f416889f7709096d86f545cf -Author: Oliver Beckstein -Date: Tue May 7 13:51:25 2019 -0700 - - add missing files to the ag_methods benchmark - - - fix MDAnalysis/benchmarks#10 - - add PSF, DCD - - add TRZ_psf, TRZ - -commit 1ea4a574134230ccac302bcdd33c5419d0ac1fe7 -Author: Mateusz Bieniek -Date: Sat May 4 10:47:03 2019 +0100 - - Added fixtures and refactored variable names. - -commit 2196bbdcb4f44d0353c72cb4f3d8bdded2693606 -Author: Tyler Reddy -Date: Sun Apr 28 17:09:24 2019 -0700 - - MAINT: compensate for NumPy load change - - * upstream changes to np.load now require - us to specify allow_pickle=True in encore - machinery - -commit c7c394e68ff862c2002a52d3b55e5bed965df32c -Author: Richard Gowers -Date: Sun Apr 21 10:01:53 2019 +0100 - - Make cython linetrace off by default - -commit 367cc60f4ec41ab4e776fe83189e4aac74677249 -Author: Fenil Suchak -Date: Sat Apr 20 19:34:44 2019 +0530 - - embedseg=False - -commit 26561ad8ad5611da437bca52536ea25082e00762 -Author: Fenil Suchak -Date: Sat Apr 20 10:36:48 2019 +0530 - - editable install travis - -commit c873b086389270f425a754ba962ca936a89b6455 -Author: Fenil Suchak -Date: Thu Apr 18 16:03:26 2019 +0530 - - remove build files - -commit da4979d2db19f0dc93fe27ecca966f5b91310482 -Author: Richard Gowers -Date: Thu Apr 18 19:32:25 2019 +0100 - - Issue 2252 pdb missing cryst (#2253) - - * fixes Issue-2252 - -commit fdeb7242017b57fd01644d6626d2c9524feff452 -Author: Oliver Beckstein -Date: Wed Apr 17 08:00:34 2019 -0700 - - re-encrypted the GH_TOKEN for doc deployment (#2250) - - * re-encrypted the GH_TOKEN for doc deployment - - travis encrypt "GH_TOKEN=" - - fix #2249 - - * set GH_TOKEN on travis-ci.com - - see https://docs.travis-ci.com/user/environment-variables/#defining-variables-in-repository-settings - - * Revert "set GH_TOKEN on travis-ci.com" - - This reverts commit 559318676f032aaf50d8612c77cca8077b7bb22f. - - * encrypted GH_TOKEN with the procedure for travis-ci.com - - Followed https://docs.travis-ci.com/user/encryption-keys/#usage - to do - - travis login --pro - travis encrypt --com 'GH_TOKEN=' - -commit da5f93428f576f95379e4e971c5ca71815fbdfd5 -Merge: 50c32a09f b49a6b001 -Author: Oliver Beckstein -Date: Thu Apr 11 15:49:04 2019 -0700 - - Merge pull request #2239 from sseyler/more-psa-tests - - - Addresses failure of `test_load()` in PSA (#2049) - - Increases test coverage in PSA module (fix #1006) - -commit 50c32a09f4152873f0f6c4dc3f53f67de85f0872 -Author: Richard Gowers -Date: Thu Apr 11 08:22:24 2019 +0100 - - Missed changelog entry in #2243 - -commit cc57aa27f4ba9f488dc6500b65441931d6b7567b -Merge: d9353e87c 8c59288fd -Author: Oliver Beckstein -Date: Thu Apr 11 15:42:39 2019 -0700 - - Merge pull request #2208 from Lp0lp/develop - - Enhancement: Adds position averaging transformation - -commit d9353e87c67806e8a710a7e0b5bfa1d6ae058ace -Author: Tyler Reddy -Date: Wed Apr 10 18:38:43 2019 -0700 - - TST: add backup pytest for MacOS CI - -commit 8c59288fd9932637f4ba90dbfe2296c641610d98 -Merge: e24805853 50713281f -Author: Lp0lp -Date: Thu Apr 11 14:52:30 2019 +0100 - - Merge branch 'develop' of https://github.com/Lp0lp/mdanalysis-PositionAverager into develop - -commit e2480585324769e6bbfe14a9a5d9cbad579db507 -Author: Lp0lp -Date: Thu Apr 11 12:14:32 2019 +0100 - - Updated the documentation. - -commit 50713281ff0c3d38a86e21870da09a94e462f334 -Merge: 5de0a8ab9 f878cc10b -Author: Luís Borges Araújo <42938615+Lp0lp@users.noreply.github.com> -Date: Thu Apr 11 10:50:52 2019 +0100 - - Merge branch 'develop' into develop - -commit f878cc10baf1ef0c25de931795117e175fb965b6 -Author: Lp0lp -Date: Tue Apr 9 19:08:39 2019 +0100 - - Fixes transformation tests not running. - - Closes #2241 - -commit 5de0a8ab9c8778dfedc19b2b28625a69c428679f -Author: Lp0lp -Date: Tue Apr 9 14:48:36 2019 +0100 - - Adds test, docs, and author/CHANGELOG info - - Added random access test - Added documentation - Updated AUTHORS and CHANGELOG - -commit e405413e34e99d0bba702ed9c6c46f468057e919 -Author: Oliver Beckstein -Date: Fri Apr 5 11:11:57 2019 -0700 - - update README build badge - - Travis-CI is now travis-ci.com (and not travis-ci.org anymore) - -commit 3f7f633c1ec3e5848ac37340bb0b02345438637d -Merge: 668e1836a 3d554a988 -Author: Oliver Beckstein -Date: Fri Apr 5 20:32:27 2019 -0700 - - Merge pull request #2219 from Yibo-Zhang/different_atoms_issue - - - different atom number error message improved - - Fixes #1998 - -commit 3d554a988710ca4f083d3bf23c506ae70d75e96c -Merge: 2f2d59daf 668e1836a -Author: Oliver Beckstein -Date: Fri Apr 5 20:31:39 2019 -0700 - - Merge branch 'develop' into different_atoms_issue - -commit 668e1836a0799c0ae2cbd10d9b73ebd494afb0e8 -Merge: 1be9f73dd 657f918b7 -Author: Oliver Beckstein -Date: Fri Apr 5 18:12:18 2019 -0700 - - Merge pull request #2226 from bieniekmateusz/survival_probability - - Survival probability: Intermittency, Step, Residues, Overlapping SP Selection Example - -commit 2f2d59daf9592d183a9a0512ae1520f2f085b205 -Author: Yibo Zhang -Date: Fri Apr 5 15:11:22 2019 -0400 - - added changelog and authors - -commit 657f918b7841f3c30c2dc4a4e85c2a1e308e334a -Merge: d2b4f082a 1be9f73dd -Author: Oliver Beckstein -Date: Fri Apr 5 11:27:31 2019 -0700 - - Merge branch 'develop' into survival_probability - -commit 1be9f73dd760eb1c3ebeb6f552a837126374e41d -Merge: 7dfb65a9b 2c929162a -Author: Oliver Beckstein -Date: Fri Apr 5 11:02:21 2019 -0700 - - Merge pull request #2221 from Fenil3510/develop - - Writes compressed output of given format (fixes #2216) - -commit d2b4f082a74e16df5e493922a2890faab0b66a56 -Merge: aaf30bc9a 3a46b347d -Author: Mateusz Bieniek -Date: Fri Apr 5 10:14:59 2019 +0100 - - Merge branch 'survival_probability' of github.com:bieniekmateusz/mdanalysis into survival_probability - -commit aaf30bc9ad61c19470e3c21530524f093f29b779 -Author: Mateusz Bieniek -Date: Fri Apr 5 10:14:44 2019 +0100 - - Numpy documentation style: PR #2226 - -commit 2c929162a6f1c92e4e0629a5ea3eeed368136c91 -Merge: 7dfb65a9b 941e3cd79 -Author: Oliver Beckstein -Date: Thu Apr 4 13:16:02 2019 -0700 - - Merge branch 'develop' of https://github.com/Fenil3510/mdanalysis into Fenil3510-develop - -commit 3a46b347d440db4b56c98eb0fe0e415bdcf66ea3 -Merge: 7dfb65a9b 970e05b48 -Author: Oliver Beckstein -Date: Thu Apr 4 13:14:06 2019 -0700 - - Merge branch 'survival_probability' of https://github.com/bieniekmateusz/mdanalysis into bieniekmateusz-survival_probability - -commit 941e3cd794d13852a76393f2ce9c51c7c35d753e -Author: Fenil Suchak -Date: Thu Apr 4 16:20:54 2019 +0530 - - updated changelog - -commit 7dfb65a9b084c9d5e1121878660b34c08230d9c8 -Merge: 6a60c8aa8 bb54223e2 -Author: Tyler Reddy -Date: Wed Apr 3 11:39:35 2019 -0700 - - Merge pull request #2234 from MDAnalysis/fix-broken-travis-2233 - - fix travis file (tab -> space) - -commit bb54223e214719e92bde1e791e6aa57189e8220b -Author: Tyler Reddy -Date: Wed Apr 3 09:53:51 2019 -0700 - - TST: pin sphinx version - - * pin the version of sphinx used - in Travis doc builds until upstream - issues are resolved in version 2.0 - -commit 970e05b48bfe7b8194148ccbb1a785a36abe8a42 -Author: Mateusz Bieniek -Date: Wed Apr 3 15:07:28 2019 +0100 - - Corrections from PR #2226 - -commit b67a7daeada6f5a0ec5fed8487a5336f48ae35bc -Author: Mateusz Bieniek -Date: Wed Apr 3 11:39:34 2019 +0100 - - Logging changes made regarding Survival Probability - -commit d84232f484195c9c70cdfa363b9d4edaa8da7ff1 -Author: Fenil Suchak -Date: Wed Apr 3 10:53:03 2019 +0530 - - added changelog and authors - -commit 28298b1165be8eac710422fbacb09824b1f7a283 -Author: Fenil Suchak -Date: Wed Apr 3 10:27:07 2019 +0530 - - changes_fixed - -commit 755e246eb4ee74b2217a93467ec8606ef31c0881 -Author: Fenil Suchak -Date: Wed Apr 3 10:13:18 2019 +0530 - - made_changes - -commit e88265df6a1f60836807171d439ab033dab42a27 -Author: Oliver Beckstein -Date: Tue Apr 2 23:53:05 2019 -0400 - - fix travis file (tab -> space) - - fix #2233 - -commit 4083378c4466af8219ad976f2adfbdd24ab542a4 -Merge: 6a60c8aa8 35769843b -Author: Oliver Beckstein -Date: Tue Apr 2 22:10:49 2019 -0400 - - Merge branch 'survival_probability' of https://github.com/bieniekmateusz/mdanalysis into bieniekmateusz-survival_probability - -commit 7d7fcbef0b65b5634caf8e37a3de4210e712308a -Merge: 6a60c8aa8 92634f0d9 -Author: Oliver Beckstein -Date: Tue Apr 2 21:32:42 2019 -0400 - - Merge branch 'develop' of https://github.com/Fenil3510/mdanalysis into Fenil3510-develop - -commit 6a60c8aa836acbcab973ae81e10e3a2c9b782fe8 -Merge: 942886673 4f8dc1723 -Author: Oliver Beckstein -Date: Tue Apr 2 21:30:51 2019 -0400 - - Merge pull request #2231 from MDAnalysis/issue-2218-2-OH - - fixed 2'-hydroxyl dihedral calculation - -commit 4f8dc1723f3fdcccd0d66d1c7ac0e93620d417fe -Author: Oliver Beckstein -Date: Tue Apr 2 15:47:09 2019 -0400 - - build docs under Python 3.7 - - I got a weird failure in PR #2231 in Travis job - https://travis-ci.com/MDAnalysis/mdanalysis/jobs/189553940 : - - Exception occurred: - File "/home/travis/miniconda/envs/test/lib/python3.5/site-packages/sphinx/ext/napoleon/docstring.py", line 703, in _parse_raises_section - m = self._name_rgx.match(_type).groupdict() - AttributeError: 'NoneType' object has no attribute 'groupdict' - - and the docs build find locally (under Python 3.6) - -commit 92634f0d9ccd0a00acee3389cf99de662faf69f5 -Author: Fenil Suchak -Date: Tue Apr 2 22:31:26 2019 +0530 - - tests_added - -commit 42418941fced75b4ab70d7d5d4d30e65b9808001 -Author: Oliver Beckstein -Date: Tue Apr 2 02:09:46 2019 -0400 - - updated tests for analysis.nucleic (for #2218) - - - replaced 1k5i.pdb (which had the 2'-OH H in strange positions) with a simulation - system of model 1 of 1k5i in CHARMM36m (generated by CHARMM-GUI and equilibrated - for 1 ns with Gromacs 2018.6). Octahedral box, K+ counter ions, TIP3P water. - - topology datafiles.RNA_PSF data/analysis/1k5i_c36.psf - - coordinates datafiles.RNA_PDB data/analysis/1k5i_c36.pdb - - added data files as gzipped datafiles (instead of bz2 because of #2232) - - removed datafiles.NUCL = data/1k5i - - updated all regression tests in test_nucleic.py with numbers appropriate for - the new test file; manually confirmed the values for the 2'-hydroxyl dihedrals - in the test by manually selecting and calculating in VMD - - replaced NUCL in atomselections test - (also removed superfluous/outdated utils/test_nuclinfo) - - updated CHANGELOG - -commit a1ae03059892b8988f5e6747022c0b7b22ecd7aa -Author: Oliver Beckstein -Date: Mon Apr 1 22:56:09 2019 -0400 - - fixed 2-hydroxyl selection - - - fixes #2218 - - RNA 2-hydroxyl selection now agrees with our docs: - H2'' (wrong) --> H2' (correct) - -commit cc4a01389aa20340026379af56989e0a846b51db -Author: Fenil Suchak -Date: Fri Mar 29 15:36:16 2019 +0530 - - GRO Zipping - -commit a7186173ee8c48cc6dc160468efd53793f02bb74 -Author: Fenil Suchak -Date: Fri Mar 29 15:01:23 2019 +0530 - - some logical fix - -commit cf36a6dd542f3c3a6a34e3df0d211db1a90b9caa -Author: Yibo Zhang -Date: Tue Mar 26 21:57:25 2019 -0400 - - add test - -commit 70a314be119b6da78fd65aafa38ac82309f4eb12 -Author: Fenil Suchak -Date: Sun Mar 24 14:54:14 2019 +0530 - - fixed util.filename by default PDB - -commit 94ccf13f14f81cf59458d87d008c5e28775847d1 -Author: Fenil Suchak -Date: Fri Mar 22 20:15:33 2019 +0530 - - fixed redundant - -commit 1b23c61974190db7a72a2e28328f9664279cc897 -Author: Fenil Suchak -Date: Thu Mar 21 22:11:45 2019 +0530 - - fixed changes due to file_format being none - -commit 35769843b6864f51e4b53bb8b0417a2101cd9409 -Author: Mateusz Bieniek -Date: Fri Mar 8 18:59:31 2019 +0000 - - An example covering the case with multiple references for the SP - analysis. This requires several runs and averaging. - -commit 417d229214735ccbb9f9a10b05616b0e98ddc35b -Author: Mateusz Bieniek -Date: Fri Mar 8 18:27:30 2019 +0000 - - Corrected documentation / proofreading. - -commit ff4d266f7604c9d632f3c2aa6b081a5583a92e63 -Author: Mateusz Bieniek -Date: Fri Mar 8 17:37:51 2019 +0000 - - The relationship between the intermittency and the window "step" - parameter is complex and was accounted for here, together with new - test cases. If necessary, we load extra frames for each window, - to account for the borders: for the first and last frame in a window. - -commit ba79bcfff9a6d41c816d72d9b27517fac6e0fb55 -Author: Mateusz Bieniek -Date: Fri Mar 8 14:30:14 2019 +0000 - - New test cases for the step+intermittency relation. - not finished - -commit 4dde01f6240877b7bf297b7b2c6aec86781521f8 -Author: Mateusz Bieniek -Date: Fri Mar 1 12:56:27 2019 +0000 - - Minor updates to the documentation. - -commit 91a1781175e781dc82eaafa9ee2b9f120a967812 -Author: Mateusz Bieniek -Date: Thu Feb 28 15:40:03 2019 +0000 - - Refactored intermittency: fewer nested blocks, giving the user access - to the selected IDs, using the selected IDs to verify the behaviour of - the intermittency. - -commit f9e829be2c6b3f621baecbc128a4a10fc6983e22 -Author: Mateusz Bieniek -Date: Thu Feb 28 14:35:57 2019 +0000 - - Intermittency added with a simple implementation. Intermittency is taken - as a gap: meaning that setting it to the value of 2 means that the atom - id 7, when in the sequence 7,X,X,7, where X means absence, will be - rewritten to 7,7,7,7. This way the intermittency does not affect the - actual routines for SP calculation. The array of IDs should never - be big so this should not add any significant computational time. - -commit 91037bc3354fa691caab39b0c626418cd09963a2 -Author: Mateusz Bieniek -Date: Thu Jan 31 17:42:00 2019 +0000 - - The SP value of entire residues can be calculated, regardless - which atoms are found. - -commit f45a005546da124089e2987e720201f347f10780 -Author: Mateusz Bieniek -Date: Wed Jan 23 18:28:41 2019 +0000 - - Better "verbose" message - avoid polluting. - -commit 036140a3e67bf5a775a8ff396c67f442e06a9350 -Author: Mateusz Bieniek -Date: Wed Jan 23 18:26:40 2019 +0000 - - Refactoring with the simpler "return_value" when possible with the mock - patch. - -commit a9abc5014089a58d7245fbc1ea2984ab35705d7d -Author: Mateusz Bieniek -Date: Wed Jan 23 18:20:08 2019 +0000 - - A test case that checks if all frames are loaded. This is the - border condition for "tau_max" and "step". - -commit a0edf640b3ad2622cfcae71630a06e025287b672 -Author: Mateusz Bieniek -Date: Wed Jan 23 18:19:05 2019 +0000 - - Use the same code for loading the frames regardless of whether the step - was set up or not. Also, manually moving between the frames rather - then using "for _ in trajectory[]". This removed unnecessary variables. - -commit 0a24544aed72109ea62b586040d729194070b717 -Author: mat -Date: Fri Jan 18 16:21:20 2019 +0000 - - Added skipping frames that are not used in the Survival Probability analysis. Before, all frames were loaded (and selection was always applied). Now, the frames which are not used are not loaded, thus improving the performance. This only happens when the step is larger than the tau_max + 1. - - Test cases cover the situation where some frames are skipped. The test checks how many times the 'select_atoms' was called. - - This is to help with the large size MD simulations analysis. - -commit 62601a372140d9c4cc8033d60ab03d393e30ca65 -Author: Fenil Suchak -Date: Thu Mar 21 13:00:56 2019 +0530 - - file_format_precedence - -commit bbc7614e20790a3c7150ecbff939faa03852a5f8 -Author: Yibo Zhang -Date: Tue Mar 19 11:16:43 2019 -0400 - - error message - -commit e7d816456555090d15483f66965e08898f1f1fb2 -Author: Fenil Suchak -Date: Tue Mar 19 12:16:33 2019 +0530 - - removed redundant format - -commit 04056e35ccaee5343718b532ff88995fc000e1d9 -Author: Fenil Suchak -Date: Sat Mar 16 18:38:05 2019 +0530 - - fix1 - -commit 231bd83dd6cd7eaa244f2d3d685a293e5455d095 -Author: Lp0lp -Date: Fri Mar 8 13:32:37 2019 +0000 - - Added tests for posavging. Fixed missing init. - -commit 94288667302c6d54321f0237e39804f69781867d -Author: Richard Gowers -Date: Wed Mar 6 08:48:40 2019 -0500 - - Update distances.py - -commit d8c429f9a3b9860fa57135c51c76b065629941a7 -Author: Ninad Bhat -Date: Wed Mar 6 11:30:25 2019 +0530 - - Reverting API change - -commit efe963c47ea68f81bbcfa1618b83c9ebc1b5dcc6 -Author: Ninad Bhat -Date: Wed Mar 6 11:26:55 2019 +0530 - - Revert "Import distance_array from lib in place of analysis" - - This reverts commit e5e4d874d6ced5bd6450c24799c5e6859084288a. - -commit 02c0872c00e9814c042f1a1ad89caa1e30ec5bad -Author: Ninad Bhat -Date: Tue Mar 5 13:22:32 2019 +0530 - - Import distance_array from lib in place of analysis - -commit c9d7a5cd0a6c4a0d28a3d8db5d16bf864b11065a -Author: Ninad Bhat -Date: Tue Mar 5 08:12:04 2019 +0530 - - Correction errors - -commit 741052f7bd61d7ec28ebc17e25c464b9c127cff9 -Author: Ninad Bhat -Date: Sat Mar 2 07:45:15 2019 +0530 - - Recommended Changes - -commit 8ac2724a6bc9462c1d6d61713b24d567963000ea -Author: Ninad Bhat -Date: Fri Mar 1 12:44:21 2019 +0530 - - updates CHANGELOG - -commit dd448cd220e37640f3d63881ef19d9bb710d6abc -Author: Ninad Bhat -Date: Fri Mar 1 12:33:01 2019 +0530 - - removing unnecessary functions - -commit eefb03f05f5768a3be3192b27ca2a61a61a7db5a -Author: Ninad Bhat -Date: Fri Mar 1 12:21:40 2019 +0530 - - Replaced distance_array in contact_matrix - -commit f51ce5f14a2f21ea30863f7c1972d49d89fc1a49 -Merge: ddab79ead 60c7a661d -Author: Johannes Zeman -Date: Fri Mar 1 00:27:22 2019 +0100 - - Merge pull request #2213 from zemanj/sp_box - - Enforce single-precision boxes - -commit 60c7a661d6b49cc67c95e931f884e4929477ddcf -Author: zeman -Date: Thu Feb 28 22:43:22 2019 +0100 - - updated CHANGELOG - -commit aa5781e51332707a8a08e9957452bd3c3fe1ef0e -Author: zeman -Date: Thu Feb 28 22:37:51 2019 +0100 - - adjust make_whole test for double precision boxes - -commit 6864c0a9b336ea630a0799107ed9db57bc00f3ce -Author: zeman -Date: Thu Feb 28 22:36:05 2019 +0100 - - add dimensions dtype checks to Universe and Timestep tests - -commit 5e65916ffb3fa3c8fd3737bc63071a8f179e99fe -Author: zeman -Date: Thu Feb 28 22:34:36 2019 +0100 - - remove obsolete box dtype conversion in make_whole() - -commit d144f8c2dcbb049bd9120df3ddd517f6d606f924 -Author: zeman -Date: Thu Feb 28 22:32:51 2019 +0100 - - enforce Universe.dimensions.dtype is always np.float32 - -commit ddab79eadb96c7b8e72f85b80f64ad8f39205b92 -Author: Ninad Bhat -Date: Mon Feb 25 10:18:32 2019 +0530 - - Using numpy operations - -commit 8caa288731464461864c6675e46b90fa52f48bd7 -Author: Ninad Bhat -Date: Sat Feb 23 13:27:08 2019 +0530 - - Update CHANGELOG - -commit 78ac16aa34cfd685ebb53e533f7c3ace99703801 -Author: Ninad Bhat -Date: Sat Feb 23 13:21:41 2019 +0530 - - Switched to capped_distances - -commit a6301ee73193ea32dcf0c070a6b1cbd1a0420086 -Author: Lp0lp -Date: Wed Feb 20 15:48:28 2019 +0000 - - updated import cycle - -commit 839410ad63154503c87237ed08dc5a2ec7c1a8c2 -Author: zeman -Date: Wed Feb 20 00:48:30 2019 +0100 - - faster tests - -commit dfadb7e2d5c74b093e16ea62b156120e087ffeec -Author: zeman -Date: Wed Feb 20 00:44:06 2019 +0100 - - fixed docs and modified attribute isinstance() check - -commit 4679d8016cf8026151897ada0b3c6edff38beb61 -Author: Philip Loche -Date: Tue Feb 19 20:19:12 2019 +0100 - - streamlined tests - -commit 31e8e019732a71e2be0fc8d62674761e4d2795ea -Author: Philip Loche -Date: Tue Feb 19 13:45:22 2019 +0100 - - revert change in centers, cleanup - -commit 18c575b82a23317c58d07ca6ae15c41e6ac1bd25 -Author: Philip Loche -Date: Tue Feb 19 12:28:13 2019 +0100 - - Added tests for residues and segments - -commit bf91d1d705d7ca07040d7ccae62283e4ea324882 -Author: Philip Loche -Date: Mon Feb 18 21:38:49 2019 +0100 - - misc. changes - - * removed NoDataError - * Clearer description for function attribute - * tiny code cleanups - -commit e31edfbaf82b9b9f4f26001d4c765f13c4bc55c8 -Author: Johannes Zeman -Date: Mon Feb 18 21:14:01 2019 +0100 - - Improved docs - - Co-Authored-By: PicoCentauri - -commit 842cab5b04d49aa38b6398354d4977372ec15fcc -Author: Philip Loche -Date: Tue Feb 19 10:09:43 2019 +0100 - - Updated CHANGELOG - -commit 46a7807bea1ad105704be5c52ac43aa8b88c64e5 -Author: Philip Loche -Date: Wed Feb 6 14:51:09 2019 +0100 - - Improved docs and tests - -commit ea01828673857c072a52d65f772e6080c69844f8 -Author: Philip Loche -Date: Tue Feb 5 16:35:47 2019 +0100 - - Allow multi-dimension arrays - -commit 6fcc6a427ef26cde2b29df452da2f0879e167d66 -Author: Philip Loche -Date: Mon Feb 4 16:48:43 2019 +0100 - - Added tests - -commit 20612402806d64499ec31cae811180a4bf0c311d -Author: Philip Loche -Date: Mon Feb 4 15:23:52 2019 +0100 - - option for array input, improved docs - -commit fdfbd6b2772f6bf7335e2cad261e9d545294bc34 -Author: Philip Loche -Date: Fri Feb 1 15:35:36 2019 +0100 - - Changed *group.sum() to general accumulate method - -commit 0f8220412c683c1096e938ad03dbdff8f7eafb33 -Author: Philip Loche -Date: Thu Jan 31 16:16:18 2019 +0100 - - Added *Group.sum() method - - This allows to add a compound parameter to *Group.total_charge() and - *Group.total_mass() - -commit 7727d209bd0e90c6ce37bb18940f88ffee8643bf -Author: Lp0lp -Date: Wed Feb 20 12:04:46 2019 +0000 - - Added posavging and updated init. - -commit 1cdd44ecd32307d7ef42ff4554c50aa96a768155 -Merge: 52707926c c7d9d9a20 -Author: Johannes Zeman -Date: Mon Feb 18 12:46:13 2019 +0100 - - Merge pull request #2205 from NinadBhat/doc_correction - - Correcting Documentation in MDAnalysis.analysis.contacts - -commit c7d9d9a2017d4bd92f96269f817dbac0a571dc40 -Merge: 3474c0568 52707926c -Author: Johannes Zeman -Date: Mon Feb 18 11:11:12 2019 +0100 - - Merge branch 'develop' into doc_correction - -commit 52707926cef8e65ff1031eacc05301a98b418383 -Author: Philip Loche -Date: Sun Feb 17 17:43:21 2019 +0100 - - Updated Changelog - -commit 57217739904a4ba592a114ffdbdc62c9e19567dd -Author: Philip Loche -Date: Wed Jan 16 10:01:25 2019 +0100 - - Ajusted fixtures to work with new fudgefactor - -commit 9e8b2c3845ab493c982d2684b859e04a123dd9f7 -Author: Philip Loche -Date: Wed Jan 16 09:19:30 2019 +0100 - - Added two more tests to bond guesser - -commit 0cf5fb949fd8148715722947fc23d0d9431cfc0c -Author: Philip Loche -Date: Wed Nov 28 16:06:13 2018 +0100 - - Adjusted fudge_factor to new radii - -commit 31ca2502acfe03ccf19738967373471794933365 -Author: Philip Loche -Date: Sun Nov 18 10:05:02 2018 +0100 - - Added more vdw radii - -commit ea05c5a62c0862c8c324967a49f8a46b5859b8f3 -Merge: 77d8f7c4c 3eda6a785 -Author: Oliver Beckstein -Date: Fri Feb 15 10:31:36 2019 -0700 - - Merge pull request #2197 from MDAnalysis/issue-2193-mmtf_optional_fields - - Fixes Issue #2193 - -commit 3474c0568867edde8d73b97dcb672aaacd4775b7 -Merge: b046713f0 77d8f7c4c -Author: Ninad -Date: Fri Feb 15 03:17:05 2019 +0000 - - Merge branch 'develop' into doc_correction - -commit b046713f0356ee44bfd9b3b5321e567f400e7a83 -Author: Ninad Bhat -Date: Fri Feb 15 08:44:31 2019 +0530 - - Making suggested changes - -commit 77d8f7c4ca776938bfe1f627e3791c87cf55ece3 -Merge: f5cea8642 b84cb6059 -Author: Richard Gowers -Date: Thu Feb 14 14:06:04 2019 -0600 - - Merge pull request #2169 from ayushsuhane/2164SegFault_Capped - - Fixes the segmentation Fault in Capped distance - -commit 3eda6a785c55839c4a29cd5e7b3e93b982099eaa -Merge: 25fc0522c f5cea8642 -Author: Richard Gowers -Date: Thu Feb 14 09:13:36 2019 -0600 - - Merge branch 'develop' into issue-2193-mmtf_optional_fields - -commit 25fc0522c9fbe055f7064decec57635c56e982ba -Author: Richard Gowers -Date: Thu Feb 14 09:10:24 2019 -0600 - - Update test_mmtf.py - -commit 387b8870b4c249955b2fe31096fae695d3a919e2 -Author: Ninad Bhat -Date: Thu Feb 14 14:13:26 2019 +0530 - - Updated CHANGELOG - -commit 2b21411b7b657c289cbe0b5506be0d9d6d2b33b4 -Author: Ninad Bhat -Date: Thu Feb 14 14:10:03 2019 +0530 - - Doc correction - -commit cb43c70f08bb2e7daeac78c98f820ceb8935f5f1 -Merge: 687beeaf5 f5cea8642 -Author: Ninad Bhat -Date: Thu Feb 14 13:21:53 2019 +0530 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit b84cb6059d129b58e51316efb889e2e9b7729127 -Merge: 962e68b83 f5cea8642 -Author: Oliver Beckstein -Date: Wed Feb 13 17:46:05 2019 -0700 - - Merge branch 'develop' into 2164SegFault_Capped - -commit f5cea86425b75ae8f4ca71accb53f66b94a9e815 -Merge: 4794389a4 9c38065f0 -Author: Johannes Zeman -Date: Wed Feb 13 21:23:30 2019 +0100 - - Merge pull request #2204 from zemanj/wrap_fixes - - Wrap fixes - -commit 9c38065f05e73d643399ca200e90326f5d44eee1 -Author: zeman -Date: Wed Feb 13 19:59:56 2019 +0100 - - corrected code comments; cast indices as np.intp instead of np.int64 - -commit 25b1785b26ad2a513ea5c9851917aa8cd722fb12 -Author: zeman -Date: Wed Feb 13 02:05:47 2019 +0100 - - added missing header to MDAnalysisTests/core/util.py - -commit 89ebf7373892e804a040824d18896f5ad4dbc3f3 -Author: zeman -Date: Wed Feb 13 01:26:56 2019 +0100 - - changelog entries for PR #2204 - -commit e937a23f243962f67c7a367af88ce107a30642a1 -Author: zeman -Date: Wed Feb 13 00:37:28 2019 +0100 - - add comprehensive *Group.wrap() tests and move relevant old tests from core.test_atomgroup to core.test_wrap - -commit 38240179e233936093ae99a1d0b292b9985b6e2a -Author: zeman -Date: Wed Feb 13 00:34:23 2019 +0100 - - make unwrap_test_universe a class UnWrapUniverse in MDAnalysisTests.core.util - -commit 196438f047320dde5865283f959befe1245efae6 -Author: zeman -Date: Wed Feb 13 00:31:41 2019 +0100 - - *Group.wrap(): better handling of invalid boxes, fix for non-unique groups, fix center precision errors - -commit 6dcfdc5600805e16fdcae8611c02577f16ea40c4 -Author: zeman -Date: Tue Feb 12 14:43:08 2019 +0100 - - avoid creating two atomgroups (unique and non-unique) in *Group.wrap() - -commit 74e51d4d276eb583b416e1b500438d448934156b -Author: zeman -Date: Tue Feb 12 13:26:54 2019 +0100 - - *Group.wrap() acts only on group members, returns wrapped positions, and can work out-of-place. Made SegmentGroup.atoms and ResidueGroup.atoms a lot faster. - -commit 4794389a41cecccce490ee434ec00aa4c6c970ed -Merge: 0fef1a381 0b05fcb2d -Author: Johannes Zeman -Date: Wed Feb 13 18:13:29 2019 +0100 - - Merge pull request #2202 from NinadBhat/self_capped - - return_distances kwarg for self_capped_distance - -commit 0b05fcb2dc410154a263e8bea88eda28c1a56f25 -Author: Johannes Zeman -Date: Wed Feb 13 16:06:33 2019 +0100 - - small doc fixes - -commit beedfbf81d75a4b7763af1c588c6e44a0e3e67f1 -Author: Johannes Zeman -Date: Wed Feb 13 14:50:29 2019 +0100 - - make CodeCov happy - - `test_self_capped_distance` now covers the new `return_distances` kwarg and also checks for correct pair/distance correspondence - -commit 687beeaf52427b9d95e34a686fdfa01f528e603e -Merge: 3d7396798 0fef1a381 -Author: Ninad -Date: Tue Feb 12 05:56:06 2019 +0000 - - Merge pull request #1 from MDAnalysis/develop - - Update new commits - -commit 32787dedd0b7b391c5383f698739536780049a4e -Merge: be8576364 0fef1a381 -Author: Ninad -Date: Tue Feb 12 05:51:17 2019 +0000 - - Merge branch 'develop' into self_capped - -commit be857636434c20b89a3914663489962718494d5b -Author: Ninad Bhat -Date: Tue Feb 12 11:18:48 2019 +0530 - - Updated AUTHORS and CHANGELOG - -commit 02a1b70a163d4a52fbc9ada7de0d883e3e978422 -Author: Ninad Bhat -Date: Tue Feb 12 11:11:35 2019 +0530 - - Removing else - -commit 0fef1a38143f4bfcb74dd44374d915b31e8b5a6c -Merge: 3d7396798 543a26521 -Author: Johannes Zeman -Date: Mon Feb 11 20:03:46 2019 +0100 - - Merge pull request #2201 from zemanj/pbc_fixes - - Pbc fixes - -commit 543a26521a4ec799367054d3568910c8fbbc950b -Author: Richard Gowers -Date: Mon Feb 11 10:38:11 2019 -0600 - - Update CHANGELOG - -commit f97e6b7ba17e63931748d2599acab5431b7a52a5 -Author: Richard Gowers -Date: Mon Feb 11 10:35:08 2019 -0600 - - Update CHANGELOG - -commit ceb638034209a07f9d4a75afb06ba54473c691f8 -Author: zeman -Date: Mon Feb 11 12:23:10 2019 +0100 - - changelog for PR #2201 - -commit 2842ac45a99fd282417f1cfb93ed7b24981be90b -Author: zeman -Date: Mon Feb 11 11:09:43 2019 +0100 - - really guarantee that wrapped coordinates lie strictly within the primary image - -commit 5c9e030ff72b1273844990590c447b35bc63c211 -Author: Ninad Bhat -Date: Mon Feb 11 12:03:16 2019 +0530 - - Updated tests - -commit 7d0713343856464a3d23e11784fe3de4739bbbc6 -Author: Ninad Bhat -Date: Mon Feb 11 11:16:07 2019 +0530 - - Added return_distances - -commit 83459f71fa6e9c682f3abb6ed385f503fdc3a1b5 -Author: zeman -Date: Sat Feb 9 03:10:31 2019 +0100 - - corrected inexact reference volume in pdb tests - -commit d2c354acda5a7365702799e3141a06fec034665c -Author: zeman -Date: Sat Feb 9 01:58:24 2019 +0100 - - three-stage wrapping to *always* guarantee that wrapped coordinates are inside the box and below upper bounds - -commit 8581589d69986fa88455ab02dbce4c6b1a289788 -Author: zeman -Date: Sat Feb 9 01:08:56 2019 +0100 - - more tests for triclinic_vectors() and triclinic_box() - -commit 7fc498dd7883a43abf9bceb57288e8a4194b299f -Author: zeman -Date: Sat Feb 9 01:07:57 2019 +0100 - - optional dtype for triclinic_vectors() which enables faster and more exact box volume computation - -commit 572bcc2f68f5c63b7df2820ba06c96afac1d98bb -Author: richardjgowers -Date: Fri Feb 8 12:27:05 2019 -0600 - - test for missing MMTF attributes - -commit cfe05df8b770e24bf0b308ca4a0ef5965f7cb90f -Author: richardjgowers -Date: Fri Feb 8 12:10:19 2019 -0600 - - tests for dimensionsless MMTF files - -commit 10fec723567ddda38ad27930dcdf106502859569 -Author: richardjgowers -Date: Fri Feb 8 11:59:02 2019 -0600 - - added extra MMTF test file - -commit 191551ffd68d0963f46e678bcee204c3e3d333a3 -Author: zeman -Date: Fri Feb 8 03:04:45 2019 +0100 - - two-stage coordinate wrapping - -commit f60f0580462e9a69134bf8b9e6e79ad048b64763 -Author: zeman -Date: Thu Feb 7 18:51:41 2019 +0100 - - more fixes - -commit 2263b7c4d1c80c6f7af284c24a1ba6c718d58e79 -Author: zeman -Date: Thu Feb 7 16:22:31 2019 +0100 - - simplified and fixed triclinic_vectors() and triclinic_box(); fixed pbc handling for zero boxes - -commit 47835e3cfb64a10365894d5a1ba792f8e9bc0c59 -Author: zeman -Date: Thu Feb 7 15:20:30 2019 +0100 - - faster and more exact coordinate wrapping - -commit 2a66f97c1e35ab27c9ef62bc9135f51926b8697e -Author: zeman -Date: Thu Feb 7 15:07:35 2019 +0100 - - faster and more exact handling of 90 degree angles in triclinic_box() and triclinic_vectors() - -commit aeba3f6d22f68367d73c51154b3950b69e07b8c0 -Author: zeman -Date: Wed Feb 6 01:49:55 2019 +0100 - - adjusted old tests to comply with more accurate box-related operations; added test for methods in lib.mdamath - -commit b655cca3a715efdb52129e9b3f8b5c50c3b8dfa2 -Author: zeman -Date: Wed Feb 6 01:48:10 2019 +0100 - - box-related computations in lib.mdamath are performed in double precision and invalid dimensions result in zero vectors - -commit 3d7396798e2bfc392157d313ddcbd3cfa99b3a5c -Author: Johannes Zeman -Date: Fri Feb 8 02:49:14 2019 +0100 - - *Group.unwrap (#2189) - - * made inplace position modification of make_whole() optional - - * added *Group.unwrap() method - - * fixed docs of make_whole() - - * cleaned up unwrap() - - * doc fixes - - * fix make_whole() for double precision boxes - - * fixed group.unwrap() for reference="com" - - * fix group.unwrap() for empty group - - * moved *group.unwrap() from core.topologyattrs to core.groups - - * tests for *group.unwrap() - - * tests for modifications in make_whole() - - * make_whole() test for double precision box - - * changed dtype of molnums from int to np.int64 - - * fixed typo and removed unneccessary "elif"s to avoid CodeCov partials - - * removed unnecessary import - - * use libc.math.fabs instead of abs in make_whole() - - * unwrap test for universe without masses - - * added changelog entry for *Group.unwrap() - - * added changelog entry for lib.mdamath.make_whole() - - * docs candy - - * eliminated another useless elif - -commit e5be7043cfa166610bbaefd410a4dbae7f5ed602 -Author: richardjgowers -Date: Fri Feb 1 13:18:33 2019 -0600 - - Fixes Issue #2193 - - properly respect optional mmtf fields - -commit 33395f6f7c52951841470fc2643d741060304d51 -Author: Richard Gowers -Date: Fri Feb 1 17:50:28 2019 -0600 - - Pdb fixes (#2196) - - * pdb conect fix - - * Fixes Issue #2194 - - added test for fixing pdb bonds - - * fixes issue #2195 - - * removed TestCase usage from test_pdb - - removed some outdated/wrong docs - -commit 992bd738f5cd6c1a16e8e55fc82cb3f442bf239c -Author: richardjgowers -Date: Thu Jan 24 13:05:36 2019 -0600 - - fixed mangled hbond autocorrel docs - -commit 5d2969eef3ef68dce2bd1e7b08db6ff0c0c6715e -Merge: a2db38784 9a44e8f98 -Author: Johannes Zeman -Date: Mon Jan 28 13:06:34 2019 +0100 - - Merge pull request #2141 from MDAnalysis/persistence_length_attention - - polymer PersistenceLength attention - -commit 9a44e8f98e9d4e218d3338f8ec9e1783720f609b -Author: richardjgowers -Date: Sat Jan 26 13:35:18 2019 -0600 - - fix plotting test - -commit 252c101c5ba8816248e6f6d537a7a5c5ec897e2c -Author: richardjgowers -Date: Sat Jan 26 13:34:03 2019 -0600 - - check error string in sort_backbone - -commit edfb42066cc432fd7cccca136aebc53f43dd62a3 -Author: richardjgowers -Date: Fri Jan 25 10:26:22 2019 -0600 - - added analysis.polymer.sort_backbone - - updated persistence length docs - -commit a2db387843874b669a63baa56cbb125fc6274486 -Author: Johannes Zeman -Date: Sat Jan 26 20:25:53 2019 +0100 - - New compounds 'molecules' and 'fragments' for COM and COG computations (#2182) - - * new compounds 'molecules and 'fragments' for com and cog computation - - * fixed *Group.center() for single-atom components; fixed typos - - * let center() return NaNs if weights.sum() is zero - - * center() tests for one- and zero-atoms groups and for zero-weights - -commit 38577cee5100d964763362d3da24575e2a554572 -Merge: ecef1c714 f6d046371 -Author: Oliver Beckstein -Date: Thu Jan 24 11:09:04 2019 -0700 - - Merge pull request #2183 from MDAnalysis/issue-2181-hbond_autocorrel_docs - - added analysis.hbonds.find_hydrogen_donors - -commit ecef1c7141823c87d520ca2d9e52d5e9c2d25696 -Author: Richard Gowers -Date: Thu Jan 24 10:52:48 2019 -0600 - - fixes for mac installation using clang on older machines (travis) (#2184) - - * fixes for mac installation using clang on older machines (travis) - - * add -mmacosx-version-min=10.7 to cpp_extra_link_args for OSX - -commit 214210d28852a407829183df1233a4b19903d01c -Author: Richard Gowers -Date: Wed Jan 23 07:47:00 2019 -0600 - - Fixed copying record_type attribute (#2179) - - * Fixed copying record_type attribute - - * added record_type to select_atoms - - * simplified record_type attribute to just store the string - -commit f6d046371dd65d77ed06f7f176f65d2cddefddc1 -Author: richardjgowers -Date: Tue Jan 22 18:07:58 2019 -0600 - - added guess_bonds example to hbond_autocorrel - -commit 52f57c5264a462ea6ffa08b746a436ad55e4da76 -Author: richardjgowers -Date: Tue Jan 22 17:59:13 2019 -0600 - - reverted automatic donor detection - -commit 6a5352f9753208d70138601a65b1b923ca1c9df1 -Author: richardjgowers -Date: Tue Jan 22 17:44:36 2019 -0600 - - derp, nitrogens are donors here - -commit d43ba8f96649b6ef0358cc6290d48788a82f1a43 -Author: richardjgowers -Date: Tue Jan 22 13:03:00 2019 -0600 - - added analysis.hbonds.find_hydrogen_donors - - updated documentation of hbonds.HBondAutoCorrel - - fixes Issue #2181 - -commit 2bb0aa72c733793a05084dd45afcde3b8e485c02 -Author: Richard Gowers -Date: Mon Jan 14 11:39:45 2019 -0600 - - add support for py3.7 on travis (#1963) - -commit 962e68b8366bf4147b8f9e65f088b6d5a2fd0f48 -Merge: 88dee03ac 1ba893ac8 -Author: ayush -Date: Sun Jan 13 21:00:05 2019 -0800 - - Changelog entry - -commit 88dee03ac076f36e28dca370c8a414e001de1546 -Author: ayush -Date: Sun Jan 13 20:55:54 2019 -0800 - - Changed the box size according to the more relevant cutoff distance - -commit 1ba893ac8fa00cf7bf71937fe7fc29c8d04fbe20 -Author: Richard Gowers -Date: Sat Jan 12 16:29:48 2019 -0600 - - fixed Issue 2172 (#2174) - - * fixes Issue 2172 - - * removed py 3.4 from test matrix - - * finalised dropped py3.4 - -commit 24972e6658be244ae7580bf6aec6dbf30d4a982f -Author: VOD555 -Date: Thu Jan 10 17:51:43 2019 -0700 - - fix texture - -commit a9077b9257f080fbec718df5301f37fcc2086fc5 -Author: ayush -Date: Tue Jan 1 16:49:20 2019 -0800 - - Added similar changes to self_search - -commit 22e9cc2aa45856a8a7d1f2b4c548b6a389257399 -Author: ayush -Date: Tue Jan 1 16:37:53 2019 -0800 - - Fixes the segmentation Fault in Capped distance - -commit abcdb1e2423ee4714c5ce7b5ce3364778a5a02f7 -Author: mnmelo -Date: Mon Dec 10 20:37:35 2018 +0000 - - Restores support for gcc on MacOS (closes #2162) (#2163) - - The actual compiler to be used at build time is now determined prior to adding clang-specific flags. - - The OpenMP compiler detection also now finds the build-time compiler. - -commit 4f204c4cd76fd728d4a04a67226cd85d2cf29661 -Merge: e65ce63a1 6f1623b70 -Author: Oliver Beckstein -Date: Thu Dec 6 14:54:34 2018 -0700 - - Merge pull request #2161 from MDAnalysis/tpx116 - - Update TPR version for Gromacs 2019 - -commit e65ce63a1705219fecd1b0c0d1363ebdcd7e0688 -Author: Richard Gowers -Date: Thu Dec 6 08:29:24 2018 -0600 - - changed encore test to be xfail for now (#2159) - - * changed encore test to be xfail for now - - can fail if it likes without slowing down development - - * added another twitchy encore test - -commit 6f1623b70a2289eaf2a2f6fda8fd9d456cf00bca -Merge: 076ae8314 aee45cb3c -Author: Jonathan Barnoud -Date: Wed Dec 5 17:30:07 2018 +0100 - - Merge branch 'develop' into tpx116 - -commit 076ae83145c28f6bb6b05a9d011a467413e8eb90 -Author: Jonathan Barnoud -Date: Wed Dec 5 17:27:18 2018 +0100 - - Update Changelog - -commit f9f16f7aded7f3a08d1a546a91c5f5bb3447cf06 -Author: Jonathan Barnoud -Date: Wed Dec 5 17:22:23 2018 +0100 - - Update TPR version for Gromacs 2019 - - Update the TPX version and add new TPR files for the tests using gromacs - 2019-beta3. - -commit aee45cb3c53b8235e40bfe392826bb08a6684737 -Author: richardjgowers -Date: Tue Dec 4 17:50:09 2018 -0600 - - fixup to gsd tests, add skip on windows - -commit ef4b583040b6a9ce6ac782732bbf8cd6ac51072a -Merge: c4e100749 e3ee5f627 -Author: Richard Gowers -Date: Tue Dec 4 07:44:07 2018 -0600 - - Merge pull request #2155 from dpadula85/issue_2112 - - Issue 2112 fixed badly - -commit e3ee5f6277d408fe34c7d8ba91f4eb846d236f36 -Author: Richard Gowers -Date: Tue Dec 4 07:43:44 2018 -0600 - - Update CHANGELOG - -commit 626d687eda13ff37c6b93f1c8749fe9e00518bd4 -Merge: f63d48f24 c4e100749 -Author: Richard Gowers -Date: Tue Dec 4 07:42:39 2018 -0600 - - Merge branch 'develop' into issue_2112 - -commit c4e100749216a42854cf0537fc80e5f2ceaa8930 -Merge: 71554d57e 937bd75a2 -Author: Richard Gowers -Date: Tue Dec 4 07:41:05 2018 -0600 - - Merge pull request #2154 from aliehlen/issue-2152-gsdbonds - - Issue 2152 gsdbonds - -commit 937bd75a2da8cb9c417fbb55f5e035a231dd5c5d -Author: Richard Gowers -Date: Tue Dec 4 07:40:30 2018 -0600 - - Update CHANGELOG - -commit 7bc0867aa22f8ecab5aeac02ef8e037d824a6993 -Merge: 45f500900 71554d57e -Author: Richard Gowers -Date: Tue Dec 4 07:39:49 2018 -0600 - - Merge branch 'develop' into issue-2152-gsdbonds - -commit 71554d57e7b234b2a8fc3890dadc4b2dfeaa8fd3 -Author: xiki-tempula -Date: Tue Dec 4 13:36:18 2018 +0000 - - fix lint error (#2149) - - * fix lint error - - * globally disable self-import - -commit 45f5009000b4d79275bd20b408c614f9e3fa67cb -Author: ali -Date: Mon Dec 3 12:42:17 2018 -0600 - - add test for specific bonds in hoomdxml parser - -commit f05eceb560fbd97dfc7979d88e509b1ac8205736 -Author: ali -Date: Fri Nov 30 11:43:31 2018 -0600 - - read in bond/angle/dihdral as list of tuples, not generators - -commit e999294c34bd655e9d894b87f0bc345fc5f895ce -Author: ali -Date: Fri Nov 30 11:41:51 2018 -0600 - - make sure that bonds, angles, dihedrals are read in as lists of tuples - - - not sure if this is the right test, but it at least catches the current problem - -commit b9090fff37c4685d74a276ee761b4bde6cbc92a7 -Author: ali -Date: Mon Dec 3 12:38:07 2018 -0600 - - add tests for specific bonds in gsd parsing - -commit f63d48f2401dd1970ceb2e198ab475b3de84af91 -Author: Daniele Padula -Date: Sun Dec 2 23:32:46 2018 +0000 - - Issue #2112 warning - -commit cae2444009543e305bf61dc853c7b1de6ef44bc6 -Author: Daniele Padula -Date: Sun Dec 2 23:29:01 2018 +0000 - - Issue 2112: added warning test - -commit b28df550e7b8711dff52a5afc4386c34037e03e1 -Author: Micaela Matta <31009265+micaela-matta@users.noreply.github.com> -Date: Sun Dec 2 15:37:09 2018 -0600 - - Issue 2144 macos fix (#2150) - - * fixed issue 2144 - -commit ecee43c9d8b0c6901a9c1b452e9af8ac61738be5 -Author: Daniele Padula -Date: Fri Nov 30 21:31:15 2018 +0000 - - Issue 2112 fixed badly - -commit 68abeab3a71e3fa258df400bb614b5461b1d7127 -Author: ali -Date: Fri Nov 30 15:18:34 2018 -0600 - - update AUTHORS and CHANGELOG for PR #2153,#2154 - -commit d2c5a4528b25b43c517a46246187475358cf1435 -Author: Richard Gowers -Date: Fri Nov 30 15:13:37 2018 -0500 - - Update datafiles.py - -commit 49576f648025dcdc160f6beeb54088adf782dd97 -Author: ali -Date: Fri Nov 30 11:49:03 2018 -0600 - - correct misspelling in gsd parsing; read in bonds as tuples - -commit c57d29f1b00e6d851912d66d8470a5a67304c131 -Author: ali -Date: Fri Nov 30 11:48:29 2018 -0600 - - add gsd file with bonds, add bond tests - - - might be easier to include just one gsd file, but I wasn't sure - -commit aaf2f9a5cd7a21a3f58cb1e7f9f71ffc71281404 -Author: richardjgowers -Date: Wed Nov 21 13:52:59 2018 -0600 - - maybe xdist is screwing up? - -commit 93c48f6061efc43ed2c9f3c042c931883c8465dd -Author: Matt Thompson -Date: Thu Nov 15 17:13:28 2018 -0600 - - Fix a docstring example so it can be run on copy+paste (#2139) - - * Fix a docstring example so it can be run on copy+paste - - * Fix another docstring typo - -commit 5d6b871f8d30fd7be5c2d44be3025f9e2419c94b -Author: Oliver Beckstein -Date: Fri Nov 9 14:44:30 2018 -0700 - - Update gowers doi (#2137) - - * added DOI to Gowers 2016 citation - - * added Gowers 2016 DOI to the comment header of all Python files - - Command used:: - - for FILENAME in `git grep -l '# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.'`; do \ - sed -i~ '/^# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy./a \ - # doi: 10.25080/majora-629e541a-00e\ - ' $FILENAME; \ - done - -commit 966391cc96918a86b4feec7b96797161682ec842 -Author: Johannes Zeman -Date: Thu Nov 8 23:15:56 2018 +0100 - - Fix #2132 (#2136) - - * Fix #2132 - - _NSGrid.coord2cellid() used to fail for coords close to box boundaries. - By defining the grid's cellsize as double precision, this is now fixed. - See Issue #2132 for details. - -commit ca2018dd55a02936384ecec0b806405e8a531e5d -Author: richardjgowers -Date: Tue Nov 6 09:58:41 2018 -0600 - - started version 0.19.3 - -commit 7aac26a3152dd1a707009cd79009cbd49a009e7a -Author: richardjgowers -Date: Tue Nov 6 09:36:46 2018 -0600 - - finalised v0.19.2 - -commit 19b3140c901f66b7c7cb641391c190adff9b4da1 -Author: richardjgowers -Date: Tue Nov 6 09:35:07 2018 -0600 - - added windows support - -commit 49552db8d617c95bd0473f5c45c9b3865d486240 -Author: richardjgowers -Date: Mon Nov 5 14:23:58 2018 -0600 - - started v0.19.2 - -commit 524f06c3abe60dc68d4160b6a09330f9a1609b94 -Author: richardjgowers -Date: Mon Nov 5 14:20:27 2018 -0600 - - fixup to changelog - -commit 333f9580a06d50cb56b1523cd43cb86fe0fe95cb -Author: richardjgowers -Date: Mon Nov 5 13:30:21 2018 -0600 - - finish version 0.19.1 - -commit 5c19974c43125c94f98ab45d2f9965c70e427eec (tag: release-0.19.2) -Merge: 9fd89139c d57172382 -Author: richardjgowers -Date: Tue Nov 6 09:38:41 2018 -0600 - - Merge branch 'start-0.19.2' - -commit d57172382b8ac55e240666bbc4a83a9d808655ba -Author: richardjgowers -Date: Tue Nov 6 09:36:46 2018 -0600 - - finalised v0.19.2 - -commit 7d8d0e6e5fa87ef044359f1d8a56d12d3965d61c -Author: richardjgowers -Date: Tue Nov 6 09:35:07 2018 -0600 - - added windows support - -commit 9fd89139ccd3b8294d5a562ea215fb80fdabffc2 -Merge: 108ffe0b1 de6f1196e -Author: Richard Gowers -Date: Mon Nov 5 18:23:37 2018 -0600 - - Merge pull request #2133 from MDAnalysis/rel-19.1 - - Release 0.19.1 - -commit a1d9f755b235cd7e686fe097df9e292c4b7829ac -Author: richardjgowers -Date: Mon Nov 5 14:23:58 2018 -0600 - - started v0.19.2 - -commit de6f1196e1101a5237fed2628c1885fe6d9ac012 -Author: richardjgowers -Date: Mon Nov 5 14:20:27 2018 -0600 - - fixup to changelog - -commit 8622a0ef687f0d085742c7174b57478e7ca25e2a -Author: richardjgowers -Date: Mon Nov 5 14:20:27 2018 -0600 - - fixup to changelog - -commit b7f36bd148f1eed47f2dc935b89d28c8cae468c4 (tag: release-0.19.1) -Author: richardjgowers -Date: Mon Nov 5 13:42:23 2018 -0600 - - updated c sources for 0.19.1 - -commit 03ae3bc7899a29d7d8d6156668faabd774f58be0 -Merge: 108ffe0b1 7c119ab4a -Author: richardjgowers -Date: Mon Nov 5 13:36:11 2018 -0600 - - Merge branch 'develop' - -commit 7c119ab4aa1efb9339e3091b577e205e816fff76 -Author: richardjgowers -Date: Mon Nov 5 13:30:21 2018 -0600 - - finish version 0.19.1 - -commit 0d7367d05f1250c2afc8be7e3768011dede1498c -Author: Richard Gowers -Date: Mon Nov 5 12:16:52 2018 -0600 - - PDB & Windows support. (#2127) - - Fixes #2125 Now supports Windows on Python 3 - Fixes #2128 PDBReader now reads DOS-style files - - switched to finding ascii offsets using bytes mode - - removed use of os.unlink inside test case - - added DOS style line ending test files - -commit 89b2299e3ae8ab548fcc932b72eb6128b2be0463 -Author: Philip Loche -Date: Tue Oct 30 21:35:28 2018 +0100 - - Fixed NumPy deprecations (#2129) - - * Changed np.matrix to np.array - - * Fixed angstrom escaping - - * Fixed tuple warning - - * Changed histogram norm - - * Fixed missing dot product - - * Removed superflous array wrapping - -commit 7b0571954d9d9c420c795a16cf678d5ccfc32095 -Author: Philip Loche -Date: Fri Oct 26 19:50:30 2018 +0000 - - Fixed error in segments, residues with 0 atoms (#2124) - - * fixed error in segments, residues with 0 atoms - - * Updated exceptions and tests. - -commit 2ffb7fbef7f5a6c32b5f2a59719441e75fec95c6 -Author: Richard Gowers -Date: Fri Oct 26 08:28:50 2018 -0500 - - Merge testsuite CHANGELOG/AUTHORS into main (#2100) - - * Merged testsuite AUTHORS and CHANGELOG into package - - * removed AUTHORS from testsuite - -commit c9a37e3a494f741014cf3fedf1fa2606c7b43a24 -Merge: e08e81748 42b856ad1 -Author: Johannes Zeman -Date: Thu Oct 25 13:14:14 2018 +0200 - - Merge pull request #2114 from zemanj/issue-2046-lib-distances-rework - - Issue 2046 lib distances rework continued - -commit 42b856ad1c69a6e45605ffc1266f3e7090a3564e -Author: zeman -Date: Sat Oct 20 04:07:38 2018 +0200 - - minor doc fix-ups for lib.util - -commit 145490d42896b3699f90d773be21109e3eefe89f -Author: zeman -Date: Sat Oct 20 03:22:45 2018 +0200 - - nsgrid docs fixup - -commit 767c5b2ffc4198cfbe786a06c316301c3170f6d1 -Author: zeman -Date: Fri Oct 19 22:51:53 2018 +0200 - - changed tests accordingly - -commit 225dfc0b3fc0533133bfd172e41080bd7d9b34fa -Author: zeman -Date: Fri Oct 19 22:45:21 2018 +0200 - - double precision distances in nsgrid; changed cutoff criterion to <= cutoff; added underscore prefix to non-user classes - -commit 5518d0b0d414ac2b83548e0b114bad1f2ba889a0 -Author: zeman -Date: Fri Oct 19 22:42:34 2018 +0200 - - moved check_box() to lib.util; changed cutoff criterion of all *capped_distances() methods to <= max_cutoff - -commit b49a6b001110f8f2efdbf264407abf3dfe9c4ad2 -Author: Oliver Beckstein -Date: Sun Oct 7 17:16:26 2018 -0700 - - pylint fix - -commit bd24ed1b65e95325abb57d6216e882833eaa1197 -Author: Oliver Beckstein -Date: Sun Aug 12 21:31:09 2018 -0700 - - more PSA tests - - NOTE: load/save fails --- maybe a bug?? - -commit e08e8174812fa604f61517c81e3ae9a3203c0776 -Author: Philip Loche -Date: Wed Oct 24 00:03:02 2018 +0000 - - Added sphinx markups for FrameIterator docs. (#2117) - - * Added sphinx markups for FrameIterator docs. - * updated CHANGELOG - -commit 983d974aa92ca77e0193db3413ea406893818a51 -Author: Philip Loche -Date: Fri Oct 19 20:59:08 2018 +0200 - - Tests for ChainReader __repr__ - -commit 37072c333183196f5f5156a37cf6b092b2f7ab0c -Author: Philip Loche -Date: Fri Oct 19 17:32:11 2018 +0200 - - Limit output of __repr__ for ChainReader class - - The output of __repr__ for the ChainReader class - is limited to 3 trajectories. For more only the first - one is printed. - -commit 044ce565232a2e82d13c45d73b3b8efea9b7f01b -Author: Richard Gowers -Date: Tue Oct 16 09:50:03 2018 -0500 - - Update test_align.py - -commit 276d5eb7de722461b71364cc504d75e831b20319 -Author: Philip Loche -Date: Tue Oct 16 09:35:22 2018 +0200 - - Updated AUTHORS - -commit a63d6783709982c68371c73c93cf3bea1182ba27 -Author: Richard Gowers -Date: Mon Oct 15 11:26:29 2018 -0500 - - Update test_align.py - -commit b951ab41fd3485e8cb48047db91eafaf703b6373 -Author: Philip Loche -Date: Sat Oct 13 16:20:00 2018 +0200 - - New default filename for align.AlignTraj - - Deprecate the default filename in align.AlignTraj and fixed - the file generation in the corresponding test. - -commit 9667c6d776491a3458843b2f75248504a1744cb1 -Merge: 25b27e13b 8a3b9473e -Author: Richard Gowers -Date: Fri Oct 12 10:01:53 2018 -0500 - - Merge pull request #2105 from MDAnalysis/pkdtree-docs - - add lib.pkdtree (and related) docs - -commit 8a3b9473e502522ce83de9725caea77245cbf8b3 -Author: Oliver Beckstein -Date: Fri Oct 12 00:07:49 2018 -0700 - - docs for transformations.translate - - - fixed missing docs - - edited intro for transformations - - made clear in which order transformations are applied - -commit 859a1dd5cf85c3f26b436ecc43d844d2d98ca1ec -Author: Oliver Beckstein -Date: Thu Oct 11 23:03:31 2018 -0700 - - add lib.pkdtree docs - - fix #2104 - -commit 25b27e13be4079e9cdb6a156d2120005e7bc9ae8 -Merge: 97db6d174 54f5ce54e -Author: Richard Gowers -Date: Tue Oct 9 17:52:57 2018 -0500 - - Merge pull request #2096 from MDAnalysis/start_0.19.1 - - Start 0.19.1 - -commit 108ffe0b19080b39975a93f947162f7371ac9144 (tag: release-0.19.0) -Merge: 39b0e4cc1 d9e58f23e -Author: Richard Gowers -Date: Tue Oct 9 14:53:57 2018 -0500 - - Merge pull request #2095 from MDAnalysis/release-0.19.0 - - Release 0.19.0 - -commit 54f5ce54ea704c2b5af35404ca596de43047b125 -Author: richardjgowers -Date: Tue Oct 9 12:25:30 2018 -0500 - - started version 0.19.1 - -commit 251f377101f55af9bc9fbc9c154ffeb4dfb298ce -Author: richardjgowers -Date: Tue Oct 9 12:17:21 2018 -0500 - - fixed compilation of cpp sources - -commit d9e58f23eb5b0855deabc20e3aa251ba0e0ef8a2 -Author: richardjgowers -Date: Tue Oct 9 12:19:27 2018 -0500 - - Updated c/cpp sources for 0.19 - -commit bd3ff7797d9a3e5b1e4af41921c7e730e9ced50f -Author: richardjgowers -Date: Tue Oct 9 12:17:21 2018 -0500 - - fixed compilation of cpp sources - -commit bd83af762881328eee27f5ee2776bd5b9c35bd01 -Merge: 39b0e4cc1 fc9e5d382 -Author: richardjgowers -Date: Tue Oct 9 11:13:43 2018 -0500 - - Merge branch 'develop' - -commit fc9e5d3825bede8799b5cf44c1fb17dc03168e71 -Author: richardjgowers -Date: Tue Oct 9 11:10:38 2018 -0500 - - finished version 0.19.0 - -commit 97db6d1742e3d16dbadf37f01f064821b6f66351 -Author: Richard Gowers -Date: Mon Oct 8 19:13:27 2018 -0500 - - Added optional forces and velocities to MemoryReader (#2080) - - Universe.empty now creates a MemoryReader trajectory - - Removed DummyReader (it was buggy) - - added varying box size to MemoryReader - - Universe.transfer_to_memory now also transfer velocities and forces - - MemoryReader now always has array of dimensions - - fixes Issue #2081 #2076 #2077 #1041 - -commit d37f87b9db93881c925848a19b6db7c63fb9e6f2 -Author: Oliver Beckstein -Date: Mon Oct 8 17:13:09 2018 -0700 - - fixed Gowers2016 reference (#2094) - - - fix #2092 - - also added explanation why we ask for both citations - - references page is again in sync with - https://www.mdanalysis.org/pages/citations/ - - added note/link at the top to the duecredit section - -commit 80560daa2fb582a5365ba1a9018d5411f91a604c -Author: Richard Gowers -Date: Sun Oct 7 21:37:55 2018 -0500 - - made GSD unsupported in Windows (#2090) - -commit edb1643c0a78f7e5447aa3ccc02712e4205ff073 -Author: Johannes Zeman -Date: Sat Sep 29 18:51:04 2018 +0200 - - bug fixes in lib.distances (#2083) - - * fix bug introduced in PR #2048 - - * allow for empty input coord arrays in lib.distances - - * tests for empty input coord arrays in lib.distances - - * fixed _bruteforce_capped() when no pairs are found; fixed _nsgrid_capped() for zero pseudobox size - - * return type testing for all functions in lib.distances - - * docs: more precise return type specifications - - * ensured _nsgrid_capped*() always returns pairs of dtype=np.int64 - - * added comments and removed unnecessary return type conversion from *capped_distance() - - * added out-of-box coordinate to TestOutputType tests - -commit 8918d42d1da0c653f41295fb7a131d7c04d46578 -Merge: 55e747504 00cf3b783 -Author: Oliver Beckstein -Date: Fri Sep 21 11:15:51 2018 -0700 - - Merge pull request #2055 from MDAnalysis/issue-1975-nomorequiet - - - Fixes #1975 - removed quiet in favour of verbose - - Fixes #1979 - deprecated start/stop/step in AnalysisBase init - - Started work on AnalysisBase API update #1463 - -commit 00cf3b783c779bf9320bdaab1f3436ec0734d7b2 -Author: richardjgowers -Date: Wed Aug 22 13:50:16 2018 -0500 - - removed quiet in favour of verbose - - updated usage of Analysis API, start/stop/step - now deprecated in __init__ and should be given in run method - - made PCA setup respect start frame more, - if start is given then initial weights are from that frame - not frame 0 - -commit 55e747504e51f873dfffdf8356ce425cdfbc6f08 -Author: Richard Gowers -Date: Fri Sep 21 10:22:37 2018 -0500 - - fixes #1795 (#2074) - - * fixes #1795 - - SphericalZone and SphericalLayer no longer shift atoms to inside - primary unit cell when calculating center of reference group - - * additional tests for sphzone - -commit 259f77811ba4af0e3dc5ca44d99766c29b6e140e -Merge: ec246c59e bab34da68 -Author: Johannes Zeman -Date: Thu Sep 13 18:19:33 2018 +0200 - - Merge pull request #2073 from zemanj/issue-2072-lib-distances - - removed obsolete functions from lib.distances - -commit ec246c59e8b26a4ff96bbcc8fd93adfe746be37c -Author: Oliver Beckstein -Date: Thu Sep 13 08:09:37 2018 -0700 - - allow import of WaterBridgeAnalysis from analysis.hbonds (#2071) - - fixes #2064 - -commit bab34da68133e01d0165b444734668c8e0f15bbe -Author: zeman -Date: Thu Sep 13 16:22:45 2018 +0200 - - moved all tests from utils/test_distances.py to lib/test_distances.py - -commit cdcf09354a3c6b7dfaada30b5c7b1edb337dbb61 -Author: zeman -Date: Thu Sep 13 13:22:33 2018 +0200 - - reduced precision in angle and dihedral tests to 4 decimals - -commit f92e072b5ded2a6db3afe725ed88243dd8b5c535 -Author: zeman -Date: Thu Sep 13 11:53:10 2018 +0200 - - improved docstring of lib.distances.calc_dihedrals - -commit 52ba2ca1eb92eb208662a7795818ec1a1f6db032 -Author: zeman -Date: Thu Sep 13 11:43:27 2018 +0200 - - removed `.. autofunction` entries of obsolete functions in lib/distances.py - -commit 16011c40f7dcb802510c48c36e3e71fd9f6b9eea -Author: zeman -Date: Thu Sep 13 11:38:51 2018 +0200 - - updated changelog (issue #2072) - -commit eb875da491df9a5dd53ccf81d0da9943daedab6c -Author: zeman -Date: Thu Sep 13 11:36:55 2018 +0200 - - improved docstrings of calc_bonds, calc_angles, and calc_dihedrals in lib.distances to better reflect the possibility of single coordinate input - -commit 0a9105ed01de38aab070a225da4432c9979839c2 -Author: zeman -Date: Thu Sep 13 10:27:25 2018 +0200 - - transformed tests for obsolete functions calc_distance, calc_angle, and calc_dihedral into tests for single coordinate input of calc_bonds, calc_angles, and calc_dihedrals - -commit ef0ee31168e02dfd08699cf1820851a2c7cafd6b -Author: zeman -Date: Thu Sep 13 10:23:50 2018 +0200 - - replaced obsolete functions calc_distance -> calc_bonds, calc_angle -> calc_angles, calc_dihedral -> calc_dihedrals in analysis.hbonds and in core.topologyobjects - -commit fdd326160238b1b9c6d86d92abde613af5a4ff30 -Author: zeman -Date: Thu Sep 13 10:20:27 2018 +0200 - - removed obsolete functions calc_distance(), calc_angle(), and calc_dihedral() from lib.distances - -commit ec8dd20a8ac5554755d311a395d7f7c75a0092d8 -Author: IAlibay -Date: Wed Sep 12 18:08:52 2018 +0100 - - Adding bond/angle reading to PARM7 TOPParser.py (#2052) - - * Adds support for reading bonds/angles - - * Adding bond/angle information for PARM7 - - * Adds support for reading bonds/angles - -commit 6741d1a2099381a4833c15f29c4334c934d4b87a -Merge: b5ba583f8 4caeea27c -Author: Johannes Zeman -Date: Wed Sep 12 18:15:01 2018 +0200 - - Merge pull request #2070 from zemanj/issue-2046-lib-distances-rework - - improved docstrings in lib/distances.py - -commit 4caeea27ce6e5f1d5397fbcd43adc111d2d0e77f -Author: zeman -Date: Wed Sep 12 14:38:04 2018 +0200 - - moved nsgrid import to top of lib/distances.py - -commit c9567dc5399f8a0ab1bff27e7576dc8c07495a46 -Author: zeman -Date: Wed Sep 12 11:52:18 2018 +0200 - - numpydoc selections for parameters with fixed value sets - -commit 791ecd970eece2ec763cec502efdfae6a0c8adb4 -Author: zeman -Date: Wed Sep 12 11:48:50 2018 +0200 - - use numpydoc `See Also` sections instead of `.. seealso::` - -commit 73ef0ebbca8bfcb83de524a4dce81cb2dbe3c0c7 -Author: zeman -Date: Wed Sep 12 11:46:44 2018 +0200 - - added back autofunction entries in MDAnalysis/lib/distances.py and removed :embers: in doc/sphinx/source/documentation_pages/lib/distances.rst instead - -commit b5ba583f8834b384a596691f36a787a3aeeef9f0 -Author: Jonathan Barnoud -Date: Wed Sep 12 00:32:03 2018 +0200 - - Fix SETTLE in TPR parser (#2068) - - * Fix SETTLE in TPR parser - - Support for SETTLE interactions in the TPR parser was added in #1953. - Though, the support was only added for the older versions of the TPR - format, causing errors with the newest files. In practice, when reading - the bonds on a recent TPR file containing SETTLE constraints, the - indices to the atoms involved in the bonds would be shifted. This is - because, the older TPR files use a different format to describe SETTLE - constraints. - - This commit should fix the issue by supporting both the old and the new - format for SETTLE. - - * Adapt the test to make sure the SETTLE issue is caught - - The test for SETTLE in TPR now checks that the index are not shifted. - -commit 1552a8b5c311089fc6068ca7077be80004b38f71 -Author: IAlibay -Date: Tue Sep 11 19:59:07 2018 +0100 - - Introduces user defined grid for density calculations (#2005) - - * Partially addresses #1928 - * Add user defined grid to density code - * Provides usage documentation user defn grid - * Adds tests for user defn grids - * Tests to capture Use Defn grid ValueError cases - * Comment fixes to density code + new tests - -commit 63c0a96739fa83c94f25f395880ba482567b93d8 -Merge: bf18cdad0 e0a2b16c4 -Author: zeman -Date: Tue Sep 11 18:50:01 2018 +0200 - - Merge branch 'develop' into issue-2046-lib-distances-rework - -commit bf18cdad0480982a16c5c92e618765409ba7edf0 -Author: zeman -Date: Tue Sep 11 18:47:57 2018 +0200 - - improved all docstrings in lib/distances.py - -commit e0a2b16c41c443f4f72b14e8af5c2b77051915c0 -Merge: cd58ce079 94a8920de -Author: Johannes Zeman -Date: Mon Sep 10 22:10:03 2018 +0200 - - Merge pull request #2067 from MDAnalysis/ci-python34-bandaid-2066 - - pin numpy version for Python 3.4 - -commit 94a8920de0be452d96d2ee2cd514e598b533b40b -Author: Johannes Zeman -Date: Mon Sep 10 18:18:12 2018 +0200 - - fixed .appveyor.yml - -commit b01f7f3b76555c52719878cf91d669ac0f52554f -Author: Johannes Zeman -Date: Mon Sep 10 10:20:46 2018 +0200 - - use conda.exe to build testing env - -commit ddb598c05d1de4f12e585a82706f617aa3f1c20e -Author: Johannes Zeman -Date: Mon Sep 10 09:49:03 2018 +0200 - - auto-update conda in appveyor builds - -commit 4e0cf0ffc7a1cc508a1c5afc8cb52e52003f16d3 -Author: Oliver Beckstein -Date: Sun Sep 9 22:36:13 2018 -0700 - - pin numpy version for Python 3.4 - - - NUMPY_VERSION=1.14 (last version known to be compatible with - Python 3.4 when installed via conda and conda-forge channel) - - fix #2066 - - This is a band-aid and should be reverted if the dependencies - in the conda-forge packages have been corrected. - -commit cd58ce0797b466d3a584beda765b58abce7f9ec2 -Author: Johannes Zeman -Date: Fri Sep 7 16:56:34 2018 +0200 - - Improved docstrings in lib/_augment.pyx (#2062) - - * added missing CHANGELOG entry for PR #2048 - - * ensured `lib.distances.distance_array()` always returns an array - -commit 280efad6da31dd463c4b1c852f2b963b950bd662 -Author: zeman -Date: Mon Sep 3 16:25:41 2018 +0200 - - improved docstrings in lib/_augment.pyx - -commit b7197052e0da2ff9701802d4e2ce2d84709be99e -Merge: 59860e70b 5fb8de84d -Author: zeman -Date: Mon Sep 3 15:42:51 2018 +0200 - - Merge branch 'develop' into issue-2046-lib-distances-rework - -commit 59860e70b765e75bd62e0ea653e3ca0988c06546 -Author: zeman -Date: Mon Sep 3 15:36:02 2018 +0200 - - improved docstrings in lib/_augment.pyx - -commit bb55d16ac6a8a71dfca60933be3cf14a54b7a7e8 -Author: zeman -Date: Mon Sep 3 09:15:24 2018 +0200 - - improved docstrings in lib/_augment.pyx - -commit 5fb8de84d7931e518faefe829a3cc4d3eae42ff6 -Merge: b89c23dfd 6fcadc055 -Author: Oliver Beckstein -Date: Thu Aug 30 22:50:48 2018 -0700 - - Merge pull request #2059 from VOD555/enh_rdf_s - - Using capped_distance instead of distance_array in rdf.InterRDF_s - -commit 6fcadc055d8b9ceb06cdedb7333821ac3e3808ef -Author: VOD555 -Date: Tue Aug 28 17:11:52 2018 -0700 - - Use capped_distance instead of distance_array - -commit b89c23dfdbf406ada5b077c32ba6e04b8d51e56d -Merge: 9cecdc92f 8cd8f55c8 -Author: Jonathan Barnoud -Date: Mon Aug 27 13:03:17 2018 +0200 - - Merge pull request #2058 from MDAnalysis/fix_cython_026 - - fixed Cython 0.26 not liking to call len inside nogil block - -commit 8cd8f55c89c5969889b6e270d36e7309a68f6d4d -Author: richardjgowers -Date: Sat Aug 25 14:39:58 2018 -0500 - - fixed Cython 0.26 not liking to call len inside nogil block - -commit 9cecdc92f6ce952f1e7ab3b6ccc49a1450781ad5 -Merge: d73b653f1 35440bfa0 -Author: Jonathan Barnoud -Date: Sat Aug 25 10:08:33 2018 +0200 - - Merge pull request #2056 from MDAnalysis/deprecate_flags - - deprecate flags - -commit 35440bfa025e2706b1fac0591b63d0187e00c464 -Author: richardjgowers -Date: Wed Aug 22 14:59:30 2018 -0500 - - deprecate flags - - add periodic kwarg to select_atoms - -commit fd80f3155504bd1b7f678e1756a6515f5069458f -Merge: 6d9e3eac5 d73b653f1 -Author: zeman -Date: Tue Aug 21 00:54:01 2018 +0200 - - Merge branch 'develop' into issue-2046-lib-distances-rework - -commit 6d9e3eac56538bcb79dd8a1e1c0a6489e45a3ca9 -Author: zeman -Date: Tue Aug 21 00:45:48 2018 +0200 - - ensured `lib.distances.distance_array()` always returns an array - -commit d487aa32905a0150cb8afc82d74595219af0be0c -Author: zeman -Date: Tue Aug 21 00:44:14 2018 +0200 - - added missing CHANGELOG entry for PR #2048 - -commit d73b653f19e8446bbb9de51bb41d71f78d148d30 -Merge: 62c35d49b 2feaaa91d -Author: Johannes Zeman -Date: Tue Aug 21 00:17:07 2018 +0200 - - Merge pull request #2028 from MDAnalysis/fast_fragments - - faster fragment finding implementation (PR #2028) - -commit 2feaaa91d54818df18beb70b25f8571e0bff40cf -Author: zeman -Date: Mon Aug 20 22:45:48 2018 +0200 - - test_find_fragments now ensures array_like input works with `find_fragments()` - -commit 40865ce39d0b99d5db98d3e2797c516baebb4e50 -Author: zeman -Date: Mon Aug 20 22:44:09 2018 +0200 - - use `bonds_view` instead of bondlist to initialize `bondmap` in `find_fragments()` - -commit bf366247dc33bd90f4542712cd353a42e12a32cc -Author: zeman -Date: Mon Aug 20 22:25:53 2018 +0200 - - more verbose docstring of `find_fragments()` - -commit 62c35d49bd9458f2b5057d28d4904391a4a38513 -Author: ayushsuhane <34154224+ayushsuhane@users.noreply.github.com> -Date: Mon Aug 20 08:56:24 2018 -0700 - - Replaced kdtree in neighborsearch with capped distances (#2054) - - * replaced kdtree in neighborsearch with capped distances - - * type modification - -commit 232bcd9b72754b2a9f7081262c1110f812cafcf5 -Author: richardjgowers -Date: Sun Aug 5 19:28:32 2018 -0500 - - Added Cython implementation of fragment finding - - Added more tests for fragment finding - -commit 5eebb18bea3a89df08dd3adfd187b9ee18a67d1f -Author: Johannes Zeman -Date: Sat Aug 18 17:48:29 2018 +0200 - - Simplified code in `lib.distances` a bit (#2048) - - * Simplified code in `lib.distances` - - * Renamed `_box_check()` -> `_check_box()` to be consistent with naming of other helper functions. - * `_check_box()` now also returns the box in the format expected by low-level C functions in `lib.c_distances`. - * Removed obsolete box type `'tri_vecs_bad'`. - * Renamed `_check_array()` -> `_check_coord_array()` to better reflect its purpose. - * Renamed `_check_results_array()` -> `_check_result_array()` since the checked parameter is always named `result`. - * `_check_result_array()` now returns a numpy array of correct shape and dtype if `result` is `None`. - * Improved docstrings of `transform_RtoS()` and `transform_StoR()` and added input coordinate shape check. Adjusted `test_augment.py` accordingly. - * Added shape check for input coordinates of `calc_distance()`, `clac_angle()`, and `calc_dihedral()`. - - * fixed wrong box types in `_check_box()` - - * tests for `transform_RtoS()` and `transform_StoR()` with single coordinate input - - * added ortho detection for tri_vecs format in `_check_box()` - - * added tests for `check_box()` helper function - - * made `_check_box()` correspond to docs and moved coord checks to `@check_coords()` decorator. - - * fixed tests to work with correct box requirements - - * Small doc fixes in `lib.util`; added check for contiguous input in `lib.util.blocks_of()` - - * added tests for `check_coords()` decorator and for `_check_result_array()` - -commit 825ee05423085521e6a718b3527be9b723409280 -Author: Oliver Beckstein -Date: Thu Aug 16 11:08:09 2018 -0700 - - tests and updated docs for analysis.data (#2047) - - - add docs explaining data and showing example use - - simple test for loading all data in analysis.data.filenames (analysis/test_data.py) - - replaced assert_array_equal with assert_equal in utils/test_datafiles.py, which I used - as a template - -commit e9ee6be5179c0589bb729774cddb7393df490f5f -Author: ayushsuhane <34154224+ayushsuhane@users.noreply.github.com> -Date: Wed Aug 15 06:06:44 2018 -0700 - - Modified the distance function in RDF (#2013) - - * using capped_distance function in rdf - - * updated docs, added cutoff in determine methods - - * extended RDF benchmarks to cover range of atoms - -commit 57d77d80a3236e9503473e2609ece2bdb59bc07e -Merge: 5cf8c5599 353f22051 -Author: Richard Gowers -Date: Tue Aug 14 18:50:15 2018 -0500 - - Merge pull request #2051 from MDAnalysis/remove-unused - - Remove unused/superfluous code - -commit 353f22051feaea8567b60a50e7c2fbe598c39aa7 -Author: Oliver Beckstein -Date: Tue Aug 14 15:17:50 2018 -0700 - - removed testsuite/__init__.py - - - fix #2040 - - instead of relying on pytest to interpret testsuite/setup.py as a package-level - setup and generate MDAnalysisTests/authors.py on Travis CI, explicitly build - the testsuite on Travis CI (see https://github.com/MDAnalysis/mdanalysis/issues/2040#issuecomment-413033864 - for details) - - made header of testsuite/AUTHORS the same as package/AUTHORS (until we merge them - according to #2050) - -commit 6cee1c1da269b501ec6006060c7a9174fed36ead -Author: Oliver Beckstein -Date: Tue Aug 14 14:20:24 2018 -0700 - - remove unused lib.mdamath.one_to_many_pointers() function - - fix #2010 - -commit 5cf8c5599e1a27c53e774c436b4e03fe71080f7a -Merge: 6f34d3cb6 8106a6c7f -Author: Richard Gowers -Date: Tue Aug 14 15:45:31 2018 -0500 - - Merge pull request #1995 from bieniekmateusz/survivalprobability - - SurvivalProbability - Readability, performance, and algorithm changes - -commit 6f34d3cb6e5e464724e991b3703051e1d99b8f5f -Author: Tyler Reddy -Date: Sat Aug 11 18:21:20 2018 -0700 - - TST: add codecov to appveyor CI run. - -commit e3966303776577e15a043daeceff5a591370398a -Author: ayushsuhane <34154224+ayushsuhane@users.noreply.github.com> -Date: Tue Aug 14 07:13:00 2018 -0700 - - Using Capped distance in distance selections (#2035) - - * modified capped function for faster computations, added search_tree in pkdtree, added tests, updated Changlog - - * updated docs, added cutoff in determine methods - - * safety condition added for bruteforce method - - * added _apply_nsgrid to selections - - * Removed dependency on kdtree flags, substituted capped_distance in class Distance based selection + point selection except CylindricalSelection - - * changed determine_method - - * minor correction for failed tests - - * updated CHANGELOG - - * minor flake8 corrections - -commit 8106a6c7f7bc848cbafe8e9e6c91dfa908b670df -Merge: 441d5baf4 d2e22ffb0 -Author: Richard Gowers -Date: Mon Aug 13 11:40:31 2018 -0500 - - Merge branch 'develop' into survivalprobability - -commit d2e22ffb0cb46af5266e39b940d7f00c1ca293c1 -Author: ayushsuhane <34154224+ayushsuhane@users.noreply.github.com> -Date: Mon Aug 13 06:43:29 2018 -0700 - - Uses faster distance evaluations in Individual methods in Capped Function (#2041) - - * modified capped function for faster computations, added search_tree in pkdtree, added tests, updated Changlog - - * updated docs, added cutoff in determine methods - - * safety condition added for bruteforce method - -commit 67d064a4515cc46404b9f15e0bab90c5db59a971 -Author: ayushsuhane <34154224+ayushsuhane@users.noreply.github.com> -Date: Mon Aug 13 06:42:18 2018 -0700 - - corrected time_guess_bonds, and added individual guess function in topology (#2045) - -commit 85ec60acd0f868005d66faead77c957b54b0d7be -Merge: 388346d38 80533cc8b -Author: Oliver Beckstein -Date: Mon Aug 13 00:53:42 2018 -0700 - - Merge pull request #2033 from hfmull/general_dihedrals - - Expansion of dihedrals analysis module - -commit 80533cc8b3f2aa9460a77e736da358a5de50f8e0 -Author: Oliver Beckstein -Date: Sun Aug 12 22:05:06 2018 -0700 - - integrate Ramachandran and Janin plots into docs and updated references - -commit b4f8484454b20326a92222d16a615852dc21b7f0 -Author: Henry Mull -Date: Sat Aug 11 08:47:03 2018 -0700 - - added ref=True to tests to increase coverage - -commit 7c4a700db52924de3f624100b289727a2e0386d8 -Author: Henry Mull -Date: Fri Aug 10 16:16:12 2018 -0700 - - Added image directory for documentation - -commit 8d94491ebe1174b8a73713507fcaf716d0b9888b -Author: Henry Mull -Date: Fri Aug 10 16:04:15 2018 -0700 - - Updated docstrings and CHANGELOG - -commit 3814fc5f05dea53d44c550a073e894b135ffb7b6 -Author: Henry Mull -Date: Fri Aug 10 15:45:24 2018 -0700 - - Added docs for analysis.data - -commit f887f76c7095ee0a53e8693234c5b441906b88b0 -Author: Henry Mull -Date: Fri Aug 10 13:59:03 2018 -0700 - - Fixed test_dihedrals, made analysis.data module - -commit e3211656d04be08515bea03d0f006cd09cee2c8d -Author: Henry Mull -Date: Thu Aug 9 17:24:32 2018 -0700 - - updated docstring and added comments - -commit 44d48add2878477402e3fdb3bc7a647100851352 -Author: Henry Mull -Date: Thu Aug 9 16:03:28 2018 -0700 - - moved ref plot data to new analysis/data directory, updated setup.py - -commit 4a52cc2fa5fe39ec309d1eaedef22f818b35f583 -Author: Henry Mull -Date: Thu Aug 9 13:21:20 2018 -0700 - - Fixed Janin plot method - -commit 556cf414d9e738305fc805ccd33a77be2f0229bd -Author: Henry Mull -Date: Thu Aug 9 12:07:01 2018 -0700 - - changed test_janin to check fewer decimals - -commit 2dd296fc1b8a5c5118aea2dd2d9d603ba9bfff41 -Author: Henry Mull -Date: Thu Aug 9 11:47:58 2018 -0700 - - Added reference plots for Ramachandran and Janin classes - -commit 6a6ec1b8877363d2d1b4778fdcdeed78d10bea92 -Author: Henry Mull -Date: Wed Aug 8 16:32:55 2018 -0700 - - updated CHANGELOG - -commit b72815becbf3449444ea0c3c9ced9ea428bcd36c -Author: Henry Mull -Date: Wed Aug 8 16:27:21 2018 -0700 - - updated docstring for dihedrals.py - -commit 92c99b7beef1af8e375cd1ad9e5b2e9feb5632e4 -Author: Henry Mull -Date: Wed Aug 8 15:57:13 2018 -0700 - - Updated test_dihedrals.py for new features - -commit 5efef65da7439fcde1c4f2fc710dc276b273f5fa -Author: Henry Mull -Date: Wed Aug 8 15:19:52 2018 -0700 - - updated to deal with selection failures - -commit 8002d04896d7799036b526897560bc8057196f87 -Author: Henry Mull -Date: Tue Aug 7 13:49:34 2018 -0700 - - fixed selections returning none in the middle of a protein - -commit 8c873c862bafc3cb679fbdadb434f398a387bf03 -Author: Henry Mull -Date: Wed Aug 1 17:15:52 2018 -0700 - - Added general Dihedral class, with tests and test data - -commit 8eadbe8a00aa3d8661c079f826003b064f390aa9 -Author: Henry Mull -Date: Wed Aug 1 14:40:23 2018 -0700 - - Made Janin class a subclass of Ramachandran - -commit c8f5d82df7fafc7a6a91a6b3c2faef408b7a6f73 -Author: Henry Mull -Date: Wed Aug 1 14:18:44 2018 -0700 - - cleaned up janin class - -commit e03fd0d8f0aeeea6019af0a7ec52596ec7001371 -Author: Henry Mull -Date: Wed Aug 1 14:17:42 2018 -0700 - - updated test_dihedrals for Janin class, added test data to datafiles.py - -commit 93e6017c8f076f7977293ea75c03e2f856e30028 -Author: Henry Mull -Date: Wed Aug 1 10:02:07 2018 -0700 - - Added Janin class to dihedrals.py - -commit 388346d38370d833b48152f61405a18942d25251 -Author: Oliver Beckstein -Date: Fri Aug 10 13:26:10 2018 -0700 - - additional PSA tests (#2036) - - * addition PSA tests - - - test functions that require seaborn (skip if cannot be imported) - - updated warning for plot_nearest_neighbors() to use run_pairs_analysis(neighbors=True) - -commit dbad72cfdc0ceb2d16e0f91c978acf8615b6e8dd -Author: Andrew McCluskey -Date: Fri Aug 10 17:58:55 2018 +0100 - - Allow read in of VERY large pdb files (#1978) - - Adds support for hybrid36 values in pdb ids - -commit 10fb62d95f52e7b6b77870a53a35e7adbc477658 -Merge: 0f18f489f 15fa3b3ec -Author: Johannes Zeman -Date: Wed Aug 8 18:32:23 2018 +0200 - - Merge pull request #2023 from MDAnalysis/issue-2018-memory-assignation - - Assigning positions on memory reader is persistent - -commit 15fa3b3ec2a1d4748b45edc4fa452c45dd6d5541 -Author: Johannes Zeman -Date: Wed Aug 8 17:08:24 2018 +0200 - - added leading underscore to internal-only method `memory.Timestep._replace_positions_array()` - -commit 0f24b89c56086948ff61c485766d3fb1517a6c32 -Author: Johannes Zeman -Date: Wed Aug 8 15:42:27 2018 +0200 - - Fixed some typos in coordinates.memory - -commit 0f18f489ff4d413f97bce9bab077d895751372a9 -Author: Henry Mull -Date: Tue Aug 7 14:44:03 2018 -0700 - - updated selection.rst to match groups.py docstring - -commit cca00f746f63f9b94fc35a3b8abc2a1b7ab09482 -Author: Oliver Beckstein -Date: Tue Aug 7 10:09:52 2018 -0700 - - doc updates/fixes for MemoryReader and Timestep - -commit e2c2b560fd198558a1be797e2dda06e968b449f4 -Merge: e90dfd244 b7751d19a -Author: Richard Gowers -Date: Tue Aug 7 07:30:15 2018 -0500 - - Merge pull request #2008 from ayushsuhane/cappedgrid - - Added capped function for grid search - -commit 8dc6894a6f2d10f83d942edaf121f428f2ebc3ad -Author: Jonathan Barnoud -Date: Sat Aug 4 17:20:01 2018 +0200 - - Assigning positions on memory reader is persistent - - Fixes #2018 - - Assigning an array to ts.positions with the memory reader does not break - the link to trajectory.coordinate_array anymore. That link needs to be - reset when switching to a new frame. This is done with the new method - ts.replace_position_array. - -commit b7751d19abda47e8fb1cf42f6fc12cfe34176728 -Merge: 0cde1ded9 e90dfd244 -Author: ayush -Date: Mon Aug 6 18:35:16 2018 -0700 - - merged develop - -commit 0cde1ded98b600d4b5c3e07ef0c8637f8c1785e7 -Author: ayush -Date: Mon Aug 6 18:30:29 2018 -0700 - - added sebastien to authors - -commit 2a0b01f8863c24abacb24db522ad23c065a9c491 -Author: ayush -Date: Mon Aug 6 17:31:25 2018 -0700 - - updated CHANGELOG - -commit e90dfd2445f2927a40a9f8e8b0317f485875e267 -Author: Tyler Reddy -Date: Mon Aug 6 13:22:51 2018 -0700 - - TST: Windows tests now xfail where needed (#2027) - - * all unit tests that currently fail or error on - Windows (Appveyor) will now strictly xfail - - * Appveyor test suite failure is no longer allowed - in CI--this prevents regressions in Windows compatibility - progress; the objective now is to reduce xfails instead - of actual failures - -commit 10e16c07b3c8ed8fc43ba7f5816496a8aa288fda -Merge: bf03cd457 fe792a1e0 -Author: Jonathan Barnoud -Date: Mon Aug 6 17:14:26 2018 +0200 - - Merge pull request #2024 from MDAnalysis/issue_2021_filesize_bytes - - BUG: Force 64-bit storage for xdr file offsets - -commit bf03cd4571dab9ab16d95348dd6805de9ffd24f3 -Author: Micaela Matta <31009265+micaela-matta@users.noreply.github.com> -Date: Mon Aug 6 08:25:20 2018 -0500 - - fixed Issue #2001 - support for Tinker periodic boundary box (#2011) - - * fixes Issue #2001 - support for Tinker periodic boundary box - -commit 76c81cf3660309ab7ab3760c5c2a1001669d9d21 -Author: ayush -Date: Mon Aug 6 02:05:31 2018 -0700 - - Added self_capped for nsgrid, moved no pbc box handling outside nsgrid and modified tests - -commit e28c70a6167123221f6993e7aec30d37c046822b -Author: ayush -Date: Sun Aug 5 18:53:07 2018 -0700 - - solved contiguous issue, fixed tests, and added checks in API - -commit 66d94e5cc760e1789b9ce185d5308b2f92f187af -Author: ayush -Date: Fri Aug 3 23:00:27 2018 -0700 - - removed parallel libraries - -commit c817b3945253b75be065c3b9fef6c3c5900e5e2b -Author: ayush -Date: Fri Aug 3 19:21:13 2018 -0700 - - returning list for get_indices, checked Docs - -commit 929fbf589d0a27ac7aeb6fc4bb3061f9647405c4 -Author: ayush -Date: Fri Aug 3 02:37:28 2018 -0700 - - docs unchecked - -commit a7264ec6cda550acf49f53ed62b70f3565b7929c -Author: ayush -Date: Thu Aug 2 02:30:58 2018 -0700 - - removed python functions, added no pbc handle using python min, max - -commit 57e9d55f5c4b546ee2cbdbe794578c550a77fe70 -Author: ayush -Date: Wed Aug 1 12:31:07 2018 -0700 - - conform tests a/c to modifications in API - -commit 7fd1f805192757464fdcd0fc22ef7344a9ba1d3d -Author: ayush -Date: Wed Aug 1 10:18:29 2018 -0700 - - added hack to handle NoPBC, tests to follow - -commit 4f1e729c143f7a13721541e3d68ea5cb1c072e0f -Author: ayush -Date: Wed Aug 1 08:57:07 2018 -0700 - - minor changes for failing tests - -commit b05e2430b5542de435e000936598e5ddb1203bf9 -Author: ayush -Date: Tue Jul 31 19:23:52 2018 -0700 - - reverted tests, removed sorting from get_indices, get_distances, modified compilation libs in setup - -commit 2c83681d155308322d2469ebe9b3c97d4edf8457 -Author: ayush -Date: Tue Jul 31 16:02:25 2018 -0700 - - mend - - Removed dict from buffers from speedup, seperated search and self_search, construct a grid and search with another grid - -commit 46f9030e95d261e89d8645c9e8262ce6934d7b5e -Author: ayush -Date: Tue Jul 31 15:57:42 2018 -0700 - - removed dict from buffers for speedup and modified tests - -commit a5d1355f90793a376642feed8b8611769d081c16 -Author: ayush -Date: Tue Jul 31 02:45:55 2018 -0700 - - Used vectors in place of lists and dict, cleaned code and modified function to take coordinates as input, modified tests accordingly - -commit e71b671af47353915ea50e849b0b8c7fd08cee04 -Author: ayush -Date: Sat Jul 28 14:32:16 2018 -0700 - - minor corrections to remove pylint error - -commit 8b8ea74933f9e2405ed8fb9a91d67012e596f032 -Author: ayush -Date: Sat Jul 28 12:16:50 2018 -0700 - - corrected name in documentation - -commit 9d52ac91889628616e63a4709e8803abcd1e272a -Author: ayush -Date: Thu Jul 26 23:10:41 2018 -0700 - - recovering accidently removed augment in setupd during rebase - -commit 08de29ba921f2c71b456a8b6f4eee9b6ec482c74 -Author: ayush -Date: Thu Jul 26 20:31:33 2018 -0700 - - added the capped function, modified the nsgrid to use box, coordinates as input parameters, modified tests - -commit 89f0b897ce5eb3efa84f9ea0964c7c493da5e69f -Author: Max Linke -Date: Sat Jul 21 20:42:25 2018 +0200 - - remove possible memory leak - -commit a738fa9b8bd4492e66141aca15662d5f76e7f42e -Author: Max Linke -Date: Sat Jul 21 15:34:59 2018 +0200 - - remove dead code - -commit f23000868a1b3b8780b7c9afd0007ac5711d2225 -Author: Max Linke -Date: Sat Jul 21 15:34:44 2018 +0200 - - use OK and ERROR as return codes - -commit 37658683132363094a86776671887e88742c79cd -Author: Max Linke -Date: Sat Jul 21 14:30:43 2018 +0200 - - make init_callable twice - -commit 7b0c56c99d5e99c4f4d092ba7d951b4052b89e76 -Author: Max Linke -Date: Sat Jul 21 14:30:23 2018 +0200 - - remove unused code - -commit 8a75a5fe81259ca5f2baee8ee780d3266a23b4cb -Author: Sébastien Buchoux -Date: Wed Jul 18 17:29:27 2018 +0200 - - Removed all references to c_gridsearch.pyx/grid module that reappeared after merge/rebase - -commit a1e03dd8bdc969e3d5dc21379fa6cee476f929e0 -Author: Sébastien Buchoux -Date: Wed Jul 18 16:44:11 2018 +0200 - - Tests written for FastNS - -commit 1a0e1507ea32bbede89e71f6ea2e5b6cbad201b4 -Author: Sébastien Buchoux -Date: Wed Jul 18 10:10:29 2018 +0200 - - Module MDAnalysis/lib/c_gridsearch.pyx renamed to nsgrid.pyx - -commit 86505097885e31040cea2a7f5360b39f0831a6bd -Author: Sébastien Buchoux -Date: Mon Jul 16 11:45:11 2018 +0200 - - Unneeded code removed from c_gridsearch.pyx - -commit 7f4a176cefa1ea1f33fd6d87ded4061944cfafce -Author: Sébastien Buchoux -Date: Sun Jul 8 20:10:33 2018 +0200 - - Memory allocation changed to PyMem to enhance speed in c_gridsearch.pyx - - Pre-converting np.resize to PyMem stuff - -commit c6339c5965f90008aeb25fbd1e4aa713bc7cdb8a -Author: Sébastien Buchoux -Date: Sun Jul 8 10:35:17 2018 +0200 - - NSResults object added to store results from NS. Started documentation - -commit 4d4a41511220599d333851f772a25b9c88acd1e6 -Author: Sébastien Buchoux -Date: Wed Jul 4 18:13:41 2018 +0200 - - Removed abort() from c_gridsearch.pyx and grid allocation moved to FastNS method. - -commit 28554002b8ea389bf82dfe1a3650a24ced8aab67 -Author: Sébastien Buchoux -Date: Sun Jul 1 16:54:21 2018 +0200 - - Removed pointer to nsgrid structure to avoid need to free it - -commit a26f437a7a73c0eec4f3f1ec3f97b56c0b5522e9 -Author: Sébastien Buchoux -Date: Sun Jul 1 16:53:22 2018 +0200 - - Corrected C (de)allocation in c_gridsearch.pyx. Should fix memory leak - -commit 97d07fe763e87bb0c94d060f7685c0bf8086c03d -Author: Sébastien Buchoux -Date: Sun Jul 1 14:06:40 2018 +0200 - - Added MDAnalysis header file to c_gridsearch.pyx - -commit 5e9fe318f42893c2b3ab5592d44a062bf24880e3 -Author: ayush -Date: Mon Jun 25 22:06:44 2018 -0700 - - removed the parallel handler to remove hard dependency on omp.h, can be added again for conditional compilation - -commit 0239d14bfdbe1cbb0f9b678b9dbb261a222c8c7e -Author: ayush -Date: Mon Jun 25 20:10:22 2018 -0700 - - Added MDAnalysis/lib/c_search.pyx for Grid NS search - -commit 579fa0088984fb4720e9b169eecf56184c6faefd -Author: Sébastien Buchoux -Date: Sun Jul 8 20:10:33 2018 +0200 - - Corrected Memory Leak - -commit ff33b2f62769b32241f0860af7b66ecfdbcfda42 -Author: Sébastien Buchoux -Date: Sun Jul 8 10:35:17 2018 +0200 - - NSResults object added to store results from NS. Started documentation - -commit f65e32bc89b930f638f81a0d87313ece89bdc471 -Author: Sébastien Buchoux -Date: Sat Jul 7 10:30:10 2018 +0200 - - grid allocation moved to FastNS method - -commit bdad5e3b3b38bb4ac96ec2b1dce58af4b067bc56 -Author: Sébastien Buchoux -Date: Wed Jul 4 18:13:41 2018 +0200 - - Removed abort() from c_gridsearch.pyx - -commit 0f35031499d97ed8e0bbbd429080a9e5c68af8c1 -Author: Sébastien Buchoux -Date: Wed Jul 4 16:17:11 2018 +0200 - - Removed pointer to nsgrid structure to avoid need to free it - -commit 02b5819a8480a69fdb09bd708155f7d38f29eeb5 -Author: Sébastien Buchoux -Date: Sun Jul 1 16:54:21 2018 +0200 - - Added Tests for grid search. Added grid in MDAnalysis.lib.__init__ - -commit 4b273a9c50b6235713b52920537c9107a799884a -Author: Sébastien Buchoux -Date: Sun Jul 1 16:53:22 2018 +0200 - - Corrected C (de)allocation in c_gridsearch.pyx. Should fix memory leak - -commit fc61e5e1ef60360bada560addbe4f5782e955c7a -Author: Sébastien Buchoux -Date: Sun Jul 1 14:06:40 2018 +0200 - - Added MDAnalysis header file to c_gridsearch.pyx - -commit 007d47da7c410289fa65d71f5420e6a95cc4bb17 -Author: ayush -Date: Sat Jun 30 01:23:12 2018 -0700 - - added the license header - -commit c3e227a863d5a505b453b0ce0167e5c8e406e0d9 -Author: ayush -Date: Mon Jun 25 22:06:44 2018 -0700 - - removed the parallel handler to remove hard dependency on omp.h, can be added again for conditional compilation - -commit c04301abd37f2268820010260cddf5e5edd40b61 -Author: ayush -Date: Mon Jun 25 20:10:22 2018 -0700 - - First commit for gridded method - -commit f92ec5da70805897bd6f874204e822fe76cb8722 -Author: ayushsuhane <34154224+ayushsuhane@users.noreply.github.com> -Date: Sun Aug 5 12:49:29 2018 -0700 - - Around keyword can use KDTree for periodic boundary conditions (#2022) - - * kdtree now works with pbc, modified _apply_kdtree method in pointselections - - * CHANGELOG - -commit 6b74bac909141477a6576b4560755708db50c632 -Author: ayushsuhane <34154224+ayushsuhane@users.noreply.github.com> -Date: Sun Aug 5 12:45:11 2018 -0700 - - Using Self Capped distance function in guess_bonds (#2006) - - * added an option to check for pairs within coordinate array using bruteforce_capped_self, pkdtree_capped_self + tests - - * Modified guess bonds to use capped function - - * seperated the self_capped_function, added tests, modified the guess_bonds function - - * modified CHANGELOG, and minor modifications - - * modified test for increased coverage, minor modifications to the self_capped_distance - -commit bf424a5d3ee43844d66fed219841ccf6acded692 -Merge: 2c9d6c50d e60b268f2 -Author: Jonathan Barnoud -Date: Sun Aug 5 19:33:52 2018 +0200 - - Merge pull request #2000 from davidercruz/rotation-transform - - corrected rotateby transformation calculation - -commit fe792a1e0aceb6ccd27ff49aa9f00bcdf607eeb4 -Author: Tyler Reddy -Date: Sun Aug 5 10:23:18 2018 -0700 - - BUG: Force 64-bit storage for xdr file offsets - - * Fixes Issue #2021 with Windows xdr large file - offset handling - - * on the Windows platform xdr file offsets are now - forced to use a 64-bit storage type so that, for example, - file seeks beyond 4 GB are correctly reported - -commit 2c9d6c50dfeb75b07f8aa87e299a717536b51931 -Author: Jonathan Barnoud -Date: Sun Aug 5 18:50:09 2018 +0200 - - Use stricter type for pkdtree indices (#2025) - - Using consistently np.int64 for the indices used in pkdtree avoids type - errors when using unique_int_1d. This should reduce the number of - failing tests on windows. - -commit c00a04a454da92acc6bf866a0b357f7987aefd20 -Author: Richard Gowers -Date: Sat Aug 4 08:15:22 2018 -0500 - - removed use of pytest.approx (#2019) - - * removed use of pytest.approx - - * removed mock decorator, playing badly with pytest fixtures - -commit 441d5baf4db55d0460309fba697fded346f86064 -Author: mat -Date: Fri Aug 3 13:50:33 2018 +0100 - - Updated comments - -commit 3331c8df1f706159665b016160756fdb0e7bd03c -Merge: 545550009 917dbec05 -Author: Richard Gowers -Date: Thu Aug 2 15:36:41 2018 -0500 - - Merge pull request #1990 from ayushsuhane/scipyKDTree - - Replace BioPython with Scipy spatial KDtree using augment function to handle Periodic boundary condition - -commit 2a1df89d292c285bd628e1f5259194c0e9d457a4 -Merge: 8536d546f a06468607 -Author: mat -Date: Tue Jul 31 14:45:48 2018 +0100 - - Merge branch 'survivalprobability' of github.com:bieniekmateusz/mdanalysis into survivalprobability - -commit 5455500094820e267689aaea30d1e2973b06dee3 -Merge: 50f430054 eb3cc9402 -Author: Richard Gowers -Date: Sun Jul 29 16:37:04 2018 -0500 - - Merge pull request #2015 from MDAnalysis/test_persistent_offsets_readonly_windows_fix - - BUG: test_persistent_offsets_readonly Windows fix - -commit 50f4300546894db3f1d36c0c9bc6bb09abca1cc4 -Merge: 461aadf67 82c84887f -Author: Richard Gowers -Date: Sun Jul 29 11:55:38 2018 -0500 - - Merge pull request #2014 from MDAnalysis/windows_test_universe_file_perm - - BUG: fix Windows file permission setting in test_universe - -commit eb3cc9402651cce0850ddb2d5e6c790aae9a2bd2 -Author: Tyler Reddy -Date: Sun Jul 29 09:06:40 2018 -0700 - - BUG: test_persistent_offsets_readonly Windows fix - - * test_persistent_offsets_readonly() now properly denies - write access to the test file on Windows - -commit 82c84887ff9a815d07f0918d4da00f5939b1f14e -Author: Tyler Reddy -Date: Sat Jul 28 17:27:45 2018 -0700 - - BUG: fix Windows file permission setting in test_universe - - * test_Universe_invalidpermissionfile_IE_msg unit test now - properly sets Windows file permission to deny read access - -commit 8536d546fa66413de5672c0e8c576b5fa1c2a7be -Author: mat -Date: Sat Jul 28 17:14:01 2018 +0100 - - Conforming to MDAnalysis overall API design. PR #1995 - -commit e60b268f279b93210f19456b0a5738a1c8aae4e4 -Author: Davide Cruz -Date: Sat Jul 28 17:02:39 2018 +0100 - - Improved docs; test point and vector in 2 shapes - -commit 46a7f69208b9bba747310e8a978578c28b201561 -Author: mat -Date: Sat Jul 28 16:41:08 2018 +0100 - - Rebased and resolved conflict with CHANGELOG - -commit 5988f96be2ec5b1968158607a8cf585b288ca778 -Author: mat -Date: Wed Jul 25 01:53:19 2018 +0100 - - Backward compatibility (and priority) with warnings. - -commit 2c36f371b42f70d5e3adc806d138952b73721b23 -Author: mat -Date: Tue Jul 24 17:44:24 2018 +0100 - - Conforming to the run() interface defined in #1463. - -commit 4b1ee1403f5b8a5a1aaf11d049453e4728c8a2e5 -Author: mat -Date: Tue Jul 24 15:41:47 2018 +0100 - - Tests adjusted to the new interface. - -commit 036ccc6925d0d1ae4b52e34bc007efa92d9a5a18 -Author: mat -Date: Tue Jul 24 15:36:52 2018 +0100 - - Documentation and requested changes PR #1995. - -commit c01c9942e303bf71668f4be3a1921f3588b67438 -Author: mat -Date: Mon Jul 23 15:42:17 2018 +0100 - - Author and changelog updated. - -commit 9f8c677cf223fca491e13d950d83e3d6343b7961 -Author: mat -Date: Mon Jul 23 15:35:50 2018 +0100 - - Trailing lines - -commit 9a208469acb19d7b5d20e17249d57360995d4c54 -Author: mat -Date: Thu Jul 19 00:40:40 2018 +0100 - - t0 testcase covers also tf. If one too many frames is used, wrong results will be given. - -commit a53a6736db3adafa0bdb4d05912a749815e8d2e4 -Author: mat -Date: Thu Jul 19 00:23:36 2018 +0100 - - Defined dataset for the test case t0 != 0. The code will be correct if the first two frames are skipped. - -commit ab21e39ef2773c33fe0ec41bbc5d598bae135745 -Author: mat -Date: Wed Jul 18 14:06:58 2018 +0100 - - Simple test that checks for the known Survival Probability. - Waterdynamics: removed an index bug that went 1 too high tau. - -commit c66f3dbf48f832c3eee87f02be552861a1407516 -Author: mat -Date: Tue Jul 17 19:41:47 2018 +0100 - - Mock data for the test case. - -commit 40e926d3e17cfc99078327f5d834bfdbc8630a36 -Author: mat -Date: Tue Jul 17 19:03:19 2018 +0100 - - Check if all tau == 1 when the same atom IDs are returned at each frame - -commit 8470c4ca83127638ef002939e0de2269000772a6 -Author: mat -Date: Thu Jul 5 17:02:22 2018 +0100 - - tiny bug - -commit 0ef10576c096ad5accf3bd49c506053fd86b8271 -Author: p-j-smith -Date: Thu Jul 5 12:24:03 2018 +0100 - - Storing a set of atom ids at each timestep, rather than a set containing - an atom group, to reduce the memory load. - - Updated the docstring. - -commit d348cc783e70d836c57fba7e77b587ed9f52337a -Author: mat -Date: Tue Jul 3 17:32:22 2018 +0100 - - The tf is inclusive. - -commit b5d07e9c71ae9fbfbd8c778804f4bc4c31076fc1 -Author: mat -Date: Tue Jul 3 17:13:27 2018 +0100 - - verbose mode added + better documentation. - -commit d8f4a60f9795d859c37490113a9c244140516b72 -Author: mat -Date: Tue Jul 3 16:36:32 2018 +0100 - - Moving the checks to the constructor. - - Saving the extracted data for the user to be able to dig deeper, if - necessary. - -commit 7cf8318b2465d8dc14f30caedf57aed412d2f6ac -Author: mat -Date: Tue Jul 3 14:37:03 2018 +0100 - - Adjusting the tests because the return function gives back taus too. - -commit 01e6fec9061cd97b781b2a3298eb40da0ecd3111 -Author: p-j-smith -Date: Tue Jul 3 14:01:58 2018 +0100 - - Returning the survival probability and the values of tau as - numpy arrays. - - Changed the name of tau_timeseries to sp_timeseries as it is a more - accurate descriptor. - - Removed some of the +/- 1 in indices to improve readability. - -commit 3cc426d7c8a1218a275b5ebf24fef737e1e0ed7e -Author: mat -Date: Tue Jul 3 11:25:12 2018 +0100 - - Using the set.intersection argument unpacking: easier to read, neater - code and no performance drawbacks. - - Tests: the user should not be forced to rely on the internal data - structures .timeseries. Returning the results with the function run(). - -commit 3928107359a5b4d807c42373cf935df2b21c5e31 -Author: mat -Date: Sun Jul 1 19:58:49 2018 +0100 - - Should the first data point be always 1? In that case first tau = 0. Or should the first data point reflect the first tau which is non-zero and therefore the first change is quantified? I believe it is the latter. This breaks the current tests which, for example, by asking for 4 datapoints, always get the first datapoint for tau=0 that is 1. - -commit 054228bec308924586bbdba1ceb069843e0ad6b3 -Author: mat -Date: Sun Jul 1 17:38:31 2018 +0100 - - If there is no atom at t, this does not need to be checked for each t+tau. - - Refactoring. - -commit cd2abb986d72f2b4240408685a3c54d20c14d075 -Author: mat -Date: Sun Jul 1 17:12:04 2018 +0100 - - No need to check t+tau for any tau if at t it is empty. - -commit da0f59482b17193f575e6f9f7be4489b8522d9a8 -Author: mat -Date: Sun Jul 1 17:05:32 2018 +0100 - - Switch the nested loops. Looping only once over the entire trajectory and more times over tau. This will lead to faster code (local memory/cache optimisation). Additionally, opens the door for combining multiple taus together. - -commit 522e7172f95c74436a44a5157f56321243d85877 -Author: mat -Date: Sun Jul 1 14:37:52 2018 +0100 - - Minor changes: - -return the list rather than require the user to access the internal list - -use tau_max variable name which is consistent with the equation, in contrast to dtmax - -commit 99ada4d8678b47fe7d4f8f8ac74a37cf8849f575 -Author: mat -Date: Fri Jun 29 20:09:37 2018 +0100 - - Changed expected output from 0.0 to Nan. - - The survival probability is a measure of how likely a selected molecule - is to remain within a specified region over a period of time. If at t0 - the selected molecule is not in the specified region, no survival - probability can be calculated. - - For example, consider that we would like to calculate the survival - probability of an ion at an interface. If the ion never approaches the - interface, the previous test would return a survival probability of 0, - which suggests that the ion comes to the interface but leaves - immediately. However, as the ion was never at the interface, no - survival probability can be calculated from this data. - -commit 6d35ed9a4901fa5fcf768dbd07072f47fb69b25e -Author: mat -Date: Fri Jun 22 17:14:13 2018 +0100 - - Syntax errors - -commit 351fc5d813944b138aa0c1b5b2b5207ab316286c -Author: p-j-smith -Date: Fri Jun 22 16:34:39 2018 +0100 - - Optimised calculation of survival probability. - - Atom selections at each frame are now stored as sets rather than lists, - so determining the intersection of selections is faster. - - Survival probability is now calculated by a single function. - -commit cdcd942db0eac4e4dd497a53a5f1501c7270d697 -Author: mat -Date: Thu Jun 21 17:01:52 2018 +0100 - - Use reverse search for number of survivors. Stop search if no survivors. - -commit b827bc09179a6ad550c30573c2865340eaa381ec -Author: mat -Date: Thu Jun 21 16:44:05 2018 +0100 - - The windows size tau + t was already accounted for in _getMeanOnePoint upstream - -commit 461aadf6733d234e0913bae774a6312a208ede27 -Merge: b50c6f02a f1e72ab0f -Author: Richard Gowers -Date: Fri Jul 27 08:10:25 2018 -0500 - - Merge pull request #2009 from MDAnalysis/unique_int_1d_win - - BUG: fix several Windows test failures with int64 type enforcement - -commit f1e72ab0fff760d3025216110d92e0fd5cc76f38 -Author: Tyler Reddy -Date: Thu Jul 26 21:06:29 2018 -0700 - - BUG: fix several Windows test failures with int64 type enforcement for unique_int_1d in selection.py. - -commit 917dbec057e0e7d6381977338f448f755d43e3ce -Author: ayush -Date: Thu Jul 26 01:01:51 2018 -0700 - - pair sorting before picking out the unique pairs. Previously resulting repeat pairs - -commit b50c6f02af8947c3cde44f08c4f5e26d1f6b7314 -Merge: 2a6f1f617 193e503fa -Author: Max Linke -Date: Wed Jul 25 07:46:22 2018 +0200 - - Merge pull request #1997 from hfmull/dihedrals - - New Dihedral and Ramachandran Analysis - -commit 182d8671a40a12257e5e16ec745ad08620fe27a3 -Author: ayush -Date: Tue Jul 24 18:31:24 2018 -0700 - - removed set_cutoff from Neighboursearch as well - -commit 666370e3aa5f394bcb8e057d2b52af602b9997e3 -Author: ayush -Date: Tue Jul 24 17:53:36 2018 -0700 - - removed set_cutoff, and modified the pbc property definition - -commit a064686070d64b076a4eda5aabed9d0af234c107 -Author: mat -Date: Wed Jul 25 01:53:19 2018 +0100 - - Backward compatibility (and priority) with warnings. - -commit eadcf3fbd692669174751bc244919f023997d38c -Author: ayush -Date: Tue Jul 24 16:35:23 2018 -0700 - - modified the sorting, and made pbc a property - -commit 193e503fae739130dcd59a0bedc1972a3b4e1345 -Author: Henry Mull -Date: Tue Jul 24 11:40:04 2018 -0700 - - Fixed imports of test_dihedral.py - -commit affc0abb0012b911606c848c38dc1066667aa82d -Author: mat -Date: Tue Jul 24 17:44:24 2018 +0100 - - Conforming to the run() interface defined in #1463. - -commit 505f5494c89a0e981a99f8e451e59598a1a36440 -Author: mat -Date: Tue Jul 24 15:41:47 2018 +0100 - - Tests adjusted to the new interface. - -commit c166ab20fcfb4e97b0f73967413c813bf4688580 -Author: mat -Date: Tue Jul 24 15:36:52 2018 +0100 - - Documentation and requested changes PR #1995. - -commit 756123291154d781c452babcf948c45b002e690d -Author: Henry Mull -Date: Mon Jul 23 13:58:20 2018 -0700 - - Fixed docstring - -commit e83bd9aade3b4392d51ba068d3ceef79725f65ce -Author: Henry Mull -Date: Mon Jul 23 11:54:20 2018 -0700 - - Fixed imports and docstring - -commit cc4db3599e74efc150048c5afb9bd441289fa975 -Author: mat -Date: Mon Jul 23 15:42:17 2018 +0100 - - Author and changelog updated. - -commit 87cce214b3aedf3c0c7f7b888694c7c9d0ddb1d0 -Author: mat -Date: Mon Jul 23 15:35:50 2018 +0100 - - Trailing lines - -commit 2a6f1f61734a53bbc2531c4f7fd5797c8be3eaaa -Merge: 238904da5 83f6cf23e -Author: Richard Gowers -Date: Mon Jul 23 08:23:14 2018 -0500 - - Merge pull request #2002 from MDAnalysis/issue_1962_cutil - - TST: test_unique_int_1d now enforces int64 type - -commit dfadeffdd52932ca6d71ade9ded9fab84faf4212 -Author: ayush -Date: Sun Jul 22 19:53:08 2018 -0700 - - Modified search pair to check the number of bonds - -commit f8d49fbfbc5bd4080792169be20d624abff3175f -Author: Davide Cruz -Date: Sun Jul 22 22:33:17 2018 +0100 - - added checks for direction ; added tests for direction - -commit 9e5db309609cd46642d06f647102393eb0ecaede -Author: davidercruz -Date: Sun Jul 22 12:51:31 2018 +0100 - - code cleanup - -commit 9ba25f1f07e173089b2edc449ef559c634d14f59 -Author: davidercruz -Date: Sun Jul 22 04:19:36 2018 +0100 - - fixed typos - -commit 83f6cf23e1afedd571d11c82910751943460f4c7 -Author: Tyler Reddy -Date: Sat Jul 21 19:36:10 2018 -0700 - - TST: test_unique_int_1d now enforces int64 type - - * the Cython function unique_int_1d() is clearly - defined and documented to accept an int64 argument - type, but its associated unit test was not enforcing - this type, which caused 6 test failures on the Windows - platform - -commit b2092cdfb85e3a665d581abd27f9a9372fa985ac -Author: ayush -Date: Sat Jul 21 17:52:11 2018 -0700 - - completely removed Biopython.KDTree and wrapper around it, replaced the name of wrapper around scipy.KDtree to PeriodicKDTree - -commit 6cffae9ab867940d56a480c80e1b8b799decb8c3 -Author: davidercruz -Date: Sun Jul 22 01:43:50 2018 +0100 - - rotateby now accepts weights - -commit 5f54fecba2d970317dafcd8c63c851e4a89e1e53 -Author: ayush -Date: Sat Jul 21 17:19:28 2018 -0700 - - Modified selections to change KDtree selections from Biopython to scipy - -commit d25e6e5e9cb57f65c8e7f2696c34da4d2042a1d5 -Author: ayush -Date: Sat Jul 21 17:18:18 2018 -0700 - - removed the dependency of Bio.KDtree and PeriodicKDTree from lib, and tests - -commit 4f23420cd12741795081bf7693be94aca1b918a3 -Author: davidercruz -Date: Sun Jul 22 00:29:20 2018 +0100 - - rotaateby now behaves as rotate, updated tests to use transform(matrix) - -commit 000f1e765c77b1cf68db999055fe1c19b067e3a2 -Author: davidercruz -Date: Sat Jul 21 02:43:38 2018 +0100 - - fixed issue with rotation from non-origin point calculation - -commit 60b1667205de120c53e5bae116113a07ec6db1ab -Author: Henry Mull -Date: Fri Jul 20 15:06:18 2018 -0700 - - Fixed plotting in dihedrals.py, added more tests to test_dihedrals.py - -commit 610368e3509ef1adb648fe567967011d0aa0aa09 -Author: Henry Mull -Date: Fri Jul 20 12:50:27 2018 -0700 - - Updated CHANGELOG - -commit 4812dc013b0f7002b034f321b26c7b5ac8cea85e -Author: Henry Mull -Date: Fri Jul 20 12:46:35 2018 -0700 - - Updated docstrings of dihedrals.py, added files to docs - -commit 0d35aefc2980c00f0085cbecddca6615da775009 -Author: ayush -Date: Fri Jul 20 01:22:27 2018 -0700 - - modified the tests and module a/c to returns of augment, added more tests - -commit fae1bee1756f380de5d9eb87dc9a083e1c780811 -Author: ayush -Date: Tue Jul 17 22:00:35 2018 -0700 - - changed the tuple sorting - -commit c9a615f68ea6b8bea3157b5583c9cf89ed9b086f -Author: ayush -Date: Mon Jul 16 02:38:27 2018 -0700 - - recover accidently deleted test from PeriodicKDTree - -commit a2090fac75a5da83d7502c6606f89ffa941fbcba -Author: ayush -Date: Mon Jul 16 02:21:09 2018 -0700 - - First commit to replace Biopython with Scipy KDTree along with tests and doc - -commit c5fcfb8d80470aa147b662a2b52400029f9f2da5 -Author: Henry Mull -Date: Thu Jul 19 17:27:49 2018 -0700 - - Removed identical frames test, switched to assert_almost_equal - -commit bfc75c9d6d8341e4951c14ec53aedb42809bdacd -Author: Henry Mull -Date: Thu Jul 19 17:21:17 2018 -0700 - - Updated test references and added them to __all__ - -commit 3b79336125117c2a397008d321da48a039220757 -Author: Henry Mull -Date: Thu Jul 19 17:20:18 2018 -0700 - - Fixed zip function - -commit 15c2bd95d2bc5bf9114587b209948cbc1e442101 -Author: Henry Mull -Date: Thu Jul 19 16:49:40 2018 -0700 - - Added six to imports - -commit f0d8030f0100a0c7c9d7e360e75fa08de161d554 -Author: Henry Mull -Date: Thu Jul 19 16:19:56 2018 -0700 - - Fixed imports - -commit 4dabf32c9861735c9aca7f0657498cdc5abd3568 -Author: Henry Mull -Date: Thu Jul 19 16:14:11 2018 -0700 - - Switched to distances.calc_dihedrals and simplified plot function - -commit 238904da5b0a055db31bbb476e63f95d3588cd89 -Merge: d7cfc2797 7ef48ef8f -Author: Richard Gowers -Date: Thu Jul 19 11:03:46 2018 -0500 - - Merge pull request #1977 from ayushsuhane/augment - - Augment Coordinates for periodic Boundary conditions - -commit 7ef48ef8f36ca795974d8be8f3dc9825c12c0394 -Author: ayush -Date: Thu Jul 19 02:30:06 2018 -0700 - - removed augment.rst - -commit 56c0b035dceeb3a7ee6f59828fdf2f7555d7d40b -Author: ayush -Date: Thu Jul 19 02:17:09 2018 -0700 - - moved _dot, _cross, _norm to _cutil.pyx, modified document structure for _augment - -commit d194cee51678a0701b426a0b878c643a874dbcf2 -Author: mat -Date: Thu Jul 19 00:40:40 2018 +0100 - - t0 testcase covers also tf. If one too many frames is used, wrong results will be given. - -commit 5bd2e0bee500fc1f7c4a7ef7fca2d0e2ac58ea5f -Author: mat -Date: Thu Jul 19 00:23:36 2018 +0100 - - Defined dataset for the test case t0 != 0. The code will be correct if the first two frames are skipped. - -commit ad4e598f1500464fe69b049663344931f25b4102 -Author: Henry Mull -Date: Wed Jul 18 10:37:10 2018 -0700 - - Updated docstring of dihedrals.py - -commit 49882ffdb208eeb8ac57b392fa5ffc751b836ed0 -Author: mat -Date: Wed Jul 18 14:06:58 2018 +0100 - - Simple test that checks for the known Survival Probability. - Waterdynamics: removed an index bug that went 1 too high tau. - -commit feebb7d69887fa8d00c0c25f7fca061cb3c2702c -Author: ayush -Date: Wed Jul 18 02:57:17 2018 -0700 - - Modified input type to undo_augment, added documentation stub - -commit d7cfc27978a8104c17340eac8339560eabde15c6 -Merge: 5f151b485 41bed97a8 -Author: Richard Gowers -Date: Tue Jul 17 17:31:27 2018 -0500 - - Merge pull request #1994 from MDAnalysis/pylint2 - - don't allow pylint to fail any more - -commit 41bed97a85271498acbe99ee11858fc48aaab925 -Author: richardjgowers -Date: Tue Jul 17 16:28:06 2018 -0500 - - don't allow pylint to fail any more - -commit 5f151b48525a5d1d3d00b73855dbf6fe88960b69 -Author: richardjgowers -Date: Tue Jul 17 15:00:23 2018 -0500 - - pylint changes for testsuite - -commit 1fbd1552feb559dbaaa32e43793c740d582b5d7f -Author: richardjgowers -Date: Tue Jul 17 12:25:48 2018 -0500 - - fixes for pylint 2 - -commit 98c83709c638a57b7e9290f692364b4f1ac931cf -Author: Henry Mull -Date: Tue Jul 17 14:02:46 2018 -0700 - - Updated residue selection of function, added test files - -commit d471bd00ae55dd7affd5698cf1963c2a105ee230 -Author: mat -Date: Tue Jul 17 19:41:47 2018 +0100 - - Mock data for the test case. - -commit 53abc628318869da3556b6f58422feb1e77322e2 -Author: mat -Date: Tue Jul 17 19:03:19 2018 +0100 - - Check if all tau == 1 when the same atom IDs are returned at each frame - -commit f7d0e4d5fb6eef62a496a18cce4a9ceea9a9d6dd -Merge: 50d8687f0 e8b2b176d -Author: Richard Gowers -Date: Tue Jul 17 09:46:47 2018 -0500 - - Merge pull request #1987 from MDAnalysis/make_whole_fix - - fixed make_whole only working on 0 base AtomGroups - -commit e8b2b176dd77d5072eae64b62d3828c2451fc5bf -Author: richardjgowers -Date: Tue Jul 17 08:04:31 2018 -0500 - - allow pylint to fail - -commit 2ed97ab87f3957af0e4cd9ffafff3a9842817b2e -Author: richardjgowers -Date: Tue Jul 17 07:51:52 2018 -0500 - - tweaked pylint - -commit 776c83aa18b1db69cf21e7e5025b24034347ced1 -Author: ayush -Date: Mon Jul 16 18:27:43 2018 -0700 - - cdef'd float instead of numpy array, changed the format of tests - -commit 1ca2bc74e6c02c7995d720073c740b6b45fc135b -Author: richardjgowers -Date: Sat Jul 14 17:23:33 2018 -0500 - - fixed segfault in make_whole with multiple fragments - -commit d7dd262b42abb3cb8cbe0e90dc66f681ac19a2d6 -Author: ayush -Date: Sat Jul 14 20:02:12 2018 -0700 - - added six.moves import - -commit 0eac39b8d2a7a485965f841f9151ea7ae781edbb -Author: ayush -Date: Sat Jul 14 18:22:48 2018 -0700 - - Modified documentation, changed the name of function - -commit 8c8edc73d2a68d9b507fa3449a3026c7a0ffdb28 -Author: ayush -Date: Sat Jul 14 15:12:20 2018 -0700 - - Added a testcase for multiple queries - -commit 900b09c6be9bd472da6c1e40409be72a13dbf188 -Author: ayush -Date: Sat Jul 14 14:56:55 2018 -0700 - - added Augment functionality, tests, modified CHANGELOG - -commit 973910c9caa3d776b7e7d8439d96ee68de5102f7 -Author: Henry Mull -Date: Fri Jul 13 16:57:35 2018 -0700 - - Added IndexErrors to function - -commit abbc3efb3bcf95125ef8c0d566ae67e8cb388272 -Author: Henry Mull -Date: Fri Jul 13 14:33:40 2018 -0700 - - updated plot function, simplified preparation - -commit 50d8687f07ac978ba18219e0a3f873015617dac6 -Author: Oliver Beckstein -Date: Thu Jul 12 16:45:25 2018 -0700 - - Update issue templates - - GitHub provides more fine grained control over issue templates. I used our standard template for *Bug report*, used their suggestion for *Feature request*, and created one for *Questions* which tells people to use the mailing list! - -commit 13ee8a0fa9eeea4f1ab30d3deec37c70607f38e0 -Author: Henry Mull -Date: Wed Jul 11 09:30:29 2018 -0700 - - Added docstring to dihedrals function - -commit 1f149adffa70538be6a4297c8f149670117273b5 -Author: Henry Mull -Date: Tue Jul 10 16:28:28 2018 -0700 - - fixed calculation errors and added plot function - -commit 30da78311e2ac87d6d83852d8127f5ff5605dada -Author: Henry Mull -Date: Tue Jul 10 14:50:23 2018 -0700 - - added imports to dihedrals.py - -commit 62a194f2895bca7b66f8198bbc001ab6df820ad0 -Author: Henry Mull -Date: Tue Jul 10 14:41:39 2018 -0700 - - First commit of dihedrals.py - -commit 675252af36128aca242af3e2d4a9cbbf554f8d3b -Merge: 4be325c3b 06e386fcd -Author: Richard Gowers -Date: Thu Jul 12 14:51:49 2018 -0500 - - Merge pull request #1934 from MDAnalysis/issue1894-iterator-len - - Proof of concept trajectory class iterators - -commit 4be325c3b46ded353a17dadec9cfa94558f17080 -Merge: 28404e26c 9d3a2fc15 -Author: Richard Gowers -Date: Thu Jul 12 14:39:28 2018 -0500 - - Merge pull request #1941 from ayushsuhane/cappedfeature - - Introduce Capped distances to evaluate the indices of pairs within a fixed radius - -commit 06e386fcd69bddfdaf6e49a2d32fda0425a86ac2 -Author: Jonathan Barnoud -Date: Thu Jul 12 02:04:45 2018 +0200 - - Address comments from @orbeckst on #1934 - -commit 28404e26ce56355a461bbfed2b4c6ebcdc72c6e8 -Merge: bba488a8a fec060c7b -Author: Richard Gowers -Date: Thu Jul 12 12:28:05 2018 -0500 - - Merge pull request #1968 from MDAnalysis/gro_benchmarks - - more GRO benchmarks - -commit fec060c7b122d16bef7a3a83e4eb6c17c41443f8 -Author: Richard Gowers -Date: Thu Jul 12 10:17:24 2018 -0500 - - Update GRO.py - -commit 9d3a2fc15efd3f99e8f5bd62610a92b06b4fa1e0 -Author: Richard Gowers -Date: Thu Jul 12 10:06:35 2018 -0500 - - Update test_distances.py - -commit edc5b2dcfb06350c6ea8bff36d7a3836aeabc864 -Author: ayush -Date: Thu Jul 12 01:58:13 2018 -0700 - - more tests - -commit 7e25ea3ea1d0b88f9a1a296bc06f960f40553afb -Author: ayush -Date: Thu Jul 12 01:03:55 2018 -0700 - - added few more tests - -commit cea2c379e5f82746d1c9390a2e32906d34ed1525 -Author: ayush -Date: Wed Jul 11 19:35:12 2018 -0700 - - Added tests for minimum cutoff - -commit bba488a8a284528fe2f011ba4be1850b5be542d6 -Author: Oliver Beckstein -Date: Sun Jan 21 15:57:40 2018 -0700 - - deprecated save*() methods (#1972) - - - fix #1972 - - important: use own util.deprecate() instead of the numpy version - - deprecated save() methods in align and contacts (#1972) - - deprecations updated 0.17.0 --> 0.19.0 - - deprecated save() in lineardensity and necesscary doc update - - deprecated save() (#1972) - - added docs explaining the results data structure - (needed anyway, but in particular when user does not get the - dated in separate datafiles) - - deprecated save() in rms (#1972) - - deprecated save() in hole (#1972) - - deprecated save() in diffusion map (#1972) - - deprecated save_table() and save_results() in all hbond analysis clases (#1972) - - doc updates for deprecations in hbonds - - removed save_table() from wbridge analysis and use it from the parent class - - deprecated save_result() PSA (#1972) - - updated CHANGELOG for #1972 - -commit 89d6f2b3298f84b58737d733400f6468e2581684 -Author: Oliver Beckstein -Date: Sat Jul 7 12:12:36 2018 -0700 - - add our own lib.util.deprecate - - The numpy.lib.util.deprecate() function messes up our doc strings. See - https://github.com/MDAnalysis/mdanalysis/pull/1763#issuecomment-403231136 - - Our deprecate() function (and _Deprecate) is based on the numpy code with the additional - enhancements - - - add util.deprecate() and util._Deprecate class - - add util.dedent_docstring() function - - requires release kwarg: note the release in which it was deprecated - - optional remove kwarg: release for which feature removal is scheduled - - properly formats the restructure doc text of the function - - add a sphinx .. deprecated:: release markup at the end of the docs - - extensive tests - -commit 1d6e67032654471cabc5c83553be70b3a8e7a653 -Merge: 86983294f fc3263581 -Author: Jonathan Barnoud -Date: Thu Jul 12 00:20:34 2018 +0200 - - Merge pull request #1976 from MDAnalysis/issue-1974-zerolength_TG - - fixes Issue #1974 - -commit fc326358126b848605edba928eb14512c18cbe22 -Author: Jonathan Barnoud -Date: Wed Jul 11 22:09:25 2018 +0200 - - Fix a typo in test_zero_size_TG_indices_angles - -commit 221868656d2acab93829ec8b30167a1fc71b8bfb -Author: Richard Gowers -Date: Wed Jul 11 15:05:31 2018 -0500 - - Update CHANGELOG - -commit 86983294f1021aae5369412363c4edec495ff514 -Merge: 1a1b2f144 7c996654b -Author: Richard Gowers -Date: Wed Jul 11 12:49:46 2018 -0500 - - Merge pull request #1980 from MDAnalysis/issue-1445-use-codecov - - switched from coverall to codecov - -commit 724cc0471435405e625a2830963cd1fb4875119a -Author: richardjgowers -Date: Wed Jul 11 11:39:22 2018 -0500 - - bit more tidying of topologyobjects.py - -commit c23c3b414b9b78caa97d5a3336e9fac097a64b03 -Author: Richard Gowers -Date: Wed Jul 11 11:24:12 2018 -0500 - - Update test_topologyobjects.py - -commit 7c996654b8d791373f9f632a3b370a1aa4ef61eb -Author: Richard Gowers -Date: Wed Jul 11 10:42:11 2018 -0500 - - tabs to spaces? - -commit aed747a6eb32206134641c02dc885a5413fd1bd9 -Author: Oliver Beckstein -Date: Wed Jul 11 03:02:27 2018 -0700 - - try coverage merge for most Linux runs (2.7, 3.x, minimal) - -commit b1939326ef031fc80d26b816287744d005d9b6ee -Author: Oliver Beckstein -Date: Wed Jul 11 02:37:39 2018 -0700 - - replaced coveralls URL with codecov URL - - - badges - - links to site - - minor formatting of reST indentation - -commit 0b02e16724f4dec1098907c62c51fc16c747c2ab -Author: Oliver Beckstein -Date: Wed Jul 11 02:25:19 2018 -0700 - - generate coverage for python 2.7 - - - merge coverage for 2.7 and 3.5 with codecov - - only install sphinx-sitemap (and sphinx) for the doc building target - -commit a8016fd010f8a39a2a8e010858f3a87dbaa873f3 -Author: Oliver Beckstein -Date: Wed Jul 11 01:21:17 2018 -0700 - - switched from coverall to codecov - - fix ##1445 (and restores full coverage reporting) - -commit 10685787f641fbab6ece1349b85df3551aad4948 -Author: ayush -Date: Tue Jul 10 18:15:05 2018 -0700 - - Modified Changelog - -commit 6197b5a7697a2c6ef51b4d4100941f8e28904004 -Merge: 32b2f06e8 1a1b2f144 -Author: ayush -Date: Tue Jul 10 18:07:46 2018 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into cappedfeature - -commit 67425318f688b40d6f208eff2ecfeb6f11aad0c2 -Author: richardjgowers -Date: Sat Jul 7 17:10:57 2018 -0500 - - fixes Issue #1974 - - zero length TG now behave properly - -commit 65423742a59ac11b4da12558242f3675d80827f0 -Author: Jonathan Barnoud -Date: Tue Jul 3 16:27:17 2018 +0200 - - Update changelog - -commit 1ef80100577f8dc5457679ea17460e37413b56b5 -Author: Jonathan Barnoud -Date: Sun Jul 8 13:22:42 2018 +0200 - - Allow ag.write to write trajectory and selected frames - - Fixes #1037 - -commit 15222e3588bfb25390b15edb4851e82a3d6920db -Author: Jonathan Barnoud -Date: Sun Jun 17 09:34:07 2018 +0200 - - Fixes #1944 - -commit 5595681741c1b1b4855d44f7073a7ce339916086 -Author: Jonathan Barnoud -Date: Tue Jun 12 12:34:24 2018 +0200 - - Frame iterables returned when indexing trajectories - - Replaces the iterators returned by the proto reader __getitem__ by an - iterable class. That class has a __len__ method to adress #1894. - - In the current implementation, each type of input for the proto reader's - __getitem__ returns a different class. This allow to test for the - correct behavior only once. Ideally, the iterables should be imutable to - avoid inconsistencies. - - Fixes #1894 - -commit 1a1b2f1442d52d1216b53b32c4c42c3b47368d38 -Merge: 01e2511af 5ed599f1f -Author: Jonathan Barnoud -Date: Sat Jul 7 11:52:35 2018 +0200 - - Merge pull request #1937 from davidercruz/rotation-transform - - Rotation transformation - -commit 5ed599f1ffb47dff76257a1e9831a68e512d7286 -Author: Davide Cruz -Date: Fri Jul 6 22:33:30 2018 +0100 - - updated tests - -commit 01e2511afe0dbb8096eef3733162da157dd2efa7 -Merge: 22dfcdb91 9ea632861 -Author: Jonathan Barnoud -Date: Fri Jul 6 19:12:01 2018 +0200 - - Merge pull request #1965 from MDAnalysis/cpp_is_contiguous - - Rewrite make_whole in Cython - -commit 9ea632861aa6cd7a9618bcc28930b1accf586a7c -Author: richardjgowers -Date: Sun Jul 1 14:58:31 2018 -0500 - - rewrote make_whole in Cython - - lib.mdamath.make_whole now supports triclinic boxes - - renamed from new to avoid cpp name conflict in calc_distances.h - - added fullerene test case for make_whole - -commit 4cd8be365e0a92d0f5640b51c4407bad072436ab -Author: Max Linke -Date: Sun Jul 1 17:33:41 2018 +0200 - - add osx compilation - -commit aebdd7bb209f9bb92957e76ad10ac3143f7e958e -Author: richardjgowers -Date: Sat Jun 30 17:29:53 2018 -0500 - - rewrote _is_contiguous in Cython, approx 2x faster - -commit f3e74c948e5012222de4f1fa4a6cd58000bec05a -Author: Davide Cruz -Date: Fri Jul 6 15:35:56 2018 +0100 - - changed pbc to wrap - -commit 39ef71964c8d448b11b1e522640f2a5aafd01f7c -Merge: cf9c6c5f0 22dfcdb91 -Author: Davide Cruz <37750297+davidercruz@users.noreply.github.com> -Date: Thu Jul 5 17:08:44 2018 +0100 - - Merge branch 'develop' into rotation-transform - -commit ebd1b33b568cc93fb82191095a16a33539a5413f -Author: mat -Date: Thu Jul 5 17:02:22 2018 +0100 - - tiny bug - -commit 683f1cbfffad7f38e40ac5fecdac680f2045086b -Author: p-j-smith -Date: Thu Jul 5 12:24:03 2018 +0100 - - Storing a set of atom ids at each timestep, rather than a set containing - an atom group, to reduce the memory load. - - Updated the docstring. - -commit 22dfcdb919d45d3b12151ea9dc873dd83921295e -Merge: b71835004 820151024 -Author: Jonathan Barnoud -Date: Thu Jul 5 11:42:38 2018 +0200 - - Merge pull request #1728 from MDAnalysis/chain-reader-continuous - - Continuous Chain Reader - -commit 820151024002fa6b349064c0b75f42bb02bdc59c -Author: Max Linke -Date: Thu Jul 5 10:30:46 2018 +0200 - - update test style - -commit ac9533b7f260977734fc36696513725e22038fc9 -Author: Max Linke -Date: Thu Jul 5 10:30:37 2018 +0200 - - improve doc texts - -commit b71835004d49f9eecc741afc5b13feff29253528 -Merge: c487972b0 94f019668 -Author: Jonathan Barnoud -Date: Wed Jul 4 21:14:48 2018 +0200 - - Merge pull request #1946 from davidercruz/center-transform - - Box centering transformation - -commit 94f0196682757ac1f9bcf879342454321a294e43 -Author: Davide Cruz -Date: Wed Jul 4 18:43:47 2018 +0100 - - style cleanup - -commit acbbf43032459707f66c986406b930cc4e77323c -Author: Davide Cruz -Date: Wed Jul 4 17:51:44 2018 +0100 - - pbc argument is now wrap; added tests in the transformations API context ; DummyReader didn't have a _transformations variable - -commit 32b2f06e8afb8aa868f51562802a3a8aac9da121 -Author: ayush -Date: Wed Jul 4 08:50:48 2018 -0700 - - Removed the seed - -commit 2c6c6d417797f15f6d65dd83db5096094d634234 -Author: Max Linke -Date: Wed Jul 4 16:00:17 2018 +0200 - - improve documentation text - -commit bc6381bdcf56e5cbfd1dea2025a0502e6f5147dc -Author: Jonathan Barnoud -Date: Wed Jul 4 07:38:43 2018 +0200 - - Make pylint happy - -commit c487972b0ecee02261a166bda6d2a0e82c0e7e09 -Author: Oliver Beckstein -Date: Mon Jul 2 11:36:22 2018 -0700 - - updated GitHub template for issues - - - add comment that tells user to use the mailing list for questions and - says that issues with question will be closed - - changed links to user and developer list in CONTRIBUTING to the Google Groups - so that we use SSL links instead the forwards to help.mdanalysis.org and developers.mdanalysis.org - -commit e0cf20a43737f2519124257130f49a2b975d96b9 -Author: Jonathan Barnoud -Date: Tue Jul 3 22:28:56 2018 +0200 - - Avoid duplicating first frame in the continuous chin reader - -commit ae6c2d991bac3c43838bf6be12ff186cb04d640a -Author: ayush -Date: Tue Jul 3 11:58:36 2018 -0700 - - Stacked decorators in tests - -commit ea1c744cf8f1210d1582a98cfd0c0149bb03d0e7 -Author: mat -Date: Tue Jul 3 17:32:22 2018 +0100 - - The tf is inclusive. - -commit c89a690e1b5f084a57d59badce107446d272f3b9 -Author: mat -Date: Tue Jul 3 17:13:27 2018 +0100 - - verbose mode added + better documentation. - -commit 3655647f64bd3b4737baf9249bd257615b549726 -Author: mat -Date: Tue Jul 3 16:36:32 2018 +0100 - - Moving the checks to the constructor. - - Saving the extracted data for the user to be able to dig deeper, if - necessary. - -commit 87b6d343c6f83babc7f18a50e120f8939a5bd282 -Author: mat -Date: Tue Jul 3 14:37:03 2018 +0100 - - Adjusting the tests because the return function gives back taus too. - -commit 9370e8f81858e2a4b8d591a0d5c0b4ad0fa23c81 -Author: p-j-smith -Date: Tue Jul 3 14:01:58 2018 +0100 - - Returning the survival probability and the values of tau as - numpy arrays. - - Changed the name of tau_timeseries to sp_timeseries as it is a more - accurate descriptor. - - Removed some of the +/- 1 in indices to improve readability. - -commit 42704d78cef5492f1a3524c85301cae86774affd -Author: mat -Date: Tue Jul 3 11:25:12 2018 +0100 - - Using the set.intersection argument unpacking: easier to read, neater - code and no performance drawbacks. - - Tests: the user should not be forced to rely on the internal data - structures .timeseries. Returning the results with the function run(). - -commit 1d19fc26edca4af9d8c86f13a32531940b5e8482 -Author: richardjgowers -Date: Mon Jul 2 17:07:24 2018 -0500 - - more GRO benchmarks - -commit 7cc6cbc17f9af3c48ce8726ced5e21d350974d92 -Author: Davide Cruz -Date: Mon Jul 2 18:47:51 2018 +0100 - - forgot :func: - -commit aecda7622d89166a4de6309962b4dc9be858a4c6 -Author: Davide Cruz -Date: Mon Jul 2 18:45:59 2018 +0100 - - code cleanup; added parameters to tests - -commit 8eb1854840a5bdd43da877f7f7490daf8273a03a -Author: mat -Date: Sun Jul 1 19:58:49 2018 +0100 - - Should the first data point be always 1? In that case first tau = 0. Or should the first data point reflect the first tau which is non-zero and therefore the first change is quantified? I believe it is the latter. This breaks the current tests which, for example, by asking for 4 datapoints, always get the first datapoint for tau=0 that is 1. - -commit 8c9326629d7e18ee06c35b42a46acdbf32ef49fa -Author: Max Linke -Date: Sun Jul 1 20:49:36 2018 +0200 - - add more test cases - -commit b711cb2ab8bc8877f02a25ef5b368fd5f7c7f20f -Author: mat -Date: Sun Jul 1 17:38:31 2018 +0100 - - If there is no atom at t, this does not need to be checked for each t+tau. - - Refactoring. - -commit d71ed58ae41e6965db5659ca3d4f1f24021481f2 -Author: mat -Date: Sun Jul 1 17:12:04 2018 +0100 - - No need to check t+tau for any tau if at t it is empty. - -commit afb48ac0132064ed37aee7ffa9d7984d975aca97 -Author: mat -Date: Sun Jul 1 17:05:32 2018 +0100 - - Switch the nested loops. Looping only once over the entire trajectory and more times over tau. This will lead to faster code (local memory/cache optimisation). Additionally, opens the door for combining multiple taus together. - -commit 9cf39289c160cabbe6167b5980a97194d4e22fbb -Author: mat -Date: Sun Jul 1 14:37:52 2018 +0100 - - Minor changes: - -return the list rather than require the user to access the internal list - -use tau_max variable name which is consistent with the equation, in contrast to dtmax - -commit 875090f577422e5cb3bc5c1a1dd8ca7f02b7aed5 -Author: Max Linke -Date: Sun Jul 1 13:01:12 2018 +0200 - - refactor test - -commit 82ff0d6502993298856ee13177f787070e11771c -Author: Max Linke -Date: Sun Jul 1 12:51:11 2018 +0200 - - check for interleaving and throw error - -commit 943df366136af1bbfdf05eec291240a985e66a0e -Author: Max Linke -Date: Sun Jul 1 11:39:23 2018 +0200 - - add failing unit test - -commit cad0ba2b42103734c6f3f3ca8e931332b9663641 -Author: Max Linke -Date: Sat Jun 30 18:55:02 2018 +0200 - - update docs - -commit 1114acb2d3a87ab4d238590162193e5543378af7 -Author: Max Linke -Date: Sat Jun 30 14:02:18 2018 +0200 - - fix warning trigger - - the trigger doesn't have false positives now - -commit 5130a6141dcb316e48855a99674b3cb84c716b7f -Author: Max Linke -Date: Sat Jun 30 14:02:12 2018 +0200 - - add test for warning - -commit 940f287a7486d4230df2f4c1ace81cd94af0cb0a -Author: Max Linke -Date: Sat Jun 30 13:44:27 2018 +0200 - - update start_frames to be introspected in a test - -commit a6880ec468a985f959e4443015ac971d1c0e49f4 -Author: Max Linke -Date: Sat Jun 30 13:18:28 2018 +0200 - - add no_warning context - -commit f38c75d87539fa1235d39a127211626aee8367b6 -Author: Max Linke -Date: Tue Jun 19 11:07:55 2018 +0200 - - remove impossible case - -commit f4d405d091ef80b0132e366b0a7d0d9da4e07899 -Author: Max Linke -Date: Tue Jun 19 11:05:29 2018 +0200 - - add untested case - - and fix errors - -commit e6ff4abacc455d3bd5390fa056a94746769c5556 -Author: Max Linke -Date: Tue Jun 19 10:43:31 2018 +0200 - - update docs and Error messages - -commit 98427d19b430c8d8067514edae14bf6f6d486584 -Author: Max Linke -Date: Mon Jun 18 21:07:43 2018 +0200 - - add documentation - -commit fcf0f23280ec833998bf8a44eebaf51becb91841 -Author: Max Linke -Date: Mon Jun 18 21:04:43 2018 +0200 - - update CHANGELOG - -commit 3ae1d8f52362ca2dc4201c5478e6a517997de675 -Author: Max Linke -Date: Mon Jun 18 21:03:02 2018 +0200 - - add tests for continuous chain reader - - Uses the build_trajectory tool from @jbarnoud - -commit e4c16b420df8825ccf734c056dafaa61e1a60550 -Author: Max Linke -Date: Mon Jun 18 21:01:49 2018 +0200 - - add a continuous chain reader option - - This option allows the chain reader to sort the given trajectories so that the - time will always increase when iterating over a trajectory. This mimics gmx - trjcat. - -commit 57363bb6bb92365602b9f41d6b168bc376300303 -Author: ayush -Date: Sat Jun 30 12:01:34 2018 -0700 - - fixed the testcase - -commit 1d0ba7c5afff41d0049ae4566b38134c0db5516e -Merge: 15e40ae44 060e2c228 -Author: ayush -Date: Sat Jun 30 11:43:44 2018 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into cappedfeature - -commit 060e2c228f2b176421f1eab0db2513ba7a9cb1c3 -Merge: 9bd5b09b5 8c55498b6 -Author: Jonathan Barnoud -Date: Sat Jun 30 13:39:34 2018 +0200 - - Merge pull request #1964 from MDAnalysis/user-warning-matplotlib - - remove matplotlib warning - -commit 8c55498b62d6aa3d0687997ed756776694d0040b -Author: Max Linke -Date: Sat Jun 30 12:42:29 2018 +0200 - - remove matplotlib warning - - this warning is issued in a user session when we load files after matplotlib is - loaded. This is annoying and not clear why this is happening to a user. - -commit 15e40ae4481e4083b556614ae11e697447fc7fa4 -Merge: 61d9c6b07 9bd5b09b5 -Author: ayush -Date: Sat Jun 30 02:33:07 2018 -0700 - - Updated with current repository and merged to remove conflicts - -commit 61d9c6b07096ac57f5be7ef682d8a5c78d5d3cf5 -Author: ayush -Date: Sat Jun 30 02:15:23 2018 -0700 - - Changes the return type - -commit ad4b44be6c62f311c46bcca304eeedf52f750a17 -Author: mat -Date: Fri Jun 29 20:09:37 2018 +0100 - - Changed expected output from 0.0 to Nan. - - The survival probability is a measure of how likely a selected molecule - is to remain within a specified region over a period of time. If at t0 - the selected molecule is not in the specified region, no survival - probability can be calculated. - - For example, consider that we would like to calculate the survival - probability of an ion at an interface. If the ion never approaches the - interface, the previous test would return a survival probability of 0, - which suggests that the ion comes to the interface but leaves - immediately. However, as the ion was never at the interface, no - survival probability can be calculated from this data. - -commit 9bd5b09b56948c6a04318dccb28d4f9f51b7e922 -Merge: 339c5106d 68446bd39 -Author: Oliver Beckstein -Date: Fri Jun 29 11:31:30 2018 -0700 - - Merge pull request #1939 from MDAnalysis/issue-1262-distances - - added single distance calculations to lib.distances - -commit 68446bd398ab83a1c3348cc94e2e039f63465ab8 -Author: richardjgowers -Date: Fri Jun 29 10:12:51 2018 -0500 - - use np.testing.assert_almost_equal not pytest.approx - -commit f3cbffdc8bee42a321c6142a5680554268c6541c -Author: richardjgowers -Date: Sun Jun 24 11:03:23 2018 -0500 - - more doc fixes in lib.distances - -commit 068934372d42048bc4e92d903fa434cfc89ee86b -Author: richardjgowers -Date: Sun Jun 24 10:51:59 2018 -0500 - - really really fixed the docs - -commit c4fc8ec6d423668d493f79e61ea0421ec6c577e0 -Author: richardjgowers -Date: Sat Jun 23 19:11:04 2018 -0500 - - maybe fixed the docs? - -commit be1ce8cfaa96dfa457efd556d5a4c7b6a5c11b45 -Author: richardjgowers -Date: Wed Jun 20 09:32:28 2018 -0500 - - removed unused import - -commit 61157394f803a73370bf01b4292a6182cb0ec500 -Author: richardjgowers -Date: Tue Jun 19 11:54:13 2018 -0500 - - completely removed HBondAnalysis' distance methods - -commit 5353f95a4ed918058e9084714db3d9936a4752cc -Author: richardjgowers -Date: Tue Jun 19 11:47:42 2018 -0500 - - fixed make_whole now Bond.length() defaults to pbc=True - -commit 0f005f2a0d0d56a966ede42b8d44febcb252911d -Author: richardjgowers -Date: Sun Jun 17 14:04:06 2018 -0500 - - changed default to pbc to True in TopologyObjects - -commit 7a11becb293eaa12127c702ea85e797c209634c2 -Author: richardjgowers -Date: Sun Jun 17 14:02:39 2018 -0500 - - finalised changelog - - defaulted Bond.value pbc to True to match other objects - -commit 0931383da977b4b851169811c939433d7ee4ae09 -Author: richardjgowers -Date: Sun Jun 17 13:59:51 2018 -0500 - - added more tests for single distance calculations - -commit 0da4f4fdc42dc6499b4d6a0b8fc9c3886983f788 -Author: richardjgowers -Date: Sat Jun 16 18:32:09 2018 -0500 - - simplified docstrings - -commit a40b33ec2a8f5fceb2330c17caf3e71ba551a7bf -Author: richardjgowers -Date: Sat Jun 16 18:29:26 2018 -0500 - - tests for new functions in lib.distances - -commit b5c2665157106a8b88600759df5fb4d3b15ea4a2 -Author: richardjgowers -Date: Thu Jun 14 07:18:44 2018 -0500 - - Added single distance calculations to lib.distances - - calc_distance, calc_angle and calc_dihedral - - Fixes Issue #1262 #1938 - - redid 180 degree angle test for new function - -commit 339c5106d8ee71d6c9a7ab88eb2fd6fbd2354140 -Author: zeman -Date: Wed Jun 27 22:05:01 2018 +0200 - - updated weblinks to PDB file format in PDB.py and PDBQT.py - -commit 36a7a5a01dfa2deaa03c8ffeaa2e277491816a4a -Author: zeman -Date: Wed Jun 27 20:00:28 2018 +0200 - - updated CHANGELOG for PR #1936 - -commit a5e235b994fbbac94d3f385f0860a3c40e8fb399 -Author: zeman -Date: Wed Jun 27 12:36:57 2018 +0200 - - input dtype conversion for all functions in lib/distances.py; modified tests accordingly - -commit 8883f906fd4d921d050573a1ead297f2624ae008 -Author: zeman -Date: Tue Jun 12 19:14:31 2018 +0200 - - enforced double precision calculations in *Group.center(); added automatic input dtype conversion to apply_PBC and (self_)distance_array - -commit f02868cf7234761e3e31c757f48569b508e72289 -Author: ayush -Date: Tue Jun 26 14:07:42 2018 -0700 - - Added rules for method selection and modifications - -commit a0bc631699f7619a12aa2ecda1e3fa06113c9507 -Author: Jonathan Barnoud -Date: Sat Jun 23 10:16:12 2018 +0200 - - Be more specific about types in unique_int_1d - - Hopefully it will solves issues on windows. - -commit e7ba5c39bcd242b3a6d18e739314cd69fa197e10 -Author: Jonathan Barnoud -Date: Sat Jun 23 09:39:22 2018 +0200 - - Make unique_int_1d accessible through lib.util - - Hide the implementation details amongst utils. The user does not need to - know that some util functions are written in pure python or in cython. - -commit 25d355d60b73d8e16fcc6974ba10a82bc38ecfd7 -Author: Jonathan Barnoud -Date: Sat Jun 23 09:16:59 2018 +0200 - - Address comments from @richardgowers on #1951 - -commit d3a7ce1baeae2aa0f38564b8048b4f3835a72fe3 -Author: Jonathan Barnoud -Date: Fri Jun 22 23:26:52 2018 +0200 - - Add a faster function to deduplicate indices - - `mda.lib.cutil.unique_int_1d` takes a 1D array of integers and returns - an array of the unique values. It has similar perormances as - `np.unique` for randomly ordered values, but is faster for sorted values. - - MDAnalysis needs to deduplicate arrays of indices for basic operations. - In most cases the indices are sorted so the deduplication can be done - in linear complexity. However, `np.unique` is a general function; it - systematically sorts the values with a quicksort, which makes the - complexity in the order of n log n. - - `mda.lib.cutil.unique_int_1d` only works on 1D arrays of integer and - does not have the optional return values `np.unique` has. It assumes - first that the values are sorted and only sorts them if they happen not - to be. - -commit cf9c6c5f068e741a235fefc4b171cfe892232374 -Author: Davide Cruz -Date: Mon Jun 25 11:20:00 2018 +0100 - - typo in doc - -commit 67142c051dfff5dd9c0198637035e5ef7fdad2f8 -Author: Davide Cruz -Date: Mon Jun 25 11:18:13 2018 +0100 - - no longer checking for lengths ; added test to rotation matrix function - -commit 0f6613fbdb37e2f37a7675f024542aa1cb54061c -Author: Davide Cruz -Date: Mon Jun 25 11:17:07 2018 +0100 - - no longer checking for lengths - -commit 8cc25fe2df0e12d9910440f7cb7664ad52f6c6b7 -Author: ayush -Date: Sun Jun 24 20:33:18 2018 -0700 - - PEP8 and added test - -commit e1dce21d0cfb28446a2bda05a5fc23ced34c4e0e -Author: ayush -Date: Sun Jun 24 19:56:46 2018 -0700 - - Capped PKDTree - -commit 9833a6909d674bcf7dc35415cc2133e25d6f9c07 -Author: ayush -Date: Sun Jun 24 17:33:28 2018 -0700 - - random seed - -commit dd12343150a16a53dcf7e05a6894a1c1965dcb7c -Author: ayush -Date: Sun Jun 24 16:29:39 2018 -0700 - - modified zip with itertools.product - -commit 23e9868801d9e572039d32c7db7f9659029a8649 -Author: ayush -Date: Sun Jun 24 15:36:27 2018 -0700 - - Modification as per the review - -commit 9e67c9d5c9f43d6e27c1c5041575135c9931edf6 -Merge: 2d9f989a6 14a404fa2 -Author: Davide Cruz <37750297+davidercruz@users.noreply.github.com> -Date: Sun Jun 24 23:33:50 2018 +0100 - - Merge branch 'develop' into rotation-transform - -commit 2d9f989a63c75cc9904677855f3925850277ada3 -Author: Davide Cruz -Date: Sun Jun 24 23:30:18 2018 +0100 - - updated docs; center is now updated every frame; added more tests - -commit cd3d29cc3ea6bb4a09be2de6d29c9844f2e1d4ba -Merge: e47ed4dad 14a404fa2 -Author: ayush -Date: Sun Jun 24 15:19:01 2018 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into cappedfeature - -commit aff66156cf0253637c41511f4acec96b0f1bc8d1 -Author: Davide Cruz -Date: Sun Jun 24 21:46:17 2018 +0100 - - removed flags reference;pbc arg defaults to False - -commit c7b6622c1e50e35824d8f287e2d61c74af9a932c -Author: Davide Cruz -Date: Sun Jun 24 21:34:34 2018 +0100 - - pbc description now includes reference to flags - -commit d32abc328dab6d0e22a7cad6012ee0c17432491e -Author: Davide Cruz -Date: Sun Jun 24 12:43:07 2018 +0100 - - defult pbc flag now in docs - -commit cbe9049727cf6a2349c05ae4b587a90eb419ee50 -Author: Davide Cruz -Date: Sun Jun 24 10:34:47 2018 +0100 - - code cleanup - -commit 1cac08ea1bbce5d0764b56f51b6e5f93fa1639a8 -Author: Davide Cruz -Date: Sat Jun 23 18:30:52 2018 +0100 - - cleaned point checking - -commit 55ef308224694daeba1cbd43e9e6fc39c0e159c7 -Merge: 177546279 91234781d -Author: Davide Cruz -Date: Sat Jun 23 18:28:58 2018 +0100 - - Merge branch 'center-transform' of https://github.com/davidercruz/mdanalysis into center-transform - -commit 1775462790bdd98f8d041f9cc63a3ee11889f772 -Author: Davide Cruz -Date: Sat Jun 23 18:27:43 2018 +0100 - - cleaned point checking - -commit 14a404fa2a0254767aec40a7c024b2f94028e1b6 -Merge: a15f2c298 52d9fa073 -Author: Jonathan Barnoud -Date: Sat Jun 23 19:23:30 2018 +0200 - - Merge pull request #1952 from MDAnalysis/issue-1950-pdbwriter - - fix MODEL and step in PDBWriter - -commit bf62c1ebae5d23a4548693fdfb836c1a4c1cf267 -Author: Davide Cruz -Date: Sat Jun 23 18:08:44 2018 +0100 - - point check and conversion now done in parent function - -commit a15f2c2989c788d78ea4c98aacba295b6bcfccaa -Author: Jonathan Barnoud -Date: Sat Jun 23 13:31:53 2018 +0200 - - TPR parser reads SETTLE constraints as bonds - - Fixes #1949 - -commit 91234781db7848fa204211bc57b967afd0042fab -Merge: 51709beb0 691e785c9 -Author: Davide Cruz <37750297+davidercruz@users.noreply.github.com> -Date: Sat Jun 23 16:41:03 2018 +0100 - - Merge branch 'develop' into center-transform - -commit 52d9fa073355133c028618a35f6f9dbc8b04f38f -Author: Oliver Beckstein -Date: Fri Jun 22 18:42:20 2018 -0700 - - PDBWriter can set start frame and ensures that MODEL is only 4 digits - - - PDBWriter now honors start kwarg as expected (well, almost, start=0 turns - into MODEL 1 because of PDB standard) - - test that we do not have 5 digit MODEL numbers but wrap around; testing white - space and that number is read correctly as int - - use fixtures for TestPDBWriter - -commit 691e785c93692b2314400c2c8163e83f2713ad85 -Merge: 61e9ed97c aae393592 -Author: Jonathan Barnoud -Date: Sat Jun 23 16:16:33 2018 +0200 - - Merge pull request #1948 from davidercruz/docs - - transformations now appear in the dev-doc - -commit 51709beb07082c7d2821cb692c58890ba6eac2f7 -Author: Davide Cruz -Date: Sat Jun 23 14:46:19 2018 +0100 - - atom group center is now calculated inside wrapped ; updated changelog - -commit aae393592b95e9558a248039e7ac72cfe90abc05 -Author: Davide Cruz -Date: Sat Jun 23 14:18:04 2018 +0100 - - angstrom symbol in code-block was causing errors - -commit de3d80e1122801f8e64865c83f674c0c2b3e6fb2 -Author: Oliver Beckstein -Date: Fri Jun 22 17:39:42 2018 -0700 - - fix MODEL format in PDB writing - - - fixes #1950 - - MODEL number is now written in columns 11-14 (right aligned) instead starting in column - 15; the maximum allowed number of digits is 4 (max 9999), as per PDB standard - http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL - - added test - -commit 1cdda248501ef2c19a57e817ce5644b2eb08ada7 -Author: Davide Cruz -Date: Fri Jun 22 23:47:11 2018 +0100 - - added more examples; fixed typos - -commit bf2faa98c5cbe1f6e153c9ae266eebef5d35dbb5 -Author: Davide Cruz -Date: Fri Jun 22 23:03:03 2018 +0100 - - replaced box with point; updated tests; fixed some typos - -commit 967a569665ae116d81f0eae46c3e68dc4bcd512f -Author: mat -Date: Fri Jun 22 17:14:13 2018 +0100 - - Syntax errors - -commit b5e1ab233b5b83dd71ef82e8c712cf4bc87a0fba -Merge: 3e65d43a3 409918703 -Author: mat -Date: Fri Jun 22 17:13:04 2018 +0100 - - Latest version by Paul to remove the unnecessary functions - -commit 40991870390115cad6d896398c542a226c493861 -Author: p-j-smith -Date: Fri Jun 22 16:34:39 2018 +0100 - - Optimised calculation of survival probability. - - Atom selections at each frame are now stored as sets rather than lists, - so determining the intersection of selections is faster. - - Survival probability is now calculated by a single function. - -commit 48f66501508dfd5e6dffb1e97d3a47bef7fcb42e -Author: Davide Cruz -Date: Fri Jun 22 01:46:37 2018 +0100 - - transformations now appear in the dev-doc - -commit 3e65d43a320ba8c0e64735d76c08129ff3e4d417 -Author: mat -Date: Thu Jun 21 17:01:52 2018 +0100 - - Use reverse search for number of survivors. Stop search if no survivors. - -commit 69be6dc5e9125a311b56566ae182fb8b3d02103e -Author: mat -Date: Thu Jun 21 16:44:05 2018 +0100 - - The windows size tau + t was already accounted for in _getMeanOnePoint upstream - -commit cff6c000e4c9b7d67c597e2d943375d952ae6d56 -Author: Davide Cruz -Date: Thu Jun 21 13:46:06 2018 +0100 - - split test on args - -commit e95b5db4feace81fa8a61a1dd3fc1bb01ff8edcf -Author: Davide Cruz -Date: Wed Jun 20 19:49:48 2018 +0100 - - clarified exceptions ; moar tests - -commit d9134faa6aae4aecf9491610759edcd63e1e6236 -Author: Davide Cruz -Date: Tue Jun 19 23:58:42 2018 +0100 - - import division from the future - -commit 1ccb38069b37e508fe51a6677139cf2539839d97 -Author: Davide Cruz -Date: Tue Jun 19 19:16:05 2018 +0100 - - improved docs - -commit 60d7195ebbc30e27ccba982fd05acf7a22c616e2 -Author: Davide Cruz -Date: Tue Jun 19 19:10:22 2018 +0100 - - cleanup - -commit 28c8072f9c0140642b65dffdb6eacfa4d6545059 -Author: Davide Cruz -Date: Tue Jun 19 19:03:26 2018 +0100 - - added a box centering transformation; added tests ; updated changelog - -commit 76e6b0312ca27edc870b4f93a263f2508391fe5c -Author: Davide Cruz -Date: Tue Jun 19 16:58:49 2018 +0100 - - some fixes; position now defaults to None - -commit cfe7b78e40bf4fb6c5c608b923852546966ed0e7 -Author: Davide Cruz -Date: Tue Jun 19 15:13:08 2018 +0100 - - more cleanup - -commit fbe09eab442f879a0643661ee2735af65e755f3d -Author: Davide Cruz -Date: Tue Jun 19 11:34:25 2018 +0100 - - some code cleanup - -commit fc03cad6ac466355fe346a1f5e2176a08e9d5798 -Author: Davide Cruz -Date: Tue Jun 19 11:31:25 2018 +0100 - - typecasting to np.float32 causes FLOP errors with rotation_matrix; tests now use make_Universe - -commit 81808d8776faf41e906ee62c72367f71997111e9 -Author: Davide Cruz -Date: Mon Jun 18 12:05:08 2018 +0100 - - changed name to rotateby; fixed typos ; dropped kwargs - -commit 61e9ed97ce074c0e2028805626c21cd4fb0c6873 -Author: richardjgowers -Date: Sat Jun 16 12:16:22 2018 -0500 - - removed osx and python=3.4 from allowed failures - -commit 3bb9a63c97ab0962f1d1dcfc4f953b5b431b8557 -Author: Oliver Beckstein -Date: Fri Jun 15 18:17:24 2018 -0700 - - fix #1942 - - Commit 8572d796a95e92bbdaa827325a1ae82e1664dcba broke XTC/TRR reading on macOS. - This fixes this issue. Only the development version 0.18.1-dev was affected; - the released 0.18.0 did NOT have this bug. - -commit 863c2f71321bea55578a0c679b4934f86f916d2e -Merge: 44631d040 2a7fe588a -Author: Oliver Beckstein -Date: Fri Jun 15 13:23:09 2018 -0700 - - Merge pull request #1922 from zemanj/duplicate_handling - - Fix duplicate handling in *Group.pack_into_box() - -commit 2a7fe588a3fc22c6a6735106960214ad51a8d25b -Author: Oliver Beckstein -Date: Fri Jun 15 11:37:41 2018 -0700 - - additional docs for changed group behavior - - - added docs/versionchanged for AtomGroup.atoms, ResidueGroup.residues, - and SegmentGroup.segments - - added extensive docs for UpdatingAtomGroup.atoms - -commit e47ed4dadeb99904a990260c5fb5ef15e4c7d9e9 -Author: ayushsuhane -Date: Thu Jun 14 18:25:39 2018 -0700 - - Clean initial Capped distance feature - -commit fe6dbb6cd9fe73011896d114a042351e438a7a66 -Author: Davide Cruz -Date: Wed Jun 13 18:02:36 2018 +0100 - - Added rotation transformation, tests, docs and update CHANGELOG - -commit 44631d040deef932bdb2e1c52b3ac457dd89684b -Merge: 70b9e9ffd 74b9d46c5 -Author: Jonathan Barnoud -Date: Wed Jun 13 13:46:45 2018 +0200 - - Merge pull request #1902 from davidercruz/develop - - on-the-fly trajectory transformations - -commit 74b9d46c5297b57c69cbb3b92c8a260ed287ed33 -Author: Davide Cruz -Date: Sat Jun 9 16:43:22 2018 +0100 - - Fixed rewind issue in the SingleFrameReader where the frame would not be re-read from the input file (#1929) - - Added tests to the rewind method in the context of transformations - -commit acf6d1e29f3a78fbcf01a8852d9f7a6ae4a45584 -Author: Davide Cruz -Date: Thu May 17 17:19:46 2018 +0100 - - Added a on-the-fly transformations API and a coordinate translation function (Issue #786) - - Transformations are applied by the readers, either by being added by the user or passed as a kwarg when instancing - the universe; added tests for the modified reader classes: ProtoReader, SingleFrameReader, ChainReader and MemoryReader - -commit 70b9e9ffd6714229294f2913a59febb4849e33e8 -Author: zeman -Date: Mon Jun 11 11:28:45 2018 +0200 - - made test_dres_convergence less likely to fail; removed printf() from CStochasticProximityEmbedding() in spe.c - -commit 20e5ecda5496392ca74109664816695416fd0d97 -Author: zeman -Date: Sat Jun 9 23:41:59 2018 +0200 - - fixed test_warn_if_not_unique_unnamed() - -commit 553416e590a91973b6fb58171dcfab487b61a439 -Author: zeman -Date: Sat Jun 9 23:07:48 2018 +0200 - - added *Group.copy() methods, duplicate warnings, and tests; updated changelog - -commit b3204dcf98bc7b5dec697963643f144b1376b54f -Author: zeman -Date: Tue Jun 5 03:15:49 2018 +0200 - - fixed error message in AtomGroup._unique_restore_mask - -commit 45126ae83f2e9735a1161c2caa9a942c9f885006 -Author: zeman -Date: Tue Jun 5 02:17:05 2018 +0200 - - updated *Group.isunique and added explanatory comments; polished docstrings in MDAnalysis/core/groups.py - -commit 0dd926e4607c88060771561210ef494e16fe48de -Author: zeman -Date: Wed May 30 19:31:16 2018 +0200 - - added PR number to changelog - -commit bbabc5cc2f421fab95d270549b6fab358b60b1b5 -Author: zeman -Date: Wed May 30 18:28:48 2018 +0200 - - fixed whitespace errors in core/groups.py and updated changelog - -commit a13863448109860f0c97e8df99d20061e415542e -Author: zeman -Date: Wed May 30 18:05:47 2018 +0200 - - fixed *Group.pack_into_box() for groups with duplicates; cached uniqueness properties of *Groups; added *Group.isunique property - -commit 9675f920f440e88c540fbf91c98b162737604a1f -Author: Tyler Reddy -Date: Wed May 30 21:21:23 2018 -0600 - - BUG: libdcd now properly handles missing input file on Windows. - -commit 347f60ffeccaf51b584add39d25704ea0ebd8c88 -Author: Tyler -Date: Wed May 23 22:05:05 2018 -0600 - - TST: skip gsd-based tests on Windows. - -commit 518091f7a2359660897365677213e25d83499ba6 -Merge: 2d35dad96 a88b57616 -Author: Oliver Beckstein -Date: Fri May 25 12:55:19 2018 -0700 - - Merge pull request #1815 from VOD555/enh-rdf - - add new rdf.InterRDF_s class for calculating rdf separately - -commit 2d35dad96a1f20ab08ff4254a5b42071e5ce27d6 -Author: Tyler Reddy -Date: Fri May 25 12:21:10 2018 -0600 - - TST: clean up extraneous writer creation in LAMMPS test_Writer() unit test. - -commit a88b57616b4780cb9df9d1d8aa14cb721bc72ff9 -Author: Oliver Beckstein -Date: Thu May 24 04:08:26 2018 -0700 - - improved docs and fixed linter complaints for RDF - -commit eab34ef026b1156ea9d65bb7490a562736b2d1f5 -Author: VOD555 -Date: Fri May 11 16:02:11 2018 -0700 - - rename functions and moved into rdf module - - - change the name of function cdf_s to avoid use the same name for the function and its output - - change name of function rdf_s - - change name of cdf_s - - move InterRDF_s into the rdf module - - add docs to explain difference InterRDF and InterRDF_s - - CHANGELOG and AUTHORS updated - -commit 0fb3867ffe0c557ed663f357d2c6ddc6f0af5587 -Author: VOD555 -Date: Thu Apr 26 13:34:06 2018 -0700 - - Add test file for rdf_s - - - Add test data files for rdf_s - - add a module-level fixture rdf and remove rdf calculation - - move YiiP_lipid files to data/analysis/ - - add the file variables to datafiles.py - - fix numpy.testing import error - - gzip the YiiP GRO data file - -commit 04db9034ab7d646b60b78e6a3234c8bd1a6a3e16 -Author: VOD555 -Date: Thu Mar 8 12:04:43 2018 -0700 - - add new analysis.rdf_s module for calculating rdf seperately - -commit 636a2097212ac7c6836cd92e688b0dd9f2fcea46 -Author: Max Linke -Date: Fri May 25 06:05:40 2018 +0200 - - Revert "clean up warnings in tests" - - This reverts commit 85bcb5d33c99406bfdf49a2c4264ce21b5196005. - -commit 18186ae3fd48d8bc149b8e890f8fd70f465930b0 -Author: Max Linke -Date: Fri May 25 06:05:40 2018 +0200 - - Revert "fix warnings in import" - - This reverts commit 72f70fe3aa75e90aad0c96291cc06b2054150406. - -commit b0106ad56c56b48669b4424740efad99b05a5214 -Author: Tyler -Date: Tue May 22 21:21:02 2018 -0600 - - TST: ignore some os.fork() related unit tests on Windows. - -commit 72f70fe3aa75e90aad0c96291cc06b2054150406 -Author: Max Linke -Date: Tue May 22 16:01:36 2018 +0200 - - fix warnings in import - -commit 85bcb5d33c99406bfdf49a2c4264ce21b5196005 -Author: Max Linke -Date: Tue May 22 15:50:53 2018 +0200 - - clean up warnings in tests - - - silence user warnings - - test for deprecation warnings - -commit 2f2c4e8ddf661ba5bd14e3637978768dfcf89156 -Author: Max Linke -Date: Wed May 23 12:54:06 2018 +0200 - - split tests into pbc and no pbc - -commit b210f45afa365d4132d75a322c32d9de19c2f890 -Author: zeman -Date: Tue May 22 21:51:04 2018 +0200 - - Modified tests for `group.center*()` methods; replaced `np.isin()` by `np.in1d()` in `center()` to support numpy < 1.13.0 - -commit df65850ef005b0cdb4bf93adc10d9eaa9c4399e0 -Author: zeman -Date: Tue May 22 18:31:28 2018 +0200 - - Changed return type of `center()` from `np.float32` to `group.positions.dtype` in order to not break a gazillion of tests - -commit e163a432f0881f489ea196421d72c04786930c3b -Author: zeman -Date: Tue May 22 18:04:34 2018 +0200 - - Fixed PBC handling in `center()`, updated docstrings. Removed uniqueness of atoms, which should first be discussed in issue #1911. - -commit 6696168e13909ce3942732981283f7dbda365910 -Author: zeman -Date: Tue May 22 17:12:51 2018 +0200 - - in `center_of_mass()`: `compound` kwarg as last parameter; removed uniqueness of atoms; streamlined docstring - -commit 41336ff9260f5cdf335ac608a556c97246a300fe -Author: Max Linke -Date: Tue May 22 12:16:56 2018 +0200 - - fix return type for compound='group' - -commit 29dfcc9da4de7120d3cb415493f1c363ddeda1c4 -Author: Max Linke -Date: Tue May 22 11:17:16 2018 +0200 - - update changelog - -commit a0cad614de46cd0b4ea1752ac1e9a5308efb33d7 -Author: Max Linke -Date: Tue May 22 11:06:43 2018 +0200 - - add tests - -commit d6e5b247a31aa780ac8df136cd21062cad3935c5 -Author: Max Linke -Date: Tue May 22 11:01:01 2018 +0200 - - add compound keyword to center - - This makes the new kwarg available to all functions related to calculation of - centroid or center of mass distances. - -commit dfb82537de81facb437440d5ab895dfde8d5198b -Author: zeman -Date: Fri May 18 02:41:18 2018 +0200 - - Added compound parameter to MDAnalysis.core.topologyattrs.center_of_mass() to support COM calculation per residue or per segment - -commit 92215af1d8a269589bbea3fa972f5ffe2e18f684 -Author: Tyler Reddy -Date: Tue May 22 10:34:42 2018 -0600 - - BUG: duecredit should now be imported properly on Windows. - -commit eeeb30a0f9cc6ddb4f7eb891fabc2ff86ffe141c -Author: Oliver Beckstein -Date: Mon May 21 16:49:17 2018 -0700 - - update PyPi meta data for package and testsuite - - - fix #1837 - - indicate content type for long description as reST - - updated links in various README, SUMMARY, INSTALL files - (also updated https://github.com/MDAnalysis/mdanalysis/wiki/Installing-from-binary-packages) - - add more metadata for the new PyPi (e.g., links to Issue Tracker and groups, specify - the Python versions) - - display various badges on PyPi - - The {package,testsuite}/setup.py were checked with - - python setup.py -r -s - - (using https://github.com/pypa/readme_renderer) - -commit 5feb9f4ffc7434f18eed85d517912c1cde4a1ac7 -Author: Oliver Beckstein -Date: Mon May 21 14:55:51 2018 -0700 - - Issue 1906 xfail duecredit (#1907) - - * skip duecredit tests if duecredit is not installed - - fix #1906 - - * renamed duecredit test from duecredits to duecredit - -commit bdb1844d17d1be6340452a25e95ed39d614d9edf -Author: Tyler Reddy -Date: Sun May 20 17:40:41 2018 -0600 - - BLD: added Python 3.6 64-bit Windows appveyor CI test. - -commit 13b1647a53d73c714085833221bd3985aa5b1b9a -Author: Tyler Reddy -Date: Mon May 21 02:33:22 2018 -0600 - - MAINT / CI: add missing imports flagged by pylint; Fixes Issue #1904. (#1905) - - * MAINT: add missing imports flagged by pylint; Fixes Issue #1904. - - * MAINT: adjust future import location in due.py - - * MAINT / CI: address additional pylint issues appearing in CI. - -commit 2e9db81a2ea2fb38b823cfbd33cdf37b9c898264 -Author: richardjgowers -Date: Fri May 11 13:26:36 2018 -0400 - - fixed lammps docs - -commit 4b31257fe5169578bc64fac13f1b0047aae741a7 -Author: richardjgowers -Date: Fri May 11 13:23:39 2018 -0400 - - redo DumpReader.close to make linter happy - -commit 002770bf9dba7bb5c08064fe1f8ad84ef077cd99 -Author: richardjgowers -Date: Thu May 10 11:37:34 2018 -0400 - - added loop over compression types for lammps tests - -commit 45bdbd834b729d54dc4ede1fd7f8debf10a69669 -Author: richardjgowers -Date: Thu May 10 11:37:19 2018 -0400 - - switched lammps test file to bz2 compression - -commit 5d5777eb277ddf6a98e36dfe6711b8743c1bbafc -Author: richardjgowers -Date: Sun May 6 16:37:57 2018 -0400 - - docs for lammps dump format - -commit 438e80af6ffc28502d2cf93db5f95dbe625d6755 -Author: richardjgowers -Date: Sun May 6 15:44:16 2018 -0400 - - Finished tests for lammps dump reader - -commit 02bf09bb95009b1b0e51e185ce3d51f864fb5342 -Author: richardjgowers -Date: Sun May 6 13:58:46 2018 -0400 - - Lammps dump parser finished - -commit be4a4179f13c2a9dde88cd5ad88f84457a306eea -Author: richardjgowers -Date: Sun May 6 13:56:17 2018 -0400 - - Added lammps dump reference file - -commit 8bab35993272ad9f1c8ad4893f85bd29928450a8 -Author: Oliver Beckstein -Date: Mon May 7 13:05:45 2018 -0700 - - create doc sitemap.xml for development site and fix for master deployment - - - sitemap.xml is appropriate for the development docs: thus we do not ship - and install a sitemap.xml that is misleading (when installing automatically - via Travis CI) - - change the loc in the sitemap.xml with the new maintainer/adapt_sitemap.py - script: parse XML tree and replace the developer site URL prefix with the - release doc prefix - - manually create the release docs from master with the - maintainer/deploy_master_docs.sh script (which is now calling - the adapt_sitemap.py script) - -commit 7d60bc504c42dd4db22ee5c69adc8a61ff31bc4d -Author: Oliver Beckstein -Date: Sun May 6 12:54:38 2018 -0700 - - add sitemap.xml to sphinx docs - - - install https://github.com/jdillard/sphinx-sitemap with pip - - create sitemap.xml that is correct for the RELEASE docs - (it is incorrect for the development docs but we do not want to - index the devdocs anyway... but we could change it so that by default - it is correct for devdocs and then we fix sitemap.xml when we manually - add the release docs with the maintainer/deploy_master_docs.sh script) - - see https://github.com/MDAnalysis/MDAnalysis.github.io/issues/78 - -commit f184da17b39f2812438c553a6427ef3a89d1ef17 -Author: richardjgowers -Date: Mon May 7 17:12:00 2018 -0400 - - added coveralls token - -commit 7a7dd60b2fc44217fca8c3702144ebdebc2bf260 -Merge: c97395b9a ee735e65c -Author: Jonathan Barnoud -Date: Mon May 7 16:54:07 2018 +0200 - - Merge pull request #1887 from MDAnalysis/1852-check-input-type-select-atoms - - 1852 check input type select atoms - -commit ee735e65c0678d6906d373905f7d92a361f3bb3c -Author: richardjgowers -Date: Sun May 6 11:30:03 2018 -0400 - - Updated 1852 against develop - -commit 7a415cdc92ce6bb30211cb84969e8e82d9d55ba3 -Author: Nabarun Pal -Date: Wed Apr 18 21:59:45 2018 +0530 - - Adds tests for modifications in MDAnalysis.core.groups.select_Atoms - -commit 2984c9f4923d9a4d905986a5feea757b3e35d481 -Author: Nabarun Pal -Date: Wed Apr 18 20:26:21 2018 +0530 - - Fixes typo in docstring - -commit df2d116d49300f6321a9e71fa1747f35733e6c76 -Author: Nabarun Pal -Date: Mon Apr 16 14:18:17 2018 +0530 - - Updates docs for MDAnalysis.core.groups.select_atoms - -commit 6f20407a8742c368b777904af80c24e1a16d2bc9 -Author: Nabarun Pal -Date: Mon Apr 16 14:17:27 2018 +0530 - - Adds a check for arbitrary atomgroups passed to MDAnalysis.core.groups.select_atoms - -commit c97395b9a7cc16a1fc0a14d75f5445a4d99320b6 -Merge: e50fc521b 3bbef5221 -Author: Jonathan Barnoud -Date: Sat May 5 10:29:07 2018 +0200 - - Merge pull request #1877 from MDAnalysis/issue-1876-topattr_types - - TopologyAttributes are now statically typed - -commit e50fc521b7ecb7dcda983c5689a0b6f09285ab89 -Merge: 8572d796a c83f33eab -Author: Oliver Beckstein -Date: Thu May 3 17:56:01 2018 -0700 - - Merge pull request #1882 from MDAnalysis/benchmark-import - - Benchmark import - -commit c83f33eab858e3d41b9567e15a69515f2c57380b -Author: Max Linke -Date: Wed May 2 15:24:07 2018 +0200 - - add benchmark for import times - -commit 3bbef5221e2d393f8466280387b9dc5f62be2f25 -Author: richardjgowers -Date: Sat Apr 28 20:53:56 2018 -0400 - - updated PDB writing occupancies test to allow floating point errors - -commit c1189a1c48faa09909234c8ccecae7c0c0ac07a2 -Author: richardjgowers -Date: Sat Apr 28 20:16:57 2018 -0400 - - TopologyAttributes are now statically typed - - Fixed Issue #1876 - -commit 8572d796a95e92bbdaa827325a1ae82e1664dcba -Author: Tyler Reddy -Date: Wed May 2 15:32:20 2018 -0600 - - BLD / MAINT: Improvements related to Windows compatibility - - * adjustments to the build process, code base, and test suite - that improve Windows compatibility; many of these are code - modernizations (i.e., broader adoption of pytest) that serve - the dual purpose of improving compatibility - -commit 3a27a7cee97f0576f6fecfa748781228d36740d2 -Author: Max Linke -Date: Wed May 2 14:44:41 2018 +0200 - - remove toplevel import of MDAnalysis in groups.py - - On a core i7-4600 with an SSD, this reduced the import times of MDAnalysis to - under a second. Tested with time python -c 'import MDAnalysis'. - - *0.18.0*: ~1.4s - *HEAD*: ~0.6s - -commit f0079dcbef86c94add1fd17550424b5c86ebfedb -Author: richardjgowers -Date: Mon Apr 30 13:18:45 2018 -0400 - - fixed HBondAnalysis not considering PBC for distances with pbc=True - -commit f2fd6c6b1dd7527e06a9fd235ff8c17551753fba -Author: richardjgowers -Date: Mon Apr 30 12:04:15 2018 -0400 - - added pbc handling to hbond_analysis distance criteria - -commit 74de372b0b77a46e4ec380afbdd2df5b920dfa5e -Author: richardjgowers -Date: Tue Apr 24 15:20:34 2018 -0400 - - added mmtf duecredit - -commit 4b81af5ac1cc503caf8bbdac32a51fe98cab442f -Author: richardjgowers -Date: Tue Apr 24 14:02:22 2018 -0400 - - updated duecredit CHANGELOG - -commit 567acdda1688cb942b6765b4d7a89fd54d946dfe -Author: richardjgowers -Date: Tue Apr 24 13:47:05 2018 -0400 - - added duecredit for encore - -commit 8b0901bcc4b7466cd6007ef9958ba66eea3f9213 -Author: richardjgowers -Date: Tue Apr 24 13:25:29 2018 -0400 - - tests for qcprot duecredit - -commit eb0fad51cecc42e2a49cd8dc7709f18e9596c177 -Author: richardjgowers -Date: Tue Apr 24 13:21:06 2018 -0400 - - added qcprot duecredit stubs - -commit 8a6cf87dce52d104052c53a40bcc02ffe45d2a57 -Author: Oliver Beckstein -Date: Tue Apr 24 02:24:55 2018 -0700 - - duecredit for LeafletFinder and HOLE - -commit d996cc395079dee1be8db0a9d6c3e4281d2d2933 -Author: Oliver Beckstein -Date: Tue Apr 24 02:01:08 2018 -0700 - - canonicalized package duecredit citations - - - shortened description to make duecredit report more concise - - use package name as path - - adjusted tests - -commit 27f03fd2bfde7cfa95f32bc2763bba9c14bb08cc -Author: Oliver Beckstein -Date: Tue Apr 24 01:49:14 2018 -0700 - - duecredit citations in analysis with tests - - - use Doi citation for hbond_autocorrel and PSA - - test that the citations are picked up - -commit 25e0b9367a11d3880dce21dc267cc8ee1cb5d98e -Author: richardjgowers -Date: Mon Apr 23 16:43:03 2018 -0400 - - added hbond_autocorrel duecredit - -commit 426b85d0467cdea4967f1875684a86c19d8c3b6d -Author: Oliver Beckstein -Date: Mon Apr 23 14:38:11 2018 -0700 - - silence duecredit import failure - - - fix #1872 - - Do not show a warning if duecredit is not installed; - if users want the functionality they can install duecredit - but we should not bother all others. - - NOTE: This was manually tested in a local installation without - duecredit but doing a real unit test is difficult and - has not been attempted. - -commit 39b0e4cc184725cd0e5e710780c8154ed4de9f4f (tag: release-0.18.0) -Author: Richard Gowers -Date: Sun Apr 22 13:55:05 2018 -0400 - - updated c files for 0.18 release - -commit 8c331d7883ccf4a61dec884f2d95110726ce7573 -Merge: 092d5a542 558d845a6 -Author: Oliver Beckstein -Date: Wed Apr 18 23:09:39 2018 -0700 - - Merge pull request #1842 from palnabarun/1685-load-new-memory-reader - - Adds a check to MDAnalysis.coordinates.memory.MemoryReader to check f… - -commit 558d845a6c009347d069558b124893d71e457e86 -Author: Nabarun Pal -Date: Sat Mar 24 16:31:38 2018 +0800 - - Updates CHANGELOG - -commit 70cd0bc45f1548e4d81fe34da7998c8b84d22f62 -Author: Nabarun Pal -Date: Sat Mar 24 16:23:53 2018 +0800 - - Adds tests for changes in MemoryReader - -commit 71ad495ae67027523dfe6962bfa0375f9c13cf0b -Author: Nabarun Pal -Date: Sat Mar 24 16:23:27 2018 +0800 - - Adds relevant docstrings to MDAnalysis.coordinates.memory.MemoryReader - -commit d2ddfc94a7bd536855e07bd49a259da5043042cb -Author: Nabarun Pal -Date: Thu Mar 22 02:01:24 2018 +0800 - - Adds a check to MDAnalysis.coordinates.memory.MemoryReader to check for special cases - -commit 092d5a5429c985b884d6a85c651f5eecda6fb8c4 -Author: Richard Gowers -Date: Wed Apr 18 19:37:30 2018 -0500 - - Issue 1868 dihedralrepr (#1869) - - * fixes #1869 - * fixed order of indices in Angle/Dihedral/Improper repr - * tests for issue 1868 - -commit 41d48e4d267d2f32721d3c3ef1e17c77eaf1ae83 -Author: Oliver Beckstein -Date: Mon Apr 16 23:18:50 2018 -0700 - - updated docs on how users should run the tests (#1866) - -commit a26e3a1fee1ee89814e2eeb9332dac865c369f00 -Author: Richard Gowers -Date: Sun Apr 15 16:21:57 2018 -0400 - - started version 0.18.1 - -commit 946f772a2da9122dd48a8749cc3763334cfe8914 -Author: Richard Gowers -Date: Sun Apr 15 15:56:24 2018 -0400 - - finalised 0.18.0 - -commit bc5be1f3c1b9ba4427081bff61f567f897a9c01c -Merge: f7a6f47e9 e8a164804 -Author: Richard Gowers -Date: Sun Apr 15 15:59:40 2018 -0400 - - Merge branch 'develop' - -commit e8a164804a0af70c57381feaeaade541141ad283 -Author: Richard Gowers -Date: Sun Apr 15 15:56:24 2018 -0400 - - finalised 0.18.0 - -commit 8ed25716afd37b54e8acf1baf9d6681959fb8eea -Author: richardjgowers -Date: Fri Apr 13 13:05:34 2018 -0400 - - removed old tests - -commit e56073fe3f24d8aaaa80491193e1e3665ea3a4ef -Author: richardjgowers -Date: Fri Apr 13 11:45:44 2018 -0400 - - updeprecated older Group.__init__ - - moved Groups to top namespace - -commit 2f0ea82e62f5095c849972786d377964f55cfd6e -Author: richardjgowers -Date: Fri Apr 13 10:53:26 2018 -0400 - - fixup! updated docs for AtomGroup to clarify init methods - -commit b205bad7e53fd769ab6a029c8597b927b6b3b53b -Author: richardjgowers -Date: Fri Apr 13 10:52:41 2018 -0400 - - updated docs for AtomGroup to clarify init methods - -commit c84c86cc455d2251b89de482d2b4efe6a7da1df0 -Merge: 63a2b0e41 b63d6854f -Author: Oliver Beckstein -Date: Wed Apr 11 08:33:34 2018 -0700 - - Merge pull request #1856 from MDAnalysis/issue-1804-pqrfix - - fixed reading PQR files from Gromacs - -commit b63d6854f8c7558f83af9abcd4f01b70d9e0bd8e -Author: richardjgowers -Date: Mon Apr 9 14:21:55 2018 -0400 - - fixed PQR coordinate reading for GROMACS flavour - -commit a67cce9aae39b155aec0edc0e15740fc222c18bb -Author: richardjgowers -Date: Mon Apr 9 08:52:41 2018 -0400 - - added test for PQR file reading - -commit ea124c1d4f12fa7d9227bcef234b7123e10cc5b0 -Author: richardjgowers -Date: Fri Apr 6 12:08:36 2018 -0400 - - added docs for PQR fix - -commit 160a9097ab7ed64ca29978c0e3f8b416e1833996 -Author: richardjgowers -Date: Fri Apr 6 12:04:59 2018 -0400 - - fixed reading PQR files from Gromacs - -commit 63a2b0e412a0b33a3240b24a8e2b08d535ae1f6e -Author: Jonathan Barnoud -Date: Tue Apr 10 21:17:49 2018 +0200 - - Update CHANGELOG and doc for TPX 112 - -commit e9fe6789119dc70600da1e1ebb6b147fc79584fa -Author: Jonathan Barnoud -Date: Tue Apr 10 17:35:57 2018 +0200 - - Add more tests for TPR and gromacs 2018 - - The file data/tprs/all_bonded/dummy_2018.tpr was generated using gromacs - 2018 from fresh rather than converted from an earlier version. The MDP - file explicitly contains the new options that have been added in v2018. - -commit b41fa2f4f0e6f3fdc1fb45973add4f747c40b54a -Author: Jonathan Barnoud -Date: Mon Apr 9 15:08:01 2018 +0200 - - Bump TPX version - -commit 149ac8b70d37c528d9b87fe514b488fdeba5c405 -Author: Jonathan Barnoud -Date: Mon Mar 12 08:51:40 2018 +0100 - - Update TPR tests for tpx 112 - - TPX 112 is the version of the TPR format used by gromacs 2018. This - commit adds a TPX 112 file to the test suite. Note that the tests fail - as the format is not yet supported. - -commit a295b2c27399a7d2a825966fc9e63084719e9e82 -Author: Tyler Reddy -Date: Mon Apr 9 16:22:53 2018 -0600 - - BUG: Fix untested MDAnalysis.visualization code - - * Fixes Issue #1617 by adding regression tests - for the 2D and 3D streamplot codes - - * Fixes a bug in the 2D streamplot code where - coordinates() were used instead of positions - to access the coordinates of an atomgroup - - * visualization code is no longer excluded - from the test coverage report - - * appropriate CHANGELOG and README adjustments - -commit 2b57a15e2b97b4d8983deb00f53f6af15130678c -Author: Richard Gowers -Date: Mon Apr 9 13:04:06 2018 -0400 - - fixed pkdtree with BioPython >= 1.71 (#1858) - - * fixed pkdtree with BioPython >= 1.71 - * bumped required version of biopython to 1.71 - -commit 1ee4ce9b76e161d9d99f6de74e6112bf23f2b37a -Merge: 5be20e3f1 224347ba1 -Author: Jonathan Barnoud -Date: Thu Apr 5 09:15:45 2018 +0200 - - Merge pull request #1855 from MDAnalysis/issue-1854-PDBresids - - Issue 1854 pd bresids - -commit 224347ba10a0f8888298504aa530be1c9a5bec06 -Author: Richard Gowers -Date: Wed Apr 4 19:58:07 2018 -0400 - - Fixed issue 1854 - -commit 0baba7c5e7537e7b06e72fadedf3fe7c3708c273 -Author: Richard Gowers -Date: Wed Apr 4 19:14:35 2018 -0400 - - added tests for issue 1854 - -commit 5be20e3f187eac73d8962d8acbf1d6efe1439044 -Author: zemanj -Date: Tue Apr 3 16:57:10 2018 +0200 - - fix HydrogenBondAutoCorrel for scipy >= 1.0.1 - - One hydrogen bond autocorrelation test fails when scipy 1.0.1 is installed. - Apparently, `scipy.optimize.leastsq()` nowadays feels kinda unhappy if the shape of a returned value / array changes between function calls. - - pytest log (shortened): - ``` - =================================== FAILURES =================================== - ______________ TestHydrogenBondAutocorrel.test_solve_intermittent ______________ - - self = - u = , hydrogens = - oxygens = , nitrogens = - - def test_solve_intermittent(self, u, hydrogens, oxygens, nitrogens): - hbond = HBAC(u, - hydrogens=hydrogens, - acceptors=oxygens, - donors=nitrogens, - bond_type='intermittent', - sample_time=0.06, - ) - - def actual_function_int(t): - A1 = 0.33 - A2 = 0.33 - A3 = 0.34 - tau1 = 5 - tau2 = 1 - tau3 = 0.1 - return A1 * np.exp(-t/tau1) + A2 * np.exp(-t/tau2) + A3 * np.exp(-t/tau3) - hbond.solution['time'] = time = np.arange(0, 6.0, 0.01) - hbond.solution['results'] = actual_function_int(time) - - > hbond.solve() - - testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py:195: - _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - [...]/MDAnalysis-0.17.1.dev0-py2.7-linux-x86_64.egg/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:519: in solve - err, p_guess, args=(time, results), full_output=True) - _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ - - func = - x0 = array([0.33 , 0.33 , 0.6 , 0.06 , 0.006]) - args = (array([0. , 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1 , - ...5.88, 5.89, 5.9 , 5.91, 5.92, 5.93, - ... 0.90015115, 0.87233986, - 0.84...0.10146257, - 0.10125294, 0.1010438 , 0.10083515, 0.10062698, 0.10041929])) - Dfun = None, full_output = True, col_deriv = 0, ftol = 1.49012e-08 - xtol = 1.49012e-08, gtol = 0.0, maxfev = 1200, epsfcn = 2.220446049250313e-16 - factor = 100, diag = None - - def leastsq(func, x0, args=(), Dfun=None, full_output=0, - col_deriv=0, ftol=1.49012e-8, xtol=1.49012e-8, - gtol=0.0, maxfev=0, epsfcn=None, factor=100, diag=None): - - [...] - - if Dfun is None: - if maxfev == 0: - maxfev = 200*(n + 1) - retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol, - > gtol, maxfev, epsfcn, factor, diag) - E ValueError: The array returned by a function changed size between calls - - [...]/scipy/optimize/minpack.py:387: ValueError - ``` - - Letting the minimized `err()` function return a value with the same shape in the "out-of-bounds" as in the "within-bounds" case seems to fix the issue. - -commit ace4dc85d701a3c3649bb686c97eaddbf0ca6621 -Merge: 8f950b6e5 d91dd3c14 -Author: Jonathan Barnoud -Date: Thu Mar 29 00:25:06 2018 +0200 - - Merge pull request #1843 from MDAnalysis/doc-fixes - - Doc fixes - -commit 8f950b6e52620e8eca5e90f8ef23484cba2c257d -Author: Davide Cruz <37750297+davidercruz@users.noreply.github.com> -Date: Wed Mar 28 23:14:59 2018 +0100 - - changed groupby function to accept multiple attributes #1839 (#1846) - - * changed groupby function to accept multiple attributes #1839 - - * Added version number to versionadded field - - * erroneously changed versionadded field instead of adding versionchanged - - * Added tests for groupby function using multiple attributes as arguments - - * Updated documentation of groupby function. Updated CHANGELOG and AUTHORS - - * Corrected formatting of versionchanged field - - * multiple functions are passed to groupby as a list. Updated tests acordingly - - * updated docs and CHANGELOG to latest version of PR - - * updated CHANGELOG - - * Modified output of groupby to flattened dict. Added dictionary flattening function to utils - - * tests updated according to changes to groupby - - * Added tests for flatten_dict function - - * updated CHANGELOG - - * now testing for string_types in groupby. explicit cast on groupby tests - - * added test on string types to groupby tests - - * documentation formatting - - * added check for and decode of bytes string - - * added bytes string compatibility - - * cleaned code and style formatting - - * corrected issues with output when using one attribute - -commit d91dd3c1441dce5d36ba9f2f048a7a4578b0e059 -Author: Oliver Beckstein -Date: Tue Mar 27 00:16:53 2018 -0700 - - improved docs for analysis.density - - fixes #1726 - -commit 4ce5ae9d69b6886eb793fc157e78bcfc2fb499fe -Author: Oliver Beckstein -Date: Sat Mar 24 13:03:50 2018 -0700 - - analysis docs: explain verbose - - - fixes #1630 - - added explanation of `verbose` for all analysis classes that are derived from - AnalysisBase - - Note: The default remains False (as in AnalysisBase), unlike the request in the - issue to set it to True. I didn't want to change the general behavior - without further discussion but if there are more voices in favor of - showing a progress bar by default then we can change to True. - -commit d404dd4f446416592105a65a24de913e0a8ae551 -Author: Oliver Beckstein -Date: Sat Mar 24 12:57:33 2018 -0700 - - make diffusionmap.DistanceMatrix full y use AnalysisBase - - Changes enable use of verbose (related to #1630) - -commit de6a58542a4c6c7d7ec8182257c850c1c4001e0d -Author: Oliver Beckstein -Date: Fri Mar 23 21:11:18 2018 -0700 - - add GSD to docs - -commit fe680455e59ad1d2d0ea50c620ed1ce572ed787a -Author: Oliver Beckstein -Date: Fri Mar 9 16:55:47 2018 -0700 - - RMSD doc improvements - -commit 4b763d3a2bbbb771886c2950b17976ffdad1f66e -Author: Oliver Beckstein -Date: Tue May 23 21:59:21 2017 -0700 - - helanal: minor doc change (numpyfication) - -commit 5a232a3168c4aaa1590bc42615ebc07773f14172 -Merge: c7c6f4006 6412516f2 -Author: Oliver Beckstein -Date: Thu Mar 22 23:04:33 2018 -0700 - - Merge pull request #1832 from MDAnalysis/issue-1819-dcd-istart - - fix DCDReader istart (#1819) - -commit 6412516f211a4f360bebdc7fd38a4a7c04724390 -Author: Oliver Beckstein -Date: Thu Mar 22 17:37:23 2018 -0700 - - updated CHANGELOG for #1819 - - - fixes #1819 - - see PR #1832 and #1767 for discussions on DCD and istart; see - also https://github.com/MDAnalysis/mdanalysis/wiki/FileFormats - -commit 994f08c02b24ab5254f89f4bab6bfc89fec50f0f -Merge: 4e7d4aa71 c7c6f4006 -Author: Tyler Reddy -Date: Thu Mar 22 16:33:16 2018 -0600 - - Merge branch 'develop' into issue-1819-dcd-istart - -commit c7c6f4006149bfc3c3e0caa788ebce7ae8a1dd94 -Author: Tyler Reddy -Date: Thu Mar 22 11:39:01 2018 -0600 - - BENCH: add rdf asv benchmarks (#1840) - - * BENCH: add rdf asv benchmarks - * Added benchmarks for MDAnalysis.analysis.rdf.InterRDF - * MAINT: Revisions requested in PR#1840. - -commit 74defb7fb168145e58388cc67af811559cf23921 -Merge: 63b70f068 f79f88b72 -Author: Max Linke -Date: Wed Mar 21 23:16:55 2018 +0100 - - Merge pull request #1833 from MDAnalysis/fix-cython28-build - - fix cython 2.8 compiler error - -commit 63b70f068ce4eb4583ada2efbe4cb0ed1ee67ba1 -Author: Navya Khare -Date: Tue Mar 20 03:40:17 2018 +0530 - - removing redundant test cases - -commit a11dce4a85ec81fa4e1db6c5fee3eb2ca63e11eb -Author: Navya Khare -Date: Mon Mar 19 19:49:42 2018 +0530 - - in copy(), seeking new reader and copying over current Timestep - -commit be3e4f784d35f98105eefe60a060546d950b4ce5 -Author: Navya Khare -Date: Sat Mar 17 19:33:50 2018 +0530 - - removing unnecessary section from copy() and adding testcases - -commit 9383f089c2b66221da6a6caf1e5f77ad730c2b3f -Author: Navya Khare -Date: Sun Mar 11 21:01:35 2018 +0530 - - Adding copy method to ChainReader - -commit 4e7d4aa710b490e2cd58b8a80bdae41cc3959a38 -Author: Oliver Beckstein -Date: Sun Mar 18 11:17:12 2018 -0700 - - DCD test: use decimal=5 for time tests - -commit 83648d2dc487b3b53bef3d0182e8521dc1344aa6 -Author: Max Linke -Date: Sun Mar 18 09:33:48 2018 +0100 - - fix rms tests - -commit 486b27bc52e82ccf9931d746457caa9c6d98b883 -Author: Oliver Beckstein -Date: Fri Mar 16 18:34:21 2018 -0700 - - fixing istart/nsavc for writers - - - fixes #1819 - - add tests for the istart and nsavc defaults in DCDWriter - - update docs for nsavc and istart - - adjust test_writer_dt() so that we get the same times for dcd and xtc - (which is a bit tricky) - - update CHANGELOG - -commit 81a44aac3ed149a83e468db7344011c5f086422b -Author: Oliver Beckstein -Date: Thu Mar 15 01:08:36 2018 -0700 - - correctly calculate start of time in DCD - -commit b23e6885504f50595623fab105f63df01bce1d8a -Author: Oliver Beckstein -Date: Thu Mar 15 01:04:13 2018 -0700 - - add tests for #1819 - -commit 2ea22fd972450be4b65edbb3d05b196d97ca3518 -Author: Oliver Beckstein -Date: Thu Mar 15 00:19:50 2018 -0700 - - add native NAMD 2.10 PSF and DCD - - - 100 steps of TMD in GBIS implicit solvent from closed AdK - to open AdK; dt = 1fs; output frequency 10, first step 10 - - NAMD version 2.10 - - created by @sseyler - - see - https://github.com/MDAnalysis/mdanalysis/issues/1819#issuecomment-373281934 - for details - -commit 543853ecc2c2148d60861fadfe883966cbe5e27b -Author: Nabarun Pal -Date: Mon Mar 19 04:37:46 2018 +0530 - - Fixes hyperlinks to external resources in docs for MDAnalysis.coordinates.PQR (#1836) - - * Fixes #1826 - * Fixes hyperlinks to external resources in docs for MDAnalysis.coordinates.PQR - * Fixes duplicate references in docs - -commit d1f6b8c1a03130a9bd8cc5760c2f249074178699 -Merge: 4e323f1b3 ffc7b7afa -Author: Oliver Beckstein -Date: Sun Mar 18 11:28:08 2018 -0700 - - Merge pull request #1822 from MDAnalysis/ayushsuhane-duecredits - - duecredits - -commit f79f88b72fcbdebd5dca63f42409245ec6dd5283 -Author: Max Linke -Date: Sun Mar 18 09:16:10 2018 +0100 - - Revert "fix cython to 0.27 as a band-aid solution" - - This reverts commit 4e323f1b36537464dce4d59963e25234c5e2ebb9. - -commit ffc7b7afa32332b9708b785e3bf14215d9af9816 -Author: zemanj -Date: Wed Mar 14 14:12:43 2018 -0700 - - mock out calls to fork() in duecredit - - See https://github.com/MDAnalysis/mdanalysis/pull/1822#issuecomment-373009050 and https://github.com/MDAnalysis/mdanalysis/pull/1794 - for background. - -commit d97c75e8ce0f0601b70ebbb2f207569b07216f34 -Author: Oliver Beckstein -Date: Tue Mar 13 20:55:35 2018 -0700 - - remove UTF-8 from duecredit citation - - Under Python 2.7 we got a decoding error internal to duecredit, see e.g. - https://travis-ci.org/MDAnalysis/mdanalysis/jobs/353008220#L3152 - -commit f68f8842c3c231f6c1f1ea46fad4feb3f5db1ec5 -Author: Oliver Beckstein -Date: Mon Mar 12 10:29:43 2018 -0700 - - duecredit: small fixes - -commit e3d5cace73f3e0cec1b14792291886673938cfab -Author: Oliver Beckstein -Date: Sun Mar 11 11:00:54 2018 -0700 - - fixed duecredit import error reporting in due stub - - When no duecredit packae is installed then MDAnalysis should not report - any errors; the stub from https://github.com/duecredit/duecredit/blob/master/duecredit/stub.py - only tests for ImportError but not ModuleImportError and wrongly issues - an error message. Fixed by checking if the exception is an instance of - ImportError. - -commit 46fe093fe85d41a35bc048360693747fe459bf75 -Author: ayushsuhane <34154224+ayushsuhane@users.noreply.github.com> -Date: Sat Mar 10 03:10:19 2018 -0800 - - omit due.py from coverage reporting - - Omitted due.py, since it is a stub file and lowers the coverage - -commit dde9250569d848ed84fd887a6eb3e2a324250d0b -Author: ayushsuhane <34154224+ayushsuhane@users.noreply.github.com> -Date: Sat Mar 10 16:27:59 2018 -0800 - - Updated docs, authors, and changelog - - - Modified the AUTHOR, CHANGELOG and added the documentation for using duecredit in the references section - - Added comments for later reference, modified references doc with code-blocks - - include duecredit link - -commit b15e8ea4562db9260491646b5e41395188b8e9a6 -Author: ayushsuhane -Date: Fri Mar 9 00:28:50 2018 -0800 - - Added the test case for Duecredit - - - modified due.py to handle import error - - Modified to install duecredit for testing - (install duecredit via ci-helpers) - - Removed import logging and modified strings according to pep8 - - Enable environment variable duecredit - -commit 006043016be30def13db0ca16c7baafb0a0e0126 -Author: ayushsuhane -Date: Wed Feb 28 01:52:58 2018 -0800 - - add citations for MDAnalysis - - - Inserted citation decorators in the __init__.py function in Universe.py. Includes Michaud-Agrawal 2011, and R. Gowers,2016 - - due.cite in __init__.py to cite everytime MDAnalysis module is called, reverted the universe.py to the previous one - -commit bbe9fe540f8ca663bbb06e8122f6b6a5dc1d6d4c -Author: ayushsuhane -Date: Wed Feb 28 12:12:48 2018 -0800 - - Changed the format of due.py to resolve the error in test - -commit 931c1700e65f8d38ec54a62fc2f17a3f7d6164fd -Author: ayushsuhane -Date: Wed Feb 28 01:36:34 2018 -0800 - - File for duecredit module to load - -commit 0658f75194774dc96422acf962dc19d50908d664 -Author: Max Linke -Date: Sat Mar 17 18:13:53 2018 +0100 - - cython setup clean-up - -commit 340ffbfea8ea82d9e67a3b75bd396623bdabf1d3 -Author: Max Linke -Date: Sat Mar 17 18:13:30 2018 +0100 - - fix copy error in cython setup - -commit 1413eac4dbd8cbe42edfc9478f44b3cafdb98867 -Author: Oliver Beckstein -Date: Wed Mar 14 22:40:41 2018 -0700 - - extensions need to be fully qualified in setup.py - - - fixes #1830 - - upgrade to cython 0.28 broke our build - -commit 6c788c6a6d2e4355c862400f0194c507bdf80e42 -Author: Matteo Tiberti -Date: Thu Mar 15 10:49:35 2018 +0100 - - fixes stochasticproxembed.pyx Cython compilation error - -commit d3f5163a7e5bd5f7c1087c8b685946c6a04128e5 -Author: Max Linke -Date: Thu Mar 15 09:08:27 2018 +0100 - - fix cython 0.28 compiler error - - I'm not sure what the actual error was. But only one function is imported and - the cleaner solution long-term is to skip the pxd file and directly import from - c. - -commit 4e323f1b36537464dce4d59963e25234c5e2ebb9 -Author: Max Linke -Date: Thu Mar 15 13:39:16 2018 +0100 - - fix cython to 0.27 as a band-aid solution - -commit bc374fad683a810b448d61d03577eda2f87b5c6b -Merge: b2fc3f905 50f0bcbaa -Author: Oliver Beckstein -Date: Tue Mar 13 22:40:39 2018 -0700 - - Merge pull request #1810 from MDAnalysis/fix-aligner-errormessages - - Fix aligner errormessages - -commit 50f0bcbaa8cbd3131e15479e28aaa08df11549dc -Author: Oliver Beckstein -Date: Wed Mar 7 15:03:05 2018 -0700 - - align.get_matching_atoms(): more checks and tests - - - added additional check, in case we could not find matching atoms - - added tests - - fixed spelling in comments - - updated CHANGELOG - - NOTE: get_matching_atoms() is not very robust (and is not very good at finding matching atoms) - and needs some TLC - -commit a5f09a09585a55bd04109cdae5edd0997da876b5 -Author: Oliver Beckstein -Date: Wed Mar 7 14:00:27 2018 -0700 - - analysis.align: fixed error messages and fixed use n_atoms - - - fixes #1809 - - error messages were not shown - - n_atoms was used as Residue.n_atoms, which does not exist anymore: fixed - as Residue.atoms.n_atoms - - similarly, fixed occurences that relied on old behavior that atoms.resids would - give a list of resids with length n_residues - - added check for having created empty selections (see also - https://gist.github.com/orbeckst/2686badcd15031e6c946baf9164a683d ) - -commit b2fc3f905b5a3f254dae1a9ac13cab0a17d2e49d -Author: zeman -Date: Fri Mar 9 23:08:37 2018 +0100 - - added comment explaining why CalledProcessError is caught and raised again - -commit 3f31d61d9455a28b290633d1a500e92b5e92554b -Author: zeman -Date: Fri Mar 9 16:16:33 2018 +0100 - - added comment explaining test_os_dot_fork_not_none - -commit 5e3bd4956cd6a552d93a80bb35de9106148a42f1 -Author: zeman -Date: Fri Mar 9 11:41:41 2018 +0100 - - cleanup: removed some unnecessary lines - -commit 068e4ea6796ca9dde73772e6008be500c9265da8 -Author: zeman -Date: Thu Mar 8 17:53:33 2018 +0100 - - moved one test back into the test module - -commit d87399684859ca850da34f7335e2c345482879ff -Author: zeman -Date: Thu Mar 8 17:26:59 2018 +0100 - - split the test into two separate ones (otherwise one could never fail) - -commit 0f30ff5a988e5d73dcd4da8f2db4f844e28957d0 -Author: zeman -Date: Thu Mar 8 16:51:30 2018 +0100 - - isolated import tests by offloading to separate Python instance - -commit f8b583b02cc021e0ac321b049c84d7b20cfa3d3b -Author: zeman -Date: Thu Mar 8 12:00:56 2018 +0100 - - Python 3 compatibility (still likely to break other tests) - -commit 44a1356ed7f4ef965d47464c94f137d6fb863a34 -Author: zeman -Date: Wed Mar 7 23:22:13 2018 +0100 - - tests for unwanted side effects when importing MDAnalysis - -commit 5209585c9055725a735aaab693bf223a9f942082 -Author: zeman -Date: Thu Mar 8 17:53:33 2018 +0100 - - moved one test back into the test module - -commit fdbd139b910939284c3eeea10b2c1262c70a6de2 -Author: zeman -Date: Thu Mar 8 17:26:59 2018 +0100 - - split the test into two separate ones (otherwise one could never fail) - -commit f0ee149d7767a7969567e03172eb437cedb81a59 -Author: zeman -Date: Thu Mar 8 16:51:30 2018 +0100 - - isolated import tests by offloading to separate Python instance - -commit a4a6d81201417e183303bf47c5ba1d64b3532589 -Author: zeman -Date: Thu Mar 8 12:00:56 2018 +0100 - - Python 3 compatibility (still likely to break other tests) - -commit 27d27270a435650aa0c5af08efff555e504b42bc -Author: zeman -Date: Thu Mar 8 17:53:33 2018 +0100 - - moved one test back into the test module - -commit 96ab1cc365dbafa7e06e86aca68c0ed1f68a13cb -Author: zeman -Date: Thu Mar 8 17:26:59 2018 +0100 - - split the test into two separate ones (otherwise one could never fail) - -commit da738bdb26870935f97d75840d194a8d9cbd418e -Author: zeman -Date: Thu Mar 8 16:51:30 2018 +0100 - - isolated import tests by offloading to separate Python instance - -commit 2f3419b326e64e569bdc803aa735e3d034e01160 -Author: zeman -Date: Thu Mar 8 12:00:56 2018 +0100 - - Python 3 compatibility (still likely to break other tests) - -commit dc706ed27e4fd7e444973a1d717d0b4a5035b143 -Author: zeman -Date: Wed Mar 7 23:35:41 2018 +0100 - - added myself to the list of authors - -commit dbafc04b497742bb344e95828fd53cf69eb00e97 -Author: zeman -Date: Wed Mar 7 23:33:27 2018 +0100 - - added changelog entry for import side effects - -commit dc324558797dfd17d114b6a7146d4c0a6a9491cf -Author: zeman -Date: Wed Mar 7 23:22:13 2018 +0100 - - tests for unwanted side effects when importing MDAnalysis - -commit 6159650038b8ba505449cd380cee30194669ba69 -Author: Tyler Reddy -Date: Sun Mar 4 13:32:01 2018 -0700 - - MAINT: Config / DOC updates for latest asv version. - -commit e94b1c412b9b73a2350e4b992fcee28ce055598a -Merge: 1fa0f8102 9b329683d -Author: Oliver Beckstein -Date: Thu Mar 8 14:43:49 2018 -0700 - - Merge pull request #1813 from MDAnalysis/issue-1807-mmap - - AMBER NCDF reader mmap=None as default - -commit 9b329683d9ffb4ccdcbc0dc6f84273b7325cf3f5 -Author: Oliver Beckstein -Date: Thu Mar 8 10:29:06 2018 -0700 - - AMBER NCDF: cleaned up mmap use - - - make mmap an explicit kwarg of the NCDFReader - - use the default mmap=None everywhere (in static method parse_n_atoms() - to avoid memory leaks, and in the writer (where it does not make a difference, as - far as I understand the docs for scipy.io.netcdf) - - updated docs with links to mmap.mmap in the standard library - -commit 139f4b9d25584ac7e934e87c421f84588cbc1547 -Author: Oliver Beckstein -Date: Wed Mar 7 16:01:37 2018 -0700 - - AMBER NCDF reader mmap=None as default - - - fixes #1807 - - The default was wrongly set to False, which means to load the trajectory - into memory, which can lead to memory problems with big trajectories - (see Issue #1807) - - added tests for value of mmap and for the reader with - (1) no arguments (default), (2) None, (3) True, (4) False - -commit 1fa0f8102e2ce1a942f5f70e3e8ebc51a8831c02 -Author: Nabarun Pal -Date: Wed Mar 7 09:31:01 2018 +0530 - - Reorders docstring elements for better consistency - -commit 713dc36c43819cf7555ab89bc43cc73eaa9266a3 -Author: Nabarun Pal -Date: Tue Mar 6 23:13:00 2018 +0530 - - Removes unnecessary docstrings - -commit 3d86c454dcad58fbcb8cd9a52b8e07c79cfdae37 -Author: Nabarun Pal -Date: Fri Mar 2 07:44:45 2018 +0530 - - Updated docstring for AtomGroup.select_atoms - -commit c4c7ad6e038ae7982d23a867fc274e857b8eff9f -Author: Nabarun Pal -Date: Fri Mar 2 07:36:13 2018 +0530 - - Removes the added versionchanged - - The versionchanged descriptor was not needed here as it is describing - a changelog in the cylayer and cyzone selections - -commit 3c6d6b1032af5a1113f15ad05efbbe834da84af0 -Author: Nabarun Pal -Date: Wed Feb 28 21:25:53 2018 +0530 - - Adds cylayer and ccyzone to docstring of AtomGroup.select_atoms - -commit e47215bdeed605ac2491afaded2f5e101201ad03 -Author: zeman -Date: Mon Mar 5 10:39:28 2018 +0100 - - added changelog entry for PR #1794 and added @zemanj to the list authors - -commit 0308d68f34e1720bc38ae7ac782960fef75ef171 -Author: zemanj -Date: Mon Mar 5 10:12:02 2018 +0100 - - applied changes suggested by @orbeckst and @richardjgowers - - See https://github.com/MDAnalysis/mdanalysis/pull/1794/files#r171996513 and https://github.com/MDAnalysis/mdanalysis/pull/1794/files#r171995836 - -commit 245762755bbe824e65ca9eadbe884fc80cf5d563 -Author: zemanj -Date: Thu Mar 1 18:31:51 2018 +0100 - - Fixed MPI fork() warning when importing MDAnalysis after MPI_Init() call - - Solved problem: - --------------- - When used in an MPI environment, importing MDAnalysis may trigger an MPI - warning because importing the uuid module in MDAnalysis.core.universe - triggers a call to os.fork(). This happens if MPI_Init() has been called - prior to importing MDAnalysis. - - Why this was fixed: - ------------------- - For the user, it is completely unclear where and why the MPI warning was - triggered and whether that is of any concern. - - How to reproduce: - ----------------- - With OpenMPI (version should be irrelevant, tested on 1.10.2) and Python < 3.7, executing - the command - echo "import mpi4py.MPI, MDAnalysis" | mpirun --mca mpi_warn_on_fork 1 -n 1 python - - yields the following output: - - """ - An MPI process has executed an operation involving a call to the - "fork()" system call to create a child process. Open MPI is currently - operating in a condition that could result in memory corruption or - other system errors; your MPI job may hang, crash, or produce silent - data corruption. The use of fork() (or system() or other calls that - create child processes) is strongly discouraged. - - The process that invoked fork was: - - Local host: (PID ) - MPI_COMM_WORLD rank: 0 - - If you are *absolutely sure* that your application will successfully - and correctly survive a call to fork(), you may disable this warning - by setting the mpi_warn_on_fork MCA parameter to 0. - """ - - If you cannot reproduce this warning, it is probably due to your Python - installation using an implementation of fork() that is named differently and, - thus, is not recognized by mpirun (can be checked for example with gdb). - - Explanation: - ------------ - The problem is actually caused by the uuid module, which is imported in - MDAnalysis.core.universe and triggers a call to os.fork() by calling a couple - of methods from the ctypes module which in turn use the subprocess module - (that's where os.fork() actually gets called). - This means that the real problem is not due to MDAnalysis itself, but it also - means that it will probably never be fixed for older Python versions. - In Python 3.7, the problem with the uuid module is solved. (see - https://bugs.python.org/issue11063 for further information) - Luckily, for Python < 3.7, the uuid module works perfectly fine with - os.fork() disabled during its import. - A clean fix is therefore simply to disable os.fork() prior to importing the - uuid module in MDAnalysis.core.universe and to re-enable it afterwards (for - Python < 3.7 only). - -commit 37f51d3288ffd27f2cca7042077a5c2c599e86f0 -Author: Richard Gowers -Date: Tue Mar 6 08:52:46 2018 +0000 - - whitespace removal - -commit a28e672f9eb4333477ea0e7fbd903cbec43cc491 -Author: Navya Khare -Date: Mon Mar 5 22:41:11 2018 +0530 - - Updates CHANGELOG and adds name to author list - -commit 7e7a154a4d2bf4369655a3b2231329b6688bf224 -Author: Navya Khare -Date: Thu Mar 1 00:31:23 2018 +0530 - - validating dimensions for self.pbc and addition of discription to docstring - -commit 5368a7ad876ce267749987f8238b3e841450c13f -Author: Navya Khare -Date: Tue Feb 27 19:25:29 2018 +0530 - - passed parameter through fixture - -commit 3366c8a51e3bb06d351592d924c118740d3343a9 -Author: Navya Khare -Date: Tue Feb 27 03:26:52 2018 +0530 - - minor changes in test_distance.py - -commit b992af41eb6798158a8b4da8366bf4a048ea87d0 -Author: Navya Khare -Date: Tue Feb 27 01:39:34 2018 +0530 - - minor error correctionin mdamath.py - -commit 38af730d51074b8983014f4e171d832d8122de75 -Author: Navya Khare -Date: Tue Feb 27 00:30:38 2018 +0530 - - added pbc to hbond_analysis and required changes made - -commit 00c785b0213cc6ced3c31ccf99d7feff60b22981 -Author: Navya Khare -Date: Mon Feb 26 23:02:49 2018 +0530 - - changing assert_almost_equal to assert_allclose to correct precision error - -commit efa08424177148a39f3cea4bdb3a8da383b2a486 -Author: Navya Khare -Date: Mon Feb 26 21:42:31 2018 +0530 - - decimal correction in test case - -commit 3b46b314e6ac66dbc47138207ec8e92667f6a755 -Author: Navya Khare -Date: Mon Feb 26 18:28:16 2018 +0530 - - added pbc to calc_angle() in hbond_analysis - -commit 3088f194555dc2f50185cdaa037d7cf746a3f7ca -Author: Navya Khare -Date: Sat Feb 24 16:26:21 2018 +0530 - - added testcase for dist w/o pbc - -commit 09680c0934bae463d1818b5ee1a16ad82f711cde -Author: Navya Khare -Date: Fri Feb 23 19:12:20 2018 +0530 - - added pbc to dist() - -commit 69746d9a080a7d20ff13864449b5a1027b5b782d -Author: Navya Khare -Date: Fri Feb 23 05:11:44 2018 +0530 - - added test case for pbc in dist() - -commit ae62b93832ca131bf59e09df1ebbc78f640ac22e -Author: Navya Khare -Date: Fri Feb 23 04:42:38 2018 +0530 - - added pbc to dist() - -commit 9761de7c1e4ff06da77c0a3659d9077f420c68c7 -Author: Nabarun Pal -Date: Tue Mar 6 05:22:52 2018 +0530 - - Updates to https urls for downloading hole - - Fixes #1802 - -commit eaaa9687be10215692073117b7047eba900c1dc4 -Merge: e97fd8ec8 48f8dc431 -Author: Oliver Beckstein -Date: Mon Mar 5 09:42:01 2018 -0700 - - Merge pull request #1793 from MDAnalysis/issue-1791-lammpsparser - - Added custom atom_style to Lammps data parser - -commit 48f8dc431ad3ab728c667235a6c1c9dc234c49e5 -Author: Richard Gowers -Date: Mon Mar 5 11:39:09 2018 +0000 - - renamed error variable - -commit eabf44f8486df61b07be20c13bd4063e1c3ad4d8 -Author: Richard Gowers -Date: Mon Mar 5 11:38:46 2018 +0000 - - made atom_style kwarg optional - -commit 3b40305990ae92b254af0c42b02d0e2353c8c43d -Author: Richard Gowers -Date: Mon Mar 5 11:37:28 2018 +0000 - - fixed up GRO and LAMMPS docs - -commit 7c6e9701e003a807dcdaf6916f0a74b54a7eb4f6 -Author: Richard Gowers -Date: Mon Mar 5 11:18:48 2018 +0000 - - doc updated for #1791 - -commit e135861f14bfb43b01a13409006dfd054595b0ce -Author: Richard Gowers -Date: Thu Mar 1 14:48:58 2018 +0000 - - added atom_style kwarg to Lammps Data file reading - - Made resids optional for Lammps data file - -commit 941afa0a21ab4bf41bd3e402a48e030a89a34d4c -Author: Richard Gowers -Date: Wed Feb 28 20:36:23 2018 +0000 - - added handling of atom_style kwarg for Lammps Data parser & reader - -commit e97fd8ec8b15590395bd0a94b5384f429f0e3f81 -Author: Nabarun Pal -Date: Mon Mar 5 09:37:09 2018 +0530 - - Updates hole download links - - Now uses the holeprogram.org download links - Fixes #1792 - -commit 41787ac555418345ca3023610a9372ef83a9bdd1 -Author: Richard Gowers -Date: Sun Mar 4 09:17:33 2018 +0000 - - fixed up tests for reindex growriter - -commit 895557007cafd8e8fc7b7f41954ee59840c972cf -Author: zhiyi wu -Date: Fri Mar 2 10:51:57 2018 +0000 - - fix (scope='class') - -commit 97561732e558ef124f95a597490644c69b545699 -Author: zhiyi wu -Date: Fri Feb 23 15:30:29 2018 +0000 - - Fix object - -commit 2f55f5035a630483f460d42215cdcffadf2aeea0 -Author: zhiyi wu -Date: Fri Feb 23 15:13:14 2018 +0000 - - pytest.fixture - -commit b78f7cecd1bd2b6df7ecd2417d46b3331e8ba430 -Author: zhiyi wu -Date: Fri Feb 23 11:49:56 2018 +0000 - - fix typo - -commit fc20c228662fe407aaf6c56e00565878a21b9efb -Author: zhiyi wu -Date: Fri Feb 23 11:46:07 2018 +0000 - - Fix docs - -commit 2322fa46c6b041d166339a3f4adf242d93634c6b -Author: xiki-tempula -Date: Thu Feb 22 17:36:37 2018 +0000 - - Update GRO.py - -commit 0bf809019f82b079c2f3440748d081af838137bb -Author: zhiyi wu -Date: Thu Feb 22 17:34:51 2018 +0000 - - Add doc - -commit 1c5d2fc60fad2f87980f8191f0d4b60f888b827f -Author: zhiyi wu -Date: Thu Feb 22 16:07:58 2018 +0000 - - Add test - -commit 97e6752659a0bd909f037d9130b896baa2448925 -Author: zhiyi wu -Date: Thu Feb 22 15:29:45 2018 +0000 - - Add reindex option to write atom id to gro file - -commit 36e12e98c958580d263c3e7c54f43c5565171787 -Author: Nabarun Pal -Date: Fri Mar 2 07:08:26 2018 +0530 - - Fixes typo in docstring of topology.guessers.validate_atom_types - -commit 1b514a863bca94e668d51796c73218efd76b313d -Author: Nabarun Pal -Date: Sat Feb 24 18:35:40 2018 +0530 - - Uses assert_nowarns for testing - -commit 7506e77cedfaebe8f3694143cdd3e9c2148075da -Author: Nabarun Pal -Date: Mon Feb 12 22:17:58 2018 +0530 - - Adds test to check for no warning when topology with MW atom type is loaded - -commit 10184af2786dca0660220f20ec4f9cef88e352c6 -Author: Nabarun Pal -Date: Mon Feb 12 22:10:49 2018 +0530 - - Fixes a bug in topology.guessers.validate_atom_types - -commit c85cc4e73a0d8a2ff30b25150736bf401db0c7c2 -Author: Nabarun Pal -Date: Mon Feb 12 21:40:45 2018 +0530 - - Add new function topology.guessers.validate_atom_types - - This is added to validate the atom types in the universe - based on whether they are present in topology.tables or not - -commit a647b2ebd7ddc3c113748afd2a3b161ce4212fbe -Author: Nabarun Pal -Date: Mon Feb 12 21:39:40 2018 +0530 - - Adds machinery to recognize dummy atoms and assign masses - -commit 0a092978399c40f7fb8fc404c00f1e9b720cc351 -Author: Nabarun Pal -Date: Wed Feb 7 18:53:56 2018 +0530 - - Refactors topology.guessers by changing the criteria when warning is raised - -commit 7b6ad00370e50c2a5a6479383984cb7a0e9333f1 -Author: Richard Gowers -Date: Fri Feb 23 20:23:17 2018 +0000 - - Fixes Issue #1771 - - Universe.empty now warns about empty Residues or Segments - -commit 323823b6783e9aebe56fa46febff873688ea4576 -Author: Oliver Beckstein -Date: Thu Feb 22 17:40:58 2018 -0700 - - fixed broken links in HOLE docs - - HOLE moved to http://www.holeprogram.org/ and is open source since 2016. - -commit 4b626048a7b04b501c0009e3271a1da7daf687d3 -Author: Oliver Beckstein -Date: Thu Feb 22 16:40:19 2018 -0700 - - fixed the PDB format of the HOLE test file PDB_HOLE - - - the file had a trailing '1GRM nnn' (nnn = linenumber) on each - line which made it illegal under PDB format v3.3 - - However, MDAnalysis still read the file but failed to assign - atomtypes (the line number was picked up as the "element") - and thus all masses were set to 0. - - - This lead to problems with the HOLE binder notebooks - (see PR https://github.com/MDAnalysis/binder-notebook/pull/1) - - - Manually fixed with - - sed -i~ 's/1GRM *[0-9]*[0-9]$//' 1grm_single.pdb - - and added an additional REMARK 500 section to explain - the difference to the original (which must date from the - late 1980s...) - -commit 34b327633bb2aa7ce07bbd507a336d1708871b6f -Author: Richard Gowers -Date: Fri Feb 23 08:12:41 2018 +0000 - - Added Universe.copy - -commit a5c16d18d7da94ba9aeb295d83a4321043f79159 -Author: Richard Gowers -Date: Fri Jul 21 01:11:17 2017 +0100 - - Added Reader.copy method - -commit 7b4bf01822aae12663a741bbc8998b3ead8262bc -Author: Richard Gowers -Date: Thu Jul 20 01:58:13 2017 +0100 - - added core.topology.Topology.copy - -commit 0a9a84a62582190ba25b8be7c11d703e1f29cc4c -Author: Richard Gowers -Date: Thu Jul 20 01:43:05 2017 +0100 - - added TopologyAttr.copy - -commit f5b3503527e7f9e40c25dca2f54218ffe7af22a8 -Author: Richard Gowers -Date: Thu Jul 20 00:43:38 2017 +0100 - - Added core.topology.TransTable.copy method - -commit acfa56a02757f440861ec7ad50583fbf5af64291 -Author: Oliver Beckstein -Date: Wed Feb 21 15:33:57 2018 -0700 - - reST formatting fixes - - Fixes to the reST docs (numpy style) were necessary because the new - Sphinx 1.7 is more stringent and flagged warnings (which we treat as errors). - -commit fc81ad0133a957d46e3bc91fb8755bd82c08c062 -Author: Oliver Beckstein -Date: Wed Feb 21 15:54:31 2018 -0700 - - raise minimum scipy version to 1.0.0 - - - fixes #1775 - - We need scipy >= 0.19.0 for the directed Hausdorff distance that was - added in PR #1758 but give the recent 1.0 release of scipy, we will - simply depend on scipy >= 1.0.0 - - only added scipy version information to package/setup.py; possibly todo: - - [ ] conda recipe - - [ ] pypi ?? - -commit 83f8383f3c6be4caf116280bced39672c41535c3 -Author: Oliver Beckstein -Date: Sun Feb 11 10:44:51 2018 -0700 - - restructured Amber docs and WebCited original Amber format pages - - - moved full-feature binary NCDF format to top so that users - see it first instead of the less-well supported ASCII TRJ - (NCDF is also the better format...) - - archived Amber format pages with http://webcitation.org/ - Added notes on which WebCite cache pages to use should the original - Amber format docs ever disappear from the web. - - [ci skip] - -commit a5517b965be6ff66c30362e1ada91c82ba28fea6 -Author: Oliver Beckstein -Date: Sun Feb 11 10:29:46 2018 -0700 - - updated Amber TRJ docs - - - added known limitation: velocities not supported - (see http://ambermd.org/formats.html#trajectory for what would need to be done) - - added note on using "crd" for Amber trj (see also https://stackoverflow.com/q/48669651): - need to use `Universe(..., format="TRJ")` - -commit daf6c1aae85dd1c9dfffc5cd2291606ff9ab1ab3 -Author: Oliver Beckstein -Date: Sun Feb 11 10:14:54 2018 -0700 - - docs: updated path to matplotlib objects - - [ci skip] - -commit 9935167c055192a08d7035dac6d15e8d9d239674 -Author: Oliver Beckstein -Date: Sun Feb 11 10:08:57 2018 -0700 - - fixed link to Amber nctraj format - - [ci skip] - -commit 2703b38b5fa7f90857d1dd5a3d2a6020861913b2 -Merge: eae5845cf 2c55dcd07 -Author: Max Linke -Date: Wed Feb 7 17:20:06 2018 +0100 - - Merge pull request #1767 from MDAnalysis/fix-dcd-witer - - fix header length in dcd - -commit eae5845cf5488ae1db1cdcc2075f68406291721e -Author: Tyler Reddy -Date: Tue Feb 6 17:52:44 2018 -0700 - - ENH: Added directed_hausdorff from scipy to speed up hausdorff calc (#1758) - - * ENH: Added directed_hausdorff from scipy from Hausdorff calculation. - - * Suggested hausdorff reshape from Oli -- tests still fail. - - * Second permutation of suggested hausdorff reshape from Oli -- tests still fail. - - * Draft of changes needed to get unit tests to pass with hausdorff when scipy is used under hood. - - * Docstring and code refinements related to performance improvements in hausdorff() function. - -commit 1ae6ed5562aadf48d03777cc35a8362cce5a6405 -Author: Max Linke -Date: Wed Feb 7 01:11:01 2018 +0100 - - add binder button (#1770) - - this will allow quick interactive usage of MDAnalysis - -commit 2c55dcd07a1c614ddeb8b7d77462e74ca69380e3 -Author: Max Linke -Date: Mon Feb 5 14:55:08 2018 +0100 - - proper null termination of remark string - - this might cause issues in other c libraries otherwise. - document and fix null termination - -commit 75b69bc839de086a385ef306e88280b73011bc90 -Author: Richard Gowers -Date: Sun Feb 4 20:39:43 2018 +0000 - - Update test_dcd.py - -commit b307e733e51f1519c779916f60617bca2cc8dab7 -Author: Max Linke -Date: Sat Feb 3 09:27:15 2018 +0100 - - update changelog - -commit adaf9d977ce8bc16f6d248f3fe5c3f68ad4e1460 -Author: Max Linke -Date: Sat Feb 3 09:22:00 2018 +0100 - - use istart information in dcd to set correct time - -commit fd68f60a4910675cf28462d8e0bd0d0e2dae9771 -Author: Max Linke -Date: Fri Feb 2 14:17:18 2018 +0100 - - DCDwriter now has a option to set istart - - Programs who use DCD have different conventions for istart, the starting frame - of the trajectory. Because of this we now allow it to be set by the user. - -commit 6fdf06dc1c0aa61d7b5db455fbe48f47e1d3399a -Author: Max Linke -Date: Fri Feb 2 09:29:03 2018 +0100 - - fix header length information in dcd - - A DCD has two byte positions to store the length of the remark section. First a - it reads number of bytes in the remark plus 4. Afterwards it has the number of - 80 character sections. These two numbers have to match. So far we wrote first - that we use 164 chars and three 80 character blocks, 164 != 80*3 + 4 - - Now we corrected that and state correctly we write 244 bytes in the remark - section. We never noticed that because our reader ignores the information about - the byte length on looks only at the number of blocks. - - As a side note here. DCD remarks always have have to be a multiple of 80 in - length. - -commit 7a82fa9fa924f740cbab823d6a46d392c1029168 -Author: Richard Gowers -Date: Sat Feb 3 11:57:46 2018 +0000 - - Update CHANGELOG - -commit f170e59e51a4edbb7b48c9c8bb21c0a214fa31a1 -Author: mat -Date: Fri Feb 2 13:42:47 2018 +0000 - - Author's name - first contribution - -commit 1fd24ebccbd54165d918f55194aaa30423110077 -Author: mat -Date: Fri Feb 2 11:46:51 2018 +0000 - - Importing explicitly waterdynamics since this is the module we are testing in this file. Decreased precision to 3 decimals. - -commit 46d90c4ad5937b59c295482bef4f1670e99acc0e -Author: mat -Date: Fri Feb 2 11:40:17 2018 +0000 - - Testing Survival Probability against actual results. Changed selection of water to be only around one interface residue GLU with a short radius to make the analysis and selection faster. - -commit 2cdf0fb8422040ca8ae405b81172ff8204b76091 -Author: mat -Date: Thu Feb 1 16:12:43 2018 +0000 - - Test case for the t0 argument being ignored. - Corrected the original test_SurvivalProbability. The first point has to be 0 (autocorrelation). - I changed the universe for the test so that the timeseries is not only 1s (meaning that nothing changes and the test is too naive). This could be further improved by using actual verified values. - -commit 9851e32791965fe1e1f0aded153dd99ad62184d3 -Author: mat -Date: Fri Jan 26 17:33:06 2018 +0000 - - Refined comments as discussed in https://github.com/MDAnalysis/mdanalysis/pull/1759 - -commit 6fb2727e0dd625b79a7c4dd16911a5669aa98f4e -Author: mat -Date: Mon Jan 22 17:06:45 2018 +0000 - - Corrected ProgressMeter to display loading correctly. - Adjusted code to adhere to the 80 character line width limit. - -commit 8664cd767352a760d8f0299b76eb57494d3e52bc -Author: mat -Date: Mon Jan 22 16:38:37 2018 +0000 - - Removed the problem where t0 was ignored. Changed the organisation of the functions and used mroe consistent variable names. - Removed the mention of parallel selection which was not implemented. - Inlined the function which did not do much. - -commit 494541510d14938ed706ea4e391c406e5f6a5d1a -Author: Nabarun Pal -Date: Fri Feb 2 17:31:00 2018 +0530 - - Adds Nabarun Pal to list of authors - -commit c5504e576a0a926475e495ac448a53b34537b3b3 -Author: Nabarun Pal -Date: Fri Feb 2 17:29:36 2018 +0530 - - Updates CHANGELOG with Fix of #1699 - -commit 0ac274e6dcf03ee4c5c6b2f2571a6d23bed5417b -Author: Nabarun Pal -Date: Fri Feb 2 10:47:29 2018 +0530 - - Refactors lib.distances._check_array and adds lib.distances._check_aray_dtype - - This is done because _check_array also checks for one more condition which may or may not be required for other scenarios - -commit 62522f53aff36255d41ded9d24b01a9ac0bf50b6 -Author: Nabarun Pal -Date: Thu Feb 1 19:18:35 2018 +0530 - - Adds tests for lib.distances.transform_StoR - -commit f658404b68517eb5d6a02b826021ae509122f340 -Author: Nabarun Pal -Date: Thu Feb 1 19:18:09 2018 +0530 - - Adds S array type validation to lib.distances.transform_StoR - -commit b56ef0165d814f898590eb18c801ec5a7b385f21 -Merge: d9ef4ec1a 7cc1e8154 -Author: Jonathan Barnoud -Date: Tue Jan 30 14:58:01 2018 +0100 - - Merge pull request #1764 from MDAnalysis/issue-1582-dimensions_copy - - AtomGroup.dimensions now always returns a copy - -commit 7cc1e81541b966aba71212327875dc1b5c82eaaf -Author: Richard Gowers -Date: Tue Jan 30 13:15:27 2018 +0000 - - Fixes Issue #1582 AtomGroup.dimensions now always returns a copy - -commit d9ef4ec1a5c0be61db887708db2eae4baf295ae3 -Merge: 10ee7ff29 4de452f52 -Author: Jonathan Barnoud -Date: Mon Jan 29 20:24:29 2018 +0100 - - Merge pull request #1762 from MDAnalysis/issue-1753-add_recordtype - - added reading of record types - -commit 4de452f528b14572f4e30d7e84bf59e63f8838e4 -Author: Richard Gowers -Date: Mon Jan 29 14:41:24 2018 +0000 - - fixed ResidueGroup and SegmentGroup RecordType access - -commit 5265b628efdbfeb157cc2ecb070ea6b513762ebe -Author: Richard Gowers -Date: Mon Jan 29 14:04:17 2018 +0000 - - encoding of RecordTypes - -commit 93aefc7d5e0d1d9969d25c8b7a9c09e38288e718 -Author: Richard Gowers -Date: Thu Jan 25 16:21:47 2018 +0000 - - added test for default record_types - -commit 911ea225656aa599b9662b61c5ad13c7f96ddc96 -Author: Richard Gowers -Date: Thu Jan 25 16:18:55 2018 +0000 - - added reading of record types - -commit f7a6f47e9c8c4637770c2c0cc0c20da841d11622 (tag: release-0.17.0) -Author: Richard Gowers -Date: Thu Jan 25 12:03:37 2018 +0000 - - regenerated c files for 0.17.0 - -commit 10ee7ff295f1a71460d6f9dc6f5b408deb1af280 -Author: Max Linke -Date: Thu Jan 25 00:44:27 2018 +0100 - - Enable pytest warnings (#1661) - - Added comments on how to enable warnings filter - - This setting would silence all the false positives and allows us to eventually get rid - of all the warnings. Enable it at a later point in time. - -commit 3961b09d35bd1144b524fa477773849d8627cc54 -Author: Richard Gowers -Date: Wed Jan 24 17:50:32 2018 +0000 - - Start of 0.17.1 - -commit b6c0086b16556f49fd1a5da443e6a899ead00228 -Author: Richard Gowers -Date: Wed Jan 24 17:47:26 2018 +0000 - - Bumped version to 0.17 release - -commit 9189429e7232f11f71ada1c4c4ee02f081c23810 -Author: Richard Gowers -Date: Wed Jan 24 17:52:19 2018 +0000 - - updated conda recipe for 0.17.0 release - -commit b07983cb1636d7798ef3fa9ecb4683cdcd0de6de -Merge: ea708b09d 2b327cdeb -Author: Richard Gowers -Date: Wed Jan 24 17:47:45 2018 +0000 - - Merge branch 'develop' - -commit 2b327cdeb173dbf07b2de1d6c2a6c1050813c16a -Author: Richard Gowers -Date: Wed Jan 24 17:47:26 2018 +0000 - - Bumped version to 0.17 release - -commit 9457fb36e5f34337579d8567e845fcc8b9aabe6c -Author: mnmelo -Date: Wed Jan 24 15:48:13 2018 +0000 - - Allows construction of minimal Universes, also for topology-less coord loading (#1533) - - * Allows construction of minimal Universes, also for topology-less coord loading - - * Added kwargs to TopologyParserBase.parse() method - - * Added `parse_n_atoms` method to Reader API - - * Added copyright to test_minimal - - * Fixed Universe.empty not generating Group classes etc - - * Added kwargs to parse_n_atoms method - - * Made order explicit in MemoryReader.parse_n_atoms - - * added test for n_atoms kwarg with MinimalParser Universe - - * Added trajectory to Universe.empty - - * Added kwargs to all Parsers.parse - - * Fixed IOErrorParser - - * Fixed LAMMPSParser using self.kwargs - - * removed relative import in testsuite - - * Added documentation pages for MinimalParser and DummyReader - - * Simplified Universe.empty by using Topology as argument to Universe - - * added tests for all_coordinates Universe kwarg - - * added example for Universe.empty - - * fixed docs for MDAnalysisTests.dummy.make_Universe - - * improved minimalparser tests - - * clarified MinimalParser docs - - * updated CHANGELOG for #1533 - -commit 06fae8b6c33f6c8763779b772a6cf2f4904bf5ac -Author: Oliver Beckstein -Date: Sun Jan 21 17:42:57 2018 -0700 - - allow Python 3.4 test to fail for the time being - - Right now, these tests fail with a conda dependency error: - - UnsatisfiableError: The following specifications were found to be in conflict: - - numpy 1.14* -> python >=2.7,<2.8.0a0 - - python 3.4* - -commit ef3cb5c2f230045ec8ab2bc8c0104364a0d3a6a2 -Author: Oliver Beckstein -Date: Sun Jan 21 16:45:39 2018 -0700 - - made tests for waterdynamics more robust - - fixes #1756 - -commit e3a6bf582f931b767096cb9650772974ef128b59 -Author: Oliver Beckstein -Date: Tue Dec 19 02:34:27 2017 -0700 - - document (and test) setting DX array type (#1725) - - - requires gridDataFormats >= 0.4.0 - - documented that PyMOL requires type="double" (see - MDAnalysis/GridDataFormats#35 for details) - - link to GridDataFormats docs for OpenDX type - - use intersphinx to the mdanalysis.org GridDataFormats docs - instead of RTD (better brand experience by staying inside mdanalysis.org...) - - added tests for Density.export(..., type=) -- note - that they really only test gridData.Grid.export() - - updated CHANGELOG - - fixes #1725 - -commit b837af1dc9d2b4dee2a5c6ea61639c369a011014 -Merge: 5a0607593 8ef999cbe -Author: Oliver Beckstein -Date: Sun Jan 21 16:53:34 2018 -0700 - - Merge pull request #1733 from jmborr/1731_spherical_tokens_pkdtree - - write a test for spherical selections tokens using the periodic kdtree - -commit 5a0607593852ecd373d8968261c8a0989857bd8c -Author: Tyler Reddy -Date: Tue Jan 16 08:12:05 2018 -0700 - - TST: Added first draft of psa module asv benchmarks. (#1750) - - * TST: Added first draft of psa module asv benchmarks. - - * TST: Patched issues in new psa asv benchmarks. - -commit ad3d811729c197a676048df9712a6fd4146a91d1 -Author: Jonathan Barnoud -Date: Mon Dec 18 21:12:43 2017 +0100 - - Fix molnums topology attr scope - - The molnum topology attribute was scoped to Atom and Residue, but not - AtomGroup nor ResidueGroup. - -commit 349c93674933bababe398973c7a56e99e82aa1af -Author: Jonathan Barnoud -Date: Thu Aug 3 17:52:45 2017 +0200 - - Address reviews on molnums - -commit a486eacb33c9270f4a1ccd62c700f9be377f5737 -Author: Jonathan Barnoud -Date: Thu Aug 3 13:45:49 2017 +0200 - - Add a molnums topology attribute to TPR parser - - PR #1557 introduced the moltype attribute that gives a name to each kind - of molecule in a topology. This commit adds the related molnums - attribute that gives an index to each individual molecules. - - The molnums attributes allows to split a system by molecule without - ambiguity when the attribute is defines. Without this commit, the only - way of splitting a system per molecule is `atom_group.fragments`. While - it works most of the time, it can fail in some topology that use other - topology tricks than bonds to connect atoms; this is the case in gromacs - with virtual sites for instance. Fragments can also be time consuming on - large systems. This commits allows to slit a system per molecule without - ambiguity with `atom_group.groupby('molnums')` or - `atom_group.split('molecule')`. - - This commit also adds the `molnum` selection keyword. To do so, this - commit refactored `mda.core.selection.SelectionRange` to avoid code - duplication. - -commit 8ef999cbe8821d01e17bbc1b3b7380a62e5200ae -Author: Jose Borreguero -Date: Sun Jan 14 17:26:38 2018 -0500 - - Refs #1731 fix accuracy of failing test - -commit ff7f4d95f8ccbaf46f395168f6e3607886ae4296 -Author: Jose Borreguero -Date: Fri Jan 12 17:42:19 2018 -0500 - - Refs #1731 resolve conflicts - -commit 7531c8f6d7d92ad644ed7cc92f0ebee91968aa84 -Author: Jose Borreguero -Date: Fri Jan 12 16:33:03 2018 -0500 - - Refs #1731 Refactor validate_dimensions - -commit f9e99df7b37ce9a6042cd7d6c16bbbd2f3be2199 -Author: Jose Borreguero -Date: Fri Jan 12 16:24:28 2018 -0500 - - Refs #1731 Refactor box and periodic definition - -commit 51b6270494c839272adc6f321768090878f613a7 -Author: Jose Borreguero -Date: Wed Dec 13 11:03:20 2017 -0500 - - Refs #21367 Validate dimensions - -commit 56c4a7cc134dd248767d145fb7c7e0ab0645e773 -Author: Jose Borreguero -Date: Mon Dec 11 14:40:12 2017 -0500 - - Refs #1731 Spherical layer selection test - -commit 4baa8a923bd03ee24e03c32e01b74e010f1d608a -Author: Jose Borreguero -Date: Mon Dec 11 14:31:07 2017 -0500 - - Refs #1731 Spherical zone selection test - -commit 6e71ffe57f4344a4911f71a698e5d25af4df6980 -Author: Max Linke -Date: Tue Jan 2 18:21:59 2018 +0100 - - update CHANGELOG - -commit dc538a4345354f27d72e91ee153feda42b7d8da9 -Author: Max Linke -Date: Tue Jan 2 17:33:23 2018 +0100 - - fix deprecation warnings occurrences in code - - check that no test code throws the deprecation warning - -commit 9f963805679fe6ae24dbf5602aefe915d7919609 -Author: Max Linke -Date: Tue Jan 2 17:33:14 2018 +0100 - - write deprecation tests - -commit 4129acd30d9d1eef4284e106e0e48bc7f3e14469 -Author: Max Linke -Date: Tue Jan 2 17:31:40 2018 +0100 - - change format -> order for timeseries method - - This now follows the agreed upon standard name - -commit 41739b1134c766eb343428bab060087e01933747 -Author: Max Linke -Date: Thu Jan 4 18:10:18 2018 +0100 - - Fix more warnings (#1752) - - * fix deprecation warnings in encore - - * fix instant selectors - - * fix build fail - - * fix wrongly modified test - - * fix even more warnings - - * add comment about deprecated call - -commit 5daf18cc2fa938f86b750358fdcd004296203b59 -Author: Max Linke -Date: Fri Dec 22 20:03:20 2017 +0100 - - Fix warnings (#1748) - - * fix docs - - * use correct mmap kwarg for netcdf files - - * more doc fixes - - * remove unused import - - * fix instant selector usage - - * use open context manager to close up files again - - * re enable test class - - * general deprecation warning fixes - - * address review comments - -commit 699697a45e0177a4cb12df67a5fd692b8ba9cbbe -Author: xiki-tempula -Date: Sat Dec 16 00:30:36 2017 +0000 - - Water bridge analysis (#1722) - -commit 311379f66dfab397fce7a56056b23ef8529f2815 -Author: Tyler Reddy -Date: Fri Dec 15 16:08:22 2017 -0700 - - TST: Added asv benchmarks for analysis.rms (#1741) - - * TST: First draft of analysis.rms asv benchmark code with time_rmsd benchmark. - * TST: Added rms.RMSD and rms.RMSF asv benchmark drafts. - -commit 15e49e9dc132eb29c90c9d210ad27b14e4783680 -Author: Richard Gowers -Date: Wed Dec 13 14:29:47 2017 +0000 - - Allow osx builds to fail - -commit bf147ef4f59ca107baa546c0117b067317884d34 -Author: Oliver Beckstein -Date: Wed Dec 13 10:35:59 2017 -0700 - - TST: show links to commits on GitHub in asv report (#1734) - - - fixes MDAnalysis/benchmarks#1 - - must use show_commit_url http://asv.readthedocs.io/en/latest/asv.conf.json.html#show-commit-url - which was not included in our asv.json - - [ci skip] - -commit a35ce016fb8301d40cd6505171907ea0af9cd584 -Merge: f878fbf32 1062ed2b1 -Author: Richard Gowers -Date: Wed Dec 13 13:13:44 2017 +0000 - - Merge pull request #1730 from MDAnalysis/issue-1712-macbuildfail - - workaround for Travis CI OSX build failure - -commit f878fbf3279fdd576a6e28975cc378b7a1a660fd -Merge: eb3678da9 71f13d22d -Author: Richard Gowers -Date: Wed Dec 13 13:13:17 2017 +0000 - - Merge pull request #1735 from MDAnalysis/issue-1732-travisfix - - Trying travis_latest image - -commit 71f13d22dfbb8b1a5a1eb0a61fd263c461180abc -Author: Richard Gowers -Date: Tue Dec 12 11:28:39 2017 +0000 - - Changed coverage build to py 3.5 - -commit 2e871f7646b3f676087ce1b444d836209d36de58 -Author: Richard Gowers -Date: Tue Dec 12 11:07:43 2017 +0000 - - removed tabs - -commit 10155d79e94aa6ebd9a06fa5f5d396b6e09653db -Author: Richard Gowers -Date: Tue Dec 12 11:00:00 2017 +0000 - - Trying travis_latest image - -commit eb3678da955b768e71f94a70f7622f1f82345666 -Merge: 88676469b b6c25ab62 -Author: Richard Gowers -Date: Mon Dec 11 13:23:40 2017 +0000 - - Merge pull request #1693 from rcortini/gsdparser-feature - - Added GSDParser - -commit b6c25ab624fc0c04fc66edb9843c597a6dd43287 -Merge: e92d07355 88676469b -Author: Richard Gowers -Date: Mon Dec 11 13:22:21 2017 +0000 - - Merge branch 'develop' into gsdparser-feature - -commit 88676469bfc4db0b16f7f3f0cca5260f6e6b2bc6 -Merge: 48aacefba 3c75a00b9 -Author: Richard Gowers -Date: Mon Dec 11 13:19:36 2017 +0000 - - Merge pull request #1508 from sseyler/issue-1006-psatests - - Issue 1006: minor fixes and several new unit tests for PSA module - -commit e92d07355e240c37ee2f47497f8fdf4322384d78 -Author: Richard Gowers -Date: Mon Dec 11 10:36:32 2017 +0000 - - Update setup.py - -commit 3c75a00b9689c9f15f2f025e4420339bc962945a -Merge: b7af4d7c3 74d51a22b -Author: Richard Gowers -Date: Sun Dec 10 21:02:24 2017 +0000 - - Merge branch 'develop' into issue-1006-psatests - -commit 1062ed2b1083da65ef5afe9868b4c09b2cbdbc71 -Author: Oliver Beckstein -Date: Sat Dec 9 09:08:39 2017 -0700 - - workaround for travis-ci/travis-ci#6307 - - Based on searchivarius/nmslib#259 - -commit 48aacefba3cb2b826615272b026b51403d556208 -Author: Max Linke -Date: Fri Dec 8 22:58:46 2017 +0100 - - better warning message for hydrogenbond analysis - -commit b7af4d7c3c7a0cc2182bccfcf6ff15808e32364c -Author: Richard Gowers -Date: Sat Dec 9 08:14:07 2017 +0000 - - Updated docstrings to numpy style in analysis.psa - -commit 251df4d490b14efa3bc3b5a73f365544cca9346e -Author: Richard Gowers -Date: Sat Dec 9 08:08:17 2017 +0000 - - Updated error strings in analysis.psa - -commit 37881f4c655a6bda6bc1917277bbdb6d3019cf90 -Author: Richard Gowers -Date: Sat Dec 9 07:49:35 2017 +0000 - - Fixed up type checking in metric filename - -commit 069af03c9009b2cbf3ad1b7c2c28826179d930af -Author: Richard Gowers -Date: Fri Dec 8 16:20:38 2017 +0000 - - Added gsd files to testsuite setup.py - -commit 98e6d9543ba6c6339783026b75dfbb48a9234dbd -Merge: 27946f228 74d51a22b -Author: Richard Gowers -Date: Fri Dec 8 09:43:44 2017 +0000 - - Merge branch 'develop' into gsdparser-feature - -commit 27946f228591c8c6c9859db1e5826437f155cb08 -Author: Richard Gowers -Date: Fri Dec 8 09:40:09 2017 +0000 - - Added gsd as dependency - -commit 74d51a22be9fe8738313c2e78f72eb0d19b8a792 -Author: Tyler Reddy -Date: Thu Dec 7 19:07:32 2017 -0700 - - TST: Adding MDAnalysis.analysis.leaflet asv benchmarks (#1724) - - * TST: Adding MDAnalysis.analysis.leaflet asv benchmarks. - * Addressing reviewer comments in PR 1724. - -commit 54d5bab1b2aa27b7f914078cc3e5a892e79ef479 -Merge: 07b8d638f de695f404 -Author: Richard Gowers -Date: Thu Dec 7 14:20:11 2017 +0000 - - Merge pull request #1186 from MDAnalysis/issue-1092-restrict_setattr - - strict attribute setting issue (#1092) - -commit de695f4048fae9e63b0e675a97db8255648abd14 -Author: Richard Gowers -Date: Wed Dec 6 18:16:24 2017 +0000 - - Updated Universe.add_TopologyAttr docstring - -commit e7104a5a8aa4a683931a6f89303bd6d6d9bf5df8 -Author: Richard Gowers -Date: Wed Dec 6 18:14:33 2017 +0000 - - Fixed up CHANGELOG - -commit 958e971d1e2449d3865af4789c2b454dc3594368 -Author: Richard Gowers -Date: Wed Dec 6 17:04:16 2017 +0000 - - reverted change to Bond TopologyAttr - -commit 3c4d607d6c0fb1bb7ec6141afff50b7f353d8557 -Author: Richard Gowers -Date: Wed Dec 6 11:47:12 2017 +0000 - - Further clarified is_group in TopologyAttrContainer.subclass - -commit b9db71d547051e6ad32ef422cbada0ad27b3572c -Author: Richard Gowers -Date: Wed Dec 6 11:41:51 2017 +0000 - - Small fix to Bond TopologyAttrs - - removed tolist() call - use .universe not ._u - -commit 4dcfb7d4c5c45e64689ed9e5aab5eec51a30901a -Author: Richard Gowers -Date: Wed Dec 6 11:37:47 2017 +0000 - - Changelog for attribute setting changes - -commit d37b6699aa0e94abe3ebcbd21fad29428a669390 -Author: Richard Gowers -Date: Wed Dec 6 11:31:09 2017 +0000 - - clarified UAG upadte procedure - -commit 68c2da4cc2598ee2d44f36b1c31c7a05a4e42ef5 -Author: Richard Gowers -Date: Wed Dec 6 10:36:37 2017 +0000 - - Renamed _TopologyAttrContainer._singular to _is_group - -commit e84c3fd6a1b84c43fc1c5e30da93f5f8d84b83b6 -Author: Richard Gowers -Date: Wed Dec 6 10:35:56 2017 +0000 - - Added explanation of _gen_initial_values - -commit b56254c70b1ee6c2f8012f3ea57de30564fe68c6 -Author: Richard Gowers -Date: Wed Dec 6 10:35:30 2017 +0000 - - Added example to add_TopologyAttr - - Expandded missing TopologyAttr docstring - -commit fa837299508aedb74203053ade9e5d38677885be -Author: Richard Gowers -Date: Sun Dec 3 13:55:19 2017 +0000 - - removed segments from WHITELIST - -commit db9a9e1179341bb735e1cabef820dd7bfafd6c0c -Author: Max Linke -Date: Sun Dec 3 14:22:32 2017 +0100 - - fix doc build error - - Need to list arguments separately. - -commit 7c50845225710617cb3390c3e05674ea3241b297 -Author: Richard Gowers -Date: Thu Nov 23 01:31:19 2017 +0000 - - added tests for universe.add_TopologyAttr - -commit 000c5f2cbc170a91d78ca6ab35a666052bce711e -Author: Richard Gowers -Date: Thu Nov 23 00:30:49 2017 +0000 - - Removed TestCase usage from test_universe - -commit 3d7aac3bcce66b5449620044f7f5468de5243b64 -Author: Richard Gowers -Date: Thu Nov 23 00:17:40 2017 +0000 - - Added u.add_TopologyAttribute with string - -commit 5c2f0deabd5533df9ee3049108a87e2191c52976 -Author: Richard Gowers -Date: Tue Nov 21 22:41:17 2017 +0000 - - TopologyAttrs now registered upon definiton - -commit 5444614ad6f32a06130b2e9cbb586e02291f3c7a -Author: Richard Gowers -Date: Tue Nov 21 21:18:40 2017 +0000 - - Fixed UAGs with restricted attribute setting - -commit 4cb43456b3e4d1db5d1284c02c254160143005b9 -Author: Richard Gowers -Date: Tue Nov 21 20:11:23 2017 +0000 - - Simplified setattr across Component and Group - -commit 5b0cf1eee4b5e2c4a2d0efa6d5f96f0bd57b8e13 -Author: Richard Gowers -Date: Tue Nov 21 19:39:35 2017 +0000 - - Fixup - -commit a71ed7084d6519cc766dca42917c3549511d9ca7 -Author: Richard Gowers -Date: Tue Nov 21 19:21:04 2017 +0000 - - Changed to a _SETATTR_WHITELIST per class, (not shared) - -commit 2c96fcaf5ef5678442a34752859f5a6cc38a7854 -Author: Richard Gowers -Date: Mon Nov 20 21:21:23 2017 +0000 - - Fixed WHITELIST for singular and plural attributes - -commit 224ee3b50d047fbda795aaf12153a302e93ca9c2 -Author: Richard Gowers -Date: Sun Nov 12 15:54:56 2017 +0000 - - More tests for attribute setting - -commit 14bd0d4da4bca69e205a45be8f5ea2276c0194ff -Author: Richard Gowers -Date: Sat Nov 11 12:31:14 2017 +0000 - - Work on Issue #1092 - - Currently failing - -commit 07b8d638f46660cf6ce04720fbb3ad2c14320eca -Author: Tyler Reddy -Date: Tue Dec 5 15:00:41 2017 -0700 - - Adding asv geometric selection benchmarks (#1695) - - * TST: Added asv geometric selection string benchmarks. - -commit 1e11a67c39e35e3fd4775a6ac759440eb0f8cabc -Merge: de46fee9f 923786b22 -Author: Oliver Beckstein -Date: Tue Dec 5 12:30:24 2017 -0700 - - Merge pull request #1720 from MDAnalysis/fix-align-step - - use correct loop counter - -commit 923786b22f34c2ef9e2495e4ff52bdd49a130aba -Author: Max Linke -Date: Tue Dec 5 00:51:14 2017 +0100 - - use correct loop counter - - The frame argument contains the current frame which might be larger then our - allocated RMSD array if we use step > 1. - -commit de46fee9fe7d7389d0610704d6ac02646ce82c15 -Author: Tyler Reddy -Date: Wed Nov 29 16:57:21 2017 -0700 - - TST: added asv benchmarks for analysis.distances (#1718) - - * TST: Added asv benchmarks for analysis.distances functions. - * TST: now using analysis subdirectory for pertinent asv benchmarks. - * asv needs __init__.py in analysis/ subdirectory - -commit 1322f55d8de7f45f0dc30bb89cb6550078c13365 -Author: Max Linke -Date: Mon Nov 27 18:01:27 2017 +0100 - - selection string can be unicode (#1710) - - * selection string can now be unicode in RMSD calculation: previously this raised a type error - * fixed similar occurrences found with `git grep 'is str'` - * update CHANGELOG - -commit fe1a196ee7ae6c3a9d85af51462b0653e6a6563d -Author: Max Linke -Date: Sat Nov 25 20:10:09 2017 +0100 - - Fix align aligntrj bug (#1716) - - * fix #1716 (default filename bug) - * added two tests - * update CHANGELOG - -commit 9b074d53ce84f40de11c9599349d75cdfc12fa8c -Merge: fed8be34a e99949cf5 -Author: Richard Gowers -Date: Thu Nov 23 21:27:53 2017 +0000 - - Merge pull request #1704 from sobuelow/develop - - Updated core/selection.py to include amber N- and C-termini resnames - -commit e99949cf5a7de0f82ab7207b03c1485d88919534 -Merge: 367108009 fed8be34a -Author: Richard Gowers -Date: Thu Nov 23 21:27:32 2017 +0000 - - Merge branch 'develop' into develop - -commit 36710800939c073e647da2fc620567c4cb4d97c4 -Merge: 3ea0bd138 fed8be34a -Author: Richard Gowers -Date: Thu Nov 23 21:26:09 2017 +0000 - - Merge branch 'develop' into develop - -commit fed8be34a3434a621bacd438d2f9307139a24511 -Author: Max Linke -Date: Wed Nov 22 22:00:25 2017 +0100 - - Speed up rotate (#1708) - - * speed up atomgroup rotation in special case - - If rotation center is coordinate system center we don't need to translate the - atoms. This should result in a noticeable speed (factor 2-3) up for this special - case. - - * update CHANGELOG - -commit d2d89dd5853a66bbb79a595494447a7968c3306e -Author: Tyler Reddy -Date: Tue Nov 21 21:05:05 2017 -0700 - - TST: Adding atomgroup method & attribute asv benchmarks (#1709) - - * TST: First draft of atomgroup methods asv benchmarks module. - * TST: Added missing MDA exception and shifted bond() to bond call in ag_methods.py asv benchmarks. - * TST: Addressing reviewer comments in PR 1709. - -commit 9ba1ab964920acfc986d8e264f78c965e062e9d0 -Merge: b5ba8278b 19799e71c -Author: Max Linke -Date: Sat Nov 18 14:04:17 2017 +0100 - - Merge pull request #1692 from jmborr/test_pkdtree - - Optimization of pkdtree - -commit 19799e71cd987c8889bf7b4f5eb68bcbe9c03956 -Author: Max Linke -Date: Fri Nov 17 20:48:27 2017 +0100 - - fix NeighborSearch - -commit d20182503816c59a97cdf3e97362ba627065bd6c -Author: Max Linke -Date: Fri Nov 17 20:47:26 2017 +0100 - - test neighbor search - -commit 8bad42896a16e4ac8662b4886c8b02edc075afeb -Author: Max Linke -Date: Fri Nov 17 20:38:18 2017 +0100 - - skip not implemented tests - -commit 75d5e8c3c5a78696e342933d3ed0b8dcce4e16c4 -Author: Jose Borreguero -Date: Thu Nov 16 12:04:46 2017 -0500 - - Refs #1691 Enable periodic tree search for selection around atoms - -commit 6a15b97b423e363635ecde2ac9017f6cb4b97eaf -Author: Jose Borreguero -Date: Wed Nov 15 17:11:39 2017 -0500 - - Refs #1691 Enable periodic tree search for selection around point - -commit 4dac2f5737740fe369c2fc72a12a039e02b128e7 -Author: Max Linke -Date: Sun Nov 12 13:20:51 2017 +0100 - - This enables pkdtree in atom selections tests - -commit 3aecc3eca68c1e6d896d81893c460b3d8d3857a9 -Author: Max Linke -Date: Sat Nov 11 16:33:26 2017 +0100 - - update CHANGELOG - -commit bd85593303084e8a13db722227c9c85772320a40 -Author: Max Linke -Date: Sat Nov 11 16:31:51 2017 +0100 - - PEP8 changes - -commit 4ba0db19ddb3d3699a3f197f7ded5152ae6593d7 -Author: Max Linke -Date: Sat Nov 11 16:26:39 2017 +0100 - - make API of pkdtree more generic and update docs - -commit b2bbc33859f286ece8391d20e70f1ffa15c91edb -Author: Jose Borreguero -Date: Tue Nov 7 15:11:10 2017 -0500 - - Test absence of images for box center point - -commit 8fedab5ae74639275cbc5922de1da73dbeeb9b9c -Author: Jose Borreguero -Date: Mon Oct 30 15:04:38 2017 -0400 - - Improve performance of pktdree - - - norm moved out of find_centers - - apply_PBC moved out of find_centers - - find_centers called only once - - more numpy in find images - - New timings: - periodic repeat n_centers radius elapsed original_elapsed - 0 False 16 16384 3.063187 0.248872 0.251313 - 1 False 16 16384 4.332000 0.497948 0.482477 - 2 False 16 16384 6.000000 0.917276 0.933354 - 3 True 16 16384 3.063187 0.781956 2.390082 - 4 True 16 16384 4.332000 1.111069 2.756319 - 5 True 16 16384 6.000000 2.147721 3.962351 - 6 False 32 131072 3.063187 1.885286 1.835147 - 7 False 32 131072 4.332000 3.292491 3.479865 - 8 False 32 131072 6.000000 8.931284 7.059998 - 9 True 32 131072 3.063187 6.532420 19.393614 - 10 True 32 131072 4.332000 9.408217 22.463955 - 11 True 32 131072 6.000000 15.984224 33.240666 - - The slow-down now ranges from two to three times. - -commit 3ea0bd138fa97df29039dc3b58b02882a6574b98 -Author: Soeren von Buelow -Date: Mon Nov 13 11:46:47 2017 +0100 - - Updated core/selection.py to include amber N- and C-termini resnames in list prot_res - - - Added unit test to test for correct recognition of all resnames by select_atoms('protein') - - AUTHORS and CHANGELOG updated - - Testsuite AUTHORS and CHANGELOG updated - -commit b5ba8278b3e09b80109aa06f77832be00f8752f0 -Author: Max Linke -Date: Wed Nov 15 06:46:18 2017 +0100 - - Compiler args (#1676) - - * use -std=c99 for all extensions - - * enable cpu specific optimizations - -commit 4226af23c25ee96de0bad4a33520ff65c904af42 -Author: Max Linke -Date: Sat Nov 11 16:41:51 2017 +0100 - - allow failure of numpy dev build - -commit 154c05cf979d6febb70861779376d81e231f0658 -Merge: c3bbe74a2 90f281dad -Author: Ruggero Cortini -Date: Tue Nov 7 15:22:44 2017 +0100 - - Merge branch 'develop' into gsdparser-feature - -commit c3bbe74a21af7d83f6d1df4a485d496a8de356a0 -Author: Ruggero Cortini -Date: Tue Nov 7 15:18:42 2017 +0100 - - no spaces between function and parentheses in GSD parsers - -commit 33122bd83c94a3aec58d5d9acccab99dc576df83 -Author: Ruggero Cortini -Date: Tue Nov 7 15:15:11 2017 +0100 - - added several new tests for GSD trajectory parsers - -commit 89c19919b61d442eadc54e3d4ea8bc49429b3afb -Author: Ruggero Cortini -Date: Tue Nov 7 15:10:21 2017 +0100 - - new test for GSD frame number - -commit fd667d6c09473083db723312e4595d3843ee38bd -Author: Ruggero Cortini -Date: Tue Nov 7 15:10:05 2017 +0100 - - corrected GSD trajectory test for particle pos - -commit 45530c8084bc8ff5668431178f8cbf457c16e085 -Author: Ruggero Cortini -Date: Tue Nov 7 14:59:41 2017 +0100 - - new: GSD topology unit test; fixed assigning resnames - -commit 664200298b27559927b8fc888aa84b05d163cf31 -Author: Ruggero Cortini -Date: Tue Nov 7 14:38:05 2017 +0100 - - updated CHANGELOGs with correct information - -commit 90f281dadc37d0305a681971d4f77db9062bbd21 -Author: Oliver Beckstein -Date: Tue Nov 7 05:28:54 2017 -0700 - - fixed CHANGELOG (#1700) - - - @jmborr had been forgotten in 0.17.0 contributor list - (should have been added with PR #1697) - - release date for 0.16.2 added - -commit 270b8760e808717ea4d74c3303c0c80295988896 -Author: Jose Borreguero -Date: Sun Nov 5 05:01:53 2017 -0500 - - Correct apply_PBC for triclinic systems (#1697) - - * Refs #1696 changed _triclinic_PBC - - * Refs #1696 fix test distances - - * Refs #1696 merge test - - * Refs #1696 changelog updated - - * Refs #1696 Hardcode test input and reference - - * Refs #1696 Unnecessary conversion to list - - * Refs #1696 Drop rounding errors - -commit 569cd20a906477c624c319153ff267c3bf32d399 -Author: Ruggero Cortini -Date: Fri Nov 3 14:22:08 2017 +0100 - - removed print statement in GSDParser - -commit 1a5477670a78ffbc7845596c3f54b5fffa388cb1 -Author: Ruggero Cortini -Date: Fri Nov 3 13:32:09 2017 +0100 - - fixed bug due to negative body indices - -commit 4d5b1d2e04b84abb92b17c1a871c3bcd85cd2778 -Author: Ruggero Cortini -Date: Fri Nov 3 11:48:50 2017 +0100 - - GSDParser sets `resid` and `resname` of atoms - -commit 13370a9a5ab26f9de1bb3edee9e684c724cd3e69 -Author: Ruggero Cortini -Date: Fri Nov 3 11:04:05 2017 +0100 - - GSDParser sets atom names - -commit 4700d048c170cb687ff439e792e778140baf8fac -Author: Ruggero Cortini -Date: Fri Nov 3 10:54:04 2017 +0100 - - wrote docstring for GSDParser - -commit fc7aa1c5cfe4723083fdd7ded8eea8d81f4837ba -Author: Ruggero Cortini -Date: Thu Nov 2 17:13:15 2017 +0100 - - added myself to AUTHORS and updated CHANGELOG - -commit e3e1dfb83fc53e9951bf64a9a8079dd83abbdedc -Author: Ruggero Cortini -Date: Thu Nov 2 17:05:46 2017 +0100 - - fixed _frame attribute of DCDReader and removed dimensions property - -commit 0bca30097f8f95e20e23d1e54407df8e0e638601 -Author: Ruggero Cortini -Date: Thu Nov 2 16:54:24 2017 +0100 - - wrote docstring for GSDReader - -commit d8ec9805aadd457f899e634658732487c1606761 -Author: Ruggero Cortini -Date: Thu Nov 2 16:31:18 2017 +0100 - - fixed Timestep frame number issues - -commit 0d66ec16f6f15deccd64cdfe643ed1bd34717cf1 -Author: Ruggero Cortini -Date: Thu Nov 2 15:20:52 2017 +0100 - - example.gsd now contains only 2 frames - -commit 026f3a6b3828990f0d12a404065281736387d6fc -Author: Ruggero Cortini -Date: Thu Nov 2 12:40:02 2017 +0100 - - GSD trajectory parser checks consistency of number of atoms - -commit b15ef4c2540a294b4dfd1afb7c8152c2b512650c -Author: Ruggero Cortini -Date: Thu Nov 2 12:25:11 2017 +0100 - - fixed bug in access to GSD trajectory at fixed frame - -commit f7cf7bf1f5bc2bae9a3ffb42b02710722c8e5edd -Author: Ruggero Cortini -Date: Tue Oct 31 17:34:16 2017 +0100 - - new: testsuite for GSD trajectory/topology - -commit 92a8a061239fe2149394653040efecbbb2f3cc56 -Author: Ruggero Cortini -Date: Tue Oct 31 14:09:36 2017 +0100 - - fixed trajectory reader to not read non existing frames - -commit 6546eaed8aa56a4172066b82eb228f3edb7ad134 -Author: Ruggero Cortini -Date: Tue Oct 31 12:35:47 2017 +0100 - - removed other debug code - -commit 803edc1b90d213f50e745f074c989bb16a1ab231 -Author: Ruggero Cortini -Date: Tue Oct 31 12:34:49 2017 +0100 - - removed debug code and comments - -commit d7c0001241b669e1195d3b4d115c41645f4773cd -Author: Ruggero Cortini -Date: Tue Oct 31 12:26:55 2017 +0100 - - fixed file close and timestep dimensions angles - -commit a913625736d18164cab4c2d28a9b9202fe14bbce -Author: Ruggero Cortini -Date: Tue Oct 31 12:21:49 2017 +0100 - - included import gsd.hoomd in try/except/pass block - -commit e96b74b53e2384427398917fdeb54ed2144aef5a -Author: Ruggero Cortini -Date: Tue Oct 31 12:20:56 2017 +0100 - - new: GSD trajectory parser - -commit c9c801b8100736e2010c7bb9b35380a6b44e517c -Author: Ruggero Cortini -Date: Tue Oct 31 11:14:31 2017 +0100 - - open GSD file with context manager - -commit a79cdf2dfa3dc88e1a4c720f1fe8767672601b4a -Author: Ruggero Cortini -Date: Tue Oct 31 10:34:37 2017 +0100 - - fixed parentheses in argument of Masses and Charges - -commit c4a8b131d28376b24227e640c69d81bc007509ba -Author: Ruggero Cortini -Date: Tue Oct 31 10:16:13 2017 +0100 - - Added GSDParser - - The topology/GSDParser.py was added, and included in the __init__.py file, in - the list __all__ and in the imports - -commit abe7933165d664ec56364f3b6f328b7c27b482a5 -Author: Tyler Reddy -Date: Mon Oct 30 18:11:08 2017 -0600 - - TST: asv benchmark tests for simple select_atoms selections (#1682) - - * Added simple selection string asv benchmark code. - * time_simple_selections() updated to handle older selectAtoms syntax when needed. - -commit 21a5f87cdf352930431c874e567db5961773d67c -Author: Jonathan Barnoud -Date: Fri Oct 27 19:19:43 2017 +0200 - - Fix the forgotten StopIteration in generator (#1688) - -commit 88b39345a1edb993d08d340665b4ce49f0ca43fa -Author: Tyler Reddy -Date: Thu Oct 26 16:22:50 2017 -0600 - - Removed spurious static function declarations in readdcd.h (#1686) - - * Removed spurious static function declarations in readdcd.h. - -commit 2e22d06e356449723ad04623311d25f2591b8106 -Merge: d833bedd8 1b0dbf6d9 -Author: Max Linke -Date: Sat Oct 21 15:34:43 2017 -0700 - - Merge pull request #1657 from MDAnalysis/fix-RMSD-mobilegroup - - fixes rms.RMSD: selections are now applied to atomgroup itself - -commit 1b0dbf6d9cc1f8d914342d515998468339cabf32 -Author: Oliver Beckstein -Date: Sat Oct 21 14:42:55 2017 -0600 - - fixed scalar/array comparisons for custom masses - - (fixed warnings) - -commit f02a1770d3ef65ddb11cad3510832f3b9fe8ff48 -Author: Oliver Beckstein -Date: Sat Oct 21 14:31:32 2017 -0600 - - added test for #1684 - - Simple test that just checks that subselecting an atomgroup in RMSD gives - a different answer than subselecting universe.atoms - -commit 318ec85acc9f005e5ee8807f55cda0732bf0d92e -Author: Oliver Beckstein -Date: Wed Aug 30 01:35:41 2017 -0700 - - fixes rms.RMSD: selections are now applied to atomgroup itself - - Previously, using an atomgroup with select was broken (the select - string was applied to atomgroup.universe). - - Note: for group_selections, the selection strings ARE still applied - to the whole atomgroup.universe for maximum flexibility - -commit d833bedd830b6314d8f23dcf79204f341a5b4924 -Merge: 3eb900ce6 b1e11bb33 -Author: Max Linke -Date: Tue Oct 17 15:17:38 2017 -0700 - - Merge pull request #1573 from MDAnalysis/asv_traj_striding - - TST: Added traj reader striding asv test - -commit 3eb900ce609f34829def4239a2e4b91701a2f38d -Merge: ad48254b5 a597437d1 -Author: Max Linke -Date: Thu Oct 12 11:21:53 2017 -0700 - - Merge pull request #1681 from MDAnalysis/issue-1643-implicit_or_docs - - Added documentation for implicit OR in selections - -commit a597437d10daa8d4928474a68ca5677bae1aea9b -Author: Richard Gowers -Date: Thu Oct 12 15:05:28 2017 +0100 - - Update groups.py - -commit bf1ba97634c23c66a562b3aaee4054b50d915c63 -Author: Richard Gowers -Date: Thu Oct 12 15:04:44 2017 +0100 - - Update groups.py - -commit 1d2dd6e141fab993c0cf064e5a544c15542b2c96 -Author: Richard Gowers -Date: Thu Oct 12 14:34:50 2017 +0100 - - Added documentation for implicit OR in selections - -commit ad48254b5da1b303d6daafd48b37a9ebd147862d -Author: Max Linke -Date: Wed Oct 11 17:11:42 2017 -0700 - - allow pickling of DCDFile - -commit 5ccd046e5a4d70d86c736f815093be4327cdd1ed -Author: Max Linke -Date: Tue Oct 10 13:57:24 2017 -0700 - - allow pickling xdr trajectory readers - - the low level __reduce__ function is used by the pickle protocol as a recipe - to reconstruct this class. - -commit b1e11bb3393aee32d041d4029badabae431929c9 -Author: Tyler Reddy -Date: Tue Oct 10 15:50:34 2017 -0600 - - Abstracted the traj_dict object in traj_reader asv benchmarks to reduce code duplication in tests. - -commit 7d7a9fb6d81995e9ba5788e903a2f691e0a0f6a4 -Author: Tyler Reddy -Date: Tue Oct 10 15:46:01 2017 -0600 - - try/except imports in traj_reader benchmarks are now grouped by format type to enhance commit hash history sampling of old vs. new features. - -commit 65e5b4f78cf211fc48c049fbbd34eac37ea74600 -Author: Max Linke -Date: Thu Aug 3 09:28:38 2017 +0200 - - add NCDF format reader - -commit f54822f52725dbe51c9dfcf8ac4c6316eb7a9f11 -Author: Max Linke -Date: Thu Aug 3 09:21:31 2017 +0200 - - MAINT: refactor wording and pep8 changes - -commit f3161a8644ab9f5a92850a084bb8a3e9d434516f -Author: Tyler Reddy -Date: Tue Aug 1 22:35:10 2017 -0600 - - TST: Added traj reader striding asv test. - -commit d5dec2b6f2be00fac35ee8f9be0106a244d6cc45 -Merge: a3e9e89d6 37834d004 -Author: Jonathan Barnoud -Date: Thu Oct 5 08:03:22 2017 +0200 - - Merge pull request #1678 from MDAnalysis/use-ssl-urls - - changed links in docs and comments to SSL-encrypted site - -commit a3e9e89d66e22321fd370c455f02bf7550fab094 -Author: Jonathan Barnoud -Date: Mon Oct 2 20:29:09 2017 +0200 - - Remove StopIteration in generators (#1679) - - Fixes #1662 - -commit 37834d0040d5c87b6d43ff127f1368a916ea3040 -Author: Oliver Beckstein -Date: Sun Oct 1 12:08:06 2017 -0700 - - changed links in docs and comments to SSL-encrypted site - - - use https://www.mdanalysis.org and https://docs.mdanalysis.org - - see MDAnalysis/MDAnalysis.github.io#61 and https://github.com/MDAnalysis/MDAnalysis.github.io/wiki/DNS - for further details - - command used: - - git grep -E -l 'http://(www|docs)?\.mdanalysis\.org' | grep -v CHANGELOG | xargs sed -i~ 's/http:\/\/www\.mdanalysis\.org/https:\/\/www.mdanalysis.org/;s/http:\/\/docs\.mdanalysis\.org/https:\/\/docs.mdanalysis.org/' - -commit 49177fd4cd5660b4107140039b1a88ef9d3a81dc -Author: Tyler Reddy -Date: Thu Sep 28 17:19:39 2017 -0600 - - TST: Added MDAnalysisTests to the asv dependency matrix along with the appropriate conda channel. When combined with modifications to our fork for asv this fixes #1577. (#1580) - -commit 88b6c200c88487d51055b00bc6c3b0893d3d8f94 -Author: Max Linke -Date: Tue Sep 26 16:39:12 2017 +0200 - - Triclinic cells (#1674) - - * use explicit image search for triclinic cells - - * add test for distance calculation - - * update CHANGELOG - - * write c89 compatible code - -commit 3ef41964e56e2a1252c2201b338c0c8d55c5a3ea -Author: Max Linke -Date: Tue Sep 26 15:30:01 2017 +0200 - - fix cython error on travis (#1675) - - * use functions instead of classes for encore cython files - - This fixes a pickle error we have seen with recent versions of cython - and our mocked imports. cython now introduced special reduce and setstate - functions to enable cross python pickling for simple classes. It also tried to - do this for some encore classes that only had a run method and would overwrite - the `__call__` special method. So lets make them function right away. - - * update sphinx rst files - - * fix rst docs - -commit 76cd70c84d3f3f53fccd583b36384461bddce2a0 -Author: Jose Borreguero -Date: Mon Sep 18 15:32:12 2017 -0400 - - Acknowledgments to Parvalli (#1671) - -commit 65a6d6be8b497433ca27cd00fb2d092dbcad9651 -Merge: 882978ee7 a99908609 -Author: Max Linke -Date: Mon Sep 18 15:58:45 2017 +0200 - - Merge pull request #1660 from camm/periodicKDTree - - Periodic kDTree - -commit a9990860908c7ef65046b9010f4809db54862e2b -Author: Jose Borreguero -Date: Sun Sep 17 11:33:00 2017 -0400 - - return empty list if no neighbors found - -commit 03508c694d2e6868dd680ed2c8123b1d48bc47df -Author: Jose Borreguero -Date: Fri Sep 15 17:20:57 2017 -0400 - - Tests for triclinic box - -commit 97cdae7be2f780eba7396f0507d905c534937885 -Author: Jose Borreguero -Date: Fri Sep 15 17:20:42 2017 -0400 - - transform fractional to real also accepts single vector - -commit 882978ee7212792240c1d5459a4a8796ee0b3ae9 -Author: Max Linke -Date: Fri Sep 15 11:02:05 2017 +0200 - - Named stream issue (#1669) - - * take care not to create NamedStream from itself - - * Avoid initializing NamedStream from same class - - * update CHANGELOG - - * add tests - -commit c428efdddcc511f830c723932846a9efa394ee60 -Author: Max Linke -Date: Wed Sep 13 11:29:06 2017 +0200 - - keep offsets on xdr reopen - - If we close a xdr file then libmdaxdr discards the old offsets. This is OK - because it can't know if the new file will have different offsets. Here we now - store the offsets before we reopen the xdrfile. - -commit 2946aa410afb7c250af5015dfd5fa25dc989a8a0 -Author: Max Linke -Date: Thu Sep 14 17:00:10 2017 +0200 - - fixup warnings (#1664) - -commit 0d673de3560f6193535fc4c6c578b9b7ff97f23e -Merge: 50c24e432 3b4d94604 -Author: Jonathan Barnoud -Date: Wed Sep 13 14:02:02 2017 +0200 - - Merge pull request #1665 from MDAnalysis/fix-assert-statement - - fix assert statements - -commit 3b4d9460463aac520442fe07a88b9713cb9569e8 -Author: Max Linke -Date: Thu Sep 7 12:15:06 2017 +0200 - - replace `assert_` with plain assert - -commit 50c24e432d9621bcef58978f46d4d1d8b0415848 -Merge: bbbd0cd9e 3697e040d -Author: Oliver Beckstein -Date: Tue Sep 12 11:13:55 2017 -0700 - - Merge pull request #1663 from MDAnalysis/remove-yield-test - - switch from test generators with yield to parameterized pytests - -commit 3697e040ddeca5591bda20b9eb5aa7f78e3eba0b -Author: Jonathan Barnoud -Date: Mon Sep 11 11:46:05 2017 +0200 - - Remove test generators in test_atomselections.py - -commit fdbd08b7f07ae7a257700304bb6b48df350e9351 -Author: Jonathan Barnoud -Date: Mon Sep 11 11:17:30 2017 +0200 - - Remove last test generator in core/test_atomgroups.py - -commit a35a5ea0eb0a5829bbdb60892f538d5229fce858 -Author: Jonathan Barnoud -Date: Fri Sep 8 19:24:58 2017 +0200 - - Remove all remaining test generators in core/test_groups.py - -commit ef9fcdcf1a2e2d59adea722df6abc4619b69dd5f -Author: Jonathan Barnoud -Date: Fri Sep 8 09:24:02 2017 +0200 - - Remove test generators in core/test_groups.py::TestGroupSlicing - -commit 48be91a386ffd355cf9cc52a28c3818039e1460a -Author: Max Linke -Date: Wed Sep 6 17:34:30 2017 +0200 - - replace yield tests with fixtures - -commit cf029a3d58dafa64e1275a4dc89344fc766e2a7a -Author: Jonathan Barnoud -Date: Thu Sep 7 12:25:47 2017 +0200 - - Fix test for group subtractions - -commit 5199241425607b1ab5accf0bd13c8a7968edd76b -Author: Max Linke -Date: Wed Sep 6 22:36:08 2017 +0200 - - ban more yields - -commit 0708d72caf880bb39b0e360a6c0cc9db422f2b6f -Author: Max Linke -Date: Wed Sep 6 22:27:34 2017 +0200 - - another commit another yield gone - -commit 9bd92f9461e54197485528b3ecb48f42e6c8c41e -Author: Max Linke -Date: Wed Sep 6 22:22:45 2017 +0200 - - fix some group yield tests - -commit 731004b9c672882ea7f153771c67bec4ff625598 -Author: Max Linke -Date: Wed Sep 6 17:54:55 2017 +0200 - - fix yield in test_atomgroup - -commit 71d514058abccf012dc87fc5b69d29cacaba2d7d -Author: Max Linke -Date: Wed Sep 6 17:43:35 2017 +0200 - - remove yield tests - -commit 596b26ec59e46cfa30cfd2e7e2239563c82aeb65 -Author: Max Linke -Date: Wed Sep 6 17:34:30 2017 +0200 - - fix yields in coordinates/test_pdb - -commit bbbd0cd9ed2839e57d694134775436b83083f052 -Author: Jonathan Barnoud -Date: Mon Sep 11 19:20:49 2017 +0200 - - Update the adress of networkx doc in the doc - - The documentation of networkx changed its URL. This means that the - objects.inv files was unreachable at the previous URL which made the - build fail. This commit updates the URL of networkx's documentation. - -commit deb1d8eb2c52d9d3b13231a7caff462946eb0ea2 -Author: Jose Borreguero -Date: Wed Sep 6 18:01:23 2017 -0400 - - test initialize_bm method - -commit 8d64c7fd735fdaac021690cfe0d6478620517cb6 -Author: Jose Borreguero -Date: Wed Sep 6 16:04:03 2017 -0400 - - Extend search to triclinic systems - -commit bc36840e81ea48ec182f0e57fe11d48572ab2996 -Merge: 5e2d0ba20 7ea2cc3e9 -Author: Max Linke -Date: Wed Sep 6 14:34:42 2017 +0200 - - Merge pull request #1606 from utkbansal/t-tprparser - - Pytest Style topology/test_tprparser.py - -commit 7ea2cc3e91163dba7d3c066dff2694e35822797e -Author: Jonathan Barnoud -Date: Wed Sep 6 12:46:08 2017 +0200 - - Rename some TPR test to have them detected - -commit bf0c199371b97a2740664e54849e0650489e2e03 -Author: Max Linke -Date: Wed Sep 6 07:55:13 2017 +0200 - - remove need for filename fixture - - This makes writing ParserBase derived classes easier - -commit ffaecc810567b082f34203b6c0dffcb0e0eafb6d -Author: Max Linke -Date: Wed Sep 6 07:36:13 2017 +0200 - - fix pep8 issues - -commit 23f4980e9a356f08bc35ddbe12e983ec0f40f695 -Author: Max Linke -Date: Wed Sep 6 07:30:17 2017 +0200 - - Use fixture parametrization instead of individual classes - -commit 5e2d0ba207b09646ff8957298fa444d20c050d3d -Merge: b138532d7 ac47b78eb -Author: Oliver Beckstein -Date: Tue Sep 5 16:47:24 2017 -0700 - - Merge pull request #1655 from utkbansal/coord-xdr - - Pytest Style coordinates/test_xdr.py - -commit 366d70c9098ab138b79904757b3fb3307134c2bb -Author: Bansal Utkarsh -Date: Mon Aug 14 00:15:51 2017 +0530 - - Make filename a fixture - -commit 979da77586ad837b3e8773e4cb2bd4892c871fbc -Author: Bansal Utkarsh -Date: Tue Aug 8 19:23:48 2017 +0530 - - Pytest Style topology/test_tprparser.py - -commit ac47b78eb60c1afb1cf686d57d684fbf0e2038eb -Author: Max Linke -Date: Tue Sep 5 17:48:18 2017 +0200 - - finish pytest transition - - - fix failing tests - - remove setUp method - - remove array asserts - - clean up - - restore old comment - - style fixes - - use best practices with context manager - - class scope for fixture - -commit 8457376ba00705cbafe30f07164dfe37266282ae -Author: Jose Borreguero -Date: Tue Sep 5 14:24:43 2017 -0400 - - Forgot to sort the list of indices! - -commit e377b797c41a7cb093bb187b4174dfe27ca82db0 -Author: Bansal Utkarsh -Date: Sat Aug 26 14:34:16 2017 +0530 - - Pytest Style coordinates/test_xdr.py - -commit 89ebb464bbd777b61b6f072ae722a198966a7c07 -Author: Jose Borreguero -Date: Tue Sep 5 11:36:32 2017 -0400 - - Parameterize tests - -commit 44dbfc190fc65e3b47696e6123bb0fbe2804ef38 -Author: Jose Borreguero -Date: Tue Sep 5 11:24:56 2017 -0400 - - Refactor search method to gain speed - -commit b138532d712a5e135fe23ea20c3cb409ddfebd0a -Author: Max Linke -Date: Mon Sep 4 22:33:04 2017 +0200 - - drop usage of assert_array_* - -commit 86c55f151279239ae05a24540f1ba0e453bd5350 -Author: Bansal Utkarsh -Date: Thu Aug 24 23:30:18 2017 +0530 - - Use assert in place of assert_equal - -commit 9a0790bf066e8d315a41a1b295ba942b4f17b3c4 -Author: Bansal Utkarsh -Date: Mon Aug 21 00:51:07 2017 +0530 - - Pytest Style core/test_atomgroup.py - -commit 6c8aa3665377cc98e31bbe8d00112863147de5a1 -Author: Jose Borreguero -Date: Mon Sep 4 18:16:52 2017 -0400 - - Use ValueError for shape checking of center point - -commit 446514ce8e142371d35d02a4495f11ac40cc7810 -Author: Jose Borreguero -Date: Mon Sep 4 18:15:37 2017 -0400 - - Use RuntimeError if coordinates not set - -commit 72f7605627d5263091b4657f6ea7915f4693d22c -Author: Jose Borreguero -Date: Mon Sep 4 18:13:56 2017 -0400 - - Use distances._box_check at initialization - -commit c791a5c81c42670791971900b4d16033af35c775 -Author: Jose Borreguero -Date: Mon Sep 4 17:40:32 2017 -0400 - - Debug insertion of additional indexes - -commit 75d42ca2dcdabd8bd261fe04234b87ffe6b47577 -Author: Jose Borreguero -Date: Mon Sep 4 17:23:37 2017 -0400 - - Entries in AUTHORS and CHANGELOG - -commit c95ad7bb9612b6d8ec4e41b861d412879e9b63b9 -Author: Jose Borreguero -Date: Mon Sep 4 17:17:22 2017 -0400 - - Switch to pytest fixtures - -commit 383e2ee4694b23e22b85c7f7a08f780ea96f6798 -Author: Jose Borreguero -Date: Mon Sep 4 16:47:49 2017 -0400 - - Use distances.apply_PBC and distances._check_array - -commit 363c94f7c5533582e89ed9ed13777b5fa3eb7f48 -Author: Utkarsh Bansal -Date: Tue Sep 5 01:53:28 2017 +0530 - - [Review Needed]Pytest Style coordinates/test_trj.py (#1651) - - * Pytest Style coordinates/test_trj.py - - * Cleanup - -commit b786cd3b22633d7faa5748d9642157443c780d22 -Author: Max Linke -Date: Mon Sep 4 14:29:02 2017 +0200 - - add assert_timestep_equal - - standalone function to replace _check_ts_equal - -commit 7dba4c520a1e4401ec3138a712de3f5171cad695 -Author: Max Linke -Date: Sun Sep 3 22:13:43 2017 +0200 - - replace yield based tests - - use fixture for timestep instead of parametrize - -commit a0024fac891e617edeb89e53d568e289a78e8e15 -Author: Bansal Utkarsh -Date: Mon Aug 21 20:11:13 2017 +0530 - - Remove yield based tests - -commit b2ac8887fd7cef70a7447962f76d5216d0c1a787 -Author: Utkarsh Bansal -Date: Mon Sep 4 10:44:02 2017 +0530 - - [Review Needed]Pytest Style core/test_updating_atomgroup.py (#1619) - - * Pytest Style TestUpdatingSelection, TestUpdatingSelectionNotraj - - * Pytest Style TestUAGCallCount, TestDynamicUAG - - * Cleanup - - * Indentation fixes - - * use builtin next method - - This is more future proof for a python3 only library in a couple of years. - -commit 211a2e0ee835463ce55a5f521ffd532da56b0716 -Author: Jose Borreguero -Date: Sun Sep 3 18:05:04 2017 -0400 - - Use six.moves.range - -commit bad5eaaebc9115823b7608438fb2ea6ab64e0648 -Author: Jose Borreguero -Date: Sun Sep 3 17:05:36 2017 -0400 - - clean up pkdtree source - -commit 20257f3ab6f3422ce20e16244a70dc2a97ed2210 -Author: Jose Borreguero -Date: Sun Sep 3 16:45:35 2017 -0400 - - Amend AtomNeighborSearch docstring - -commit 53edb84fe7c6e81c96b281ad68dea033f2229e49 -Author: Jose Borreguero -Date: Sun Sep 3 16:38:53 2017 -0400 - - Unit test for PeriodicKDTree.search - -commit 3703d7d3b1c00f203539fbf5d71e61e0ec2a5b21 -Author: Utkarsh Bansal -Date: Mon Sep 4 00:38:38 2017 +0530 - - Pytest Style: coordinates/test_gro.py (#1659) - -commit 49aaf082578fe3947a7d6a41ff6ec7c5feb2caee -Author: Utkarsh Bansal -Date: Mon Sep 4 00:36:24 2017 +0530 - - [Review Needed]Pytest Style TestEncore (#1609) - - * Pytest Style TestEncore - - * Pytest Style TestEncoreClustering - - * Pytest Style TestEncoreClusteringSklearn - - * Pytest Style TestEncoreDimensionalityReduction - - * Cleanup - - * Fix assert comparisions - - * Use step parameter in transfer_to_memory - - * Use transfer_to_memory in place of np.copy() - -commit b270733d1e2c7717654c5d61f50e20ce5e8eb3b9 -Author: Jose Borreguero -Date: Sun Sep 3 13:02:58 2017 -0400 - - Fixed bug in initializing self.box - -commit 9b11a67d42ad4f8dd07d90d67448b988b5c55700 -Author: Jose Borreguero -Date: Sun Sep 3 13:02:32 2017 -0400 - - test_find_centers added - -commit 7049b087e910404ab07a6721529e9f072a91b42d -Author: Jose Borreguero -Date: Sat Sep 2 14:39:42 2017 -0400 - - source and some testing - -commit 141dc1159cc82e548c5b301f83fed96e79345015 -Author: Utkarsh Bansal -Date: Mon Aug 28 16:58:56 2017 +0530 - - Pytest Style coordinates/test_netcdf.py & coordinates/test_trj.py (#1647) - -commit e9f0cb9564d6b2ec9379db0a787846fb5067c2ed -Author: Utkarsh Bansal -Date: Mon Aug 28 11:42:17 2017 +0530 - - Pytest Style coordinates/test_timestep_api.py (#1650) - - * Pytest Style coordinates/test_timestep_api.py - * Remove redundant class: no need to skip if netCDF4 cannot be found because we can always read Amber NETCDF files with scipy.io.netcdf (#503) - -commit ec1e983d87d232520248ee266313cdde668110fe -Merge: db2cc3cb3 a3bae230e -Author: Jonathan Barnoud -Date: Sun Aug 27 17:07:54 2017 +0200 - - Merge pull request #1652 from utkbansal/coord-trz - - [Review Needed]Pytest Style coordinates/test_trz.py - -commit db2cc3cb33d85799b12e5146ac1a7303f73d4d7a -Author: Utkarsh Bansal -Date: Sun Aug 27 13:25:51 2017 +0530 - - [Review Needed]Pytest Style core/test_residuegroup.py (#1624) - - * Pytest Style core/test_residuegroup.py - - * Delete commented code - -commit be5d599b79d8bf4d73773daa2f4a57124ed150ec -Author: Utkarsh Bansal -Date: Sun Aug 27 13:19:15 2017 +0530 - - [Review Needed]Pytest Style coordinates/test_lammps.py (#1644) - - * Pytest Style coordinates/test_lammps.py - - * Better path joining - -commit e0307aa0b8d1e237305b5a94beb722d589421ef1 -Author: Utkarsh Bansal -Date: Sun Aug 27 13:15:43 2017 +0530 - - Pytest Style coordinates/test_writer_registration.py (#1654) - -commit d15c51ec30f6da2260586952bfaf3dbba2cd763e -Author: Utkarsh Bansal -Date: Sat Aug 26 22:36:55 2017 +0530 - - Pytest Style coordinates/test_xyz.py (#1656) - -commit fba975ee1c311386a3bf039f41c115cef1c96d03 -Author: Utkarsh Bansal -Date: Sat Aug 26 22:34:42 2017 +0530 - - PEP8 fixes for coordinates/test_txyz.py (#1653) - -commit a3bae230e09ef2969541b42f309ce29e9834db33 -Author: Bansal Utkarsh -Date: Sat Aug 26 12:39:56 2017 +0530 - - Pytest Style coordinates/test_trz.py - -commit 93a8d8c3929738f1b67a4940f78f06a14e1e39bd -Merge: 2ce3e7547 164ea6560 -Author: Jonathan Barnoud -Date: Fri Aug 25 13:52:18 2017 +0200 - - Merge pull request #1648 from utkbansal/coord-null - - [Review Needed]Pytest Style coordinates/test_null.py - -commit 2ce3e75477c29a5d678d474bfb73edeb97b2e311 -Author: Utkarsh Bansal -Date: Fri Aug 25 16:56:13 2017 +0530 - - Pytest Style coordinates/test_pdbqt.py (#1649) - -commit 1215ca301a51a3859efb1472a726338082b0b8b4 -Author: Utkarsh Bansal -Date: Fri Aug 25 14:46:29 2017 +0530 - - Pytest Style coordinates/test_memory.py (#1645) - -commit e8de75d6a610f7452a80da0dd25ffc03f59f396b -Author: Utkarsh Bansal -Date: Fri Aug 25 14:45:43 2017 +0530 - - Pytest Style coordinates/test_mmtf.py (#1646) - -commit b997234b1dc6360acd06493cee15fcca664f49a9 -Author: Utkarsh Bansal -Date: Fri Aug 25 14:21:36 2017 +0530 - - Pytest Style core/test_atomselections.py (#1634) - -commit 2364f1327c8fc550854f42ca15032f93f92fadbf -Author: Utkarsh Bansal -Date: Fri Aug 25 14:20:46 2017 +0530 - - Pytest Stylecore/test_topology.py (#1621) - -commit 164ea6560415dd2c0960d8a9f0f8105500ecfddc -Author: Bansal Utkarsh -Date: Fri Aug 25 13:33:54 2017 +0530 - - Pytest Style coordinates/test_null.py - -commit ef5dee9cf5f29051d2062193f12ebad45e29bc87 -Author: Utkarsh Bansal -Date: Fri Aug 25 12:40:49 2017 +0530 - - [Review Needed]Pytest Style coordinates/test_gms.py (#1639) - - * Pytest Style coordinates/test_gms.py - - * Move fixture to base class - -commit bf47a6abee82572dfdb453afe520b4ed191a58c0 -Author: Utkarsh Bansal -Date: Fri Aug 25 05:53:15 2017 +0530 - - Pytest Style coordinates/test_crd.py (#1641) - - * Pytest Style coordinates/test_crd.py - * Use ordered dict so that the order of fixture data is deterministic - -commit f08aa4f791eeeb067940cdd0eb770f76eb801541 -Author: Utkarsh Bansal -Date: Fri Aug 25 02:54:51 2017 +0530 - - [Review Needed]Pytest Style coordinates/test_chainreader.py (#1640) - - * Pytest Style coordinates/test_chainreader.py - - * Drop trajectory fixture - -commit 56776ef50c6e9d3583ef7b9bd0273293df7e1036 -Author: Utkarsh Bansal -Date: Thu Aug 24 03:37:07 2017 +0530 - - Pytest Style analysis/test_rms.py (#1610) - - * Pytest Style analysis/test_rms.py - * Remove useless fixture - * Fix test_with_superposition_equal - * testing RMS requires independent universes in fixtures - * removed spurious print() - * removed remaining tempdir use from test_rms - -commit 2cd27612ead580cd722c0f73cfbc8574b6d0e2e2 -Author: Bansal Utkarsh -Date: Mon Aug 21 19:37:57 2017 +0530 - - Pytest Style coordinates/test_dms.py - -commit 09d8b684a75eb14023e60dd9e9a61e9cee48805f -Author: Bansal Utkarsh -Date: Mon Aug 21 19:32:36 2017 +0530 - - Pytest Style coordinates/test_dlpoly.py - -commit f240c55cc89687fe3191b9312011d58982db8310 -Author: Max Linke -Date: Mon Aug 21 12:57:42 2017 +0200 - - use minimally version 0.7.0 of seaborn - - This version does not depend on a specific numpy version in either the default - or conda-forge channel and also have python 3.4 packages available. - -commit 38e9e92adad7d8f9d515d1224700a6dd8e655903 -Author: Utkarsh Bansal -Date: Mon Aug 21 14:51:39 2017 +0530 - - Pytest Style core/test_requires.py (#1626) - - * Pytest Style core/test_requires.py - - * Fix pytest.fail() call - -commit c7a47410f28b6f33980c735c76b51e31d012f66e -Author: Utkarsh Bansal -Date: Mon Aug 21 14:42:17 2017 +0530 - - Pytest Style core/test_fragments.py (#1633) - -commit 4a8f881051b5da5816e84f2989af95c9c72be15b -Author: Utkarsh Bansal -Date: Sun Aug 20 04:45:08 2017 +0530 - - Pytest Style core/test_topologyattrs.py (#1620) - - * Pytest Style core/test_topologyattrs.py - - * Move class attr to fixture - -commit 8a075f205a5ee5fa645f9e2335b191e13102552d -Author: Oliver Beckstein -Date: Fri Aug 18 08:34:14 2017 -0700 - - changed exceptions raised by lib.util.get_weights() - - Following @kain88-de 's comments: - - raise TypeError only if it is not an array_like or one of the special values - "masss" or None - - raise a ValueError in all other problematic cases (array_like of wrong length - or shape) - - changed docs for rms.RMSD - - changed tests for rms.RMSD and util.get_weights - -commit 85a2786572f53c31a1797e91c7917d621945dba2 -Author: Oliver Beckstein -Date: Thu Aug 17 18:31:13 2017 -0700 - - doc improvements for RMSD and RMSF - -commit ebf171bd54e92ddd98a2136056fede7634e62821 -Author: Oliver Beckstein -Date: Wed Aug 16 18:29:47 2017 -0700 - - add lib.util.get_weights(atoms, weights) function - - - checks that weights are approriate and raises TypeError otherwise - - transforms weights="mass" --> atoms.masses - - inserted get_weights() in align and rms - - added tests - -commit d5b6bf47a74002c6db93b266c3aefdc307ec8d9f -Author: Oliver Beckstein -Date: Wed Aug 16 16:59:24 2017 -0700 - - analysis.psa: removed deprecated mass_weighted - -commit 81d1352a1eeb2fe4026f73f28789f2b8109e7b50 -Author: Oliver Beckstein -Date: Wed Aug 16 16:48:07 2017 -0700 - - analysis.align: cleaned up imports and docs - -commit b345f66315e6db05d4c2213cfcb7eef51ce60c6e -Author: Oliver Beckstein -Date: Wed Aug 16 16:04:44 2017 -0700 - - analysis.align: removed deprecated mass_weighted - - - removed kwarg mass_weighted from all functions/classes - - updated docs - - fixed example that used mass_weighted - - updated CHANGELOG - - removed tests for deprecated functionality - -commit 50925938392f2421ee8c067eae7173efdb5a86af -Author: Oliver Beckstein -Date: Mon Aug 14 23:58:17 2017 -0700 - - improve handling of weights in analysis.rms - - - class RMSD() - - check that weights is either "mass" or None or iterable of the - correct size - - fix: cast weights to np.array if necessary (failed if it was a simple - iterable) - - removed deprecated mass_weighted keyword (deprecated in 0.16.0, scheduled - for removal in 0.17.0) - - raise TypeError (or ValueError) and document the behavior if weights - are not correct - - add tests for failures and use of a list - - slightly updated tests according to style guide https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide%3A-Tests - - use assert_almost_equal() instead of assert_array_almost_equal() - - use bare assert instead of assert_ - - class RMSF() - - removed unused weights keyword (and updated docs): weights were never used anywhere - in the RMSD code - - removed the corresponding rmsf weights test - - updated CHANGELOG - -commit 12467b09e353356172c6f3df0395e079d5db7537 -Author: Oliver Beckstein -Date: Mon Aug 14 22:53:38 2017 -0700 - - analysis.rms: removed deprecated mass_weighted kw and doc improvements - -commit a8a2de58c23c42f29457996ce7de9f04557491ab -Author: Oliver Beckstein -Date: Thu Aug 10 00:32:21 2017 -0700 - - RMSD groupselections are not superimposed any more - - - fixes #720 - - only allow groupselections with either weights="mass" or weights=None - - adjusted tests (the values increased as expected for the new tests - compared to the old ones that used an implicit superposition) - - updated CHANGELOG - -commit 31319117ad27702b278d839698d0698b2a7950f9 -Author: Oliver Beckstein -Date: Thu Aug 10 00:06:54 2017 -0700 - - analysis.rms: code cosmetics - -commit 9b3cc87c2a8a8fc457582c2dcbce93856c4fb98c -Author: Oliver Beckstein -Date: Thu Aug 10 00:00:28 2017 -0700 - - improved docs in analysis.rms - -commit eda6c13c41f887677e4ba82a4f0aa78d56ad15c8 -Author: Oliver Beckstein -Date: Thu Aug 3 18:16:41 2017 -0700 - - fix MDAnalysis.analysis.rms.RMSD with select != "all" fails - - - closes #1487 - - properly rotate the whole universe, not just the mobile selection - - NOTE: To be fixed: RMSD for groups should be calculated WITHOUT implicit - fitting by qcprot - -commit 0d11e113c935b76ad77e50af67321ab572131d12 -Author: Oliver Beckstein -Date: Thu Aug 3 17:01:17 2017 -0700 - - test for #1487 - -commit a8ae6c938fa871353aaa9c905a33f441eb044e80 -Author: Richard Gowers -Date: Fri Aug 18 07:07:59 2017 +0100 - - updated TXYZ docs (#1631) - - * updated TXYZ docs - * generate more extensive docs for TXYZ - -commit 0acb79661255cb39228b8734eb614eb8a3c3f990 -Author: Bansal Utkarsh -Date: Tue Aug 15 22:08:59 2017 +0530 - - Drop TestCase inheritence - -commit 0acc0f93d47baea8c50d41765ba45366e5a4261b -Author: Richard Gowers -Date: Wed Aug 16 17:39:28 2017 +0100 - - fixed TXYZ.py rst bullet list - -commit 59e2c225e5f7ad5d9ee06808e6ce49847a225f65 -Author: Richard Gowers -Date: Wed Aug 16 17:36:29 2017 +0100 - - Update TXYZ.py - -commit c5125953931a4f0f56c81f21685be9ab4ed13d05 -Author: Richard Gowers -Date: Wed Aug 16 17:33:13 2017 +0100 - - Update TXYZParser.py - -commit 77fa82e62d128687eb2d0bf254a37909cd77dea0 -Author: Richard Gowers -Date: Tue Aug 15 17:24:55 2017 +0100 - - Update __init__.py - -commit 8440f6676a094d9fa855ebb16802efe5a2d8bb81 -Author: Micaela Matta -Date: Tue Aug 15 11:12:40 2017 -0500 - - Added reference to ARC files in test_txyz.py - -commit c60860ea6652effab577928edee0b8097182cbe9 -Author: Micaela Matta -Date: Tue Aug 15 11:02:46 2017 -0500 - - Added reference to Tinker file formats in tables: topology/__init__.py and coordinates/__init__.py - -commit d2101fca3c0d5c16da15635a1a5f69954a4d912e -Author: Micaela Matta -Date: Tue Aug 15 10:40:23 2017 -0500 - - Fixed imports in Tinker coordinates reader - -commit cebbb707fa825d52ccdf2526a4a1240d0880058b -Author: Micaela Matta -Date: Mon Aug 14 14:20:39 2017 -0500 - - relative imports on Tinker coordinate reader and topology parser - -commit f65c1ee8cc431920f4865087dd43cc79bd625b07 -Author: Micaela Matta -Date: Mon Aug 14 12:02:10 2017 -0500 - - fixed imports on Tinker coordinate reader and topology parser - -commit f67a99e5ce53cbf1b66a8d10e5b305f7973d5076 -Author: Micaela Matta -Date: Mon Aug 14 11:50:55 2017 -0500 - - Added documentation for Tinker file format - -commit d4f04eaae54a99b7105a6f8d19362e23f2804711 -Author: Micaela Matta -Date: Mon Aug 14 10:45:29 2017 -0500 - - added rst stubs for tinker - -commit 36ae1d30376f98d673d2d1fa85bb13eab61cb748 -Author: Micaela Matta -Date: Mon Aug 14 10:43:08 2017 -0500 - - docs and changelog - -commit 5408508c1a05a34adcd60c4f9f206d2a5787d6c4 -Author: Micaela Matta -Date: Mon Aug 14 10:39:12 2017 -0500 - - Added Tinker coordinate reader - -commit a6be297934840598fbb228c3544393699aad8bbf -Author: Micaela Matta -Date: Mon Aug 14 10:16:56 2017 -0500 - - Added Tinker topology reader - -commit beb08df3f45c40555a0b1e0a7739c4df96842de7 -Author: Micaela Matta -Date: Mon Aug 14 09:41:49 2017 -0500 - - Added Tinker testfiles - -commit 9085e7b414ed1423d784add408bc57dbc22eb113 -Author: Max Linke -Date: Wed Aug 16 18:43:26 2017 +0200 - - run pylint on python 3.6 (#1589) - - * run pylint on python 3.6 - - * ignore false positives - - * fix pylint error - - * simplify travis pylint setup - - * remove todo in travis config - -commit 6b136c4a2fb79d3a761da4ed67beed5c62be4bbe -Author: Utkarsh Bansal -Date: Wed Aug 16 21:16:08 2017 +0530 - - Pytest Style core/test_group_traj_access.py (#1629) - -commit 150865cd64c0c390301781ecb20ea1d64da9789d -Author: Utkarsh Bansal -Date: Wed Aug 16 01:14:49 2017 +0530 - - Pytest Style core/test_index_dtype.py (#1627) - -commit 4fd0215b3bb2afea13a466245a11f4760c5c3578 -Author: Utkarsh Bansal -Date: Tue Aug 15 21:27:12 2017 +0530 - - Pytest Style core/test_residue.py (#1625) - -commit 6840e49fde6059462e87dd707d564993949ce0c3 -Author: Utkarsh Bansal -Date: Tue Aug 15 21:26:07 2017 +0530 - - Pytest Style core/test_segmentgroup.py (#1622) - -commit 5428d7ec1aba709846caf0523d7cf539b48c7d2f -Author: Utkarsh Bansal -Date: Tue Aug 15 21:20:41 2017 +0530 - - Pytest Style core/test_segment.py (#1623) - -commit 69730f4a5f19e3bed621a70de5f0b89cd69b0b6b -Merge: 7b383c1ac ab5b5d991 -Author: Jonathan Barnoud -Date: Tue Aug 15 08:07:08 2017 +0200 - - Merge pull request #1590 from utkbansal/topology-gro - - [Review Needed]Pytest Style topology/test_gro.py - -commit 7b383c1acaf1639a4b70b3b088147d06c29b22af -Merge: 4c465e91e 3a21ed4e1 -Author: Jonathan Barnoud -Date: Tue Aug 15 08:00:47 2017 +0200 - - Merge pull request #1597 from utkbansal/t-mol2 - - [Review Needed]Pytest Style topology/test_mol2.py - -commit 4c465e91e697c050a54492a9462a185cf0ddb173 -Merge: 6f9ff86c0 9801d05d8 -Author: Jonathan Barnoud -Date: Tue Aug 15 07:57:08 2017 +0200 - - Merge pull request #1600 from utkbansal/t-pqr - - Pytest Style topology/test_pqr.py - -commit 6f9ff86c02c4e65ef70dd63d0f963b4934842a96 -Author: Oliver Beckstein -Date: Mon Aug 14 11:57:01 2017 -0700 - - change Universe.load_new() to return universe itself - - - Universe.load_new() returns self (instead of tuple filename_or_array, - file_type) so that one can more easily chain methods (see #1613) - - closes #1613 - - added comments for why load_new() accepts None: to build Universes - with empty coordinates; now make sure that this case ALSO returns - the universe itself (and not just None as before, which was inconsistent) - - added tests for load_new(DCD) and load_new(None) - -commit 995201211b309a87bc43b76ef129949066ce6350 -Author: Oliver Beckstein -Date: Mon Aug 7 17:54:40 2017 -0700 - - DOCS: disable travis button in docs menu - -commit 09d168c14820172ff1d3e2cab52d8f80823c344c -Author: Utkarsh Bansal -Date: Mon Aug 14 20:27:31 2017 +0530 - - [Review Needed]Pytest Style analysis/test_hydrogenbondautocorrel.py (#1611) - - * Pytest Style analysis/test_hydrogenbondautocorrel.py - - * Cleanup - - * Use np.arange - -commit ab5b5d9913f14715288e17343c4044e3bb09628f -Author: Bansal Utkarsh -Date: Mon Aug 14 00:34:11 2017 +0530 - - Move asserts out of loop - -commit 64f9816a7bf0b6213e12d0bfff6f54b3a433eec8 -Author: Bansal Utkarsh -Date: Tue Aug 8 18:37:45 2017 +0530 - - Pytest Style topology/test_topology_base.py - -commit d98f063799e2f72999ae96dc4025fcc4c0d5d0c0 -Merge: 4fde59649 929867e15 -Author: Jonathan Barnoud -Date: Fri Aug 11 20:28:37 2017 +0200 - - Merge pull request #1605 from utkbansal/t-str - - PEP8 fixes topology/test_topology_str_types.py - -commit 4fde59649831972fb4112f4094a9c68041b8d519 -Merge: ed1772851 0d7ada4a9 -Author: Jonathan Barnoud -Date: Fri Aug 11 20:27:13 2017 +0200 - - Merge pull request #1607 from utkbansal/t-xpdb - - Pytest Style topology/test_xpdb.py - -commit ed17728516801a1002e607a4c606c400fccbd4d5 -Merge: 8fb4f0ae5 262fd3e94 -Author: Jonathan Barnoud -Date: Thu Aug 10 08:12:16 2017 +0200 - - Merge pull request #1608 from utkbansal/t-xyz - - Pytest Style topology/test_xyz.py - -commit 8fb4f0ae56d36282ba0fd5c577ef9c8b19b4f546 -Author: Utkarsh Bansal -Date: Wed Aug 9 01:02:31 2017 +0530 - - Pytest Style topology/test_psf.py (#1601) - -commit 262fd3e940f79183937d48710046303f59c7df4a -Author: Bansal Utkarsh -Date: Tue Aug 8 19:28:05 2017 +0530 - - Pytest Style topology/test_xyz.py - -commit 0d7ada4a9cc5a592e5a2542d71b09f776ba5e873 -Author: Bansal Utkarsh -Date: Tue Aug 8 19:26:48 2017 +0530 - - Pytest Style topology/test_xpdb.py - -commit 929867e1582a60eca9c0d8830c41f52815adb411 -Author: Bansal Utkarsh -Date: Tue Aug 8 18:44:14 2017 +0530 - - PEP8 fixes topology/test_topology_str_types.py - - * Replace hard tabs with spaces for indentation - * Order imports - -commit 1cc027534bb0722f97cb9cd22f6cadfc76fe9b21 -Author: Bansal Utkarsh -Date: Tue Aug 8 18:26:11 2017 +0530 - - Undo parametrize - -commit 753edd829d6224450020ee44d21f701700008c2a -Author: Utkarsh Bansal -Date: Tue Aug 8 17:38:52 2017 +0530 - - Pytest Style topology/test_top.py (#1602) - -commit 559a4590724d9998b5704e58c56563b0467033a9 -Author: Utkarsh Bansal -Date: Tue Aug 8 17:38:12 2017 +0530 - - Initial work (#1595) - -commit 1c19bd33281e3ae618f90487b89c8ca2aca59f7f -Author: Utkarsh Bansal -Date: Tue Aug 8 13:04:55 2017 +0530 - - Pytest Style topology/test_pdbqt.py (#1599) - -commit 6a856aa7168a0ac048136108370e28938d9105cd -Merge: 76f98c50c 812df80b1 -Author: Jonathan Barnoud -Date: Tue Aug 8 08:56:48 2017 +0200 - - Merge pull request #1598 from utkbansal/t-pdb - - Pytest Style topology/test_pdb.py - -commit 76f98c50c2406d1f6aef95622446c2baa3cef9d5 -Merge: 2a702aab3 782cd7b05 -Author: Jonathan Barnoud -Date: Tue Aug 8 08:30:13 2017 +0200 - - Merge pull request #1596 from utkbansal/topology-laamps - - Pytest Style topology/test_lammpsdata.py - -commit 9801d05d8f7272b676861f60e831c1bae78c650d -Author: Bansal Utkarsh -Date: Tue Aug 8 09:48:32 2017 +0530 - - Pytest Style topology/test_pqr.py - -commit 812df80b15fe95bc722b004c04f181d299f66c78 -Author: Bansal Utkarsh -Date: Tue Aug 8 09:44:21 2017 +0530 - - Pytest Style topology/test_pdb.py - -commit 3a21ed4e1015cb7ead4b10ceda8a7601acf2404f -Author: Bansal Utkarsh -Date: Tue Aug 8 09:40:01 2017 +0530 - - Pytest Style topology/test_mol2.py - -commit 782cd7b059e0d8a55c9b7833b74640ad30d6861f -Author: Bansal Utkarsh -Date: Tue Aug 8 09:17:11 2017 +0530 - - Pytest Style topology/test_lammpsdata.py - -commit 2a702aab36ac2d46e48fa259e17031835cc88c72 -Author: Utkarsh Bansal -Date: Mon Aug 7 21:33:06 2017 +0530 - - Pytest Style topology/test_guessers.py (#1592) - -commit f15526ba42fd1a0668d5f065cf8b6c1f199ff474 -Author: Utkarsh Bansal -Date: Mon Aug 7 21:32:23 2017 +0530 - - Pytest Style topology/test_hoomdxml.py (#1593) - -commit 8f5d4db8c91a3891b0f810a68e62b6efb068b457 -Merge: 833d83a8a b939af1c2 -Author: Jonathan Barnoud -Date: Sat Aug 5 21:33:45 2017 +0200 - - Merge pull request #1587 from utkbansal/topology-dms - - Pytest Style topology/test_dms.py - -commit 833d83a8a8945a6732888e92f26d5542ab3478b8 -Author: Utkarsh Bansal -Date: Sun Aug 6 01:02:47 2017 +0530 - - Pytest Style topology/test_gms.py (#1588) - - * Pytest Style topology/test_gms.py - - * Whitespace fixes - -commit 2542b16826c9238edaf758141a4d585a50962c79 -Author: Utkarsh Bansal -Date: Sat Aug 5 23:47:58 2017 +0530 - - [WIP]Pytest Style analysis/test_density.py (#1543) - - * Pytest Style analysis/test_density.py - - * Fix test_grid - - * Use pytest's tmpdiR - -commit 60d013bb8f7226e7a4273337ecd63db6807f0e79 -Merge: 1703f85bb 59299cc6e -Author: Jonathan Barnoud -Date: Sat Aug 5 12:35:05 2017 +0200 - - Merge pull request #1585 from MDAnalysis/note-about-python2-only-package - - add note about mock for python3 removal - See #1584 - -commit d4705e824484da79d89545e6bc598336f06bc80c -Author: Bansal Utkarsh -Date: Sat Aug 5 15:50:32 2017 +0530 - - Pytest Style topology/test_gro.py - -commit 1703f85bbe42e19d9c592d491c191fe9e79c51e7 -Author: Bansal Utkarsh -Date: Sat Aug 5 14:17:41 2017 +0530 - - Pytest Style topology/test_dlpoly.py - -commit 0b9066c989265efa548837fd626c615315bf5c55 -Author: Bansal Utkarsh -Date: Sat Aug 5 13:09:17 2017 +0530 - - Use pytest.importorskip - -commit ef1b0d4aae3088b1c2d6d954bd8da750408a167d -Author: Bansal Utkarsh -Date: Thu Aug 3 20:19:45 2017 +0530 - - Drop nose - -commit 4e070eaabdfabdc348542278baeb5391352da19d -Author: Bansal Utkarsh -Date: Thu Aug 3 19:33:48 2017 +0530 - - Remove all occurences of @dec - -commit 36e5b14d4390c266b22e15604d1306c79ab9df65 -Author: Bansal Utkarsh -Date: Wed Aug 2 21:36:44 2017 +0530 - - Get rid of assert_raises - -commit b939af1c267e3f8181a673d45795f8064c040589 -Author: Bansal Utkarsh -Date: Sat Aug 5 14:21:31 2017 +0530 - - Pytest Style topology/test_dms.py - -commit 59299cc6e6a70b6770471a320322222f345f189a -Author: Max Linke -Date: Sat Aug 5 09:53:47 2017 +0200 - - add note about mock for python3 removal - - [skip ci] - -commit 1f69ba0266f2e029ac9314520ca2d1fb54d80b6c -Author: Utkarsh Bansal -Date: Sat Aug 5 13:12:06 2017 +0530 - - Pytest Style analysis/test_lineardensity.py (#1548) - - * Pytest Style analysis/test_lineardensity.py - - * Typo fix - - * Cleanup - - * Delete dead code - - * Use assert_almost_equal - - * Use the default precision - -commit 74b5e23b4847fca597b6b84460f6d4af5dc149dd -Author: Max Linke -Date: Fri Aug 4 20:37:31 2017 +0200 - - TST: speed up gnm tests - - The close contact tests run over a full trajectory and needed to compute the - verlet-list for over 10000 particles for every frame in the trajectory. Cutting - down on the number of frames analyzed doesn't change the tests but reduces the - runtime significantly. - -commit 4cb8c087f115340de7fbee20a8cfbfdfbb98aa8a -Author: Max Linke -Date: Fri Aug 4 19:56:46 2017 +0200 - - MAINT: yapf gnm - -commit a5a584d901e29d67feb25e24d70712f13657df0d -Author: Max Linke -Date: Fri Aug 4 19:43:21 2017 +0200 - - TST: test for deprecation warnings - -commit 0fa638a501c15b5a64e271492613bedf27b4668b -Author: Max Linke -Date: Fri Aug 4 19:41:35 2017 +0200 - - MAINT: simplify neighbor search algorithm - - use itertools.product instead of a nested loop. - -commit 559528f3349bebcaeb82e7f97fd6b76ae8aecce2 -Author: Max Linke -Date: Fri Aug 4 17:38:41 2017 +0200 - - Gnm speed up (#1579) - - * MAINT: micro optimize in _dsq gnm - - This seems to be faster by roughly a factor of 1.5 - - * MAINT: Use generator to calculate possible neighbors - - This simplifies the generate_kirchoff functions and separates the slow code into - it's own function that we can test and improve later on. - - This also includes some minor improvements in the generate_kirchoff functions. - - * update CHANGELOG - - * MAINT: simplify generate_grid return values - -commit ea2ca62f7834b2943a656239cbbf7e6724f0d03c -Author: Utkarsh Bansal -Date: Fri Aug 4 05:37:23 2017 +0530 - - Pytest Style: topology/test_crd.py (#1527) - - * Parametrize the base test class - - * Adds back the old ParserBase so that old tests keep working - - * Nuke topology/test_crd.py - - * Rename base.py for pytest discovery - - * Revert to subclassing - -commit 858069f3e97a49d53c574e1b65cfa7cac4a47647 -Author: Utkarsh Bansal -Date: Thu Aug 3 23:49:22 2017 +0530 - - [WIP]Pytest Style analysis/test_align.py (#1546) - - * Pytest Style analysis/test_align.py - - * Cleanup - - * Fix name - - * Cleanup - -commit b6a7cbcf8eced94766a70ca2f179bfc6fa10473c -Author: Utkarsh Bansal -Date: Thu Aug 3 21:48:28 2017 +0530 - - Pytest Style analysis/test_hbonds.py (#1544) - -commit 0f9ef862a79b1b9aa7970a7d35e492fe2df0b5e8 -Author: Nestor Wendt -Date: Wed Aug 2 15:29:29 2017 +0100 - - Fixed _calc_dihedral and Dihedral.dihedrals (#1566) - - * Fixed _calc_dihedral and Dihedral.dihedrals - - Closes #1554, #1565 and #1572 - - * Fixed nuclinfo.tors() not converting delta to 0-360 - - * Makes calc_dihedral_angle consistent with numpy - - * Changed _calc_dihedral* to be consistent with numpy implementation - -commit d8af6c76ec65bff71a8638d9c0bed500f7855c82 -Merge: 8e3f0e1ac 5b00422e9 -Author: Oliver Beckstein -Date: Tue Aug 1 17:20:59 2017 -0700 - - Merge pull request #1553 from MDAnalysis/asv_bench_simplified - - ENH: Added basic asv benchmark suite to MDAnalysis - -commit 5b00422e9ef79b4b336a22b44a392780ac764183 -Author: Tyler Reddy -Date: Tue Aug 1 17:58:31 2017 -0600 - - DOC: Added MDA asv docs. - -commit 8e3f0e1ac38cd35c22192c473f80f3858c844db7 -Author: Utkarsh Bansal -Date: Wed Aug 2 02:15:52 2017 +0530 - - Pytest style analysis/test_persistencelength.py (#1568) - -commit 081429ac47f003c4ffc11ca6b2f7bc7e50b3bc1c -Author: Utkarsh Bansal -Date: Wed Aug 2 00:51:32 2017 +0530 - - Pytest Style analysis/test_waterdynamics.py (#1571) - -commit 1db2aaf2059d9c708dd3ad42d5feacaffba9d4f8 -Author: Tyler Reddy -Date: Thu Jul 27 22:02:29 2017 -0600 - - TST: Added first draft of trajectory reader asv benchmark tests. - -commit 3d73f446cccd6940b9a124e22b82e16e10612c42 -Author: Tyler Reddy -Date: Sun Jul 23 18:48:27 2017 -0600 - - TST: Removed some scipy-specific info from asv JSON file. - -commit 13da40b82f612fef361fcf6a0bd8b2ed7ba18594 -Author: Tyler Reddy -Date: Sun Jul 23 18:28:25 2017 -0600 - - TST: Changes needed to get MDAnalysis asv benchmarks working with NO relocation of setup.py. - -commit afa87d15d4fbb6b95d43319a1071787fdf02b551 -Author: Tyler Reddy -Date: Tue Jun 13 22:09:56 2017 -0600 - - ENH: early work adding asv benchmark suite to MDA. - -commit 3f87c79fde1db57296fd9e45dacc5ba5b9ed7dc8 -Author: Sean Seyler -Date: Mon Jul 31 12:38:59 2017 -0700 - - get_path_metric_func now raises KeyError with error string; it's unit test now checks KeyError is raised - -commit 5fb8893553d434874bb52db954776a1b8823670d -Author: Jonathan Barnoud -Date: Mon Jul 31 17:41:39 2017 +0200 - - Replace the deprecated logger.warn (#1564) - - The `warn` method from the `logging` module is deprecated at least in - python 3. This results in deprecation warnings being displayed instead - of the legitimate warning we want to log. - - This commit replaces all occurrences of `logger.warn` by - `logger.warning`. - -commit a4e57912a24ea44bf4db4bbf145618465bffa6c5 -Author: Utkarsh Bansal -Date: Sun Jul 30 23:53:57 2017 +0530 - - Pytest Style analysis/test_psa.py (#1569) - - * Pytest Style analysis/test_psa.py - -commit b307b2c2ae7703b172061b2c0a9beaedc13b021f -Author: Utkarsh Bansal -Date: Sun Jul 30 16:56:11 2017 +0530 - - Pytest Style analysis/test_rdf.py (#1570) - -commit 0cb6d088e90e0d6ccfb34cfb198e096b9a781d73 -Author: Utkarsh Bansal -Date: Sun Jul 30 16:48:21 2017 +0530 - - Pytest Style analysis/test_gnm.py (#1542) - - * Pytest Style analysis/test_gnm.py - - * Cleanup - - * Import zip from six - -commit 0ad6d9bb922ce994076e1bac2caf854bffb228f3 -Author: Utkarsh Bansal -Date: Sat Jul 29 23:45:04 2017 +0530 - - Pytest Style analysis/test_base.py (#1547) - - * Pytest Style analysis/test_base.py - - * Drop the class - -commit a1e49ba10e1e556fe5fc6e33af2ce00cb0b4e413 -Author: Utkarsh Bansal -Date: Sat Jul 29 23:42:32 2017 +0530 - - Pytest Style: test_util.py (#1494) - - * Fixes - - * Fix TestMakeWhole - - * Fix TestCachedDecorator - - * Fix TestConvFloat - - * WIP TestGuessFormat - - * WIP TestGuessFormat - - * WIP3 TestGuessFormat - - * WIP4 TestGuessFormat - - * Fix TestGuessFormat - - * Supress pylint warning - - * Fix TestGetWriterFor - - * Fix TestNamespace - - * Fix TestTruncateInteger - - * Cleanup - - * Do _load_bonds in fixture - - * Move body of function to fixture - - * Convert map to list comprehensions - - * Remove all calls to lambda - - * Rename format to format_tuple - - * Cleanup - - * Cleanup - - * Remove python3 checks - - * Whitespace and name fixes - -commit b4e044bad08b77c982765efc7bc1d744831b65b7 -Author: Utkarsh Bansal -Date: Sat Jul 29 23:21:07 2017 +0530 - - Pytest Style analysis/test_leaflet.py (#1551) - - * Pytest Style analysis/test_leaflet.py - -commit a46cf63712bc2c8332598e8604c3b7c81064eed0 -Author: Utkarsh Bansal -Date: Sat Jul 29 20:42:36 2017 +0530 - - Pytest style analysis/test_distances.py (#1541) - - * Pytest style analysis/test_distances.py - - * Cleanup - - * Use more fixtures - -commit fda6e366a584c9d5cb0737e1f7423cd9a8bbd25f -Author: Utkarsh Bansal -Date: Sat Jul 29 13:21:13 2017 +0530 - - Pytest Style analysis/test_diffusionmap.py (#1540) - - * Pytest Style analysis/test_diffusionmap.py - - * Cleanup - - * Increase fixture scope to module - -commit 2b6052474e8545916478667d974cc5e3f4dab6c4 -Author: Jonathan Barnoud -Date: Sat Jul 29 09:38:00 2017 +0200 - - Fix tests about moltypes (#1567) - - Changes merged in MDAnalysisTests.topology.base broke the tests about - the moltype topology attribute. Indeed, the topology object being tested - is now a pytest fixture while it used to be a object attribute. - - This commit fixes the tests. - -commit 3271028d734aa2d2b24081798a159021fc3e01f3 -Author: Utkarsh Bansal -Date: Fri Jul 28 21:02:50 2017 +0530 - - [WIP]Pytest Style analysis/test_helanal.py (#1550) - - * Pytest Style analysis/test_helanal.py - -commit dc1612406c1dee327ced2a8dead3ddd7e352ae03 -Author: Jonathan Barnoud -Date: Fri Jul 28 14:59:10 2017 +0200 - - Issue 1555 moltype (#1557) - - * Add moltypes as topology attribute for TPR - - The TPR parser now exposes the molecule type as the moltypes topology - attribute. The moltypes attribute is defined at the residue level, but - can be accessed at the atom level as well; it behave in the same way as - the resnames attribute. - - The molecule type is the name of the molecule to which the atom/residue - belongs. Two molecules that share a molecule type has the same topology - template, so by definition they will have the same number of atoms, - residue, bonds, angles ... On the contrary to segments, moltypes do not - have to be contiguous so multiple occurrences of the same moltype can be - defined in a topology with other molecule types in between; this happens - for instance in lipid bilayer simulations where the lipids are sorted by - leaflet. - - In the specific case of gromacs, the molecule type is defined as the - first field in the `[moleculetype]` section of an ITP file. Only the TPR - parser implements the moltype attribute, though the attribute is generic - in principle and can be implemented in any other parser assuming the - format can name molecules. - - * Add the moltype selection keyword - -commit ed3018af4bfa228157ef8d8f193bb8063118e7d2 -Author: Utkarsh Bansal -Date: Thu Jul 27 02:33:11 2017 +0530 - - [WIP]Pytest Style analysis/test_contacts.py (#1545) - - * Pytest Style analysis/test_contacts.py - - * Cleanup - -commit 5672a7ae03c4852cc272b68bd72bcb57cf375c25 -Author: Utkarsh Bansal -Date: Thu Jul 27 02:25:45 2017 +0530 - - Pytest Style analysis/test_hole.py (#1539) - - * Pytest Style analysis/test_hole.py - - * Cleanup - - * Make fixture a static method - -commit aaff9a150cbf16ff77c1368b95ea5e19864e6b2e -Author: Richard Gowers -Date: Wed Jul 26 12:51:33 2017 -0700 - - Fixed Angle.angle when angle~=180. (#1559) - - Converted test_topologyobjects to pytest - -commit 53410cdf3772b79bcbd5c275d2046fb76a8cdde9 -Author: Utkarsh Bansal -Date: Thu Jul 27 01:20:56 2017 +0530 - - Pytest Style analysis/test_nuclinfo.py (#1549) - -commit 1b8c667e97660cf3da1950df6b1effe1f6d2b167 -Author: Utkarsh Bansal -Date: Wed Jul 26 00:02:28 2017 +0530 - - Pytest style topology/base.py (#1526) - -commit d97da42b874ffea5a46b0651bd556734c2700a4b -Author: Utkarsh Bansal -Date: Tue Jul 25 23:42:54 2017 +0530 - - Pytest Style: core/test_atom.py (#1535) - -commit e0bc3034042411ecfb9eb123e5bb207c593eba28 -Merge: 51ce9876f d76c93489 -Author: Max Linke -Date: Sat Jul 22 07:41:30 2017 +0200 - - Merge pull request #1517 from MDAnalysis/py3builds - - Made Py3.6 main language - -commit d76c93489d11d06bc83cd29e4b23961f937cf059 -Author: Richard Gowers -Date: Fri Jul 21 19:48:54 2017 +0100 - - added coveralls to dep list - -commit 9a500e4c1e3f9ac28ef4bac46f14f83dfd033ed1 -Author: Max Linke -Date: Fri Jul 21 12:20:59 2017 +0200 - - fix hole download - -commit b71471b8e5a873dbee45e62b12e3260660c476a0 -Author: Max Linke -Date: Fri Jul 21 09:30:17 2017 +0200 - - skip hole on osx for now. - - we don't have the correct binary to download - -commit 0e2745f9b26ed7ab2d3dfc5070989538ea8eaf0f -Author: Max Linke -Date: Thu Jul 20 18:31:24 2017 +0200 - - general clean up of travis.yml - - - fix hole installation for max - - simplify test scripts - -commit 179444d3a9e57d761d2b3d227a2d2f74def3f6ae -Author: Richard Gowers -Date: Tue Jul 18 20:03:23 2017 +0100 - - Added python3 to build matrix - -commit 51ce9876f85f64d3ecc3ca595de71aabe4eb24d4 -Author: Utkarsh Bansal -Date: Thu Jul 20 23:16:04 2017 +0530 - - Pytest Style: test_streamio.py (#1472) - - * Pytest Style test_streamio.py - - * Fix yield based tests - - * Use tmpdir - - * Adds skipif - - * Refer issue #1534 for segfaults - -commit 36d1351c3a94d4cce6193be020a9674518b8f8e7 -Author: Oliver Beckstein -Date: Thu Jul 20 07:11:15 2017 -0700 - - fixed Python 3 errors in analysis.hole and tests (#1532) - -commit 6698c62329f02541a6db98af3f47c9f28771502c -Author: Richard Gowers -Date: Thu Jul 20 06:42:56 2017 -0700 - - Re-enabled parallel pytest (#1531) - - * Re-enabled parallel pytest - - Fixes issue #1529 - -commit 8420368e87956e9222e9390963521ecd09e4775b -Author: Richard Gowers -Date: Wed Jul 19 15:07:34 2017 -0700 - - Fixes Issue #1495 (#1519) - - * Fixed Issue #1495 - - phi_selection and friends no longer raise deprecation errors - - * Combined atom selections - - * Added nodep tests for phi_selection - - Moved no_deprecated_call to top namespace of Test package - -commit 301c7eb1577cbeda4493b744ce85115e8f1b75d6 -Merge: 01e9fa056 1208eb135 -Author: Max Linke -Date: Wed Jul 19 22:33:24 2017 +0200 - - Merge pull request #1524 from MDAnalysis/issue-260-py3 - - Made python 3 support official - -commit 7a5b9a7197835217c24b6c662b5838db1cb5651e -Author: Sean Seyler -Date: Wed Jul 19 12:35:47 2017 -0700 - - Added docstring in PSAnalysis.cluster for dist_mat kwarg - -commit 86273c6e7899be9cae365afe380aa808910a46a7 -Author: Sean Seyler -Date: Wed Jul 19 12:28:03 2017 -0700 - - Small fixes/changes: - - Added future division and six.range to test_psa.py - - Separated pairs analysis (_run_pairs_analysis) from _run; moved plotting before - - Adding a couple distance matrix checks to PSAnalysis methods - - PSAnalysis.cluster now uses generated distance matrix D by default - and checks for proper dist matrix format if dist_mat kwarg is specified - - updated docstring for PSAnalysis.cluster - -commit 6b6fde1338e86c6d6b5745590710bf5390c17dbe -Author: Sean Seyler -Date: Tue Jul 18 10:58:46 2017 -0700 - - Changed to old-style division in dist_mat_to_vec to ensure integer output - -commit 2ee4e6590121cc5519dc7db20a2a8666f08cfef0 -Author: Sean Seyler -Date: Mon Jul 17 18:41:45 2017 -0700 - - Added fix, change, author sseyler to CHANGELOG; updated run_pairs_analysis docs for dist matrix D - -commit 3e3ac062389cc520b678a01f2058a643f5f206fa -Author: Sean Seyler -Date: Mon Jul 17 17:15:16 2017 -0700 - - New test for Hausdorff pair frames in pairs analysis; pairs analysis now also gives distance matrix - -commit 6bfbf1c5f1dda515f3b30032a7b5a59d425e7b4a -Author: Sean Seyler -Date: Mon Jul 17 14:41:37 2017 -0700 - - Added two tests for Hausdorff neighbors--only the distances - -commit 46448c92883a8f109331624929eac4eb7ee5a9bf -Author: Sean Seyler -Date: Mon Jul 17 14:16:58 2017 -0700 - - New names for (w)avg_hausdorff tests + reverting back to old (same) test names: test_asymmetric_weight() - -commit b48275ea28c93a286c3c497bb9e1f4f1ddc2d458 -Author: Sean Seyler -Date: Mon Jul 17 14:02:50 2017 -0700 - - Changed test name(s) from test_asymmetric_weight() to test_asymmetric_wavg_weight() and test_asymmetric_avg_weight(); need diff names for each test. - -commit 01e9fa056760749c39c5d566de517758a02cde7e -Author: Tyler Reddy -Date: Wed Jul 19 12:12:47 2017 -0700 - - Fixed analysis_class warning. Fixes #1511. (#1522) - - * Fixed analysis_class warning. Fixes #1511. - - * Revised test_analysis_class_decorator() based on feedback in PR 1522; context manager is now more specific. - -commit 283c617f9e5d56bda704c09efc58fc5b53620755 -Author: Tyler Reddy -Date: Wed Jul 19 12:12:18 2017 -0700 - - TST: Added a test for segid str type in test_str_types(). Fixes #1523. (#1528) - -commit 1208eb1351f1dce02ce1d23a578342e428c4ed63 -Author: Richard Gowers -Date: Wed Jul 19 18:07:24 2017 +0100 - - removed pytest xdist - -commit 8826b5e08093aa07f367e648171207375972ff50 -Author: Jonathan Barnoud -Date: Wed Jul 19 19:05:15 2017 +0200 - - Fixes segid from TPR parser on python 3 (#1521) - - Fixes #1520 - -commit c3a0abdb33c802c958874adfe116840a46076c81 -Author: Richard Gowers -Date: Wed Jul 19 01:09:15 2017 +0100 - - Made python 3 support official - -commit 704107beec76b3613909bc3dae53f1a18a4c9213 -Author: Richard Gowers -Date: Tue Jul 18 14:16:48 2017 -0700 - - Remove parsernotfound (#1516) - - * Removed python 3 import warning - - * Removed parser_not_found - - Can import everything in python 3 now, including parsers - -commit 3e420cfb24664c6ecff4f71faba2a5099bee820f -Author: Max Linke -Date: Tue Jul 18 23:01:26 2017 +0200 - - Test log fix warnings (#1509) - - * remove warnings in log tests - - * use new division - -commit f3514752794ef150b63127b972c5871acdaf2d44 -Author: Tyler Reddy -Date: Tue Jul 18 13:56:43 2017 -0700 - - Added tests for topology string types with various formats. Fixes #1336. (#1518) - -commit a97753ff44860b813714343a397fc0c35ceb2c9a -Author: Richard Gowers -Date: Tue Jul 18 12:19:22 2017 -0700 - - Fixed get_writer_for in py3.6 (#1515) - -commit 4ca3235b8a98fb5d958037eaad4e11d9195d9f36 -Author: Richard Gowers -Date: Tue Jul 18 10:39:32 2017 -0700 - - Fixes Issue #1174 (#1505) - - GMS Reader now works out file offsets in bytes mode - -commit f1647ecf39473005c38a3929c108ca9841ea9e4d -Author: Max Linke -Date: Tue Jul 18 18:46:37 2017 +0200 - - fix test_streamio python3 (#1510) - - StringIO can't be initialized from a file handle. Fixes #1513. - -commit 192e75b57d4f249a203e5a9d3aa97d0951419f32 -Author: Utkarsh Bansal -Date: Tue Jul 18 20:30:02 2017 +0530 - - Pytest Style: auxiliary/base.py (#1492) - - * Pytest style auxiliary/base.py - - * Fix raises - - * Fix raises errors - - * Fix assert calls - -commit 3dd9d3c2c01fff6992cbfd200a6c182b3f02f78f -Merge: 82e100e3c 299a939ad -Author: Max Linke -Date: Tue Jul 18 16:57:02 2017 +0200 - - Merge pull request #1480 from utkbansal/f-u-nose - - Dropping nose as a dependency - -commit 299a939adfd0e3e946e6e07fe250a69e92dd0180 -Author: Bansal Utkarsh -Date: Fri Jul 14 20:42:43 2017 +0530 - - Drop comments for running tests with nose - - Fix Install docs - - Update CHANGELOG - - Cleanup docs - -commit 82e100e3ca3af940055359d11bc314daf41fd346 -Author: Tyler Reddy -Date: Mon Jul 17 20:42:38 2017 -0700 - - The NamedStream class now has the required __fspath__ method (#1504) - - * The NamedStream class now has the required __fspath__ method for Python 3.6 os.PathLike behavior. - - * os.PathLike is now handled with a try/except block in util.py; empty class used for Py < 3.6. - -commit 9616de701963c9cda19a30fbfc6c84595af0e4ea -Author: Richard Gowers -Date: Mon Jul 17 17:25:20 2017 -0700 - - Rewrote TestLAMMPSDATAWriter to use pytest fixture (#1499) - - * Rewrote TestLAMMPSDATAWriter to use pytest fixture - - * More pytesting of test_lammps - - * Removed whitespace - -commit 680fdbdfb7fa8af9ec9115297ef246859577c6be -Author: Tyler Reddy -Date: Mon Jul 17 17:11:18 2017 -0700 - - Patched argument type checking logic in function dist_mat_to_vec(), and corresponding unit test is now more thorough (checks the specific error message string). Fixes #1498. (#1500) - -commit 02101295331fba254f6f8945890591ae38834c64 -Author: Richard Gowers -Date: Mon Jul 17 16:31:52 2017 -0700 - - Fixes Issue #1502 (#1503) - - use `np.savetxt(..., header='')` to write header, rather than trying to - open the file handle ourselves - -commit 16eae41a1b195ed411720a7e868d895cafa186b1 -Author: Bansal Utkarsh -Date: Fri Jul 14 19:47:16 2017 +0530 - - Remove mda_nosetests and nose plugins - - Remove nose from dependencies & implement run method - -commit fac3e8d50df64a3d3183b5f548dbaa0e6365a480 -Author: Bansal Utkarsh -Date: Fri Jul 14 19:29:39 2017 +0530 - - Get rid of @attr - -commit 316eb858fbdff6270ad5f4698ad9695888da806a -Author: Jonathan Barnoud -Date: Sun Jul 16 18:23:22 2017 +0200 - - Issue a deprecation warning for Universe. (#1491) - - Fixes #1478 - -commit 8bfa78ae85436ba3d142aeed0070a0431031a0a4 -Author: Max Linke -Date: Sun Jul 16 09:14:24 2017 +0200 - - refactor PCA tests (#1485) - -commit 7173fcf75f59b684deff71e20b48a4b92f64f142 -Author: Utkarsh Bansal -Date: Sun Jul 16 12:09:43 2017 +0530 - - Pytest Style test_xvg.py (#1493) - -commit c3e9cc5ac43c30ce5d7a73b644d39e3833abac87 -Author: Max Linke -Date: Sat Jul 15 17:09:55 2017 +0200 - - print slowest tests (#1486) - - * print slowest tests - - * remove explicit pytest dependencies - - it should be installed automatically by ci-helpers - - * remove pytest-cov and pytest-xdist requirement - - These packages are only giving new runtime options for pytest. The testsuite - can be run without them. - - * remove pytest-raises dependency - - * use SETUP_CMD for ci-helpers to recognize options - -commit e71888e92899b0a6959b1b4b32d434b34d23ef29 -Author: Jonathan Barnoud -Date: Sat Jul 15 12:33:15 2017 +0200 - - Prevent tests from littering (#1490) - - Running the tests creates files that stay after the end: failure.txt, - output.txt, and test.dcd. This commit makes sure that output.txt and - test.dcd are created in temporary directories. failure.txt is only - created when the MDA_FAILURE_TEST environment is set. - -commit 277127c8ace815235784e15a6f154913852023e2 -Merge: a355d99a6 f51f49a61 -Author: Jonathan Barnoud -Date: Fri Jul 14 11:35:07 2017 +0200 - - Merge pull request #1450 from utkbansal/pytest-analysis - - Port analysis module to pytest - -commit a355d99a6ad80f83a6fc94b1035a85fbc947fb25 -Author: Jonathan Barnoud -Date: Fri Jul 14 10:06:11 2017 +0200 - - Fix missing edge case with TypeError on aux (#1484) - - Fixes #1457 - -commit 9f24e0e6ded824f7f96a9a724c93ae583ff409dc -Author: Max Linke -Date: Thu Jul 13 22:29:19 2017 +0200 - - only add a commit if there is something staged - -commit f51f49a61dfe9f980124cd1d91c680d7af1b7862 -Author: Bansal Utkarsh -Date: Thu Jul 13 23:31:33 2017 +0530 - - Removes mda_nosetests - -commit 5f6de0ead8a9820b4101a08f70d5afc3d3954092 -Author: Bansal Utkarsh -Date: Thu Jul 13 18:53:40 2017 +0530 - - Fix test_hbonds.py - - Hack in parameterize - - Cleanup - - Use itertools - - Cleanup - -commit 51e285cb8c608b9543def97f22a116144097423f -Author: Max Linke -Date: Thu Jul 13 18:49:56 2017 +0200 - - add python 3 to travis (#1479) - - * add python 3 - - * no coveralls! - -commit 4b30b98a9cbc41e4a20d0938be4ad4eec6c13700 -Author: Jonathan Barnoud -Date: Thu Jul 13 17:56:03 2017 +0200 - - Fix deprecation warning missfires (#1477) - - * Fix deprecation warning missfires - - `u.segments` and `u.residues` should not issue a deprecation warning. - This commit applies the same strategy than - a9f9655a3b45b8486a1aadb5ad903f8bfe68ef3f to avoid the unwanted warning. - - * Ignore `exec-used` pylint warning in a test - - The exec built-in is used in the tests about the deprecation warnings - for the instant selectors. This causes a warning from pylint as `exec` - can be a security concern in some context. Here, the input given to - `exec` is fully controlled and exec is not more dangerous than typing - the input instructions directly. As `exec` improves the readability of - the tests, this commit disable the warning for the two specific use of - `exec`. - -commit d4b27a6f5bdfeae5bc2a1d8d0332edd7bef758af -Author: Utkarsh Bansal -Date: Thu Jul 13 18:52:54 2017 +0530 - - Pytest Style: test_persistence.py (#1470) - - * Pytest Style test_persistence.py - -commit ae6fca7968e635b77e6de32b31d4a5d7b0e6ed4c -Author: Utkarsh Bansal -Date: Thu Jul 13 17:30:55 2017 +0530 - - Pytest Style: test_log.py (#1467) - - * Pytest Style test_log.py - - * Cleanup - - * Get the error message back - - * Use fixtures - - * Rename variables - - * Fix deprecated warning checks - -commit 26e63326838d8e48c1635983d88896607dbb55df -Author: Utkarsh Bansal -Date: Thu Jul 13 14:08:01 2017 +0530 - - Pytest Style: test_nuclinfo.py (#1469) - - * Pytest Style test_nuclinfo.py - -commit c6106f0d67fe959c20dfa65d519c58b2cda19f93 -Author: Utkarsh Bansal -Date: Thu Jul 13 13:00:01 2017 +0530 - - Pytest Style: test_modelling.py (#1468) - - * Pytest Style test_modelling.py - - * Refactor - - * Remove unused imports - - * rename variables - -commit 4c6bc8b4394128ca70bbc5574dd380b3258155b5 -Author: Utkarsh Bansal -Date: Wed Jul 12 13:41:29 2017 +0530 - - Pytest Style: test_selections.py (#1471) - - * Pytest Style test_selections.py - - * Cleanup - - * Cleanup - -commit 7cb8500a4f8e8c9592f2f24db0a8eecb2b721cfe -Author: Utkarsh Bansal -Date: Wed Jul 12 13:10:31 2017 +0530 - - Pytest style: test_datafiles.py (#1465) - - * Pytest style test_datafiles.py - -commit 4398642f623ff77d2f7bf9083dbc6e52b675c8be -Author: Utkarsh Bansal -Date: Wed Jul 12 13:02:17 2017 +0530 - - Pytest Style: test_deprecated.py (#1466) - - * Pytest style test_deprecated.py - - * Use fixture - -commit 97526a5f8aa06b7c0fc6e2db44dc6e73351bc31d -Author: Utkarsh Bansal -Date: Wed Jul 12 10:56:17 2017 +0530 - - Fix coverage drop in coordinates module (#1441) - - * Fix TestGROReader - - * Fix TestGROWriter - - * Fixes remaining GRO Reader classes - - * Fixes remaining GRO Writer classes - - * Fix test_xyz.py - - * Fix test_memory.py - - * Fix test_xdr.py - - * Band aid fix for TestBaseTimestep - - * Get rid of yield - - * Minor fixes - - * Fix BaseTimestepTest yield cases - - * Refactor - - * Refactor base reader - - * Move fixture to BaseReader class - - * Fix test_getitem - - * Fix TestBaseTimestep - - * Fix dcd tests - - * Try using asser_almost_equals - -commit 5a1b55c6381db06522c3f4dc471ab1dd0303c83b -Author: Utkarsh Bansal -Date: Tue Jul 11 23:54:36 2017 +0530 - - Pytest Style: test_imports.py (#1473) - - * Pytest Style test_imports.py - -commit d996cfe87d1e2238b01290c34108521e594136f9 -Author: Oliver Beckstein -Date: Tue Jul 11 06:02:46 2017 -0700 - - updated README (removed vm) (#1474) - -commit 94faa8c968e6a9c474bc1a108386ddb69a4e02ec -Author: Max Linke -Date: Tue Jul 11 14:55:05 2017 +0200 - - Convert libmdaxdr test (#1442) - - * Use EOFError in libmdaxdr when end of file is reached - - also improves the docs - - * convert libmdaxdr test to proper pytest style - - * update CHANGELOG - -commit 47d8016ed3d0a0eff34591d88c2c1bf1421210cc -Author: Utkarsh Bansal -Date: Tue Jul 11 00:46:16 2017 +0530 - - Pytest Style: test_altloc.py (#1464) - - * Pytest style test_altloc.py - - * Drop the class - -commit 4923639b57e7aecf0fe9829b71abc1c60f5be8fe -Author: Oliver Beckstein -Date: Sun Jul 9 22:17:04 2017 -0700 - - remove unmaintained virtual machines from repository (#1462) - - closes #1461 - -commit d0dfa98321928cbe3cb55484bb101667bc629ad7 -Author: Max Linke -Date: Sun Jul 9 22:37:00 2017 +0200 - - open in 'rt' mode by default - -commit 189df6803a3002ee5fca063d0fa19dc65f0b6d64 -Author: Jonathan Barnoud -Date: Sun Jul 9 22:05:19 2017 +0200 - - Fix comparison of None with int in auxiliary (#1459) - - See #1457 - -commit a952501fef185f7eb9f2eaf9f7d89fe6c71d04c6 -Author: Max Linke -Date: Sun Jul 9 18:58:41 2017 +0200 - - add explicit byte encoding to Amber netCDF files (#1455) - - * add explicit byte decoding to utf-8 to Amber netCDF files for Python 3 - * fix netcdf tests: also need decode('utf-8') for Py3 - * fix usage of deprecated warn function in NCDF logger - -commit cc34959fa025981472cc815b05c355d66c091b51 -Merge: 6ea0eb129 3214bd897 -Author: Jonathan Barnoud -Date: Sun Jul 9 10:58:31 2017 +0200 - - Merge pull request #1458 from MDAnalysis/anyopen-py3 - - anyopen in rt mode - -commit 3214bd8976c1fe3964fc3d9b0275e86b1aa46736 -Author: Max Linke -Date: Sun Jul 9 09:08:16 2017 +0200 - - anyopen in rt mode - -commit 6ea0eb129e16b5e50b2b338dc87bd89c13c6ce47 -Merge: 742d7c460 b4aa1dd23 -Author: Jonathan Barnoud -Date: Sun Jul 9 08:15:17 2017 +0200 - - Merge pull request #1456 from MDAnalysis/testing-deps - - install pytest-raises with setup.py for testing and keep dependencies only in MDAnalysisTests setup.py - -commit b4aa1dd237e2a22a71c9a3590cc417c93d7ad8a4 -Author: Oliver Beckstein -Date: Sat Jul 8 18:04:37 2017 -0700 - - install pytest-raises with setup.py for testing and keep dependencies only in MDAnalysisTests setup.py - - If pytest-raises is not installed, a number of tests fail because - exceptions are not properly caught and recognized. - - Removed explicit testing dependencies from package/setup.py except the - MDAnalysisTests package itself; all required dependencies are solely - defined in MDAnalysisTests's setup.py. - -commit fd129d6545f9432f0ff95c485d5427ebce3b4e39 -Author: Bansal Utkarsh -Date: Sat Jul 8 22:38:22 2017 +0530 - - Fix test_encore.py - -commit 742d7c460badd2e0f73c49fe30bdc4fa62b9dc3b -Merge: 77f5ea460 42c710576 -Author: Max Linke -Date: Sat Jul 8 13:37:55 2017 +0200 - - Merge pull request #1372 from MDAnalysis/dcd-cython-rebase - - DCD-Cython - -commit ebc342e89f8305cd4d05d621a7a164bece424fc6 -Author: Bansal Utkarsh -Date: Sat Jul 8 14:58:54 2017 +0530 - - Fix test_rms.py - -commit 42c71057601f5221904b2fcc2a7f62725fb0b66e -Author: Oliver Beckstein -Date: Sat Jul 8 02:04:08 2017 -0700 - - install hypothesis for tests with setup.py - - (Also added pytest-{cov,xdist} which are not absolutely required but very handy.) - -commit 8cbac38757846443716ceafa97425005842c64a2 -Author: Max Linke -Date: Fri Jul 7 22:51:53 2017 +0200 - - update license header - -commit 9bec7bdcab7ffb80d9adad9fd63ae51994d7df33 -Author: Max Linke -Date: Fri Jul 7 10:05:45 2017 +0200 - - use pytest style for test_dcd - -commit 6423abb30249630205915fb31a673646a49be184 -Author: Max Linke -Date: Fri Jul 7 10:03:05 2017 +0200 - - update test_libdcd with pytest style guides - -commit 25bfb7c0b36e30b9b44834a623fe96299a71cd26 -Author: Max Linke -Date: Fri Jul 7 09:44:45 2017 +0200 - - improve unitcell decoding - -commit 32efca9169a23febbdb5b5c861572eec38d8edae -Author: Max Linke -Date: Mon Jul 3 22:15:04 2017 +0200 - - improve docs for libdcd and DCD - -commit 6f2001f7ecb0f4160e384cf2639a9b4bc4316922 -Author: Max Linke -Date: Tue Jul 4 19:02:32 2017 +0200 - - don't change dt when using nsavc for writing - -commit 23e3d28e76722ed534416eb99a39c7fc9ec2befc -Author: Max Linke -Date: Tue Jul 4 09:50:01 2017 +0200 - - refactor libdcd header API - - We now don't expose the CHARMM bitfield directly anymore in the header. The - bitfield is a internal implementation detail of readdcd.h and the wrong value to - expose to a user of libdcd. Rather we expose `is_periodic` to enable - reading/writing box information. With this change the write/read header - test symmetric now. - -commit 2d2ce49e815808adcd7591cb4eee2fcf3a81cf0b -Author: Max Linke -Date: Tue Jul 4 09:49:56 2017 +0200 - - modify changelog - -commit 619526c385f14d7dfd9e4f6e0891e4bc7c00cd00 -Author: Max Linke -Date: Mon Jul 3 22:15:15 2017 +0200 - - avoid copy in dcd writer - -commit 015f15a736bba3b658df52a90b1dc3b7397470ca -Author: Max Linke -Date: Mon Jul 3 22:08:09 2017 +0200 - - use assert_array_equal - -commit 00970991637a6e0c356e4b742a3b54f268b00655 -Author: Max Linke -Date: Mon Jul 3 22:08:02 2017 +0200 - - update libdcd - -commit ceb7313d516682d8e84911fedc5daa9f2755503a -Author: Max Linke -Date: Mon Jun 26 10:24:19 2017 +0200 - - push test loop into pytest parametrize - -commit ce6573bb28e1823d025427911b0752c5e43b0a61 -Author: Max Linke -Date: Mon Jun 26 09:49:29 2017 +0200 - - add libdcd to rst docs - -commit bd9c425c1845f1369f5e10634209f807ad2453ec -Author: Max Linke -Date: Sun Jun 25 20:19:00 2017 +0200 - - reach 100% coverage of DCD.py - -commit 366290ee18d7847c494dc7cc073cb67849180535 -Author: Max Linke -Date: Sun Jun 25 20:33:36 2017 +0200 - - remove unnecessary check - -commit 717346a7783f2666e4b63398ef959df227d3c9b6 -Author: Max Linke -Date: Sun Jun 25 17:37:28 2017 +0200 - - add Exception names to libdcd docs - -commit 134199ec35db67126f4184dbfbaa1226db6df99c -Author: Max Linke -Date: Sun Jun 25 17:15:14 2017 +0200 - - fixup DCD sphinx error - -commit 7420bd3fbca659dee66a376140c8a033a8c55b12 -Author: Max Linke -Date: Sun Jun 25 17:08:23 2017 +0200 - - uniformly use xyz to refer to coordinates in libdcd - -commit 8ca3fd316ba82b692692bbcbe4938e422b3998c5 -Author: Max Linke -Date: Sun Jun 25 17:04:26 2017 +0200 - - add information about charm bitfield - -commit ad64253a98c74eee0832030bca384900b390d10c -Author: Max Linke -Date: Sun Jun 25 15:59:48 2017 +0200 - - prefer to use format over string interpolation - -commit 76290ee5542bd9393c71b8d1de2c8013583f0bfd -Author: Max Linke -Date: Sun Jun 25 14:20:36 2017 +0200 - - add random unit cell test to test_dcd - -commit 49f3e54880e0e7335016d49475160bb76ef44ac6 -Author: Max Linke -Date: Sun Jun 25 14:20:30 2017 +0200 - - fix DCD writer errors - -commit 36105ae6d2255ef63814cd87317907071b9e6a80 -Author: Max Linke -Date: Sun Jun 25 13:51:17 2017 +0200 - - fixup CHANGELOG & setup.py with rebase cleaning - -commit ae5222986a4d8e9cfbe134ece099182f42537620 -Author: Max Linke -Date: Sun Jun 25 13:48:53 2017 +0200 - - delete old files - -commit 8ed06ce6929a75196f2dc03c23687ec40d74668c -Author: Max Linke -Date: Sun Jun 25 07:03:49 2017 +0200 - - Convert test_libdcd.py to pytest - - - no more test classes - - yapify - -commit 82de16a5b23dbcddb503e7de23a11240d85ff509 -Author: Max Linke -Date: Fri Jun 16 09:30:06 2017 +0200 - - add new timeseries tests to test_dcd - -commit 64093cb18bee0f4674341edfe20f895fd221a666 -Author: Max Linke -Date: Fri Jun 16 08:21:53 2017 +0200 - - fix backwards step in readframes - -commit 3bc9c0296c2eb9504ad07134aafcd7db09620bd6 -Author: Max Linke -Date: Fri Jun 16 08:15:49 2017 +0200 - - add readframes tests - -commit 3d5e2d73c8152958327b26bd8017751414e21695 -Author: Max Linke -Date: Fri Jun 16 07:54:01 2017 +0200 - - reorder tests - - This way the alternatives where we test CHARMM and NAMD are sorted directly after - declaring the initial test class - -commit 11bef65c59d0bb6269648fd877e8d8db13f26ae3 -Author: Tyler Reddy -Date: Thu Jun 15 17:23:48 2017 -0600 - - test_libdcd test_seek_over_max() now appropriately checks for EOFError instead of IOError. - -commit 19316df2b6759e79f791e84c3d0f0496f2235a87 -Author: Max Linke -Date: Thu Jun 15 21:59:09 2017 +0200 - - fix test for dcd - -commit 9f790046ec79a7b7fbdc7f30d189ea970e569dcc -Author: Max Linke -Date: Thu Jun 15 21:59:01 2017 +0200 - - fix error in DCD Reader and remove confusing comment - -commit f9492eedb7796e0b1920e2a8af4536f30db46fe9 -Author: Max Linke -Date: Thu Jun 15 19:46:09 2017 +0200 - - yapify DCD - -commit d3c437dca77213697c3482f4c160b9e340d8b66f -Author: Max Linke -Date: Thu Jun 15 19:45:49 2017 +0200 - - update libdcd and DCDReader docs - -commit eb1c00181c088012ddc69a28401753dd3051f814 -Author: Tyler Reddy -Date: Tue Jun 13 22:49:09 2017 -0600 - - DCD test improvements - - - test_libdcd self.testfile generation switched to os.path.join based on reviewer comments in PR 1372. - - libdcd test_written_unit_cell() adjusted to use assert_almost_equal, as requested by reviewer in PR 1372. - - libdcd test_relative_frame_sizes() has simplified assert statement based on reviewer request in PR 1372. - - test_libdcd.py adjusted with (commented) knownfailure decorators for appropriate unit cell writing tests as requested in PR 1372. Comments are used because the tests pass, but we do not explicitly support this writing behavior. - - Added knownfailure unit tests for unit cell writing in unsupported formats. - - Clarified header writing unit test comments as requested by reviewer in PR 1372. - -commit f0170be38eaf87f83a807c8846bf244fbc188ba4 -Author: Max Linke -Date: Sun Jun 4 18:16:38 2017 +0200 - - update changelog - -commit 9b1d607146ad7bb0fb77fe62e345c7c5909d6dbf -Author: Max Linke -Date: Sun Jun 4 18:10:54 2017 +0200 - - fixed known failure in transition - - fix unit tests - -commit 2c754d4da83fd850011669c021dc6c9c7e6a578f -Author: Max Linke -Date: Sun Jun 4 17:38:21 2017 +0200 - - copy timestep - - this avoids that ts points to the same reference in a loop. - -commit 66d42a2caadbfe76b10642a06c3e1b2c77d98599 -Author: Max Linke -Date: Fri Jun 2 23:10:19 2017 +0200 - - add docs - -commit 9a07c00bf8ce10808671e0aa2de74f70b6901d97 -Author: Max Linke -Date: Fri Jun 2 19:50:04 2017 +0200 - - speed up - -commit 51ba896c92ad20c4a2487f1678f397be88a53f97 -Author: Max Linke -Date: Fri Jun 2 19:30:38 2017 +0200 - - allow subset reading in readframes - -commit 4d0a44f1147cd6a69b6dc4766c0d7934247e8081 -Author: Max Linke -Date: Fri Jun 2 19:26:17 2017 +0200 - - support ordered readframes - -commit 4c308c7ecb488a4cb2a6a8c08b94aa3e7204fffe -Author: Max Linke -Date: Fri Jun 2 14:21:21 2017 +0200 - - fix unitcell initialization - -commit 8ba9f19ff05f95e79ea3f08edbf6b2a1f104874c -Author: Max Linke -Date: Fri Jun 2 13:51:31 2017 +0200 - - remove dcd from timestep API test - -commit 979c8dd4bc28ea6aff200d43f910085e6f7e4593 -Author: Max Linke -Date: Fri Jun 2 13:41:36 2017 +0200 - - fix linter problems - -commit f1895105498f37a00c02f63f468542ebc5282a69 -Author: Max Linke -Date: Fri Jun 2 08:23:19 2017 +0200 - - have readframes with start,stop,step - - this will support slices now. Saves memory - -commit 65ea67b4058a7a7d365c6c4b80198d4611b44ef1 -Author: Max Linke -Date: Fri Jun 2 08:05:41 2017 +0200 - - fix timeseries - -commit 64098d8986cc121799a55fe66427e20e7e3bdbab -Author: Max Linke -Date: Fri Jun 2 08:05:33 2017 +0200 - - fix ndims DCD reader error - -commit e651f598613c8408389b6758db13cb7b6dc0cd2d -Author: Max Linke -Date: Thu Jun 1 22:52:09 2017 +0200 - - use timeseries - - doesn't work right now - -commit fcfbf5da36e5e7c03d6ba2fc037822390ebab25f -Author: Tyler Reddy -Date: Thu Jun 1 22:21:59 2017 +0200 - - reactivate hypothesis tests - -commit b409b20898e5ecd845279eabccee56069e35de2c -Author: Max Linke -Date: Thu Jun 1 21:18:17 2017 +0200 - - general clean up - -commit ccbf0ba44e87de16d906cd008337d3b2514ab1bd -Author: Max Linke -Date: Tue May 30 17:56:22 2017 +0200 - - DCD header improvements - - - add header writing and getter methods - - fix headers in libdcd - - use header dictionary - - make header writing public - -commit 95a58085cb3138da0e64d562ad1dc649bd72d99f -Author: Max Linke -Date: Thu Jun 1 15:56:46 2017 +0200 - - add hypothesis to travis tests - -commit 4ea19bb9fc276aa96047fe6ee5f8d01ba18f13d0 -Author: Max Linke -Date: Tue May 30 17:33:56 2017 +0200 - - move unitcell handling from libdcd to DCDReader - - - remove unitcell handling from libdcd - - add dimensions handling into MDAnalysis DCD reader - - fix box tests for libdcd - -commit 911bff5b3c76d99d2d2c0b4ebaba9230e90e3406 -Author: Max Linke -Date: Tue May 30 17:32:29 2017 +0200 - - remove old module from setup.py - -commit 188813003f13e6e3732221f7f3c98b7c2b97f7cf -Author: Max Linke -Date: Tue May 30 08:19:33 2017 +0200 - - add header property - -commit e64127fc30652049e5aa76f02842ddc4f68e2da6 -Author: Max Linke -Date: Tue May 30 08:11:09 2017 +0200 - - remove duplicate tests - -commit 9e75910afe9c58b8031b15c32a508e71fd89f880 -Author: Max Linke -Date: Tue May 30 08:05:36 2017 +0200 - - remove old C dcd reader - -commit 71668a9017cf49dfbb76466996e80c1b4be1f90f -Author: Max Linke -Date: Tue May 30 08:04:22 2017 +0200 - - fix up docs - -commit 473f1c548c144c46e5c407e4474c97604979e955 -Author: Max Linke -Date: Tue May 30 07:58:49 2017 +0200 - - enable new style reader/writer tests - -commit 54abc2dbeef52e0e5faf4df22141c53277566178 -Author: Max Linke -Date: Mon May 29 21:29:06 2017 +0200 - - fix failing tests - -commit e06b0ff94d322df6f0e596444d1e3e9db38f5d2d -Author: Max Linke -Date: Sun May 28 15:38:15 2017 +0200 - - Fix unitcell handling - - Unitcells are not handled uniformly. We take a [A, B, C, alpha, beta, gamma] - and return the same as well. - -commit 5fb38787521b5092c4ed07c3c833f889ba4b8a13 -Author: Max Linke -Date: Sun May 28 15:39:52 2017 +0200 - - improve dt unit handling - -commit d446fcd6dd69cde2f0914bef10d7ee7deb0542be -Author: Max Linke -Date: Sun May 28 14:45:11 2017 +0200 - - fix unicode name in open - -commit e2e8e84aed4ed576abe9542167331c09648b8456 -Author: Max Linke -Date: Sun May 28 13:54:48 2017 +0200 - - start work on new dcd reader - -commit 23272c5c71926d283b906f37d3ee368e08eca3f4 -Author: Max Linke -Date: Sun May 28 13:36:59 2017 +0200 - - deactivate correl tests for now - -commit f919d79cafcc32a3f8f397a6ffb7ea7953c0b500 -Author: Max Linke -Date: Sun May 28 13:27:23 2017 +0200 - - restucture libdcd test order - -commit 7632871f2fd3af89a9b84dfd9286a9b7e94d5fbe -Author: Max Linke -Date: Sun May 28 13:24:53 2017 +0200 - - remove double definition - -commit 2596974b0de335d17079d6bd4723c20e4fc9e7a7 -Author: Max Linke -Date: Sun May 28 13:23:18 2017 +0200 - - use sensible warnings when only a header is written - - We shouldn't do that but other programs might produce a dcd with a header and - no frames stored. - -commit e4382e3ef440a0f37a5a3c4705b9ad827244f6e7 -Author: Max Linke -Date: Sun May 28 13:12:38 2017 +0200 - - check tell in iteration - -commit 24656c32233cd31fdf33b964594095c723f5eb33 -Author: Max Linke -Date: Sun May 28 13:03:38 2017 +0200 - - add write dtype handling - -commit d14ffb5e632872e4fac5a13a5e7b608e001ffd27 -Author: Max Linke -Date: Sun May 28 12:11:23 2017 +0200 - - fix write_file function - - use testfile from function arguments - -commit c8d50d224cfb4b486722c14c33f4c0cccdd8d038 -Author: Tyler Reddy -Date: Fri May 26 11:36:34 2017 -0600 - - Added new property-based unit test, test_written_remarks_property(), which reveals that DCDFile is not able to handle writing when an empty REMARKS string is provided. - -commit b26de04de28db57e451341b4b10ffdfdd6bb4a22 -Author: Max Linke -Date: Tue May 23 14:26:26 2017 +0200 - - Refactor libdcd test - - - remove TestCase usage - - use context manager with short lived files - - stop leaking of file dscriptors - -commit 9091ac932729002fdb34e6d34d173c72fd723e9b -Author: Max Linke -Date: Mon May 22 09:20:00 2017 +0200 - - fixes in libdcd - - fix repeated iteration of dcd file - fix repeated context manager of dcd file - -commit 6d7e8b6b9feec3bfc180d2ad81b872c22a9b13d8 -Author: Tyler Reddy -Date: Wed May 10 22:15:45 2017 -0600 - - DCDWriteTestRandom now pins down the random seed for testing robustness. - -commit 0d605769a6c871138f17d136ea0f5a36dd2a63f7 -Author: Tyler Reddy -Date: Wed May 10 22:02:23 2017 -0600 - - Simplified code in test_iteration() unit test based on PR comments. - -commit 021665d69186e430cc729df9038fe66eae209540 -Author: Tyler Reddy -Date: Wed May 10 21:55:06 2017 -0600 - - test_header_remarks has been adjusted to perform a direct string comparison, as requested in PR comments. - -commit f247e7b2449dff6a0337892c1ae5bd5b6874366e -Author: Tyler Reddy -Date: Tue May 9 15:06:10 2017 -0600 - - DCD unit cell data handling and tests - - - The use of read_dcdsubset in DCDFile Cython code has been replaced by the expected read_dcdstep. Unit cell handling behavior in the latter C-level function has been patched to reflect previous adjustment in MDA relating to DCD file unit cell formatting. All unit tests passing, including the reading of the NAMD DCD unit cell info - - Testing of unit cell data writing has been restricted--NAMD unit cell data writing is not currently supported. - - Adjustments to DCD unit cell handling code that enable a read-write-read unit cell cycle for the DCD test file, and also allow a read-write-read cycle for randomly generated charmm unit cell data. - - Added Charmm36 triclinic trajectory data unit tests -- all of them pass. - - Removed extraneous unit cell handling code from C-level read_dcdsubset. - -commit 0d43e4f0ada0fd10fcd24d73c11e7d70fffef76c -Author: Tyler Reddy -Date: Fri Apr 21 16:01:39 2017 -0600 - - added DCD regression tests against data from old DCDReader - - Added unit test test_read_coord_values, and associated testing data, for DCDFile reading fidelity. - test_libdcd.py adjusted to allow pickle to open new test data under python 2 and 3 execution. - The testsuite included data now covers Python pickle files as some were added for the new DCDFile framework testing. - DCDFile unit testing now uses .npy for archival coord storage instead of pickle, for long-term format stability reasons. - -commit 60929805d8af8f22d822a10675c8555a83fd5e0e -Author: Tyler Reddy -Date: Thu Apr 20 22:34:02 2017 -0600 - - Attempted formatting fixes in test_libdcd.py. - -commit 6c7a691d37dde933a99958dab5b41abaab0ad232 -Author: Tyler Reddy -Date: Thu Apr 20 19:32:12 2017 -0600 - - Patched issue with frame iteration in test_coord_match -- all unit tests now pass. - -commit fdb768578ed13026dbf53504192a2963a77e3826 -Author: Tyler Reddy -Date: Thu Apr 20 17:14:25 2017 -0600 - - Removed spurious header writing; fixed an issue in write() method of DCDFile such that single-frame NAMD DCD trajectory writing exactly reproduces the coordinates from the input file. - -commit d3573e11f7d84fb91c316fb9209fd9dac1c77c81 -Author: Tyler Reddy -Date: Thu Mar 16 17:55:43 2017 -0600 - - current_frame variable is now updated in write method of DCDFile. - -commit 7bcec2666dd87fc5e86d6867bff3fa9ba420f4a4 -Author: Tyler Reddy -Date: Thu Mar 16 17:38:08 2017 -0600 - - DCDFile now allows overwriting, based on feedback in PR#1155. - -commit 04de2c087d5d00c9aa8c7ad1bdb408b3fd67cffe -Author: Tyler Reddy -Date: Thu Mar 16 17:30:54 2017 -0600 - - Replaced a standard library assertion with a numpy assertion in the libdcd test suite, based on reviewer feedback in PR#1155. - -commit ced318bb4168e6b4001d435ad0bbe17487db837a -Author: Tyler Reddy -Date: Thu Mar 16 17:21:58 2017 -0600 - - DCDFile variables that are testing-only / implementation details are now prefixed with an underscore in response to comments in PR#1155. - -commit 0020b3e50bf096a75e02c035d1abaea0b5c5327f -Author: Tyler Reddy -Date: Thu Mar 9 13:55:15 2017 -0700 - - ENH: Added proper DCDFile remarks / header string handling -- all unit tests now pass in python 2.7 & 3.5 - -commit a93d37c49ff7beb27e68cf4e34c162eb3aefa0c5 -Author: Tyler Reddy -Date: Mon Feb 13 11:52:46 2017 -0700 - - DCD unit test improvements - - ENH: Added unit tests for NAMD-format DCD file input to DCDFile. Minor adjustments to code to handle new format. One unit test currently fails -- writing the NAMD-formatted REMARKS section to a new DCD file. - ENH: Added more thorough / correct unit test code for header remarks section string handling in test_libdcd.py, and removed extraneous debug print statements. - ENH: patched minor error from accidental deletion in test suite for new DCD code. - -commit c783f2d47d30c04c80506ed94a87bc344d719a59 -Author: Tyler Reddy -Date: Sun Jan 29 19:51:21 2017 -0700 - - DCD writing - - ENH: DCDFile now has an early draft of the write() method & there's a crude associated initial unit test. - ENH: added additional arguments and docstring to write method of DCDFile, based on the write method in libmdaxdr.pyx. - ENH: The write method of DCDFile now calls the header writing code first, as required. Also, fixed a unit test to account for the recently increased number of arguments accepted by the write method of DCDFile. - ENH: DCDFile unit tests updated to reflect the fact that the write method can now be called with various arguments, without raising an exception (though the actual DCDFile that is written is not quite right yet). - ENH: DCDFile write method arguments now accepting python input, though the C-level method is temporarily disabled. - ENH: Reactivated the write_dcdstep C code in the write method of DCDFile. A unit test modification confirms that a binary output file is produced by the latter, although it is not yet a proper DCD file as DCDFile can't read it back in. - ENH: Initial cleanup of ctypedef statements in libdcd.pyx based on reviewer comments in PR#1155. - ENH: The DCDFile write method now requires the double type for box and unit tests have been adjusted accordingly, based on reviewer comments in PR#1155. - ENH: Expanded the DCDFile header writing capabilities. - ENH: Added more unit tests for DCDFile write() method. - use consistent double dimensions - ENH: Added 2 new unit tests for DCDFile writing behaviour. - ENH: Added initial code to allow REMARKS section of DCD file written by DCDFile to be user-controlled. Currently, the title and time fields from the C-header file seem to get intermingled in the .remarks property of the DCDFile read back in. - ENH: General cleanup of DCDFile write() method arguments in code proper and unit tests. - ENH: Removed an extraneous variable from the setUp of DCDWriteTest. - ENH: python 2/3 string handling compatiblity fixes for DCDFile. - ENH: DCDFile writing of REMARKS section has been adjusted to allow specification of a properly formatted string up to 160 chars in length. - ENH: Added 3 new writing-related tests for the new DCDFile object. - ENH: The number of 80 character title strings written by default to new DCD files has been increased to 3, allowing exact preservation of the remarks section from the MDA test DCD file when writing. - ENH: the DCDFile firstframesize property has been patched to the apparently correct arithmetic. - -commit 5df264e59a988b3a43f84632d4e25614cfc2750a -Author: Tyler Reddy -Date: Sun Jan 29 19:29:32 2017 -0700 - - ENH: Fixed an IOError message in libdcd.pyx that referred to TRR files instead of DCD files. - -commit 1475c996e0835db3cddf9bc7f769398dd907f990 -Author: Tyler Reddy -Date: Sat Jan 28 19:31:05 2017 -0700 - - ENH: New DCD reading code now appears to handle unit cell information properly. All tests in test_libdcd.py pass in python 2.7 and 3.5. - -commit 09ff489b746b9a0a695548446f44430e063227a3 -Author: Max Linke -Date: Mon Jan 16 13:03:59 2017 +0100 - - compile _dcdmodule again - - This will help to pass travis tests during development. - -commit 6182da5749bf937cd3742ef7dd3a1fca6734f5df -Author: Tyler Reddy -Date: Sat Jan 14 16:08:27 2017 -0700 - - ENH: added py3 compatibility for block_import. - -commit c749a134696e76ab438fc974017021570887f140 -Author: Tyler Reddy -Date: Sat Jan 14 16:05:41 2017 -0700 - - exception handling in DCD - - ENH: Replaced all usage of RuntimeError exception with IOError in libdcd.pyx, for consistency with MDA codebase. - ENH: test_libdcd.py now correctly expects IOError instead of RuntimeError from libdcd. - -commit ab0f981f7b1cea73e4de1f270ff9ce8216bf118d -Author: Tyler Reddy -Date: Sat Jan 14 09:06:34 2017 -0700 - - ENH: restored DCD-related import checking in MDAnalysis/coordinates/__init__.py after upstream python 3 fixes. - -commit a2ccb3d367cbfd67b4c36a88f4e1bbd0bde90cdc -Author: Tyler Reddy -Date: Tue Jan 10 16:05:52 2017 -0700 - - initial work on DCD writing - - ENH: rebase against develop / handle merge conflicts / remove old DCD imports from package. - ENH: Very early draft of DCD header writing Cython code and very crude associated unit test. - ENH: libdcd.pyx now avoids file overwriting and handles writing more robustly for _write_header. - ENH: Updated DCD unit tests to accommodate improvement to DCD file header writing. - -commit f4d7740755476ce94e944fd9c96e70f40011926c -Author: Tyler Reddy -Date: Fri Oct 21 16:45:15 2016 +0100 - - TST: Added first draft of testing module for new Cython-based DCD file handling interface. - - TST: All libdcd unit tests now pass, except one related to unit cell dimensions. - TST: Added several more unit tests to test_libdcd.py. - TST: updated unit tests to reflect appropriate Error raising for test_read_write_mode_file and test_open_wrong_mode. - -commit 9e40e7aadf3c1e2847778c908be60e90889ea790 -Author: Max Linke -Date: Sat Oct 1 22:40:30 2016 +0200 - - implement frame reading - - - estimate number of frames - - work on read_next_frame - - improve reading API - - finish reading and iteration protocol - - add seek support - -commit 671f1b46a1ee62bea0573260ccf1411039721e4a -Author: Max Linke -Date: Thu Jun 30 21:45:36 2016 +0200 - - new Cython-based DCD file handling code - - first dcd stumb cython file - first working darft of dcd reimplmentation - This is a good wirst step - open and close dcd files - add context manager support - remove pass statement - correctly handle is_open flag cases - start dcd read header stub - add include guards for fastio.h - read DCD Header - free memory when closing - remarks handling - comment all the things - convert remarks to python strings - make n_atoms public in dcd - make delta public - make more stuff public - periodic property - -commit 77f5ea460a278a13f3cfe8ba2a5137632fc4c582 -Author: Matteo Tiberti -Date: Mon Jun 12 13:14:31 2017 +0100 - - fixed ENCORE compilation warnings - -commit 566bcca95dcc98e75c0b6c2dc855ef4939b4cd43 -Merge: b97f2abd7 3860ccd63 -Author: Oliver Beckstein -Date: Mon Jul 3 12:40:16 2017 -0700 - - Merge pull request #503 from MDAnalysis/scipy-ncdf-debug - - closes #506: Replacing netCDF4 with scipy.io.netcdf - -commit 3860ccd63d7f35612cc16281173de9309dc89ca2 -Author: Oliver Beckstein -Date: Sun Jul 2 20:28:18 2017 -0700 - - removed bundled lib.netcdf - - We do not need the copy of of scipy.io.netcdf that was added in - 68ff0d5709052025ffff6ea3cc1a135b3288fd06 because scipy is now - a full dependency (see #1361) - -commit 2b16b6abede4ae67a0c59f3deaf67a33aa7cc1c1 -Author: Oliver Beckstein -Date: Fri Jun 30 00:34:55 2017 -0600 - - use netcdf for reading Amber netcdf but netCDF4 for writing - - - closes #506 - - netcdf reads MUCH faster than netCDF4 but writes MUCH, MUCH - slower than netCDF4: always read with netcdf but write with - netCDF4 if available, otherwise use slow netcdf and warn - - implements @swails 's solution from ParmEd/ParmEd#722 -- thank you!! - - minimal testing: write the same trajectory with netcdf and with - netCDF4 - - NOTE: netCDF4 is not installed by default, use the re-introduced - [AMBER] install target - - pip install MDAnalysis[AMBER] - - to request its installation but Amber users should also be aware - of potential issues with the bundled netcdf library of Amber; see - https://github.com/MDAnalysis/mdanalysis/issues/506#issuecomment-225081416 - for details - - removed zlib and cmplevel kwargs from NETCDFWriter (only used with netCDF4) - - comprehensive docs with background and reference to #506 - - updated CHANGELOG (@tylerjereddy and @orbeckst as authors) - -commit 17a9a47f80e50d523e5f476302174bf1efe8d9fc -Author: Bansal Utkarsh -Date: Mon Jul 3 04:27:26 2017 +0530 - - Delete useless file - -commit 123139f9f4225c40f680b7e9458c5a0e5b79f517 -Author: Bansal Utkarsh -Date: Mon Jul 3 04:25:30 2017 +0530 - - Shift analysis to PYTEST_LIST - -commit 1f0d2f96cc5c437c2ffacf7316deb457820b8695 -Author: Bansal Utkarsh -Date: Mon Jul 3 04:23:55 2017 +0530 - - Partially fix test_rms.py - -commit e025e639fb4247b27aa1f3106e37ab2fba8434e6 -Author: Bansal Utkarsh -Date: Mon Jul 3 04:20:00 2017 +0530 - - Fix test_rdf.py - -commit 0b5aced3d0be099d4fe7cd69526d6d9ad803d0bd -Author: Bansal Utkarsh -Date: Mon Jul 3 04:18:03 2017 +0530 - - Fix test_psa.py - -commit 80c4cba43d485bf5e923753ffe727f243741ff74 -Author: Bansal Utkarsh -Date: Mon Jul 3 04:14:37 2017 +0530 - - Fix test_persistencelength.py - -commit f3946f3c9c38f6aed74a9eaaba7ac4df84b2c097 -Author: Bansal Utkarsh -Date: Mon Jul 3 04:12:51 2017 +0530 - - Fix test_pca.py - -commit a7f050eacbbcfe2bc6f2423bc9caaf02ec02e3a1 -Author: Bansal Utkarsh -Date: Mon Jul 3 04:12:00 2017 +0530 - - Fix test_nuclinfo.py - -commit c9f2038d43c74f6ae9eaf3412e4026fb48916b3b -Author: Bansal Utkarsh -Date: Mon Jul 3 04:09:45 2017 +0530 - - Fix test_hydrogenbondautocorrel.py - -commit 2deec4e8f8f2847aa323e6b188721fd2b86d07ca -Author: Bansal Utkarsh -Date: Mon Jul 3 04:05:33 2017 +0530 - - Partially fix test_hbonds.py - -commit c1e7cf2299979e5da83019b4f5f61e4c0e6c7197 -Author: Bansal Utkarsh -Date: Mon Jul 3 04:02:18 2017 +0530 - - Fix test_gnm.py - -commit ed4c80ad5101a156309a9276304beaeab0bc47bd -Author: Bansal Utkarsh -Date: Mon Jul 3 03:50:02 2017 +0530 - - Fix test_diffusionmap.py - -commit c773c0f3e9a9d543b85c756bb091a515dbcf9bec -Author: Bansal Utkarsh -Date: Mon Jul 3 03:47:13 2017 +0530 - - Fix test_density.py - -commit 60cb030f305322c11e7bf29649078c6c2f6aca71 -Author: Bansal Utkarsh -Date: Mon Jul 3 03:44:50 2017 +0530 - - Fix test_contacts.py - -commit 3b4841b22805bb5234b90c426a4bfecea79b8025 -Author: Bansal Utkarsh -Date: Mon Jul 3 03:39:51 2017 +0530 - - Fix test_base.py - -commit f0a8204194548c25328921b0553af730535cf793 -Author: Bansal Utkarsh -Date: Mon Jul 3 03:37:02 2017 +0530 - - Fix test_align.py - -commit b97f2abd7463a1f4a6750ec44385385061839156 -Author: Utkarsh Bansal -Date: Sun Jul 2 22:46:35 2017 +0530 - - Port core module to pytest (#1443) - - * Fix test_group_traj_access.py - * Move core to PYTEST_LIST - * Fix test_atom.py - * Fix test_atomgroup.py - * Fix test_atomselections.py - * Fix test_groups.py - * Fix test_index_dtype.py - * Fix test_residue.py - * Fix test_residuegroup.py - * Fix test_segment.py - * Fix test_segmentgroup.py - * Fix test_topology.py - * Fix test_topologyattrs.py - * Fix test_topologyobjects.py - * Fix test_universe.py - * Fix test_updating_atomgroup.py - * Use @pytest.mark.skipif in place of @dec.skipif - -commit dbdaf609dbf591db695ccaf2e0f1f02f79ebbbfe -Author: Oliver Beckstein -Date: Sat Jul 1 02:22:08 2017 -0600 - - install pytest >= 3.1.2 (#1447) - - Fixes #1438 - -commit 68ff0d5709052025ffff6ea3cc1a135b3288fd06 -Author: Oliver Beckstein -Date: Thu Jun 29 22:15:49 2017 -0600 - - added scipy.io.netcdf (v0.19.1) as lib.netcdf (fallback for Amber Reader/Writer) - - - netcdf.py was added as a fallback in case scipy.io.netcdf is - not available - - adjusted imports (e.g. use six instead of scipy._lib.six) - - small doc string changes - - The Amber netcdf reader will try to load scipy.io.netcdf first - but will use MDAnalysis.lib.netcdf if scipy is not available. - - Added the test_netcdf.py file as test_scipy_io_netcdf.py and the - example_1.nc data file; adjusted the test to use tempdir and - other MDAnalysis conventions. lib.netcdf is thus always tested. - - Removed the skipif decorators from all Amber NC tests because - from now on, Amber trajectories should always be readable and - writable. - - Fixed test failure testing NC dimensions attributes (with - scipy.io.netcdf) - - Removed setup.py [AMBER] install target, which installed scipy, because - scipy is a required dependency since 0.16.2 - - netcdf tests run under pytest - - updated test MANIFEST to ensure that everything is included - -commit 31e5e88a757ab8f219288402294012d92e0d85a7 -Author: Oliver Beckstein -Date: Tue Dec 1 10:54:27 2015 -0700 - - NCDFReader supports mmap kwarg and tests - - - Note: default is None so that for files mmap=True and for file-like objects - mmap=False, as described for http://docs.scipy.org/doc/scipy-0.16.0/reference/generated/scipy.io.netcdf.netcdf_file.html - -adapted netcdf float32 test for scipy.io.netcdf - NOTE: currently fails for me on Linux (which might explain - problems in #551) with the dtype('>f4') instead of - np.float32 == dtype('f4') (i.e. - big-endian) whereas the native np.float32 is little-endian (' -Date: Mon Oct 19 17:46:16 2015 -0700 - - replaced netCDF4 with scipy.io.netcdf (issue #506) - - - removed all imports of netCDF4 - - API is different (less feature rich in the pure python - implementation) so it is not straightforward to support - both netCDF4 and fall back on scipy.io.netcdf (or perhaps - even pupyere, which is a single-file package from which the - scipy code originated) - - uses float32 for - - positions - - velocities - - forces - (port of resolution of issue #518) - - change NCDFReader, NCDFWriter and test_netcdf - - see discussion of issue #506 for performance benchmarks - - fixed skipif in netcdf tests - -commit be8db1cc1955927320eb952bf12dfbaf191539c6 -Author: Utkarsh Bansal -Date: Wed Jun 28 16:21:54 2017 +0530 - - Port auxiliary module to pytest (#1439) - -commit ea708b09d75ded215e541175c023276a9afc72f7 (tag: release-0.16.2) -Author: Richard Gowers -Date: Tue Jun 27 11:16:04 2017 +0100 - - Updated c sources for 0.16.2 release - -commit 3fa9bf74879977f07d3b854083633ef1ebb0ca43 -Author: Richard Gowers -Date: Tue Jun 27 11:11:55 2017 +0100 - - Bumped version to 0.16.2 release - -commit 5b55e0e1f247e2030b239596b8a9f685f1d75516 -Merge: 723cd8985 ae72fe9a7 -Author: Richard Gowers -Date: Tue Jun 27 11:08:34 2017 +0100 - - Merge pull request #1421 from MDAnalysis/release-0.16.2 - - Release 0.16.2 - -commit ae72fe9a7b8d953a8e34e2b37d3999dfa3f38f6d -Merge: f8464279f 723cd8985 -Author: Richard Gowers -Date: Tue Jun 27 10:14:28 2017 +0100 - - Merge branch 'master' into release-0.16.2 - - Conflicts: - package/CHANGELOG - -commit ea608e83147d6d7514e88e5bcf3562bb78e5e9c5 -Author: Jonathan Barnoud -Date: Mon Jun 26 07:27:35 2017 +0200 - - Make topology pass tests in python 3 (#1436) - - Tests for the topology module now pass on python 3. This especially fix - the issue of topology attribute types (bytes/string) for TOP, XVG, and - TPR (see #1363). - -commit 62dbab815d34f8fa5ba0a8c5455f731e74ae18f7 -Author: Max Linke -Date: Sun Jun 25 17:52:01 2017 +0200 - - pytest-raises is not available on conda - - I have a feeling that conflicts in the installation drastically drive up the - time needed for ci-helpers to run conda installation. - -commit 2d969b71e647c903008ffb411e0c27e94652a155 -Author: Utkarsh Bansal -Date: Sun Jun 25 20:50:29 2017 +0530 - - Run the pytest testsuite in parallel (#1418) - -commit e9a32c50d5ae2a8e9ab7d06bb3cd203b51667bd0 -Author: Jonathan Barnoud -Date: Sun Jun 25 12:38:37 2017 +0200 - - Fix python 3 imcompatibilities in core (#1435) - -commit 0c8522c7e4a312172fc1bbe0f0d3accfe2505fd9 -Author: Bansal Utkarsh -Date: Fri Jun 23 22:05:02 2017 +0530 - - Remove useless file - - Fix changelog - -commit 647698732ee364ae1511ed2b525abcf2c8011371 -Author: Richard Gowers -Date: Thu Jun 22 11:06:30 2017 +0100 - - Added pytest-raises - - Converted test_units to use parametrize - - Some hacking of test_distances to use pytest features - - Completed moving test_distances to pytest style - - rewrote test_transformations into pytest style - -commit 18bbfd3df05f61c6c37a6f0412b4b9bf671c83c8 -Author: Bansal Utkarsh -Date: Thu Jun 22 00:12:20 2017 +0530 - - Port utils to pytest - - Move utils module to run with pytest - - Get rid of staticmethods - - Fixed import ordering - -commit fe0b8867ba391f9fa79126e927b2804ebb53c61f -Author: Jonathan Barnoud -Date: Sat Jun 24 16:01:47 2017 +0200 - - Fix a syntax error in MDAnalysis.__init__ (#1432) - - * Fix a syntax error in MDAnalysis.__init__ - - The PR #1375 introduced a syntax error in MDAnalysis.__init__. This - commit fixes the defective line. - - * Remove deprecation test about Timeseries collection - -commit f8464279fa4f95ffba0e18d5c77a4ca0c9c56e07 -Author: Max Linke -Date: Sat Jun 24 14:09:41 2017 +0200 - - add @utkbansal to changelog - -commit ff3e4ebea208b8a168249183ea309dae4592bde2 -Author: Richard Gowers -Date: Sat Jun 24 12:24:35 2017 +0100 - - Fixing up CHANGELOG (#1430) - - CHANGELOG took a battering, this fixes it - -commit c5479f9bd632c265497dd99689a38da3126fcaa1 -Author: Max Linke -Date: Sat Jun 24 13:06:26 2017 +0200 - - Remove planned deprecations (#1297) - - * remove old analysis class - - * remove deprecations in rms.py - - * remove deprecated rms_fit_trj - - * Remove tests - - * remove 0-based index for hbond - - also cleans up the docs - - * remove old contact docs - - * update CHANGELOG - -commit d99abba565f051747bbd8dd0b1139e74cd91b02e -Author: Max Linke -Date: Sat Jun 24 13:01:16 2017 +0200 - - remove TimeseriesCollection (#1375) - - * remove TimeseriesCollection - - * update CHANGELOG - -commit 3cb61d67c0ff40f4ee744886c1304b0110feda50 -Merge: 01bd06604 46bc9857c -Author: Richard Gowers -Date: Sat Jun 24 11:56:28 2017 +0100 - - Merge pull request #1427 from MDAnalysis/fix-trz-endian - - Fix trz endian - -commit 46bc9857cc1fa2c8882e8a91a5a031bb25a15581 -Merge: 3f5874047 01bd06604 -Author: Richard Gowers -Date: Sat Jun 24 11:55:32 2017 +0100 - - Merge branch 'develop' into fix-trz-endian - -commit 01bd06604a4236a60aecfa63bf71df1cf23c050f -Author: Utkarsh Bansal -Date: Sat Jun 24 16:20:13 2017 +0530 - - Port coordinates module (#1414) - - Moved coordinates tests to use pytest - -commit c27ace3e653d5189aaa1f9b1f005c04515aa02e6 -Author: Utkarsh Bansal -Date: Sat Jun 24 16:19:18 2017 +0530 - - Port topology module (#1420) - - * Port topology to pytest - -commit 47f956f430fa2554e61071507608b152acb253b1 -Author: Max Linke -Date: Sat Jun 24 12:47:35 2017 +0200 - - update version number to 0.17.0 (#1426) - -commit 3f5874047398087c2189ae44410c69b8885e7318 -Author: Dominik 'Rathann' Mierzejewski -Date: Thu Jun 22 13:19:09 2017 +0200 - - fix TRZ file reader on big-endian arches - - - Numpy dtype int (iN) and float (fN) specifiers assume native-endian - by default, so force them to be little-endian. - - Closes #1424. - - added CHANGELOG entry and docs - -commit 853447cad69746f7c3cd93ba717a6c4806b5db3a -Merge: 87dbe0ed4 f2f45f87e -Author: Max Linke -Date: Thu Jun 22 16:09:04 2017 +0200 - - Merge pull request #1404 from MDAnalysis/issue-1159-analysis-deps - - make scipy and matplotlib required dependencies (#1159) - -commit f2f45f87e51de55e683a108fd632e00f51442c44 -Author: Max Linke -Date: Sat Jun 17 13:38:24 2017 +0200 - - minor clean ups - -commit 677924098bd919d1a52142ebc7c3b6b822e9e5d6 -Author: Oliver Beckstein -Date: Thu Jun 15 20:44:17 2017 -0700 - - removed conditional skipping of tests when scipy or matplotlib are missing - -commit a56ec2a1425e01c59c1b2138df3d2a390efa416b -Author: Oliver Beckstein -Date: Thu Jun 15 19:37:48 2017 -0700 - - scipy and matplotlib are imported at top in analysis - - - updated all modules - - removed any code that guards against scipy or matplotlib import - - conforms to style guide https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide#module-imports-in-mdanalysisanalysis - - fixes #1159 - - fixes #1361 - -commit 4eab969e90205d318eb93ff7e602acd4fc91e25f -Author: Oliver Beckstein -Date: Thu Jun 15 17:18:13 2017 -0700 - - make scipy and matplotlib full dependencies (#1159) - -commit 87dbe0ed4108d9b3db6535edfa63110c155b9d49 -Author: Utkarsh Bansal -Date: Wed Jun 21 22:39:34 2017 +0530 - - Flip formats module to run using pytest (#1417) - -commit fba80e2f7237a3218bf646065ba586ec79a2ce66 -Author: Utkarsh Bansal -Date: Wed Jun 21 16:38:59 2017 +0530 - - Port lib/test_util.py to pytest (#1413) - -commit 85c0c561761a704c57a6eac9be35032d3650b391 -Author: Max Linke -Date: Sat Jun 17 13:38:24 2017 +0200 - - minor clean ups - -commit 12a795e0cbc292759c25b54c36ca485e10287010 -Author: Oliver Beckstein -Date: Thu Jun 15 20:44:17 2017 -0700 - - removed conditional skipping of tests when scipy or matplotlib are missing - -commit 47340573db5319eecc11cf4d7d10412b107ff120 -Author: Oliver Beckstein -Date: Thu Jun 15 19:37:48 2017 -0700 - - scipy and matplotlib are imported at top in analysis - - - updated all modules - - removed any code that guards against scipy or matplotlib import - - conforms to style guide https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide#module-imports-in-mdanalysisanalysis - - fixes #1159 - - fixes #1361 - -commit fbc16880eaf9b87ac9c88ff8e86158598001da5c -Author: Oliver Beckstein -Date: Thu Jun 15 17:18:13 2017 -0700 - - make scipy and matplotlib full dependencies (#1159) - -commit e24da325980732efc04adb6366dafb3162d6e687 -Author: Max Linke -Date: Tue Jun 20 16:18:02 2017 +0200 - - only issue _get_named_atom warning on successful call - - This allows code to use the `getattr` function and only throw - an error if the requested attribute is an atom name. - -commit 50f5d5a9a1a39a2cfbc6285dbd2c3e353ffc99be -Author: Oliver Beckstein -Date: Sat Jun 17 17:03:32 2017 -0700 - - removed explicit DeprecationWarning for AtomGroup["name"] - - It turns out that with this warning in place we raise two deprecation warnings because we also - have a warning on _get_named_atom(item). - - Example output: - - >>> w.atoms['AAA'] - .../mdanalysis/package/MDAnalysis/core/groups.py:1520: DeprecationWarning: Using the [] operator with strings is deprecated and will be removed in 1.0. Please use `select_atoms('name AAA')` instead. - category=DeprecationWarning) - .../mdanalysis/package/MDAnalysis/core/groups.py:1522: DeprecationWarning: `_get_named_atom` is deprecated! - Instant selector AtomGroup[''] or AtomGroup. is deprecated and will be removed in 1.0. Use AtomGroup.select_atoms('name ') instead. - return self._get_named_atom(item) - - -commit 84354d8b978f9a67defeb9ebacd386331e6b302d -Author: Oliver Beckstein -Date: Sat Jun 17 16:52:52 2017 -0700 - - AtomGroup.__getitem__ depreaction warning: added removal release - -commit abc11e6122bab31b2628991265b6748b2df925b6 -Author: Oliver Beckstein -Date: Sat Jun 17 16:49:55 2017 -0700 - - minor cleanups in tests - -commit e15f1be7391f04f222418ce4d6532a6c422b6b92 -Author: Oliver Beckstein -Date: Sat Jun 17 16:49:37 2017 -0700 - - test for no warnings raised by AtomGroup.segid - - See comment https://github.com/MDAnalysis/mdanalysis/pull/1403#discussion_r122565617 - -commit b6646dabca41fa4991a08fe74630be30671cfc60 -Author: Max Linke -Date: Sat Jun 17 11:15:33 2017 +0200 - - use explicit deprecation warning - -commit fae031e9a4a3b7abe1d540cd4b552cbbf223b922 -Author: Max Linke -Date: Sat Jun 17 08:39:52 2017 +0200 - - add getitem warning message - -commit 3e57373d9f683681ca2f30cb37626a740aaa4491 -Author: Max Linke -Date: Sat Jun 17 08:24:52 2017 +0200 - - fix sphinx warnings - -commit 3de936c8bbdee7b437d915b98a8fd82f3901a080 -Author: Oliver Beckstein -Date: Fri Jun 16 14:10:29 2017 -0700 - - make instant selectors emit DeprecationWarning - - - instant selectors AtomGroup[''], AtomGroup., ResidueGroup., - Segment., Segment.r, SegmentGroup. emit warnings - - added tests - - updated docs with detailed deprecation and alternatives - - Thanks to @richardjgowers for insights https://github.com/MDAnalysis/mdanalysis/pull/1403#issuecomment-309136416 - -commit c238a40b8630e7bfbfc0d7bdfd486eda5f6c04a7 -Author: Oliver Beckstein -Date: Fri Jun 16 13:55:02 2017 -0700 - - new MDAnalysisTests.core.util.assert_nowarns() function - -commit 250ed47cade2f512f21bf687a4cdf198eff255e3 -Author: Oliver Beckstein -Date: Fri Jun 16 00:56:12 2017 -0700 - - removed top-level imports of Timeseries - - - removed imports in core and MDAnalysis - - replaced MDAnalysis.collection with a mock object that issues - warnings and raises NotImplementedError - - added a test for MDAnalysis.collection - -commit 6e0abb0c32a74c793b835796f66765823598e334 -Author: Oliver Beckstein -Date: Thu Jun 15 23:05:13 2017 -0700 - - mention optional/full dependencies in docs - - - improved installation instructions (minimal/full install for pip, always full - install for conda; also added entry on installation of tests) - - analysis landing page: better explained optional packages, removed scipy as example - and replaced with sklearn and HOLE. - -commit e9784a791870a865c6e25fbd87588f73068cf707 -Author: Richard Gowers -Date: Tue Jun 13 09:17:54 2017 +0100 - - Deprecated DCDReader.correl - -commit bd3b4df241cd31fb47f04f673982ea4701954f5f -Author: Richard Gowers -Date: Tue Jun 13 09:16:34 2017 +0100 - - deprecated core.Timeseries module - -commit 0a37e9e33166fcc065c7ceeae971e929f10796e3 -Author: Oliver Beckstein -Date: Thu Jun 15 16:26:13 2017 -0700 - - add deprecation warnings for API changes - - - closes #1383 - - included deprecations: - - #1373 Timeseries (targeted for 0.17) - Note that the deprecation for core.Timeseries will always show up; - this is deliberate so that users WILL see it as it will be gone in - the next release! - - #1377 Quick selectors (target 1.0) - - #782 flags (target 1.0) - - updated CHANGELOG - -commit 49496c37a5566fe232b7c32f4cbd1b840ac72195 -Author: Utkarsh Bansal -Date: Mon Jun 19 20:51:31 2017 +0530 - - Break build packagewise (#1370) - - Merge into single command - - Fix for root dir files - - Move files in root dir to utils folder - - Drop plugins directory - - Merge coverage files - - Fix covage run command - - Fix test list env variable - - Fix output coverage file - - Fix covegae file - - Fix case - - Commnet out test__set_verbose - - Fix minimal build - - Fix merge command - - Undo minial build change - - Fix multiline command - - Fix lint build - - Remove plugins from the minimal build - - Try to fix the doc build - - Adds the test flags to the minimal build - - Reactivate tests that pass in test_log.py - - Remove if-else logic from "script" phase - - Adds missing call to evail in "script" phase - - Filip test flags and test directories - - Adds cover package argument - - Split command into constituent variables - - Fix MAIN_CMD in full build - - Have the same order of execution for all builds - - Add lib folder to the testing command - - Make the lib folder a python package - - * Adds __init__.py file to the lib folder - - Adds __future__ import - -commit 1f36502b2b58cb8dd36d242945c935f42b711c24 -Author: rathann -Date: Mon Jun 19 11:01:41 2017 +0200 - - fix int type in asserts in TestDownshiftArrays (#1410) - - Fixes #1362 - - this was missed in eed776181c90646d960eb00a275bffb3ffb36a20 - -commit 785cfc4418c648f209d7c4330752d35b102f3582 -Author: Max Linke -Date: Sat Jun 17 11:30:17 2017 +0200 - - update copyright year - -commit 9dc173783fae2712c9ccba27f8032bfb440ec4cb -Author: Brigitta Sipocz -Date: Sat Jun 17 19:37:12 2017 +0100 - - Use common setup script rather than OS specific ones (#1408) - -commit ebe2b84e64456aa7ef9d665a281f096f4dbfbb00 -Merge: 6e6aa9d0c e3d58188b -Author: Oliver Beckstein -Date: Tue Jun 13 17:16:12 2017 -0700 - - Merge pull request #1398 from MDAnalysis/issue-1397-group-hash - - - Explicitly define __hash__ for groups: - Groups (AtomGroup, ResidueGroup, SegmentGroup) cannot be stored in sets - or used as dict key if they are not hashable. In python 3, the hash - method is not defined implicitly anymore when a class has a eq method. - - fixes #1397 - -commit e3d58188bb1670a4831328fbca64bc3dd4f36890 -Author: Jonathan Barnoud -Date: Tue Jun 13 19:26:29 2017 +0200 - - Explicitly define __hash__ for groups - - Groups (AtomGroup, ResidueGroup, SegmentGroup) cannot be stored in sets - or used as dict key if they are not hashable. In python 3, the __hash__ - method is not defined implicitly anymore when a class has a __eq__ method. - - Fixes #1397 - -commit 6e6aa9d0c7e9436ec07e4da979589d8d8a8bedbf -Merge: 3e4a973c7 eed776181 -Author: Oliver Beckstein -Date: Tue Jun 13 17:03:38 2017 -0700 - - Merge pull request #1393 from MDAnalysis/issue-1362-int_types - - Issue #1362 : use np.intp types for indexing instead of np.int64 - - - According to numpy/numpy#4384 (comment), `np.intp` is the recommended dtype for indexing: - "... use np.intp as dtype whenever things have to do with indexing or are logically related to - indexing/array sizes. This is the natural dtype for it and it will normally also be the fastest one. - - see https://docs.scipy.org/doc/numpy/user/basics.types.html - - see also PR #1391 for discussion - - This change should go some way towards increasing compatibility with i386/i696 (32 bit) platforms. - - NOTE: No dedicated testing on 32 bit yet (see WIP PR #1392 ) - -commit eed776181c90646d960eb00a275bffb3ffb36a20 -Author: Richard Gowers -Date: Mon Jun 12 07:58:40 2017 +0100 - - More work on making indexing arrays use intp (#1362) - - - Added tests for 32 bit index support - - added @rathann to AUTHORS - -commit 8641226001e876f5e0360c4d74d4c239aab3d539 -Author: Dominik 'Rathann' Mierzejewski -Date: Fri Jun 9 11:49:09 2017 +0200 - - relax test_symmetry test due to lower precision on 32bit - -commit 39ad792b939bdd26e461f9a6e801f4f54ea789fd -Author: Dominik 'Rathann' Mierzejewski -Date: Fri Jun 9 11:42:19 2017 +0200 - - use correct int types - - This fixes ERRORs and FAILs in the testsuite on 32bit: - - TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' - - and - - assert_(out[0].dtype == np.int64) - File "/usr/lib/python2.7/site-packages/numpy/testing/utils.py", line 92, in assert_ - raise AssertionError(smsg) - AssertionError - -commit 3e4a973c7f2946bc54f8e8b9720f80d8a60c69fa -Merge: 76527108a abd205b8f -Author: Oliver Beckstein -Date: Tue Jun 13 14:29:24 2017 -0700 - - Merge pull request #1396 from MDAnalysis/issue-1395-gro_resid_truncate - - Issue 1395 gro resid truncate - -commit abd205b8f8d4814d647f3f0062b7f8958cd416bb -Author: Richard Gowers -Date: Mon Jun 12 17:11:09 2017 +0100 - - Changed coordinate writers to use ltruncate_int - - Fixes issue #1395 - -commit 930bb6349fde760eaa315a747a914aa469185f55 -Author: Richard Gowers -Date: Mon Jun 12 16:03:51 2017 +0100 - - Added lib.util.ltruncate_integer - -commit 6a5fa2ce17e8747f4e72b35f8e762a545ac2377f -Author: Richard Gowers -Date: Mon Jun 12 15:30:08 2017 +0100 - - Added tests for issue #1395 - -commit efd9fc5fa40a808da0bf2095581983442b2b32c9 -Author: Richard Gowers -Date: Mon Jun 12 14:47:13 2017 +0100 - - Aesthetic fixes to test_gro - - Removed TestCase usage - -commit 76527108a83030d69c6db270be313c11dd27c05b -Author: Max Linke -Date: Tue Jun 6 12:12:04 2017 +0200 - - update conda badge (#1386) - - point to new conda-forge release version - -commit a0d61f904d9cc8aa19918c0ca033fe99221626a4 -Author: Max Linke -Date: Sun Jun 4 15:18:00 2017 +0200 - - change definition of tests (#1382) - -commit 805c6c222a6176c1866156d8f852523804ca7776 -Merge: 6f906c0a1 a16483057 -Author: Max Linke -Date: Sun Jun 4 07:23:33 2017 +0200 - - Merge pull request #1381 from MDAnalysis/start-0162 - - Start of 0.16.2 - -commit a1648305773117953b20db3e2412edcb28e4958f -Author: Richard Gowers -Date: Sat Jun 3 23:52:01 2017 +0100 - - Started version 0.16.2 - -commit 723cd8985052e359bc0cf1c47dc45e70c0f6951a (tag: release-0.16.1) -Author: Richard Gowers -Date: Sat Jun 3 21:36:24 2017 +0100 - - Updated c sources for 0.16.1 - -commit dfb09d6c400a1ebe7d0c81613769d98c1ae25e58 -Merge: 6a274d7a4 34f237010 -Author: Richard Gowers -Date: Sat Jun 3 20:48:53 2017 +0100 - - Merge branch 'develop' - - Conflicts: - maintainer/conda/MDAnalysis/meta.yaml - package/CHANGELOG - package/MDAnalysis/version.py - package/setup.py - testsuite/CHANGELOG - testsuite/MDAnalysisTests/__init__.py - testsuite/setup.py - -commit 34f237010fa2a4da0ae00e5e3bfee8b38e64110a -Author: Richard Gowers -Date: Sat Jun 3 20:45:57 2017 +0100 - - Finalised version 0.16.1 - -commit 6f906c0a11248a03ff0aa88be25ed9e3037c78ee -Author: Richard Gowers -Date: Sat Jun 3 18:32:51 2017 +0100 - - Updated CHANGELOG for issue #1378 (#1380) - -commit 5222fc300cf24db11fe2deffa6540a6a54d38d40 -Author: Kathleen Clark (Kacey Reidy) -Date: Sat Jun 3 09:33:13 2017 -0700 - - Updated PCA Tutorial (#1379) - - * Fixes issue 1378 - - * Update pca.py - - * Update AUTHORS - -commit 0b499e9564e6840a88c0a763821f7cf53a477ca5 -Author: Max Linke -Date: Fri May 26 15:45:26 2017 +0200 - - remove * imports in align docs - -commit 2e2ad9f10063e8baf69c6198e7c7901a1cf2c81c -Author: Max Linke -Date: Sun May 28 15:42:18 2017 +0200 - - Fix weights deprecations (#1356) - - * deprecate mass_weighted in psa - - * update CHANGELOG - -commit e12a64749ffc690918e97b682982c0ede77cca63 -Merge: afcd60632 b60c9244a -Author: Oliver Beckstein -Date: Fri May 26 01:49:38 2017 -0700 - - Merge pull request #1367 from MDAnalysis/reader-speed-boost - - Reader speed boost. - Fixes #1357. - -commit b60c9244a887b12068149c1be71e48d2bf9776c9 -Author: Richard Gowers -Date: Fri May 26 08:15:00 2017 +0100 - - Use Timestep API more in reader speed boost - -commit 13f219237ac49c1b2e73a4016121741cf19366ad -Author: Max Linke -Date: Sun May 21 18:19:31 2017 +0200 - - add comments - -commit 8bb6f4a79474cf87ee2e5412153ebd948b6b3f1d -Author: Max Linke -Date: Fri May 19 23:08:19 2017 +0200 - - update changelog - -commit 74997bd0a62bb3c1060ac40bc20148bd4c1422d8 -Author: Max Linke -Date: Thu Apr 13 17:56:07 2017 +0200 - - speed up pdbqt - -commit 97c1cc51e2cb12e30cc1692740a91b4738fa6fe5 -Author: Max Linke -Date: Thu Apr 13 17:53:47 2017 +0200 - - speed up pdb reading - - the testsuite is about 1 second faster for pdb files alone - -commit 7527a924e096d3a3e1c4d09aa51d4b575cf7d4f3 -Author: Max Linke -Date: Thu Apr 13 17:46:27 2017 +0200 - - speed up PQR - -commit 3ecd7bf2b3b32600ce517b74aa72d485193a02c1 -Author: Max Linke -Date: Thu Apr 13 17:44:48 2017 +0200 - - speed up xyz reader - -commit afcd60632105b673532c135470157dd1cb1450a5 -Author: Oliver Beckstein -Date: Tue May 23 22:32:42 2017 -0700 - - changed URL for docs to new http://docs.mdanalysis.org - - - closes #1315 - - master docs were moved to their own repo https://github.com/MDAnalysis/docs and are - served as GitHub pages - - replaces obsolete https://pythonhosted.org/MDAnalysis - - updated CHANGELOG (also added notes on #378) - -commit ad5ff75c26bb4caa2191a37e1391b32d72b77507 -Merge: f6bc4861a 5da4146ea -Author: Oliver Beckstein -Date: Tue May 23 21:48:06 2017 -0700 - - Merge pull request #1126 from MDAnalysis/new-sphinx-style - - switched sphinx theme to Alabaster with MDAnalysis styling - - alabaster: https://github.com/bitprophet/alabaster (used under BSD-3 clause license) - - uses CSS from https://github.com/ignacysokolowski/sphinx-readable-theme (MIT license) - -commit f6bc4861a0b997f2e29979101a6265f263e4a382 -Merge: dc2dd7e00 dc8b90c69 -Author: Jonathan Barnoud -Date: Sun May 21 16:08:58 2017 +0200 - - Merge pull request #1358 from MDAnalysis/issue-1104-selection-writer-docs - - improved selection exporter docs - -commit dc8b90c699a1e6e0e106f078affd7f66f03ee26c -Author: Oliver Beckstein -Date: Sun May 21 01:54:09 2017 -0700 - - improved selection exporter docs - - - fixes #1104 - - added docs for selections.get_writer (numpy style) - - fixed tcl markup - - used examples from #1104 and reorganized the selections_modules.rst - page - -commit dc2dd7e0045994504c991a1b68b62cb4fe420b2a -Author: Max Linke -Date: Fri May 19 08:01:17 2017 +0200 - - FIX: rmsf.run should return itself - - This is the standard for normal analysis today - -commit 5da4146eac147d15fccd9f29ad38f3bfe0538ec6 -Author: Oliver Beckstein -Date: Thu May 18 11:12:15 2017 -0700 - - use sphinx-readable CSS with alabaster - - We use a stripped-down version of the readable.css_t from https://github.com/ignacysokolowski/sphinx-readable-theme - as a custom CSS (included in custom.css). Minor touch-ups are performed in custom.css. - - The overall effect is Alabaster fancyness with readable style. - -commit 8cd760379e6b7d8437cac7901cbebb083a1b819c -Author: Oliver Beckstein -Date: Tue May 16 13:29:52 2017 -0700 - - documentation updates and fixes - - - doc front page update: added key information - - use sections (now that the TOC has been removed, we - have a bit more space to include stuff that people - want to know right away) - - Getting Involved: includes link to Code of Conduct - - Installation: abbreviated quick install (with link) - and correct conda channel (MDAnalysis/MDAnalysis.github.io#54) - - Source Code: git clone - - added link to Topology formats table - - must cite each reference somewhere - Newer sphinx versions (1.6.x or so) throw a warning for any reference that is not - cited anywhere. - - Now we cite every reference in the Reference page itself instead - of linking these references to the individual module reference sections. - - Touched up encore docs references. - - small reST fix in coordinates/__init__ and analysis.pca - -commit bf4733dc3874293611fd6cec1f4c096cb4950095 -Author: Oliver Beckstein -Date: Tue May 16 15:27:22 2017 -0700 - - maintainer/deploy scripts - - - new deploy_master_docs.sh script for pushing to https://github.com/MDAnalysis/docs - - EXPERIMENTAL --- only use manually at the moment. - - nuke the html/.git --- only needed for manual testing - - commit message with fullgy GitHub-linked commit SHA1 - - fixed syntax error in die() in maintainer/deploy_docs.sh - -commit 5f2e0f11c1b2fd16b925c3b9f77baaad320f39f4 -Author: Oliver Beckstein -Date: Wed May 17 23:49:51 2017 -0700 - - removed Mock class from sphinx/conf.py - - Not needed. - -commit bcba12420d00de6975a195fe1fb92ac4312d5c72 -Author: Oliver Beckstein -Date: Wed Dec 14 16:50:22 2016 -0700 - - switched sphinx theme to alabaster with MDAnalysis styling - - - https://alabaster.readthedocs.io/en/latest/ for notes on styling; - note that CSS has to be entered as strings, not as Python lists. - - use normal non-floating sidebar in alabaster - Using the standard sidebar avoids funny rendering artifacts when the pages are short - - collapsible sidebar navigation - - only show the TOC in sidebar - - enable depth 4 in sidebar, but 2nd level is collapsed until one - navigates to the page; we want 4 levels because this is where most - of our analysis docs has the per-page headings - - use MDA gray for the background in the mobile menu (or when page is - very narrow) - - enabled Related Topics in sidebar and adjusted font sizes - - custom.css: smaller Notes/See Also (admonition) title - -commit a59cd631b8da396c0e6e3e4b1f455887291e7347 -Author: Max Linke -Date: Tue May 16 22:05:27 2017 +0200 - - re-enable cron job - -commit 26149a1001a26d6ac84ada1d88d6ba23bc1172ca -Author: Oliver Beckstein -Date: Tue May 16 13:34:14 2017 -0700 - - numpy-docs for visualization module (#1346) - - - closes #1277 - - updated citation for Chavent2014 - - shortened module headings - - better formatting for return values - - added more parameter/return sections to the undocumented helper functions - (possibly refactor into underscore-hidden functions) - - made clear that "coordinate files" are really "topology - files" in MDAnalysis parlance: changed variable names and docs accordingly - -commit c9f5cd0e8b657691ce993e339ff313be70561058 -Author: xiki-tempula -Date: Tue May 16 20:48:08 2017 +0100 - - added OC1 and OC2 to default list of hydrogen bond acceptors - - - added C-terminus OC1 and OC2 (Amber FF) to default list of acceptors in HydrogenBondAnalysis - - closes #1342 - - updated docs - - updated CHANGELOG - -commit f1897587ec38402f0f6147ff4b01264ce3ca9440 -Author: Richard Gowers -Date: Sun May 14 20:10:27 2017 +0100 - - Fixed Issue #1347 (#1348) - - PSFParser now considers segid and resname when splitting into residues - -commit 1f9a31fd2676bddb16a884b422cb9cb2af9231d1 -Author: Oliver Beckstein -Date: Sun May 14 02:37:32 2017 -0700 - - hbond analysis: fixed incorrect residue handling with trailing numbers (#1339) - - * test for correct TIP3P resname in hbond analysis table (#801) - - * Fixed incorrect handling of residue names with trailing numbers in HydrogenBondAnalysis (issue #801) - - - fixes #801 - - analysis.hbond.hbond_analysis.HydrogenBondAnalysis now correctly stores and parses - donor and acceptor names and is not tripped up by resnames that end in numbers, such - as TIP3 - - store timeseries as _timeseries with donor and acceptor atom identifiers as - tuples instead of strings (avoids the use of fragile lib.util.parse_residue()) - - made timeseries a property that is generated on the fly so that old code does not break, but - it is not cached (to avoid memory consumption for big trajectories) and so users should cache - themselves if needed - - added tests - - rewrote parts of the docs and added notes on use of timeseries - - updated DEPRECATION warning for 1-based indices to 0.17.0 (should have been removed in - 0.16.0 but we forgot) - - * hbond analysis doc fixes/improvements - - - mostly numpy style (whenever possible): - Apparently, napoleon does not like a single Notes and See Also section, need to - use reST. - - named the 1-based indices "idx" in the docs. - - added example for analysis - - describe convenience analysis functions - - how to use pandas - - * HydrogneBondAnalysis: internal clean up - - Use atom.index instead of atom.index+1 internally and for debug output. - - * Hbond analysis: fixed docs (stated wrong defaults for updating) - - * hbond analysis: addressed review comments - -commit 429795a071eddb6cb351c4d2769b9e0537d4175e -Author: Max Linke -Date: Fri May 12 20:20:45 2017 +0200 - - remove failing cron build job - -commit 1c8f87d1eda2dda30407b1bd63eaf08adbd593ed -Author: Max Linke -Date: Wed May 10 23:36:38 2017 +0200 - - fix start, stop, step values of AnalysisBase (#1340) - - * fix start, stop, step values of AnalysisBase: - We have to set them after the trajectory slice check. That way the None values - get converted correctly. (This regression was introduced in #1195.) - * add new analysis base test - * update changelog - * correctly ignore doc build - -commit 36be0d9f73d837bf502fb53d92bc6b7e5c0d4daa -Author: Oliver Beckstein -Date: Mon May 8 22:28:22 2017 -0700 - - changed OAuth token for doc deployment from Travis CI (#1338) - - - fixes #1337 - - new token was generated because the old token was exposed due to a security - incident at Travis CI, see https://blog.travis-ci.com/2017-05-08-security-advisory - - followed #386 for generating new token and encrypting for Travis CI - -commit 303574b72d6160855e3b7380c4e2737025b9e786 -Author: Richard Gowers -Date: Mon May 8 12:59:42 2017 +0100 - - Fixes issue #1330 (#1332) - - * Fixes issue #1330 - - * Added tests for Lammps data rearranging positions and ids correctly - -commit d5667ae9b52c1f14d9cc0fe3cb77799c9a5635c2 -Merge: afe690bad c1db03380 -Author: Oliver Beckstein -Date: Sun May 7 12:42:39 2017 -0700 - - Merge pull request #1247 from MDAnalysis/minor-fixes - - Various fixes, primarily docs. See PR #1247 for details. - -commit c1db03380a20229818522d446a000e96d8e1e704 -Author: Max Linke -Date: Sun May 7 20:09:41 2017 +0200 - - use consistent formatting - -commit ecc39197672fb3ef4be36c05fdb1c1a19eb1e133 -Author: Oliver Beckstein -Date: Fri May 5 14:41:05 2017 -0700 - - more reST fixes - - - @kain88-de suggestions - - even more fixes (everywhere in coordinates, elsewhere where I found something - to fix). In particular - - adde Parameter/Return/Raises sections to many functions in lib.util - - made sure that there were two empty lines above .. versionchanged etc sections - - made proper Example sections - - fixed/clarified text - - ensure that *all* classes are shown and can be linked (added autoclass markup - where necessary) - - PDB: removed any mentioning of the simple/Bio.PDB parser stuff, only left a - versionchanged entry - -commit 7817f96b1d13884871a4ee49fa654f324fee1168 -Author: Jonathan Barnoud -Date: Fri May 5 09:37:35 2017 +0200 - - Fix small rendering errors in the doc - -commit afe690bad8657b442cfcd5487c01870e8fe7fe1e -Merge: bb9bb5771 ce80e91b5 -Author: Jonathan Barnoud -Date: Fri May 5 09:29:18 2017 +0200 - - Merge pull request #1333 from QuantumEntangledAndy/Issue1331 - - This handles the case where number of items is exactly divisible by number of items per line. Previously the code would always round up, where instead it should only round up when not exactly divisible. - - Fixes #1331 - - Changes made in this Pull Request: - - Changes how amber prmtops are loaded such that the number of lines is only rounded up when neede - - Added to the change log - - Added a prmtop to the test suite that fails without this corrected rounding - -commit ce80e91b525963a6a16b889c6548bdec90b4a030 -Author: QuantumEntangledAndy -Date: Fri May 5 11:07:00 2017 +0700 - - Fixes Issue 1331 - This handles the case where number of items is exactly divisible by number of items per line. Previously the code would always round up, where instead it should only round up when not exactly divisible. - -commit 4f3d59cdbb2129ff3469ef7176cefde793a22ed4 -Author: Oliver Beckstein -Date: Thu May 4 16:18:07 2017 -0700 - - fixed remaining sphinx warnings and doc touchups - - - I fixed everything until local - cd doc/sphinx - make html - passed without errors.... but I am sure that more - errors will come up. - - reformatted and rewrote various portions of the docs while - fixing the errors - - completed the ENCORE citations in encore/similarity.py - -commit e25d2c753b968d6cfe5dc0bd13c0b504c5875508 -Author: Oliver Beckstein -Date: Thu May 4 18:13:30 2017 -0700 - - sphinx: make sphinx fail on warnings and be verbose (local sphinx Makefile) - - Normally we build the docs with - python setup.py build_sphinx - but for more fine-grained control one can also locally build with - cd doc/sphinx - make html - This is useful for debugging reST issues. - -commit 279351937763845a9995c3a950fc9d221d865700 -Author: Richard Gowers -Date: Mon Mar 20 15:15:30 2017 +0000 - - Update guessers.py - -commit a8f5157ebbdb81d054106456be6e47aab3c437b8 -Author: Jonathan Barnoud -Date: Sun Mar 19 12:43:37 2017 +0100 - - Numpyfy docstrings - - Update the docstrings everywhere in the package but in the anlysis. - -commit 352ec8086be2a7efabdd6820ffa2c88cc9d769fd -Author: Jonathan Barnoud -Date: Sun Mar 19 11:26:11 2017 +0100 - - Avoid isinstance(something, int) - - Testing that arguments where integer by using `isinstance(arg, int)` has - proven itself detrimental on several occasions. Indeed, the test refuses - other types that would be legitimate such as numpy integers. This commit - replaces the remaining occurences of the too narrow test by the solution - that has already been used on multiple places of the code: testing - against `numbers.Integral`. This new way matches everything that looks - enough like an integer, and behave the same on python 2 and python 3 on - the contrary to testing against `int`. - -commit a8ea0365277646c4cb6a46de4377c54a8ed4f522 -Author: Jonathan Barnoud -Date: Sun Mar 19 11:11:07 2017 +0100 - - Remove windows end of lines - -commit bb9bb5771465e822b545901eadf47730244068a7 -Author: Max Linke -Date: Wed May 3 21:11:15 2017 +0200 - - fix doc deploy - - Closes #1316 - -commit c1e751e2e3d7b455081052df3c5820c47c3ac7bc -Author: Sang Young Noh -Date: Tue May 2 00:15:39 2017 -0700 - - fixed docs for PDBParser "conect" keyword (#1329) - - - fixes #1246 - - supercedes and closes PR #1279 by @Shtkddud123 - - added @Shtkddud123 to AUTHORS - - updated CHANGELOG - -commit ac27e28b636cfcd429193dd6f49e633bcea012a4 -Author: Richard Gowers -Date: Mon May 1 21:05:13 2017 +0100 - - PQRParser now reads icodes (#1328) - - * PQRParser now reads icodes - * Fixes Issue #1317 - * Updated PQR docs - -commit d5bc8f5108b75170b8e742c431dd9914509adff5 -Author: xiki-tempula -Date: Fri Apr 28 16:10:44 2017 +0100 - - Fix hbond cannot deal with atoms too far (PR #1325) - - * add check that s2 selection is empty - * add test - * add change log entry - -commit 5c6700b1eaeb56f57566638055277ea1a369a4ef -Author: Alejandro Bernardin -Date: Thu Apr 27 12:26:38 2017 -0300 - - wateranalysis: Formatted according to PEP8 - - - Adapted to PEP8, not fully, but most - - CHANGELOG formatting fixes - -commit ce4891115af64a09365a9634128ba10b783222f9 -Author: Alejandro Bernardin -Date: Wed Apr 26 16:08:59 2017 -0300 - - wateranalysis: Fixed case when no water molecules in selection. - - - wateranalysis could not handle empty selections: now we check - explicitly and return 0 or (0, 0, 0) when necessary - - Improved print to screen format; now uses ProgressMeter - - Avoiding hidden return inside if/else (improves code readability) - and made lg2(x) a static method - - Added test - - Fixed some orthography. - - CHANGELOG updated. - -commit 401c36636a5c12d250d2edd08ef44f678fe8ba45 -Author: Wouter Boomsma -Date: Sat Apr 29 18:21:21 2017 +0200 - - Fix #1324 (encore required reader with timeseries capabilities) - - * Encore: Added transfer_to_memory() in get_distance_matrix to ensure that it is compatible with all Universe types. - * Added test (for XTC) - * Added CHANGELOG entry - * Fixes #1324 - -commit 2c479783cf1d8ec828326f8992a2f1a85ad16d7c -Author: Jon Kapla -Date: Thu Apr 27 02:18:43 2017 +0200 - - Changed dt to include step in Universe.transfer_to_memory() (#1321) - - * Changed dt to include step in Universe.transfer_to_memory(). Test in core/test_universe.py:TestInMemoryUniverse - - * Cleaning up. Entries added to AUTHORS and CHANGELOG - -commit 68e4c17a2dfb47365f77909a3468ca808ec7e022 -Author: Max Linke -Date: Tue Apr 25 18:17:47 2017 +0200 - - replace .. SeeAlso:: with numpy section (#1314) - - * replace .. SeeAlso:: with numpy section - * fix obvious formatting errors - * addressed comments from @jbarnoud - * fix rendering issues - * some more usability changes - * add ExtendedPDBReader to docs - * fix last link issue - - I used the following command to replace all occurrences. - - find . -name '*py' -exec sed -rie 's/^(( *).. SeeAlso::( *))/\2See Also\n\2--------\n\2/g' {} \; - - Following a comment of @jbarnoud at https://github.com/MDAnalysis/mdanalysis/pull/1240#discussion_r111933801 - -commit ca30efa938a0123b546429ec295e8d6a151bb8fd -Merge: a3c2fca15 c9f76b21f -Author: Max Linke -Date: Mon Apr 17 23:41:37 2017 +0200 - - Merge pull request #1312 from MDAnalysis/doc-warnings - - fix sphinx warnings - -commit c9f76b21fb14953da0c10780cf92486593cc4c93 -Author: Max Linke -Date: Mon Apr 17 10:29:30 2017 +0200 - - update CHANGELOG - -commit 7a768282151da0d7abb27b64d5ef2078b89b0484 -Author: Max Linke -Date: Mon Apr 17 10:27:06 2017 +0200 - - update mathjax cdn - - The original cdn will be taken down on 30 April 2017 - -commit 373c1fbbbf6126b2ad5508759a0e9a7acc508a12 -Author: Max Linke -Date: Mon Apr 17 10:22:44 2017 +0200 - - remove pylint warnings - - They are triggered now. I don't know how to fix them. - I think they are triggered now because pylint used to be tripped by errors - in the docs. Why that happened I'm not sure. - -commit d249fd7dc0734c3468c5dfe40b2fee649218808b -Author: Max Linke -Date: Mon Apr 17 10:13:45 2017 +0200 - - update travis file - - use more ci-helpers goodies. - -commit 322bbb91ab1a96955d2ceef07c896e8af2a18fa5 -Author: Max Linke -Date: Mon Apr 17 10:13:37 2017 +0200 - - turn doc warnings into errors - -commit 317dedf3dd3785cdb94de37393ff754e57e60a5c -Author: Max Linke -Date: Mon Apr 17 10:13:10 2017 +0200 - - fix errors in rst files - - This also activates the .. TODO:: sections to be legal - -commit dfad88c3ca62fc0d6b594c022ddae07447700b78 -Author: Max Linke -Date: Mon Apr 17 10:12:26 2017 +0200 - - Fix doc warnings in MDAnalysis package - -commit a3c2fca15981988a5738f67d685713d6c09e443a -Author: xiki-tempula -Date: Thu Apr 13 13:22:46 2017 +0100 - - Residues with the same residue ids are not merged by default (#1307) - - * Residues with the same residue ids are not merged by default - - Fixes Issue #1306 - -commit 9ba5078423cff691c44e00dae9ecd33b3f0dad13 -Author: xiki-tempula -Date: Thu Apr 13 13:19:18 2017 +0100 - - changes string.uppercase to string.ascii_uppercase for py3 compatibility (#1309) - - * changes string.uppercase to string.ascii_uppercase for py3 compatibility - - * update change log - -commit 46cc08f7e1044f44d0eaa5ca232e8fc7cf07d436 -Author: Max Linke -Date: Thu Apr 13 12:11:37 2017 +0200 - - Enable more pylint warnings (#1302) - - * enforce print function - - * enforce py3 style range function - - * enforce py3 style map and zip generators - - * update changelog - -commit b87a20a5a0a6b465f6355477adf114ab458a25b6 -Author: Utkarsh Bansal -Date: Wed Apr 12 13:59:56 2017 +0530 - - Fix changelog (#1304) - - * Fix changelog - - * Fix year - -commit 0faa8a04b2abaa63e24eab93a89ff5445bfeab6f -Author: Utkarsh Bansal -Date: Wed Apr 12 13:59:13 2017 +0530 - - Universe now works with StringIO objects (#1254) - - * Universe now woks with StringIO objects - -commit 2521d78b7bf4b480fc993ede0bcc365177a702f9 -Merge: 445d679e5 b2561a128 -Author: Jonathan Barnoud -Date: Tue Apr 11 00:03:20 2017 +0200 - - Merge pull request #1294 from MDAnalysis/lint-absolut-import - - Lint absolut import - -commit b2561a1286e9a473aa76f601001f955f030b4113 -Author: Max Linke -Date: Mon Apr 10 18:16:44 2017 +0200 - - remove duplicate imports - -commit 5bb6a9b9dc3f46c89e119ecb7fede75c8cc378c9 -Author: Max Linke -Date: Sun Apr 9 09:27:48 2017 +0200 - - fix test errors - -commit c3130ca1635f3342eacef459eff35c9852c1f7e4 -Author: Max Linke -Date: Sat Apr 8 19:44:32 2017 +0200 - - use absolute imports - - - add copyright info if missing - -commit 445d679e598e6287f1bcb1cdf10855ab0f0a2524 -Merge: 924340a7e 2aad424cd -Author: Jonathan Barnoud -Date: Mon Apr 10 16:43:46 2017 +0200 - - Merge pull request #1293 from MDAnalysis/lint-division - - Always use new division - -commit 924340a7ebeffd521ff0cc32563d4e651eb818d9 -Author: Richard Gowers -Date: Mon Apr 10 07:46:02 2017 +0100 - - Start of v0.16.1 (#1296) - - * Bumped version for 0.16.1-dev0 - - * Updated conda build version - -commit 6a274d7a42a16ceb30db3523a4c1a02ebd15729e (tag: release-0.16.0) -Author: Richard Gowers -Date: Mon Apr 10 07:42:40 2017 +0100 - - Updated conda build version - -commit e464e9a449310850565897530e2d1b8940b6134d -Author: Richard Gowers -Date: Mon Apr 10 07:22:00 2017 +0100 - - Fixed version in testsuite - -commit 2d474e94f4be8157b136cf71694a5667fe1168d4 -Author: Richard Gowers -Date: Mon Apr 10 06:51:08 2017 +0100 - - Updated Cython C files - -commit b55e64ffc2e351f18947e44610686e579422fb21 -Merge: cc64b4506 a28739a05 -Author: Richard Gowers -Date: Mon Apr 10 06:22:57 2017 +0100 - - Merge branch 'develop' - - Conflicts: - package/CHANGELOG - package/MDAnalysis/version.py - testsuite/CHANGELOG - testsuite/setup.py - -commit a28739a0572ae2c09689fd868ae6d72506f2a01c -Author: Richard Gowers -Date: Mon Apr 10 06:19:15 2017 +0100 - - Finalised CHANGELOG for v0.16.0 - -commit 4b4e110743891bb4082e3ed4ff5c6fa964220eaf -Author: Max Linke -Date: Sun Apr 9 10:16:42 2017 +0200 - - Numpy bump (#1291) - - * bump numpy version - - * add new numpy=1.9.3 build job - - * update CHANGELOG - - * change numpy builds - - allow failure for old numpy versions - check new numpy version in a cron job - - * use numpy 1.10.4 - -commit 2aad424cdba06ecfe7511d3376d319575b8f91e8 -Author: Max Linke -Date: Sun Apr 9 09:03:59 2017 +0200 - - fix division errors - -commit d776d73a8d8aab1ba0b4383a1ad552f63c8f74c8 -Author: Max Linke -Date: Sat Apr 8 22:53:43 2017 +0200 - - fix integer division - -commit 0015d693cccfe549b0716fdd0e6722df0442a881 -Author: Max Linke -Date: Sat Apr 8 19:15:24 2017 +0200 - - always use py3 division - -commit ce6e09a1e7f1f3bac4470e84f9b0b3daeb93804d -Author: Max Linke -Date: Sat Apr 8 11:06:49 2017 +0200 - - Fix __repr__ if topology loaded from PDB (#1288) - - * Fix __repr__ if topology loaded from PDB - - Fixes #1287 - -commit 68cade414ac0028fd2aa4481ddaf9b2d44cc34d5 -Author: Jonathan Barnoud -Date: Sat Apr 8 09:50:39 2017 +0200 - - The XVG auxiliary readers now use anyopen - - Fixes #1289 - -commit 217d501a18cfcfa746396ba91164bac0844f0f4e -Author: Jonathan Barnoud -Date: Sat Apr 8 08:27:21 2017 +0200 - - Remove windows end of line in XVG aux reader - -commit 14a47591b06ab81187a1d5c4be33890d48ca1cff -Author: Max Linke -Date: Fri Apr 7 14:25:06 2017 +0200 - - Get OSX and different Numpy builds running (#1282) - -commit 4f794831402dad715bed017bdb1eb66183b5ca25 -Author: Brigitta Sipocz -Date: Thu Apr 6 08:20:26 2017 +0100 - - Using ci-helpers (#1284) - -commit 7263f42a4a41cf220303439b85f58d0b346c7c99 -Author: Richard Gowers -Date: Tue Apr 4 12:31:09 2017 +0100 - - Fixes Issue #1108 (#1280) - - Adds better documentation for unique methods - -commit 297c40b342d24367acb527e178dba0570635fef5 -Author: Max Linke -Date: Tue Apr 4 13:30:42 2017 +0200 - - allow to change dimensions from basegroup (#1281) - - restores 0.15.0 behavior - -commit 09f822e80356a03b5d68846f09b4df39d1959e4b -Author: Richard Gowers -Date: Tue Apr 4 08:40:22 2017 +0100 - - Issue 728 gr oresidwrap (#1278) - - * Fixes Issue #728 - - GRO Files with > 99,999 resids now get treated properly - - * Slightly improved GROParser performance - - iter(filehandle) is slightly faster than repeatedly calling .readline() - - * Fixed 0 resid corner case for Issue #728 - -commit 0add228401b0baefea7b1be4205ab91207dbaf4f -Author: Max Linke -Date: Mon Apr 3 10:48:35 2017 +0200 - - Updated Travis build (#1273) - - Overall builds a little faster - -commit 3aecf99811eb0c14506048a042cef6045e7167eb -Author: Oliver Beckstein -Date: Sun Apr 2 05:27:33 2017 -0700 - - transition analysis docs to numpy style (#1240) - - * analysis.density: fixed top level Example section in docs - Do not use Examples as a heading UNLESS inside a function/class doc because the NumPy reST - parser changes it to a rubric heading. This breaks document structure. - * analysis.psa: doc fixes - * analysis.align: formatting fixes - * analysis.contacts: formatting fixes - * analysis.diffusionmap: formatting fixes and section headers (cannot use - 'Examples' as a normal section header because it is rewritten by - sphinx.ext.napoleon as a rubric) - * analysis.distances: numpyfied - * analysis.hbonds.hbond_analysis: numpyfied - * analysis.helanal: doc update and code cleanup - - - removed kwargs start and end for resid selection from def helanal_main() - and helanal_trajectory() because this can be easily done inside the - selection string and neither start nor end are used further in the code. - helanal_trajectory() uses the resid of the first and last residue extensively - for reporting so we now get these resids from the selection itself. - * analysis.leaflet: numpified docs and added test for optimize_cutoff() - * analysis.legacy.x3dna: numpified docs and use OrderedDict - * analysis.nuclinfo: numpyfied docs - * analysis.rdf: fixed numpy reST - * analysis.waterdynamics: numpyfied docs (TODO: PEP8) - -commit 536c24521c4be0794d4be451c4867fca10e29272 -Author: Max Linke -Date: Fri Mar 31 13:38:05 2017 +0200 - - Update conda package files (#1271) - - - ensure that no dependencies are installed - - update dependencies - - deactivate open files plugin - - [skip ci] - -commit 71589b95f2e559356b7bd2275d0f4cb7f9f6c853 -Author: Oliver Beckstein -Date: Fri Mar 31 02:08:59 2017 -0700 - - analysis.gnm: optimizations and doc/code cleanup (PR #1272) - - - optimization - - eliminated costly lookup of residue sizes - - reduces run time of TestGNM.test_closeContactGNMAnalysis by about - a factor of 5 (!) --- should go a long way to improve #1191 - - made sure that numpy arrays are used - - argument changes and deprecations - - new weights="size" kwargs - - deprecated MassWeight for 0.17.0 (but have tests until then that - check that it works and overrides weights) - - in GNMAnalysis, replaced skip kwarg with start/stop/step - (without going through deprecation because of limited use) - - added/adapted tests for new kwargs - - code cleanup - - removed unused backup_file() function - - made GNMAnalysis._generate_output() a private method (so that I do not have - to document it...) - - numpy-style docs in whole module - -commit 90dbc149e842fb4af528b0df0526d7300aa5e5f6 -Author: Max Linke -Date: Mon Mar 27 19:39:32 2017 +0200 - - Fix automated doc build - - The MDA_DOCDIR folder is now fixed. I'm not sure why the folder has changed - when using setup.py sphinx_build and why the change is only visible on travis. - -commit 212338bf1eb5dc20e445703cb296b89f9c51cd7f -Author: Max Linke -Date: Mon Mar 27 23:57:37 2017 +0200 - - remove deprecated functions / flags / classes (#1259) - - * remove deprecated functions / flags / classes that were scheduled for removal - * remove doc for deprecated PrimitivePDBParser - * add changelog info - -commit 847f459af8a57af0206edccfb1aea9065b5e7ca1 -Author: Max Linke -Date: Mon Mar 27 15:26:14 2017 +0200 - - fix script location (#1263) - -commit 0780b499f696f0cf146507aba7cb62019a84258d -Author: Max Linke -Date: Mon Mar 27 14:09:31 2017 +0200 - - Refactor Travis into smaller jobs (#1261) - - - * add doc build - * add lint build - * modularize build with MAIN_CMD and BUILD_CMD - * update sphinx and add setup to sphinx checks for a PR (no active yet) - * general clean up of travis config - -commit bc77b3e391208f577751d4c3eb0989239a4dc341 -Author: Max Linke -Date: Sun Mar 26 13:55:34 2017 +0200 - - Pca test times (#1260) - - * change pca testfile to smaller PSF, DCD - - This has a change of 6.5 seconds on my develop machine. It should also - be a significant chunk of time on the travis test machines. - -commit 2ff2ee6ae1386a9356155f1a2b4afca8aa2073cc -Author: Utkarsh Bansal -Date: Thu Mar 23 16:40:16 2017 +0530 - - Port GRO tests to new BaseReader/Writer Test classes (#1196) - - * Adds basic TestGROReader class - - * splits BaseReaderTest into BaseReaderTest & MultiframeReaderTest - - * Update test.gro to the first frame - - * Adds velocities to GROReference - - * Adds test.gro to MDAnalysisTests.datafiles.__all__ - - * Adds n_atoms attribute to GROWriter - - * Set totaltime in GROReference - - * Adds basic TestGROWriter - - * Adds basic TestGROReaderNoConversion class - - * Adds postion, velocity and other attrs to GRONoConversionReference - - * Adds TestGROReaderIncompleteVelocities class - -commit 6f337060483ce49edcc9f1dbf863e3a9376eedc4 -Merge: e9af17194 4032398f8 -Author: Oliver Beckstein -Date: Wed Mar 22 23:03:39 2017 -0700 - - Merge pull request #1256 from MDAnalysis/issue-1027-extra-fix - - Fix confusion in transfer_to_memory - -commit e9af1719429bb8996802721ff0a3ddef32fd596c -Merge: e48153fe1 1a6627280 -Author: Oliver Beckstein -Date: Wed Mar 22 23:01:33 2017 -0700 - - Merge pull request #1255 from MDAnalysis/issue-1251-merge-memory - - universe built with Merge now use the MemoryReader - - - Fixes #1251 - - Universes built with Merge now use the MemoryReader. This slightly streamlines the code of the Merge function, and makes universes built that way full featured. - -commit 4032398f891821710dc190cfa27844a6eaeb2f3b -Author: Jonathan Barnoud -Date: Thu Mar 23 00:24:47 2017 +0100 - - Fix confusion in transfer_to_memory - - I reviewed #1252 too fast and missed a mixup in the filename passed - to the memory reader. The topology filename was passed instead of the - trajectory one. This commit fixes the confusion. - -commit 1a6627280ae6a0e219d0dea3778a3a74ff815cdc -Author: Jonathan Barnoud -Date: Wed Mar 22 23:25:32 2017 +0100 - - universe built with Merge now use the MemoryReader - - Fixes #1251 - -commit e48153fe16766c30b59f06cd3231834c71938ed8 -Author: Utkarsh Bansal -Date: Thu Mar 23 01:37:20 2017 +0530 - - Adds filename attribute to MemoryReader & associated tests (#1252) - - Fixes #1027 - - Changes made in this Pull Request: - - Adds filename attribute to MemoryReader - Adds tests - -commit 7f9c36d83cf1ed92892bcee721fa503687a87a9e -Author: Jonathan Barnoud -Date: Sat Mar 18 22:19:48 2017 +0100 - - Make selection writers more pythonic (#1245) - - * Make selection writers more pythonic - * Remove the `wa` mode - * Add a `close` method - * Close the file when leaving the context manager rather than at every write - * Factorize the tests - * Update docstring format in selections/base.py - * Fixes #1244 - -commit f3db4fa7ceeec5017153d061cdc4649dc61aa850 -Merge: 1b165be7a 5a89efeb3 -Author: Oliver Beckstein -Date: Thu Mar 16 10:52:22 2017 -0700 - - Merge pull request #1242 from kain88-de/rotate-fix - - Revert rotate default to before #1022 - -commit 5a89efeb3ef5e0d52ab388daaad1f5b24b646ca0 -Author: Max Linke -Date: Mon Mar 13 11:22:18 2017 +0100 - - update CHANGELOG - -commit 9c002e14389394c2199ffa7093a75206edb6c161 -Author: Max Linke -Date: Mon Mar 13 11:18:12 2017 +0100 - - add two protein alignment test - - This aligns a partial universe of two proteins. - -commit ff038b010af74f25a655d223361cc92adcf05308 -Author: Max Linke -Date: Mon Mar 13 08:27:43 2017 +0100 - - add default rotation center test - -commit 8c4fb51b4d5859e87dec88e259dfd41e976c5724 -Author: Max Linke -Date: Mon Mar 13 08:12:20 2017 +0100 - - revert #1022 - - To not break a lot of old code restore the old behavior of rotate to - use (0, 0, 0) as center of the rotation. - -commit 1b165be7a06b7c6505a4430dcca98503c7102e5a -Merge: aca9fd337 04391b4b4 -Author: Oliver Beckstein -Date: Wed Mar 15 16:25:43 2017 -0700 - - Merge pull request #1239 from MDAnalysis/set-operators - - Introduce operators to groups - - Fixes #726 - -commit 04391b4b4f8b9c9095ea247aa4079d1a0e5eb142 -Author: Jonathan Barnoud -Date: Wed Mar 15 16:10:26 2017 +0100 - - Polish set operators - -commit b7281dd50225f8f23bcec4f8ab17f739e144c5b9 -Author: Richard Gowers -Date: Tue Mar 14 11:48:43 2017 +0000 - - Updated docstrings for set operators - -commit 0f687ec905326646e337ac10d2c512bab0216555 -Author: Richard Gowers -Date: Sun Mar 12 14:31:02 2017 +0000 - - Suggested changes for PR #1239 - - substract -> subtract - - reworked subtract to use numpy set operations - - tried to use self.ix and self.universe rather than shortcutting - -commit 8be793043b83a2bf6852930675821ab7147a4a17 -Author: Jonathan Barnoud -Date: Thu Mar 9 20:16:08 2017 +0100 - - Introduce operators to groups - - See #726 - - This commit introduce several method to the GroupBase class, including - all the set operators, and a subtract method. Some operator symbols are - overridden. - -commit aca9fd337f47d085b25650e8346de939215be383 -Author: xiki-tempula -Date: Thu Mar 9 12:18:55 2017 +0000 - - Correct the display error of Hbond analysis (#1224) - - * Correct the display error of Hbond analysis - - * Change the progress meter to include the current time frame - - * update the format string and use enumerate instead - - - * Add to the change log - -commit a4491e381e36b7e49ce8355f2e08d9d3f439f2e1 -Author: Oliver Beckstein -Date: Wed Mar 8 16:54:27 2017 -0700 - - [DOC] added note to RMSD that molecules must be whole - - - fixes #1182 - - restructured class docs - -commit 3e445f1f5371cde7b1c74eb786fc904612ab5b04 -Author: Oliver Beckstein -Date: Wed Mar 8 15:58:36 2017 -0700 - - [DOC] fixed all SEVERE sphinx issues - - Mainly badly formatted Parameters sections and needing raw strings when escape sequences - or maths are discussed (which use backslashes). - - Rearranged some class docs so that the Parameters section is now at the class level and - __init__ is empty: this makes for a better structure when there are long Examples sections - in the class docs. - -commit f7f95a03318ae9785451cde82ab7d1ed84478532 -Author: Oliver Beckstein -Date: Wed Mar 8 15:55:38 2017 -0700 - - [DOC] updated intersphinx links (avoids redirects) - -commit 7bc420ffabe0984abe8e1ad9401599475da06344 -Author: Oliver Beckstein -Date: Wed Mar 8 15:55:13 2017 -0700 - - [DOC] removed all traces of pdb.extensions - -commit 568e39a79733f52340d09d115e350f13b7b1da93 -Author: Oliver Beckstein -Date: Wed Mar 8 12:02:37 2017 -0700 - - [DOC] density.analysis fixes - - - fix title formatting in analysis.density - - parameter formatting - - various doc fixes throughout (mostly formatting) - - link to gridDataFormat docs - -commit 686079bb8ec633e46221e5602b501d3b4c1ccded -Author: xiki-tempula -Date: Wed Mar 8 17:28:38 2017 +0000 - - fix frame slice problem introduced by np.int object (#1233) - - * fix the np.int slice problem - * tests with super comprehensive list of all the numpy integer object that you could ever think of. - * add entry to CHANGELOG - -commit 675eb10f482436f5e01c171bb3451930175959d6 -Author: Richard Gowers -Date: Mon Mar 6 15:47:52 2017 +0000 - - Fixes Issue #921 - - Renamed various base classes: - - IObase -> IOBase - Reader -> ReaderBase - SingleFrameReader -> SingleFrameReaderBase - Writer -> WriterBase - SelectionWriter -> SelectionWriterBase - TopologyReader -> TopologyReaderBase - -commit 03f1ed40828069d5adebb35b555ff5e34d82170b -Author: Kashish Punjani -Date: Wed Mar 8 04:25:17 2017 -0700 - - added tests for exceptions in Density._check_set_unit() (#1231) (#1237) - - - fixes issue #1231: tests for bad input to Density._check_set_unit() all raise - ValueError for: - - wrong unit type - - wrong unit value - - missing unit length - - Update AUTHORS and CHANGELOG - - moved new tests for exceptions in density.Density into TestDensity (@orbeckst) - - (update for PR #1235 which fixes issue #1231) - -commit 174f1b52223aec7f2b9e26af6eb7584f0d578978 -Author: Oliver Beckstein -Date: Wed Mar 8 04:18:59 2017 -0700 - - fixes density_from_Universe() (#1211) (#1236) - - * fixes density_from_Universe() (#1211) - - - This fixes a bug in PR #1232 that slipped through (found by @macraild), - namely, a spurious groupselection --> atomselection - - added test case for density_from_Universe() when using not-within coordinates - - * cleaned up docs in analysis.density - - - use numpy formatting (mostly) - - removed docs for Grid (imported from gridData: just link) - - split generated docs into section for users and for developers - - simplified density_from_Universe() by removing kwargs and just using - explicit 'parameters' parameters (the only thing that was actually used - in kwargs) - - * fixed test for dynamically updating density - - The test wrongly used kwarg 'update_selections' but the correct kwarg is - 'update_selection' (singular!). However, until the last commit, density_from_Universe - would swallow ANY unknown kwargs instead of raising an error and thus this buggy - test slipped through. - - The reference value was updated for the dynamic selection and now the actual - updating code path should be checked. - -commit 18962da7a2ae371ce7c8d7ccc682b108de33be9e -Author: Jonathan Barnoud -Date: Sat Mar 4 03:45:04 2017 +0100 - - Make an error message more useful in MemoryReader - - When the MemoryReader raise an exception because of a mismatch in the - number of atoms, the problematic numbers of atoms are displayed as part - of the exception. This make the error message more useful. - -commit 8b4d540b7c8c70c011600e3657c1e015a0238217 -Author: Richard Gowers -Date: Wed Mar 8 00:20:15 2017 +0000 - - Fixes for analysis.density (#1232) - - * Fixes Issue #1211 : notwithin_coordinates_factory now uses new KDTree and AtomGroup syntax - * Fixed analysis.density with updating selections: Updating selections can now be used within the notwithin_coordinates_factory - * docs for notwithin_coordinates_factory updated - -commit c82512bb3a35336727387fd6ca2f9dc84415a918 -Author: Jonathan Barnoud -Date: Mon Mar 6 11:23:40 2017 +0100 - - Fixes #1227 (#1228) - - At Universe creation, the coordinates were not read when the topology - was provided as a Topology object. Skipping the coordinates was likely - there to by accident because of the case where only the topology is - given. This commit moves the skip, so trying to read coordinates is - skipped only when no coordinates are provided: we do not try to read - coordinates from a Topology object. - -commit 80946b1e4537c2f64ceec978b690e14b2006bae2 -Author: Juan Eiros -Date: Thu Mar 2 15:21:13 2017 +0000 - - Smart repr and str for Groups (#1225) - - * Add __str__ method to GroupBase class - - Smart reporting of groups with more than 10 items - - * Remove individual __repr__ method of groups - -commit 23eeda8f7aad3c2316a5bef6ff28ae34e7e905c4 -Author: Richard Gowers -Date: Wed Mar 1 18:39:35 2017 +0000 - - Fixed reprs to match 0.15 behaviour (#1222) - - Fixed reprs to match 0.15 behaviour: - - verbose reprs for Atom, SegmentGroup and ResidueGroup - - terse for AtomGroup - - see #1223 for discussion of future changes: this PR is only restoring 0.15.0 - behavior so that we have a good starting point for future changes. - -commit 4d0f3e3127c1a6ade53c04bf7f93d916cebcef39 -Merge: d2cafc579 f786a64b4 -Author: Jonathan Barnoud -Date: Sat Feb 25 16:07:46 2017 +0100 - - Merge pull request #1220 from MDAnalysis/issue-1219-lowercase_format - - Remove case sensitivity for format in get_reader and get_writer - -commit d2cafc579a44ed3d2510594e80fcef5ac04e719e -Author: akshay0724 -Date: Sat Feb 25 14:56:40 2017 +0530 - - [MRG] Make knownfailure work even without parentheses (#1218) - - * Added support for knowmfailure to work without parentheses - - * Removed parentheses from existing @knownfailure() usage - -commit f786a64b4ce36e7552e91b59fc4b62aea32799b2 -Author: Richard Gowers -Date: Fri Feb 24 21:19:17 2017 +0000 - - Added tests related to issue-1219 - -commit 803d8134b994a225a0337c9be652d14f307cc365 -Merge: f4c7207da b50e68c58 -Author: Jonathan Barnoud -Date: Thu Feb 23 10:31:54 2017 +0100 - - Merge pull request #1216 from kain88-de/deactivate-osx-test - - Deactivate OSX Travis test - - The tests don't execute correctly at all right now because the install - instructions don't take care of mac/ubuntu incompatibilities. Also the OSX - builders are very limited (128 total) on travis and usually have a long backlog. Therefore - we should not use OSX to allow other projects to make better use of the - resources. - -commit b50e68c582dafc7acdedfe553d6d3c6dfe119a4d -Author: Max Linke -Date: Thu Feb 23 09:38:28 2017 +0100 - - Deactivate OSX Travis test - - The tests don't execute correctly at all right now because the install - instructions don't take care of mac/ubuntu incompatibilities. Also the OSX - builders are very limited on travis and usually have a long backlog. Therefore - we should not use OSX to allow other projects to make better use of the - resources. - -commit f4c7207dad0cd7f20d7dbd3b6ade7436e3716740 -Author: Max Linke -Date: Sat Feb 18 02:00:31 2017 +0100 - - Add links to useful tutorials in readme (#1214) - - [skip ci] - -commit bcfb1bfdd3a7c553b2123d834ae52757f652bf3a -Author: John Detlefs -Date: Fri Feb 17 15:29:29 2017 -0800 - - Reverse orders for ag.principal_axes() to reflect documentation. (#1167) - - * Reverse principal_axes order so that the eigenvectors are now sorted by *highest* eigenvalue first (as it was always stated in the docs) - * Updated CHANGELOG - * Updated tests - * Fixes #1167 - -commit 232a4e77378a7a01f6fb9fab12dddd920b7e7245 -Merge: 561540548 6273d5fd2 -Author: Max Linke -Date: Fri Feb 17 22:24:49 2017 +0100 - - Merge pull request #1213 from kain88-de/update-conda-recipe - - update conda recipe [skip ci] - -commit 6273d5fd2b465df12c811fff785a07e4a7f6c9c2 -Author: Max Linke -Date: Fri Feb 17 14:08:28 2017 +0100 - - update conda recipe - - The recipe is now updated to build the current develop branch by - default. We also acknowledge that we build against specific python - versions now. This is important since we actually build against the - numpy C-API. - -commit 561540548d862d8070c91466871abe326ef8b55a -Author: Richard Gowers -Date: Thu Feb 16 16:42:07 2017 +0000 - - Update AUTHORS (#1210) - -commit 14bad0a22bc60f9d90a324d3530375896d064eef -Author: xiki-tempula -Date: Thu Feb 16 16:00:02 2017 +0000 - - fix the typo problem for density plot. (#1208) - - When np.histogramdd is called, numpy calls the np.isfinite to check if - the range is finite or not. However, np.isfinite cannot deal with the - zip object. - -commit e45493d45ab0abd9a279a4b6554b61a3f07291ae -Merge: bb5d106a6 5e926748b -Author: Jonathan Barnoud -Date: Tue Feb 14 17:16:26 2017 +0100 - - Merge pull request #1201 from MDAnalysis/issue-1199-writerregistration - - Issue 1199 writerregistration - -commit bb5d106a64056e542e1a9e49f45d9bebd5630a44 -Merge: 39d5daa10 aad74e46a -Author: Oliver Beckstein -Date: Mon Feb 13 19:41:24 2017 -0600 - - Merge pull request #1197 from MDAnalysis/refactor-align - - Refactor align. - - use arbitrary weights in align.py and rms.py - - rewrite RMSF to use AnalysisBase - - fix centering bug in RMSD (should be done with chosen weights) - -commit aad74e46a85d3f1d7215e66b27f32ce286a74d24 -Author: Matteo Tiberti -Date: Mon Feb 13 09:56:49 2017 +0000 - - changed description for options "selection" and "superimposition_selection" in conformational_distance_matrix - -commit d516bc74101662bd5282a7503e89e912bd7a2076 -Author: Max Linke -Date: Mon Feb 13 09:47:50 2017 +0100 - - use uniform verbose/quiet arg handling - -commit a2317fb0db68ceca3854e97f3da6f08b31332825 -Author: Max Linke -Date: Sun Feb 12 20:27:32 2017 +0100 - - add more tests for the weights - -commit 705e38484acb4d1dc1622a13f879cb6954e7a1a8 -Author: Max Linke -Date: Sun Feb 12 18:40:21 2017 +0100 - - remove useless deprication warnings in confdist.py - - These warnings don't make sense since we haven't published any code with encore. - -commit af56e574c7c885bbb035d98e9d295e8afc2ab085 -Author: Max Linke -Date: Sun Feb 12 18:25:21 2017 +0100 - - fix numpy warning in weights arg check - -commit 0d6496d2682cd08fe1d6ef98b007efc24312fea5 -Author: Max Linke -Date: Sun Feb 12 17:35:05 2017 +0100 - - add RMSF.run to deprecate it later - -commit 2253984288e49f5ca8824dbcb41241bf5883ceb5 -Author: Max Linke -Date: Sun Feb 12 17:28:17 2017 +0100 - - add dummy rmsf run method - -commit 616e1293c9ca73123ab4611b2a31b81431f5c20a -Author: Max Linke -Date: Sun Feb 12 17:13:32 2017 +0100 - - add deprecation notes - -commit feca58cd92acbc1bbfb7e0edf67d1d89683f0f8f -Author: Max Linke -Date: Sun Feb 12 15:39:40 2017 +0100 - - add custom weights tests - - This makes a comparison of tests when I chose mass as weights or directly - the mass arrays from the atomgroup - -commit 60af3b258fd5ca2807787b06ca448db79c766628 -Author: Max Linke -Date: Fri Dec 30 22:23:16 2016 +0100 - - Change encore to use arbitrary weights - - This changes the methods in encore to the new arbitrary weights system. - - - fix docs and default parameters - -commit 9863cd4b1ec3258124ed0c0adc48688da6601a6e -Author: Max Linke -Date: Fri Dec 30 21:55:03 2016 +0100 - - add deprecation tests - -commit eac64f321b39b79e4a92daea858ea1a37d8249af -Author: Max Linke -Date: Thu Dec 29 11:12:11 2016 +0100 - - update CHANGELOG - -commit 9103264c3e2d6f00c4d0e4713708ac7fc636a005 -Author: Max Linke -Date: Thu Dec 29 11:09:52 2016 +0100 - - add deprecation warnings - -commit e361d6336dc2dc5b3738bb449a2955f26bd23983 -Author: Max Linke -Date: Thu Dec 29 11:05:45 2016 +0100 - - fix docs from using deprecated method - -commit 16444be0dc7786a50cd5a9e85398e63567480978 -Author: Max Linke -Date: Thu Dec 22 20:57:12 2016 +0100 - - convert RMSF to AnalysisBase - -commit 70848c6a9f6885d9152f281f27d9b440b03ba183 -Author: Max Linke -Date: Thu Dec 22 18:03:14 2016 +0100 - - correct test results! - - The old results have been wrong due to a centering bug in the RMSD code - -commit 855475271e4ce5076cacd42e3a351dd570e11956 -Author: Max Linke -Date: Thu Dec 22 18:03:04 2016 +0100 - - RMSD uses new weights kwarg, fixes bug as well - - This also fixes a centering bug. Previous the center of mass was used - independent of the used weights. Now we center with the chosen weights. This - means results might change! - -commit adc82ea4a638bd47673567f83a0c50d84cbe8335 -Author: Max Linke -Date: Thu Dec 22 08:15:04 2016 +0100 - - introduce weights kwargs also for AlignTrj - -commit 369877ce5f8da2d06b41a7420119650f5b9564b5 -Author: Max Linke -Date: Thu Dec 22 08:09:11 2016 +0100 - - Add weights kwarg to alignto - - This new general weights kwarg can take an mass argument or arbitrary weights to - allow new fitting algorithms. - -commit 6e37376bce26cac44c3d3b7aa811c5e27f59da87 -Author: Max Linke -Date: Thu Dec 22 07:55:50 2016 +0100 - - refactor rms.py:rmsd - - simplify weights handling - -commit 39d5daa10556ac00dd0de03945bc9d75fd302462 -Merge: 683967015 cc2d75d14 -Author: Max Linke -Date: Fri Feb 10 14:55:02 2017 +0100 - - Merge pull request #1204 from MDAnalysis/issue-1200-progress-transfer - - Fix transfer_to_memory progress meter call - -commit cc2d75d145be01119a31d090ad0f107fff937210 -Author: Jonathan Barnoud -Date: Fri Feb 10 14:07:30 2017 +0100 - - Fix transfer_to_memory progress message - -commit 683967015a379085efff4e709c444a00cbc90601 -Author: Shobhit Agarwal -Date: Fri Feb 10 18:11:51 2017 +0530 - - Trajectory slicing made completely Pythonic #918 (#1195) - - Makes trajectory slicing completely pythonic #918 - - Original commit messages: - - * Trajectory slicing made completely pythonic #918 - * Adds test cases - Fixes some logical error - * Merged develop branch with forked develop branch - * Adds test cases - Fixes some logical error - * Merged develop branch with forked develop branch - * Trajectory slicing made completely pythonic #918 - * Adds test cases - Fixes some logical error - * Merged develop branch with forked develop branch - * Adds some more test cases for pythonic slicing - * Fixed minor bugs - * Reduced the lines of code for the pythonic slicing logic - The tests which no longer raises an Error are removed - The values for the removed tests are moved into the test generator. - * Fixes import order - * Refractored analysis/base.py - Added warning docstring to check_slice_indices - * Modifies AUTHORS and CHANGELOG - -commit 010475643457fffc1ebea5a81b83a588497bdf05 -Author: Jonathan Barnoud -Date: Fri Feb 10 13:38:06 2017 +0100 - - Fix the number of frames in transfer_to_memory pm - - The number of frames passed to the progress meter by transfer_to_memory - was wrong, especially in the case of truncated trajectory. - - This commit pass the correct number of frames to the progress meter, and - adapt the progression message. - -commit 517b12dab722eb2d99f6e9db7ed78feaff683b68 -Author: Jonathan Barnoud -Date: Thu Feb 9 17:29:52 2017 +0100 - - Fix transfer_to_memory progress meter call - - Since I merged #1030, Universe.transfer_to_memory could instanciate a - ProgressMeter with an invalid interval. By default, that interval was - set to None, which is an invalid interval since interval must be an - integer (or must be castable to an int). - - Here, I make sure Universe.transfer_to_memory always use 1 as interval - for the progress meter. This leads to the same behaviour as before #1030 - was merged: the progress meter updates at every frame transferred. Note - that this behavior is not the default behavior of the progress meter, - and that the default behavior may be preferable. - - Fixes #1030 - -commit 5e926748b5b65ffd6b743989210833f1e0b48acf -Author: Richard Gowers -Date: Thu Feb 9 16:04:38 2017 +0000 - - added ENT format to MultiPDBWriter - -commit 393f452d820f74fdf55937947b634f7f41553c89 -Author: Richard Gowers -Date: Thu Feb 9 15:49:08 2017 +0000 - - Refactored get_writer_for - -commit 05e7115f40447d78ec6dce0bfdb1c3dca21b979b -Author: Richard Gowers -Date: Thu Feb 9 15:38:15 2017 +0000 - - Fixes Issue #1203 - - Declared null, NCDF, TRR and XTC as multiframe Writers - -commit 6940d0cc2baf4716daa293ded385262d4041cf38 -Author: Richard Gowers -Date: Thu Feb 9 15:10:59 2017 +0000 - - Added test for getting MemoryReader - -commit 652d313cb79d517ca483a1d37706a30646e838f3 -Author: Richard Gowers -Date: Thu Feb 9 14:59:45 2017 +0000 - - Adjusted test_pdb now that singleframe PDB writer is used in that case - -commit c09cb57e0cd8dc338d29b5fedb287b9b8218e006 -Author: Richard Gowers -Date: Wed Feb 8 11:27:15 2017 +0000 - - added tests for writer registration - -commit 879bc7aa50091317b4f153b7f0bd6ab51568939d -Author: Richard Gowers -Date: Wed Feb 8 11:14:43 2017 +0000 - - Changed MultiPDBWriter to *not* support single frame writing - -commit e7553dec659fad25bbbcff3ab42d332da67572b1 -Author: Richard Gowers -Date: Wed Feb 8 11:11:58 2017 +0000 - - Added support for `singleframe` keyword for Writers (default True) - -commit 180f3144976a6394503ff9b6e4ba9656f81c848a -Merge: 1af51af0c e1d0bd049 -Author: Max Linke -Date: Tue Feb 7 15:57:02 2017 +0100 - - Merge pull request #1165 from MDAnalysis/coc [skip ci] - - add code of conduct - -commit 1af51af0cb26b7deb17fbdc2a7b0096e82ee1cfb -Author: Jonathan Barnoud -Date: Sat Feb 4 12:14:43 2017 +0100 - - Deactivate open-files plugin in travis (#1198) - - The nose plugin that list open files has compatibility issues with the - plugin that captures stderr. To avoid obscure traceback in travis, this - commit deactivate the open-files plugin from travis runs. - -commit da70c1f5b685e7ad4e5d6b2f7b1bac1675be04c8 -Merge: 94f918048 bd9400724 -Author: Max Linke -Date: Sat Feb 4 08:22:30 2017 +0100 - - Merge pull request #1183 from vedantrathore/develop - - Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) - -commit bd940072418db5a90968a6720d9597514168c407 -Author: Vedant Rathore -Date: Sat Feb 4 00:57:19 2017 +0530 - - Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) - -commit 376b0b1798fb9c2002d7278bf907cd2b59a493e6 -Author: Vedant Rathore -Date: Fri Feb 3 16:36:56 2017 +0530 - - Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) - -commit 36acf58aea7020823af2b46996ca054f17b09aca -Author: Vedant Rathore -Date: Fri Feb 3 14:28:03 2017 +0530 - - Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) - -commit ece534a23614cb135d6b2d2cea6c4f2d77611a79 -Author: Vedant Rathore -Date: Thu Feb 2 17:49:25 2017 +0530 - - Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) - -commit f12458e9df61c6721b78d8725d7e1270a203eac5 -Author: Vedant Rathore -Date: Wed Feb 1 02:37:10 2017 +0530 - - Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) - -commit b706493a158322946fd239dc20618bd0d684e927 -Merge: 3943ddc44 94f918048 -Author: Vedant Rathore -Date: Wed Feb 1 02:33:57 2017 +0530 - - Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis into develop - -commit 3943ddc4480ae6d9bb9fc15f0042832e6bef93f1 -Author: Vedant Rathore -Date: Wed Feb 1 02:33:43 2017 +0530 - - Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) - -commit 94f91804815b9b531bba38cad6e67240d59a3009 -Merge: e879b4221 6b0e845fd -Author: Max Linke -Date: Mon Jan 30 23:08:46 2017 +0100 - - Merge pull request #1161 from MDAnalysis/chainid-selector-fix - - Fixed Universe chainID quick selector not grouping segments - -commit e1d0bd0496db28056efd6344b3b140240abfc9dd -Author: Max Linke -Date: Mon Jan 30 23:06:13 2017 +0100 - - fix more grammar errors - -commit ddb87121a8e7774c543af539dbce0a9da7e22988 -Author: Max Linke -Date: Mon Jan 30 12:15:15 2017 +0100 - - move COC to root folder - - [skip ci] - -commit 6127da112b23a2480ed71662111d519e6575befb -Author: Max Linke -Date: Mon Jan 30 12:14:27 2017 +0100 - - include @mnmelo comments - -commit e879b4221a673a50a2b5ce3e22b431970b580ec4 -Merge: a725b16e1 e7edff0c8 -Author: Jonathan Barnoud -Date: Sun Jan 29 09:26:54 2017 +0100 - - Merge pull request #1193 from MDAnalysis/issue-1191-timingtests - - Added timing to travis #1191 and clean a bit GNM - -commit 1dc8403600744add77ab85ceae9572331ab04e4a -Author: Max Linke -Date: Sat Jan 28 22:36:04 2017 +0100 - - minimal wording change - -commit cecc350dec45be42f4e729975d0d061cd044f967 -Merge: dcc6168ac a725b16e1 -Author: Vedant Rathore -Date: Sun Jan 29 02:23:35 2017 +0530 - - Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis into develop - -commit dcc6168ac578a8a76e62cf87ff66390f536872a6 -Author: Vedant Rathore -Date: Sun Jan 29 02:23:20 2017 +0530 - - Adds validation for dist_mat_to_vec function inputs - -commit 9090715f6e50666dd7b33176dfb426b983a1c475 -Author: Max Linke -Date: Sat Jan 28 10:38:48 2017 +0100 - - fix grammar error - -commit 0ae08ac26e923f96e6f41c5abf7fec7211de97fc -Author: Max Linke -Date: Sat Jan 28 10:35:59 2017 +0100 - - fix spelling and add form address - -commit 917d978403cd283b7e991be4c5991a4d934ba957 -Author: Max Linke -Date: Fri Jan 27 23:22:59 2017 +0100 - - add TOC [skip ci] - -commit 4e63ac2d3098c20d15030796acd4902deb8b836f -Author: Max Linke -Date: Fri Jan 27 23:21:55 2017 +0100 - - add short enforcement guideline - -commit e7edff0c8d932fc46e1421a1f4c86e04771c4d02 -Author: Richard Gowers -Date: Fri Jan 27 14:54:11 2017 +0000 - - Remove time workaround in analysis/gnm - - Timestep.time now part of API - -commit ea09574106b33452fa54700f340c6fe782fa6c51 -Merge: 16523c01e 5244c2f22 -Author: Richard Gowers -Date: Fri Jan 27 14:50:05 2017 +0000 - - Merge branch 'issue-1191-timingtests' of github.com:MDAnalysis/mdanalysis into issue-1191-timingtests - -commit 16523c01e0b445ae28207d3408450f748c3eb011 -Author: Richard Gowers -Date: Fri Jan 27 14:46:34 2017 +0000 - - Optimised analysis/gnm slightly - -commit 5244c2f22adb5115fdd10c6cb47e750b0d8b17a3 -Author: Max Linke -Date: Fri Jan 27 14:44:26 2017 +0100 - - report top 50 slowest tests - -commit 3e58007bd44c982be517176fa4a2c887b7b07d0b -Author: Richard Gowers -Date: Fri Jan 27 12:59:08 2017 +0000 - - Added timing to travis #1191 - -commit a725b16e15a15039e19cab9aac4ec52f2a4f42ad -Author: Utkarsh Bansal -Date: Fri Jan 27 16:19:48 2017 +0530 - - Add support for start and stop in transfer_to_memory (#1030) (#1189) - - * Adds start & stop parameters to transfer_to_memory - - * Rename frame_interval to step in transfer_to_memory - - * Update docstrings - - * Adds tests - - * Adds more tests - - * Update CHANGELOG and AUTHORS - - * Rename usages of in_memory_frame_interval to in_memory_step - -commit 6b8c66d0a2f421ff0f18f7725f9a4d928d7567ec -Author: David Dotson -Date: Thu Jan 26 13:27:35 2017 -0800 - - Beginnings of new topology docs (#1176) - -commit 6b0e845fd61fda01f6bb0871822d5e81924cbf0e -Author: Richard Gowers -Date: Thu Jan 26 16:27:27 2017 +0000 - - Update test_universe.py - -commit 9ba96d1c1e44e76d430e1765e22b3657bafd01b1 -Author: Max Linke -Date: Thu Jan 26 14:37:01 2017 +0100 - - changes - -commit 3b655df466baa20344bf51a09192c4e4395c51c1 -Merge: 85e5b178b dad6b32f2 -Author: Richard Gowers -Date: Thu Jan 26 13:36:39 2017 +0000 - - Merge branch 'develop' into chainid-selector-fix - -commit dad6b32f29d89cd91688588426a256d0495b2a6a -Merge: 9ef4a64a3 7e81e09fb -Author: Jonathan Barnoud -Date: Thu Jan 26 14:31:27 2017 +0100 - - Merge pull request #1164 from MDAnalysis/split_test_atomgroup - - Fixes #466 - Fixes #1178 - Fixes #940 - - Changes made - - * test_atomgroup split into many smaller files - * AtomGroup[atomname] access reimplemented (eg u.atoms['HT1']) - * size checks for topology attribute assigning - * populated MDAnalysisTests.util from __init__ - * moved make_Universe to top test namespace - * added better error messages to setting attributes from wrong level - -commit 7e81e09fb4c030ea051eb607d163ce681ce7b42f -Author: Richard Gowers -Date: Thu Jan 26 11:22:40 2017 +0000 - - TST: Commented cryptic test about setting topologyattrs - -commit cf0a47981b4b7967552e605fe44268813ad41a9d -Author: Richard Gowers -Date: Thu Jan 26 11:05:17 2017 +0000 - - TST: Added tests for setting Component attr to wrong length values - -commit 0375bf4c0cb73cb034589792873dc9d632ef0b3a -Author: Richard Gowers -Date: Thu Jan 26 10:55:34 2017 +0000 - - Updated docs for topologyattrs._check_length - -commit 3df584b0f6c6ad7e42967b180ddccde5afcf8b23 -Author: Richard Gowers -Date: Thu Jan 26 10:52:29 2017 +0000 - - TST: Added use of context manager to test writer - -commit cda6c5767dfa78fe88243c562b23afb28cf4f541 -Author: Vedant Rathore -Date: Mon Jan 23 22:35:13 2017 +0530 - - Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) - -commit bf8765b5750d685fdd35855184a6b7157ee83bae -Author: Vedant Rathore -Date: Mon Jan 23 22:21:49 2017 +0530 - - Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) - -commit 8f5740474fffd6d55f536eec0a1a8b218405ad25 -Author: Richard Gowers -Date: Mon Jan 23 11:58:17 2017 +0000 - - Fixed error message definition - -commit 85e5b178bedb05d220c9ae74efd95683cc9f5999 -Author: Richard Gowers -Date: Mon Jan 23 11:28:30 2017 +0000 - - fixup - -commit 54156cf382ea65be5645a565ab41bcc378a2370b -Merge: ce5bb30f3 326c86b9e -Author: Richard Gowers -Date: Mon Jan 23 11:24:13 2017 +0000 - - Merge branch 'split_test_atomgroup' of github.com:MDAnalysis/mdanalysis into split_test_atomgroup - -commit ce5bb30f31ee5389f48ff855788f3cb58faddf85 -Author: Richard Gowers -Date: Mon Jan 23 11:23:41 2017 +0000 - - Finished moving tests from test_atomgroup - -commit 3af71be906c365872becf7b8eba07f97baa8e364 -Author: Vedant Rathore -Date: Mon Jan 23 16:43:04 2017 +0530 - - Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) - -commit 1b0420590bb8490bc4f68f21a7b9435ab4824aea -Merge: ceb1618fd 9ef4a64a3 -Author: Vedant Rathore -Date: Mon Jan 23 16:36:25 2017 +0530 - - Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis into develop - -commit e1f77672735099661630dc4363d0a78e9bf9ee94 -Author: Richard Gowers -Date: Mon Jan 23 11:03:15 2017 +0000 - - Removed Universe topology setting tests - not valid any more - -commit 89dabea4cb6d192cda71f6769a33e6894ccc5aca -Author: Richard Gowers -Date: Mon Jan 23 10:54:53 2017 +0000 - - Added better errors for setting Attributes from wrong level - -commit 326c86b9ee4def8d7c3c46bf929589c6cb8db52f -Author: Richard Gowers -Date: Mon Jan 23 10:28:20 2017 +0000 - - Update topologyattrs.py - -commit 9ef4a64a3fbc997b14aabf22a2bced304bc16e1b -Author: Utkarsh Bansal -Date: Mon Jan 23 15:57:37 2017 +0530 - - Fix error message in case of unidentified file format (#1184) - - * Fix error message in case of unidentified file format - - * Adds testcase to check raising of correct error - - * Update CHANGELOG - -commit ceb1618fd75f97e430ad3a7485520d578647f98a -Merge: 9a49244fe 790d4816e -Author: Vedant Rathore -Date: Mon Jan 23 04:31:53 2017 +0530 - - Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis into develop - -commit 9a49244fe04961f7d9546b69af80d0d71608be61 -Author: Vedant Rathore -Date: Mon Jan 23 04:27:36 2017 +0530 - - Added exception and unittest for function dist_mat_to_vec of analysis/psa.py (part of #597) - -commit 440e1a893c56d062e03e32050f3ea247b6251eb2 -Author: Max Linke -Date: Sun Jan 22 11:59:18 2017 +0100 - - update mail address - -commit 55f66f300ba2e722d0216bfbad788b04e7e21eff -Author: Max Linke -Date: Sat Jan 21 19:21:04 2017 +0100 - - refine reporting with contributor covenant text - -commit 790d4816efbbb8ceb5f0f6fd6d6981f222aadfab -Author: Utkarsh Bansal -Date: Sat Jan 21 13:02:23 2017 +0530 - - Raises IOError if the toplogy file doesn't exist or can't be accessed (#1177) - - * Raises IOError if the toplogy file doesn't exist or can't be accessed - - * Fixes raising of IOErrors - - * Adds testcase to check non existant file - - * Adds testcase to check for invalid file (something with the wrong content) - - * Adds testcase to check for file with invalid permissions - - * Adds comments and updates CHANGELOG & AUTHORS - -commit ebacb4f2b7a18a43ea41aebb640dae066c19e90f -Merge: 282e57fbc 002d22bf0 -Author: Jonathan Barnoud -Date: Fri Jan 20 08:24:12 2017 +0100 - - Merge pull request #1181 from MDAnalysis/logic-error - - fix typo in a test - -commit 2f8b003d58aa7022f52ec7554ff950a766d78d56 -Author: Max Linke -Date: Thu Jan 19 23:53:03 2017 +0100 - - update with jupyter changes - - they have some really good additions since I checked last time - -commit 282e57fbc899adf1b4cedebe36a760555bd908cc -Author: Jonathan Barnoud -Date: Thu Jan 19 23:50:31 2017 +0100 - - lib.util.Namespace raises the expected exception (#1169) - - * lib.util.Namespace raises the expected exception - - `lib.util.Namespace` allows to query a namespace by index or by - attribute. It allows to use both the following syntaxes to access the - same element: - - ns = lib.util.Namespace() - ns['key'] = 'plop' - - ns['key'] # Access by index - ns.key # Access by attribute - - The class is used to permit some flexibility when accessing auxiliary - data attached to trajectories. - - Prior to this commit, accessing a non-existing item from a namespace by - attribute would raise a KeyError while an AttributeError should be - raise. This breaks functions that test the features of an object by - looking for some attributes, and are therefore capturing AttributeError - as a sign the attribute is missing. - - In particular, raising the wrong exception confused - `numpy.lib.type_check.iscomplexobj` in numpy 1.12.0. This confusion lead - to `assert_equal` to miss behave in that version of numpy, therefore - breaking the tests for MDAnalysis when upgrading from python 1.11.3 to - 1.12.0. - - This commit makes sure that the expected exception is raised when - accessing an non-existing item by attribute in a Namespace object. - - * Remove unnecessary mention in the CHANGELOG - - * Fixed lib.util.Namespace setattr - - Added tests for lib.util.Namespace - - Moved test_util to lib/test_util - -commit 0ccfdf34a839115a38ad894b8891b79bf20685d4 -Author: Max Linke -Date: Thu Jan 19 23:47:43 2017 +0100 - - include @orbeckst suggestions - -commit 4c2c15c3fec17f58ea180634c000f50d8a71a726 -Author: Richard Gowers -Date: Tue Jan 17 12:22:12 2017 +0000 - - Update CODE_OF_CONDUCT.md - -commit fecdaafeeb10db69b023c4b0340e971f3215e0de -Author: Max Linke -Date: Mon Jan 16 21:16:05 2017 +0100 - - add code of conduct - -commit 002d22bf00ed7db7e120341eb11435d9f262ee0c -Author: Max Linke -Date: Thu Jan 19 23:26:26 2017 +0100 - - fix broken logic - - should check for masses - -commit 7032b27b8e7080a61ee28e3bd0fa0273fdb42b63 -Author: Max Linke -Date: Thu Jan 19 21:48:44 2017 +0100 - - cast values for PureRMSD to float64 (#1179) - -commit 9ded575784673baefc181161f80bfb91b5f7c2be -Merge: 2dd43e1ea 08898c06a -Author: Max Linke -Date: Thu Jan 19 17:39:51 2017 +0100 - - Merge pull request #1173 from jbarnoud/fix_error - - Fix the error format with the open-file plugin - -commit cf05e87b2da4bfd7e37f168e0fb6d4764770896e -Author: Richard Gowers -Date: Wed Jan 18 15:54:36 2017 +0000 - - Fixed setting topology attr with wrong length values - -commit 08898c06a94c042ccd341f6e9ac41b5d04d1dee3 -Author: Jonathan Barnoud -Date: Wed Jan 18 16:15:29 2017 +0100 - - Fix the error format with the open-file plugin - - When the open-file plugin is used in mda-nose, the captured error output - is non formatted correctly. This commit fixes the formatting. - -commit 2dd43e1ea7c7280eb7655958e856ace75948f2bf -Author: Jonathan Barnoud -Date: Wed Jan 18 13:19:23 2017 +0100 - - MOL2 parser stores bond order again (#1171) - - Fixes #1170 - -commit 9ef4db2baf18de6ea5f4ee7b493458a9be5463bf -Merge: f24df4a20 5926312d9 -Author: Jonathan Barnoud -Date: Wed Jan 18 13:04:24 2017 +0100 - - Merge pull request #1172 from MDAnalysis/joblib-warning - - Removed redundant warnings in analysis/encore - -commit 5926312d921280569b79ae57f2bbdbfe49b08161 -Author: Richard Gowers -Date: Wed Jan 18 11:18:06 2017 +0000 - - Removed redundant warnings in analysis/encore - -commit e6c8e52efb30e9ebdadaf298a828bd639fb97679 -Author: Richard Gowers -Date: Tue Jan 17 16:54:42 2017 +0000 - - More splitting of test_atomgroup - -commit 933fe7628b8148b8495c84de02b42c72473f99bb -Author: Richard Gowers -Date: Tue Jan 17 14:12:09 2017 +0000 - - Moved MDAnalysisTests.core.groupbase to core.util - - Made make_Universe available at MDAnalysisTests top namespace - - Moved more tests out of test_atomgroup - -commit 59fa15251e94586fd88fa67ccbeeeddfcdb147b0 -Author: Richard Gowers -Date: Tue Jan 17 12:23:01 2017 +0000 - - Moved test utilities to MDAnalysisTests/util - - Removed check for assert_ import, should be covered in setup.py rather - than runtime - -commit a39da5bf7837ed5ccd85639d0f28bb8eaf5be06b -Author: Richard Gowers -Date: Mon Jan 16 17:08:42 2017 +0000 - - Migrated many tests from test_atomgroup into smaller test files - -commit 7222de06a066e94b255936ae3ada23ebd00ebf02 -Author: Richard Gowers -Date: Mon Jan 16 16:55:05 2017 +0000 - - (Re)Added named atom slicing to AtomGroup - -commit 9856e0455e235fcb6830cd2301d7317be60b7f10 -Author: Richard Gowers -Date: Mon Jan 16 16:32:58 2017 +0000 - - Added checks for type when adding Components and Groups - -commit f24df4a202c4248405b52695c377845543102a30 -Merge: e35660492 0087bb4d0 -Author: Max Linke -Date: Mon Jan 16 07:05:19 2017 +0100 - - Merge pull request #1135 from kain88-de/psa - - PSA use AlignTraj, fixes #1099 - -commit 0de561d2fa2526ecd5c27e7ce935b5abdefd78a7 -Author: Richard Gowers -Date: Sun Jan 15 15:29:02 2017 +0000 - - Added docs for Universe segment quick selection - -commit e35660492586d587d500a056bfadb4d2239ab7b6 -Merge: 789a96c73 2be647797 -Author: Max Linke -Date: Sun Jan 15 16:11:32 2017 +0100 - - Merge pull request #1132 from wouterboomsma/issue-1063-memory-reader-layout - - Changed default memory layout of MemoryReader to 'fac' - -commit 789a96c73c35292110e07f8f0ee2e92753c77c92 -Merge: d88567f18 c0699584f -Author: Max Linke -Date: Sun Jan 15 16:07:33 2017 +0100 - - Merge pull request #1145 from kain88-de/refactor-encore-confdist - - Refactor encore `conformational_distance_matrix` - -commit fe85f4541557d7a504c149fd3068d110ac1b4983 -Author: Richard Gowers -Date: Sun Jan 15 11:24:35 2017 +0000 - - Fixed Universe chainID quick selector not grouping segments - -commit c0699584f78c1cbc422f93eb30702e2e3f01f8c0 -Author: Max Linke -Date: Fri Jan 13 23:21:08 2017 +0100 - - switch to use standalone joblib package - - We don't use the sklearn packaged version to have most of the - encore distribution run normally inside of MDAnalysis - -commit 0dcbd8d57c5fc43589a5b99272b22e54d8c7feb6 -Author: Richard Gowers -Date: Mon Jan 9 16:06:57 2017 +0000 - - TST: Fixed block_import not blocking subpackages - -commit 8e1e525af35dfec80259365c61e9f2f31ef5c64a -Author: Max Linke -Date: Sun Jan 8 21:26:48 2017 +0100 - - fix failing test suite - -commit c2656bf0c6524197d916baea8c401e0e8bac6c96 -Author: Richard Gowers -Date: Thu Jan 5 15:08:57 2017 +0000 - - Update test_encore.py - -commit a541e15ff766a54dfed1ca4a8ef6ab6dbd96e25b -Author: Richard Gowers -Date: Thu Jan 5 14:21:35 2017 +0000 - - TST: Added tests for analysis.encore import warnings - -commit 89503205e25245c579b5cb031cacbc7068f3c284 -Author: Max Linke -Date: Sun Jan 8 16:33:32 2017 +0100 - - fix trm_indices spelling - -commit 0d068da33ae3058488d82eb28f1e8e8e3835f840 -Author: Max Linke -Date: Wed Jan 4 13:03:20 2017 +0100 - - remove ProgressBar - - it isn't used anymore and there were license issues with it - -commit e7ddb3fd049c14cbca68ea16b7eb794ca90c362f -Author: Max Linke -Date: Mon Jan 2 22:30:03 2017 +0100 - - use include guards for joblib - -commit 47858ca1a57db2209d99e387fdef7af174f09e1b -Author: Max Linke -Date: Sun Jan 1 16:47:09 2017 +0100 - - deactivate tests in minimal build - -commit 0f3dd34470d1dafdbdbcd818ecf77dbccad0cf3d -Author: Max Linke -Date: Sat Dec 31 15:10:44 2016 +0100 - - update docs - -commit 91e3a2a95547a006710c41efa6fb3eef64139c3b -Author: Max Linke -Date: Sat Dec 31 15:04:34 2016 +0100 - - use n_jobs instead of ncores - -commit a0c545582ccb819e238cbda4445d95ccb4bd0cd9 -Author: Max Linke -Date: Sat Dec 31 14:58:51 2016 +0100 - - remove unused progressbar code - -commit eb7bf3bbba4ae5a79056c24e9aba10309fb94dcd -Author: Max Linke -Date: Sat Dec 31 14:54:08 2016 +0100 - - refactor TriangularMatrix - - This gives the initialization more freedom. We can have more types to choose - from and the metadata can be passed in as a dict and still be correctly handled. - -commit 74be2a21c37f3f0f6429799ed70b625e0036f310 -Author: Max Linke -Date: Sat Dec 31 14:53:46 2016 +0100 - - remove multiprocessing completely - - now we only rely on numpy functions and joblib - -commit de0d0684c8b5e821bc8513aed7c5600c7b6ecb86 -Author: Max Linke -Date: Sat Dec 31 14:45:34 2016 +0100 - - switch to joblib parallel processing - - This is included in scikit-learn. It does work stealing job balancing for us - that helps to use the full processor power. The absolute biggest advantage of - this is though that I can now include print/exception errors for debugging in - the `conf_dist_function`. - -commit d88567f1842ca059088f0b47f986ffc3f80ef95c -Merge: 39c29e515 59288ea42 -Author: Oliver Beckstein -Date: Fri Jan 13 22:40:06 2017 -0700 - - Merge pull request #1160 from kain88-de/travis-clean-up - - clean up travis config - -commit 59288ea428198037f912d89533db9434c9490e74 -Author: Max Linke -Date: Fri Jan 13 23:31:56 2017 +0100 - - clean up travis config - - - remove old branch config - - have a common minimal install section - - install as much as possible from conda - -commit 2be6477971fc5b7146da79a9b4458e24ab4ba0f3 -Author: Wouter Boomsma -Date: Fri Jan 13 09:52:41 2017 +0100 - - Added test for default memory layout - -commit 39c29e5154d316f41ef0f47910cb04c6c7c0ba1f -Merge: 59af18fb6 2f5764938 -Author: Max Linke -Date: Thu Jan 12 22:58:34 2017 +0100 - - Merge pull request #1158 from jbarnoud/py3 - - Some fix for python 3 - -commit 2f5764938095113e5a840c8a8c366afaa5e99142 -Author: Jonathan Barnoud -Date: Thu Jan 12 22:14:39 2017 +0100 - - Some fix for python 3 - -commit 0087bb4d0192c75eed32a6b03de2ca0b6d97539c -Author: Max Linke -Date: Thu Dec 22 17:46:35 2016 +0100 - - update CHANGELOG - -commit 22dcbb2aca52066f1f854aa0e152f18c26d228a4 -Author: Max Linke -Date: Thu Dec 22 17:44:30 2016 +0100 - - switch PSA to use AlignTraj - -commit 59af18fb67cd5c4aadf02dc2614aa417001015ab -Author: David Dotson -Date: Thu Jan 12 05:48:56 2017 -0700 - - groupby method for GroupBase (#1112) - -commit f6ee182dc5252b9cfc65002df4b9b2344e3c4a15 -Author: Richard Gowers -Date: Thu Jan 12 12:38:21 2017 +0000 - - Fixes issue #1011 (#1156) - - * Reduced sensitivity to whitespace in select_atoms property selection - - * Added operator flipping in select_atoms property selection - -commit 0ada503f21a5c09b2deac68ba5ec29693088be7d -Author: Richard Gowers -Date: Thu Jan 12 12:33:56 2017 +0000 - - Pickling (#1125) - - Pickling now uses uuid rather than filenames to hash the Universe. - -commit f940c4ce324bc44523902850bf38e62712658e8f -Author: Richard Gowers -Date: Tue Jan 10 21:55:57 2017 +0000 - - Issue 1083 pdb0atoms (#1103) - - * Fixed Issue #1083 - - Writing an empty PDB file now raises an IndexError - - * Changelog for #1083 - -commit 5838d5f482b43ea3ed1c7d4400e4dbdc712fd8b0 -Merge: 64ee2319a 677057b8a -Author: Max Linke -Date: Tue Jan 10 15:57:58 2017 +0100 - - Merge pull request #1150 from jbarnoud/issue-903-verbose - - Issue 903 — Deprecate quiet in favor of verbose - -commit 64ee2319af02b0c45d5be277c677902d74956f48 -Author: Max Linke -Date: Tue Jan 10 15:02:25 2017 +0100 - - raise error if shape isn't equal in rotation_matrix (#1153) - -commit 9fca0fbe4bb729485f23635562bf2881fb54135d -Author: Richard Gowers -Date: Tue Jan 10 14:00:35 2017 +0000 - - Removed python as travis language (#1148) - - * correct minimal install environment - - griddataformats pulls scipy when installed from conda. This now installs griddataformats from pip. I have also changed the mmtf-python installation and switched to conda-forge as a channel to pull packages from. - - * only import scipy if needed in pca module - -commit 055abca036fb21ef0f1de4498d186d4d5e99c5bb -Author: Tyler Reddy -Date: Tue Jan 10 06:14:57 2017 -0700 - - TST: Added unit tests for MDAnalysis.analysis.density handling of gridData import. (#1151) - -commit 677057b8a227f9920bfbe67b690fa777ead4e98a -Author: Jonathan Barnoud -Date: Tue Jan 10 11:10:32 2017 +0100 - - Deprecate quiet in hbond_analysis - - MDAnalysis.analysis.hbonds.hbond_analysis is a peculiar case for the - deprecation of the *quiet* keyword argument in favor of *verbose*. - Indeed, the *verbose* keyword argument is already in use to toggle the - debug outputs. - - Here we deprecate the use of *quiet* in favor of *verbose*, and we - deprecate the use of *verbose* in favor of *debug*. A deprecation - warning is issued in two cases: - - * the user creates an instance of HydrogenBondAnalysis using the - *verbose* keyword argument. In this case, the user wants to set up the - debug mode and should have used *debug* in the new version. - * the user calls HydrogenBondAnalysis.run with the *quiet* argument. - There, the user wants to toggle the progress meter and should use - *verbose*. - - If the user calls HydrogenBondAnalysis.run with the *verbose* keyword - argument, then we cannot now if he intended to toggle the progress meter - following the new usage, or to set the debug output following the old - usage. Therefore, such call cannot issue a deprecation warning. Yet, the - change in behavior is visible as soon as the first step of the analysis. - -commit b9a50f44bc3090277f8d6b48a340ba2e57158360 -Author: Jonathan Barnoud -Date: Mon Jan 9 11:58:02 2017 +0100 - - Issue a deprecation warning when _quiet is defined - - If a class inherit from AnalysisBase and define self._quiet in __init__ - without going through the base class __init__, then a deprecation - warning is issued. - -commit bb0130197da7be716680e72c552e844396fe5e83 -Author: Jonathan Barnoud -Date: Mon Jan 9 11:20:01 2017 +0100 - - Test for _set_verbose use explicit arguments - -commit f5f3e798c385d538fe8cfbf9306336e1eb6a6a0c -Author: Jonathan Barnoud -Date: Mon Jan 9 10:38:28 2017 +0100 - - Move the quiet keyword at the end of signatures - - The quiet keyword is deprecated. Having it at the end of the - functions/methods signature makes it clearer it is not to be used - anymore. - -commit b029a382874282ba70b246416d28372493a699d1 -Author: Jonathan Barnoud -Date: Mon Jan 9 10:27:49 2017 +0100 - - Test _set_verbose - -commit ac36d26553534d518c6963549ba65dfe408c7e12 -Author: Jonathan Barnoud -Date: Sun Jan 8 15:49:16 2017 +0100 - - Update the changelog for the deprecation of quiet - -commit a0eed430d330c12984134ccd3e927c2b7fa4cddf -Author: Jonathan Barnoud -Date: Sun Jan 8 15:29:14 2017 +0100 - - Adapt tests to the verbose keyword - -commit f729b980ee841dc21daf8855ccc2f486716f119a -Author: Jonathan Barnoud -Date: Sun Jan 8 15:05:16 2017 +0100 - - Deprecate quiet keyword in analyses and memory reader - - The quiet keyword is *not* deprecated in hbond_analysis yet, as a - verbose keyword argument is aready used for an other purpose. - -commit 9fd96d191247acdd43c5a93a59f9d3bf2556eaa7 -Author: Jonathan Barnoud -Date: Sun Jan 8 10:48:52 2017 +0100 - - Deprecate quiet in AnalysisBase - - AnalysisBase._quiet remains for compatibility. Its use does not trigger - a deprecation warning as it is not a documented API; it could issue a - warning if defined as a property but such definition would be heavier. - - Instructions on how to deal with the post deprecation phase are added in - the docstring of the new private function lib.log._set_verbose. Thet - function handles most of the logic behing the deprecation of the quiet - keyword. It issues the deprecation warning if needed, raises an - exception if the user provided contradictory values of quiet and - verbose, and gives the value of verbose based on verbose and quiet. - -commit cd2f1aaa4ec840db8b78290e8c57e2801c9abb03 -Merge: e15836f0c 19b0a3584 -Author: Max Linke -Date: Sat Jan 7 18:16:53 2017 +0100 - - Merge pull request #1115 from MDAnalysis/issue-877-write-kwarg - - BUG: Writing a PDB file from an ag with invalid kwargs - -commit 2e1ca5af265175579a3ec90fd6a01910f6e63a9a -Author: Jonathan Barnoud -Date: Sat Jan 7 10:17:46 2017 +0100 - - Deprecate quiet keyword in progress bar - - The *quiet* keyword argument in lib.log.ProgressBar is deprecated in - favor of the new *verbose* argument. If *quiet* is used, then a - deprecation warning is issued. The class also checks that the user does - not explicitly provide contradictory values for *verbose* and *quiet*. - -commit 19b0a358422b663cf35b3fff51eb8224cfd5c79f -Author: Richard Gowers -Date: Fri Jan 6 15:02:33 2017 +0000 - - Fixup of last - -commit e15836f0c31115824611b70cb23c6f102b0ba590 -Merge: 58200c876 d0c1a93ff -Author: Max Linke -Date: Wed Jan 4 14:15:00 2017 +0100 - - Merge pull request #1146 from MDAnalysis/level-simplify - - Remove core.levels to simplify things - -commit d0c1a93ff970045eb75c3eb037e228b90b98381d -Author: Richard Gowers -Date: Tue Jan 3 17:28:02 2017 +0000 - - Update groups.py - -commit b83026a87b980d4b54e4140996b5233cad333398 -Author: Richard Gowers -Date: Tue Jan 3 17:24:33 2017 +0000 - - Added docs on levels - -commit 7c68e2a2d512a5a0b6accfa155c15bd82e25f044 -Author: Richard Gowers -Date: Tue Jan 3 14:06:30 2017 +0000 - - Replaced core.levels.Level with namedtuple - -commit eb2fac2274a1ff09c68dbbf8a63f95c69a30bb6e -Author: Richard Gowers -Date: Tue Jan 3 13:53:38 2017 +0000 - - Reworked core.levels to simplify them - - TST: reworked test_groups to not use level string comparison - -commit 58200c876b381a006b42285c44e762defc332241 -Merge: 6e5183000 47abb63f9 -Author: Max Linke -Date: Tue Jan 3 11:39:32 2017 +0100 - - Merge pull request #1119 from MDAnalysis/topologyobjects-coverage - - Topologyobjects coverage - -commit 6e51830006cdfdb83c9c0abb3c53ca74b41bda46 -Author: Tyler Reddy -Date: Sun Jan 1 10:58:42 2017 -0700 - - TST: Added scipy import warning unit test to test_distances.py. (#1141) - - * TST: Added scipy import warning unit test to test_distances.py. - - * TST: Added block_import to MDAnalysisTests.util (#1143) - - * TST: Attempted fix of relative imports in PR#1141. - - * TST: updated test_distances.py to use new block_import decorator. - - * TST: TestImportWarnings now clears analysis.distances from sys.modules to properly test import warnings. - - * TST: TestImportWarnings now checks for the exception raised if scipy is absent when using contact_matrix. - -commit bf378bf72fbfe1211e41355d3abd328504b39806 -Merge: 543084e69 ab4d2076e -Author: Max Linke -Date: Thu Dec 29 23:39:08 2016 +0100 - - Merge pull request #1138 from kain88-de/totaltime - - totaltime assumes first frame is at time 0 - -commit ab4d2076e0f59350b0277c43e0b0ef33fad7b702 -Author: Max Linke -Date: Fri Dec 23 19:45:13 2016 +0100 - - totaltime assumes first frame is at time 0 - -commit 543084e6945cc57a0003a5fa0aa3ce5a03644634 -Author: mnmelo -Date: Wed Dec 28 18:01:47 2016 +0000 - - Made UAG.ensure_updated a private method. (#1142) - -commit 7c81dd28768003621fd769a9c78cb5677aeba615 -Author: mnmelo -Date: Wed Dec 28 13:55:21 2016 +0000 - - Added dynamically updating atomgroup selections (#175 and #1074) (#1080) - - * Added dynamically updating atomgroup selections (#175 and #1074) - - Cleaned up some selection docs - - Updated some uses of itertools.izip to six.zip - - Cleaned up some variable names in groups.py that could eventually clash with - the six module. - - Made AtomGroup __repr__ fancier by inflecting with the number of - elements. - -commit bc05a221dae97085dd2ac49a80d89c16b20a9737 -Merge: c6050648f 83b4b8e16 -Author: Oliver Beckstein -Date: Sun Dec 25 23:01:04 2016 +0100 - - Merge pull request #1139 from MDAnalysis/docs-build - - Build docs only in full configuration - -commit 83b4b8e16e45ccc7bff3a50a8ee29bca5003723a -Author: Max Linke -Date: Sat Dec 24 06:49:10 2016 +0100 - - Build docs only in full configuration - -commit c6050648f526436cbe4fee944e2d0828eb9daa60 -Merge: 6eece4d27 16d5c6cc8 -Author: Max Linke -Date: Fri Dec 23 19:33:53 2016 +0100 - - Merge pull request #1123 from MDAnalysis/core-coverage - - Added tests for groups accessing the Reader - -commit 6eece4d2774d8aa37498576d99ea7c42a005e9e3 -Merge: 6a4e42fd9 8bcab6b0d -Author: Max Linke -Date: Fri Dec 23 16:27:55 2016 +0100 - - Merge pull request #1127 from MDAnalysis/core-selections-coverage - - Test coverage increase for core/selection - -commit 6a4e42fd925e925e389bc879432f9605b22f9c76 -Merge: ca690007d 8dd8f0f42 -Author: Max Linke -Date: Fri Dec 23 16:25:39 2016 +0100 - - Merge pull request #1131 from alejob/develop - - Solved issue #935. Improvement of documentation of Waterdynamics module. - -commit ca690007daa33e60a72a5ab0c97fba1febf44612 -Merge: 4de2b70db d5ac1bf3a -Author: Oliver Beckstein -Date: Wed Dec 21 19:25:31 2016 -0700 - - Merge pull request #1134 from kain88-de/cython-setup-check - - warn about missing cython for dev builds, fixes #836 - -commit d5ac1bf3af38ebd7a7f1622861f8618a141d00a4 -Author: Max Linke -Date: Wed Dec 21 23:41:02 2016 +0100 - - warn about missing cython for dev builds - -commit 2f71f11eb4180d08827fa56d6fde09c3963ce8a9 -Author: Wouter Boomsma -Date: Tue Dec 20 23:05:51 2016 +0100 - - Changed default memory layout of MemoryReader to 'fac' - -commit 8dd8f0f424195a398731a3fbb1447a49af93c747 -Author: Alejandro Bernardin -Date: Tue Dec 20 15:10:31 2016 -0300 - - Updated CHANGELOG - -commit 4272db226d1c1d60369589190dae597dc3ae16ef -Author: Alejandro Bernardin -Date: Tue Dec 20 14:58:42 2016 -0300 - - Solved issue #935. Improvement of documentation of Waterdynamics module. - -commit 8bcab6b0d470d00cb12ef5d36527005d57dae64f -Author: Richard Gowers -Date: Thu Dec 15 14:35:08 2016 +0000 - - Tests: Added tests for model keyword in select_atoms - -commit f35514581b1f7bcf52f9642e97f2f71476b1901d -Author: Richard Gowers -Date: Thu Dec 15 14:24:15 2016 +0000 - - Tests: Added test for RangeSelection error - -commit 5971db58bd51ece2c3823f1504e3ddea9dbb7032 -Author: Richard Gowers -Date: Thu Dec 15 13:04:10 2016 +0000 - - Removed core.selection.unique in preference of AG method - - AtomGroup has intrinsic unique method so use this over an auxiliary - method - - Tests: - - Reactivated skipped tests in test_atomselections - - Removed TODO about nucleic tests, these have now been added - -commit ac40860c2e6465e04ffe4d9bb54cc060294142ce -Author: Richard Gowers -Date: Tue Dec 13 12:24:29 2016 +0000 - - Updates to AG.write and SelectionWriters - - Updated AtomGroup.write method. Errors from Writer should now propogate - properly. - - SelectionWriters now have a Registry similar to Coordinate Writers - - SelectionWriters now support the `with` statement (like Coordinate - writers) - -commit 16d5c6cc8761a183fc5864f81ba4ed4fd2f16139 -Author: Richard Gowers -Date: Mon Dec 12 22:01:39 2016 +0000 - - Tests: Added tests for groups.n_GROUP - -commit 0e8099ade5ee93d9cbd52321277f1d7101d805a3 -Author: Richard Gowers -Date: Mon Dec 12 21:52:30 2016 +0000 - - Tests: Fixed TypeError tests for ResidueGroup.segment assigning - -commit b625e963f38ac82ad91fc65d585408772760dab4 -Author: Richard Gowers -Date: Mon Dec 12 21:51:52 2016 +0000 - - Moved AtomGroup.split tests into new directory - -commit 3a8ff5d2e3b755f318e0fdb66a5656ba14b04b25 -Author: Richard Gowers -Date: Mon Dec 12 15:36:30 2016 +0000 - - Added tests for errormessage of NoDataError on velocity/force access - - Fixed velocity/force access propagating the wrong error message - -commit d5e44ae0836f702aa4e5ce28b5d569272081436e -Author: Richard Gowers -Date: Mon Dec 12 14:17:48 2016 +0000 - - Added tests for groups accessing the Reader - - Added velocities and forces kwargs to MDAnalysisTests make_Universe - - Migrated all velocity and force related tests together - -commit 4de2b70db0a0a74909b4f9bdcf46b98f8352f3f6 -Author: Richard Gowers -Date: Fri Dec 9 22:40:33 2016 +0000 - - Fixes Issue #1120 (#1121) - - Fix: MMTFParser now converts null strings to empty strings - - * Fixes Issue #1121 - * Fixed \x00 -> '' for altLoc (and iCode) in mmtf - -commit 47abb63f92de201e5509127b6ab9cf07ee02ae39 -Author: Richard Gowers -Date: Fri Dec 9 12:50:12 2016 +0000 - - More tests for core/topologyobjects - - Fixed weird bug in lib.util.unique rows when a view of array was used - -commit ec76ea42bc662246c6c09f1e055e34ecf19c6555 -Author: Richard Gowers -Date: Fri Dec 9 12:16:49 2016 +0000 - - Fixed Bond.length(pbc=True) returning an array (should be float) - - Fixed numpy giving DepWarning on array comparison. Use np.array_equal! - -commit 74d2a606dd0d1641f900e0050a084d9aadd65bbb -Author: Richard Gowers -Date: Fri Dec 9 11:38:06 2016 +0000 - - Readded tests for TopologyGroup Cython methods - -commit efdeec503a1cc39fe60e65fd77522345ad523252 -Author: Tyler Reddy -Date: Thu Dec 8 13:39:01 2016 +0000 - - BUG: Writing a PDB file from an ag with invalid kwargs now raises an appropriate exception. Fixes #877. - -commit 8891fcb11cefcc5fb755c3a96db59e084a11c35d -Merge: 4a1113df3 1400ee979 -Author: Oliver Beckstein -Date: Wed Dec 7 13:33:22 2016 -0700 - - Merge pull request #1113 from MDAnalysis/netcdf-tests - - Netcdf fixes and tests - -commit 1400ee9790f66fdcd1fccf36a7040367ed238c9f -Author: Richard Gowers -Date: Tue Dec 6 12:24:09 2016 +0000 - - Fixed netCDFWriter sometimes writing velocities as forces - - - Wrote velocities as forces if convert_units was False - - new tests pass - -commit 00437f08e74d754b5ee91770f3d8be1f14da650a -Author: Richard Gowers -Date: Tue Dec 6 12:15:14 2016 +0000 - - Added tests for errors in netcdf format Reader/Writer - -commit 4a1113df3baa316c1b073245f2dc7859df6331e0 -Merge: efaf156a9 6b1b97b0f -Author: Max Linke -Date: Tue Dec 6 22:30:05 2016 +0100 - - Merge pull request #1111 from MDAnalysis/issue-1110 - - Fix for issue-1110 - -commit 6b1b97b0f334f06abfef50740ef743a290843c29 -Author: Richard Gowers -Date: Mon Dec 5 13:50:11 2016 +0000 - - Added tests for issue #1110 - -commit 2e321076e7a9494dc3f43fe6244ff7c746d7b7af -Author: Richard Gowers -Date: Mon Dec 5 10:59:08 2016 +0000 - - Fix for issue-1110 - - PDBParser: New residue now triggered when ChainID changes - -commit efaf156a923507623ea0669176065458bbe60bff -Merge: 69f9a950a 58fc4e5b5 -Author: Max Linke -Date: Mon Dec 5 07:22:37 2016 +0100 - - Merge pull request #1106 from MDAnalysis/issue-1003-libmdaxdrdoc - - docs for libmdaxdr and XDR-based Gromacs formats fixes: #1003 - -commit 58fc4e5b50256b8434ffc66404449b734fe7ff24 -Author: Max Linke -Date: Sun Nov 27 20:49:22 2016 +0100 - - docs for libmdaxdr and XDR-based Gromacs formats - - - closes #1003 - - libmdaxdr (under formats) - - coordinates.XDR - - coordinates.{XTC,TRR} - - notes of offsets - -commit 69f9a950a99b1bf078c02c7eedd66e3d2d77408b -Merge: 118563038 aecbc8787 -Author: Max Linke -Date: Fri Dec 2 14:40:55 2016 +0100 - - Merge pull request #1102 from MDAnalysis/issue-1089-encore-rms_fit_trj: Fixes #1098 - - ENCORE - replace align.rms_fit_trj with align.AlignTraj(...).run() - -commit aecbc8787bc1c7c5bab567a9d51b687844aae1b0 -Author: Matteo Tiberti -Date: Fri Dec 2 12:26:31 2016 +0000 - - fixed indentation of AlignTraj() calls - -commit cd3434c5155bdbb46190193f2907b637a192618a -Author: Matteo Tiberti -Date: Fri Dec 2 11:44:49 2016 +0000 - - replaced align.rms_fit_traj with align.AlignTraj(...).run() - -commit 118563038ddfd5c59d267a6475d6d78cbf017dac -Author: Tyler Reddy -Date: Wed Nov 30 18:20:00 2016 +0000 - - DOC: Wrapping up updates to MDA citation requirements (#1096) - - * DOC: Updates to MDA citation requirements in SUMMARY and README. - - * cleanup of README/INSTALL/LICENSE - - - removed all licensing with respect to KD-tree/Biopython: we do not ship any - Biopython code anymore - - changed license description for Gromacs xdrlib: it is now BSD-2-clause (like); - the LICENSE file is correct - - removed any mentioning of LGPL for libmdaxdr because it is GPL v2 like everything else - - changed wiki and doc links to use our redirects docs.mdanalysis.org and wiki.mdanalysis.org - - cleaned up INSTALL: added quick install at top, removed most of the crud, and just link - to the wiki - - changed the copyright in README to be in line with #993 - - * updated citation header in C files - - * fixed size of test data files (~70 MB) - -commit 1a0cb95f65a7324e427720470e704c4c58b3c73e -Author: Max Linke -Date: Wed Nov 30 18:03:45 2016 +0100 - - Encore license switched to GPL v2, fixes #1094 (#1097) - - * Switch encore to GPLv2 license (with explicit consent of all authors @wouterboomsma , @mtiberti , @tbengtsen): Now all the encore code has the same license and header as the rest of MDAnalysis. - * remove all GPL notices (we ship the GPL v2 in the LICENSE file) - * remove leftover file - * fixes #1094 - -commit a5de9922eefcf9c4de84ea715b0abef9d1535b5e -Author: Max Linke -Date: Wed Nov 30 15:27:29 2016 +0100 - - generalized centering for groups (#1090) - - * add new center method - - A more generalized function of center_of_geometry and center_of_mass. This will - allow to write more general algorithms in the future. Add docs and tests as well - - * update CHANGELOG - - * Added failure tests to AtomGroup.center - - Added example to center docs - -commit a6a6db3f9147500f05e61bc8a8e1629be46a3505 -Merge: df97b5054 66749f41a -Author: Max Linke -Date: Wed Nov 30 13:37:41 2016 +0100 - - Merge pull request #1100 from MDAnalysis/groups-testcoverage - - TST: Nudging up core/groups coverage - -commit 66749f41aee09d021c407702f917d57d9cf00960 -Author: Richard Gowers -Date: Wed Nov 30 11:40:57 2016 +0000 - - TST: Nudging up core/groups coverage - -commit df97b5054980f2c96e4f7ca122d95088a053cb5e -Merge: bff425cbc c6435d83e -Author: Max Linke -Date: Tue Nov 29 15:03:46 2016 +0100 - - Merge pull request #1086 from MDAnalysis/issue-1081-randomaccess - - Issue 1081 randomaccess - -commit bff425cbc672245dcfbd6f236732e213bc1e19b6 -Merge: d08025055 2e37f68a9 -Author: Richard Gowers -Date: Tue Nov 29 10:43:43 2016 +0000 - - Merge pull request #1088 from MDAnalysis/update-citation - - update all headers - -commit c6435d83ec87d781d59dabb4c2e898c695855338 -Merge: a98dcaa3d d08025055 -Author: Richard Gowers -Date: Tue Nov 29 10:38:32 2016 +0000 - - Merge branch 'develop' into issue-1081-randomaccess - - Conflicts: - .travis.yml - -commit a98dcaa3d2b10fc0b8c2e98ab5d9c8e1f7304824 -Author: Richard Gowers -Date: Thu Nov 24 13:03:13 2016 +0000 - - Added random access to GMS Reader - - Added random access to TRJ Reader - - Refactored GMS tests - - Added slicing tests for TRJReader - - Added random access tests for gms reader - - Updayed hbond_autocorrelation tests now TRJReader has random access - - Added mock to travis requirements - - Added mock to testsuite requirements - -commit d080250554d89504641b762bd84cd275eae57c4e -Merge: dd5836509 3d7d8a07d -Author: Richard Gowers -Date: Tue Nov 29 10:33:30 2016 +0000 - - Merge pull request #1082 from MDAnalysis/issue-810-fetchmmtf - - Issue 810 fetchmmtf - -commit 3d7d8a07d81c323ff05a26ecc0da211037393681 -Author: Richard Gowers -Date: Tue Nov 22 11:48:50 2016 +0000 - - Refactored Universe.__init__ to separate topology and coordinate logic - -commit 0b7f68cc3b6c8a4c8266ccb953d21cde785a13e1 -Author: Richard Gowers -Date: Tue Nov 22 11:22:24 2016 +0000 - - Changed format special cases to upper case - -commit cd37cce93e8203c35ce778b00407cc531b095b21 -Author: Richard Gowers -Date: Tue Nov 22 11:14:47 2016 +0000 - - Removed circular imports in core/universe - -commit 84f55c1474b4fc519f82d3aa53d5deed837df93a -Author: Richard Gowers -Date: Tue Nov 22 11:12:17 2016 +0000 - - get_reader_for now detects if format is a Reader - -commit 9bb1b4724efc0f6802b805c2b4b63fe35f086bca -Author: Richard Gowers -Date: Mon Nov 21 15:20:21 2016 +0000 - - Added fetch_mmtf function! - - Added mocked mmtf_fetch tests - -commit dd583650955d7b8bc07ad46bec1f158c5d6666b3 -Author: Tyler Reddy -Date: Sun Nov 27 18:45:16 2016 +0000 - - BUG: rms.RMSD now properly leverages ProgressMeter. Fixes #1084. - - * BUG: rms.RMSD now properly leverages ProgressMeter. Fixes #1084. - - * BUG: Addressed reviewer comments in PR#1085. - - * BUG: Added unit test for fix in PR#1085. - - * update rms to use new pm format - -commit 2e37f68a9b0ccf458bd369ca442d36f768b5f76f -Author: Max Linke -Date: Sun Nov 27 12:07:49 2016 +0100 - - update all headers - -commit 37d107ef260b82ad17a75cf89f528900bf3223ae -Author: David Dotson -Date: Fri Nov 25 01:11:39 2016 -0700 - - MMTF now properly installs automatically (#1087) - -commit 6422f709359e320560f2d3875e7282eabff53c94 -Author: Richard Gowers -Date: Mon Nov 21 14:58:32 2016 +0000 - - Moved get_*_for to lib/util - - get_reader_for, get_writer_for and get_parser_for now in lib/util - - MMTFReader and MMTFParser now accept a MMTFDecoder object as 'filename' - -commit df5a555327c5d8a94ad1d9ca13d1f79f201e531a -Author: Richard Gowers -Date: Mon Nov 21 13:36:27 2016 +0000 - - Refactored Reader&Parser registries to top module namespace - - Avoids annoying circular import problems - -commit d2a8c6a52c4f91905534c9de561ce41475cb1e14 -Author: Oliver Beckstein -Date: Mon Nov 21 06:19:43 2016 -0700 - - Refactor chain reader (#1079) - - * refactored ChainReader: base.ChainReader --> chain.ChainReader - - - new coordinates.chain module - - split old test_coordinates.py into test_amber_inpcrd.py and - test_chainreader.py - - updated docs throughout (and changed/updated/fixed docs - related to readers/writers/Trajectory API) - - added sphinx docs for chain.ChainReader - - updated CHANGELOG - - * test_modelling: removed unused output file that littered tests - - * renamed ChainReader.get_flname() and fixed QC minor problems - - ChainReader.get_flname() is effectively a private method that is only - used inside ChainReader: renamed to ChainReader._get_filename() without - any deprecations or stubs (no user should have ever used it). - - Also fixed various QuantifiedCode complaints. - -commit 4722e070a0f7394975d3a6bee2fce1f37dc07fe6 -Merge: 578c52520 e8fa15ac1 -Author: Max Linke -Date: Sat Nov 19 23:29:00 2016 +0100 - - Merge pull request #1076 from MDAnalysis/issue-1059-ALignTraj-MemReader - - Issue 1059 add _in_memory to AlignTraj - -commit e8fa15ac18ea0f46fa25b47fabdb54af0c814b57 -Author: Oliver Beckstein -Date: Sat Nov 19 00:30:32 2016 -0500 - - changed core.get_write_for() - - - first argument filename is now required (no default None - anymore) - - filename=None selects the NullWriter - - updated CHANGELOG - -commit 390a3025a511edb4fe4f43e6a8cf95ab38d433aa -Author: Max Linke -Date: Fri Nov 18 23:57:23 2016 +0100 - - add test for partial fit - -commit a1768b873757e92eaffbefe476e39b15b3867c73 -Author: Max Linke -Date: Fri Nov 18 09:23:32 2016 +0100 - - fixes in AlignTraj that are required for in_memory - - - write whole atom universe in AlignTraj - - initialize base after reader conversion - -commit fd1d56021860ea4b40e6262f2def5d552481b133 -Author: Oliver Beckstein -Date: Thu Nov 17 01:44:12 2016 -0700 - - adding in_memory to alig.AlignTraj - - fixes #1059 - -commit ff93ad6a54622ab561814ce2c387d85797611339 -Author: Oliver Beckstein -Date: Thu Nov 17 01:16:44 2016 -0700 - - adds NullWriter - - The NullWriter ignores all input but provides the Writer API (think of - /dev/null that can be used wherever MDA uses Writers): allows suppressing - of output. - - - added coordinates.null.NullWriter - - added simple test - - added docs - -commit 578c52520e838d9e5940f3a76c8ee5ec7d847ec0 -Author: Oliver Beckstein -Date: Fri Nov 18 22:43:00 2016 -0500 - - doc fixes (especially new topology system) (#1077) - - - added missing docs for new topology system (#363) - - removed some of the obviously old outdated topology discussions (but still need proper discussion of #363 changes – see issue #1078 ) - - added rst sphinx stubs for new modules in core - - updated rst docs (added links, reformatted, fixed, found out that - Napoleon REQUIRES two lines before .. versionchanged/versionadded) - - removed AtomGroup.rst - - restructured core_modules - - fixed Universe and AtomGroup reST references (core changes in #363) - - find . -name '*.rst' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Universe (MDAnalysis.core.universe.Universe)g' - find . -name '*.py' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Universe)(MDAnalysis.core.universe.Universe)g' - find . -name '*.rst' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.AtomGroup)(MDAnalysis.core.groups.AtomGroup)g' - find . -name '*.py' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.AtomGroup)(MDAnalysis.core.groups.AtomGroup)g' - - - fixed reST links for other changes in core (#363) - - AtomGroup.Atom --> groups.Atom - - AtomGroup.Merge --> universe.Merge - - AtomGroup.ResidueGroup --> groups.ResidueGroup (no SegmentGroup needed to be fixed, no Residue or Segment found) - - core.Selection --> core.selection - - find . \( -name '*.py' -o -name '*.rst' \) -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Atom)(MDAnalysis.core.groups.Atom)g' - find . \( -name '*.py' -o -name '*.rst' \) -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Merge)(MDAnalysis.core.universe.Merge)g' - find . \( -name '*.py' -o -name '*.rst' \) -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.ResidueGroup)(MDAnalysis.core.universe.ResidueGroup)g' - - - many more doc fixes everywhere - - broken reST links - - added more cross references and SeeAlso - -commit a294166068c6f28aee195d9b089430bf736056c3 -Author: Richard Gowers -Date: Fri Nov 18 12:59:39 2016 +0000 - - new MMTF Reader (Issue #907) (PR #1069) - - * Added support for MMTF format (#907) - * closes #907 - -commit 66987a66acfdb0927fa295505c3b6725279c8045 -Merge: 7cb24316a 4bb1b5584 -Author: Max Linke -Date: Mon Nov 14 21:13:32 2016 +0100 - - Merge pull request #1073 from kain88-de/pca-clean-up - - Pca clean up #953, #954 - -commit 4bb1b558433173aaf7e90c519a633212821333b2 -Author: Max Linke -Date: Mon Nov 14 16:12:21 2016 +0100 - - fix tests - -commit 4e7132c302ab2cb5d63564c9573b10319e82081c -Author: Max Linke -Date: Mon Nov 14 16:07:49 2016 +0100 - - remove performance warning, fix #954 - - It's a note now. This helps since the normal use now won't trigger a - warning. - -commit 062239f264b76ea1dd36975b11ea9ece8ba030b4 -Author: Max Linke -Date: Mon Nov 14 15:45:52 2016 +0100 - - accept universe instead of AtomGroup, fixes #953 - - Now we accept a universe directly. This way the Atomgroup was handeled - internally before. - -commit 7cb24316a6810e7574b5d6767899ac9eaf89ebc3 -Author: Max Linke -Date: Sun Nov 13 21:59:21 2016 +0100 - - Add AtomGroup stub, fixes #1067 (#1070) - - * Add AtomGroup stub - - Any class used from this module will raise a warning. The classes work - without needed to be specially imported. - - * fix Universe Warning Message - - * update changelog - - * add test for deprecation warning - - * Added compatibility for old AtomGroup init methods - - * Added tests for deprecated Group init methods - -commit 9912e153a5a7095a1d7a6ff1f63f5922d1bf165f -Merge: 992aaa42d 1f60b047d -Author: Max Linke -Date: Fri Nov 11 15:04:14 2016 +0100 - - Merge pull request #1066 from MDAnalysis/issue-839-icodeselection - - Issue #839 - Resid selection with icodes - -commit 1f60b047d29323a9245c7ddc02b05da727e58b66 -Author: Richard Gowers -Date: Fri Nov 11 12:30:22 2016 +0000 - - Docs for issue 839 - -commit 2fa757d17ae663cf01b9bf2bf971981791d352ff -Author: Richard Gowers -Date: Fri Nov 11 12:24:04 2016 +0000 - - Changelog for 839 - -commit 8d7b19c21706b3468d4faaa008fca003c280b008 -Author: Richard Gowers -Date: Fri Nov 11 12:21:35 2016 +0000 - - Tests for icode selection failure - -commit ac1a351638b5ef1e3f9860ab0ebd57eb15e7f65b -Author: Richard Gowers -Date: Fri Nov 11 12:16:04 2016 +0000 - - Fixes for selections with icodes being respected - -commit 992aaa42d6aafb82cf45a75c757d566a78dbd65a -Author: Max Linke -Date: Tue Nov 8 16:20:10 2016 +0100 - - make kwargs read only (#1068) - -commit e6f0464371a8c26f6246869821b892e78af162c5 -Author: Richard Gowers -Date: Mon Nov 7 14:53:11 2016 +0000 - - WIP of Issue #839 - -commit 94f1d75a378677a2ebc6ba4e9f242b5b64cfb277 -Merge: 168e592a2 a53c5c39a -Author: Max Linke -Date: Mon Nov 7 12:08:16 2016 +0100 - - Merge pull request #815 from MDAnalysis/issue-363 - - WIP: Issue 363 - New Topology System - -commit a53c5c39a761d796ed6e2ad43523a2ebb906f087 -Merge: c62c3be67 168e592a2 -Author: Richard Gowers -Date: Mon Nov 7 10:22:10 2016 +0000 - - Merge branch 'develop' into issue-363 - - Conflicts: - package/AUTHORS - package/CHANGELOG - testsuite/MDAnalysisTests/analysis/test_psa.py - -commit c62c3be678d8dcffdc98c1c12d2ce59514e46704 -Author: Richard Gowers -Date: Mon Nov 7 10:17:28 2016 +0000 - - TST: Added tests for DATAWriter - -commit 168e592a28e2d642c6d5be92eba5504302b779e3 -Merge: a377e11aa 8ac406ede -Author: Max Linke -Date: Fri Nov 4 09:19:45 2016 +0100 - - Merge pull request #1056 from MDAnalysis/issue-1047-encore-docs - - Issue 1047 encore docs - -commit 8ac406ede0b678d0ca2ecbb22068948dea48e654 -Author: Oliver Beckstein -Date: Thu Nov 3 17:07:28 2016 -0700 - - reST fix for encore.similarity and updated analysis.density gridData import error message - - [ci skip] - -commit b99d4934e6520e588fc985e681da3366209b4f6f -Author: Wouter Boomsma -Date: Thu Nov 3 09:31:43 2016 +0100 - - Issue 1047 encore docs (#1062) - - * Fixes in Encore and MemoryReader documentation to make it render with sphinx. - - * Edits in Encore and MemoryReader documentation. - - * Renamed PrincipleComponentAnalysis to PrincipalComponentAnalysis. Minor edits in documentation. - - * Changed spacing issues - -commit 0438c255c33a5dee815beb1a005cc1545768f09c -Author: Richard Gowers -Date: Wed Nov 2 14:23:35 2016 +0000 - - Issue 363 pqrwrite (#1061) - - * Finished checking PQRWriter - - * MOL2Writer now cleanly doesn't write non mol2 sources - - * Finished checking PDBQT - -commit bbda282d98d6b72f058da8d71cbd288de0fb9070 -Author: Oliver Beckstein -Date: Wed Nov 2 00:41:08 2016 -0700 - - added Matteo Tiberti and Tone Bengtsen (ENCORE) to AUTHORS - -commit 5a24204416e95245bfdc18d15e266b23a6d1bdb5 -Author: Oliver Beckstein -Date: Wed Nov 2 00:32:35 2016 -0700 - - include docs for MemoryReader - - - fixes https://github.com/MDAnalysis/mdanalysis/pull/1056#issuecomment-257536667 - - added entry to reST sphinx docs - - added/changed docs in coordinates/memory.py: - - included AnalysisFromFunction example from https://github.com/MDAnalysis/MDAnalysis.github.io/pull/30#discussion_r85888977 - - included transfer_to_memory() example - - included example for how to make a in-memory trajectory of a sub-system with Merge() and Universe.load_new() - from https://github.com/MDAnalysis/mdanalysis/issues/915#issuecomment-256225321 - - minor reST fixes in the MemoryReader docs (e.g., renamed the Examples section because the - numpy format napoleon parser treats this heading special and does not recognize it as a standard - section) - -commit e2d05ace88ae4b59f5bd4b585b654320f27d4a4b -Author: Max Linke -Date: Tue Nov 1 18:17:59 2016 +0100 - - WIP: Issue 363 tests (#1052) - - * Add tests - - * TST: Added tests for get_named_residue - - * fix imports and pylint warning - -commit 64bad77fea49e4e925438ba08325fa159c8c1f97 -Author: Max Linke -Date: Mon Oct 31 23:20:13 2016 +0100 - - Issue 363 pylint fix: #1044 (#1058) - - * Add pylintrc - - * activate pylint during CI - -commit fa150d71628a3aa514341acde25ecabaea9a60de -Author: Shantanu Srivastava -Date: Sun Oct 30 13:46:29 2016 +0100 - - Added ProgressMeter to transfer_to_memory function - -commit 8704d48335a739ec086ace54246e0fad8a4c6419 -Author: Oliver Beckstein -Date: Thu Oct 27 23:26:26 2016 -0700 - - reST for analysis.encore (#1047) - - - created top level encore.rst that reproduces some text from encore.similarity - - added stubs for complete automodule loading when possible or wrote small rst files - with header and automodule/member loading - - combined Clustering submodules and Dimensionality Reduction submodules each into - one file - -commit dcd85788cb517e01e0925498e3fd32e2d2095ddd -Author: Oliver Beckstein -Date: Thu Oct 27 16:14:56 2016 -0700 - - updated references - - - collected references in references.rst; removedt the full MDAnalysis references from - the index page and just link to the citations in references.rst - - use reST citation syntax so that one can refer to the citations from *anywhere* in the - docs; in this way we only need to maintain them in a single place - - added ENCORE reference - - added MDAnalysis SciPy reference - - reformatted all references to a common style; note that I needed to manually break some - lines to avoid starting lines with character followed by period (such as 'O. Beckstein') - because reST/sphinx interpretes 'O.' as a enumerated list and messes up the format. - -commit 2ea209940994056043d020a5260179dc3e6ea9e7 -Author: Richard Gowers -Date: Thu Oct 27 13:46:06 2016 +0100 - - TST: Migrated some tests from test_atomgroup to universe - -commit 33c2b7cdfdab1aa6a9826ca8b5a8943b4ccdd79f -Author: Richard Gowers -Date: Thu Oct 27 12:43:04 2016 +0100 - - TST: Added tests for Universe creation failures - -commit 6ea8046728fcf30b753ee7b5077854ecfcdce4cf -Merge: 869d61a07 6cd78a75a -Author: Richard Gowers -Date: Wed Oct 26 10:38:47 2016 +0100 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 869d61a0772479342024b2e9eb2e3615d698ba48 -Author: Richard Gowers -Date: Wed Oct 26 10:38:21 2016 +0100 - - Added test for subclassing AtomGroup - -commit 6cd78a75aad3c79465d8770a004a23e707462b8c -Author: Richard Gowers -Date: Tue Oct 25 17:45:20 2016 +0100 - - TST: Unskipped more atomgroup tests - -commit 58810c68e6a1e9fdfe752cf76cbce9cd97ef6163 -Author: Richard Gowers -Date: Tue Oct 25 14:18:25 2016 +0100 - - Fixed Segment residue name selection - -commit a3e601f46bdca2f83c54f692487f640a56be7f25 -Author: Max Linke -Date: Tue Oct 25 14:14:40 2016 +0200 - - Issue 363 align pa (#1051) - - * fix bug and docs in rotaxis - - If a == b this used to return [nan, nan, nan] due to the division by 0. - - * pep8 changes test_transformations.py - - * add rotaxis test - - * add align_principal_axis test - - * update changelog - -commit c0ddc8969b6a17e90e64b94d8bd42f4627bda5cd -Author: Richard Gowers -Date: Tue Oct 25 13:12:59 2016 +0100 - - Hardcoded Segment and ResidueGroup getattrs - -commit d5c9314436d18058dbc02a8db29dfcc6ca460c6d -Author: Richard Gowers -Date: Tue Oct 25 10:48:15 2016 +0100 - - Permanently removed some invalid tests - -commit a800c881d74115bd1332670eac203f7b7c57aa3f -Author: Richard Gowers -Date: Tue Oct 25 10:45:28 2016 +0100 - - Readded Segment.r# access to Residues - - Readded tests for phi_selection and friends - -commit a9b93e81d1e88b2feef046311bed153fc8564b1a -Author: Richard Gowers -Date: Mon Oct 24 14:26:45 2016 +0100 - - Fixed segid selector when starting with s - -commit e97efe5ac85846acda08fef0978c85a82d4f4b02 -Author: Richard Gowers -Date: Mon Oct 24 11:44:20 2016 +0100 - - TST: Improved core/topology coverage - -commit a377e11aa630b5e68bca99b8344aaa92c8be04a0 -Author: Max Linke -Date: Mon Oct 24 08:28:34 2016 +0200 - - update tests - -commit 5407fd59ab75b10f8c67ea5d2ef3ac546a155c16 -Author: Max Linke -Date: Mon Oct 24 08:26:36 2016 +0200 - - update CHANGELOG - -commit aa3c064a1e4355876a46e4ef9a07ce868a0f1c60 -Author: Max Linke -Date: Mon Oct 24 08:24:46 2016 +0200 - - Only return IOError - - It was a mistake to use anything else but an IOError for this class. - Especially I only raise an exception if something with the I/O has gone - wrong. - -commit 886a02c4798c109342f228e026f55c97b2d989fd -Author: Richard Gowers -Date: Sun Oct 23 16:43:04 2016 +0100 - - Added tests for topology.guessers module (#1048) - - * Added tests for topology.guessers module - - * TST: More tests for test_guessers - -commit 3b0ed059d38b1fa5edb101a27b173751413a8685 -Author: Richard Gowers -Date: Sat Oct 22 18:44:18 2016 +0100 - - Changed Masses attribute back to float64 precision - -commit e37a5cea060f9bbed9974f86d605326a7e237ce8 -Author: Richard Gowers -Date: Fri Oct 21 16:07:40 2016 +0100 - - Fixed PDBParser not setting types attribute to np array - -commit ff2f135449e5975d91de5ac472b3276086e58e94 -Author: Richard Gowers -Date: Fri Oct 21 11:26:01 2016 +0100 - - Changed element attribute (back) to atomtype - -commit 1d6f6e77e731041144d1a7d82392c78bec891ae9 -Author: Max Linke -Date: Fri Oct 21 11:47:44 2016 +0200 - - Issue 363 pep8 (#1039) - - * PEP8 Changes - - Make code more PEP8 compliant - - * remove 0.16 deprecated function - - The time of deprecating this was lost in some merge. - - * test PEP8 Changes - - * test hash function - - * insert future TODO - -commit 52140a3f3941ef887a5864b2ce3e6d838db831a9 -Author: Max Linke -Date: Fri Oct 21 11:45:11 2016 +0200 - - PEP8 changes to topologyattrs: Fixes #1045 (#1042) - - * pep8 changes topologyattrs - - * pep8 changes test file - - * add license to test - -commit af941ad5d591c220f6c275bc1bc5a82bbae67a87 -Author: Max Linke -Date: Thu Oct 20 19:24:27 2016 +0200 - - refactor load_new (#1043) - - This is to ensure that **kwargs only contains arguments indented for - functions that are called and every named argument used by this function - is stated explicit. - -commit 80a84bf354e92199633c1db1027c9c0641acd90e -Author: Tyler Reddy -Date: Thu Oct 20 12:57:09 2016 +0100 - - TST: Added remaining unit tests for PDBWriter handling of missing topology attributes. - -commit 353fc5fe957dd24f4a152bdc088f027d54fe8192 -Author: Tyler Reddy -Date: Thu Oct 20 12:02:11 2016 +0100 - - TST: Unit test for PDBWriter handling of missing altloc attribute now passes (accepts an empty string, which is equivalent to the length 1 blank string in this case). - -commit 94e0fe1b1d87b937f9a80b142d9ee8c7b89520ff -Author: Tyler Reddy -Date: Thu Oct 20 11:42:51 2016 +0100 - - TST: new unit test for PDBWriter handling missing altlocs (currently fails due to obliteration of length 1 blank string). - -commit a152798dd71bfc67735856e07f163d769051888f -Author: Tyler Reddy -Date: Thu Oct 20 11:01:39 2016 +0100 - - guess_atom_element() function now properly handles blank atom names. - -commit 820930cd2d2b780ecb8b509f2e21e7721808b263 -Author: Tyler Reddy -Date: Thu Oct 20 11:00:43 2016 +0100 - - PDBWriter adjustments that enabling handling of missing topology attributes: residue or atom names. - -commit 400918ea95c3f75e9f41b201a49646537819c68f -Author: Tyler Reddy -Date: Wed Oct 19 17:24:43 2016 +0100 - - TST: Added unit test for PDBWriter handling missing topology attributes. - -commit 63cef11b06d5630e17f6ec2956b831b7a0e414ec -Author: Richard Gowers -Date: Thu Oct 20 17:40:02 2016 +0100 - - Fixed guess_bonds to use elements if no atomtypes present - -commit 99b07ac17cd2f381fc4862f0581769df90a69814 -Author: Richard Gowers -Date: Thu Oct 20 17:27:54 2016 +0100 - - Updated topology docs - -commit a94d31fffa53f0d54b36bd8affa2307e2127366a -Author: Richard Gowers -Date: Thu Oct 20 13:44:39 2016 +0100 - - Checked DATAParser - -commit 38707c7f16d13f37e88a638d599587ae61b96e12 -Author: Richard Gowers -Date: Thu Oct 20 12:54:07 2016 +0100 - - Checked PDBParser - -commit f94c3ec85d6236dd67916d415eb6b67e237e4b21 -Author: Richard Gowers -Date: Thu Oct 20 12:23:18 2016 +0100 - - Checked DLPoly Parsers - -commit 753a7e8de77a0ff0e9f60b0d22ac8082dd5dd660 -Author: Richard Gowers -Date: Wed Oct 19 21:29:13 2016 +0100 - - Checked TPRParser - -commit f2eabece661181f5820eb8e2663aa724ec8dd3a6 -Author: Richard Gowers -Date: Wed Oct 19 20:59:25 2016 +0100 - - Check DMSParser - -commit 1049f5e712b6b78e9bf1dd298431b03b49bb66f6 -Merge: ff364d403 32be45c87 -Author: Richard Gowers -Date: Wed Oct 19 12:51:28 2016 +0100 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit ff364d40355cf123d60b86b95e0f91ab65fa0f8b -Author: Richard Gowers -Date: Wed Oct 19 12:51:11 2016 +0100 - - Checked HoomdXML Parser - -commit 32be45c87fef9ef337745372ff16040903e47486 -Author: Tyler Reddy -Date: Wed Oct 19 12:49:55 2016 +0100 - - WIP: GROWriter 363 testing (#1033) - - * TST: a unit test for GROWriter resid truncation has been adjusted to conform to the integer precision limitations imposed by the new topology system. - - * TST: Added GROWriter unit tests for missing topology attribute handling. - - * MAINT: restored an accidentally removed slow decorator in TestGROWriter. - - * TST: Addressed initial reviewer comments in PR#1033. - - * TST: Added trajectory mocking to tests in PR#1033. - - * TST: Fixed issues in PR#1033 related to expected values for GROWriter given blank universe attributes. - -commit ce0b08bdfea5531c9ca2bed7b020afc47b7b7180 -Author: Richard Gowers -Date: Wed Oct 19 12:19:19 2016 +0100 - - Checked GMSParser - -commit 5a8d76ad2f37e390d2860fd7341d8bdf3cf6e31e -Author: Richard Gowers -Date: Wed Oct 19 11:44:51 2016 +0100 - - Checked MOL2Parser - -commit c086eb951b22abe2bb6532a619d572295b3f8a3e -Author: Richard Gowers -Date: Wed Oct 19 11:26:49 2016 +0100 - - Check PDBQTParser - -commit 185e6115f48175142d5063970e1542673cc14591 -Author: Sean Seyler -Date: Wed Oct 19 02:28:19 2016 -0700 - - Issue 1035 psa pdbtobinarytraj remove (#1036) - - * Tweaked module imports - - * Fixed PDBToBinaryTraj bugs + tweaked topology writing behavior - - * Added skeleton test class for PDBToBinaryTraj class - - * Fixed PDBToBinaryTraj function + tests for traj + single frame - - * Removed PDBToBinaryTraj + corresponding tests. Simplified imports in test_psa - - * Fixed spacing for long line - - * Fixed more code broken across lines - - * Updated changelog - -commit 890980ce06f9a6148800fdaf77fc1a5229d93943 -Author: Richard Gowers -Date: Tue Oct 18 23:26:02 2016 +0100 - - Checked PQRParser - -commit 0ec4147b89daaefb9378dab7da9ce9d7d08a5861 -Author: Richard Gowers -Date: Tue Oct 18 13:49:54 2016 +0100 - - Added tests for guessed attributes - - Checked GROParser - -commit c6ac4537d2c00378ccb3b010222786fe922e9087 -Author: Richard Gowers -Date: Tue Oct 18 11:49:14 2016 +0100 - - Check XYZParser - -commit 7ff7f91848132743051d7722046365eb249527c7 -Author: Richard Gowers -Date: Mon Oct 17 20:26:04 2016 +0100 - - Finished checking TOPParser - -commit 263d11f1174407454baeda2c6843ca21002d1a62 -Author: Richard Gowers -Date: Sun Oct 16 23:28:53 2016 +0100 - - Added atomic number to element name table to topology/tables - -commit 71a9bb4a1eaff2bee46a5d6ccbb9e723bb1176fd -Author: Richard Gowers -Date: Sun Oct 16 21:06:15 2016 +0100 - - Checked PSFParser - -commit e82228c88c78ff705b9515d0f4969fcb99cb9ee7 -Author: Richard Gowers -Date: Sun Oct 16 20:42:14 2016 +0100 - - Checked new implementation of CRDParser - - Fixed Elements topology attr being called Element - - Added tests for mandatory attributes - -commit 643315abad02668ca7d4b099810cddf61bd28905 -Merge: 34829ae43 36d934289 -Author: Richard Gowers -Date: Sun Oct 16 18:16:05 2016 +0100 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 34829ae43c9a5ee004f46673448081bc6132ee4b -Author: Richard Gowers -Date: Sun Oct 16 18:14:27 2016 +0100 - - Check CRDWriter - - CRDParser now groups residues by either a change in resid or a change in - resname. - - Added tempfactors to make_Universe - - make_Universe atom names now 3 characters - - make_Universe can now attach a trajectory through a keyword - -commit 36d934289b5016b72a4c6aa202c6bc9e37396325 -Merge: 0ee3c37af c281138e6 -Author: Richard Gowers -Date: Sat Oct 15 19:51:12 2016 +0100 - - Merge pull request #1032 from kain88-de/iterator-fix - - Reset Trajectory after sliced iteration - -commit c281138e633892e450fd042ae9f7479c35264add -Author: Max Linke -Date: Fri Oct 14 14:06:13 2016 +0200 - - Reset Trajectory after sliced iteration - - Reset to 0 for a sliced iteration like we do for a normal iteration. - -commit 0ee3c37afeed9b117d928e2d62b4c68a85def851 -Merge: 6f8d1c1a5 930186779 -Author: Richard Gowers -Date: Fri Oct 14 11:58:12 2016 +0100 - - Merge pull request #1026 from kain88-de/issue-363-transform-api - - Issue 363 transform api - -commit 930186779aedccc8535b7fe10e6eef0b70748fb9 -Author: Max Linke -Date: Fri Oct 14 09:26:41 2016 +0200 - - Update CHANGELOG - -commit 9c2ac812e910d8fb2fb0a3f6468be27143f701e0 -Author: Max Linke -Date: Fri Oct 14 08:07:03 2016 +0200 - - add tests to rotate about arbitrary point - -commit 8c5a5de83f273e7746cb9c5219b0f65bbd07b031 -Author: Max Linke -Date: Fri Oct 14 08:03:04 2016 +0200 - - refactor tests to be more robust - -commit 6648264a5adf2108fe9430869e171659dc3d341b -Author: Max Linke -Date: Fri Oct 14 07:59:40 2016 +0200 - - add point kwarg to rotate - - This kwarg allows to specify the center of rotation. This changes the - default behavior from using the center of origin to using the centroid - of the group. - -commit 6bb53dd0daf70549329977310e1bc597d1d13216 -Author: Max Linke -Date: Fri Oct 14 07:45:28 2016 +0200 - - return self for 4 group member functions - - rotateby, rotate, translate, transform now return self. This allows - chaining their operations like this - - ``` - ag = ag.translate(vec).rotate(R) - ``` - -commit 63e6acecd92f98c2a99f1e8c4fb317cbd3eae4e2 -Author: Max Linke -Date: Fri Oct 14 07:42:07 2016 +0200 - - remove AG param from rotateby - - This removes all notice that rotateby or translate accepted atomgroups - as well. It makes the interface more consistent and easier to document. - -commit 6dc73550aacc7109d4514c90b66cac25be7b8385 -Author: Sean Seyler -Date: Thu Oct 13 01:47:14 2016 -0700 - - Issue 1018 psa scipy bugfix (#1019) (#1024) - - * closes #1018 - * Removed 'color_list' and changed 'orientation' kwargs in dendrogram() in PSAnalysis.cluster - * Commented out import from brewer2mpl as well; leaving there in case alternative dendro coloring arises. - * Removed brewer2mpl import and corresponding call to get_map - * Updated changelog with reference to issue 1018 - * Added small test to check dendrogram returns a dict - * Fixed test method name for dendrogram test - * Added missing line to psa tests to generate plot - * Added decorators to psa tests to skip when matplotlib/scipy not installed - * Added import for module_not_found for psa tests - -commit 6f8d1c1a52f7be19b2bcdccba237c0820f447bbe -Author: Richard Gowers -Date: Thu Oct 13 21:43:36 2016 +0100 - - Fixed up some masses being float32 - -commit 0a3d59f8220ca8affe328f84810416eeb7bc0423 -Author: Richard Gowers -Date: Thu Oct 13 18:11:14 2016 +0100 - - Fixed masses not being cast to float64 in analysis/rms - - Fixed old import of AtomGroup in analysis/distances - -commit 2c33de889b475557742bcc92df7badc9f0900df4 -Author: Richard Gowers -Date: Thu Oct 13 17:52:43 2016 +0100 - - Fixed diffusionmap usage of Universe - - Removed deprecated usage of coordinates() from analysis/distances - - Updated Universe import in pca - -commit f893703a2432509d9a829e05619bf4893efd1f9b -Author: Richard Gowers -Date: Thu Oct 13 17:13:42 2016 +0100 - - Fixed up RMS test - -commit 8165301323f96c6a2f76940a2c34c48e696e30fd -Author: Richard Gowers -Date: Thu Oct 13 16:57:07 2016 +0100 - - Updated test_pdb tests - -commit 32597c2a6776510f33e7f7d7dd3fe55f65101a1c -Author: Richard Gowers -Date: Thu Oct 13 16:51:16 2016 +0100 - - Fixed old import of AtomGroup.AtomGroup - -commit 6ead2dd15a05a46574f4a3b0b79ceba9a40ebea0 -Author: Richard Gowers -Date: Thu Oct 13 14:40:48 2016 +0100 - - Readded memoryreader - -commit 3f6a5fb6bf95b3a9e38ed8cb741c4caec9ea5244 -Author: Richard Gowers -Date: Thu Oct 13 14:21:34 2016 +0100 - - Fixed PDBParser - -commit bad25f7c08e63dbb1e6fcf793ddad29f7eb16fb2 -Author: Max Linke -Date: Thu Oct 13 14:44:48 2016 +0200 - - update doc strings - -commit 8259bbe2e75c5f0f9e62663c27af4b5567187801 -Author: Max Linke -Date: Thu Oct 13 14:12:26 2016 +0200 - - clean whitespace - -commit ecad9ed8d564f7f822d196a03bd8f27372c293ef -Author: Max Linke -Date: Thu Oct 13 13:53:55 2016 +0200 - - start new docs - -commit 242997e180e5336cf15132be80f0b2293843871c -Author: Max Linke -Date: Thu Oct 13 10:10:51 2016 +0200 - - simplify rotate function - -commit d152dd4b58cf6a2274744a0601c8a37433ec40ff -Author: Max Linke -Date: Thu Oct 13 10:00:50 2016 +0200 - - add more transform tests - -commit 851a51523b41497a1aba40aef5d435fafbda40e5 -Author: Max Linke -Date: Thu Oct 13 09:57:50 2016 +0200 - - add test for rotateby - -commit 72440c65a16071c3b4651c22dcdd54abf7376b19 -Author: Max Linke -Date: Thu Oct 13 09:52:55 2016 +0200 - - add transform tests - -commit 30862a3d186651cb2bdfaa8abba04015c56ad424 -Author: Max Linke -Date: Thu Oct 13 09:52:30 2016 +0200 - - add rotate test - -commit 00482bb57a9364ca7df1bbff703064dc3a494d47 -Author: Max Linke -Date: Wed Oct 12 20:25:29 2016 +0200 - - add translate test - -commit 6977b96e6df5456406f2ed976a1add92ca2b8d8a -Merge: af0bdd78c 8d806c8fd -Author: Richard Gowers -Date: Thu Oct 13 11:15:33 2016 +0100 - - Merge branch 'develop' into issue-363 - - Conflicts: - package/MDAnalysis/coordinates/DCD.py - package/MDAnalysis/coordinates/GRO.py - package/MDAnalysis/core/AtomGroup.py - package/MDAnalysis/topology/PDBParser.py - package/MDAnalysis/topology/TPRParser.py - testsuite/MDAnalysisTests/formats/test_libmdaxdr.py - testsuite/MDAnalysisTests/test_atomgroup.py - testsuite/MDAnalysisTests/test_util.py - testsuite/MDAnalysisTests/topology/test_pdb.py - testsuite/MDAnalysisTests/topology/test_tprparser.py - -commit af0bdd78cede3fc05fc9719135f05887b610679d -Merge: 4370b7470 c6749ccf5 -Author: Richard Gowers -Date: Thu Oct 13 10:48:39 2016 +0100 - - Merge pull request #967 from MDAnalysis/issue-363-resmove - - Issue 363 resmove - -commit 8d806c8fdb0138da7c09ad2d9d909f94ef224fb9 -Author: Oliver Beckstein -Date: Thu Oct 13 01:47:14 2016 -0700 - - Issue 1018 psa scipy bugfix (#1019) (#1024) - - * closes #1018 - * Removed 'color_list' and changed 'orientation' kwargs in dendrogram() in PSAnalysis.cluster - * Commented out import from brewer2mpl as well; leaving there in case alternative dendro coloring arises. - * Removed brewer2mpl import and corresponding call to get_map - * Updated changelog with reference to issue 1018 - * Added small test to check dendrogram returns a dict - * Fixed test method name for dendrogram test - * Added missing line to psa tests to generate plot - * Added decorators to psa tests to skip when matplotlib/scipy not installed - * Added import for module_not_found for psa tests - -commit c6749ccf572a2a0febd09f39f81de22811092318 -Author: Richard Gowers -Date: Wed Oct 12 14:33:55 2016 +0100 - - tests: make_Universe now allows specifying size of Universe - -commit 4a4bc0dd877126e4b1c47f148a7592470c70fa77 -Author: Richard Gowers -Date: Wed Oct 12 13:15:16 2016 +0100 - - Error messages for Residue and Segment creation - -commit fc2400542d23ff2f8bee6e61a485ad0b0c717ffb -Merge: 94759076f 98f7c1fa8 -Author: Richard Gowers -Date: Wed Oct 12 09:56:07 2016 +0100 - - Merge pull request #797 from encore-similarity/feature-encore - - Inclusion of ENCORE into MDAnalysis - -commit 6185482d1460546d788cef4c82e1f36fb40fbd20 -Author: Richard Gowers -Date: Tue Oct 11 23:31:49 2016 +0100 - - Residue and Segment creation now implemented - -commit aefe842495ee79dcd9eaf4c5aa76ad33b866d8d0 -Author: Richard Gowers -Date: Mon Oct 10 14:51:05 2016 +0100 - - Fixed unsorted atoms in residues - -commit a7ff5aeddc0f03f7d15e2a4bc32c079ac9530fb4 -Author: Richard Gowers -Date: Mon Oct 10 14:47:40 2016 +0100 - - Fixed residue->atoms conversion - -commit 299941c0e7f4aa11373bc920974362997be8d012 -Merge: ab87d4a5b 4370b7470 -Author: Richard Gowers -Date: Sun Oct 9 11:12:25 2016 +0100 - - Merge branch 'issue-363' into issue-363-resmove - - Conflicts: - package/MDAnalysis/core/groups.py - -commit 4370b7470489a08d485a7936d0ab60dbb5ffe417 -Author: Max Linke -Date: Sun Oct 9 10:34:52 2016 +0200 - - PEP8 changes (#1021) - - * PEP8 changes - - just clean up most complains of my PEP8 checker (flake8) - - * more PEP8 changes - - * fix ag.write - - - make code simpler - - no filename given means pdbs are written - - * add ag.write tests - - should cover it all now - - * add transformation tests - - * tests forces setters/getters - -commit 3669d0d23cef2cfb0a3ac2dc806ca4bb08bce435 -Author: Kyle Huston -Date: Thu Oct 6 17:03:00 2016 -0400 - - test atom order in topology groups, residues, segs (#1017) - - Add tests to verify atoms are ordered by index within each residue and - segment. - -commit ab87d4a5b2bc24a0449007c1a810fa1fd65086de -Author: Richard Gowers -Date: Thu Oct 6 19:26:18 2016 +0100 - - Added functionality and tests for moving atoms between existing residues - -commit bf32a515bc4ac915406e23db2cdabe8e75c1d58b -Author: Richard Gowers -Date: Thu Oct 6 12:45:52 2016 +0100 - - Added __ne__ to all classes with __eq__ - -commit 33aa27f4e3b087887063002fc1c3d25d7e9f5567 -Merge: b16851da6 9c5594145 -Author: Richard Gowers -Date: Thu Oct 6 09:41:56 2016 +0100 - - Merge branch 'issue-363' into issue-363-resmove - - Conflicts: - package/MDAnalysis/core/topologyattrs.py - testsuite/MDAnalysisTests/core/groupbase.py - -commit 9c5594145b4b9efe6fbed2fb32c7904050c8191e -Author: Richard Gowers -Date: Wed Oct 5 14:47:40 2016 +0100 - - Fixed local import in test_libmdaxdr - - Fixed errors in TopologyGroup addition - -commit 0d90248864a1e5e50a7d000e7d9a21e781ac951b -Author: Richard Gowers -Date: Wed Oct 5 14:30:43 2016 +0100 - - Ugly hack to make multiple getatttrs work - -commit 9cf8654630893bdf44816c08c209ca138c78c5f4 -Author: Richard Gowers -Date: Wed Oct 5 13:29:16 2016 +0100 - - Fixed tests in test_modelling - - Previously used same resid with different resname, but atoms had - different resnames in same residues - - New system doesn't allow this (by design), so different resids must be - used to get a different resname - -commit b29f0103632fa6c4189a8130b509d24923bb1aeb -Author: Richard Gowers -Date: Wed Oct 5 11:03:26 2016 +0100 - - Added special error message for fragments (more to follow) - - PDB serials now wrap rather than being None - -commit 531819b030b5b7e32b03bb48ccd32a249b2d0fbe -Author: Richard Gowers -Date: Wed Oct 5 10:45:17 2016 +0100 - - Marked persistence tests for skipping - - Need reworking - -commit 64cb00642dbc6a53e6be386466bbe0bf00ae41e6 -Author: Richard Gowers -Date: Wed Oct 5 10:44:05 2016 +0100 - - readded order to Bonds - -commit 94759076fe7c468e5ad19547889d5085258b2927 -Author: Tyler Reddy -Date: Wed Oct 5 09:50:06 2016 +0100 - - Added unit test for discrete Frechet distance. (#1013) - -commit 2f07deb9467ea914397c20994e697a1e6363245f -Author: Richard Gowers -Date: Tue Oct 4 18:59:04 2016 +0100 - - Fixed use of set_segid - -commit e51ef59f2c2fd3e2a11ff82d6a5d29bbbf447d49 -Author: Richard Gowers -Date: Tue Oct 4 18:56:04 2016 +0100 - - Removed invalid properties from TestAtomGroupProperties - -commit 3d37887ca3f5089144a3555e55d65c51026fa1d6 -Author: Richard Gowers -Date: Tue Oct 4 16:08:11 2016 +0100 - - Fixed import in analysis/density - -commit 5fab3d9451499a4e0faea163a793960390f09dc3 -Author: Richard Gowers -Date: Tue Oct 4 15:12:11 2016 +0100 - - Fixed PDBQT tests - -commit 848e98b30ea6cbeb1666e9c57ba70a4cf06acd8b -Author: Richard Gowers -Date: Tue Oct 4 14:01:19 2016 +0100 - - Rewrote fragments tests - -commit e3490806d2faace16775b3685745901c38599b00 -Author: Richard Gowers -Date: Tue Oct 4 10:35:39 2016 +0100 - - Testfix: Universe doesn't have bonds by default - -commit becdd7bb805201a352ffdbc4434ed844ecdb5974 -Author: Richard Gowers -Date: Tue Oct 4 10:33:50 2016 +0100 - - Removed tests for unordered residues - -commit 8391c93f9b4bd6480686ef0f76d43822d5e2ca5a -Author: Richard Gowers -Date: Mon Oct 3 09:54:33 2016 +0100 - - Fixed wrapping serials making PDBParser fail - -commit b19a460654e4401683942896301da90e2c59c149 -Author: Richard Gowers -Date: Mon Oct 3 09:37:55 2016 +0100 - - Fixed errors with TopologyObjects - -commit 8f5a2f208801a3f64de9fd0516e95a4508ed74dd -Author: Richard Gowers -Date: Mon Oct 3 08:55:20 2016 +0100 - - Universe checks again for guess_bonds - -commit 10d5b6828618699ec477f8bcad7d7484743b265d -Author: Richard Gowers -Date: Mon Oct 3 08:12:21 2016 +0100 - - Readded guess_bonds to AtomGroup - -commit 81c97977b2dfcbc1b8ea76337276b9514584cdf1 -Author: Richard Gowers -Date: Sun Oct 2 11:52:21 2016 +0100 - - Fixup for XPDBParsing icodes - -commit fc6aedcc1ffba4e339e2257888eb27f1dbbadc96 -Author: Richard Gowers -Date: Sat Oct 1 19:09:11 2016 +0100 - - Reworked PDBParser to respect insertion codes - - Can now squash Residues based on multiple criteria (resids and icodes) - -commit 3773943a61b4c372f5a52b0c46204ba8a1ee477b -Author: Richard Gowers -Date: Sat Oct 1 19:08:27 2016 +0100 - - Changed insertion codes to work on Residue basis - -commit 7b170b38236ffb747197be20478bb7405c422384 -Author: Richard Gowers -Date: Thu Sep 29 21:34:37 2016 +0100 - - Fixed setting atom.resid in test_modelling - -commit b6f3ee1739006932cef5ff47363bc25aec906e7e -Author: Richard Gowers -Date: Thu Sep 29 21:07:43 2016 +0100 - - Fixed import in test_persistence - -commit 2231841e07b8b28003e7dda4ba79e0c374dda8b6 -Author: Richard Gowers -Date: Thu Sep 29 16:45:33 2016 +0100 - - Removed checking len of itertools cycle in coordinates/XYZ - -commit e90b873b54f9cde6d1abd9295e4d9c0de4247294 -Author: Richard Gowers -Date: Thu Sep 29 14:52:58 2016 +0100 - - Rewrote TestAtomProperties tests - -commit 88e22fe01b3bcc2c191f32ffc1c270f41665a960 -Author: Richard Gowers -Date: Thu Sep 29 14:30:56 2016 +0100 - - PDBParser guesses off atom names if types aren't present - -commit 4956350f9fe24f222c7b51f4fcc81905ea46f0cf -Author: Richard Gowers -Date: Thu Sep 29 14:00:09 2016 +0100 - - Added tests for XYZWriter atom names - -commit 30f3c140186514fd2261207ce50c81292363cc13 -Author: Richard Gowers -Date: Thu Sep 29 12:32:24 2016 +0100 - - Fixed PDBQT Parser tests - - ParserBase tests now give better error message - -commit f81eb871f339c5ca949e280ba942b72f4bd103cd -Author: Richard Gowers -Date: Thu Sep 29 12:16:03 2016 +0100 - - Added tests for resid_change_squash - -commit 8cbff8cc9e1b23da8b358313aa0a81c9d0bd4ce0 -Author: Jonathan Barnoud -Date: Thu Sep 29 12:53:03 2016 +0200 - - Fragments are ordered by their first atom index (#1008) - - * Fragments are ordered by their first atom index - - Fixes #1007 - - * Atoms in fragments are now sorted by index - -commit 3f46c9446d7ec111cd40d498e88c2edf525ebbdf -Author: Richard Gowers -Date: Wed Sep 28 18:21:14 2016 +0100 - - Add requires guard around Lammps writer - -commit ad35b561a71f1611d388ef7089391e2a4d6ee01d -Author: Richard Gowers -Date: Wed Sep 28 18:21:06 2016 +0100 - - Added resid change squasher - - Started fixing PDBQT parser... - -commit c514756503460da84299a0e8dcc20d5f5b1d9bbf -Author: Richard Gowers -Date: Wed Sep 28 17:52:59 2016 +0100 - - Fixed possible silent test failure - - Fixed deprecated usage of Error.message - -commit 98f7c1fa8b05026413d0afef8d7079023f4b9464 -Merge: d50c3d7ea 96344fcc1 -Author: Tone Bengtsen -Date: Wed Sep 28 18:27:03 2016 +0200 - - Merge branch 'feature-encore' of https://github.com/encore-similarity/mdanalysis into feature-encore - - merged with Matteos latest changes - -commit d50c3d7ea4feadd42338fa2a83497326df0528d5 -Author: Tone Bengtsen -Date: Wed Sep 28 17:50:57 2016 +0200 - - Updated docstrings, updated/added examples - - - Updated the docstrings. - - Added examples to the functions dres, ces to show how to use different - clustering/dimensional reductions methods and different parameters at ones. - - Added examples to the functions dres_convergence, ces_convergence - -commit 824ec971d0cb451cf3d012c3ab60644ce9efa77c -Author: Richard Gowers -Date: Wed Sep 28 16:24:11 2016 +0100 - - Improved error message of requires - -commit ffa6d0676d18785b3e526d13a18d0f35369f1416 -Author: Richard Gowers -Date: Wed Sep 28 15:47:07 2016 +0100 - - Added requires decorator to core/groups - -commit 101cffdad8f17f3ab486cd0c8332ff9730c0028f -Author: Richard Gowers -Date: Wed Sep 28 13:53:37 2016 +0100 - - CRDWriter: Fixed missing * in title - - Added more tests for CRDWriter - -commit f9f5ac60b001d236f1a5f1cefb7447ec4f8c59b0 -Author: Richard Gowers -Date: Wed Sep 28 12:14:01 2016 +0100 - - Rewrote CRDWriter to expect missing attributes - - Now uses "".format style strings - -commit 90602c6c58260f5190dc4d526fcad701c2fc3d84 -Author: Tyler Reddy -Date: Tue Sep 27 03:03:51 2016 +0100 - - Hausdorff distance unit tests (#1005) - - * Added unit for asymmetry of Hausdorff distance - * Tests for average Hausdorff distance - * Tests for weighted average Hausdorff distance - - * Added 'undirected' clarification to psa hausdorff docstrings. - - * Improved / refactored Hausdorff tests. - - * Suppressed docstring changes for Hausdorff-related code (not needed). - - * Whitespace cleanup to reverse psa.py docstring changes. - -commit 7f54182cf53e63a17a22fabe35450f7694913791 -Author: John Detlefs -Date: Fri Sep 23 12:33:37 2016 -0700 - - analysis.rms.RMSD now confirms to new Analysis API (PR #934) - - * fixes #893 - * RMSD refactored with AnalysisBase class and confirms to the new analysis API (see #719) - * Tests added - * Documentation and chaining functions - * Fixed and updated documentation - * Addressed broadcasting and other issues - * Updated CHANGELOG - -commit 0970a38d3aa9a583edc79fd2051323a208340f98 -Author: Richard Gowers -Date: Fri Sep 23 16:55:04 2016 +0100 - - WIP CRD rewrite - -commit 10750c6595a49e92131e42d02b3ea98228efa2cc -Author: Richard Gowers -Date: Fri Sep 23 15:52:21 2016 +0100 - - Added Topology.guessed_attributes & read_attributes - -commit 72900d04f70fefcf44c5aef24e825f2fe7e3e144 -Author: Richard Gowers -Date: Fri Sep 23 14:42:33 2016 +0100 - - Updated analysis/leaflet to 363 - -commit 861e73d58ef883b71b9518e0d336a05e499ce78f -Author: Richard Gowers -Date: Fri Sep 23 14:18:40 2016 +0100 - - Added resnums to PSF and PDB - -commit 7afd8c4defd57172b9757bd23ad80308d16d0def -Author: Richard Gowers -Date: Fri Sep 23 14:10:36 2016 +0100 - - Tests: Fixed gnm tests - -commit 97bd9cf5e2df29e665f35c129f2c81992a113499 -Author: Richard Gowers -Date: Fri Sep 23 13:55:25 2016 +0100 - - Tests: Hbond tests now passing - -commit 7a22f4aa9a5c01b31144eccf8b4b6e26677653a1 -Author: Tyler Reddy -Date: Fri Sep 23 13:51:35 2016 +0100 - - Unit tests / exception handling in psa module (#999) - - * Added two unit tests for psa analysis module exception handling. - - * Updated testsuite CHANGELOG to reflect new unit tests for exception handling in psa module. - - * get_coord_axes() function in psa module now properly raises a ValueError when input path dimensions are not correct. - - * Removed entry from testing CHANGELOG. - -commit bda971f5da41c5e17d0c1633fcd64f6bf02242ba -Merge: e6bf1f9db 022bfc96d -Author: Richard Gowers -Date: Fri Sep 23 13:50:53 2016 +0100 - - Merge pull request #1000 from MDAnalysis/unit_test_polymer - - Two unit tests for polymer.py - -commit ddda1c4618b0b736adc02e5dfd589277aa4c54ff -Merge: 775563a8f 15c02477e -Author: Richard Gowers -Date: Fri Sep 23 13:30:59 2016 +0100 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 15c02477e1ca41bdbe68cd8d2143fb77cb3a935a -Author: Richard Gowers -Date: Fri Sep 23 13:29:57 2016 +0100 - - First draft of writing missingn attributes (#991) - -commit 775563a8fb754249d47d57d04c9afa56d6b3750a -Author: Richard Gowers -Date: Fri Sep 23 12:14:15 2016 +0100 - - PDBParser now guesses masses - -commit 022bfc96d0eac067f483a6efab209baedee0d5a0 -Author: Richard Gowers -Date: Fri Sep 23 11:59:00 2016 +0100 - - Went back to using nose testing functions in test_persistencelength - -commit 49bfbf8e26c994a0206019be8a054f11a9eb4d80 -Author: Richard Gowers -Date: Fri Sep 23 11:55:48 2016 +0100 - - Started adding guessing to PDBParser - -commit 59984755a8f498b46754b06b39c8068c092edbb4 -Author: Tyler Reddy -Date: Fri Sep 23 10:58:02 2016 +0100 - - Added two unit tests to test_persistencelength.py. Covers an exception handling scenario and a plotting scenario. - -commit e6bf1f9dbf169dcf2c32f827201dad150e5d5ab9 -Merge: e7a7bbbba 1f0641ecb -Author: Jonathan Barnoud -Date: Fri Sep 23 09:28:44 2016 +0200 - - Merge pull request #990 from MDAnalysis/leaflet_selection_test - - Test for LeafletFinder selection string - -commit 1f0641ecbeab2e5f7d7a102c1e10c70cbd3d149f -Author: Tyler Reddy -Date: Sun Sep 18 15:51:12 2016 +0100 - - Added unit test that ensures that LeafletFinder handles a selection string properly in place of an atomgroup proper. - -commit 1524f75248e30afcc9b3d8ff9d99555bffb9bf18 -Author: Richard Gowers -Date: Thu Sep 22 14:55:08 2016 +0100 - - Added guessed masses and types to GROParser - -commit 66f8d0e4281e747218f2cc1b99bb3abc1c3b6dcb -Author: Richard Gowers -Date: Thu Sep 22 14:54:32 2016 +0100 - - Added topology.guessers module - -commit e7a7bbbba58cf49105857b379533a0369a641fdf -Author: Tyler Reddy -Date: Thu Sep 22 13:55:41 2016 +0100 - - Add unit test for MDAnalysis.analysis.distances.between() (#998) - - * Added unit test for MDAnalysis.analysis.distances.between(), which was completely uncovered by tests and also completely broken. - - * Updated testsuite CHANGELOG to reflect new unit test for MDAnalysis.analysis.distances.between(). - - * MDAnalysis/analysis/distances.py has been fixed to add a missing import required for between() and to fix a call to a non-existant method in the latter function. - - * Updated CHANGELOG at package level because between() is no longer broken. - -commit 4c556ecc5bbdbf8a7bf874fa4767fbdeadda0bd6 -Author: Richard Gowers -Date: Thu Sep 22 11:29:05 2016 +0100 - - Removed obsolete tests in test_atomgroup - -commit 96104b9089af285c62f52c61e6e1c98e05201673 -Author: Richard Gowers -Date: Thu Sep 22 11:24:02 2016 +0100 - - Removed set_* usage in test_atomgroup generator - -commit 286ca0c05075f20065e2703145abc526806cb0d0 -Author: Richard Gowers -Date: Thu Sep 22 11:01:50 2016 +0100 - - Added saving kwargs to Universe - -commit 22ab2deac508bfd0cfdce1b1aae62d884ad81cdf -Author: Tyler Reddy -Date: Wed Sep 21 19:24:52 2016 +0100 - - Add unit tests for MDAnalysis.analysis.distances.dist() (#997) - - * Added unit tests for MDAnalysis.analysis.distances.dist(). - - * Added one more unit test for MDAnalysis.analysis.distances.dist() related to matching the lengths of the input atomgroups. - -commit 3106c5b1b2f8ffc34bff520fcb5e9217d1e38571 -Author: Tyler Reddy -Date: Wed Sep 21 14:33:41 2016 +0100 - - Clip matrix frustrum boundary tests (#996) - - * Corrected the upcoming release version number in the testsuite CHANGELOG. - - * Added 3 unit tests to check frustrum bounds handling by clip_matrix in the transformations testing module. - - * Added CHANGELOG entry for clip_matrix frustrum boundary checks. - -commit a5f2eddf8acc239c580ad7506bcea57e24721949 -Merge: a491e1528 40d149566 -Author: Richard Gowers -Date: Tue Sep 20 21:39:43 2016 +0100 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - - Conflicts: - package/MDAnalysis/lib/NeighborSearch.py - -commit 40d14956688b6a5307d88ec27b2062059e82e382 -Author: Tyler Reddy -Date: Tue Sep 20 21:36:57 2016 +0100 - - WIP: Issue 363 test failure squashing (#992) - - * Fixed test failures in test_gro.py -- setting the position of an atom now requires a shape (3,) array and will not work with with an index-based assignment to a single x, y, or z coordinate value. - - * Assignment of atom position in test_pdb.py now properly uses a required shape (3,) array-like object as indexing is no longer supported. - - * Fixed a test failure in test_atomgroup.py -- selecting a single residue now returns a Residue instead of ResidueGroup. - - * Fixed the floating point stringency of test_Writer_dimensions in test_lammps.py -- was causing a failure on Travis (though not locally). - - * lib/NeighborSearch.py adjusted to properly handle indexing of an ag with an empty list and bug fix in AtomNeighborSearch, both of which relieve 5 errors in test_hbonds.py. - - * Fixed 4 errors in test_nuclinfo.py related to the need to use residue.atoms to access certain properties. - - * Fixed 1 error in test_atomgroup.py caused by PSFParser.py no longer raising the appropriate exception when fed PSF_BAD data file. - -commit a491e15280c63e34d030ff8910cddbbd8b13afde -Author: Richard Gowers -Date: Tue Sep 20 21:31:19 2016 +0100 - - Added guessing types for GRO in hbond tests - -commit 556d71ddbdf1e4073a2d9b7dd0a73bec442d739e -Author: Richard Gowers -Date: Tue Sep 20 21:14:04 2016 +0100 - - Added generator to test_hbonds - - Fixed Residue.select_atoms in hbond_analysis - - Fixups in NeighborSearch - -commit 5a0a123d1106de4157d64da26606a56fa9df1f36 -Author: Richard Gowers -Date: Tue Sep 20 20:56:03 2016 +0100 - - Force Groups to cast input indices to array - -commit 96344fcc1675e5c5888b079fe9a9dcdbbb05be9c -Author: Matteo Tiberti -Date: Tue Sep 20 10:14:22 2016 +0100 - - added test for * and + operators in utils.TriangularMatrix - -commit 232a0a584777b678a6344027b5372af868057d6c -Author: Matteo Tiberti -Date: Tue Sep 20 10:13:57 2016 +0100 - - added error messages and fixed error types - -commit d4eee36a424fe9e499de9ea2b4977a4bdfd79a9c -Author: Matteo Tiberti -Date: Tue Sep 20 10:07:51 2016 +0100 - - added __imul__ and __iadd__ to TriangularMatrix - -commit abf1eb7af3d735e372b7d0716194974dc92ddbf5 -Author: Richard Gowers -Date: Mon Sep 19 13:15:40 2016 +0100 - - Added shortcut to bonds from Universe - -commit 67174aef0bf2912025fb06dc5617084cc3dac66b -Author: Richard Gowers -Date: Mon Sep 19 13:02:04 2016 +0100 - - Fixing PDB tests - - Removed occupancy tests from PDB - -commit a38b88cc53544117ae479274ce60c8c013eb161d -Author: Richard Gowers -Date: Mon Sep 19 12:58:57 2016 +0100 - - Tests: Fixed some PQR tests - -commit b1bec17121f48ccca78ffc9d0846d691904803ea -Author: Richard Gowers -Date: Mon Sep 19 11:36:06 2016 +0100 - - Tests: Rewrote Atom comparison tests - -commit 07d022156f565673e3b7a4841d7e6cca197afbf5 -Author: Richard Gowers -Date: Sun Sep 18 20:50:33 2016 +0100 - - Fixed NeighborSearch use of AtomGroup() - -commit e4bc5004c589d3bed4808bac2cc139b75d4764e6 -Author: Richard Gowers -Date: Sun Sep 18 20:32:55 2016 +0100 - - Fixed reference to core.Selection -> core.selection - -commit e419e04256744f74f9b2157871370b994970e345 -Author: Richard Gowers -Date: Sun Sep 18 20:31:48 2016 +0100 - - Fixed bad imports in test_xdr - -commit a81e9b837adc44b32317609e390d66488554670b -Author: Richard Gowers -Date: Sun Sep 18 20:30:26 2016 +0100 - - Removed deprecated use of write_selection - -commit 7ae31638a6152591ea203c25337310efea7e3929 -Author: Richard Gowers -Date: Sun Sep 18 20:26:33 2016 +0100 - - Fixed views of position/velocity/force being returned - -commit 3c904ffe796696b2cd3518814e6bb24a2ebb9a7c -Author: Richard Gowers -Date: Sun Sep 18 19:51:02 2016 +0100 - - Tests: Fixup for persistencelength tests - -commit 2b5fec94d2573ccba2044d1e40f039f1e56bad56 -Author: Tyler Reddy -Date: Sun Sep 18 16:16:14 2016 +0100 - - unit tests for SelectionWriter file mode (#989) - - * Added unit tests to ensure that a ValueError is raised by SelectionWriter when using an invalid file mode. - - * Moved test suite specific enchancements to the test suite CHANGELOG. - - * Unit tests for SelectionWriter file mode have been abstracted to a base class. - - * Whitespace cleanup in test_selections.py. - -commit a71ef5eea1b3503d40ee9b31857afc49fd0498de -Merge: ddf87d543 69d7752dd -Author: Matteo Tiberti -Date: Fri Sep 16 17:49:39 2016 +0100 - - Merge remote-tracking branch 'upstream/develop' into feature-encore - -commit 16f4b5e9d33ffd6f0693f7dc600dcdd5b5f6debb -Author: Richard Gowers -Date: Fri Sep 16 16:01:41 2016 +0100 - - Added 363 to travis build matrix - -commit 69d7752dd7549b78b20440e85504ae9ebc3419ca -Author: Oliver Beckstein -Date: Thu Sep 15 12:09:57 2016 -0700 - - updated AUTHORS - - - changed "Maintained by Oliver Beckstein and Elizabeth Denning" to - "Maintained by the MDAnalysis Core Devs Team" - - added Wouter Boomsma (for PR #976) - - removed explicit mentions for KDTree (Hamelryck) because since 0.11.0 - we do no longer include the actual code (see PR #395 and #383) - - removed explicit mentions for helanal (Hall) because Ben Hall is - a contributing author - -commit ebde209cc54edabf65d6570ba8a52c61fd0aafd4 -Author: Oliver Beckstein -Date: Thu Sep 15 11:52:55 2016 -0700 - - set release to 0.16.0-dev0 - - - reported release should be in sync with CHANGELOG - - ran `maintainer/change_release 0.16.0-dev0` (and manually undid the - change in the conda yml config --- still left at the 0.15.0 values - to avoid creating wrong conda packages by chance) - - fixed 0.15.1 -> 0.16.0 reference in analysis.align - -commit 3240973ab5a0a26a598b13e7f242cc6a6957f07b -Author: Oliver Beckstein -Date: Thu Sep 15 11:47:21 2016 -0700 - - documentation fixes - - - fixed legacy/x3dna docs (and added versionchanged) - - updated CHANGELOG (missing PCA entry, mention analysis API) - - fixed reST in PSA and PCA modules - - updated object.inv link for networkx docs - -commit c4e26d9a55b047536b5bd7210cbdefb12c1a6b15 -Author: Richard Gowers -Date: Thu Sep 15 16:10:16 2016 +0100 - - Updated CHANGELOG for Issue #976 - -commit 2ee7bbf7c1bf3e09c42f01319887bce66ffa7db0 -Author: Wouter Boomsma -Date: Thu Sep 15 17:05:47 2016 +0200 - - MemoryReader. (#976) - - * Added MemoryReader and tests. - - * Added documentation, and removed unused import - - * Minor bugfixes and documentation updates related to MemoryReader. - - * Changed reader format string: memory->MEMORY - - * Removed check for existence of group.universe - - * Use isinstance instead of checking against format class variable. - - * Inreased travis process timeout to 400s - - * Bugfix in MemoryReader: now forces numpy array copy when using in_memory option of Universe constructor - - * Extra documentation and minor bugfix - -commit 8688adaea6ab7bdd1e3a6a83011ae63f59c0a1ee -Author: Oliver Beckstein -Date: Thu Sep 15 08:03:47 2016 -0700 - - moved analysis.x3dna to analysis.legacy.x3dna (#987) - - * moved analysis.x3dna to analysis.legacy.x3dna - - - created new MDAnalysis.analysis.legacy package - - directory - - docs - - x3dna is now considered legacy code (no/minimal testing, no maintenance) - - see #906 for reasons (mainly because the x3dna license does not allow us - to just install it for testing on travis, or rather, licensing and access - to x3dna is unknown/too complicated) - - closes #906 - - see #743 on background for legacy code and also https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide#tests-for-mdanalysisanalysis - - added stub with deprecation warning: until release 1.0, MDAnalysis.analysis.x3dna is still accessible - - added test case that the stub is there - - * updated CHANGELOG - - - legacy module (#743) - - x3dna is now legacy code (#906) - - updated upcoming release number to 0.16.0 - - [skip ci] - - * Removed legacy submodule from coverage - -commit ddf87d543884cebef4473037a29c0af880391df5 -Author: Wouter Boomsma -Date: Thu Sep 15 09:59:30 2016 +0200 - - Extra documentation and minor bugfix - -commit f328b8258ea05b40c4a6eefa4dee9db7887bad2d -Author: Oliver Beckstein -Date: Wed Sep 14 15:41:13 2016 -0700 - - improvements to travis-ci configuration (#986) - - - language is Python - - allow fast finishing https://docs.travis-ci.com/user/customizing-the-build#Fast-Finishing - - only run coveralls for the FULL build - - closes #979 - - see also @jdetle's https://github.com/MDAnalysis/mdanalysis/commit/03570d37ad363b525fef36c06281a0d2cbfc2989 - -commit d8ba3f78e03945efbf3e0f0c43706af806896995 -Author: Richard Gowers -Date: Wed Sep 14 21:18:56 2016 +0100 - - Doc updates for TopopologyAttrs - -commit 6274d5ac1f511c36fde76bdab8b18d7989539b5b -Author: Richard Gowers -Date: Wed Sep 14 20:48:19 2016 +0100 - - Tests: Fixed some missing imports in tests - -commit 6e82e584c3d7835672be37f7fd7e36755b791872 -Author: Richard Gowers -Date: Wed Sep 14 20:29:43 2016 +0100 - - Fixed GROParser not raising error for missing atom name - -commit f048ea34e49c37f24bf9397efd7ecc83179bdd0d -Author: Richard Gowers -Date: Wed Sep 14 20:29:32 2016 +0100 - - Tests: Fixed missing import in test_psf - -commit b7edd0b93a21977d48cddca11606ef9f0126ab7e -Author: Richard Gowers -Date: Wed Sep 14 20:12:32 2016 +0100 - - Tests: removed usage of .pos (deprecated and removed) - -commit 9eeeb7da5e969aa8319256c617b7192e72f03728 -Author: Richard Gowers -Date: Wed Sep 14 19:56:03 2016 +0100 - - Testsuite; Marked moving atoms via resid as knownfailure - -commit 2769c1b637368ae2614a02c3f3203e742efdbf94 -Author: Richard Gowers -Date: Wed Sep 14 19:52:43 2016 +0100 - - Testsuite: Moved test_atomselections into core/ - -commit 40814435057a06c07b811b9687dc28e9478bf9e6 -Author: Richard Gowers -Date: Wed Sep 14 19:24:32 2016 +0100 - - testsuite: make_Universe can now add TopologyAttrs to mock Universe - -commit 2728557570e8e4d71e4e7131e1bc358092febe15 -Author: Richard Gowers -Date: Wed Sep 14 11:51:36 2016 +0100 - - Fixed incorrect alignment in nucleic selection test file - -commit 6cbed67e43c0e92a006ebe19e30a7196d1e8545e -Author: Matteo Tiberti -Date: Wed Sep 14 10:58:18 2016 +0100 - - revised tests in documentation - -commit 4a73b242002483802d357a66288ef0f6fb7fba28 -Author: Matteo Tiberti -Date: Tue Sep 13 17:58:30 2016 +0100 - - first pass on documentation - -commit bd4b8e5d34d79904fc18fb4bb8018865dca86959 -Author: Max Linke -Date: Tue Sep 13 11:34:19 2016 +0200 - - Issue 363 flags (#969) - - * reactivate flag tests - - * fix asphericity flag handling - -commit abb55d2e206b294ce614386334c80781560077d1 -Author: Wouter Boomsma -Date: Mon Sep 12 21:14:47 2016 +0200 - - Bugfix in MemoryReader. Minor cleanup in similarity.py - -commit 16ae695276c93b56095035729aeaa9657722ae8a -Author: Wouter Boomsma -Date: Mon Sep 12 13:23:21 2016 +0200 - - Use isinstance instead of checking against format class variable. - -commit 02441a3b5a9d7e71b19968d86ec66124df446790 -Author: Wouter Boomsma -Date: Mon Sep 12 13:07:23 2016 +0200 - - Removed check for existence of group.universe - -commit dcb72bad76e17131d24cd12b34c8557395787ed7 -Author: Wouter Boomsma -Date: Mon Sep 12 13:03:39 2016 +0200 - - changed reader format string: memory->MEMORY - -commit 89e6633d1da593d8bde7dbf17f17a23b0be3ea91 -Author: Tyler Reddy -Date: Mon Sep 12 10:13:02 2016 +0100 - - Added remaining regression tests need to full cover analysis.nuclinfo module. Fixes #790. (#978) - -commit 43c21590f44aa33bbf5c3d1aa209e1bd0e14bf5e -Author: Wouter Boomsma -Date: Sun Sep 11 22:36:33 2016 +0200 - - Cleaned up merge_universes function. - -commit e56e6b58092012d00d1898eae2f06ffbbe7423b4 -Author: Wouter Boomsma -Date: Sun Sep 11 22:00:32 2016 +0200 - - Minor bugfixes and documentation updates related to MemoryReader. - -commit 080f86194ac73ae8d76f3810608748f37fe4e05d -Author: Tyler Reddy -Date: Sun Sep 11 11:27:05 2016 +0100 - - Regression tests for nuclinfo.minor_pair (#977) - - * Added two regression tests for MDAnalysis.analysis.nuclinfo.minor_pair - - * Added CHANGELOG entry for new MDAnalysis.analysis.nuclinfo.minor_pair regression tests. - -commit 1556203b730e2349b9898797706d6df7389f7dcf -Author: Wouter Boomsma -Date: Sat Sep 10 13:01:33 2016 +0200 - - Added documentation, and removed unused import - -commit 77abc7e939d5bde627433aa6b8e4ae7eb541a52f -Author: Wouter Boomsma -Date: Sat Sep 10 12:50:30 2016 +0200 - - Inreased travis process timeout to 400s - -commit 291b462ea4fa5d911b727eaf9cdf2305b26f0b68 -Author: Wouter Boomsma -Date: Fri Sep 9 23:01:30 2016 +0200 - - Increased robustness of test - -commit f43c77b2576a99347fa395d72cd6daf14f5efef0 -Author: Wouter Boomsma -Date: Fri Sep 9 21:47:58 2016 +0200 - - Removed debugging print statements - -commit 27ecd9926253e3af084192bf1063cc017eccd033 -Author: Wouter Boomsma -Date: Fri Sep 9 20:31:30 2016 +0200 - - Removed obsolete code. - -commit 04f459fe1f031b95fe2d744e38ef9a15ed08ede7 -Author: Wouter Boomsma -Date: Fri Sep 9 17:35:14 2016 +0200 - - Speeded up tests. Reverted back to 300s process timeout. Bugfix in hes error estimation. - -commit b16851da6807a9639bc290be937a2edec9516253 -Author: Richard Gowers -Date: Thu Sep 8 15:06:00 2016 +0100 - - Added more tests to check that group attrs affect entire group - -commit 8f5f722c5cf19bfa0cd6c738f4547a6ebf520c42 -Author: Wouter Boomsma -Date: Thu Sep 8 14:47:06 2016 +0200 - - Inreased travis process timeout to 400s - -commit ec81d486fa22bd44d09e909f568dc4ffd3bce042 -Author: Richard Gowers -Date: Thu Sep 8 11:28:23 2016 +0100 - - Added setting resid/segid with iterable - -commit 56f8efb13b01dfdae17aed19a7697fd4d7a258c5 -Author: Richard Gowers -Date: Thu Sep 8 09:40:06 2016 +0100 - - Added tests for setting resids/segids with iterable - -commit c000a5c55b236f4fd73e281095b36ba74ede29c3 -Author: Wouter Boomsma -Date: Thu Sep 8 00:12:53 2016 +0200 - - Changed ParallellCalculation to run in main thread when ncores==1. Added tests. - -commit 5893b12ce5f0f2074081361b7517c7691c0cbd47 -Author: Wouter Boomsma -Date: Wed Sep 7 22:57:53 2016 +0200 - - Fixed QuantitiveCode issue - -commit 7dea72d2206978c10a370ccb77a7fa088d9cdb0a -Author: Wouter Boomsma -Date: Wed Sep 7 22:52:37 2016 +0200 - - Fixed QuantitiveCode issues. Added sklearn availability tests to several tests. - -commit 2a421e1db0f363390d498cd197ead9a47118d671 -Author: Wouter Boomsma -Date: Wed Sep 7 20:39:51 2016 +0200 - - Added sklearn availability tests to two tests. - -commit 1c6fc9d5ab2e7e884dd40e3a211bb0b18fdf1d04 -Author: Wouter Boomsma -Date: Wed Sep 7 16:53:26 2016 +0200 - - Added missing warnings import - -commit cd125011c50af4bde234de3b280ff4255abede3b -Author: Wouter Boomsma -Date: Wed Sep 7 11:14:42 2016 +0200 - - sklearn -> scikit-learn in setup.py - -commit 9355a6eba79f5b45541c72443df39d011c8a78d1 -Author: Wouter Boomsma -Date: Tue Sep 6 23:20:26 2016 +0200 - - Removed debugging print statements. - -commit b8b5a36c1079cc3ed8a33e5d91b95eb9e06ee7b5 -Author: Wouter Boomsma -Date: Tue Sep 6 23:14:25 2016 +0200 - - Minor corrections to MemoryReader code, tests and documentation. - -commit 5ba05a4b7b7134c6ed807904b62075b1a08c86a4 -Author: Wouter Boomsma -Date: Tue Sep 6 22:42:18 2016 +0200 - - Added sklearn as optional requirement in setup.py and .travis.yml. Minor bugfixes. - -commit f8dafb54107819c93143d237c7f53c6eb3ece785 -Author: Wouter Boomsma -Date: Tue Sep 6 22:09:34 2016 +0200 - - Bugfix in similarity.py - -commit 01424ccc447d166a8508b8e415d27a1f828c9a6f -Author: Wouter Boomsma -Date: Tue Sep 6 21:06:32 2016 +0200 - - Fixed test_reader_w_timeseries_frame_interval test - -commit 9b9c60783f8c976c6239b047656557510d98324c -Author: Wouter Boomsma -Date: Tue Sep 6 20:57:13 2016 +0200 - - Added missing warnings import - -commit c60d69e6fd6ae31c154a893297c4596aee124bf1 -Author: Wouter Boomsma -Date: Tue Sep 6 16:52:13 2016 +0200 - - Decreased sensitivity of hes_align test. - -commit adee6a984f56697ecc56384b6dbde07fc9a9e5bd -Author: Richard Gowers -Date: Tue Sep 6 10:45:43 2016 +0100 - - Clarified downshift docs - -commit e8ad9b2ae77e0af061f1128cdebb82af830cae00 -Author: mnmelo -Date: Mon Sep 5 21:43:59 2016 +0200 - - test_imports now recursively checks subdirs (closes #964) (#965) - - * test_imports now recursively checks subdirs (closes #964) - * Rebased and fixed testsuite/CHANGELOG conflicts - - Also fixed a wrong-order CHANGELOG entry from #961 - -commit 735c1a4f262c24128165e9b0fb2e8b97cb7ef3bb -Author: Richard Gowers -Date: Mon Sep 5 14:08:57 2016 +0100 - - Added tests for make_downshift_arrays - -commit a897d8376e9e8e312a8762d2046129b3df6b780f -Author: Max Linke -Date: Mon Sep 5 13:06:42 2016 +0200 - - WIP: fix error in principle axis (#963) - - * fix error in principle axis - - The code was using unimported functions and unnecessary ifs - - * fix imports - - * activate test - - * improve argument handling - -commit 9b47f00faf5cef33fbf7c74342570eb17e0d74e5 -Author: Kyle Huston -Date: Sun Sep 4 05:59:41 2016 -0400 - - Dataparser image flags (#968) - - * Allow for image flags in lammps data file - - During the conversion of DATAParser to the new shiny Topology format, - the position parser was changed to just read the last three numbers as - the x,y,z positions. Sometimes, the image flags are added after the - x,y,z positions, so I restored this detection. - - * rectify difference with mdanalysis/issue-363 - - * simplify DATAParser position assignment - -commit 930570ed0f19bbf2955e57d575a66ec397ff656f -Author: Wouter Boomsma -Date: Sat Sep 3 12:44:29 2016 +0200 - - Fixed test in test_encore to reflect change in slicing behavior of MemoryReader. - -commit 04c2fc2ce1e1334c0a9d452d6ac2682a0aea46c8 -Merge: f6ec6e107 396e04084 -Author: Matteo Tiberti -Date: Sat Sep 3 08:38:30 2016 +0100 - - Merge remote-tracking branch 'upstream/develop' into feature-encore - -commit 64d98a25edaa8d978629fa8f8631a0280bc7b643 -Author: Richard Gowers -Date: Fri Sep 2 13:32:40 2016 +0100 - - Moving to existing residues and segments works - -commit 7c9428fa07d7ad5355f180f47af956c5cee7a862 -Author: Richard Gowers -Date: Fri Sep 2 12:01:04 2016 +0100 - - added tests for changing AtomGroup's resid/resindex - -commit 76f7db4e6050d1881ff0b6c213777d2d037a6d2f -Author: Richard Gowers -Date: Fri Sep 2 11:09:05 2016 +0100 - - Resid setting now goes via resindex - -commit 6ea8494de3910d2f9d1f610b522d0083b2d8a8d4 -Author: Richard Gowers -Date: Thu Sep 1 16:47:20 2016 +0100 - - Tests for 363: - - groupbase.make_Universe returns Universe with resnames, resids and - segids - - Fixed Residue->AG, Segment->RG and Segment->AG moves not working - properly - -commit e9655c17c4204260f0ad80543f9254e909b505b6 -Author: Richard Gowers -Date: Thu Sep 1 13:03:21 2016 +0100 - - Fixed issue with downshift arrays for rectangular outputs - -commit 3133e110a6bfd7c9981bc02f223fae846c2ddc3c -Author: Richard Gowers -Date: Tue Aug 30 21:33:04 2016 +0100 - - Removing random numbers from tests (#961) - - * Removed random numbers from test_persistencelength - - * Fixed transformations inverse by using fake random numbers - - * Removed random numbers from test_util - - * Removed random numbers from test_density - - * Used RandomState in test_transformation - - * closes #958 - -commit 508907082f82fb51f950353290af84d17f1be2e0 -Author: Max Linke -Date: Thu Aug 25 16:27:34 2016 +0200 - - Issue 363 test (#931) - - * delete outdated test_attributes_pos - - the alternative 'position' is still tested - - * delete test_atom_centroid - - This function doesn't exist anymore. - - * fix test_undefined_occupancy - - apply hint - - * add atom attribute setting tests - - It has to be skipped right now because some functions aren't - implemented. - - * fix getitem tests in TestAtomGroup - - * fix test_sequence_nonIUPACresname - - The test passes but I'm not sure if the fix is correct. - - * fix test_set_resname_single - - * add explanaition to test_residues INVALID - -commit 39b4324c0abe3952aee0afde1e282480f0992707 -Merge: ffa4835ff 94a58765b -Author: Jonathan Barnoud -Date: Thu Aug 25 14:56:48 2016 +0200 - - Merge pull request #956 from MDAnalysis/issue-939 - - test_imports now looks in the right directory (closes #939). - -commit 94a58765b25d5c4a154fd8f45cb1572136f715af -Author: mnmelo -Date: Thu Aug 25 14:55:42 2016 +0200 - - Update testsuite CHANGELOG - -commit ed7fa6b53489c50416bbacfead0f8eea97a16be4 -Author: mnmelo -Date: Thu Aug 25 10:44:44 2016 +0200 - - Small reorganization and optimization (#952) - - * The roles of GroupBase and TopologyAttrContainer are now separate. - - Container base classes in Universe are now kept in an explicit dict. - - Universe class dictionaries now hash merged classes by their main class - object only. - - * Made TopologyAttrContainer private and reflowed base class initialization. - -commit 60c75c14305e9c0ce8a443504f765da743d3c364 -Author: Manuel Nuno Melo -Date: Wed Aug 24 16:39:05 2016 +0200 - - test_imports now looks in the right directory (closes #939). - -commit ffa4835ff6caee39af5845e6883ce0861fad1bf7 -Merge: 6a383dcfc 0a3ca6bdd -Author: Jonathan Barnoud -Date: Wed Aug 24 16:02:34 2016 +0200 - - Merge pull request #949 from MDAnalysis/issue-936-PDBfixes - - Fixes for Issue #936 and #937 - -commit 0a3ca6bddf87f45d1fc6a3a915e1fe780634500c -Author: Richard Gowers -Date: Wed Aug 24 14:03:13 2016 +0100 - - Fixed up test files for 936 - -commit 4a1332aa74911b747c09351de32c5eb7875d13f5 -Merge: fb2dc45c4 6a383dcfc -Author: Richard Gowers -Date: Wed Aug 24 13:59:35 2016 +0100 - - Merge branch 'develop' into issue-936-PDBfixes - - Conflicts: - package/CHANGELOG - -commit fb2dc45c411eac135e842708659027891725a9f2 -Author: Richard Gowers -Date: Wed Aug 24 12:41:43 2016 +0100 - - Added warnings for Issue#936 - - Aesthetic changes to PDBParser, removed indentation level - -commit 6a383dcfc32bbd2db54308020ebaf6a2b4f9e19d -Merge: 7e5b00329 770eba479 -Author: Max Linke -Date: Tue Aug 23 12:46:11 2016 +0200 - - Merge pull request #944 from jbarnoud/issue-927-progressbar-notebook - - Fix progress meter on jupyter notebook - -commit 770eba479e365835e29d2f819cff0c6973dc7b1f -Author: Jonathan Barnoud -Date: Tue Aug 23 11:52:19 2016 +0200 - - More detailed changelog entry for PR 944 - -commit 7e5b003299810c54240853473c4f3a8162983706 -Merge: 8f803a45b c95e79fe1 -Author: Jonathan Barnoud -Date: Mon Aug 22 22:37:47 2016 +0200 - - Merge pull request #950 from MDAnalysis/analysis-decorator - - Analysis decorator fixes #946 - -commit c95e79fe122dda239e5e42b871ad3c1feb8b42f4 -Author: Max Linke -Date: Mon Aug 22 17:44:23 2016 +0200 - - update CHANGELOG - -commit 66bb1828018296de247a6f2ff460b173b1520f36 -Author: Max Linke -Date: Mon Aug 22 17:31:14 2016 +0200 - - Add tests for new functionality - -commit e11c306f4598cf2ba121c0c18f20f342767d2b3a -Author: Max Linke -Date: Mon Aug 22 08:17:04 2016 +0200 - - Create Analysis from functions - - Adds a class `AnalysisFromFunction` that creates a analysis class - directly and a decorator `analysis_class` to define the class during - function definition. - -commit f54d76afda47478fa4597a970b138b2f40ac70a1 -Author: Richard Gowers -Date: Sun Aug 21 10:22:47 2016 +0100 - - Fixes Issue #937 - - Single CONECT records (CONECT A\n) are now handled properly - -commit 59916ed93e36788d4ce7ff129c686096df8c5960 -Author: Richard Gowers -Date: Sun Aug 21 10:13:52 2016 +0100 - - Fixes for Issue #936 - - CONECT records to unknown entries (hopefully TER) are now ignored - -commit b79e5a2de65e5aebdf9c15bf5d2bf2ac9ce2861f -Author: mnmelo -Date: Sat Aug 20 12:22:59 2016 +0200 - - Deferred AtomGroup class mixing to __new__, allowing subclassing. (#938) - - * Deferred AtomGroup class mixing to __new__, allowing subclassing. - - * Tests now create a fully initialized dummy Universe. - - * __new__ cache shortcut implemented in its own class. - - New order of class merging allows for subclasses of AtomGroup et. al. to - override the TopologyAttrs brought with Universes. - - * Removed legacy Segment.__getattr__. - - * Cleaned docstring. - -commit 8f803a45b70375adfa584e2d62b9d3f96f2a5852 -Merge: 396e04084 5923b117f -Author: Max Linke -Date: Sat Aug 20 10:41:28 2016 +0200 - - Merge pull request #948 from jbarnoud/tpr-gromacs-2016 - - Minor fixes for easier mainetance of the TPR parser - -commit 5923b117fdc2a51394a61e1c0ac48e17e80db784 -Author: Jonathan Barnoud -Date: Fri Aug 19 17:39:33 2016 +0200 - - Additional fixes for TPRparser maintenance - -commit f60a68b94e3142b404cb49efae0df1e666a45602 -Author: Jonathan Barnoud -Date: Fri Aug 19 14:06:57 2016 +0200 - - Adapt details of read_tpxheader to gromacs-2016 - - Small name changes to follow the gromacs function. These changes are - minor and do not change anything to the logic, but following the names - used in gromacs helps with maintenance. - -commit 944167854dccd730758778030cb73588e3531e84 -Author: Jonathan Barnoud -Date: Fri Aug 19 13:55:59 2016 +0200 - - Backward compatibility with TPX 77-79 dev - -commit 62969f4e418593e233ab190f0e427d2add27c7d9 -Author: Jonathan Barnoud -Date: Fri Aug 19 13:45:12 2016 +0200 - - Fix mystery readings in read_tpxheader - - read_tpxheader reads the header of a gromacs TPR file. This function - follows the C function do_tpxheader in fileio/tpxio.cpp. - - Two integer were read in the python version without apparent - correspondence in the original C function from gromacs. It appears that - these integer are in fact the length of the strings read right after. - The reading that integer is hidden deep in the gromacs source code in - gmx_system_xdr.c:454 (gromacs-2016). - - This shows a discrepancy in the way python and gromacs read strings from - a XDR file. The new python function do_string emulate gromacs's - gmx_fio_do_string, and read the size prior to the string. - -commit b7130aef8434f0bf01377f2658aa5fcee887cff2 -Author: Jonathan Barnoud -Date: Thu Aug 18 13:14:42 2016 +0200 - - ProgressMeter accepts both new and legacy formats - - A previous commit, translated the formats from the legacy to the new - syntax. This would break user's code. - - This commit adds a keyword `format_handling`. When the keyword is set to - "new", the format string is handled with the new {}-based syntax. When - the keyword is set to "legacy", the format string is handled with the - old %-based syntax. By default, the keyword is set to "auto"; then the - kind of syntax is guessed. - -commit f6ec6e107b559446233709c5226da787da28d3a4 -Author: Matteo Tiberti -Date: Thu Aug 18 11:14:06 2016 +0100 - - streamlined convergence functions - -commit f099f675272a1cca9a450f80a2a7762b54799677 -Author: Jonathan Barnoud -Date: Wed Aug 17 20:51:35 2016 +0200 - - Document changes to ProgressMeter in CHAMGELOG - - Also add a .. versionchanged:: entry. - -commit db69f5b2f3249a05d3af9a55c4876f7dfb4925c4 -Author: Jonathan Barnoud -Date: Wed Aug 17 20:29:58 2016 +0200 - - Progress meter format do not contain \r anymore - - The implementation details of the progress meter should not be the - responsibility of the end user. Therefore, the end user should not have - to deal with the \r at the beginning of its custom format for the - progress meter. This is especially True as having the \r at the - beginning or at the end of the format may cause different behavior. - - This commit removes the responsibility of the \r from the end user. - Instead, it adds a `dynamic` keyword to the ProgressMeter class. If set - to True (default), the \r is added at the beginning. Else, the format is - left untouched. - -commit 65fe9ec1f4f30bd73defbc2d9b1749708e7d2473 -Author: Jonathan Barnoud -Date: Wed Aug 17 19:22:37 2016 +0200 - - Fix progress bar in jupyter notebook - - Fixes #927 - - Place the \r at the beginning of the format rather than at the end. This - caused the progress bar not to be displayed on jupyter notebooks. - - This commit also change the string formatting of the progress bar from - the old % syntax to the new {} one. - -commit 396e04084bc1dc3e1bfe5542c5f7ba2127cabf12 -Author: Jonathan Barnoud -Date: Wed Aug 17 16:01:22 2016 +0200 - - Temporarily remove python 3 builds, allow osx to fail (#943) - - Python 3 builds are to far from passing to be relevant on travis. This - commit disable them. - - OS X builds fail because of an issue with surviving file descriptors - that is fixed in the new topology scheme. This commit allows the os x - build to fail. - -commit 06c3e14c6e2c8df0e5dd18451e4bea2f61075d69 -Merge: 843530c5e a9e067dd1 -Author: Jonathan Barnoud -Date: Wed Aug 17 14:32:54 2016 +0200 - - Merge pull request #868 from fiona-naughton/issue-785-add-auxiliary - - [WIP] Issue 785 add auxiliary - -commit 843530c5ecf5c1171896d7917948bff3233f13a9 -Merge: b375b4b74 7909ac55c -Author: Max Linke -Date: Wed Aug 17 13:20:55 2016 +0200 - - Merge pull request #941 from jbarnoud/issue-932-TPX110 - - [WIP] Issue 932 -- TPR from Gromacs 2016 fixes #932 - -commit 7909ac55cf149629c6ed09cb0d83b056f4575b1d -Author: Jonathan Barnoud -Date: Wed Aug 17 11:25:21 2016 +0200 - - Update CHANGELOG for issue 932 (TPR 110) - -commit 8bf9107d57d97ddbc5a97afd3c7bd3b9c2340bd3 -Author: Jonathan Barnoud -Date: Wed Aug 17 11:11:14 2016 +0200 - - Support TPX 110 used by gromacs-2016 - - Adding 110 as a supported version is enough to have the test pass. Yet, - gromacs-2016 deprecate a number of gromacs feature and reorganize how - TPX versions are handled. Detailed inspection of gromacs-2016 may be - needed to make sure the tests cover all use cases. - -commit 336ff1d5238b1bfaa1d9a38fd142db54e35d5104 -Author: Jonathan Barnoud -Date: Wed Aug 17 10:52:43 2016 +0200 - - Add gromacs-2016 in the TPR test suite - - Gromacs-2016 bumps the version of the TPR files. This commit adds the - files needed to test the support of that new TPR version, and include - the files in the test suite. - - 2lyz_gmx_2016.tpr was build from 2lyz_gmx_5.1.tpr using - - echo 0 | gmx convert-tpr -s 2lyz_gmx_5.1.tpr -o 2lyz_gmx_206.tpr - - dummy_2016.tpr was build using gmx grompp on the source files in - data/tprs/all_bonded. - -commit a9e067dd12f5689ddf4223820f53e111f831c101 -Author: fiona-naughton -Date: Tue Aug 16 16:29:15 2016 +0100 - - update changelog - -commit 5cf376ad12e02b711816f3d008040fd58137519a -Author: fiona-naughton -Date: Sat Aug 6 00:33:06 2016 +0100 - - methods for accessing aux attributes from traj reader; iter/next as aux take into account cutoff - tidy docs + tests - -commit 99b0419808c9b64545405e8dfd6848944d3dcae0 -Author: fiona-naughton -Date: Thu Aug 4 21:32:39 2016 +0100 - - make default time/data selector; add a guesser to return an instance; various renaming and doc fixes - -commit 0474544683e2c72026653023633112f21e6b6930 -Author: fiona-naughton -Date: Wed Aug 3 18:40:57 2016 +0100 - - fix auxreader slice so last step is included - fix step_to_frame when trajectory starts after 0 - -commit f0dc612ea8b7e09828ff2044996dff78773ddd87 -Author: fiona-naughton -Date: Wed Aug 3 14:54:20 2016 +0100 - - stop at first '&' + deal with blank lines in xvg reader - -commit 15754f381820d6bfd4fc0f997bab37e2dbcb055d -Author: fiona-naughton -Date: Tue Jul 26 14:54:54 2016 +0100 - - remove extra aux bit from XDR/PDB readers - -commit 6d17219c72f0f521a165fbeb94f2863e277ce582 -Author: fiona-naughton -Date: Fri Jul 22 12:51:35 2016 +0100 - - tidy + various fixes (AuxReader __getitem__, AuxStep data, tests) - Optimise perf from use of range in auxiliaries - -commit cb3f88fc79a65f86f098972d846b2d4ebd73e62f -Author: fiona-naughton -Date: Fri Jul 22 12:36:00 2016 +0100 - - add getitem to Namespace - -commit 302f832d812304d8c52385eff3950e82297e47f7 -Author: fiona-naughton -Date: Mon Jul 18 18:36:14 2016 +0100 - - add __getitem__ for auxreader; assort. small fixes - -commit fdb81d047087eac6725d459f55042cde49c45d09 -Author: fiona-naughton -Date: Fri Jul 15 22:55:01 2016 +0100 - - add a AuxStep class - -commit 2d5f4117e0b4f193e9e4e380303004914cf8e329 -Author: fiona-naughton -Date: Tue Jul 12 17:46:02 2016 +0100 - - generalise time/data selection beyond column; various renaming; move Namespace to Utils - -commit e453c31b2fb075be64f3fb5a142088a59820741b -Author: fiona-naughton -Date: Thu Jun 30 20:17:39 2016 +0100 - - add methods for recording AuxReader info for reloading - -commit e60a24759782b98aa83ea3ee0dcef2c5a46779f1 -Author: fiona-naughton -Date: Thu Jun 16 23:16:34 2016 +0100 - - add a read-all-to-memory xvg reader; update tests+docs - -commit 03c279f08548d15b22c5240f834bc5d3860d81e9 -Author: fiona-naughton -Date: Thu Jun 16 12:22:24 2016 +0100 - - fixes for iter/next as aux; force aux rewind in PDB + XDR readers - -commit baf10b07d4861634e154965911695c89a67139fa -Author: fiona-naughton -Date: Sat Jun 11 02:02:53 2016 +0100 - - add tests; add auxreader guesser; update Namespace; fix defaults + add error-raises when options invalid - -commit a692f06764dfcd17a8b07a6ea555eaba73981800 -Author: fiona-naughton -Date: Fri Jun 10 14:51:17 2016 +0100 - - add next/iter as aux - -commit 42e17820b666f334a9ec592db05a822f08ab3d40 -Author: fiona-naughton -Date: Wed Jun 8 18:48:53 2016 +0100 - - aux steps now 0-based, store n_steps + time for each; allow columns selection; assort fixes - -commit 3d808515fae4ca9d1c933f8d0223f8830c142b37 -Author: fiona-naughton -Date: Mon Jun 6 22:33:12 2016 +0100 - - update auxiliaries with trajectory change by next() or jump - -commit 11e1c147a8848f42079be21bf1fe081406a05132 -Author: fiona-naughton -Date: Fri Jun 3 19:18:13 2016 +0100 - - add auxreader time/dt/etc attributes + method to move to particular timestep - -commit a947f67ae65f49afc006242ad9e6e5f8213666f5 -Author: fiona-naughton -Date: Wed Jun 1 21:55:14 2016 +0100 - - add aux namespace to timestep and give reader add/remove auxiliary methods - -commit 0fc664f61dad150947663eb468e678258335df2e -Author: fiona-naughton -Date: Mon May 30 20:20:15 2016 +0100 - - first xvgreader attempt - -commit fc7e40f27b5c4c44ff449f9f8ed7d18e7afd4342 -Author: Wouter Boomsma -Date: Tue Aug 16 00:08:59 2016 +0200 - - Added cluster.py - -commit 8bccc3a1ce76ba615ec2b22fdac29ba24bff3646 -Author: Wouter Boomsma -Date: Mon Aug 15 23:57:21 2016 +0200 - - Code reorganization, cleanup and bugfixes. - Bugfix in AffinityPropagation code. - Clustering and Dimensionality reduction now available as separate functions, and separated from similarity code. - The clustering and dimensionality reduction similarity scores now support different methods. - -commit b375b4b74bf42e716eaa35d65e5a39ed20762b46 -Merge: 54d48dbaf 1cf340c71 -Author: Max Linke -Date: Sun Aug 14 19:01:31 2016 +0200 - - Merge pull request #896 from jdetle/PCA - - [WIP] Bauhaus PCA - -commit 1cf340c71b376f7c204ca340d5fdf3c7514f6221 -Author: John Detlefs -Date: Sat Aug 13 11:31:44 2016 -0700 - - PCA docs updates - -commit 54d48dbaf1af9360af550bfc6f10c5d4e432f527 -Merge: 2f873541d 88664cac3 -Author: Oliver Beckstein -Date: Sat Aug 13 14:34:44 2016 -0700 - - Merge pull request #930 from rbrtdlgd/qcprot - - Input coordinate arrays for qcprot do not need to be transposed anymore. Speed up between 20% to 40%. - - - keep float64 to maintain precision to 1e-10; - using float32 decreases it to 1e-5 or even 1e-4 - - input arrays should now be (N, 3) instead of (3, N): - this saves two transposes and gains up to about 30% in speed - - added tests and updated existing tests - - * changed analysis code to use new qcprot (no transposes) - - - code in align and rms - - adapted test case - - Changed rms.py so that there are no more .T's. - - updated docs everywhere - - * Finalized qcprot. Various cleanups. - - Modularized tests for qcprot. - - Cleaned up variable names. - - PEP8 compliant. - - Added the change in qcprot to CHANGELOG where it now uses N x 3 - arrays instead of 3 x N. - - Added Robert Delgado to authors. - -commit 88664cac3cb4be7bb9cf9a0726828d178544b1ae -Author: Robert Delgado -Date: Tue Aug 9 10:31:51 2016 -0700 - - Finalized qcprot. Various cleanups. - - Modularized tests for qcprot. - - Cleaned up variable names. - - PEP8 compliant. - - Added the change in qcprot to CHANGELOG where it now uses N x 3 - arrays instead of 3 x N. - - Added Robert Delgado to authors. - -commit efdd22f060c81b40a343578cae2aa070badb9a9f -Author: Robert Delgado -Date: Mon Aug 1 17:35:18 2016 -0700 - - changed analysis code to use new qcprot (no transposes) - - - code in align and rms - - adapted test case - - Changed rms.py so that there are no more .T's. - - updated docs everywhere - -commit 310038057862f29093d1373b4cb12a4a05a9115e -Author: Robert Delgado -Date: Fri Jul 29 16:41:45 2016 -0700 - - qcprot does not need a transpose anymore - - - keep float64 to maintain precision to 1e-10; - using float32 decreases it to 1e-5 or even 1e-4 - - input arrays should now be (N, 3) instead of (3, N): - this saves two transposes and gains up to about 30% in speed - - added tests and updated existing tests - -commit 6099a79679cb3e9afd64c12cf3a529dc2823571b -Author: John Detlefs -Date: Fri Aug 12 14:01:30 2016 -0700 - - Doc fix [skip ci] - -commit e0617e07dbd5048be30a9033f99f73bcd0bec9fd -Author: John Detlefs -Date: Fri Aug 12 13:43:06 2016 -0700 - - More docs fixes - -commit a52d9b86990109f9c8a12430c0b1bc6c5c8f5159 -Author: John Detlefs -Date: Fri Aug 12 11:10:15 2016 -0700 - - Doc fixes, test updates - -commit 2f873541d3c405a0eaca5aede05566dea94100cd -Author: Oliver Beckstein -Date: Thu Aug 11 14:31:48 2016 -0700 - - fixed docs for TPRParser: submit NEW issue for missing formats - - See https://github.com/MDAnalysis/mdanalysis/issues/2#issuecomment-239297956 - - [ci skip] - -commit 50e329fd4497a0f1ae15d2444fb99511e5e3d550 -Author: John Detlefs -Date: Thu Aug 11 13:54:38 2016 -0700 - - Added autofunction autoclass docs, made cosine_content static method, updated tests accordingly. - -commit fc2f4d45a3c0696892fdd84180799e0519f6461d -Author: John Detlefs -Date: Wed Aug 10 13:27:23 2016 -0700 - - Fix up some docs - -commit 159b9180b72df37a9f98d4f035ae20a7f2c9563d -Author: John Detlefs -Date: Wed Aug 10 13:17:30 2016 -0700 - - Moved cosine content, changed and added documentation. - -commit 6257bd762194cf325305dee6952c252d8e5439b1 -Author: John Detlefs -Date: Wed Aug 10 12:36:26 2016 -0700 - - Format change for mean progress meter. - -commit bc8d15a72cb7eb4004bfea2b901ae6151b358401 -Author: John Detlefs -Date: Wed Aug 10 11:56:44 2016 -0700 - - Fixed tests for new random walk files. - -commit 84fc3ce0f87bdec3118a778d706af54dc34dec02 -Author: John Detlefs -Date: Mon Aug 8 14:24:35 2016 -0700 - - Made changes to pca to align with Scikit-learn, specifically demeaning in transform. - Added random walk trajectory and tested for cosine content. - Added some more functionality and testing - - Docs fixes and reverting some mistakes. - - Updated docs, added testing for universe as inputs, added mean positions as atom group. Some other style fixes. - - Updated CHANGELOG - - Progress meter added, switch to XTC - -commit 9812f9e6d6383c39faa7cea89bb51a330f9b78bf -Author: John Detlefs -Date: Thu Aug 4 13:17:07 2016 -0700 - - Accepts a Universe as a transform argument, added tests that fails - -commit 32db2cc6d66faf9d37d7a1ad65c8b9d85697b1a2 -Author: John Detlefs -Date: Thu Aug 4 12:46:48 2016 -0700 - - Fixed broken tests - -commit 8938ff0a163b2006925d0e751aeaba133bc9d4bf -Author: John Detlefs -Date: Wed Aug 3 14:15:03 2016 -0700 - - Warnings added - -commit 8e3f8abd96a39cbac574ada0f64c8022d0db69a5 -Author: John Detlefs -Date: Wed Aug 3 13:27:20 2016 -0700 - - I came, I saw, I analyzed some principal components. - -commit 6c11174405bd5d7b172391c04ade2753df36ca7c -Author: John Detlefs -Date: Mon Aug 1 13:01:51 2016 -0700 - - small changes - -commit e0ec9ff9dd16e39c02f43c07d93ad426e5ce3a30 -Author: John Detlefs -Date: Mon Aug 1 13:01:07 2016 -0700 - - PCA covariance test - -commit f0e6501c5cb9626c83775e9bcd0512f9549f9399 -Author: John Detlefs -Date: Fri Jul 29 14:29:55 2016 -0700 - - Removed inverse_transform function, fixed rather large issue in transform function - -commit f318a3e370c34852bd02e72844723e7ecd41ac22 -Author: John Detlefs -Date: Fri Jul 29 13:14:38 2016 -0700 - - Transform changes - -commit 736d95a68eacd79cd8e9005d9a27ee63a925aae6 -Author: John Detlefs -Date: Thu Jul 28 14:15:31 2016 -0700 - - Fixed transform function per Maxs comments - -commit b22b2dfb886c376cee9de00124adcc1e5af8e733 -Author: John Detlefs -Date: Thu Jul 28 13:12:38 2016 -0700 - - Reset previous commit, force pushing the appropriate changes - -commit c15d339c6ae0929ed077922d0597861a31133b51 -Author: John Detlefs -Date: Thu Jul 28 11:29:22 2016 -0700 - - updated docs - -commit dae191ae29ee9ece7f76294b3a0105e4e89f62bf -Author: John Detlefs -Date: Tue Jul 26 16:07:01 2016 -0700 - - Get transform working, add calculated protected attribute. - -commit 4ed2070b9ca89ecf89c34827fd8fc325077d4a16 -Author: John Detlefs -Date: Tue Jul 26 15:57:11 2016 -0700 - - Iteration over crappy code to get things working. - -commit bb24f2b14348804b0269f78271334fca184a043d -Author: John Detlefs -Date: Tue Jul 26 15:34:05 2016 -0700 - - Crappy code to jump off from. Demeaning using _fit_to. - -commit 740fc89c9460123b7feac672939d7fbdf6d6afe1 -Author: John Detlefs -Date: Mon Jul 25 15:17:12 2016 -0700 - - Some demeaning fixing, work in progress - -commit 9aa086d140824d1f491160f3a079b60d61790528 -Author: John Detlefs -Date: Mon Jul 25 12:25:09 2016 -0700 - - Updated transform - -commit 5dc007668d310227ca6b3691e61666fff9c5a510 -Author: John Detlefs -Date: Sat Jul 23 18:32:07 2016 -0700 - - Tests working after refactor - -commit 1678d58122170bea80f0ed24da311e56e830ca2f -Author: John Detlefs -Date: Sat Jul 23 17:26:31 2016 -0700 - - Switched to new base api - -commit b945237147fcf5a47dcf3fd31f08f64251e642e8 -Author: John Detlefs -Date: Thu Jul 21 16:21:00 2016 -0700 - - Transform update - -commit bdb3848934bc9b0e4bd40d3337598a7a5c9c8139 -Author: John Detlefs -Date: Thu Jul 21 16:04:43 2016 -0700 - - update to Covariance algorithm - -commit f59c1ba354ece6eeae1fc3e5f88fc87e907bddbe -Author: John Detlefs -Date: Fri Jul 8 13:26:09 2016 -0700 - - Test driven bug fixing - - Updated tests - -commit 7501982d445aa10dab54f7ff3626c3e4f41e6ef8 -Author: John Detlefs -Date: Thu Jul 7 13:09:29 2016 -0700 - - Transform function done - -commit c673951d261cb290f7e7c1a2b728539068387c2c -Author: John Detlefs -Date: Thu Jul 7 11:57:28 2016 -0700 - - Mostly finished with docs - -commit 9fdc3906cfe5123e457d4f1d30202c426ec3c425 -Author: John Detlefs -Date: Wed Jul 6 21:08:33 2016 -0700 - - more docs - -commit c732a922683bf3455ca62086fc56591f9b987b33 -Author: John Detlefs -Date: Wed Jul 6 15:52:50 2016 -0700 - - More work done, Docs update, added variance attribute - -commit ad250484806e00ebd63a1dfa5446e619bcff5591 -Author: John Detlefs -Date: Wed Jul 6 14:06:24 2016 -0700 - - More work done - -commit dbbef39bc0cbd30bbef82bbd29d0a51f356d9f05 -Author: John Detlefs -Date: Wed Jul 6 11:17:43 2016 -0700 - - Work started on actual details - -commit 74941884722270a9077a4eda364647aae75426bb -Author: John Detlefs -Date: Mon Jul 4 10:16:30 2016 -0700 - - Fleshed out API - -commit 8ce6291a4388d8a99994fbbcb70d489edd50f885 -Author: John Detlefs -Date: Wed Jun 22 17:26:29 2016 -0700 - - Initial PCA Work - -commit 39f4cad413c56ca8190b721e68d9be29ab17a4a0 -Merge: 58e3b25d9 5ccb6cae0 -Author: Richard Gowers -Date: Mon Aug 8 20:53:40 2016 +0100 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 5ccb6cae0458ee54fee03fd063b0bc838356322c -Author: David Dotson -Date: Mon Aug 8 12:34:49 2016 -0700 - - More VALID/INVALID markings. - - We're basically done here. However, need @richardjgowers to look over - `test_atomgroup.TestGuessBonds` to see what's VALID/INVALID there. I did - some marking of that class, but wasn't sure about most of it. - -commit 4d466c3b0420bbbc1dd089aaf81e584ec328c850 -Author: David Dotson -Date: Fri Aug 5 15:20:37 2016 -0700 - - More VALID/INVALID marks; about to start on `TestUniverse` - -commit 9306a72c01c1d35b4fe443e6450d2dca59116edb -Author: David Dotson -Date: Fri Aug 5 15:01:22 2016 -0700 - - 70% coverage of `test_atomgroup` with VALID/INVALID - -commit ec46c9ce4dfdb782a8213bd0835485e0c2de2ec7 -Author: David Dotson -Date: Fri Aug 5 14:07:51 2016 -0700 - - More progress on VALID/INVALID marking. At 60% of `test_atomgroup` - -commit 58e3b25d95c869ec5b51a1283ef40b5506791fb3 -Merge: 2945a839b 0adc855ca -Author: Richard Gowers -Date: Fri Aug 5 13:22:36 2016 +0100 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit d293435a3142ab3ba97bd5fb4efcbdf0e0cd79c3 -Author: Richard Gowers -Date: Fri Aug 5 13:21:11 2016 +0100 - - Started hacking resid moves - -commit 0adc855ca7bede2bc42105f86cc6f1e33ff641d6 -Author: David Dotson -Date: Thu Aug 4 17:33:20 2016 -0700 - - TestAtomGroup methods now fully marked VALID/INVALID - - Instances where behavior was valid but not yet reflected in codebase - were fixed. This included getitem behavior for e.g. residues. We should - see what else we are missing as we continue. - - Halfway done with marking the entire file. - -commit fdfac03c3dbba738ee51dca08358de8a6a63f708 -Author: David Dotson -Date: Thu Aug 4 12:40:57 2016 -0700 - - Replaced pytest usage with nose-compatible components. - - Sticking with nose for now. - -commit e1e3064db9e6bd67cc02b756bd46dc1b3a3ebe4a -Merge: a670101e2 6d4f56803 -Author: David Dotson -Date: Thu Aug 4 10:57:15 2016 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit a670101e2bd01ef8cd22ca5f6c0f64c02fec882c -Author: David Dotson -Date: Thu Aug 4 10:56:15 2016 -0700 - - More VALID/INVALID marks on old test_atomgroup - - Also moved sequence from hardcoded in ResidueGroup to a transplant in - Resnames. - -commit d09073eb89a5809657336aa4cf322637f16b228f -Author: Richard Gowers -Date: Thu Aug 4 18:15:04 2016 +0100 - - Reworked transtables to use array of arrays - -commit 6d4f56803ecaed917f6c1582e5dd5076dafdfc01 -Merge: 904e457dc e12f8a8f2 -Author: Richard Gowers -Date: Thu Aug 4 15:27:48 2016 +0100 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 904e457dcbf3b1cad6c342349b3e1200b4d1b654 -Author: Richard Gowers -Date: Thu Aug 4 15:24:23 2016 +0100 - - All TopologyObject tests now pass! - - TopologyObject repr always sorts indices - -commit 0527a565dafa01a0ebae72ad643351acbaac9dec -Author: Richard Gowers -Date: Thu Aug 4 15:11:20 2016 +0100 - - Added return_index to lib.util.unique_rows - -commit e12f8a8f2a623a361ec8adff307d1b5fe45aafe6 -Author: David Dotson -Date: Wed Aug 3 17:00:45 2016 -0700 - - Beginnings of marking old test_atomgroupy tests. - - We want to preserve old AtomGroup tests for now to make it clear what is - breaking and what is not from old behavior. I've begun marking each test - with either VALID or INVALID. VALID means that the test should pass - under the new system. INVALID means that the test should not pass, and - so the test should be altered or removed. - - Tests that fail in either case I am marking with `pytest.mark.skip` - so that we can continue moving forward with tests that are failing and - haven't been reviewed yet. - -commit 89f094eef7b3187ea9986324ae205a82fdf2c126 -Merge: a1aa84449 f0d4dfd09 -Author: Richard Gowers -Date: Wed Aug 3 12:55:04 2016 +0100 - - Merge pull request #925 from kain88-de/rdf-reset - - Reset InterRDF variables in `_prepare`, fixes #924 - -commit f0d4dfd0942d19b3f694aa1a184678487180b4a1 -Author: Max Linke -Date: Wed Aug 3 11:37:24 2016 +0200 - - update tests - -commit 66c9541c66e7c90f04a6e2f346941158b16cc08c -Author: Max Linke -Date: Wed Aug 3 10:07:07 2016 +0200 - - update changelog - -commit 70825c7839a8d71933b15e8eedff4e5ecb44b7f5 -Author: Max Linke -Date: Wed Aug 3 10:02:18 2016 +0200 - - Reset InterRDF variables in `_prepare` - - This hasn't been done so far. This leads to wrong results if `run` is - called twice. - -commit a1aa84449f45ef967c96a7b95ad31d3bfce4db66 -Merge: 286e327b8 0f62787ec -Author: Richard Gowers -Date: Tue Aug 2 09:34:29 2016 +0100 - - Merge pull request #916 from jdetle/slicing_fixes - - Slicing fixes - -commit 0f62787ec3a667ff4f77807df03e9ec5c403865c -Author: John Detlefs -Date: Mon Aug 1 13:13:46 2016 -0700 - - Added known failures - -commit 286e327b830617c856da8141e4ef028e72025d33 -Author: Richard Gowers -Date: Mon Aug 1 18:33:51 2016 +0100 - - Added regression tests for hydrogenbondautocorrel (#917) - -commit 76ec586cb22a520dcf21fa5ac390948deafece6a -Author: John Detlefs -Date: Mon Aug 1 10:04:40 2016 -0700 - - Added tests that cause failures - -commit 9abf11d69d5cbe533cb3f7e13a967bb11bd376de -Merge: a8f8c1abd 736619aa8 -Author: Richard Gowers -Date: Mon Aug 1 15:24:47 2016 +0100 - - Merge branch 'DATAWriter' into issue-363 - - Conflicts: - package/MDAnalysis/coordinates/LAMMPS.py - package/MDAnalysis/coordinates/__init__.py - testsuite/MDAnalysisTests/coordinates/test_lammps.py - -commit 6833e3a772be12069a9953f667fd395b9893c55a -Author: John Detlefs -Date: Sun Jul 31 14:53:17 2016 -0700 - - Undo comment removal [skip ci] - -commit d3d4dadac56fef66101e461140d0856143198081 -Author: John Detlefs -Date: Sun Jul 31 11:50:03 2016 -0700 - - Added comments. - -commit 0c268ed06c1034336a0c2dfc9ab07e0d3894bc62 -Author: John Detlefs -Date: Sat Jul 30 21:04:36 2016 -0700 - - More testing - -commit d036859610ca8253a179078e3c0e725e33f757e9 -Author: John Detlefs -Date: Sat Jul 30 20:55:44 2016 -0700 - - I made a silly mistake in Timeseries - -commit e476ee5c2d913aabc936c7330f391f666f3fe6c1 -Author: John Detlefs -Date: Sat Jul 30 19:48:25 2016 -0700 - - Changed to logic to take advantage of new default, simplify code. - -commit 6f9e57d874524887eee4e9fe96a3d4b6731b924e -Author: John Detlefs -Date: Sat Jul 30 18:47:03 2016 -0700 - - Changes to DCD correl functions - -commit 68ae89786ab022d73ca3b0575a4bc14b1d80c6e0 -Author: John Detlefs -Date: Sat Jul 30 13:13:06 2016 -0700 - - Fixed incomplete logic - - Changed tuples - - Eliminated _testDCD - -commit 32fce067fefbef6b569d7af2e78063472f98a8e8 -Author: John Detlefs -Date: Fri Jul 29 21:08:02 2016 -0700 - - Reduced number of tests by a signifcant margin, removed test of test - -commit 6b275882712faaea80e3ab14b6766281f4c38862 -Author: John Detlefs -Date: Fri Jul 29 16:13:14 2016 -0700 - - Fixed issue caused by integer division, when stop-start / nframes has no remainder it should remain 1. - -commit df6cec8d5521311817b619608ab53d748f397b2d -Merge: e5c98deb0 6ab7b2682 -Author: Oliver Beckstein -Date: Fri Jul 29 15:11:05 2016 -0700 - - Merge pull request #909 from MDAnalysis/issue-883-openmpflag - - Added flag at lib.distances.USED_OPENMP - - closes #883 - -commit 6ab7b268247ca4fc8860bcc379aaff9f02f5a3cc -Author: Richard Gowers -Date: Fri Jul 29 22:09:47 2016 +0100 - - Added test for USED_OPENMP flag - -commit 6893abdb220980432cb51c136036fc526d3376ea -Author: John Detlefs -Date: Fri Jul 29 09:01:10 2016 -0700 - - Fixed silly correl bug - - Simple arg changes - -commit d687cc7492b611c51517569bad1d74b32b95c77b -Author: John Detlefs -Date: Fri Jul 29 08:00:41 2016 -0700 - - Changed to warnings.warn() because decorator wasnt working - -commit 8e24480f247759aeb05216ae5e6823d361e1e9f3 -Author: John Detlefs -Date: Thu Jul 28 15:43:12 2016 -0700 - - Deprecated skip for step - -commit beffbeaa923c85598fc67a918d8dee8d7f2930b2 -Author: John Detlefs -Date: Thu Jul 28 11:02:28 2016 -0700 - - Added generator but it appears to not be working, please help. - -commit 83c7e4f962122b684074f9fa770115a724a5922c -Author: jdetle -Date: Wed Jul 27 22:40:47 2016 -0700 - - Elaborated on docs - -commit 55910a0a279ca6e76998142355cf061345e14d8c -Author: jdetle -Date: Wed Jul 27 21:49:21 2016 -0700 - - Change to ++ - - Small fixes to make code work better - -commit 320b1dcc7de8aec5d89d1e1abe0aaa825311b27a -Author: John Detlefs -Date: Wed Jul 27 16:49:59 2016 -0700 - - Everything working. - Fixed logic error in code. - Removed printing of debug statement. - -commit 1b1d4f28b33684277f56e33712a213f0b9f5a4f5 -Author: John Detlefs -Date: Wed Jul 27 15:57:04 2016 -0700 - - DCD.py changes - -commit cb5852e9cea9fa1affdd04297e00a06b51a66d7e -Author: John Detlefs -Date: Wed Jul 27 15:56:26 2016 -0700 - - Added test for slicing, slowly changing DCD source for timeseries slicing. - -commit 1983709a197ef8d4be98734d481d62783521a8c5 -Author: John Detlefs -Date: Tue Jul 26 18:30:55 2016 -0700 - - Updated changelog [skip ci] - -commit 04dc85d1d8be6c8ccd9875fb396453b25738b7c9 -Author: John Detlefs -Date: Tue Jul 26 18:07:22 2016 -0700 - - Changed RMSFarray to reflect correct data - -commit e9b65862e4b17d10ec037fe22130a4d0a6475d62 -Author: John Detlefs -Date: Tue Jul 26 17:49:04 2016 -0700 - - DCD fix - -commit 9e7d439bde51cdb42190db70ae6cd95b1531ec4e -Author: John Detlefs -Date: Tue Jul 26 17:40:25 2016 -0700 - - Check_slice index fix - -commit 0649737a6780e9725c7f1d71297d275cc2bbeb1f -Author: John Detlefs -Date: Tue Jul 26 17:35:06 2016 -0700 - - Fixed analysis docs - -commit 814542109f200125d3055f775103b84e203ee9a4 -Author: John Detlefs -Date: Tue Jul 26 17:24:12 2016 -0700 - - Fixed DCD defaults and documentation. - -commit 9a58b1b802e7411618370c31158cd185ef7bb0e7 -Author: John Detlefs -Date: Tue Jul 26 17:13:27 2016 -0700 - - RMSF fix - -commit 93b52b00a65d6acb24caf105ffa1881ea5c5afab -Author: John Detlefs -Date: Fri Jul 29 10:53:31 2016 -0700 - - Reformatting commit - -commit e5c98deb0c21a9acf7c88debab83f0cb6c697e1c -Merge: d00244c13 98c568cd0 -Author: Oliver Beckstein -Date: Mon Jul 25 11:17:01 2016 -0700 - - Merge pull request #912 from jbarnoud/docs - - Some fixes for the formatting of the documentation - -commit 98c568cd029db76e2829126307c96ff663dfe997 -Author: Jonathan Barnoud -Date: Fri Jul 22 13:28:03 2016 +0200 - - Fix some documentation rendering issues - - Minor missformatting of docstring can cause part of the documentation - not to be rendered. This commit fixes some of this formatting issues. In - some occurences, it also updates some docstring refering to deprecated - methods. - - The commit also restores the documentation for gromacs trajectory - formats. - - Fixes 855 - -commit d00244c1357ab78ca6146e56dd6597449e46ae6e -Author: Oliver Beckstein -Date: Fri Jul 22 16:17:52 2016 -0700 - - added @euhruska as author - - - see his contributions to #894 - - also sent invitation to join MDAnalysis as a collaborator - -commit abbb7d33965a48251bac3786c489fd0e01f529df -Merge: 3f934d705 58fb0c7d5 -Author: Jonathan Barnoud -Date: Fri Jul 22 18:08:00 2016 +0200 - - Merge pull request #910 from MDAnalysis/issue-733-natomsdoc - - better documentation for Reader API and n_atoms kwarg - -commit 3f934d705720b9f9fce29ae24e7d8a06d1ddcd51 -Merge: 9a632a91f af677cd4c -Author: Max Linke -Date: Fri Jul 22 13:11:34 2016 +0200 - - Merge pull request #908 from MDAnalysis/issue-902-rewinds - - unify rewind behavior of Readers, fix #902 - -commit 58fb0c7d59050d88029e59e77c73b34c1f994a7d -Author: Richard Gowers -Date: Fri Jul 22 11:21:39 2016 +0100 - - better documentation for Reader API and n_atoms kwarg - -commit 0832ec3583c562b97ec81bd693e4ba50f0c7582a -Author: Richard Gowers -Date: Fri Jul 22 11:01:27 2016 +0100 - - Added flag at lib.distances.USED_OPENMP - - Fixes #883 - -commit af677cd4c03d1d612eeb895f14993010f01722df -Author: Richard Gowers -Date: Fri Jul 22 10:46:39 2016 +0100 - - Started Issue#902 - - Removed extra rewind methods, force all readers to follow base - implementation - -commit 9a632a91f23efb7f20a23c750eced293cd930494 -Merge: 6c6510c87 10283076b -Author: Richard Gowers -Date: Wed Jul 20 22:50:21 2016 +0100 - - Merge pull request #901 from MDAnalysis/issue-898-external-code - - install external packages for tests - -commit 10283076be961a4aeecb2c6b05f27014777c52cf -Author: Oliver Beckstein -Date: Tue Jul 19 22:54:49 2016 -0700 - - adjusted HOLE open file descriptor test (#129) for Darwin - - In order to provoke the failure described by issue #129 we artificially lower the open file descriptors. - On Mac OS X on travis this always leads to failing tests, as discussed under - https://github.com/MDAnalysis/mdanalysis/pull/901#issuecomment-231938093 ; this hack increases the allowed - open fds when we are running on Darwin. According to @jbarnoud, this problem is solved by #363 so once that - corresponding PR #815 is merged we should be able to revert this commit. - -commit 6c6510c87fa63678158a12ca8e7d5d330ecc78b2 -Merge: 054a9de26 313a174bb -Author: Richard Gowers -Date: Wed Jul 20 10:41:31 2016 +0100 - - Merge pull request #894 from jdetle/diffusion_rebase - - Diffusion Maps rebase, new PR for final review - -commit d291ae8d3ebe849f965a6886768c0a731ed6188a -Author: Oliver Beckstein -Date: Tue Jul 19 17:14:37 2016 -0700 - - analysis.hole: suppress output from sos_triangle and test for HOLE VMD surface creation - - - tests that the programs sph_process and sos_triangle can be run - - these two programs litter the terminal: captured stdout/stderr in HOLE.create_vmd_surface() - (at the moment, the output is never shown, which might make debugging harder) - - added new utility context manager in_dir() to the MDAnalysisTests.__init__ to make - directory jumping easier - -commit 90c750558b90fa7a7435a981091436fb7b7fef0b -Author: Oliver Beckstein -Date: Tue Jul 19 16:38:44 2016 -0700 - - simple test for plotting methods in analysis.hole - - - just run the plot() and plot3D() methods and check that - we get appropriate matplotlib objects - - removed unnecessary checks for hole executable from the - code: we already use the executable_not_found() decorators - on the tests so we are guaranteed to have hole available - - similarly, removed unnecessary checks for resources (rlimits) - -commit 1e42ce980058614a2f36b55f2811f1fd561b5fc4 -Author: Oliver Beckstein -Date: Tue Jul 19 17:56:49 2016 -0700 - - tests: set matplotlib agg backend - - On travis, the DISPLAY variable is not set and we need to choose a simple backend - like agg to make tests pass. - -commit e500355e085d240800f70ffbafbc9fe055d89a7e -Author: Oliver Beckstein -Date: Mon Jul 11 17:01:10 2016 -0700 - - added clustalw2 to full build environment - - - conda packages for clustalw2 from https://biobuilds.org/ - https://anaconda.org/biobuilds/clustalw - - enables more tests for analysis.align to pass - - see issue #898 for discussion - -commit e56d786c7621a772b4484a887b0bf4acd6bac9db -Author: Oliver Beckstein -Date: Mon Jul 11 15:33:54 2016 -0700 - - install HOLE for full tests (see #898) - -commit 313a174bb33bfc28ced2b38205ac505d38733617 -Author: John Detlefs -Date: Tue Jul 19 10:58:55 2016 -0700 - - Fixed docs, returned self - -commit cc384f1a35cf2a3e4a3b31e2ce207d52d369888d -Author: John -Date: Sat Jul 16 12:09:08 2016 -0700 - - Updated tests, updated docs - -commit 2945a839bc22967e1ff99379bdc2cca4c24fbe81 -Author: Richard Gowers -Date: Fri Jul 15 19:39:22 2016 +0100 - - Updated bond repr test - lower index first - -commit 054a9de26d29e1df9d424bf9d8f3a7d156d47465 -Author: Max Linke -Date: Thu Jul 14 11:05:02 2016 +0200 - - Analysis progmeter (#892) - - * PEP8 Changes - - * Add progressmeter to AnalysisBase - - This also adds an initialization function to AnalysisBase. This is done - now because we need to do more then just to setup the iteration. - - * Adopt Contacts - - * Follow best practices for matplotlib - - Returning an axis object is considered to be better since the user is - able to adjust the plot by himself if he wishes to do so. - - * Addopt Persistencelength - - * Adopt InterRDF - - * Adopt LinearDensity - - * Adopt AlignTrj - - * update changelog - - * Ensure old API still works - - Since user code might already exist we keep make sure the old API still - works as well. - -commit 736619aa8eb852e94d74477d0c8ef80d2299ab9f -Author: khuston -Date: Wed Jul 13 14:38:13 2016 -0400 - - DATAWriter bond types and Masses made valid - - Writer raises an exception if there are bonds but bond types are not - _explicitly defined_ as integers >= 1, i.e. will raise an exception - given the default output of `bond.type`. - - The Masses section is written for all atomtypes up to the maximum - atomtype represented in the written selection. If the mass for an - atomtype cannot be determined from the selection's universe, then it - is taken to be 1. - -commit 98d5c1076147ecb48834ee289328088c741c20cc -Merge: 4dcf071db 8d8268841 -Author: Oliver Beckstein -Date: Mon Jul 11 09:38:12 2016 -0700 - - Merge pull request #899 from MDAnalysis/tests-align-sequence_alignment - - test and doc updates for align.sequence_alignment - -commit 4dcf071db20a3dfa4187334db448dde153b35900 -Author: Oliver Beckstein -Date: Mon Jul 11 05:41:01 2016 -0700 - - various improvements to analysis.hole (#895) - - * small fixes in analysis.hole - - - updated for matoplotlib 1.5.1 - - default to cmap viridis instead of jet - - small code refactoring - - * replaced HOLE test trajectory - - The old HOLE test trajectory XTC_HOLE was replaced with MULTIPDB_HOLE. - The old one contained repetitions of a static frame, the new one the dominant - mode from an elastic network model (generated by elNemo server). The new one - is a better example for future test cases and also to demonstrate the - function of the module --- see eg https://gist.github.com/orbeckst/64c0bd5a037b3e434cc8ee6732030252 - - * added raseed argument for analysis.hole.HOLE and HOLEtraj classes - - - sets HOLE RASEED card to initialize the random number - generator; this allows reproducible HOLE runs - - added tests for HOLE and HOLEtraj that use MULTIPDB_HOLE - (and which *rely* on having RASEED --- otherwise each run - gives different output) - - Note that the test will not run on Travis because HOLE is not - available. We *could* install it, though: - - curl -L 'https://www.dropbox.com/s/jukpwlohhi20r17/hole2-NotForProfit-2.2.004-Linux-x86_64.tar.gz?dl=1' -o hole2-NotForProfit-2.2.004-Linux-x86_64.tar.gz - cd ~ - tar xvf hole2-NotForProfit-2.2.004-Linux-x86_64.tar.gz - export PATH=${PATH}:${HOME}/hole2/exe - - There is also a Mac OS X version: - - curl -L 'https://www.dropbox.com/s/5mzrsyp48i32je4/hole2-NotForProfit-2.2.004-Darwin-i386.tar.gz?dl=1' -o hole2-NotForProfit-2.2.004-Darwin-i386.tar.gz - cd ~ - tar xvf hole2-NotForProfit-2.2.004-Darwin-i386.tar.gz - export PATH=${PATH}:${HOME}/hole2/exe - - * HOLE updates: work with axes and changed docstrings to NumPy style - - - addressed @kain88-de's comment: plot() and plot3D() now properly - honor existing axes - - converted all doc strings to NumPy - - added more docs and examples - -commit 8d82688413d7a844aaac0da16c6b0b0b3d5fd9d4 -Author: Oliver Beckstein -Date: Mon Jul 11 01:18:17 2016 -0700 - - test and doc updates for align.sequence_alignment - - - added unit test - - turned **kwargs into kwargs with defaults - - updated docs - -commit b450f5390f4e35bdd20fc1ac539f3130eca95388 -Author: Oliver Beckstein -Date: Mon Jul 11 01:55:41 2016 -0700 - - fixed test for align.rms_fit_trj() with default filename - -commit c3fd22a1030151b0850e5e6471f20f090dfacc6c -Author: Oliver Beckstein -Date: Mon Jul 11 01:34:36 2016 -0700 - - added skipif(no DCD parser) to new RMS tests - -commit b299d891789d7668b6ac5fde90118a41a19cd9b2 -Author: John Detlefs -Date: Thu Jul 7 14:22:10 2016 -0700 - - Changed n_frames warning to 5000, - eliminated reference to anisotropic kernel in docs - fixed sphinx linking, documented metric API. - - Changes to documentation and some style fixes. - - More work on docs - - Change to license v2 - - Fixed tests - - Docs fixes, protected eigenvectors - -commit e801d35bbd11dccbece75877d8c2f2ea989aa94b -Author: John Detlefs -Date: Sun Jul 10 10:45:53 2016 -0700 - - Fix and cover RMSD (#889) - - Fixed (temporarily) broken analysis.rms.RMSD and added missing tests - - - fixes #897 - - full testing of the RMSD class - - Updated CHANGELOG - - * Added tests for RMSD, added a testfile. - Changed RMSD class to save rmsd array as numpy file instead of text. - - * Tested saving - - * Test group selections - Reverted back to save. - Updated test coverage for exceptions. - Found some errors with logging requiring a message. - Reverted inclusion of unnecessary RMSD array. - Fixed a small error and combined save and mass_weighted test. - No Data Error. - Covered RMSD.save(). - - * Fixed error messages - - * Asserted everywhere, fixed error messages. - -commit a4c185a95555f1a40ac8302cac100127658ef4ca -Author: John Detlefs -Date: Thu Jul 7 13:45:37 2016 -0700 - - Added space to get sphinx pages to build properly. [skip ci] - -commit b24364e192389283bcc30e27cc7db68947df4b6a -Author: John Detlefs -Date: Wed Jul 6 15:59:00 2016 -0700 - - Added link to jupyter notebook [skip ci] - -commit aa98fa72a02ab171f319438932d983ee915f68e3 -Author: John Detlefs -Date: Tue Jul 5 11:04:05 2016 -0700 - - Updated docs to remove references to anisotropy, update tutorial [skip ci] - -commit 9418cdc767043fcee476385dd6da3f94bce69cb2 -Author: John Detlefs -Date: Sun Jul 3 14:18:19 2016 -0700 - - Removed anisotropic kernel creation. Figured out that I was - unneccesarily exponentiating a diagonalizable matrix. Removed - timescaling init, removed tests for anisotropic kernel and - timescaling. - -commit 7492455f5b89fb5bb4a90be69b3e0508ef759b38 -Author: John Detlefs -Date: Wed Jun 29 11:33:12 2016 -0700 - - Removed epsilon class from pull request, now must supply a constant as a scale parameter. - - Added exception to be thrown for large distance matrices. - - Updated diffusion map after some test-driven development, added error thrown for large frame size. - - Change to warning - - Removed exception test, fixed typo - - Fixed transform, kwargs acceptance, removed Epsilon after accidentally adding it back in. - Minor fixes to docs. - - Fixes as suggested to be more pythonic and elegant - - Fixes to docs, Transform function. - -commit a9a5dbe09a4ee62883f5aca31a77f7083a2bc445 -Author: John Detlefs -Date: Tue Jun 28 18:38:46 2016 -0700 - - Refactor of code to stop DiffusionMap inheriting from AnalysisBase - Changed code further to make transform a simple iteration. - Provided functionality for doing a diffusion map with just a distance matrix. - -commit aea25a787aacd51e140b4fbe8acd2bdd10239e7b -Author: John Detlefs -Date: Sat Jun 18 20:44:59 2016 -0700 - - Fixed bug in _single_frame() - - Eliminated spectral gap function... for now - - Fixed matrix multiplication bug - - Fixed save issue - - Better single_frame loop - - Name changes, styling updates and doc fixes. - -commit 32a9655bd15f118f5c3cb74ecb791ed564a0ba06 -Author: John Detlefs -Date: Fri Jun 17 20:44:15 2016 -0700 - - Now witness the firepower of this fully armed and - operational diffusion map - -commit 786ef01fc53514cd45c257b2dbf3e0d30ea42774 -Author: John Detlefs -Date: Thu Jun 16 15:39:03 2016 -0700 - - Automodule added, Changed some object oriented stuff around - DistMatrix is its own AnalysisBases subclass, DiffusionMap still is an AnalysisBase subclass - but only for the actual diffusion map embedding. Previous _conclude function renamed to - kernel_decompose. - - Changed things around to get embedding working - - Added tests, found bugs, squashed bugs. - - Eliminated square of distance, random mistake - -commit 19c3675c08064a4f363a044f4d6d1792805c47ba -Author: John Detlefs -Date: Fri Jun 10 13:52:53 2016 -0700 - - Separated calculation of distance matrix from diffusion - map calculation decided to calculate epsilon as a - function outside of class for maximum usability. - - Change of direction in API, more work to be done implementing everything - - Changes to docs, functions, tried to make it very evident - how we were following the lafon paper in terms of algorithm. - - added timescaling, fixed some parts - -commit 38f2352712141b3277ee34522732a98d8677d720 -Author: John Detlefs -Date: Sun May 29 17:15:11 2016 -0700 - - added tests, fixed logger issue - - style fixes, protection fixes, added docs - - fix of some broken areas - - fixed selections and updated tests accordingly - - switched order of imports [skip ci] - -commit a14242206e3fa9bc5ad27d78924ee2d38eb43536 -Author: John Detlefs -Date: Sun May 29 13:49:17 2016 -0700 - - refactor of @euhruska diffusion map - -commit f2ae4a406aca350b6940eb5525d2e3386bb79193 -Author: John Detlefs -Date: Mon May 23 21:08:24 2016 -0700 - - initial work for refactor - -commit e77350012ea7301e69eacfcb468488fff3a80c39 -Author: Eugen Hruska -Date: Thu Mar 10 18:44:18 2016 -0600 - - included notes - -commit b6f8632754831e3c6d6600b4e04fce6f986d40c4 -Author: Eugen Hruska -Date: Wed Mar 2 15:55:50 2016 -0600 - - diffusionmap faster test - -commit 6f8e8cc02341e55502e1116931c303265e1f13b4 -Author: Eugen Hruska -Date: Wed Mar 2 15:30:16 2016 -0600 - - test for diffusionmap - -commit ce7dd68e97c1e65002b57f54359348449e5f3a41 -Author: Eugen Hruska -Date: Wed Mar 2 13:08:01 2016 -0600 - - diffusionmap minor fix - -commit 5fdd7b6e5352173b54885b74b991b78425f078a2 -Author: Eugen Hruska -Date: Wed Mar 2 12:46:24 2016 -0600 - - description of diffusion map - -commit ffcd3f27f7cd705f7f165a80fe88f00000187a4f -Author: Eugen Hruska -Date: Wed Mar 2 11:29:23 2016 -0600 - - new analysis feature: diffusion map - -commit 5d78f0302bf55180c34a80fa897dc2a960cd298a -Merge: c11cb7424 852daecf9 -Author: Oliver Beckstein -Date: Wed Jul 6 17:34:55 2016 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit c11cb74243cf5ceb13208fad71ceb12a4550cf35 -Author: Oliver Beckstein -Date: Wed Jul 6 17:34:28 2016 -0700 - - cleaned up reST in MDAnalysis.analysis.contacts - -commit 852daecf9eb9b20700d9a71160efb9baa2490ba5 -Merge: 7220db53f 80eb6d305 -Author: Max Linke -Date: Thu Jul 7 00:20:29 2016 +0200 - - Merge pull request #891 from jdetle/nframes - - Changed nframes to n_frames, fixes #890 - -commit 80eb6d3051ca438fabdb612349e4bd4adbce714f -Author: John Detlefs -Date: Wed Jul 6 14:12:32 2016 -0700 - - Changed nframes to n_frames - - Updated CHANGELOG - - Removed references to nframes in tests - -commit 7220db53f2dd7b9660258e2dce90221b0996fa08 -Author: Tyler Reddy -Date: Wed Jul 6 17:52:30 2016 +0100 - - Resolving Truncation of resids for GRO file writing (Issue 886) (#887) - - * Fixes #886. When .gro files are written their resids will now be properly truncated to 5 digits. - * Added a new unit test for Issue 886 -- dealing with residue number truncation when writing GRO files. - - - * The fix for Issue #886 has now been added to the CHANGELOG. - - * Added a comment regarding usage of class-level fixtures for the unit test covering Issue 886. - - * output file specification in unit test for Issue 886 has been fixed. - - * Fixed the formatting of CHANGELOG following fixes to Issue 886. - -commit 16cd195c6352b7a5565cd6e46f7a950e8526b6b1 -Author: kain88-de -Date: Fri Jul 1 13:49:16 2016 +0200 - - Only filter MDAnalysis deprecation warnings (#885) - - This gets rid of the annoying deprecation warnings in - ipython when MDAnalysis is loaded. - - [skip ci] - -commit 01e4d45cdfcc8ccfd116080e93f77cfcbe6cc27f -Merge: 9c1f8fb99 1b7b82b5e -Author: Jonathan Barnoud -Date: Thu Jun 30 10:49:14 2016 +0200 - - Merge pull request #882 from jdetle/baseAnalysis - - Added self._frame_index for easy array operations using AnalysisBase - -commit 1b7b82b5e0f7601023cd71d65ea41aa3eda0a1ba -Author: John Detlefs -Date: Tue Jun 28 13:33:17 2016 -0700 - - Name change and CHANGELOG updated - -commit c921196294f209617a7f4beff610f926a9ec2a32 -Author: John Detlefs -Date: Mon Jun 27 12:58:44 2016 -0700 - - Added self._index for easy array operations - -commit a8f8c1abd8b62f276cf9e098c86d84e61932e56b -Author: Richard Gowers -Date: Sat Jun 18 08:04:04 2016 +0100 - - Fixed TopologyObject missing _bondtype attribute - - Fixed adding single TopologyObject to TG - -commit 1cf32ba043ed5bb4d647eef00d01c596578834f5 -Merge: 0feec7bec e07619894 -Author: Richard Gowers -Date: Wed Jun 15 10:09:08 2016 +0100 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 9c1f8fb99f5504d8d5726a856ed91ebadd8cb03e -Merge: debae2b9e aff3e9af3 -Author: kain88-de -Date: Mon Jun 13 14:21:58 2016 +0200 - - Merge pull request #874 from jbarnoud/opened_files - - Plugin to display the open files upon test failure - -commit aff3e9af32f7751407e50ce778242356e86be07e -Author: Jonathan Barnoud -Date: Fri Jun 10 15:10:49 2016 +0200 - - Plugin to display the open files upon test failure - - The plugin is enabled by default. It displays the path to the files that - have a open file handler. To disable the plugin, run mda_nosetests with - the --no-open-files option or with the NOSE_NO_MDA_FILES environment - variable set. - - The commit also introduces a test that fails if the MDA_FAILURE_TEST - environment variable is set. This test comes handy to test nose behavior - upon failure. - - The open-files plugin requires psutil. That requirement has been added - to setup.py. - -commit debae2b9e92e88bce9eff6c8bc9c242029a0d1ed -Merge: 1eaba07d6 ac1f681e3 -Author: mnmelo -Date: Mon Jun 6 23:20:49 2016 +0200 - - Merge pull request #872 from MDAnalysis/issue-869-fixup - - Added tests for calling next at end of Reader - -commit ac1f681e38156a08e7ce6df1379d6c33a2a95670 -Author: Richard Gowers -Date: Mon Jun 6 20:48:02 2016 +0100 - - fixup - -commit 000c1a32205b8357dd7ecd72f852c226fda6400b -Author: Richard Gowers -Date: Mon Jun 6 20:10:10 2016 +0100 - - Added tests for calling next at end of Reader - - SingleFrameReader now correctly raises a StopIteration on call of next - -commit 1eaba07d600f0763d13ef576f0d3cbfbaaca223a -Author: Fiona Naughton -Date: Mon Jun 6 19:54:17 2016 +0100 - - fix Reader iter/next (#870) - -commit ca51e1db1991b1b2523af74ed32e2eaedd5f2f39 -Merge: d68cf73ef cc2d886f9 -Author: kain88-de -Date: Sun Jun 5 23:22:26 2016 +0200 - - Merge pull request #856 from jdetle/refactor_align - - Refactor align - -commit cc2d886f93f2cdf067e101b04b030dfb56c7e82e -Author: jdetle -Date: Sun Jun 5 11:50:29 2016 -0700 - - removed version changed reference - -commit 0737c0f1b87175048b5aa7e88826e670b97e082d -Author: John Detlefs -Date: Fri Jun 3 11:08:05 2016 -0700 - - changed scope of variables, added docs for unprotected attributes - -commit 0596f596f04c9fd05b5768453423a5d3b4431a15 -Author: John Detlefs -Date: Thu Jun 2 00:22:02 2016 -0700 - - Fixed CHANGELOG, Docstring added and fixed logger info, Fixed docs - -commit 7d12fd8cf9f96fcb5ef3c7de6a94ef468dd3bc1d -Author: John Detlefs -Date: Sat May 28 23:32:12 2016 -0700 - - Fixed docs and added comments, style fixes for PEP8. - -commit 0feec7bec7b9b7f4256c4484c532b2eeeed9a04b -Author: Richard Gowers -Date: Wed Jun 1 10:18:23 2016 +0100 - - Resids no longer required in pdb files - -commit 3541a5c4a390d84c3ff3acaa7b4957b4e5d5b66e -Author: Richard Gowers -Date: Wed Jun 1 10:18:16 2016 +0100 - - Fixed old usage of coordinates() - -commit 9b8d120d7ecb68932a5f467e49a8d36771260921 -Author: John Detlefs -Date: Thu May 26 11:03:55 2016 -0700 - - Updated CHANGELOG [skip ci] - -commit 6d613289e157dd51cb7ce8d163e107e70af74504 -Author: John Detlefs -Date: Wed May 25 22:59:49 2016 -0700 - - Updated Biopython sequence alignment docs [skip ci] - -commit 8f75e1ef7bb04203e3468718f9a0a4dccb74546d -Author: John Detlefs -Date: Wed May 25 22:38:06 2016 -0700 - - Saved some doc changes before redoing other docs in case of revert [skip ci] - -commit f2401a7896f2c0627f8e450a31b76a0abf13cc70 -Author: John Detlefs -Date: Wed May 25 21:53:57 2016 -0700 - - docs fix [skip ci] - -commit 752d9257556bbee871c8953511af18b18ae85749 -Author: John Detlefs -Date: Wed May 25 20:22:38 2016 -0700 - - coverage increase - -commit c1662d318f5571b607a88ddcc23edc239f63207a[m -Author: John Detlefs -Date: Wed May 25 20:00:01 2016 -0700 - - fixed error - -commit 8d16241735cbb27cbb9fcec37d1fb608be6fa484 -Author: John Detlefs -Date: Wed May 25 18:59:08 2016 -0700 - - simple fixes - -commit cfd664f6284ce2120f0f914f4fe916e0cfadbc94 -Author: John Detlefs -Date: Wed May 25 18:48:50 2016 -0700 - - Increased coverage revealed an error! - -commit 467dd4a27af7bdc4f551bee4d05e33528e2dcf88 -Author: John Detlefs -Date: Wed May 25 12:07:08 2016 -0700 - - center of mass/vs center of geometry backwards - - Updated tests, align - -commit 17d50c59c8cf0b273a1edabd3cad7e1c1fac81a2 -Author: John Detlefs -Date: Wed May 25 10:43:53 2016 -0700 - - QC fix and docs update - -commit 162fc7b683d7a1db7e113a105a7f9e7e8c73da67 -Author: John Detlefs -Date: Wed May 25 10:37:07 2016 -0700 - - changed order of selection and rmsd calculations to get proper selections - -commit c125aad0c4e6366b63c9045ec1a78137f8fde4b5 -Author: John Detlefs -Date: Thu May 19 21:31:47 2016 -0700 - - Fixed some tests to delete files after creation, - Updated docs to satisfy numpy doc strings - Updated alignto to return old_rmsd, new_rmsd - Created _fit_to wrapper for min_rmsd calc and atom translation - AlignTraj now calls simple _fit_to class in single_frame - - changes to _fit_to, align_to, AlignTraj - - updated docs - - updated alignTraj, fit_to - - commity mcCommitface - - commity mcCommitface - -commit b697ae312743d9587c45fa0a7c042f8e99766978 -Author: John Detlefs -Date: Thu May 19 18:01:07 2016 -0700 - - Reverted the addition of progress meter to base.py - -commit 46f915b12401efa9e28c9fc745a5d1870863d234 -Author: John Detlefs -Date: Tue May 17 20:31:22 2016 -0700 - - First refactor to fit_trj, new class named AlignTraj fixed some minor issues in other functions - Made changes to fit_trj to conform to style and look cleaner - Added deprecation warning for rms_fit_trj in align - Fixed numerous errors to get tests passing, changed references to new names in tests. - Added tests for AlignTraj - Removed class protection from process selection as it is used by align.py - Updated docs to satisfy style guide - -commit f4936b9bcf1f71ea4f8d4b66871068b58907189a -Author: Wouter Boomsma -Date: Wed May 25 15:45:19 2016 +0200 - - Encore: Adjusted expected results for hes tests: test failures were due to minor bug in previous version. - -commit d68cf73efca409f5c7718290fc88d6147bcdd8fc -Merge: aa3d19b68 7ab0ad28f -Author: Jonathan Barnoud -Date: Tue May 24 11:55:37 2016 +0200 - - Merge pull request #854 from MDAnalysis/conda-build-update - - Conda build update - -commit 7ab0ad28f2fb0810ff243271c010d155eda94106 -Author: Max Linke -Date: Mon May 23 14:32:33 2016 +0200 - - increase build number - -commit 1b01462ee1c0fa8067dac0a89f99a85c5ee5c11f -Merge: 50a9edceb aa3d19b68 -Author: Matteo Tiberti -Date: Mon May 23 13:28:53 2016 +0100 - - Merge remote-tracking branch 'upstream/develop' into feature-encore - -commit 50a9edcebe1e8a7723ba8c3a2e3dbb84b40e1227 -Author: Matteo Tiberti -Date: Sun May 22 09:25:49 2016 +0100 - - Merge remote-tracking branch 'upstream/develop' into HEAD - -commit aa3d19b68f9a924a204698517db95702618ddd16 -Merge: 004125eb9 eb52ea491 -Author: Oliver Beckstein -Date: Sun May 22 23:15:14 2016 -0700 - - Merge pull request #860 from kain88-de/fix-lambda - - Fix lambda (fixes #859) - -commit eb52ea4910649a3e1c0193a97862814b3f460c25 -Author: Max Linke -Date: Sat May 21 15:50:56 2016 +0200 - - Update CHANGELOG - -commit 1a78edbed92f075cc3b4c1cc2c677ab86ec50d5b -Author: Max Linke -Date: Sat May 21 15:45:37 2016 +0200 - - PEP8 changes coordinates/base.py - -commit 9c08c45e4ded826a51c443245d393b403f8962d9 -Author: Max Linke -Date: Sat May 21 15:39:43 2016 +0200 - - Read and store lambda value for trr files - - The lambda value is stored in the data dictionary of the TimeStep. - If no value is found a dummy value of 1 is used. - -commit e07619894863acf75511a205dd851cd8477f7e60 -Author: Richard Gowers -Date: Fri May 20 21:17:38 2016 +0100 - - Fixed filename in MOL2Parser - -commit 454b221e799df6388880390abbaac1ce2d6bebb0 -Author: Richard Gowers -Date: Fri May 20 20:36:51 2016 +0100 - - Fixed various tests in pbb - - Fixed Universe breaking when given empty segids - -commit 3e664ab8ed1ea831e3730108992757b4869bc33c -Author: Richard Gowers -Date: Fri May 20 19:56:48 2016 +0100 - - Reworked PDB writing - - Now makes no assumptions on contents of AtomGroup - -commit ba99fcb7c59f9dbecf6a54308836fe7df128ed2b -Author: Matteo Tiberti -Date: Fri May 20 16:21:07 2016 +0100 - - moved cython/c file according to the new paradigm and modified setup.py accordingly - -commit fa08f757622b9f27234dd284e1042b59fd069fa4 -Author: Richard Gowers -Date: Fri May 20 10:09:58 2016 +0100 - - Fixed some topologyattr tests - -commit 34cc7b1950c0b35a6b1968b909af3a561a885355 -Author: Richard Gowers -Date: Thu May 19 20:41:13 2016 +0100 - - Added write method to AtomGroup - - XYZ write selection now doesn't use resid - - Fixed bad lammps data file - -commit 1ee9b31b13586f5347e6bcad99c8ed952f97dfc7 -Author: Richard Gowers -Date: Thu May 19 17:05:14 2016 +0100 - - Removed references to SYSTEM from gro tests - - Default segid removed - -commit 8856096977c50bfefd0f38fc819df48732d1afd3 -Author: Richard Gowers -Date: Wed May 18 18:40:37 2016 +0100 - - AtomNeighborSearch now accepts Atoms as well as AtomGroups - - various small 363 fixes - -commit 83f55be95e19c799cf8b6e259bb7977a1ffe2c49 -Merge: 777209bb2 004125eb9 -Author: Richard Gowers -Date: Wed May 18 10:10:14 2016 +0100 - - Merge branch 'develop' into issue-363 - - Conflicts: - package/MDAnalysis/coordinates/PDB.py - package/MDAnalysis/core/AtomGroup.py - package/MDAnalysis/topology/ExtendedPDBParser.py - package/MDAnalysis/topology/GROParser.py - package/MDAnalysis/topology/PDBParser.py - package/MDAnalysis/topology/PrimitivePDBParser.py - testsuite/MDAnalysisTests/coordinates/test_gro.py - testsuite/MDAnalysisTests/coordinates/test_pdb.py - testsuite/MDAnalysisTests/test_topology.py - -commit 5193ee7c4d3a1da0b4496b5b41985d14f6dbb41c -Author: Max Linke -Date: Mon May 16 13:13:51 2016 +0200 - - update travis build - - install griddata also from conda. This should give a minimal speed up in - build times. - -commit f8e74ed921d10984909e19f4fffaa175936c66c5 -Author: Max Linke -Date: Mon May 16 12:49:33 2016 +0200 - - fix last tempdir occurences - - Looks like we overlooked some of them at the first try - -commit 345853dd4402157df5f74e1cf6b1cb52a2391b65 -Author: Max Linke -Date: Mon May 16 12:29:17 2016 +0200 - - update buildscript for mda 0.15.0 - -commit 004125eb9c02047e2d593b3b1ed09e531f5d6832 -Author: Richard Gowers -Date: Mon May 16 10:00:35 2016 +0100 - - Started next develop version after release - -commit cc64b450601fd556b638e38c37db5d134d499cf9 (tag: release-0.15.0) -Merge: 13a97e481 f906b949f -Author: Richard Gowers -Date: Sun May 15 21:19:55 2016 +0100 - - Merged 0.15.0 release into master - -commit f906b949f251b8d23879d70cfc419bc7a2f58179 -Author: Richard Gowers -Date: Sun May 15 21:14:48 2016 +0100 - - Finalised 0.15.0 release - -commit 69039dfb9d9ea2f1795e69ad0897f341d61595a2 -Merge: aa27b03e7 dc522c4f2 -Author: kain88-de -Date: Sun May 15 17:10:47 2016 +0200 - - Merge pull request #852 from MDAnalysis/issue-851-dlpfix - - Fixed HistoryReader using 1 based frame indices - -commit dc522c4f2f71a1f9ce24353f75b6fe9c8ed14aac -Author: Richard Gowers -Date: Sun May 15 12:05:47 2016 +0100 - - Fixed frame numbering on rewind - - #851 - -commit 98394615879c4aeb010d2a1b47bf1573378f6cf6 -Author: Richard Gowers -Date: Sun May 15 11:23:38 2016 +0100 - - Fixed tests for issue #851 - -commit 35a7e7269036db0a4da01ca97607f4790798ad90 -Author: Richard Gowers -Date: Sun May 15 11:18:25 2016 +0100 - - Fixed HistoryReader using 1 based frame indices - -commit aa27b03e70773be81f935558cd084f8733e4d700 -Merge: d989f27fa 1a4c7cba6 -Author: kain88-de -Date: Fri May 13 15:57:43 2016 +0200 - - Merge pull request #849 from MDAnalysis/issue-848-fasterpdb - - First draft of faster pdb reading (fixes #848, #850) - -commit 1a4c7cba61ba138309350c71d9ca39a8e1e45b0f -Author: Richard Gowers -Date: Fri May 13 14:00:33 2016 +0100 - - Added tests for compressed PDB file seeking and reading - -commit fa5d50b2b0063abc5c8d320eda4286930a2a36f1 -Author: Richard Gowers -Date: Thu May 12 17:49:26 2016 +0100 - - tests for standalone PDBReader - -commit 5928dbc00ce2a16e700f21016a00eb80090579d7 -Author: Richard Gowers -Date: Thu May 12 17:07:39 2016 +0100 - - Fixup - -commit ea70fd4aece67348fa581169f37ea79859b62b71 -Author: Richard Gowers -Date: Thu May 12 16:25:29 2016 +0100 - - For issue #850 - - PDBReader only opens a single file handle in its lifetime - -commit 48571e157fbdccc8dea65b77418a07ca64fbc359 -Author: Richard Gowers -Date: Thu May 12 15:17:33 2016 +0100 - - Updated to handle CRYST entries that precede model headers - -commit 0269cf01976a0bf6f18a8b1644e70a35afb0fae8 -Author: Richard Gowers -Date: Thu May 12 12:22:08 2016 +0100 - - First draft of faster pdb reading - -commit d989f27fa9269252f6000eb20e5c70a2d5a6dc10 -Author: kain88-de -Date: Wed May 11 11:08:36 2016 +0200 - - Amber trj format (#847) - - * PEP8 Changes - - * Add crdbox as TRJ formated file - - * Update Changelog - -commit 0f1683131f057c19e35157345a50fcd16de1ce20 -Author: Matteo Tiberti -Date: Mon May 9 14:13:18 2016 +0100 - - removed all other flavours of SPE except for the classical one - -commit 190ed95f7e94250982daf0bc35577bb65e3d5c2c -Author: Matteo Tiberti -Date: Mon May 9 14:04:24 2016 +0100 - - changed math.h import - -commit b750c24e90121e852451c7015401775c2c1aea22 -Merge: f914568f4 439901fa6 -Author: Richard Gowers -Date: Mon May 9 09:14:07 2016 +0100 - - Merge pull request #833 from jdetle/hbonds - - Added zero-based indices for donors and acceptors in HBond Analysis. - -commit 439901fa62248155f6861f969ed3bd901c468f15 -Merge: 730bc3d3e 64596fc26 -Author: John Detlefs -Date: Sat May 7 19:13:25 2016 -0700 - - Merge pull request #1 from richardjgowers/hbonds - - Hbonds fixup - -commit 730bc3d3e1eef787ff7c1c885a8f79e913edb6d5 -Author: John Detlefs -Date: Fri May 6 20:41:50 2016 -0700 - - Added real trajectory test - -commit 64596fc26c1f66df93080b898b131d1f0e06eba5 -Author: Richard Gowers -Date: Sat May 7 12:14:05 2016 +0100 - - Tidied hbond_analysis slightly - - Changed distance metrics to staticmethods - - Reworked selections to use implicit OR syntax - - Used direct bool comparison of Groups - -commit 3892406e7c9090ce4238eea8eef32dcf15e1eb7d -Author: Richard Gowers -Date: Sat May 7 11:06:19 2016 +0100 - - Fixed up test - -commit 777209bb2dcb43354b7c7882d66df6ae393401b6 -Author: Richard Gowers -Date: Sat May 7 11:03:05 2016 +0100 - - Fixed single file Universe creation - -commit 58687ec61cfcb8873591ba5546c6b700e02f025b -Author: John Detlefs -Date: Fri May 6 20:41:50 2016 -0700 - - Added real trajectory test - -commit f914568f4a48e91afe486e4bda0e369d127cfb47 -Merge: a7fb27414 94ce366d8 -Author: Richard Gowers -Date: Fri May 6 20:02:55 2016 +0100 - - Merge pull request #844 from kain88-de/tempdir-removal - - Tempdir removal - -commit 94ce366d88552e5eebbc472f0e64261644cb1f42 -Author: Max Linke -Date: Fri May 6 19:14:10 2016 +0200 - - remove tempdir from conda scripts - -commit 222e0d9c0adc7549f8434d05d0f27a02a077700d -Author: Max Linke -Date: Fri May 6 19:10:13 2016 +0200 - - remove tempdir requirement - - and some general clean up of the setup.py - -commit a7fb274141173d9a1bec27c43273a3509a9d7be7 -Merge: 5ccd344ba 7a77bf115 -Author: kain88-de -Date: Thu May 5 15:49:09 2016 +0200 - - Merge pull request #840 from jbarnoud/pdb-p3-regression - - Fix a regression with PDB files on python 3 - -commit 7a77bf115bb4eec942a1b07ab86004c4b7eed9aa -Author: Jonathan Barnoud -Date: Thu May 5 10:17:08 2016 +0200 - - Fix a regression with PDB files on python 3 - -commit 71fcc6df9bc6cd249c2709b94ee9dcc0c2f45455 -Author: Richard Gowers -Date: Wed May 4 14:23:21 2016 +0100 - - Fixed icodes being read as integers - - Added icode selection - -commit 92b544581c246e53d90069166b28b69155b99c7b -Merge: 0bf9c0708 0f5de8a03 -Author: Matteo Tiberti -Date: Tue May 3 09:21:26 2016 +0100 - - Merge branch 'feature-encore' of https://github.com/encore-similarity/mdanalysis into feature-encore - -commit 9142426c908f8c654bbd971a97143c9619b6ea6e -Author: John Detlefs -Date: Mon May 2 21:08:48 2016 -0700 - - Updated docs [skip ci] - -commit 2bea8be04ec8e5b3b41e7a7a2c090e99272266af -Author: John Detlefs -Date: Mon May 2 20:33:26 2016 -0700 - - Updated tests, fixed some issues in docs - -commit c231374d95a34f8e77104158aae0d84dac67b972 -Author: John Detlefs -Date: Wed Apr 27 16:44:46 2016 -0700 - - Updated CHANGELOG - -commit ed9ece5fc2daa0d968cd95aa12725551b8ecbcee -Author: John Detlefs -Date: Sun Apr 24 13:51:07 2016 -0700 - - Added zero-based indices for donors and acceptors in HBond Analysis, - updated docs to reflect change. Added deprecation warning for the - 1-based index. - -commit 5ccd344baf9ec35496117ac55bd7bae86ea8937f -Merge: 2567a1aa3 218a9c332 -Author: Jonathan Barnoud -Date: Fri Apr 29 23:56:53 2016 +0200 - - Merge pull request #835 from jdetle/issue-834 - - Added ENT file extension to PDBReader, Writer and Parser. - -commit 218a9c332e440deb2e6c60e4470f19561620c6bc -Author: John Detlefs -Date: Wed Apr 27 17:44:03 2016 -0700 - - Added ENT file extension to PDBReader, Writer and Parser. - Updated tests to check succesful loading of PDB file from ENT extension. - Updated CHANGELOG, allowed for reading of .ent files in testsuite, shortened - '.ent' testfile. Updated docs to show ent extension supported by trajectory - readers/writers and topology parser. Changed name of truncated ENT test file - to reflect testing purpose. - -commit 0bf9c0708f76152430a7df829cfcdc06d9e64001 -Author: Matteo Tiberti -Date: Fri Apr 29 12:56:20 2016 +0100 - - cosmetical changes - -commit f7a1eafd6aaf2877cd638ad3628518922924de3f -Author: Matteo Tiberti -Date: Tue Apr 26 10:56:48 2016 +0100 - - removed debug prints - -commit 2567a1aa36ff2cfd7d5814677a632ed96a3ea202 -Merge: 2bd06e54b 1a0943c56 -Author: Jonathan Barnoud -Date: Mon Apr 25 08:23:52 2016 +0200 - - Merge pull request #809 from BartBruininks/issue597_units_unittest_Raises - - Added exception test for units.py (part of #597) - -commit 2bd06e54b8d9cede15782fbd25f456a64938877a -Merge: 2de129031 719a3915b -Author: David Dotson -Date: Sun Apr 24 23:14:58 2016 -0700 - - Merge pull request #756 from MDAnalysis/issue-755-atomTSview - - Fixes #755: Atom timestep properties now return copies, not views. - -commit 719a3915b11fcdfd1ada24961db4e30e2504081b -Merge: a7def5f1d 2de129031 -Author: Richard Gowers -Date: Sun Apr 24 18:40:10 2016 +0100 - - Merge branch 'develop' into issue-755-atomTSview - - Conflicts: - testsuite/MDAnalysisTests/coordinates/test_pdb.py - -commit a7def5f1de9b1fb03df66d2f30df288642e74ccb -Author: Richard Gowers -Date: Tue Apr 19 19:27:44 2016 +0100 - - Fixed failing tests for Issue #755 - - These were incorrectly settings the position of the atom (using the - returned view) - -commit 2de12903198343ade57274e118de954259ead68c -Merge: ba2fd3a39 aad5e1a60 -Author: Richard Gowers -Date: Sun Apr 24 18:36:59 2016 +0100 - - Merge pull request #832 from MDAnalysis/issue-777-remove-BioPDB - - remove Bio.PDBParser (Issue #777) - -commit aad5e1a604098840e3b87047d68a7506024ae7b3 -Author: Oliver Beckstein -Date: Fri Apr 22 01:40:24 2016 -0700 - - removed tests related to permissive PDBReader - -commit 964a4b48e829863b0a60346e61e049a85d1e6eb5 -Author: John Detlefs -Date: Tue Apr 19 16:52:55 2016 -0700 - - doc fixes for removal of Bio.PDBParser - - - Removed references to Permissive_PDB - - Updated CHANGELOG, fixed errors in tests, updated docs - -commit 3084ad3768a0500bbfccbcd92c279dd1b5ec2e88 -Author: John Detlefs -Date: Wed Apr 13 19:41:55 2016 -0700 - - removed supporting code for Bio.PDBReader and cleanup - - - Removed references to permissive flag in docs, and its use as an argument. - - Updated tests in test_pdb and test_topology, updated tests to remove - references to the permissive flag. - - Updated docs to identify deprecated modules, - - removed structure builder and updated the CHANGELOG - -commit a9751d8759ecde1318e8aa87c1a7b2d6eedc3074 -Author: John Detlefs -Date: Mon Apr 4 13:09:25 2016 -0700 - - cleanup related to BioPDB removal (#777) - - - Changed tests to eliminate known failures caused by BioPython - - Updated CHANGELOGs and fixed wrong version number in AtomGroup.py, - - fixed indentation issue in PDB.py - - Fixed doc references to version strings and the permissive flags, - - got rid of extraneous text in PrimitivePDBParser, fixed scope of warnings - - Used boolean property of collections as suggested by QC - -commit 8d1dc5482a095cf03faca452f6a0627a1c209b0c -Author: John Detlefs -Date: Sat Apr 2 15:31:31 2016 -0700 - - Eliminated Biopython PDB Reader/Writer and Parser (#777) - - - 'permissive'=False has no effect anymore - - Added deprecation warnings for Primitive Readers/Writers and Parsers. - - Changed doc strings to eliminate references to - BioPython Reader/Writer. - - Updated CHANGELOG to reflect changes. - -commit ba2fd3a3944c93cc8031c7276929ef74cc340078 -Merge: 9ce60e67f 0ebbbe6a6 -Author: Oliver Beckstein -Date: Thu Apr 21 23:10:10 2016 -0700 - - Merge remote-tracking branch 'origin/contact-improvements' into develop - -commit 9ce60e67f84046babd408b0624aae13056fd6562 -Merge: 9e049f68e 0492d9a06 -Author: Oliver Beckstein -Date: Thu Apr 21 19:30:40 2016 -0700 - - Merge pull request #827 from kain88-de/include-tempdir - - include tempdir module into testsuite - - (Simplifies conda packaging. If we find a better solution we will unbundle again.) - -commit 1a0943c5630c6143081e0b9db62a814a3beda6e6 -Author: Bart Bruininks -Date: Wed Mar 30 18:55:57 2016 +0200 - - Added exception test for units.py (part of #597) - - Also found and fixed a formatting error in units.py for unknown unit - types also fixed a small printing bug and made the format of the - touched files up to the current standard. - -commit d2ed4003d860d9d7bc618e648e1b9f3417c1849b -Merge: da35a5ce2 9e049f68e -Author: Richard Gowers -Date: Tue Apr 19 19:25:21 2016 +0100 - - Merge branch 'develop' into issue-755-atomTSview - - Conflicts: - package/CHANGELOG - -commit 9e049f68e8292f68c854687e6a3587877276f72a -Merge: a4c31d467 330db1cd7 -Author: kain88-de -Date: Tue Apr 19 06:30:35 2016 +0200 - - Merge pull request #825 from MDAnalysis/depremovals - - Removed some use of deprecated methods - -commit ec3ac90701a17c55fbe9772244236e0e1fa6f16e -Merge: c4dd45df8 30218af74 -Author: David Dotson -Date: Mon Apr 18 17:44:01 2016 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit c4dd45df87dc3a32ec52bdd729455bb6091e8434 -Author: David Dotson -Date: Mon Apr 18 17:43:05 2016 -0700 - - Needed to flatten corresponding indices for downward group conversions - -commit a4c31d46749a9253586a98c4e55f66e54d37f3c3 -Merge: aa7e87155 6a47ed73a -Author: Oliver Beckstein -Date: Mon Apr 18 16:39:43 2016 -0700 - - Merge pull request #829 from MDAnalysis/warnonce - - Deprecation warnings now only appear once per deprecated feature - -commit 30218af743d1d8c6ce2c7c9a550d6caa99a08ff2 -Author: Richard Gowers -Date: Mon Apr 18 22:53:22 2016 +0100 - - Added tests for contains in Groups - -commit 2bb30fadb1b9668866bc86d4e580c08479d679e5 -Author: Richard Gowers -Date: Mon Apr 18 19:32:15 2016 +0100 - - Added tests for using Sum on Groups and Components - - Fixed components not summing correctly - -commit 6a47ed73a5f69fa6de65a316af050179c267e167 -Author: Richard Gowers -Date: Mon Apr 18 10:57:40 2016 +0100 - - Deprecation warnings now only appear once per deprecated feature - -commit aa7e871550b16864dd378115d8a1330253b37143 -Merge: 432498e37 613184952 -Author: kain88-de -Date: Mon Apr 18 09:31:21 2016 +0200 - - Merge pull request #821 from MDAnalysis/issue-820-grovels - - fixes #820 read gro files with missing velocities - -commit 432498e375bc26d7b20ece0f7c6c2c4c1a5931c1 -Merge: d2aff3359 66115e11e -Author: kain88-de -Date: Mon Apr 18 09:29:15 2016 +0200 - - Merge pull request #826 from jdetle/rmsd-weighting - - Updated rms to factor in weighting (fixes #814) - -commit 66115e11e4f6de705abc6dac3dd1f5f00e6437b6 -Author: John Detlefs -Date: Thu Apr 14 18:30:17 2016 -0700 - - Updated rms.py and tests to account for weighting - - Updated tests to check weighting with superposition - -commit 6131849525aca63ef0f91efce5a822476815676a -Author: Richard Gowers -Date: Sun Apr 17 22:50:53 2016 +0100 - - fixup - -commit 330db1cd7ce9776aa3adbd7d63b5f9245cc53b0f -Author: Richard Gowers -Date: Sun Apr 17 22:47:33 2016 +0100 - - Removed use of Residue.name and Segment.id - -commit d2aff335938eaaf5a2b11388201de68e222c1f00 -Author: kain88-de -Date: Sun Apr 17 23:01:59 2016 +0200 - - fix pos warnings (#828) - -commit 0492d9a068656ee1494a629439739aceda0f66fc -Author: Max Linke -Date: Sat Apr 16 22:13:07 2016 +0200 - - replace string interpolation with format() - -commit 21060d52acafef28452eadebf63677313bc233b5 -Author: Max Linke -Date: Sat Apr 16 22:03:23 2016 +0200 - - Update CHANGELOG and LICENSE - -commit 2e1bd189712102bb8f02815f47848b70375633af -Author: Max Linke -Date: Sat Apr 16 21:52:05 2016 +0200 - - Update all tests to use MDAnalysisTests tempdir - -commit 8c84df85cb70195e50c5dc4fdd648e57b152afc0 -Author: Max Linke -Date: Sat Apr 16 21:51:14 2016 +0200 - - add tempdir module - - We ship our own copy now. This isn't to much code and it - helps us slim down on dependencies (especially the ones - not provided by conda) - -commit 0ebbbe6a6824bd8def168657d93042442b9871d3 -Author: Max Linke -Date: Sat Apr 16 20:21:37 2016 +0200 - - Update CHANGELOG - -commit 5d871af32e9642e51891e6411066aaa34f6f90d6 -Author: Max Linke -Date: Fri Mar 18 08:14:03 2016 +0100 - - Update tests and add new tests - - This updates all the old test with some refactoring. Each function gets - its own test now as well. According to coverage all code that isn't - deprecated is covered to 100% - -commit 3aacb27e4cd35e6926c508a1cb5b31927047d00a -Author: Max Linke -Date: Tue Mar 1 18:11:12 2016 +0100 - - Refactor Contacts class - - This is a list of all the changes done in this commit - - - PEP8 changes - - allow arbitrary method to be passed to Contacts - - contact_matrix is a separate function - - simplifies Contacts class, cut everything non essential - - update docs - - removed plot functions - - analysis saving is done with extra function call - - deprecate ContactAnalysis and ContactAnalysis1 - - Use python3 division in module - - add explicit q1q2 analysis - -commit 0f5de8a03578f7bc2c4e914d1a9ed07c55f90feb -Author: Wouter Boomsma -Date: Fri Apr 15 14:07:27 2016 +0200 - - Changed behavior so clusters are returned even when not fully converged (warning is issued). - -commit 96c927262daeb21d00c33b9112e5be283f45b78a -Merge: d73c18a65 d07237769 -Author: kain88-de -Date: Wed Apr 13 19:45:10 2016 +0200 - - Merge pull request #823 from MDAnalysis/issue-822-simple-rmsd-broken - - fix for simple rms.rmsd() (Fix #822) - -commit 3f1f36d5c05f1026078a82a4a856462472c57500 -Author: Richard Gowers -Date: Tue Apr 12 10:18:16 2016 +0100 - - Removed some use of deprecated methods - -commit d0723776953feedb9a784d75f63e8598cf37ba91 -Author: Max Linke -Date: Tue Apr 12 15:01:27 2016 +0200 - - update changelog - -commit 928e88545f9c3f3595cbbeb8389e33030f5cd649 -Author: Max Linke -Date: Tue Apr 12 14:19:54 2016 +0200 - - Add more rmsd test - - I know compare also the results when the superposition theobald - algorithm is used. - -commit 868fa851407e9eb91f0bb5e51449c951f4d5f4a3 -Author: Max Linke -Date: Tue Apr 12 14:03:15 2016 +0200 - - fix rms tests - -commit 06b275b23fa12096e8c95eebeb045ff9d6d5dc81 -Author: Richard Gowers -Date: Mon Apr 11 17:45:41 2016 +0100 - - Fixes Issue #820 - - Added warning to incomplete velocity read - -commit cf1e6b6271cc2004d847fd6d62a296a5bcad175f -Author: Oliver Beckstein -Date: Mon Apr 11 18:10:53 2016 -0700 - - fix for simple rms.rmsd() (Issue #822) - -commit e95294506fecb0f6a7eb910882f82bece08b4827 -Author: Richard Gowers -Date: Mon Apr 11 17:29:47 2016 +0100 - - tests for issue #820 - -commit d73c18a651ad4667a3e4de431b27ad3ec7263521 -Author: David Dotson -Date: Sun Apr 10 15:24:26 2016 -0700 - - All deprecations on AtomGroup and friends getters and setters. (#698) - - * All deprecations on AtomGroup and friends getters and setters. - - The new topology system for #363 will arrive in 0.16.0, and this removes - redundant getters and setters of various `Atom`, `Residue`, and - `Segment` properties. These methods predated the properties that replace - them, and this commit features deprecation warnings for each with - instructions on what to use instead. - - Some `Atom` properties, such as `number`, `pos`, `serials`, have themselves been - replaced in the new scheme (`index`, `position`, `id`, respectively). - - The methods `AtomGroup.translate` and `AtomGroup.rotateby` no longer - take tuples of `AtomGroup` objects as optional arguments, but only take - explicit vectors. Because `Residue`, `ResidueGroup`, `Segment`, and - `SegmentGroup` are no longer `AtomGroup`s themselves, leaving this in - creates a minor convenience at the cost of method complexity. The - documentation is correspondingly complex, and in the course of updating - the docstrings to numpy-style for #363, simplifying the method also - simplified the documenation. - - Also deprecated `as_Universe` function. This has yet to be discussed on - the `issue-363` branch, but discussion should happen on what its purpose - is. - - Not addressed in this commit: - - 1) In #363, `__getattr__` behavior for the Groups - have changed to a slightly different scheme. No warnings have been added - for this change to the `__getattr__` methods yet. The new scheme goes - as:: - - SegmentGroups __getattr__ can select by segment name - Segment __getattr__ can select by residue name - ResidueGroup __getattr__ can select by residue name - Residue __getattr__ can select by atom name - AtomGroup __getattr__ can select by atom name - - Should only require the following in `AtomGroup.__getattr__`, or - pehaps override in `ResidueGroup` and add after a `super`: - - ```python - if isinstance(self, ResidueGroup): - warnings.warn("In version 0.15.0 this will select " - "residue names, not atom names ", DeprecationWarning) - ``` - - - * Added deprecations to Residue angle methods. - - The methods `phi_selection`, `psi_selection`, `omega_selection`, and - `chi1_selection` rely on particular atom names and the contiguity of - resids to work properly. Although these are not bad assumptions for most - topologies with a protein, they are inherently fragile. They have not - been included in the new topology system addressing #363. - - * Added warnings for property access at the appropriate level. - - Also added warning that getattr on ResidueGroups will work only for - residue names, not atom names. - - * _FIFTEEN -> _SIXTEEN; Segment now has segid property - - In the new topology scheme, atomid is just a label present defined by - the topology format (gro and PDB files have them) that don't need to - start from 0 or be unique. Atoms are uniquely identified by atom *index* - instead, which is mostly internal to the topology system but is unique - between atoms and starts from 0. - - Given this, we make atom id in the old system roughly behave as it will - for the new scheme. Strangely, atom ids up until this point were defined - by residues. I have no idea why, or what a good reason might have been - for this. - - * Added kwarg support to atom_property decorator - - * Removed "id" from Atom slots. - - Since `Atom.id` is now a property, it shouldn't be a slot. - - * Added deprecations for Residue, Segment plural residue, segment props respectively - - Since Residues are an AtomGroup subclass here, a Residue has e.g. `resids`, - which gives per-atom resids (all the same, *hopefully*). This doesn't - exist in #363, so added proper deprecations. Ditto for segment - properties that spit out per-residue results. - - Also, since we don't want our own recommendations for setters using the - deprecated setters internally, did simple copy-paste of setter code to - appropriate property. - - Also deprecated Residue.id, Residue.name, and added Residue.resid and - Residue.resname as the proper alternatives. - - * Fixed neglected changes to copy-pasted code for property setters - - * Removed deprecated use of Segment.id - - * removed usage of deprecated functions Universe init - - * Removed deprecations on anchor mechanisms. - - The anchor mechanisms of a Universe deserve further discussion. They are - used for AtomGroup pickling/unpickling, which may or may not make sense - under the new system. De-deprecating for now, though. - - * Added deprecations to changelog; fixed some omissions. - - Also, moved warning decorator outside of cached decorator if present so - it displays every time. - -commit d365548e89342f374268d84e5b2c5c58ec901415 -Author: Kyle Huston -Date: Sun Apr 10 18:00:50 2016 -0400 - - Fix Merge for issue-363 branch (#781) - - * Fix Merge for issue-363 branch - - Rewrote mda.Merge to work for new topology style. - - I also changed the default argument for attrs in core.Topology() beacuse - the default argument of None caused an error, whereas using an empty - list instead will return a blank Topology. - - * fix atomgrps for same universe, enable sum - - My first attempt at collecting atom groups for the same universe was - flawed if args contained more than one atom group from the same - universe. Hopefully this one is correct. - - I also override __rsum__ on AtomGroups to allow use of sum. - - * cleanup and describe which topologyattr get Merged - - * correct Merge atom order, segind, add top tests - - I changed my previously proposed mda.Merge to align more closely with - the old Merge behavior, in that it preserves the atom order as given to - Merge. Given the introduction of residue and segment indices (distinct - from ids), the behavior of this new Merge assigns separate residue and - segment indices to each argument of Merge. That is, if two arguments to - merge are atomgroups from the same universe with the same residue - indices, in the post-merge universe, they will have different residue - indices. If the user doesn't want this, s/he should add together the - atom groups before merging. - - My understanding is that resid is just an attribute of a residue, - whereas the residue index is the unique identifier of that residue - instance. I didn't think it would make much sense for Merge to duplicate - atoms by giving them different indices while keeping their residue - indices the same, such that you have doubled or tripled (etc.) the - number of atoms in a residue or segment. - - Before I was sending the per-atom segment indices to Topology instead of - the per-residue segment indices. Topology.__init__() or - TransTable.__init__() should probably check that the correct length - index arrays are passed on. - - I added an attribute to the TopologyAttrs called `per_object` where the - value of this attribute is 'atom', 'residue', or 'segment' if the length - of the TopologyAttr value should equal n_atoms, n_residues, or - n_segments. The Universe method `_process_attr` now checks if the - TopologyAttr has `per_object` attribute, and raises a ValueError of the - length of the value array is not as expected. - - Finally I updated `test_modelling.py`. This actually increased the - number of errors raised during testing by 2, because instead of stopping - at an error in the first few lines of the test file, it goes on and - errors occur for Capping and `atoms.write`. - -commit bf0816de1c911f26a7c3cb0d54b67eae22421b88 -Author: Richard Gowers -Date: Sat Apr 9 12:17:04 2016 +0100 - - More tests for group slicing - - Fixed slicing group with empty list - Fixed contains on groups - - Added test for group getitem singular - - Added tests for slicing with numpy integer array - - More tests for group getitem - - First tests for Group addition - - Fixed Components eq comparison - - Added tests for groups TypeError - - Started tests for Group level transitions - - Fixed downward level transitions in Groups - - Added tests for up and down shifts in Groups - - Added tests for Group.unique - - Added component to group tests - -commit 78331d5435a5287322c04203aeeecab4edb1d9fc -Merge: 86d1eae41 50629b706 -Author: kain88-de -Date: Fri Apr 8 22:04:45 2016 +0200 - - Merge pull request #796 from MDAnalysis/groparser-coveragefix - - Changed bare except in GROParser to try and fix coverage detection - -commit c328a67f11b9539384ed86faa458e1c79f3f3aef -Author: Richard Gowers -Date: Fri Apr 8 13:06:06 2016 +0100 - - Started slicing tests - -commit 1fb0c92cc4a698fae22e1f0cc156848fa0c163f2 -Author: Matteo Tiberti -Date: Fri Apr 8 09:16:40 2016 +0100 - - removed debug print statement - -commit 86d1eae41418a94d8bf5b79e8354ab010227c66d -Merge: fdd5dca12 fdec85492 -Author: Oliver Beckstein -Date: Thu Apr 7 15:46:28 2016 -0700 - - Merge pull request #817 from MDAnalysis/issue-816 - - Closes #816 - MOL2 without substructures - -commit 7eddb935ec000f1e1c453b8e191d13fb25854f65 -Author: Richard Gowers -Date: Thu Apr 7 22:49:41 2016 +0100 - - More tests for group slicing - - Fixed boolean slicing with list - -commit da57201b61e583f38a5afc13a0389d1d9e3c4ed8 -Author: Wouter Boomsma -Date: Thu Apr 7 21:37:21 2016 +0200 - - Changed slice convention in MemoryReader to follow that of numpy. - -commit a12a6308f3d47074fe213c59a0968b0ce9babf30 -Author: Matteo Tiberti -Date: Wed Apr 6 17:27:44 2016 +0100 - - changed the AP algorithm to use floats instead of double for memory efficency - -commit dfaf296457fb5123bedc8d1ee2e106910bbab839 -Author: Matteo Tiberti -Date: Wed Apr 6 15:05:42 2016 +0100 - - removed duplicate test - -commit fdec85492a7dca11c2c53f6eea15a1d7cef61626 -Merge: f19cdcc39 fdd5dca12 -Author: Richard Gowers -Date: Wed Apr 6 13:40:14 2016 +0100 - - Merge branch 'develop' into issue-816 - - Conflicts: - package/CHANGELOG - -commit f19cdcc39b69ea0a45ee2ee9d5167a0511cf32f4 -Author: Richard Gowers -Date: Wed Apr 6 13:36:37 2016 +0100 - - Finished Issue #816 - -commit 07fc902deff851e6761b4f4ab1a04c6ad0297eb0 -Author: Richard Gowers -Date: Wed Apr 6 13:32:27 2016 +0100 - - MOL2 Writer no longer requires substructure - -commit b443a4d00e693c411f894dbde6df9e1f42b0698e -Author: Richard Gowers -Date: Wed Apr 6 13:21:56 2016 +0100 - - Removed list appending for MOL2 coordinate reading - -commit ac9afb90424735f9acbf30e7e086d0d4accebdd6 -Author: Richard Gowers -Date: Wed Apr 6 13:08:38 2016 +0100 - - Fixes issue #816 - -commit de62a9b0cf9a8ada5916b7d18daf464a8ee8150b -Author: Richard Gowers -Date: Wed Apr 6 13:00:47 2016 +0100 - - Added tests for Issue #816 - -commit 36f2949329a55179c983f526c5a2d15d9604b903 -Author: Matteo Tiberti -Date: Wed Apr 6 11:23:31 2016 +0100 - - Removed problematic test - -commit 4d97e18d7fb5ff836ece674a109cbd26cde719ea -Merge: c3c127461 0608d161c -Author: Matteo Tiberti -Date: Wed Apr 6 11:05:10 2016 +0100 - - Merge branch 'feature-encore' of https://github.com/encore-similarity/mdanalysis into feature-encore - -commit c3c12746158f0b1a50ea0c61a69ab9ea63b3371b -Author: Matteo Tiberti -Date: Wed Apr 6 10:51:08 2016 +0100 - - fixed parallel execution in conformational_distance_matrix - -commit 434d8b111e6b9a997811d2d64e664bdf6db637bc -Author: Matteo Tiberti -Date: Wed Apr 6 10:33:13 2016 +0100 - - Refactored the confdistmatrix module - functions instead of classes - -commit fdd5dca1216e2a8f43952144fd8a7ecc9e47d5d9 -Author: David Dotson -Date: Tue Apr 5 21:40:32 2016 -0700 - - A Universe now holds onto its initialization kwargs. - - * A Universe now holds onto its initialization kwargs. - (Fixes #292) - This is useful for external libraries, such as MDSynthesis - (https://github.com/datreant/MDSynthesis), to re-initialize a Universe - from its arguments. - - * Added tests for Universe keeping a copy of its init kwargs. - - Basic test that it holds on to these as we'd expect in - test_atomgroup.TestUniverse. Another test that these work as expected in - guess_bonds tests. - - * Test equality of full kwargs dict - - * Exposed Universe kwargs with read-only property - - * Updated changelog with Universe kwargs exposure - - * guess_bounds -> guess_bonds - - * Made test for universe kwargs staticmethod since we don't use self - - * Removed `self` from staticmethod test. - -commit 0608d161c72283a0bddb2a7809ac6d465f8a816d -Author: Wouter Boomsma -Date: Tue Apr 5 22:26:58 2016 +0200 - - Added special case in Selection.AllSelection to speed up "all" selections. - -commit ce6d6e5783b8acf6e1423b05da2c85860cc47fdc -Author: Wouter Boomsma -Date: Tue Apr 5 22:07:52 2016 +0200 - - Removed call to np.cov in covariance.py - ML case. - -commit 8edefade0c3da44467f214dca2e8a2bb7f611fed -Merge: 8145ccf20 9b554804b -Author: Richard Gowers -Date: Tue Apr 5 10:04:49 2016 +0100 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 8145ccf20f223ba3d23fa099533d15d833577fcb -Author: Richard Gowers -Date: Tue Apr 5 10:04:26 2016 +0100 - - Started tests for group slicing - -commit bbcbd3618daf08eacd762a8fbb513076f9b49ded -Author: Wouter Boomsma -Date: Tue Apr 5 01:34:20 2016 +0200 - - numpy -> np in covariance.py - -commit f8733d588ac004653128c42bf9744e61b3255bc9 -Author: Wouter Boomsma -Date: Tue Apr 5 01:27:42 2016 +0200 - - Removed check for empty selection string in Universe.select_atoms() - Introduced check for all-atom selection MemoryReader. - -commit 9b554804b07b52fa4a346f98bfbe4eea16fa52bb -Merge: b8f033414 3f3f07fac -Author: David Dotson -Date: Mon Apr 4 16:14:56 2016 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit b8f033414dd48c50558833cd231b4d88fb3cc48e -Author: David Dotson -Date: Mon Apr 4 16:13:32 2016 -0700 - - Getting atomindices are resindices gives iterable same len as caller - - This is to match decided behavior for accessing attributes at various - levels. - -commit f26cd38b240c462c1bd2ff18105bc76ecd45a69d -Author: Wouter Boomsma -Date: Tue Apr 5 00:04:47 2016 +0200 - - Bugfix in coordinate extraction in Universe.transfer_to_memory(). - Added test for matching skip convention in timeseries() and MemoryReader. - -commit be24a915929a192039e0c6c8d3bb1efbfe299738 -Author: Matteo Tiberti -Date: Mon Apr 4 15:10:16 2016 +0100 - - defaulted number of cores to 1 in confdistmatrix - -commit eb4e393dc6bdbda3f3b1d416dde085368136d99e -Author: Matteo Tiberti -Date: Mon Apr 4 15:07:32 2016 +0100 - - changed numpy.array to numpy.asarray to avoid making useless copies - -commit d319957dbab1e54475f96b420fbf9f4b19b28133 -Author: Matteo Tiberti -Date: Mon Apr 4 15:01:47 2016 +0100 - - Changed dict.iteritems() to six.iteritems(dict) - -commit c70dafe20f6272df6c13c3307492b88bdeb40342 -Author: Wouter Boomsma -Date: Mon Apr 4 15:34:49 2016 +0200 - - Added dimensions and dt support to MemoryReader. - TestMemoryReader now inherits from BaseReaderTest. - -commit 14b16279d3f2ec027a430c55bf00fb3f18dc4bad -Author: Wouter Boomsma -Date: Mon Apr 4 13:35:42 2016 +0200 - - Simplified coordinate extraction code in Universe.transfer_to_memory - -commit 3f3f07fac5c2fdf07cad24874ed6b516da13df34 -Author: Richard Gowers -Date: Mon Apr 4 12:15:30 2016 +0100 - - Readded AtomGroup to TopologyObject conversions - -commit 7d86cb9fdcbe9aea3b0481661db10911f44ab147 -Merge: a22539af0 ee9210f14 -Author: Richard Gowers -Date: Mon Apr 4 11:35:21 2016 +0100 - - Merge branch 'develop' into issue-363 - - Conflicts: - package/MDAnalysis/coordinates/MOL2.py - package/MDAnalysis/coordinates/PDB.py - package/MDAnalysis/core/AtomGroup.py - package/MDAnalysis/core/Selection.py - package/MDAnalysis/core/Timeseries.py - package/MDAnalysis/core/__init__.py - package/MDAnalysis/core/topologyobjects.py - package/MDAnalysis/lib/util.py - package/MDAnalysis/topology/CRDParser.py - package/MDAnalysis/topology/DLPolyParser.py - package/MDAnalysis/topology/GMSParser.py - package/MDAnalysis/topology/GROParser.py - package/MDAnalysis/topology/HoomdXMLParser.py - package/MDAnalysis/topology/PDBParser.py - package/MDAnalysis/topology/PDBQTParser.py - package/MDAnalysis/topology/PSFParser.py - package/MDAnalysis/topology/PrimitivePDBParser.py - package/MDAnalysis/topology/TOPParser.py - package/MDAnalysis/topology/XYZParser.py - package/MDAnalysis/topology/base.py - package/MDAnalysis/topology/core.py - package/MDAnalysis/topology/tpr/utils.py - testsuite/MDAnalysisTests/test_atomselections.py - testsuite/MDAnalysisTests/test_topology.py - testsuite/MDAnalysisTests/test_util.py - testsuite/MDAnalysisTests/topology/test_gro.py - testsuite/MDAnalysisTests/topology/test_tprparser.py - -commit e9eb097963665a52ff3ed3dc3e528628d247917d -Author: Wouter Boomsma -Date: Sun Apr 3 21:14:12 2016 +0200 - - Removed Ensemble class - Fixed bug in MemoryReader - -commit ee9210f1477139d805cbb66affa51b14a0577b1c -Merge: b739cecf2 9b3167dce -Author: Richard Gowers -Date: Sat Apr 2 16:44:48 2016 +0100 - - Merge pull request #803 from Endle/develop - - Started tests for gnm. - -commit 667225da31cae49928940faaefacc1bb2cd319c6 -Author: Wouter Boomsma -Date: Sat Apr 2 16:08:12 2016 +0200 - - ArrayReader renamed to MemoryReader - in_memory option added to Universe - in_memory option added to rms_fit_trj - timeseries() now default to asel==None - -commit 9b3167dce188801d7767bc5c697eccf2eb4a875e -Author: Zhenbo Li -Date: Sat Mar 26 21:27:07 2016 +0800 - - Add tests for gnm. - - Signed-off-by: Zhenbo Li - -commit b739cecf217505d7a4a64e9e0c2845ebebcf4f2c -Merge: 7a329b9e7 45846d87c -Author: kain88-de -Date: Thu Mar 31 22:36:30 2016 +0200 - - Merge pull request #811 from jdetle/develop - - Updated comments in init to reflect nose test docs - -commit 45846d87c892a0afb4a18d2333d7a431ea3c208d -Author: John Detlefs -Date: Thu Mar 31 12:23:57 2016 -0700 - - Updated comments in init to reflect nose test docs [skip ci] - -commit a22539af08816d0f3807381647b42ba418eda0c9 -Author: David Dotson -Date: Wed Mar 30 17:19:43 2016 -0700 - - Added element topologyattr. - - Probably useful for PDB files or any other topology file that gives an - element name. - -commit 9b6ecb8701c5d009ed74e2abe29770bcc5cb8c4f -Author: Wouter Boomsma -Date: Tue Mar 29 22:48:21 2016 +0200 - - Switch to new-style string formatting. - -commit cd9bba239f5690cdb1023c53143dc790ebd15fc9 -Merge: 5461d12aa a3a5f00d5 -Author: Matteo Tiberti -Date: Tue Mar 29 16:21:10 2016 +0100 - - Merge branch 'feature-encore' of https://github.com/encore-similarity/mdanalysis into feature-encore - -commit 5461d12aa55e2742e0c313ae0eec615b10c2a0f1 -Author: Matteo Tiberti -Date: Tue Mar 29 16:20:31 2016 +0100 - - fixed few other QuantifiedCode issues - -commit a3a5f00d5686de721a4952924f5a07fedc5a8bc6 -Merge: f2d60781c 5447bdbbf -Author: Wouter Boomsma -Date: Tue Mar 29 16:37:19 2016 +0200 - - Merge branch 'feature-encore' of https://github.com/encore-similarity/mdanalysis into feature-encore - -commit f2d60781c9718a70bfdd1edce576aabf1f417356 -Author: Wouter Boomsma -Date: Tue Mar 29 16:37:14 2016 +0200 - - Switch to new-style string formatting. - -commit 5447bdbbf2f96231f1a271802b479edd94f421b6 -Author: Matteo Tiberti -Date: Tue Mar 29 15:29:21 2016 +0100 - - solved most issues raised by QuantifiedCode - -commit d8faaec4fdaca9751cacf784e0862d7f118a1619 -Author: David Dotson -Date: Sun Mar 27 23:16:12 2016 -0700 - - Small notes to re-add removed functionality for translate and rotate_by - -commit dbe6d061e35f45104317e2c3662601f19b9ea44e -Author: David Dotson -Date: Sun Mar 27 22:00:55 2016 -0700 - - Moved residue angle selections to Atomnames. - - I consider these very fragile since they depend on particular atom names - (however customary), but included them where they should go since they - depend on atom names. They will need to be refactored, though, since - they depend on getitem working for atom names, which is not something - we've included (so far) for any groups. - -commit 7a329b9e7d28cd2ef21088e0dc58cbbba73ff67e -Merge: 58f13b1ab f06710190 -Author: Oliver Beckstein -Date: Sun Mar 27 20:41:11 2016 -0700 - - Merge pull request #806 from jbarnoud/issue-804-coverage - - Update the README to reflect #804 - -commit 366e713dcc1b3c1faf5a3912c74b3aeec1f21059 -Author: David Dotson -Date: Sun Mar 27 20:21:00 2016 -0700 - - Moved as many things out of AtomGroup and into GroupBase as reasonable. - - We want ResidueGroups and SegmentGroups to behave roughly in the same - way as before, that is having methods they had when they were subclasses - of AtomGroup. Not everything makes sense, but most things do. - - This was consensus from discussion in #703 - (https://github.com/MDAnalysis/mdanalysis/issues/703#issuecomment-181569563) - -commit ada354ec9e2c8165356066482d53f91541290e1d -Author: David Dotson -Date: Sun Mar 27 18:31:54 2016 -0700 - - Accessing topologyattrs always gives iterable of same length as caller. - - This in accordance with the consensus on #599 - (https://github.com/MDAnalysis/mdanalysis/issues/599#issuecomment-183540437). - -commit f067101905619fad1d9b8ed2aa4ef33d74bb10eb -Author: Jonathan Barnoud -Date: Sun Mar 27 22:54:16 2016 +0200 - - Update the README to reflect #804 - -commit 58f13b1ab80981554d38da123f29e33e8a4b6d99 -Merge: bddbd81c6 7306f1720 -Author: kain88-de -Date: Sun Mar 27 21:17:49 2016 +0200 - - Merge pull request #805 from jbarnoud/issue-804-coverage - - Activate coverage report for analyses (fixes #805) - -commit 7306f1720e0711676e10240ff71bbefab7b72865 -Author: Jonathan Barnoud -Date: Sun Mar 27 21:00:56 2016 +0200 - - Activate coverage report for analyses - - See issue #804. - -commit c539d54c586be1320fa171e1ff5b4b0ca03b0213 -Author: Matteo Tiberti -Date: Thu Mar 24 20:08:48 2016 +0000 - - solved most issues raised by flake8 - -commit 5b2971e6de8269b1c4f9baa846264eddf08ebcba -Author: Matteo Tiberti -Date: Thu Mar 24 18:15:24 2016 +0000 - - fixed code style according to pep8 - -commit 80af13e9d59385063f16d236f02608f5266033d9 -Author: Matteo Tiberti -Date: Thu Mar 24 17:54:49 2016 +0000 - - removed debug print - -commit c857da9ea48257126d93c6700397bf43f90e87fe -Author: Wouter Boomsma -Date: Thu Mar 24 07:40:26 2016 +0100 - - Added decorators around scipy-dependent tests. - -commit 349974cdd64bb4fd63e0690c786a248b277cdfb8 -Author: Wouter Boomsma -Date: Thu Mar 24 01:24:43 2016 +0100 - - Added decorators around scipy-dependent tests. - -commit 4e1cee0e04cdb6a1e30303dbbaf26197f5373d95 -Author: Wouter Boomsma -Date: Thu Mar 24 01:16:51 2016 +0100 - - Added Python3 support. Fixed import style. - -commit b83f4b96afba075fb4c1e88986a9b8fd6ac7fed9 -Author: Wouter Boomsma -Date: Wed Mar 23 13:44:29 2016 +0100 - - Removed __iter__ from ArrayReader. - -commit 024d8723e606a6c24b1b259f462520383ec3f15f -Author: Wouter Boomsma -Date: Wed Mar 23 13:24:25 2016 +0100 - - Removed topology_filename attribute from Ensemble class. - -commit 50629b706859b5260f3a421c07f1d04c6c3405a0 -Author: Richard Gowers -Date: Tue Mar 22 23:08:24 2016 +0000 - - Changed bare except in GROParser to try and fix coverage detection - -commit 96c72717f788308d0f895cff8201dbfbc5339b9a -Author: Matteo Tiberti -Date: Tue Mar 22 13:58:23 2016 +0000 - - added test - -commit 81f834ab514a5b3f3815a42fd290a5bf63dbe43e -Author: Wouter Boomsma -Date: Tue Mar 22 10:37:39 2016 +0100 - - Increased test coverage in encore. - -commit bddbd81c6e784aceb8d38b51b211ba1dce4c66bd -Merge: c282d663f 93b5841be -Author: mnmelo -Date: Mon Mar 21 19:53:13 2016 +0100 - - Merge pull request #794 from jbarnoud/issue-784-dynamic-authors-py3 - - Dynamic author list works on python 3 - -commit 93b5841be8f6bc4de5fb193d88d47dc09418a42a -Author: Jonathan Barnoud -Date: Mon Mar 21 19:01:31 2016 +0100 - - Wrap dynamic author list generation in setup.py - - If the user cannot write in the MDAnalysis source directory, writing the - list of authors will fail. This commit wrap the generation so the - install proceed with a warning instead of crashing. - -commit c282d663fcd0f80279bd35cd4459d58fd94eb5c8 -Merge: feefee668 ea126c8e8 -Author: Jonathan Barnoud -Date: Mon Mar 21 18:11:12 2016 +0100 - - Merge pull request #783 from fiona-naughton/develop - - added test for exception raise in GROParser (per issue #597) - -commit ea126c8e89dc83229297ebfd64d216d47163a20f -Author: fiona-naughton -Date: Sat Mar 19 04:05:14 2016 +0000 - - added tests for exception raise in GROParser - -commit 0de57c87568a485f3ac380e95d1fdb839bc315ba -Author: Jonathan Barnoud -Date: Mon Mar 21 18:03:25 2016 +0100 - - Dynamic author list works on python 3 - - The dynamic author list introduced in #787 did not work on python 3 - because of the way encoding was handled. This commit fixes the handling - of file encodings by using the codecs library. - -commit 98db2b7bb59fa71ad36fb7ee723ca25d156ebf6d -Author: Matteo Tiberti -Date: Mon Mar 21 11:23:41 2016 +0000 - - fixed regression from botched merge - -commit 0126e27b81c29ce17048ceb6c3151cd2a332d00c -Merge: cf5198ba4 feefee668 -Author: Matteo Tiberti -Date: Mon Mar 21 10:32:08 2016 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit cf5198ba46b68c2fe420cec3f32ddab46f803433 -Author: Matteo Tiberti -Date: Mon Mar 21 09:56:24 2016 +0000 - - fixed dobule RELEASE issue - -commit feefee668aa9b10ce04ade61e3e46636dbfaf61d -Merge: 2cc1cc31d 33ac4f694 -Author: Oliver Beckstein -Date: Sun Mar 20 23:38:13 2016 -0700 - - Merge pull request #789 from pedrishi/issue724 - - Closes #724 - Removing assert statements from test units - -commit 33ac4f694df2a3fd974f2e4d44cb7e45ed01a959 -Author: pedrishi -Date: Sun Mar 20 02:40:43 2016 +0000 - - Issue 724 - Removing assert statments from test units - -commit 2cc1cc31d3e9af2a773b85ef986d6443521d652c -Merge: 33e15b60d c7a1593f1 -Author: Richard Gowers -Date: Sun Mar 20 16:17:58 2016 +0000 - - Merge pull request #791 from jbarnoud/issue-784-dynamic-authors - - Remove relative imports introduced in #787 - -commit c7a1593f14d0871a1db21e6f192977d5e450d837 -Author: Jonathan Barnoud -Date: Sun Mar 20 14:26:54 2016 +0100 - - Remove relative imports introduced in #787 - - We prohibit relative imports in the tests (see #189). When adding tests - for the dynamic author list (#787), I introduced some such relative - imports. - -commit 33e15b60df0a2a6e4e4a0b216e5125b7316c1eec -Author: Richard Gowers -Date: Sun Mar 20 11:06:06 2016 +0000 - - Started tests for nuclinfo - -commit 3de4db6cecfe61919578d43588bc219cdcfb26b6 -Merge: b27e41d7f a68eedfd6 -Author: Richard Gowers -Date: Sun Mar 20 09:48:03 2016 +0000 - - Merge pull request #787 from jbarnoud/issue-784-dynamic-authors - - Issue #784 -- Dynamic author list - -commit a68eedfd628809ecea0ddd17f40b31a45e6df8d7 -Author: Jonathan Barnoud -Date: Sun Mar 20 02:12:24 2016 +0100 - - Wrap the imports of authors.py - - MDAnalysis should not fail if authors.py cannot be generated and - therefore imported. If authors.py is not present, then __authors__ is an - empty list. - -commit eee3cee0fbc95670d9cb94f046eb08572a2f1ba6 -Author: Jonathan Barnoud -Date: Sun Mar 20 01:40:16 2016 +0100 - - Update CHANGELOGs for __authors__ - -commit 5b1aadf754796e92a499e3a0356f3af4989f5ffc -Author: Jonathan Barnoud -Date: Sun Mar 20 01:03:53 2016 +0100 - - Test that __authors__ is defined - -commit 2937b7467fede2f20b6e07e9638e1548e353c617 -Author: Jonathan Barnoud -Date: Sun Mar 20 00:53:26 2016 +0100 - - Generate authors.py from AUTHORS for the tests - -commit 1c2e62fc48805c08f5e1a5e25baa03b5a829564c -Author: Jonathan Barnoud -Date: Sat Mar 19 23:10:24 2016 +0100 - - Sphinx uses __authors__ - - The list of authors used by sphinx is the one in authors.py. - -commit 4e5d502da05106b09ceb6abede062c732d199ad8 -Author: Jonathan Barnoud -Date: Sat Mar 19 21:56:12 2016 +0100 - - setup.py writes authors.py in package - - A list of authors usable from python is generated from the AUTHORS file - by 'package/setup.py'. That list allows to maintain a single list of - authors instead of one list in AUTHORS and one list in the sphinx - documentation. - - MDAnalysis.__init__ imports authors.py to give access to - MDAnalysis.__authors__. - -commit c7a1ba0d5ba2fd75f548f3d12727348ea4beb1b3 -Author: Jonathan Barnoud -Date: Sat Mar 19 23:05:22 2016 +0100 - - Add missing Lennard van der Felzt in AUTHORS - -commit b27e41d7f5124214529cec5778e7789b5de55ae9 -Merge: e3a345d07 861caefa3 -Author: Jonathan Barnoud -Date: Sat Mar 19 23:03:41 2016 +0100 - - Merge pull request #779 from jdetle/develop - - updated change_release to fix regex - - Fixes #776 - -commit 861caefa3a62d5de46d4b8fc14c31146c7b29c08 -Author: jdetle -Date: Fri Mar 18 13:14:08 2016 -0700 - - Updated change_release.sh to improve regex - (original change of "dev|rc*[0-9]" to "dev*[0-9]|rc*[0-9]") - - Updated CHANGELOG to add my githup id (jdetle) - - Updated AUTHORS to add my own name (John Detlefs) - - Added fix to CHANGELOG ("change_release finds number and dev") - - Fixed change_release.sh to allow for dev and rc with no numerics - ("0.15.0-dev" should be a legal version name") - - Fixed change_release.sh to allow for spaces in __version__ and version: - (regex changed to "__version__= to "__version__.=") - - Fixed changed_release.sh to allow for any amount of whitespace - ("__version__.=" to "__version__ *=") - [skip ci] - -commit e3a345d07bd7afbfa95694c5773478e6f165fe8c -Merge: e39ace4ad abf7aa7a1 -Author: kain88-de -Date: Fri Mar 18 16:56:23 2016 +0100 - - Merge pull request #751 from kain88-de/conda - - conda build scripts (fixes #608) - -commit c7bab6ffa54e08afeeb016456b47fc8dab0c61c2 -Author: khuston -Date: Fri Mar 18 11:13:25 2016 -0400 - - Made recommended style fixes - - I also removed the part of the docstring describing the - not-yet-implemented feature because it would probably cause more - false hope than good. - -commit 58a5cc6f5f2fef61ac39e955f811d5e18d2ce747 -Author: khuston -Date: Thu Mar 17 16:51:47 2016 -0400 - - fix dataparser atype truncation, clean writer test - -commit abf7aa7a168fbad11c6f769ba8d39b07c06eeb02 -Author: Max Linke -Date: Thu Mar 17 19:23:03 2016 +0100 - - update release script. - - Also change the versioning in the conda install files. - -commit 778b5a5b266b57efec754ab67831e2487244d83e -Author: Max Linke -Date: Tue Mar 8 08:35:17 2016 +0100 - - Add changelog - - [skip ci] - -commit 487f855e19ec36c9bced56acb5a824b9319fff99 -Author: Wouter Boomsma -Date: Thu Mar 17 09:14:41 2016 +0100 - - Increased test coverage of Ensemble.py and array.py - -commit 43e8d9f11ef80e42090ee1df5d165456d27b2771 -Author: khuston -Date: Wed Mar 16 18:49:12 2016 -0400 - - include only bonds etc. whose atoms are in atomgrp - - I added an associated test and fixed part of a test that was passing in - an invalid way. - -commit 3a15fb52b3e70da26724d75e471f48c21498f53a -Author: khuston -Date: Wed Mar 16 17:42:31 2016 -0400 - - DATAWriter, velocity unit conversion, unit test - - Writes selection at current trajectory frame to file, including sections - Atoms, Masses, Velocities, Bonds, Angles, Dihedrals, and Impropers (if - these are defined). Atoms section is written in the "full" sub-style if - charges are available or "molecular" sub-style if they are not. - Molecule id in atoms section is set to to 0. - - No other sections are written to the DATA file. - As of this writing, other sections are not parsed into the topology - by the `DATAReader`. - - If the selection includes a partial fragment, then the outputted DATA - file will be invalid, because it will describe bonds between atoms - which do not exist in the Atoms section. - - By default the writer assumes "conventional" or "real" LAMMPS units - where length is measured in Angstroms and velocity is measured in - Angstroms per femtosecond. If other units are desired, they must be - specified. - - Raises ValueError if atom types are not convertable to integers or if - atoms of the same type don't all have the same mass. - - An AttributeError will be raised if the atom group doesn't have masses. - - I added tests to make sure topology attributes of the written file - (after being read again) match the topology attributes read from - the original file. Checks types, bonds, positions, velocities, etc. - - There was a problem with test data mini.data because it had atom type - 3 which had undefined mass, so I changed the atom type to 1. - - The DATAParser before was not converting velocity units, so I added - default units Angstroms/fs which are the "real" units in LAMMPS. - -commit 37addac122407ace102cbbcfc903144548689f3c -Merge: 12cb064cc 5b564584b -Author: Richard Gowers -Date: Wed Mar 16 16:58:21 2016 +0000 - - Merge pull request #772 from khuston/DATAWriter - - Fix DATA type parsing and add explicit bond types - -commit e39ace4adc3d60499cfa95552d4ed4cdd101bed2 -Merge: 247424b8e ac15aed54 -Author: Richard Gowers -Date: Wed Mar 16 12:01:08 2016 +0000 - - Merge pull request #771 from Endle/develop - - Make Travis run tests on OSX. - -commit 9927b6a8717b7cf135e78a3ad770406e095504ae -Author: Max Linke -Date: Tue Mar 8 08:32:25 2016 +0100 - - Add anaconda badge - - [skip ci] - -commit e068ce692872afd4bbe69e54ea4328135f7c12bf -Author: Max Linke -Date: Tue Mar 1 22:52:58 2016 +0100 - - conda build scripts - - Scripts to build tempdir dependency conda package and a combined - MDAnalysis and MDAnalysistests package. - - [skip ci] - -commit 5b564584bd19a6c542140c07cd2e0396f03b481e -Author: khuston -Date: Wed Mar 16 01:28:12 2016 -0400 - - Fix handling of empty TopologyGroups - - If parser told universe to create empty TopologyGroup, the resulting - group was an attribute of atoms but gave IndexError on trying to access - it. Seems to work as expected now... creating TopologyGroup with 0 - TopologyObjects - -commit 906c46c59359b14b021e972a443b5a5266db723f -Author: khuston -Date: Tue Mar 15 17:50:41 2016 -0400 - - Restore unique_rows to lib.util - -commit 9bb9c49cf2f93cb6cc06ca733317874e6e0ee16f -Author: khuston -Date: Tue Mar 15 16:57:13 2016 -0400 - - replace unique_row with np.unique and np records - - The function `unique_row` was causing problems because bond type could - be None, and the containing numpy array had dtype==object. I replaced - `unique_rows` with `np.unique` by first converting the bond indices and - bond types into a numpy record, and then breaking this record back into - the bond indices and bond types. - - I also simplified some of what I'd written in `topologyattrs.Bonds`. - -commit 044fc695f2bed56e174a9ec67d039331ccc1b856 -Author: khuston -Date: Tue Mar 15 14:18:15 2016 -0400 - - Fix DATA type parsing and add explicit bond types - - **NOTE:** `atoms.bonds` is broken for atom groups without explicit bond typing - in this commit. - - In order to write a LAMMPS.DATAWriter, I first need explicit typing of bonds, - angles, dihedrals, and impropers beyond the tupling of atoms types done now. - To hack bond types into the topology, I branched issue-363 and tried the - following: - - 1. Add optional `types` keyword to `topologyattrs.Bonds`. This is stored - in the class instance a `self._bondtypes`. A topology parser can pass `types` - to the Bonds topologyattr. - 2. When `topologyattrs.Bonds` is called upon to generate a TopologyGroup, - these values are passed on via a new keyword in `TopologyGroup.__init__()`. - They are stored in the TopologyGroup instance as `self._bondtypes`. - 3. I modified `TopologyGroup.__getitem__` to yield a Bond with attribute - `_bondtype`. If `_bondtype is not None` then it overrides the default behavior - of `bond.type`. - 4. I modified `TopologyGroup()` calls wherever I could find them to pass on - `_bondtype` in the instantiation. - - I found that the DATAParser in branch #363 is slightly broken, because - the atom types are saved as integers which breaks `select_atoms` (I think it - expects strings, and typing the types as strings on parsing fixes this issue). - It seems there is currently no test for atom selection from LAMMPS DATA files, - so this might have gone undetected. - - An error is raised for `ag.bonds` for an atom group that doesn't have bonds, - but this seems to also be the case for branch issue-363 right now, so I didn't - try to fix this. - - Two places are especially ugly. One is where I tried to hack `_bondtypes` - into the existing code to remove duplicate bonds. This is also where - the code seems to be broken for non-explicit bond types. In this case, - I set `_bondtypes` to be a numpy array full of `None` with `dtype=object`. - It seems that `unique_rows` fails for this case, although it works fine - when `_bondtypes.dtype == "|S1"`. - -commit 138122c51563d9634d69d3d48f4b07d51d9eddb5 -Author: Matteo Tiberti -Date: Tue Mar 15 12:51:38 2016 +0000 - - removed useless is_int function - -commit ac15aed54a6a229b901859b22d6100a2b95d94c8 -Author: Zhenbo Li -Date: Tue Mar 15 16:25:42 2016 +0800 - - Make Travis run tests on OSX. - - Signed-off-by: Zhenbo Li - -commit 0973a93495d0dab27edfa03abefe45c425b2738c -Merge: 11f5a5f84 259e14cc1 -Author: Matteo Tiberti -Date: Mon Mar 14 16:09:11 2016 +0000 - - Merge branch 'develop' of https://github.com/encore-similarity/mdanalysis into develop - -commit 11f5a5f847cd804c0e32d8deedd968dbf298e05f -Merge: 0d2177228 247424b8e -Author: Matteo Tiberti -Date: Mon Mar 14 16:07:29 2016 +0000 - - Merge remote-tracking branch 'upstream/develop' into develop - -commit 247424b8ec67eb2dc4b69ab7a88b03d84fd2ac96 -Merge: f552580ca 1fb1a06a9 -Author: Jonathan Barnoud -Date: Sun Mar 13 09:32:59 2016 +0100 - - Merge pull request #769 from abhinavgupta94/issue-766-no-import-star - - Replace `import *` by explicit imports in tests - -commit 1fb1a06a9648f0589b221cb995929d3f5be3adf0 -Author: Abhinav Gupta -Date: Sat Mar 12 23:38:34 2016 -0500 - - added explict imports - -commit f552580cae27b7fcd3b1ec9245f521890cbb6194 -Author: Oliver Beckstein -Date: Sat Mar 12 10:53:21 2016 -0800 - - metadata update: link download_url to GitHub releases - - - in setup.py, added download_url for https://github.com/MDAnalysis/mdanalysis/releases - (package and testsuite) - - should allow Depsy to properly attribute to all committers - (see https://github.com/Impactstory/depsy/issues/47 ) - - closes issue #749 - - also added @richardjgowers as maintainer to the testsuite setup.py and harmonized - its metadata with package/setup.py - -commit 259e14cc112d068f14f1483dda92c201556daf6e -Merge: b81cee414 0d2177228 -Author: Wouter Boomsma -Date: Fri Mar 11 12:01:46 2016 +0100 - - Merge branch 'develop' of https://github.com/encore-similarity/mdanalysis into develop - -commit b81cee41440171b260263147fbf7e86a2a37ca92 -Author: Wouter Boomsma -Date: Fri Mar 11 11:54:30 2016 +0100 - - Minor bugfix in ArrayReader - -commit 33b563bc935f0f9fd47a115768ef873c7a250928 -Merge: 05a8aa600 22d17a9dc -Author: Jonathan Barnoud -Date: Fri Mar 11 09:59:55 2016 +0100 - - Merge pull request #761 from abhinavgupta94/develop - - Ensure HEADER and TITLE occur just once in a PDB file - - Fixes #741 - -commit 22d17a9dc49410c76c624dad1b2748b1c0690f1f -Author: Abhinav Gupta -Date: Wed Mar 9 12:14:18 2016 -0500 - - ensure HEADER and TITLE occur just once in a PDB file - -commit 0d217722873d3538e4a31fd9a9e12bb72c0ccebb -Author: Matteo Tiberti -Date: Thu Mar 10 18:53:52 2016 +0000 - - edited documentation - -commit 6d26f6dccc940d7ac301378c00e55078e62d1bee -Author: Wouter Boomsma -Date: Wed Mar 9 14:43:03 2016 +0100 - - Added unit tests for ArrayReader - Fixed minor issues in ArrayReader - Updated documentation strings in all Encore files. - -commit 469766f9ee9220f45d154393c0e8c28d88782464 -Merge: 29b536d61 7281e66cf -Author: Wouter Boomsma -Date: Wed Mar 9 00:05:36 2016 +0100 - - Merge branch 'develop' of https://github.com/encore-similarity/mdanalysis into develop - -commit 29b536d61506630fd8b9b0672d7243cf9570e5bf -Author: Wouter Boomsma -Date: Wed Mar 9 00:05:14 2016 +0100 - - Removed selections attributes from Ensemble object. Selections are now passed to the individual methods instead. - Removed coordinates attributes from Ensemble object. This is now delegated to the new ArrayReader trajectory reader - Added ArrayReader trajectory reader for reading from a numpy array through the standard trajectory interface - -commit 05a8aa600915290596a70f983350bcc45517fc41 -Merge: 622ebf3a8 0e4c042be -Author: David Dotson -Date: Tue Mar 8 14:26:40 2016 -0700 - - Merge pull request #714 from kain88-de/rmsd - - Rmsd (fixes #562) - - This changes the current API and default behavior. Superposition for `MDAnalysis.analysis.rms.rmsd` is now controlled by a new keyword. Centering is also controllable by a keyword. - -commit 0e4c042beec9297876ec03399b031641e15666e7 -Author: Max Linke -Date: Tue Mar 8 19:49:05 2016 +0100 - - Move changelog into to new version - -commit e1b4182c23c3424748f78cd70e5fb36cfe318404 -Author: Max Linke -Date: Tue Mar 8 19:02:45 2016 +0100 - - Fix citations in docs - -commit 104ae483a60c615d6141a1aad2e5360139dcde38 -Author: Max Linke -Date: Tue Feb 16 18:20:57 2016 +0100 - - correct align function - - The old function actually didn't calculate the previous rmsd because - there was always an implicit alignment. This now calculated the RMSD - after centering (geometry or mass) and compares that to the correctly - rotated rmsd. - -commit 4f949b9416d8536fc85c4df303e26e7ce44a0bfc -Author: Max Linke -Date: Tue Feb 16 18:20:42 2016 +0100 - - update align tutorial to new rmsd behavior - -commit 16fe0f7b8ffe4bc70ee02a4311bc0885534e8e28 -Author: Max Linke -Date: Thu Feb 11 23:57:16 2016 +0100 - - fix align tests - - I had to change the expected value aswell. This is because the - superposition also does a centering now. - -commit c853f1660b7d46b4ed6cd57aafefb77e200a9f4c -Author: Max Linke -Date: Thu Feb 11 21:41:15 2016 +0100 - - Add changelog - -commit 8675b63fd9cc56a4d33eba0711da9d5949ccd4da -Author: Max Linke -Date: Thu Feb 11 21:38:16 2016 +0100 - - Add tests for rmsd function - -commit f6e372ae235fb391e8c686d03aade8a7db236446 -Author: Max Linke -Date: Thu Feb 11 21:22:38 2016 +0100 - - Don't superposition for RMSD on default - - This adds a new keyword 'superposition' to control if a - superposition should be performed before the RMSD is calculated. - - The default for *center* is changed as well. - - This way rmsd should just work for most users - -commit 0b90ebd997de3935430ba9d13d6f2bea2ce0da63 -Author: Max Linke -Date: Thu Feb 11 21:09:24 2016 +0100 - - Numpy-style doc-strings - -commit 502503a2ab899904fc51a3648b938aee53b6832e -Author: Max Linke -Date: Thu Feb 11 20:49:27 2016 +0100 - - PEP8 Changes - -commit 7281e66cf5b13331c84340120822236496efbc36 -Author: Matteo Tiberti -Date: Tue Mar 8 09:03:48 2016 +0000 - - added mantainer name in similarity.py - -commit 622ebf3a8fd9b99f937ce88643469ddbcc2e228b -Merge: 5b6471d93 267068e09 -Author: Richard Gowers -Date: Mon Mar 7 08:30:30 2016 +0000 - - Merge pull request #758 from kain88-de/shear-test - - Shear test (fixes #757) - -commit 267068e09f4cc93d3a89affb2942a40f42abafbd -Author: Max Linke -Date: Sun Mar 6 23:22:09 2016 +0100 - - Add CHANGELOG entry - -commit 1a6343d6783e92491eb0b9a86991f79ea32fa222 -Author: Max Linke -Date: Sun Mar 6 23:17:44 2016 +0100 - - Remove dependencies and conda pinning. - - We don't need the dependencies because of conda. The pinning is removed - because conda has changed it's libgfortran and only the most recent - scipy version links correctly against it. Because scipy links against - numpy we need the most recent version of it too. - -commit 094115a1f3035118425c538c7fbe4a220229d6dd -Author: Max Linke -Date: Sun Mar 6 23:13:53 2016 +0100 - - Update shear test numbers to pass with MKL - - As it turns out the method to calulcate shear forces back from a shear - matrix doesn't work for all input cases. Their are some edgecases. These - new numbers let the test pass under numpy 1.10.4 build with MKL and - LAPACK. - -commit da35a5ce2014d07ce262130a524f2fa3fa25588b -Author: Richard Gowers -Date: Fri Mar 4 18:20:45 2016 +0000 - - Fixes for Issue #755 - - Atom properties now return a copy - -commit 953c06dbf819e9c084d13bbb2094fea73acc154f -Author: Richard Gowers -Date: Fri Mar 4 18:17:46 2016 +0000 - - Added tests for Issue #755 - -commit 08633e91d87c2a529fc49fe60f5312d8b764da69 -Author: Matteo Tiberti -Date: Fri Mar 4 09:42:34 2016 +0000 - - fixed error message in tests - -commit b5ace0fbe0971b047cb08cdcf47701b1eaca8e46 -Author: Matteo Tiberti -Date: Fri Mar 4 09:41:18 2016 +0000 - - added tests for convergence and error estimation and few changes in output formats - -commit a4f3f50b5588e23dc7ce44821b9d6d697df733fe -Merge: 897060c78 f9579b124 -Author: Matteo Tiberti -Date: Wed Mar 2 14:40:08 2016 +0000 - - Merge branch 'develop' of https://github.com/encore-similarity/mdanalysis into develop - -commit 897060c784207aadc5c88b1d347023d5d2dae8f6 -Author: Matteo Tiberti -Date: Wed Mar 2 14:38:27 2016 +0000 - - fixed import bug for utils module - -commit 5b6471d93a36581d06ec73a1a0bddc8a460d4213 -Author: Richard Gowers -Date: Tue Mar 1 16:03:15 2016 +0000 - - Moved .github to correct location (repo root) - -commit 00163359d1bfc57d93f550ddc347133ea5d82b7b -Merge: c824225b4 41038e1da -Author: kain88-de -Date: Tue Mar 1 17:01:36 2016 +0100 - - Merge pull request #750 from MDAnalysis/issue-508-contributingrst - - First draft of CONTRIBUTING file. Closes Issue #508 - -commit 41038e1daf6fbc88ff23c8db49bd4533453d2707 -Author: Richard Gowers -Date: Tue Mar 1 15:57:14 2016 +0000 - - Fixed code getting mashed in md - -commit e57933994cf7b54387d55977054fc4042169d7f9 -Author: Richard Gowers -Date: Tue Mar 1 15:55:17 2016 +0000 - - First draft of CONTRIBUTING file - - Closes Issue #508 - -commit c824225b4a1ad95dc27af2c53b49a5a421939722 -Merge: a4ee46b31 5c4324fdf -Author: Oliver Beckstein -Date: Mon Feb 29 20:52:41 2016 -0800 - - Merge pull request #748 from MDAnalysis/issue-746-missing-docs - - added missing function/class docs - -commit 5c4324fdf873e61901d143b02e9c0de19a37814e -Author: Oliver Beckstein -Date: Mon Feb 29 17:27:08 2016 -0800 - - added missing function/class docs - - - closes #746 - - added :members: directive - -commit a4ee46b31139978cca3bee5a7b25a84853d73b01 -Merge: d2288c182 7d98d485c -Author: Max Linke -Date: Mon Feb 29 10:31:53 2016 +0100 - - Merge branch 'issue-702-contacts' into develop - -commit 7d98d485c6d2f2f3cb68ff62c66f4ef19e1743c4 -Author: Jan Domanski -Date: Fri Feb 26 10:44:26 2016 -0500 - - Remove any self calls from load method, to make it nice and static - -commit b0007f421862cf5fd8031c33c3c974ba2df3099b -Author: Jan Domanski -Date: Thu Feb 25 12:20:23 2016 -0500 - - Upated CHANGELOG, brought back the old ContactAnalysis class - -commit d261919c631c132500d1eafdf0063eca28cf4883 -Author: Oliver Beckstein -Date: Wed Feb 24 15:24:09 2016 -0700 - - added back ContactAnalysis - - - ContactAnalysis was removed by @jandom but needs to - stay because the functionality does not exist in the - new Contact class - (But it needs to be rewritten with AnalysisBase.) - - updated doc strings (numpy style) - -commit 0e3811e7c75f1f7600f0649519fedccb98ea8cd1 -Author: Oliver Beckstein -Date: Wed Feb 24 13:35:33 2016 -0700 - - doc string upgrades in analysis.contacts - -commit 0b318502a33fc222a7621937cfc96541788ce84d -Author: Oliver Beckstein -Date: Wed Feb 24 13:06:35 2016 -0700 - - improvements for distances - - - numpy style docs - - guard scipy.sparse import and warn - - see PR #708 for discussion - -commit b8c0245fa82727db44e537dbb31521c881ee2889 -Author: Jan Domanski -Date: Wed Feb 24 15:14:11 2016 -0500 - - Test and docstring cleanup - - numpy style docs, - - renamed a few methods, - - @staticmethod annotation in tests - -commit 21243559bef304b899710a6e5eaa7ec90703535a -Author: Jan Domanski -Date: Tue Feb 23 17:06:34 2016 -0500 - - Corrected docs, moved things around - general feature cleanup - -commit 17dec2d1e8475dc72c7e591ab87a2bf586670367 -Author: Jan Domanski -Date: Sun Feb 14 19:19:42 2016 -0500 - - Deprecate the old ContactAnalysis1 class - - checked if tests pass - -commit 5588e1570e209fbf8d08ee9672cb41e9f7e627b2 -Author: Jan Domanski -Date: Sun Feb 14 19:03:30 2016 -0500 - - Moved all the remaining methods from ContactAnalysis1 to Contacts - -commit 094b7f2ab5f51b14d90174196b48b2060a9ef0fd -Author: Jan Domanski -Date: Sun Feb 14 17:56:52 2016 -0500 - - Re-link to gro.bz2 files in setup.py - -commit cad0d59a0575f478808f666bf62f37443c62fc33 -Author: Jan Domanski -Date: Sat Feb 13 16:13:58 2016 -0500 - - Trying to make the new Contacts class as close to ContactAnalysis1 class... - -commit 485c0c40a92d14b12950b5640cad31140196ed17 -Author: Jan Domanski -Date: Fri Feb 12 17:49:31 2016 -0500 - - Clean-up docs, bzip conf files - -commit 15cc3a468b01ace700f826783d4bd5c6938c05e2 -Author: Jan Domanski -Date: Fri Feb 12 11:15:06 2016 -0500 - - Single class that supports both cutoff and best-hummer contacts - - scipy.sparse will cause an ImportException - - updated tests (appear to be passing...) - -commit b2262d4476df16679206b885286780d279a4a7ef -Author: Jan Domanski -Date: Thu Feb 11 17:12:11 2016 -0500 - - Fixed imports (iii) - -commit c4df4b5888ebcdb021ca72bbb215cf6edf59a342 -Author: Jan Domanski -Date: Thu Feb 11 16:55:14 2016 -0500 - - Fixed module imports (ii) - -commit 605118c70765bc85a3a576945a5789579c2c921a -Author: Jan Domanski -Date: Thu Feb 11 16:27:18 2016 -0500 - - Fixed module import - -commit 91538ddc4e890c50d9ff0529f88349994d64efe5 -Author: Jan Domanski -Date: Thu Feb 11 15:24:56 2016 -0500 - - Correct typo in tests - -commit 98b9c11bfaf6c55aaa6456e428439b1ea8d5f54d -Author: Jan Domanski -Date: Thu Feb 11 14:12:11 2016 -0500 - - Contact analysis: move the example to cookbook - - remove accidentally included CoordinateNeighborSearch, - - single test class in test_contacts.py, remove test_contacts_best.py, - -commit a07c6eebcddd1f0db6f41e807bbe5ef296281c36 -Author: Jan Domanski -Date: Wed Feb 10 15:29:53 2016 -0500 - - Add test files to package, rename test class for contacts - -commit 4d5c798bf8f75c0a71333e13704993e487c06396 -Author: Jan Domanski -Date: Wed Feb 10 14:17:18 2016 -0500 - - Refactor universe identity check between groups, optional scipy.sparse import - -commit 25655f11ef6851a92b6d0c24fd7a9e0a4359fb2f -Author: Jan Domanski -Date: Wed Feb 10 12:49:28 2016 -0500 - - Arguments refactored, numpy-style docs - -commit 88dc958142fc1ff3bd4f057bc513c6a883fd46d1 -Author: Jan Domanski -Date: Wed Feb 10 12:13:20 2016 -0500 - - Revert to changes to contacts.py - - removed a dependancy on pandas, update tests - -commit eaf6da3369a24d751e39983b7679ff06f44d6a28 -Author: Jan Domanski -Date: Tue Feb 9 16:59:28 2016 -0500 - - Improved, Best-like contact analysis (Issue #702) - - A worked example with GpA dimer in a bilayer - - Added tests to the BestHummerContacts calculation - - Tests for fraction of native contacts (Q) - -commit d2288c182187338e796944bdd563d867f608ff3f -Author: Richard Gowers -Date: Sun Feb 28 13:56:53 2016 +0000 - - Bumped version to 0.14.1-dev0 - -commit 13a97e481a49cedf6d5e45041f96db35cf563880 (tag: release-0.14.0) -Author: Richard Gowers -Date: Sun Feb 28 13:29:01 2016 +0000 - - Finalised CHANGELOG - -commit b5e5906165958b597becb4388f52133833fa9456 -Author: Richard Gowers -Date: Sun Feb 28 12:41:10 2016 +0000 - - Bumped version to 0.14.0 release - -commit ada0f2f708e69f5fd4602e0e2ba2fc0a8ee06582 -Author: Richard Gowers -Date: Sun Feb 28 12:40:53 2016 +0000 - - Added c files - -commit 7ef61fe623f8391e458f3c9943cb710953c225fa -Author: Richard Gowers -Date: Sun Feb 28 12:23:13 2016 +0000 - - Added mattihappy to CHANGELOG - -commit df5c2420284f3705ec3a6104a94491fdfbeda1f6 -Merge: 277afec87 382b3e25c -Author: Jonathan Barnoud -Date: Sat Feb 27 18:28:47 2016 +0100 - - Merge pull request #745 from kain88-de/xdr-test-coverage - - Only use python 2/3 compatible exception printing - - The old `e.message` seems to be from older python versions and has been - removed in python 3. For python 2.7 and later just printing the - Exception works fine. - - This brings coverage for the XDR class to 100% again. - -commit 382b3e25c01f666d3807fbb06a97191572551d9c -Author: Max Linke -Date: Sat Feb 27 18:01:18 2016 +0100 - - Only use python 2/3 compatible exception printing - - The old `e.message` seems to be from older python versions and has been - removed in python 3. For python 2.7 and later just printing the - Exception works fine. - -commit 277afec87897125668c4e5020c73a598cd1413fa -Merge: b877c3bec dbf45f178 -Author: Jonathan Barnoud -Date: Sat Feb 27 16:03:41 2016 +0100 - - Merge pull request #744 from kain88-de/xdr-dimensions - - Xdr dimensions (fixes #740) - - Box dimensions are updated every frame. Fix a regression. - -commit dbf45f178d56007b176b095ce19d0cb2585bbd9d -Author: Max Linke -Date: Sat Feb 27 11:57:45 2016 +0100 - - Modernize test_libmdaxdr - -commit a87dad1250af9d68402e756cfe5f9a239ce62774 -Author: Max Linke -Date: Sat Feb 27 11:51:42 2016 +0100 - - use non integer box sizes and angles - - This way we can also be sure to see some rounding errors we might miss - otherwise. - -commit 919bfe69e31d3e5b453725509ac6d8cc14ad8263 -Author: Max Linke -Date: Fri Feb 26 21:04:35 2016 +0100 - - Replace naked assert with assert_equal - -commit 9904a1d67a5f64df4d8df6a7b886ba2ca1f9184f -Author: Max Linke -Date: Fri Feb 26 20:16:15 2016 +0100 - - Add explicit dimensions tests to XDR reader/writer - - This adds functionallity to enable box dimensions tests - for file formats. During the test we see if we can read dimensions from - the provided files and if we can save them with changed dimensions. - The corresponding test files for xtc and trr have been changed. - -commit 8d108ac7518fdcd1aac045cda8a880b58e6470cd -Author: Max Linke -Date: Fri Feb 26 19:36:09 2016 +0100 - - XDR read box information - - We now read the changing box information from XTC/TRR files as well. - To write files like we read them I also changed libmdaxdr to allow - writing with changing box size. - -commit b877c3becea806f9dbcb10d92ef5e774b900fdcc -Merge: b6bd755f8 25883d489 -Author: David Dotson -Date: Fri Feb 26 12:38:23 2016 -0700 - - Merge pull request #742 from Saxenauts/syntax_err - - Syntax error in psa.py fixed - - Fixes #738 . - -commit 25883d48988e7c0a7cb7d5782074f85e8a7ee732 -Author: Saxenauts -Date: Fri Feb 26 23:31:44 2016 +0530 - - fixed syntax psa.py - -commit 72b3689c627db7e8f1ba1b6c8f34a39647ce116e -Author: Saxenauts -Date: Fri Feb 26 23:28:39 2016 +0530 - - Fixed syntax error psa.py - -commit de563b184ca03f5b2a3b5a2c0ff80c92ab23c92a -Author: Saxenauts -Date: Fri Feb 26 23:23:39 2016 +0530 - - Syntax error fixed in psa.py Issue #738 - -commit b6bd755f876ff85baa9321f7715b15fd5a928f27 -Merge: c81ece31f 61246305f -Author: Richard Gowers -Date: Tue Feb 23 20:23:37 2016 +0000 - - Merge pull request #737 from kain88-de/offset-checking - - Don't fail when loading old offset formats. (fixes #736) - -commit 61246305f61f34ea1cc9fb0f8353fd2fb07f84ba -Author: Max Linke -Date: Tue Feb 23 20:43:25 2016 +0100 - - Don't fail when loading old offset formats. - - In case we change the format again in the future it won't bother users. - -commit c81ece31f7cffc73c8b146bb4c8854789c0a02c1 -Merge: 693b4782a 8750c720e -Author: kain88-de -Date: Tue Feb 23 00:21:42 2016 +0100 - - Merge pull request #732 from MDAnalysis/issue-669-test-offsets-cleanup - - New cleanup plugin that deletes offset files after tests (closes #669) - -commit 8750c720eabb125b2a1cb373db01399aa7ea949e -Author: Manuel Nuno Melo -Date: Fri Feb 19 15:34:55 2016 +0100 - - New cleanup plugin that deletes offset files after tests (closes #669) - -commit f9579b124e13aa03601a29e6e938309f9e5dedbf -Author: Tone Bengtsen -Date: Mon Feb 22 13:15:22 2016 +0100 - - changed documentation - - changed returns back to numpy array - - added note about None in return array - -commit c001ada140462a98b2d58bbcc32f05f3d4c57427 -Author: Tone Bengtsen -Date: Mon Feb 22 13:08:52 2016 +0100 - - changed docs - - changed return values header back to numpy array - -commit 01704be106a6c64b586e6d1269fba6f63a7926c2 -Author: Wouter Boomsma -Date: Sat Feb 20 23:05:27 2016 +0100 - - Fixed Encore unit tests in response to API change. - -commit 693b4782acb046c5a5b7807d5ef00b1601085373 -Author: Richard Gowers -Date: Sat Feb 20 20:38:10 2016 +0000 - - Removed trailing semicolons from pyx - - Issue #615 - -commit 516ddd94136a344ba5fbe602530a99497cdd6083 -Author: Matteo Tiberti -Date: Sat Feb 20 20:35:18 2016 +0000 - - fixed load_matrix bug - -commit 12885b0de1377b03e7825acc893116dcf808e8dd -Author: Matteo Tiberti -Date: Fri Feb 19 19:18:26 2016 +0000 - - partially revised documentation - -commit 673dc8204dade5dde327dcad5fd74d058763c45a -Author: Matteo Tiberti -Date: Fri Feb 19 18:12:14 2016 +0000 - - modified output types and input types for parameters - -commit 1b8b6244c2a26e25e517a552ee58ab93d5808508 -Merge: 78992cffd e338d39ea -Author: Jonathan Barnoud -Date: Fri Feb 19 16:07:27 2016 +0100 - - Merge pull request #730 from MDAnalysis/issue-725-boolindex - - Boolean indexing fixes - -commit 1205f8c74f0464ea21915a54af39774eb6619ead -Author: Tone Bengtsen -Date: Fri Feb 19 15:48:26 2016 +0100 - - change documentation - - updated examples to work - - added description of the stocastic nature of dres - - added note of stocatic nature of dres - -commit 7a07bb7fd68fe1f31b8126443d183539a1a1ea9c -Author: Wouter Boomsma -Date: Thu Feb 18 22:55:46 2016 +0100 - - Added Encore unit-tests - -commit 1b554742c1b5d28f34087d163cefaf70c668d441 -Author: Matteo Tiberti -Date: Thu Feb 18 18:13:52 2016 +0000 - - fixed conf. dist. matrix bug in dres and refactored similarity_mode options - -commit e338d39eac9a194e510d98cf9c858cff43c90f39 -Author: Richard Gowers -Date: Wed Feb 17 20:36:51 2016 +0000 - - Boolean indexing fixes - - AtomGroup can now be sliced with a list of bools (as well as an array) - Closes Issue #729 - - Trajectory can be sliced using an array of list of bools - Closes Issue #725 - -commit f752ed5d2bdd2c7366f3b75249fec3083accc540 -Author: Matteo Tiberti -Date: Wed Feb 17 13:46:51 2016 +0000 - - added to Author information to docstrings; minor fixes - -commit 024ed871a4fec114a29802c281ddcf3516bd2b9b -Author: Tone Bengtsen -Date: Wed Feb 17 13:08:52 2016 +0100 - - fixed cluster.py problem - -commit 128a9e69e9ca494b1c02e920856286f1c83aa6de -Author: Tone Bengtsen -Date: Wed Feb 17 13:05:21 2016 +0100 - - fixed indentation - -commit 1d4a3379d75aed642670ba2b244e8c0b9ba9c6b3 -Author: Tone Bengtsen -Date: Wed Feb 17 13:01:18 2016 +0100 - - fixed indentation - -commit 12cb064cc8d90d76f0aa32943dd7bb5946fef96c -Author: Richard Gowers -Date: Wed Feb 17 09:17:30 2016 +0000 - - Updated topologyattr tests - -commit c035ca8112ff424d85b09974597a7cf90a773ff9 -Author: Richard Gowers -Date: Wed Feb 17 08:48:39 2016 +0000 - - Fixed transtable tests - -commit 074f139189fe4114552ae6f41a1ee6a98d8874f5 -Author: Tone Bengtsen -Date: Tue Feb 16 13:40:41 2016 +0100 - - updated documentation and codestyle - - - added header to similarity - - Updated header to Ensemble - - added examples for - - hes() - - ces() - - dres() - - Ensemble - - added docstrings for hes(),ces(),dres() - - updated docstrings to follow numpy style doc - - updated codestyle to follow PEP8 - -commit 78992cffd40682ffa644c486ccbc638232497ae4 -Author: Balasubra -Date: Fri Feb 12 17:55:27 2016 +0100 - - Fix used number of frames in density_from_Universe - - When used on a slice of trajectory, density_from_Universe average using - the total number of frames of the trajectory rather than the number of - frames actually used. - -commit b1e7d29c73de8a2766c4e122e968b1b13fd7cac3 -Author: Richard Gowers -Date: Mon Feb 15 10:03:36 2016 +0000 - - Final test coverage for get_writer_for - -commit 4d06f6540d1c77c99e7b460d9a6af29b6f033de6 -Merge: 42defaadc 10e20655a -Author: Richard Gowers -Date: Mon Feb 15 09:52:37 2016 +0000 - - Merge pull request #723 from jbarnoud/issue-712-get-writer-for - - Add some test coverage to coordinates.core - -commit 10e20655a7f05d547c26b272bda21dc16a08fb18 -Author: Jonathan Barnoud -Date: Mon Feb 15 09:07:42 2016 +0100 - - Add some test coverage to coordinates.core - -commit 42defaadceef5d848a2f18ac25b8b3fb721e61d3 -Merge: 36d2482da 69baaf8a1 -Author: Richard Gowers -Date: Sun Feb 14 20:05:27 2016 +0000 - - Merge pull request #721 from jbarnoud/issue-712-get-writer-for - - Fix get_writer_for with NamedStream #712 - -commit 69baaf8a10e0aa9ca80a91a33f06fe3c5345ae4a -Author: Jonathan Barnoud -Date: Sat Feb 13 18:33:24 2016 +0100 - - Fix get_writer_for with NamedStream - - Also change the default behavior of the function. Now, - MDAnalysis.coordinates.core.get_writer_for uses the format given via the - *format* argument in priority. If *format* is not provided, then the - function try to deduce the format from the file extension of the file - name given via *filename*. - -commit 36d2482da7124f0f8a772260136c52274199dfb9 -Merge: 173ff2652 cbac0d40b -Author: kain88-de -Date: Sun Feb 14 15:56:45 2016 +0100 - - Merge pull request #722 from jbarnoud/issue-647-pdb-atom-name - - Fix atom name formatting in PrimitivePDBWriter, Fixes #647 - -commit cbac0d40bede98c629ccdc2537fdb432688b584c -Author: Jonathan Barnoud -Date: Sun Feb 14 14:25:05 2016 +0100 - - Move the lists used to get PDB atom name at class level - - This avoids the lists to be recreated each frame - -commit d370b925e7b57ba5acf8e09ab9f87485fe3acfae -Author: Jonathan Barnoud -Date: Sun Feb 14 02:45:42 2016 +0100 - - Fix atom name formatting in PrimitivePDBWriter - - Fixes #647 - -commit 173ff26522717af14c798106a87d5c328416336f -Merge: 17159a20d 22fb2e8bb -Author: kain88-de -Date: Fri Feb 12 19:06:20 2016 +0100 - - Merge pull request #709 from MDAnalysis/issue-707-fix_knownfailure - - Make knownfailure plugin numpy-1.11-ready (closes #707) - -commit 17159a20d3ffcb8dd28c193bf17290b3da046bb8 -Merge: 419d7aa2b dd0c0f35e -Author: kain88-de -Date: Fri Feb 12 13:12:26 2016 +0100 - - Merge pull request #711 from MDAnalysis/issue-710-cyzonefix - - Fixes for Issue #710 - -commit 419d7aa2b56377413cadb5021ec4de91e5b5f0dd -Merge: 8e06aa505 9c2661843 -Author: kain88-de -Date: Thu Feb 11 22:11:13 2016 +0100 - - Merge pull request #713 from kain88-de/tempfile-clean-up - - Tempfile clean up (fixes #440) - -commit 9c2661843bbf3891e7c07334fce939c4c9df9cd8 -Author: Max Linke -Date: Thu Feb 11 18:35:23 2016 +0100 - - PEP8 changes test_atomgroup - -commit 6f7c7bcc5fa22c9aa0cde59dbbef2021c58e6d32 -Author: Max Linke -Date: Thu Feb 11 18:32:37 2016 +0100 - - PEP8 changes test_altloc - -commit f31eb6eb89c070d006e92121f053c59e0b33171e -Author: Max Linke -Date: Thu Feb 11 18:31:20 2016 +0100 - - replace tempfile test_log - -commit 144a87f3b729a11d59297c82f1e977cfa8f13a51 -Author: Max Linke -Date: Thu Feb 11 18:30:11 2016 +0100 - - replace tempfile test_modelling - -commit 860e877b98c9ba93755fbe0141dcbcfec946048c -Author: Max Linke -Date: Thu Feb 11 18:27:46 2016 +0100 - - remove unnecessary import test_streamio - -commit 79ac73e4d885297136cb42b559d458f57f6380c4 -Author: Max Linke -Date: Thu Feb 11 18:27:20 2016 +0100 - - minor PEP8 changes test_util - -commit 97edf40730ed84edf908b51142d5e908a6fb553d -Author: Max Linke -Date: Thu Feb 11 18:26:23 2016 +0100 - - replace tempfile test_altloc - -commit 035c175e555ed56f0e22bb40d4d74201e2bd3163 -Author: Max Linke -Date: Thu Feb 11 18:24:58 2016 +0100 - - replace tempfile test_mol2 - -commit 99596ec86825442aa652a1d48aa62797bea38fcd -Author: Max Linke -Date: Thu Feb 11 18:23:34 2016 +0100 - - test_pdbqt replace tempfile - -commit 01c108ea274f04883f021bbed1b1fc57617de085 -Author: Max Linke -Date: Thu Feb 11 18:21:59 2016 +0100 - - test_rms remove tempfile - -commit 3214e675d3e0b644f9fcfca262beb7fce1330aba -Author: Max Linke -Date: Thu Feb 11 18:18:02 2016 +0100 - - remove tempfile in test_psa - -commit 577cbf2e90ce35e2b53bb46108e149d5fba1240e -Author: Max Linke -Date: Thu Feb 11 18:16:18 2016 +0100 - - remove tempfile in test_atomgroup - -commit ca78c467e3ecef62a166cf85ce3dade631541f0c -Author: Max Linke -Date: Thu Feb 11 18:12:51 2016 +0100 - - clean up imports - -commit 8e06aa505ed7e864cce65f05c95144160d5eadf9 -Merge: 4c0070109 0f0aefac3 -Author: Richard Gowers -Date: Thu Feb 11 15:23:16 2016 +0000 - - Merge pull request #670 from mattihappy/feature-LinearDensity - - Analysis - Linear Density module - -commit dd0c0f35eff8b8f77b30b064a202d7158cae3cc6 -Author: Richard Gowers -Date: Thu Feb 11 15:21:18 2016 +0000 - - Fixes for Issue #710 - -commit 9c7b60cb9ff23850a38957b599f12c3317dd890e -Author: Matteo Tiberti -Date: Thu Feb 11 11:17:22 2016 +0000 - - tweaks to details output - -commit 4d6062f58db60a2a217c10fe2937bf9529c6df3d -Author: Matteo Tiberti -Date: Thu Feb 11 09:02:54 2016 +0000 - - fixed error and convergence estimation - -commit 22fb2e8bb1dd8f860068d6644107852b53e9ab78 -Author: mnmelo -Date: Thu Feb 11 01:10:46 2016 +0100 - - Make knownfailure plugin numpy-1.11-ready (closes #707) - -commit 4c0070109bc5fcf7af86570950a2bfa87e591129 -Merge: eee993292 d0740d8fb -Author: kain88-de -Date: Thu Feb 11 00:10:34 2016 +0100 - - Merge pull request #706 from kain88-de/rotation - - fix TypeError when no rotation matrix is found (fixes #705) - -commit d0740d8fb14ee98e33c6f270eedd54df3a5fd2f5 -Author: Max Linke -Date: Wed Feb 10 09:43:07 2016 +0100 - - Add changelog info - - [skip ci] - -commit 68b98708d7434ea9042d4e80e37b2a0f15e68d84 -Author: Max Linke -Date: Wed Feb 10 07:57:31 2016 +0100 - - Add test for various input types - -commit 73f0591e9d0eae12647365771cbbfa3a9be89b1b -Author: Max Linke -Date: Wed Feb 10 07:51:09 2016 +0100 - - Be more liberal with rotation_matrix args - - The old code didn't properly type cast the arguments to be used in the - qcprot module. This is done now. - -commit 4ddd3f81d0be8cc3664bc98dd0ca68a1881642e7 -Author: Max Linke -Date: Wed Feb 10 09:36:43 2016 +0100 - - Fix qcprot bug when no rotation can be found - - It can happen that no rotation matrix can be found for the input. In - that case the rmsd is `None`. But in CalcRMSDRotationalMatrix we - expected a typed rmsd for all cases. Includes also a clean up of - test_align. - -commit 743e84de08a4e5e53fe617da92f0ed22222ffbf4 -Author: Max Linke -Date: Wed Feb 10 09:34:57 2016 +0100 - - Numpy-style docs pqcprot.pyx - -commit d4e203813f4ebb678af8f4de57cdfb54fe4fb7d8 -Author: Max Linke -Date: Mon Feb 8 15:47:23 2016 +0100 - - Convert doc-string to numpy-style - -commit eee993292a1686b1c9328ec56c1c5601a375449b -Merge: 41c86ed12 9b577f140 -Author: Richard Gowers -Date: Tue Feb 9 10:35:50 2016 +0000 - - Merge pull request #692 from MDAnalysis/issue-667-untrack-cythonized - - Cythonized files now deleted after setup. (closes #667 / #629) - -commit 9b577f14036a758c0f8c1b343889ccd45bc926cf -Author: Manuel Nuno Melo -Date: Tue Feb 2 04:25:59 2016 +0100 - - Cythonized files now deleted after setup. (closes #667) - - Default behavior now depends on release or dev status. When in dev mode - default is to use Cython and delete cythonized files. When in release - mode default is to skip Cython but keep existing cythonized files. - - setup.py now reads the version string directly from version.py. - - Environment variable handling in setup.py enhanced to recognize strings - with boolean meaning (fixes #629). - - Travis' minimal build now also rebuilds cythonized files. - -commit 3a58f6f444ffddc57a246d65163756749120183f -Author: David Dotson -Date: Mon Feb 8 14:08:16 2016 -0700 - - Added total_charge function to Charges TopologyAttr. - - Somehow missed this one during the migration of old AtomGroup functions. - -commit 41c86ed12af3da2f2ed72e6073f14185b394fedb -Merge: 8bd70bf8d b9d2e1443 -Author: Oliver Beckstein -Date: Mon Feb 8 14:03:10 2016 -0700 - - Merge pull request #700 from kain88-de/pdb-charge-alignment - - PDB charges are not written anymore. - -commit 8bd70bf8df0d7dc28dca2ce176780f098abdc020 -Merge: 795e5737f 2a48d50ed -Author: kain88-de -Date: Mon Feb 8 21:09:42 2016 +0100 - - Merge pull request #699 from MDAnalysis/issue-679-xdr_licenseinfo - - Updated LICENSE and AUTHOR info regarding xdrfile (closes #679) - -commit b9d2e1443ba6bb42934066a94c726afdd5b8a787 -Author: Max Linke -Date: Mon Feb 8 20:29:56 2016 +0100 - - Add changelog and doc info - -commit 2a48d50edf93408e58e42962aaec9137453358d0 -Author: Manuel Nuno Melo -Date: Mon Feb 1 19:40:05 2016 +0100 - - Updated LICENSE and AUTHOR info regarding xdrfile (closes #679) - - Rebranded our xdrlib with cython bindings as libmdaxdr. - - Further standardized XDR error message reporting and exceptions - (now mostly IOError). - - Removed reference to the old SWIG numpy.i in the credits. - - Made logo LICENSE info consistent - -commit c46aee3755d3fe853cbfc0115a0f6a82fe88a473 -Author: Max Linke -Date: Mon Feb 8 15:32:25 2016 +0100 - - Remove charges from PDBWriter - - PDB can't handle charges properly and the guide states that these fields - are mostly left empty anyway. One should use the more apropriate PQR - files to save charge information. - -commit ffda652e083f677ede553c4249c377e56474b3ca -Author: Max Linke -Date: Mon Feb 8 14:32:42 2016 +0100 - - PDB charges are integers with 1 column width - - http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM - This says that charge only goes from column 79-80. - -commit 795e5737f2a1f5c1a16eec8a0e749191344dc616 -Merge: 73d6f59fc d6ca51ba9 -Author: mnmelo -Date: Sun Feb 7 13:07:32 2016 +0100 - - Merge pull request #656 from kain88-de/xdrlib-offset-checking - - Xdrlib offset checking, issue (631) - -commit 0f0aefac3a9987cfc20dc2454a28276f05c2ddaa -Author: mattihappy -Date: Sat Feb 6 22:22:37 2016 +0100 - - Trajectory name taken from variable filename and not dcdfilename, removed print statements from test - -commit fd44b72854108e76a053177a664e6ad0f7e52232 -Author: mattihappy -Date: Wed Feb 3 22:21:32 2016 +0100 - - Test added - -commit 90c574cd6b5169a1d5b72c3dbeeda80533a9115d -Author: mattihappy -Date: Wed Feb 3 22:21:01 2016 +0100 - - Lineardensity does not take universe as argument anymore and is compatible with AnalysisBase of MDAnalysis 0.13.0 - -commit 38d09a272d43465b1ea1b2e0cef695174dd6d86e -Author: mattihappy -Date: Wed Feb 3 00:49:03 2016 +0100 - - Modified changelog - -commit a3a9550f77a726e856ccb9a33a1f4bcbf46ba0e1 -Author: mattihappy -Date: Wed Feb 3 00:40:23 2016 +0100 - - Added myself to authors - -commit 5605394a5f70afd8665c8d2c6bad38979369be7c -Author: mattihappy -Date: Wed Feb 3 00:28:24 2016 +0100 - - Created stub rst for the analysis module and added link under Volumetric Analysis - -commit a6771157b071c50f2275c3be8650fba915d8f549 -Author: mattihappy -Date: Wed Feb 3 00:23:35 2016 +0100 - - Added standard header - -commit f38bc451a3c3c23575d14ba03aa99e1c364ac208 -Author: mattihappy -Date: Sun Jan 31 02:50:22 2016 +0100 - - Fixed improper use of list comprehension; Added docstrings - -commit eadb51af0d4b7bc60930b17143f4335e3e8ea144 -Author: mattihappy -Date: Wed Jan 27 19:26:58 2016 +0100 - - Fixed: np arrays instead of lists for charges and masses, correct import order, added save method, use of in-place sum of np arrays - -commit b6dfa8809d1a006a26d290c9870b62f22b74dd60 -Author: mattihappy -Date: Wed Jan 27 13:40:53 2016 +0100 - - Added lineardensity module - -commit d72b9dcac8dc9781a894234d61b43a049e3e6dcf -Author: David Dotson -Date: Sat Feb 6 13:44:00 2016 -0700 - - np.concatenate can't take a generator. Using list comprehension instead. - - Also, some other subtle bugfixes. - -commit 73d6f59fca6fbd1491d5d1701b1ca603a3d2df40 -Merge: 2da2f8486 5a959e686 -Author: Richard Gowers -Date: Sat Feb 6 18:46:12 2016 +0000 - - Merge pull request #697 from kain88-de/pdb-atomtype-rightalignment - - Right align atomtype (#648) - -commit 5a959e68618d1c7ddd9cf57597e360011b786adb -Author: Max Linke -Date: Sat Feb 6 18:24:07 2016 +0100 - - Right align atomtype - - Fixes #648 - -commit 2da2f848683a749cb84ae8c0000ce2b4b894752c -Merge: 21ca62b41 87fe7b078 -Author: Richard Gowers -Date: Sat Feb 6 16:45:00 2016 +0000 - - Merge pull request #696 from MDAnalysis/docs-hbondautocorrel - - Fixed hbond_autocorrel doc strings - -commit 87fe7b078a61f9938df5ffa313fc01cc612badb7 -Author: Richard Gowers -Date: Sat Feb 6 14:43:55 2016 +0000 - - Fixed hbond_autocorrel doc strings - -commit d6ca51ba97b2f88ae3f1b9af99f77ded09a7840e -Author: Max Linke -Date: Sat Feb 6 13:55:15 2016 +0100 - - Change warning message for xdr - -commit ed008c2f165975dd5a55410fd6e9bf889d4dce77 -Author: Max Linke -Date: Sat Feb 6 13:51:27 2016 +0100 - - Use n_atoms from xdr file in offsets check - -commit 456b00dc7fc566627ad5bc647e0a0faf45d5ebe2 -Author: David Dotson -Date: Fri Feb 5 22:17:01 2016 -0700 - - Implements the decision for level jumps as decided in #599. - -commit 21ca62b41a37c6d83f08361348a9d8a1dc1cce66 -Merge: 0c918f4dc 07a384059 -Author: Richard Gowers -Date: Fri Feb 5 10:05:15 2016 +0000 - - Merge pull request #694 from kain88-de/pdb-connect-fix - - Pdb connect fix, fixes #693 - -commit 07a3840595fa5c6d7f1d56a4db4bd682713f5e2e -Author: Max Linke -Date: Fri Feb 5 07:51:59 2016 +0100 - - Add changelog info - -commit b64cf72ba62ba7d8c6670383fb94f1a04c7075a9 -Author: Max Linke -Date: Fri Feb 5 07:48:18 2016 +0100 - - Performance improvements in PDBReader - - It turns out that numpy arrays can be given a list of strings directly. - The array object takes care of the type conversion for us. This results - in a performance increase of up to 10% (results may vary). - -commit da9e619e97eb272116ee825228e6624f93b68242 -Author: Max Linke -Date: Thu Feb 4 18:28:51 2016 +0100 - - Parse PDB CONECT line based on position - - The old split approach didn't work for PDBs with more then 10000 atoms, - because there isn't a whitespace anymore between atom ID's. The new - approach works with those as well. - -commit 09b70ad9ea84e894d01aba8cb8279fccb9e87b5f -Author: Max Linke -Date: Thu Feb 4 18:12:27 2016 +0100 - - Change doc-strings to numpy style - -commit 5be9d613c4c122b1baa4f75be98321ae46c8c603 -Author: Max Linke -Date: Thu Feb 4 18:09:21 2016 +0100 - - PEP8 changes - -commit 34f034eda8531f985b7ffa997deb3b6edc8b0f41 -Merge: ee8933ae3 080f97e68 -Author: Richard Gowers -Date: Wed Feb 3 10:12:58 2016 +0000 - - Merge pull request #651 from MDAnalysis/issue-363-groupmigrate - - WIP: Almost done migrating all Group functionality. - -commit 0c918f4dc7e4edb9a20bfbd1723b5c02096e2397 -Merge: ac8a98c49 b5f00ffd9 -Author: Richard Gowers -Date: Wed Feb 3 10:09:51 2016 +0000 - - Merge pull request #685 from MDAnalysis/issue-647-qc-authorship - - include quantifiedcode under Other Contributions in AUTHORS - -commit bf9307fd9cb2cfed7e2c073440761d416022667c -Author: Max Linke -Date: Wed Feb 3 07:59:48 2016 +0100 - - Retry seek with refreshed offsets on fail for xdr - - When reading after a seek doesn't work because of a RuntimeError it - could be because of wrong offsets. Now we recalculate them and try the - seek again. If this fails as well we raise an exception. - -commit 72e40d8cab0d90dd29f139c504a3cc415267adfe -Author: Max Linke -Date: Mon Feb 1 23:37:52 2016 +0100 - - Always catch warnings in xdr tests - -commit 604ddd8ce0f1bce4ecd35e85b6628162cb1eb263 -Author: Max Linke -Date: Mon Feb 1 23:30:49 2016 +0100 - - Check for n_atoms as well in xdr offsets - -commit b5cddbd82e36a45f2b8faa08d0b3da0640dac1b3 -Author: Max Linke -Date: Mon Feb 1 23:26:14 2016 +0100 - - Use function to read offsets into dict - -commit 080f97e68c20d804f4567a0eef43c61959517906 -Author: David Dotson -Date: Tue Feb 2 21:20:10 2016 -0600 - - Replacing deprecated functionality in tests. - - Mainly now using `positions` or `position` instead of `coordinates()` - and `pos`. Not done yet. - -commit 48968125e9a6ae94f2cb74c97e4771968b845fa0 -Author: David Dotson -Date: Tue Feb 2 18:10:35 2016 -0600 - - _get_named_* __getattr__ now work for groups. - - AtomGroup and Residue can get AtomGroups of atoms with a specific atom - name with, e.g. ag.CA or r.CA, respectively. ResidueGroups and Segments - can likewise get ResiduGroups of residues with a specific resname. - Likewise SegmentGroups can get SegmentGroups of segments with specific - segids. - - We achieve this with transplants for the corresponding TopologyAttr, - namely Atomnames, Resnames, and Segids. - - This is about the same as the previous behavior. - - Also, finally moved AtomGroup.ts property to new AtomGroup. It's needed - for the current trajectory writing functionality. - -commit 04caf3a8c583ebc40a39886814002f62b5e2c53f -Author: David Dotson -Date: Tue Feb 2 14:29:04 2016 -0600 - - Fixing imports of old AtomGroup module. - -commit ac8a98c4900b52fb3e8e175d7b03d7bdeb54abc3 -Merge: 34ce8fa44 767a9bedc -Author: Richard Gowers -Date: Mon Feb 1 20:13:25 2016 +0000 - - Merge pull request #690 from jbarnoud/issue-260-fix-trz - - TRZ reader and writer are compatible with python 3 - -commit 767a9bedc4f51ace47eb3eee6548c583a3be7f85 -Author: Jonathan Barnoud -Date: Mon Feb 1 20:14:47 2016 +0100 - - Simplify unused redundant generator - - Following @richardjgowers comment on #690 - -commit fd918d1c438fb3260823886961c269a7fb989989 -Author: Jonathan Barnoud -Date: Mon Feb 1 19:24:02 2016 +0100 - - Update changelog after changes in TRZ title handling - -commit d16f30c706c6d11a2192c2da0cf11d2d0a8d7e99 -Author: Jonathan Barnoud -Date: Mon Feb 1 19:11:42 2016 +0100 - - Remove trailing spaces in TRZ titles - - TRZ titles shorter than 80 characters are read with trailing spaces. - These spaces are striped as they are not expected by the users. - -commit e6b6a26bbeffbde20a30575745ed9869afa7205f -Author: Jonathan Barnoud -Date: Mon Feb 1 19:03:32 2016 +0100 - - TRZ writer raises an exception for too long titles - - The length of the title in a TRZ file is limited to 80 characters. - -commit 4a5e48e83264b50e9138930fdc86192901a19948 -Author: Jonathan Barnoud -Date: Mon Feb 1 18:48:58 2016 +0100 - - Make TRZ reader and writer python 3 compatible - -commit cfaff2466607a8d6074532e00bf62fd8587ae546 -Author: Jonathan Barnoud -Date: Mon Feb 1 18:36:36 2016 +0100 - - Test the title written and read for TRZ files - -commit a5b905737c6f44186a992d99dd99eadbca2d4aa9 -Author: Jonathan Barnoud -Date: Mon Feb 1 16:54:49 2016 +0100 - - Make TRZ reader importable on python 3 - - Work around the merge of int and long int in python 3. Note that there - is no test for that work around as it would require a heavy TRZ file. - -commit 34ce8fa44a1250853eac4cec0d36840aec429dee -Merge: 6b7839bdb 2e26655e1 -Author: Jonathan Barnoud -Date: Mon Feb 1 15:38:47 2016 +0100 - - Merge pull request #684 from MDAnalysis/fix-missing_datafiles_all - - Fix missing datafiles in __all__ - - Also adds a test to make sure all the constant defined in `datafiles.py` are in `datafiles.__all__`. - -commit 6b7839bdb74a3e9047391c032849c96695536028 -Merge: 68b587a54 cab91d560 -Author: kain88-de -Date: Mon Feb 1 15:13:36 2016 +0100 - - Merge pull request #687 from MDAnalysis/issue-676-netcdfDT - - Issue 676 netcdf dt - - fixes #676 - -commit 68b587a54e09b0eb8d2f6823c130a8ed9b2ee1e3 -Merge: 4e4f0fac9 2cdcb2ad6 -Author: Richard Gowers -Date: Mon Feb 1 11:21:42 2016 +0000 - - Merge pull request #683 from jbarnoud/issue-260-more-fix - - Issue #260 More python 3 compatibility fix - -commit cab91d560dea7d544282a25d2dd757616b77bbe5 -Author: Richard Gowers -Date: Mon Feb 1 10:55:52 2016 +0000 - - Fixed NetCDF Reader not reading DT properly - - Removed useless type check in _read_frame (use base.Reader checks) - -commit 7238df900660d954d2cd7e2aa81e98339f57d4a0 -Author: Richard Gowers -Date: Mon Feb 1 10:51:08 2016 +0000 - - Moved Timestep handling of Reader reference into Timestep - -commit b5f00ffd9ac55c926fc47cb978315366305ac956 -Author: Oliver Beckstein -Date: Sun Jan 31 12:29:25 2016 -0700 - - include quantifiedcode under Other Contributions in AUTHORS - - Closes issue #674 - -commit 2e26655e10feccd081c83ac6666d0f649a93a9dd -Author: Oliver Beckstein -Date: Sun Jan 31 11:45:44 2016 -0700 - - simple tests for MDAnalysis.tests.datafiles - - (Note that MDAnalysis.tests.datafiles really belongs to MDAnalysisTests.datafiles - so the tests need to be installed.) - -commit e64989b5a9ee1979d6bbaad1622fb9aca915c77e -Author: Oliver Beckstein -Date: Sun Jan 31 11:18:26 2016 -0700 - - added missing datafiles variable names to datafiles.__all__ - - - only PRM7 and NCDFtruncoct were missing - - removed `resource_filename` at end of datafiles.py to have a clean - namespace: everything that looks like a variable is then a filename - - useful to have them in __all__ so that `from MDAnalysis.tests.datafiles` works - - use something like - - import MDAnalysisTests.datafiles - [name for name in dir(MDAnalysisTests.datafiles) if not name.startswith('_') and name not in MDAnalysisTests.datafiles.__all__] - - to check manually. - - We do not have tests to test the tests although we could test - MDAnalysis.tests.datafiles because we are using it often in tutorials - and tell users to use it for reporting bugs and creating minimal failing - cases. - -commit 2cdcb2ad67bb4a352b65821053fa7c3a985aca90 -Author: Jonathan Barnoud -Date: Sun Jan 31 16:20:46 2016 +0100 - - Remove a forgotten debug line - -commit 317d8035131e30834309a71164a6608fa9ff3c1e -Author: Jonathan Barnoud -Date: Sun Jan 31 12:48:11 2016 +0100 - - Simplify a list(map()) into a list comprehension - - Following a suggestion by @kain88-de on #683 review. - -commit 081e5ca8e91b29f9eac4b5f5a532d3b4ce335844 -Author: Jonathan Barnoud -Date: Sun Jan 31 12:45:55 2016 +0100 - - Move the definition of bz2_open in the try/except - - Following suggestion by @richardjgowers in #683 review. - -commit 0ba5677b5eed02353006fed9f582af83e3930610 -Author: Jonathan Barnoud -Date: Sun Jan 31 12:37:06 2016 +0100 - - Remove debug lines - -commit 4e4f0fac998a6f5e846943ed07720be1df350afe -Merge: 481b56087 5ed8a9ab5 -Author: kain88-de -Date: Fri Jan 29 22:55:52 2016 +0100 - - Merge pull request #673 from MDAnalysis/fixes-ContactAnalysis1 - - Fixes for analysis.contacts.ContactAnalysis1 - -commit 5ed8a9ab5b46c4643e0a26f0f3ffc85cec237e6c -Author: Oliver Beckstein -Date: Wed Jan 27 11:42:55 2016 -0700 - - ContactAnalysis1: addressed remaining comments from PR #638 - - - removed code that wrongly ignored stop=0; added test that is - now passing (because bug #672 was fixed recently) - - added tests for general slicing - - cleaned up warnings imports - - added log message if 0 frames are analyzed - - use np.arange() instead of range() (so that I dont have - to mess with six or list(range()) - -commit 79d87d023cc8e81b0fc1e3d13580b1a2771a7997 -Author: Oliver Beckstein -Date: Wed Jan 27 10:37:07 2016 -0700 - - fixed contact docs - - As mentioned by @tylerjreddy in #638. - -commit 4c8883155e009f1db8580edfe5ad44c2fa228e0a -Author: Jonathan Barnoud -Date: Thu Jan 28 21:51:52 2016 +0100 - - Fix python 3 compatibility issues - - Mostly bytes/strings issues - -commit 481b5608738455450b743c1cf7ddb7f263f32b77 -Merge: 7b26bcf0a 9844015b3 -Author: Richard Gowers -Date: Fri Jan 29 11:14:53 2016 +0000 - - Merge pull request #680 from MDAnalysis/issue-632-itervalues - - removed usage of itervalues (py3) - -commit 9844015b3b2944ab3070e3d459164ee506d22158 -Author: Richard Gowers -Date: Fri Jan 29 10:55:19 2016 +0000 - - removed usage of itervalues (py3) - - Part of #632 - -commit 7b26bcf0a664be258aef5dfa1a29d75ae40567bd -Author: Richard Gowers -Date: Fri Jan 29 10:50:05 2016 +0000 - - Changed travis to only build master & dev branches - -commit dd384fd4f25ff0c5584e9350b367fe054574c2f2 -Merge: a5548e0a9 b92a5f1bd -Author: mnmelo -Date: Fri Jan 29 10:25:20 2016 +0100 - - Merge pull request #678 from MDAnalysis/issue-677-xdr_largefile - - XDR file seeks and tells working again on large files (closes #677) - -commit b92a5f1bd6f6c08d529ca2997f77e3692563c07f -Author: Manuel Nuno Melo -Date: Fri Jan 29 00:24:13 2016 +0100 - - Cleanup of cython cdefs and comparisons to XDR error codes. - -commit 02149895f37f729e4a7e9a0f74d0f3ad95d4ab7d -Author: Manuel Nuno Melo -Date: Thu Jan 28 18:54:45 2016 +0100 - - Fix XDR seek exception types and tests. - -commit 4b634b2cbfb751c9847c328dda30a09ff04e8427 -Author: Manuel Nuno Melo -Date: Thu Jan 28 17:16:19 2016 +0100 - - Added _bytes_seek and _bytes_tell XDR methods - - On error xtc_seek now returns the system errno value, which is printed as - is. This is more informative and fixes an IndexError looking up the error - message, that occurred when xtc_seek failed and returned exdrNR. - - Added testing for _bytes_seek and _bytes_tell, also beyond 4GB filesize - limits. - -commit a5548e0a90441038a8507b657a9bc049bae39c1e -Merge: 6e1f26d7d fd6ff1f17 -Author: Jonathan Barnoud -Date: Thu Jan 28 11:55:33 2016 +0100 - - Merge pull request #675 from MDAnalysis/issue-672-Readerindex0 - - Fixed Readers not working when stop in slice was 0 - - See #672 - -commit fd6ff1f1741551e138c58b38290c4258fa4e17c0 -Author: Jonathan Barnoud -Date: Thu Jan 28 11:52:04 2016 +0100 - - Use is not rather than not ... is in #675 - - Following a suggestion from Quantified Code and @kain88-de - -commit 89bd40b0586dc12129c6d15157e5b2e3e91b000d -Author: Richard Gowers -Date: Thu Jan 28 10:24:51 2016 +0000 - - Fixups for #672 following review - -commit 00885ad56aac340e3f5a9240838995a531086afd -Author: Manuel Nuno Melo -Date: Thu Jan 28 05:06:51 2016 +0100 - - XDR file seeks and tells working again on large files (closes #677) - -commit d3b0148144b7370319fe12faf7d444760ef7afd5 -Author: David Dotson -Date: Wed Jan 27 17:42:28 2016 -0700 - - Most of the tedious work done in moving things to new Groups. - - Some things to figure out/lingering thoughts: - 1. The `Group.ts` property makes a kind of copy of the Reader's timestep - object but with pre-sliced attributes. This feels like it could allow - some weird stalenss to creep in, and compared to the topology system - it's very clunky. Need to figure out what to do. - 2. Convenience getters like Residue. and Segment. - amount to __getattr__ modifications for those Components. However, - these are dependent on TopologyAttrs that are not always present, - so should be implemented as transplants. But just putting in a - `__getattr__` method into a `TopologyAttr` overrides its own special - `__getattr__`. Could just have it exist under a different name, - but would need special machinery to graft it on under a different - name. *sigh* - 3. Bonds. I leave this to @richardjgowers. - 4. Angle conveniences for proteins. Leave in? Or should these be - deprecated? - -commit c68b9aef1a7d2ef84d68c33119340134684e7c72 -Author: Richard Gowers -Date: Wed Jan 27 21:29:55 2016 +0000 - - Fixed Readers not working when stop in slice was 0 - - Closes Issue #672 - - Rewrote tests to use generator - -commit 970e896f61831362847e1f8495aee72ee61ecaa3 -Merge: b5108cf44 ee8933ae3 -Author: David Dotson -Date: Wed Jan 27 13:15:05 2016 -0700 - - Merge branch 'issue-363' into issue-363-groupmigrate - -commit 6e1f26d7d8c1228cacf65f4c2f636e3c1d89cb6f -Merge: 9b70936c1 0ef13b6e5 -Author: kain88-de -Date: Wed Jan 27 16:25:53 2016 +0100 - - Merge pull request #671 from MDAnalysis/issue-662-fixtravis - - Removed conditional memleak testing--always on now - -commit 0ef13b6e586fddc7c4f8cb11d06f847aa00d15fd -Author: mnmelo -Date: Wed Jan 27 15:43:21 2016 +0100 - - Removed conditional memleak testing--always on now - - This should have accompanied PR #668 - -commit 9b70936c1b18baf6159a439f91a162b0359a8ca5 -Merge: 448cd70ec 3206aa3a5 -Author: mnmelo -Date: Wed Jan 27 15:34:35 2016 +0100 - - Merge pull request #661 from kain88-de/xdrlib-reorder - - move libxdrfile seek functions into separate files - -commit 3206aa3a56ee26b8db65475b0d48cdac90f0bb97 -Author: Max Linke -Date: Tue Jan 26 08:05:35 2016 +0100 - - move libxdrfile seek functions into separate files - - This now puts the functions we have added to enable the calculation of - the byte offsets for xtc/trr trajectories explicitly under the GPL. - - Changes to the original libxdrfiles follow the license stated in that - files. This now includes the missing coordinate/velocity/forces - detection for trr, seek/tell for xdr files and moving function - declarations into header files. - -commit 448cd70eca3df8b49438fb76c02ee1a61f14151e -Merge: 3f2ca5b86 02364c96d -Author: Richard Gowers -Date: Wed Jan 27 11:35:52 2016 +0000 - - Merge pull request #668 from MDAnalysis/issue-662-memleaktest-python3 - - Made memleak testing python 3 compliant (closes #662) - -commit 3f2ca5b86180035ce95bf37643dd2341ae4611d2 -Merge: 926007fa8 a0bf251ee -Author: Jonathan Barnoud -Date: Wed Jan 27 07:29:41 2016 +0100 - - Merge pull request #665 from MDAnalysis/issue-594-QC-fixes - - Issue 594 qc fixes - - * Useless `pass` statement - * Use list.insert rather than list + list - -commit 02364c96d20099ecc679eb83da014fb2f95584d2 -Author: Manuel Nuno Melo -Date: Wed Jan 27 04:37:14 2016 +0100 - - Made memleak testing python 3 compliant (closes #662) - - (The memleak testing in python 3.4 may be unneeded anyway since - it now cleanly handles leaks.) - - Also fixes an empty line before the setup.py shebang in the testsuite. - -commit a0bf251ee3dd2c1407a8e6e50bc93629f4ff5a83 -Author: Oliver Beckstein -Date: Tue Jan 26 18:13:02 2016 -0700 - - fixed QuantfiedCode "Avoid unnecessary `pass` statements" - - Closes issue #594. - -commit 74521961b02ad5992f9d743e1b7e55c00915b36c -Author: Oliver Beckstein -Date: Tue Jan 26 18:08:31 2016 -0700 - - fixed QuantifiedCode 'Use `extend()` for list concatenation' - - In fact, this needed prepending (not extending) so the next - best thing is list.insert(0, x); it is not a performance issue - (so not worthwhile changing program flow or data structures) - but hopefully the QC issue goes away. - - See also http://stackoverflow.com/questions/8537916/whats-the-idiomatic-syntax-for-prepending-to-a-short-python-list - -commit 113a2837234221e870668324cf65fff055ffa4f5 -Author: Matteo Tiberti -Date: Tue Jan 26 16:43:22 2016 +0000 - - fixed regression - -commit d473b97a197a7591e42c832bc7a0e221a5d74e45 -Merge: 926007fa8 5d914cc0b -Author: Matteo Tiberti -Date: Tue Jan 26 15:55:11 2016 +0000 - - Merge branch 'master' into develop - -commit 5d914cc0b6186c6ab550a6690ee56438983b72f1 -Merge: f39d3e9dd 9a80de068 -Author: Matteo Tiberti -Date: Tue Jan 26 15:43:49 2016 +0000 - - Merge branch 'master' of https://github.com/encore-similarity/mdanalysis into HEAD - -commit f39d3e9dd64de9f0661221a0d016fc1f4e714d51 -Author: Matteo Tiberti -Date: Tue Jan 26 15:41:19 2016 +0000 - - added encore to release 0.12.1 - -commit 926007fa8e5b006273a58638980df3cccd210d30 -Merge: ebc2f591c 9df7d634e -Author: kain88-de -Date: Tue Jan 26 13:30:18 2016 +0100 - - Merge pull request #663 from MDAnalysis/issue-559-camelCaseCases - - Added description of when camelCase deprecations will happen - -commit ebc2f591cb9ea604e78a380b93d582174c6e0d0e -Merge: 5330a7c7a 187272c01 -Author: Richard Gowers -Date: Tue Jan 26 12:12:51 2016 +0000 - - Merge pull request #658 from jbarnoud/issue-260-python-3 - - Issue #260 Partial python 3 compatibility - -commit 9df7d634edbf6e1c1cde15fd0b561b6d61ba8d54 -Author: Richard Gowers -Date: Tue Jan 26 11:56:24 2016 +0000 - - Added description of when camelCase deprecations will happen - - Part of Issue #599 - -commit ee8933ae3f6c799d7dcc6651c842100f6b0e3686 -Merge: 07cbacf24 2848f6b43 -Author: Richard Gowers -Date: Tue Jan 26 10:18:49 2016 +0000 - - Merge pull request #650 from MDAnalysis/issue-363-unifromtop - - Can now initialize a universe with a Topology object - -commit 187272c01bcef25b329a3fa846f84f9e25dc6a05 -Author: Jonathan Barnoud -Date: Mon Jan 25 15:18:50 2016 +0100 - - Random fixes to improve python 3 compatibility - -commit b0f0364acb85428184df181cfa7f293794ec13ee -Author: Jonathan Barnoud -Date: Mon Jan 25 14:47:32 2016 +0100 - - Skip a test that relies on the LAMMPS parser - -commit b51ba1c26b75e9dc9c9f08f1d37fdce6c77abc10 -Author: Jonathan Barnoud -Date: Mon Jan 25 14:25:10 2016 +0100 - - Make test_topology.py pass on python 3 - - Note however than some tests are skipped because they rely on files in - unsupported formats. - -commit 3acef5be1f328b8df3e3d53e9afcccc5e636b4dc -Author: Jonathan Barnoud -Date: Mon Jan 25 13:54:34 2016 +0100 - - Add a warning when MDAnalysis is imported on py 3 - -commit c4281f3f5cfc8ed5a206de07cefc8bd8340e484c -Author: Jonathan Barnoud -Date: Mon Jan 25 13:52:53 2016 +0100 - - Simplify the __hash__ function of `TopologyObject` - - Following the comment of @richardjgowers on #658 - -commit 18beb92d40619ab86fdd71a288d40ba8e85d9e25 -Author: Jonathan Barnoud -Date: Mon Jan 25 11:46:44 2016 +0100 - - Make Travis run the tests on python 3 - - The python 3 tests are allowed to fail so they will not mark pull - requests as broken. - -commit 5330a7c7a7e0e780824f10a445567757c9355862 -Merge: f13d8c8b3 8bb8d3846 -Author: kain88-de -Date: Mon Jan 25 12:11:12 2016 +0100 - - Merge pull request #653 from MDAnalysis/issue-461-nucleicselections - - Added extra resnames to 'nucleic' selection - - closes #461 - -commit fde8735e40001845a7a92cb7ed3c4f58f69b4b96 -Author: Jonathan Barnoud -Date: Mon Jan 25 11:37:28 2016 +0100 - - On python 3 skip tests that use unsupported reader - - Tests that relies on DCD, LAMMPS, or TRZ test files ends with an error - because the reader is not supported on python 3 yet. This creates a lot - of noise in the nose report that hides the other failures. Hereby we - make these tests being skipped if the parser is not loaded. - - Note that this reduce dramatically the test coverage on python 3! - -commit c739bbeca1b4ea3f4a8f09c678207afeffc1773f -Author: Jonathan Barnoud -Date: Mon Jan 25 11:23:22 2016 +0100 - - Avoid import * in test_atomgroup.py - -commit d7d956289265a241b74eac68139f24ef3904d36f -Author: Jonathan Barnoud -Date: Mon Jan 25 11:03:42 2016 +0100 - - Avoid import * in test_topology - -commit 20d0ab0d39288098cad2a6ed4518a01caf8b5f01 -Author: Jonathan Barnoud -Date: Mon Jan 25 10:38:16 2016 +0100 - - Avoid import * in test_modelling.py - -commit 64ad46790492e6e7db6dc247d8e6663d9dfc675c -Author: Jonathan Barnoud -Date: Sun Jan 24 22:19:49 2016 +0100 - - Fix some call to map that expected a list output - - In Python 3, map returns a generator rather than a list. - - Make coordinates/test_dl_poly.py pass on python 3 - -commit b1640c3d0344b1c6165fcb0f0d23d77328ca0192 -Author: Jonathan Barnoud -Date: Sun Jan 24 20:37:01 2016 +0100 - - Make test_tprparser.py pass on Python 3 - - Read the TPR file as binary (mode='rb'). - -commit 269c629939af29da8faf0571340764e8a4c7b305 -Author: Jonathan Barnoud -Date: Sat Jan 23 15:59:11 2016 +0100 - - Use six for StringIO and cPickle everywhere - - An odd failure about StringIO remains in test_streamio.py on Python 3. - -commit 6fed1960d7e9a5d68184b2e64915b768d24e70dc -Author: Jonathan Barnoud -Date: Sat Jan 23 15:09:34 2016 +0100 - - Make test_persistance.py pass on Python 3 - - * use six for cPickle - * use the `next` builtin rather than the `next` method - -commit fa990ecc345eaa7e17b51dc116770692b866718c -Author: Jonathan Barnoud -Date: Sat Jan 23 14:57:32 2016 +0100 - - Male test_log.py pass on Python 3 - - * replace seek(0L) by seek(0) - * use six for StringIO - -commit 6a5c60fdaf8348739d110e90a4b8f5b1cbe9d69b -Author: Jonathan Barnoud -Date: Sat Jan 23 14:39:09 2016 +0100 - - Make test_altloc.py pass on Python 3 - - In python 3, numpy integers are not instances of int anymore. - -commit 9f191b63ec363e1b5d299e4cb726577e5e94ece7 -Author: Jonathan Barnoud -Date: Sat Jan 23 14:15:05 2016 +0100 - - Make tests from test_util.py pass on python 3 - - * The test for format guessing ignore DCD, DATA, and LAMMPS on python 3 - * fix some call to the `map` function that do not return a list on - python 3 - * other minor fixes - -commit 23b8cddebfd6fe23da7d7a7a554242ea466a9194 -Author: Jonathan Barnoud -Date: Sat Jan 23 13:28:44 2016 +0100 - - Replace print statement by print function - -commit 2dc601cf4d7667ae5d1668a07a37993737bca021 -Author: Jonathan Barnoud -Date: Sat Jan 23 10:31:28 2016 +0100 - - Make topology objects hashable on Python 3 - - On python 2, user defined object are hashable by default unless the - __hash__ method is overloaded to return None. On python 3, user objects - are not hashable if the __eq__ method is overloaded. - - This commit defines a __hash__ method that returns a hash based on the - sorted indices of the atoms involved in the topology object. This should - reproduce the behavior advertised in the topology object documentation. - Yet, it is different from the previous behavior. In the previous behavior, - two different objects with the same atoms were equal for __eq__ but - different regarding the hash. - -commit da8bfa548bf9a018141affacc082c4996624e557 -Author: Jonathan Barnoud -Date: Fri Jan 22 21:02:50 2016 +0100 - - Fix how unicode Angstrom symbol is encoded - - The unicode representation for the Angstrom symbol in the dictionary - used for unit conversion was wrong. While the escaping sequence was - correct, it was used as a series of bytes rather than like a unicode - string. Also, the same key was created twice as two escaping sequences - were used (utf-16 and utf-8) and they were synonymous. - - The tests were passing because they were testing against the same series - of bytes. - - This commit use a proper unicode string as key and remove the redundant - definition. It also adds a test with the actual unicode symbol rather - than an escaping sequence. - -commit 7b1fded506274a4d3fd29139346a4117a499a29b -Author: Jonathan Barnoud -Date: Fri Jan 22 19:48:26 2016 +0100 - - Replace iteritems with six.iteritems - - See #632 - -commit 36a38a518579f2f29251a76172f89a863b2da29b -Author: Jonathan Barnoud -Date: Fri Jan 22 19:47:53 2016 +0100 - - Fix implicit relative import in test plugins - -commit 0f4eec11260cd9e6f3540b95405cc5111a578354 -Author: Jonathan Barnoud -Date: Fri Jan 22 19:12:29 2016 +0100 - - Make some coordinate parser optional on Py3 - - The DCD parser is not compatible with python 3, this commit makes it - optional on that version of python. As the LAMPPS coordinate parser uses - the DCD parser, it is made optional as well. - - The TRZ parser requires some small modifications to be compatible. It is - made optional until is can be tested. - -commit 756ca76360a1e9e51dfbf4a0f99db244e1a124e7 -Author: Jonathan Barnoud -Date: Fri Jan 22 19:11:08 2016 +0100 - - Fix print for py3 in LAMMPS topology parser - - Why is there a print here anyway? - -commit bd6663da3061e1dcc7118b36821d27d394b37b89 -Author: Jonathan Barnoud -Date: Fri Jan 22 19:08:42 2016 +0100 - - Fix implicit relative import in the PDB parser - -commit b5108cf4430740f65d8f817b90e9ca2cd83028b6 -Author: David Dotson -Date: Fri Jan 22 20:44:14 2016 -0700 - - Moved most of the transformations. - - Only a few things left in AtomGroup. The remaining things in Atom, - Residue, and Segment are either bond stuff or the convenience names - (Segment.). - -commit f13d8c8b327ff9e0ff93555e90090109c35aee1a -Merge: 6e7c7da1f b57895401 -Author: Richard Gowers -Date: Fri Jan 22 22:35:35 2016 +0000 - - Merge pull request #657 from MDAnalysis/feature-NamedStream-hacks - - NamedStream cleanup - -commit b57895401bf0a811ca978941cf8b007c4b2e6b38 -Author: Oliver Beckstein -Date: Fri Jan 22 13:22:13 2016 -0700 - - minor QC fixes related to NamedStream tests and use tempdir - -commit 92464cde735d015406e9e8d54347218c30089967 -Author: Oliver Beckstein -Date: Fri Jan 22 13:11:40 2016 -0700 - - updated docs for NamedStream - -commit 532c19dc743ff088dbb4bf00e9cb0ece3bdb74f0 -Author: Oliver Beckstein -Date: Fri Jan 22 12:54:04 2016 -0700 - - additional NamedStream/os.path tests - - - test expanduser: works but behaves unexpectedly (but consistently) in that it - returns the expanded string if a tilde was in the name but does nothing (as - described in the docs) when it does not do a substitution, which means that - it now returns the original NamedString. Kind of messy but probably tolerable. - - test expandvars: does not work - - note: some of the tests related to expandvars and expandusers generated - Segmentation fault on my Mac OS X 10.6 with Python 2.7.11 and I disabled - the tests. - -commit e4c395509ae6268f0d004fffef20355a96d15852 -Author: Oliver Beckstein -Date: Fri Jan 22 11:12:34 2016 -0700 - - added __add__, __radd__, __mul__ to NamedStream + test cases for add and radd - - This enables full string addition, both string + NamedStream and NamedStream + string. - Many of the os.path functions will now work with NamedStream. - - (Thanks to @richardjgowers for __radd__!) - -commit 3ad14f9a8995c5d40226a932176dd3e52fc27621 -Author: Oliver Beckstein -Date: Fri Jan 22 10:57:49 2016 -0700 - - tests for interaction of NamedStream with os.path functions - - (see discussion at #652) - -commit 6e7c7da1f3ecc24f4edb785fe946ad430f6a3b8c -Merge: 848aedf4a 7c56ad25d -Author: Richard Gowers -Date: Fri Jan 22 16:28:45 2016 +0000 - - Merge pull request #655 from jbarnoud/issue-632-basestring - - Replace `basestring` by `six.string_types` - -commit 7c56ad25df0f20ec7170ffedff2bd73788cc5f53 -Author: Jonathan Barnoud -Date: Fri Jan 22 16:26:06 2016 +0100 - - Replace `basestring` by `six.string_types` - - `basestring` got removed from Python 3. This commit replaces all its - occurrences by `six.string_types`. - - See #643 and #260 - -commit 848aedf4adb368be061135f7a4b29e02a8382494 -Merge: 5dc4fde07 c707b59ad -Author: Richard Gowers -Date: Fri Jan 22 15:09:38 2016 +0000 - - Merge pull request #654 from jbarnoud/issue-649-docstring - - Issue 649 docstring - -commit c707b59ad4b5ac69db7b80d93248fc16647c9a85 -Author: Jonathan Barnoud -Date: Fri Jan 22 15:57:17 2016 +0100 - - Update the docstring of `util.iterable` as well - -commit 8bb8d38468e60d6521e56ad5df95bf67118657c2 -Author: Richard Gowers -Date: Fri Jan 22 14:54:30 2016 +0000 - - Updated nuclres tests to include non selected atoms - -commit 9cf7204879bd750def9db968d01a4cf0dec16752 -Author: Jonathan Barnoud -Date: Fri Jan 22 15:53:26 2016 +0100 - - Update the docstring of NamedStream - - Remove the reference to `NamedStream` inheriting from `basestring` as it - is not true anymore since #652 - -commit 5dc4fde0704486d5fa4c7fc03359087d8ee7a873 -Merge: bff74158c c45daa83f -Author: Jonathan Barnoud -Date: Fri Jan 22 15:46:29 2016 +0100 - - Merge pull request #652 from MDAnalysis/issue-649 - - Removed inheritance of basestring from NamedStream - -commit d22606a18d25a85e697638f019cfa9b95b4ab207 -Author: Richard Gowers -Date: Fri Jan 22 14:18:06 2016 +0000 - - Added extra resnames to 'nucleic' selection - - Closes issue #461 - -commit c45daa83f67d10958eeb48222d611fd09cd365b2 -Author: Richard Gowers -Date: Fri Jan 22 10:49:56 2016 +0000 - - Removed inheritance of basestring from NamedStream - - But still isn't considered iterable - -commit bff74158cb349de42d4d44e40c94995a34a0c6f3 -Author: Richard Gowers -Date: Fri Jan 22 09:27:00 2016 +0000 - - Fixup to core/Selection tests - -commit 479cd28468a3f1e50793fe948310c27f4a467bd2 -Author: David Dotson -Date: Fri Jan 22 00:47:10 2016 -0700 - - Almost done migrating all group functionality. - - Moving what used to be in each of AtomGroup, ResidueGroup, and - SegmentGroup into the new classes, many of which are now transplants - from TopologyAttrs. Also doing the same for Atoms, Residue, and Segment - classes. - - As I go, I'm updating docstrings to numpy style. - -commit 2848f6b4378e1453f1af3a14dda8fe56415a756b -Author: David Dotson -Date: Thu Jan 21 22:05:37 2016 -0700 - - Can now initialize a universe with a Topology object - -commit 07cbacf24f21f640cd965347f2f00f7c3d6de2d1 -Author: David Dotson -Date: Thu Jan 21 17:16:38 2016 -0700 - - Changed short transtable method names to extended names. - - To make things clearer, changed e.g. `a2r` to `atoms2residues`. - -commit 40831d942c4bda65fec8987f4627ede2c643de0e -Merge: 7c25ebbe7 217c13f95 -Author: David Dotson -Date: Thu Jan 21 12:56:16 2016 -0700 - - Merge pull request #630 from MDAnalysis/issue-345-implicitOR - - Implicit or in selections (Issue #345) - - Allows selections such as: - ``` python - - u.select_atoms('name C* N* O*') - # == u.select_atoms('name C or name N') - - u.select_atoms('name N and resname GLY LEU') - # == 'name N and (resname GLY or resname LEU)' - - u.select_atoms('resid 1:10 14 15') - - u.select_atoms('resid 1:100 200-300 and not resname MET GLY') - ``` - Defines how to detect keywords in selection strings with `is_keyword` (Issue #347). - -commit 217c13f95be22b00878749ee56e58f7184297488 -Merge: f18e6ac4e 7c25ebbe7 -Author: Richard Gowers -Date: Thu Jan 21 19:34:29 2016 +0000 - - Merge branch 'develop' into issue-345-implicitOR - - Conflicts: - package/CHANGELOG - -commit f18e6ac4e899a0c25e7fbabeeb99564c09c7a674 -Author: Richard Gowers -Date: Thu Jan 21 19:33:40 2016 +0000 - - Fixed deprecation of fullgroup - - Fixed missing group error, now raises SelectionError rather than missing - token error - -commit 7c25ebbe79ded36fd20cba8a58d74511427963e8 -Merge: 804d5d27e f512fcdd4 -Author: Richard Gowers -Date: Thu Jan 21 11:49:02 2016 +0000 - - Merge pull request #638 from MDAnalysis/issue-624-ContactAnalysis1 - - Issue 624 -- ContactAnalysis1 - -commit f512fcdd4ebb80f377587b763574d1708a9ed834 -Author: Tyler Reddy -Date: Thu Jan 21 11:22:51 2016 +0000 - - Deprecated argument handling in ContactAnalysis1 run() method now uses kwargs.pop(deprecated_arg). - -commit deb0f669e0406ac8cbae08926fc90f8c00af2af2 -Author: Tyler Reddy -Date: Thu Jan 21 11:10:11 2016 +0000 - - Added 0.15.0 as the target version for removal of deprecated slicing arguments to ContactAnalysis1 run() method deprecation warning messages. - -commit fbc3fc38f424533b140d79133461972d2a83d499 -Author: Tyler Reddy -Date: Thu Jan 21 11:01:48 2016 +0000 - - ContactAnalysis1 run() method now uses DeprecationWarning category for warning messages related to start, stop, and step. - -commit 565ac1a44686102536468a0fc3472ba3732b9d35 -Author: Richard Gowers -Date: Thu Jan 21 09:55:14 2016 +0000 - - Changes for #345 following review - -commit 22027d0679fd6675c6f48df62d7e35a923ecb947 -Merge: 0920ae2c8 804d5d27e -Author: Richard Gowers -Date: Wed Jan 20 18:14:33 2016 +0000 - - Merge branch 'develop' into issue-624-ContactAnalysis1 - - Bumped version to 0.14.0-dev0 - - Conflicts: - package/CHANGELOG - -commit 0920ae2c808a8645654e1fe2fd97e3a3e7ff00ba -Author: Tyler Reddy -Date: Wed Jan 20 17:26:47 2016 +0000 - - Some of the kwargs in the run() method of MDAnalysis.analysis.contacts.ContactAnalysis1 have been adjusted (deprecated), along with corresponding changes to the docs. - -commit 804d5d27e8f780a6ff8cf45f2393f5683acf2a96 -Merge: af0e2e136 15a05bf9d -Author: Jonathan Barnoud -Date: Wed Jan 20 13:38:52 2016 +0100 - - Merge pull request #645 from MDAnalysis/issue-632-izipremoval - - Removed izip usage - - Move `izip` usage to `zip` and `six`. Use `six` also for `map`, `cPickle`, and remaining `xrange`. - -commit 15a05bf9d6e075b354a1063d161a158cd48f3454 -Author: Richard Gowers -Date: Wed Jan 20 11:13:54 2016 +0000 - - Removed imap usage #632 - -commit 3d3b14df951d6c66b6b62226907d20ad1a9db06b -Author: Richard Gowers -Date: Wed Jan 20 10:23:14 2016 +0000 - - Removed izip usage - - Issue #632 - -commit af0e2e13643790e0dd8261bf999627e52d63432f -Merge: 7c907c247 56bf30e38 -Author: Richard Gowers -Date: Tue Jan 19 23:07:48 2016 +0000 - - Merge pull request #640 from jbarnoud/cleanup - - Some minor clean up - -commit 56bf30e383f4b60dc36540d0ac19e0e4c5f2be12 -Author: Jonathan Barnoud -Date: Tue Jan 19 23:34:43 2016 +0100 - - Adapt analysis/nuclinfo.py after #644 got fixed - - See discussion in #640 - -commit 77bc9cfd193e6b5a78fd36d9e81172669d85275c -Author: Jonathan Barnoud -Date: Tue Jan 19 22:31:18 2016 +0100 - - `atom` selection token allows empty selection - - Fix #644 - -commit b9eef5fe20263430e61d06d640a122ab3a27927e -Author: Jonathan Barnoud -Date: Tue Jan 19 19:11:00 2016 +0100 - - Change how some selection are cut in nuclinfo.py - - Make the cuts follow the logic of the selection string that is cut. - -commit 28421e0c8b68d7b841b0c6193edea1b255fb99fa -Author: Jonathan Barnoud -Date: Tue Jan 19 18:48:35 2016 +0100 - - Use `is not` rather than `not ... is` - - Make Quantified Code happy by fixing the suggestion entitled "`not ... - is` used instead of `is not`. - - Also remove some trailing spaces. - -commit 26c2ac45838b99854d3db75730979529677ffb13 -Author: Jonathan Barnoud -Date: Tue Jan 19 18:15:31 2016 +0100 - - Fix some untyped exception handlers - - Using try/except without an specified exception can hide major issues. - It also hide the intent of the code by not telling what is expected to - go wrong. This commit fix some occurrences of that bad practice when I - could understand the intent of the code. - - Makes Quantified Code happier by fixing part of the suggestion untitled - "Avoid untyped exception handlers". - -commit e506a12c37f68d78e01aad3930471257fb01e4da -Author: Jonathan Barnoud -Date: Tue Jan 19 17:30:00 2016 +0100 - - Cut long lines in analysis/nuclinfo.py - - Long lines were cut only if the cut was obvious enough and would not - impair readability. Error message and the first line of the docstrings - were never cut. - -commit 6b4d13b96dfd3b8992a06544e19172e5fbfe5437 -Author: Jonathan Barnoud -Date: Tue Jan 19 17:02:39 2016 +0100 - - Use set comprehension instead of set(list()) - - Make Quantified Code happy by fixing the "Consider set comprehensions - instead of passing lists to 'set()'". - -commit 936429e3e7c2244fbe80292dd89c91ac97a0bf8c -Author: Jonathan Barnoud -Date: Tue Jan 19 16:59:24 2016 +0100 - - Use new-style Python classes - - Make Quantified Code happy by fixing the "Use new-style Python classes" - suggestion. - -commit bbceab2a9ed9838d51e411ef13bb0a4b2bdc6f3d -Author: Richard Gowers -Date: Tue Jan 19 22:01:19 2016 +0000 - - Additional tests for selections - -commit 7c907c247832b7d396510fc568e5bc891b69591d -Merge: fedf0a2b0 c9d2e0f9c -Author: Richard Gowers -Date: Tue Jan 19 20:21:05 2016 +0000 - - Merge pull request #636 from jbarnoud/port-py3 - - Make xrange and range call python 3 compatible - -commit fedf0a2b0ef31d144ebf6fda7c43d4e9b125981e -Merge: ac500caaa d175f92af -Author: Richard Gowers -Date: Tue Jan 19 19:00:48 2016 +0000 - - Merge pull request #641 from MDAnalysis/issue-639-pdbwritefix - - Issue 639 PDBWrite fix - -commit d175f92afe9157c825edb1655555483dc339bc40 -Author: Richard Gowers -Date: Tue Jan 19 18:25:05 2016 +0000 - - Fixes Issue #639 - - Start on 2nd column if less than len 4 - -commit 4f5f82cf51a38e171931607e2df0398b128da9ca -Author: Richard Gowers -Date: Tue Jan 19 18:23:39 2016 +0000 - - Added tests for Issue-639 - -commit 3a598af474160f3fb1cafc40b14325a8119f3ea9 -Author: Tyler Reddy -Date: Tue Jan 19 17:38:07 2016 +0000 - - Replaced the usage of tempfile with tempdir module in test_contacts.py - -commit 20d40c5eb6698a8fed2a66a2dc176062e3c73d0a -Author: Tyler Reddy -Date: Tue Jan 19 16:22:08 2016 +0000 - - ContactAnalysis1 run method now starts at frame index 0 by default. Fixes #624. This update includes the docstring fix for the default setting as well. CHANGELOG has also been updated accordingly. - -commit 4fbcb5cbeea095d3dbe4ba49bf0da89b510784b4 -Author: Tyler Reddy -Date: Tue Jan 19 16:08:46 2016 +0000 - - Added a unit test for Issue #624. - -commit ac500caaa04b2e7aab37f9d131b5e456b6007f85 -Merge: ae755d8da 46ed3fb29 -Author: kain88-de -Date: Tue Jan 19 17:03:04 2016 +0100 - - Merge pull request #637 from jbarnoud/gitignore - - Update gitignore to ignore annoying stuff - -commit 46ed3fb292c32e3ab19e9a5ff766854382186a9a -Author: Jonathan Barnoud -Date: Tue Jan 19 16:36:05 2016 +0100 - - Update gitignore to ignore annoying stuff - - * Ignore the .eggs directory created by pip - * Ignore the temporary files created by vim - * Ignore the MDAnalysis log files - -commit c9d2e0f9cc61ca63ddba571bf3f21118b259d2bf -Author: Jonathan Barnoud -Date: Tue Jan 19 15:52:39 2016 +0100 - - Make xrange and range call python 3 compatible - - The `xrange` function disapears in Python 3. In the same time, the - meaning of the `range` function changes in python 3 to behave in a - similar fashion as `xrange`. Therefore, in Python 3, `range` produces a - generator and `xrange` does not exist anymore. - - This commit replace all calls to `xrange` by calls to `range`. It also - overload the `range` built-in to use the one provided by `six` that - reproduce the behavior from Python 3. - - No Cython file got touched, even though some use xrange, as xrange seems - to keep existing in Cython. - - This commit changes the behavior of the `range` built-in! - - In the future, `xrange` should not be used anymore. When `range` is - used, it should be overloaded with `from six.moves import range`. When a list - is needed rather than a generator, `list(range(x))` should be used. - -commit ae755d8da449d73d8f3ecff4d8015affa742d236 -Merge: 4fdc9be5e c8268bc15 -Author: Richard Gowers -Date: Tue Jan 19 13:43:03 2016 +0000 - - Merge pull request #634 from jbarnoud/port-py3 - - Small changes to improve python 3 compatibility - -commit 52fcb572c312b48740ab447ed5eff65efb9af728 -Author: Richard Gowers -Date: Tue Jan 19 12:41:54 2016 +0000 - - Moved select_atoms docstring onto AG.select_atoms not Universe.select_atoms - - AG version is surely used more often? - -commit c8268bc15d9ad3bb052f1b9b5d6e12cf6d54cbec -Author: Jonathan Barnoud -Date: Tue Jan 19 13:33:19 2016 +0100 - - Small changes to improve python 3 compatibility - - This commit fix few small things that prevented MDAnalysis to be - imported in python 3. MDAnalysis can still not be imported in python 3, - though. - -commit 5cdebf11c9e816f07ffcd333266c9fdd240627a6 -Author: Richard Gowers -Date: Tue Jan 19 12:28:15 2016 +0000 - - Updated select_atoms docstring - -commit 230a352b2ed883557b7782fd760e8b156f74d043 -Author: Richard Gowers -Date: Tue Jan 19 11:25:00 2016 +0000 - - Added implicit OR to RangeSelection (resid) - - Allows selections such as: - 'resid 1:10 20:30' == 'resid 1:10 or resid 20:30' - -commit 020f7aae94fe74146ca15f58b1ba143b92de5119 -Author: Richard Gowers -Date: Tue Jan 19 10:45:37 2016 +0000 - - Added tests for Implicit ORs - - Updated LogicOperation metaclass to py2/3 style - -commit 71b81547103f5e5362fc47495ab7b7020f023e95 -Merge: 6bcdc8bd3 4fdc9be5e -Author: Richard Gowers -Date: Tue Jan 19 09:36:42 2016 +0000 - - Merge branch 'develop' into issue-345-implicitOR - -commit 4fdc9be5e42f246abeb29cb644db854eeede629d -Merge: 554d27620 60b36a9c7 -Author: Richard Gowers -Date: Tue Jan 19 09:34:44 2016 +0000 - - Merge pull request #633 from MDAnalysis/issue-632-py3metaclasses - - Using six for Py2/3 metaclass usage - -commit 60b36a9c7b4102f3f597b0ce2593e93a28c63856 -Author: Richard Gowers -Date: Mon Jan 18 19:48:55 2016 +0000 - - Using six for Py2/3 metaclass usage - - Part of #632 - -commit 554d2762091aad87b2b4657b8eb357b6b4c9bfb7 -Author: Richard Gowers -Date: Mon Jan 18 16:30:02 2016 +0000 - - Moved examples out of main repo (now in MDAnalysisCookbook) - - Closes Issue #627 - -commit 6bcdc8bd30c1f60c5c5f7973a7bd53fa8ac3c0eb -Author: Richard Gowers -Date: Mon Jan 18 10:40:12 2016 +0000 - - Fixup of missing brackets as keywords - -commit 3dcf57dc0d12a397087e72440bedf5dc1536f144 -Author: Richard Gowers -Date: Mon Jan 18 10:11:06 2016 +0000 - - Implicit or in selections (Issue #345) - - Allows selections such as: - u.select_atoms('name C N') == u.select_atoms('name C or name N') - u.select_atoms('name N and resname GLY LEU') == 'name N and (resname GLY - or resname LEU)' - - Defines how to detect keywords in selection strings (`is_keyword`) - Issue #347 - -commit b91e0abf5c3df5917e5e22d985e3e8d055aaec67 -Merge: 74e6f82f7 6002e9f1c -Author: Richard Gowers -Date: Sun Jan 17 14:50:36 2016 +0000 - - Merge pull request #441 from kain88-de/cython-xdrlib - - Cython xdrlib - -commit 6002e9f1c79cd539e1eaa0427aae57f039f93ca5 -Author: Max Linke -Date: Sun Jan 17 15:00:36 2016 +0100 - - Add changelog info - -commit afcd9da2c812c3f767bffa532a4ad7ccb7990e20 -Author: Max Linke -Date: Thu Jan 14 18:14:31 2016 +0100 - - ignore *.npz files created during testing - -commit eb80ca91c714d79bf580c19167d98364838d68f3 -Author: Max Linke -Date: Thu Jan 14 18:12:16 2016 +0100 - - Fix up doc strings - -commit 9a3c3fcc6f1e4af2fd25ec90b492e2b1a5bb092f -Author: Max Linke -Date: Thu Jan 14 18:12:09 2016 +0100 - - Fix up doc strings - -commit a2508e393805cf2e0c9c1d355a29955e4033bc4d -Author: Max Linke -Date: Thu Jan 14 18:11:25 2016 +0100 - - Fix Doc strings - -commit c42c528930f3ffd91e19dddf7916dacbf5e4462d -Author: Max Linke -Date: Thu Jan 14 18:03:27 2016 +0100 - - Fix test Error - - Base test classes in test files seem to be needed to start with an - underscore otherwise nose picks them up and tries to lets their tests - run. - -commit 7149ed1d9657451a5e7d2aae41ec0f5bd8127e58 -Author: Max Linke -Date: Thu Jan 14 10:34:47 2016 +0100 - - Various QC fixes in XDR.py - -commit 568067d74644dfd80d29db499d1b8b25831efef4 -Author: Max Linke -Date: Thu Jan 14 08:16:01 2016 +0100 - - really test offset mismatch - -commit 7b7242eb0fb8f3039c6975daad1e8a20ddb71b13 -Author: Max Linke -Date: Thu Jan 14 08:15:53 2016 +0100 - - XDR fix spelling error - -commit 03cb2ae5050b8510576e63cefd0e6b3520422459 -Author: Max Linke -Date: Thu Jan 14 00:10:36 2016 +0100 - - Add XTC sub selection test - -commit 405eff1837096b8f39e7cdf0654a15640c0d99e0 -Author: Max Linke -Date: Wed Jan 13 23:57:32 2016 +0100 - - deactivate unused tests - -commit 4f2a2086d5b81e5e74ee67c4b3d373f750d2b7a1 -Author: Max Linke -Date: Wed Jan 13 23:54:37 2016 +0100 - - test precision setting in xtcwriter. - -commit 3128f23bc9ee7d7e5ac9908a37e9b9a028ab62cb -Author: Max Linke -Date: Wed Jan 13 23:48:32 2016 +0100 - - use float type for precision - -commit 7fde350e7ad48f1558b1ddda7933412f77b4fbbe -Author: Max Linke -Date: Wed Jan 13 08:07:20 2016 +0100 - - Add test to write non default xtc precision - -commit b3f48d83aee433af709b44b50dcb8adb1f3ce631 -Author: Max Linke -Date: Wed Jan 13 07:44:09 2016 +0100 - - Add information how test.xtc/trr was created - - This also includes information how to read the content of the files - in ascii without using MDAnalysis - -commit ddc8cafaef0520de9a3209284824bfaeda3c6932 -Author: Max Linke -Date: Mon Dec 28 12:31:33 2015 +0100 - - Fix type in doc-string - -commit 1e6b5a3a5072ec9c84df8878c5d6354093b2b48e -Author: Max Linke -Date: Mon Dec 28 12:30:54 2015 +0100 - - convert to xdrlib precision for XTC saving - - Use a more sensible precision definition inside of MDAnalysis. - -commit ec6df6f8b94b6f6d0ebe264b9e3d21a05da03221 -Author: Max Linke -Date: Mon Dec 28 12:26:44 2015 +0100 - - Use old gromacs precision in xdrlib - - This is to better deal with the precision return value here. - -commit 0f95627bfcf33d4f24ecc2c38e2d8b6413a85cf2 -Author: Max Linke -Date: Sun Dec 27 13:09:00 2015 +0100 - - Offer precision keyword in XTCWriter - - The old class supported this so I should do this here as well - -commit a081c3f14768916f177968bd95efa3e5b3919970 -Author: Max Linke -Date: Sun Dec 27 13:07:47 2015 +0100 - - Use better precision interface for xtc writing - - This new interface is more intuitive. - -commit c890331d06f331a319f34bf9cb2655d2f9dd3242 -Author: Max Linke -Date: Sun Dec 27 12:42:54 2015 +0100 - - Forget offsets when xdrfile is closed. - - This ensures that offsets are recalculated if another file is opened - with the same xdrfile instance. - -commit 405121fe0c39e3bebe6e2db072b7cc8b1348dbdc -Author: Max Linke -Date: Sun Dec 27 12:42:11 2015 +0100 - - Add smal docstring to XTC and TRR reader - -commit 4546a61e1a32ba0b2c7246f6e8717ebe3277306a -Author: Max Linke -Date: Sun Dec 27 12:31:29 2015 +0100 - - Remove unused variable - -commit 58ede09e990a8725177f48733305786f21f10bb2 -Author: Max Linke -Date: Fri Dec 18 16:31:11 2015 +0100 - - Combine xdrlib tests - -commit 2507b8f074550788601e7ddf6d3d7e2f657a2e68 -Author: Max Linke -Date: Fri Dec 18 16:26:02 2015 +0100 - - Add licence info the each file - -commit a2659fc1207ac30bcb1d5cef049d04b1d275e156 -Author: Max Linke -Date: Fri Dec 18 16:18:48 2015 +0100 - - completely remove test_vel_src. - - The code has been removed. - -commit ca0af8884720ab48ba6c23ebd0ed57b9c1685538 -Author: Max Linke -Date: Fri Dec 18 16:18:37 2015 +0100 - - clean up test_xdr.py - -commit ac8b116b5374159def24a8a14fec1d72a89eb541 -Author: Max Linke -Date: Fri Dec 18 16:13:31 2015 +0100 - - clean up test_timestep_api - -commit b1c910948fc27663cb6c7a865649b86ee306c7d2 -Author: Max Linke -Date: Fri Dec 18 16:03:02 2015 +0100 - - Reactivate timestep tests - -commit 72354330f57c26e17bfbb596cbdb6b8500e51e8e -Author: Max Linke -Date: Fri Dec 18 15:59:37 2015 +0100 - - improve xdrlib doc strings - -commit 3898986ed681e643b07a8000002e596b241d24f3 -Author: Max Linke -Date: Fri Dec 18 15:43:08 2015 +0100 - - Fix small things in XDR.py - -commit b522357992d5c0e3911f4599ea29aeb68e6d5f3b -Author: Max Linke -Date: Fri Dec 18 10:29:57 2015 +0100 - - Get 100% coverage in XDR.py - - This will only test that the code path is run. Not that the does - anything correct. - -commit 9afeffbb69415e4c720850a781b0debbfcca0800 -Author: Max Linke -Date: Fri Dec 18 10:22:55 2015 +0100 - - merge xdr test files - -commit 2308848d0ac56b1cbac643ac98f6198d10cd9f5f -Author: Max Linke -Date: Fri Dec 18 10:18:37 2015 +0100 - - Move xdr persistence test to xdr tests - -commit 563f6e0d4e5badf66a1c7479c928a7700476b018 -Author: Max Linke -Date: Fri Dec 18 10:16:06 2015 +0100 - - Deactivate mismatch tests - - Since I can't possibly test for them right now they have to be - deactivated. - -commit 9151a3fa7fb5f85450aa4c8219b2669163230ebb -Author: Max Linke -Date: Fri Dec 18 10:03:15 2015 +0100 - - Only try a savez - - It can fail when the directory is read-only or when something - else happens to the directory. In that case just fail silently - -commit 6d3081e97c37071e6271f0c622464d77bf258b16 -Author: Max Linke -Date: Fri Dec 18 10:02:44 2015 +0100 - - remove cruft from persistence tests - -commit a4002672d2710cb56bc303f9e2d152029ec96edd -Author: Max Linke -Date: Fri Dec 18 09:16:45 2015 +0100 - - Refactor from tempfile to tempdir - - This ensures cleaning up for us and we don't have to do those unlink - things. - -commit 3f6a1e7294fcf6509fb59989423202197c2a7458 -Author: Max Linke -Date: Fri Dec 18 09:09:52 2015 +0100 - - remove lazy loading persistence offset tests - - The new XDR-classes don't support lazy loading for the - offsets anymore. - -commit dc1ce75cd1dfc1d48e4aa1b90dda25f7cfa669cb -Author: Max Linke -Date: Fri Dec 18 00:10:09 2015 +0100 - - get most persistence tests to pass - -commit 64575a97e804c4e71e5e5a985cef4606d4cbb6eb -Author: Max Linke -Date: Fri Dec 18 00:09:29 2015 +0100 - - better warning message - - the new system doesn't abort the offset loading. It just - reloads them directly with construction then. - -commit 7b08f9139197473a1954db7f3fef5a4c2c4e4bb3 -Author: Max Linke -Date: Thu Dec 17 22:54:40 2015 +0100 - - Fix offsets path algorithm - - The algorithm could only deal with relative paths. This - works also for absolute paths - -commit f3517cc8734d30914077789ead26fbf3fcf0e6ab -Author: Max Linke -Date: Thu Dec 17 22:27:00 2015 +0100 - - PEP8-fy test_persistence.py - -commit 8b051cc58027e91825eacbc386881edb9c602d9d -Author: Max Linke -Date: Thu Dec 17 18:00:48 2015 +0100 - - Persistently save offsets - -commit 109f7e208d55409530f5220889c8e2c3211e805e -Author: Max Linke -Date: Thu Dec 17 17:26:29 2015 +0100 - - Avoid offset calculation in XDRBaseReader init - -commit cbcf57d1179e81acd9d3878714d28df5563d7517 -Author: Max Linke -Date: Thu Dec 17 17:24:11 2015 +0100 - - Don't look into offsets when seeking to frame 0 - - Looking into the offsets array would trigger a calculation of the - offsets. This modifocation allows to still use lazy loading in the - XTCReader and still inspect the second frame to calculate a dt. - -commit e41f1ee50a0db2045d0c1a6a932bfa85fac34716 -Author: Max Linke -Date: Thu Dec 17 16:47:20 2015 +0100 - - Make n_frames a property - -commit 5dcedd4e9f796655bfe7dec7793e59057f7698fb -Author: Max Linke -Date: Wed Dec 16 23:23:48 2015 +0100 - - Create XDR base class and adopt XTC/TRR - -commit 4c65354efd0b2973af1b977e48bfaaaa2afdb601 -Author: Max Linke -Date: Tue Dec 15 14:38:09 2015 +0100 - - test common xdrlib functions in a base class - -commit 6585913d500da8e2ebeccd42dddc65fef7c52da3 -Author: Max Linke -Date: Tue Dec 15 08:20:00 2015 +0100 - - Unify xtc/trr file wrappers - - Use a common base class for the two. This reduces duplicated code. - - Check BOX tolerance to 2 decimal places xdrlib - - Upto 2 decimal places accuracy is enough for box vectors. - Well it's exactly the value I need to have the tests pass. - -commit e291468f8ba0e6570e1d39b496a04a833edf0cd8 -Author: Max Linke -Date: Thu Dec 10 22:47:59 2015 +0100 - - remove libxdrfile2 tests - -commit 735b7b29caa2e9e027fc5539e8e758d4812afe9d -Author: Max Linke -Date: Thu Dec 10 21:28:00 2015 +0100 - - deactivate some tests - - deactivate persistence test - deactivate timestep tests - deactivate atom_group velocity source test - what was this testing anyway??? - -commit a0d14ab0c5b9f1bf90b58e447a48d44184a6afe4 -Author: Max Linke -Date: Thu Dec 17 09:35:36 2015 +0100 - - Add C_ptr to ndarray wrapper - - I need a way to convert pointers to numpy arrays in cython that is - portable across numpy versions and python versions. This file should to - exactly that. It will help me to treat the xdrlib correctly. The - wrapper - is a bit more complex then just setting the OWN_DATA flag in a newly - created array to allow us a fine controll over the used deallocator. - Then numpy can change it's allocater in the future and this will still - work. - -commit 140681b96d04b3df7686264d704e59c5ce478828 -Author: Max Linke -Date: Thu Oct 29 19:43:00 2015 +0100 - - Add new tests for XTC and TRR reader/writer - - Delete also old TimeStep tests since that object doesn't exists - anymore in the code. - -commit 561352f39e56f1c0152e2030cf2a9daa4f38e83f -Author: Max Linke -Date: Fri Sep 18 11:18:55 2015 +0200 - - Readd the TRR-Reader/Writer classes - - Basically it is the same as the XTC module. Just small - changes for the TRR format. - -commit 34b0090db0503ca0d57bd4ec6e926b53368965d5 -Author: Max Linke -Date: Tue Sep 15 15:50:52 2015 +0200 - - Readd XTC-Reader/Writer class - - This is now a 'simple' wrapper around the xtcfile object. - That simplifies the code quite a lot and it looks like we have a proper - seperation of responsibilities in the code - -commit 99063b1cd56ce105520c13626e3fe0f33bb61583 -Author: Max Linke -Date: Tue Sep 15 07:41:03 2015 +0200 - - Add tests for trr module - -commit f9446db4250b55b95950ed5f8aa50579db3336e9 -Author: Max Linke -Date: Mon Sep 14 23:27:40 2015 +0200 - - Add TRRFile module - - This is a copy of the xtc module enabling to use trr files. - -commit 4bfe4d26b071a2d2c9d3b1d626a1f14bc0a8da65 -Author: Max Linke -Date: Sun Sep 13 15:16:46 2015 +0200 - - Add test for new XTCFile object - - This adds a comprehensive set of tests for the new XTCFile class. - It tests most error conditions that are easy to generate and comes - with it's own set of small test files. Even though I'm doing some IO - everything runs very fast because the files involved are small. - -commit 312b5fe3369694df38e150c85b5aa7d91332c14d -Author: Max Linke -Date: Sat Sep 12 18:29:16 2015 +0200 - - Add XTCfile object module - - This adds a clean wrapper for xtc functions in the xdrlib of GROMACS. - The object acts similar to a normal file object in python. This should - be the a clean wrap and enable to use xtc files with little fuss inside - of mdanalysis. It currently is still somewhat slow. After fixes edges - with the API and integrating it into a Reader class I'll have a look - into optimizing it. - -commit a95001226598dcead0e0d65067cf1716265025ee -Author: Max Linke -Date: Wed Nov 25 10:48:40 2015 +0100 - - Fix memleak in xtc offset calculation - - It was never returned how the the offsets array actually had become. - This means there was no way of taking back controll over a small part of - the allocated memory. Resulting in a memory leak. This new version also - returns the information about the actual size of the offsets array. - -commit a2b451c802cf3c8cb950e6878a4b5228bc979980 -Author: Manuel Nuno Melo -Date: Thu Nov 19 21:52:55 2015 +0100 - - Readd original changes for seeking in XDR files - - These are the changes that have been made my Manuel to enable seeking in - the xtc/trr files. The C modules compile besides of some changes I need - to make to the cython wrappers. - - Signed-off-by: Max Linke - -commit 3feecfaa364f0d7ca8982438479bf54291cb5ce6 -Author: Max Linke -Date: Sat Sep 12 17:59:50 2015 +0200 - - Add currentversion of xdrlib - - This is the newest version accessible from the GROMACS - devs. - -commit 8a6c68b5011d1b5ed00944c869d7f2c14513b5bb -Author: Max Linke -Date: Sat Sep 12 15:47:01 2015 +0200 - - Remove old XDR code - - Refactoring this is not really worth it. I'll start the xdr - interface from scratch. - -commit 74e6f82f7797724a03e09fcf561029bbeebaac2e -Author: Richard Gowers -Date: Sun Jan 17 12:52:07 2016 +0000 - - Bumped version to 0.13.1-dev0 - -commit 9a80de068cd9057e7e3dc665345840c28ab247fd (tag: release-0.13.0) -Author: Richard Gowers -Date: Sun Jan 17 11:15:29 2016 +0000 - - Finalised testsuite changes for 0.13.0 release - -commit 3fab8ada828ef21c871bf4f8f2dd6a9fde9b2ee2 -Author: Richard Gowers -Date: Sun Jan 17 11:06:16 2016 +0000 - - Removed tests to check openmp was used - - OpenMP is optional, so this test should still pass if openmp wasn't used - -commit 9cb2162d895135eb2331822474ff2ddc4ef40785 -Merge: 83d9167f0 5f950845e -Author: Richard Gowers -Date: Sun Jan 17 10:37:18 2016 +0000 - - Merge pull request #628 from jbarnoud/Add-six-requirement - - Add `six` to the requirements - -commit 5f950845eeb05f59611f5afde0fe94c48e4b6c1f -Author: Jonathan Barnoud -Date: Sat Jan 16 15:25:44 2016 +0100 - - Add `six` to the requirements - - Part of the code already use the `six` module in prevision for python 3 - support. Yet, `six` was not declared as a requirement in setup.py. - - This commit declares six>=1.4.0 in setup.py. Not all test pass with - older version of six. - -commit 83d9167f05c2936aa03fd06ac16570a223e09194 -Author: Richard Gowers -Date: Sat Jan 16 07:58:22 2016 +0000 - - Finalised changes for 0.13.0 release - - Release candidate for Issue #600 - -commit 57934b628a5d61538a08670a60abc617270aeb42 -Merge: d826144e4 6723d7463 -Author: Richard Gowers -Date: Fri Jan 15 22:44:12 2016 +0000 - - Merge pull request #626 from MDAnalysis/issue-615-cythonsemicolons - - Removed semicolons from Cython source files - -commit d826144e411dc66bce16e514c8e08ec13f3323d5 -Merge: 960d9ba79 b48845eee -Author: Richard Gowers -Date: Fri Jan 15 22:11:55 2016 +0000 - - Merge pull request #625 from jbarnoud/Issue-622-precision-test-helenal - - Reduce the precision of a helenal test - -commit 6723d74633eb999f46a7e0c70fe3a616299742fd -Author: Richard Gowers -Date: Fri Jan 15 22:11:23 2016 +0000 - - Removed semicolons from Cython source files - - Closes Issue #615 - -commit b48845eee4dc35b1546452f46360c5b9bb096c7b -Author: Jonathan Barnoud -Date: Fri Jan 15 22:37:09 2016 +0100 - - Reduce the precision of a helenal test - - Make a test about helenal less stringent. - - Fix #622 - -commit 960d9ba79f7be52a97c1e2dccef3dca240624ca1 -Merge: 5044e906b 01c42a1ae -Author: kain88-de -Date: Fri Jan 15 22:19:31 2016 +0100 - - Merge pull request #621 from MDAnalysis/issue-620-pdbwriting - - Closes Issue #620 - -commit 01c42a1ae030cc360c658288532d93adba7b6a64 -Merge: e02355122 5044e906b -Author: Richard Gowers -Date: Fri Jan 15 20:50:43 2016 +0000 - - Merge branch 'develop' into issue-620-pdbwriting - - Conflicts: - package/MDAnalysis/coordinates/PDB.py - -commit 5044e906bb52f8ae758980b5a7a5ad267c63dd57 -Merge: 5437ca786 8cc2e5af2 -Author: Richard Gowers -Date: Fri Jan 15 20:19:23 2016 +0000 - - Merge pull request #623 from jbarnoud/Issue-592-format-redo - - Issue 592 format redo - -commit 8cc2e5af273e73da3e6ce8c26d5c586fcc7b5f2e -Author: Jonathan Barnoud -Date: Fri Jan 15 20:02:28 2016 +0100 - - Fix Cody/QC error with format - - Cody/QC suggested a fix to replace all string replacements using % by - string replacements using the `format` method. Yet, the suggested - replacement introduce a syntax error by replacing all occurences similar - to '%4s' to something like '{0:4!s}'; where what follows the column is - the format for the replacement and what follows the bang is the type for - the conversion. - - Cody's replacement leads to the following exception: - - ValueError: Invalid conversion specification - - It appears that the column part and the bang part of the format should - be written the other way around so '{0:4!s}' should actually be - '{0!s>4}'. Note that the > character is important as it describes how - the data should be aligned. By default, without the >, strings are flush - to the left while '%4s' flush strings to the right. Note that '{0!d:4}' - does flush to the right on the contrary to what happens with strings. - - In MDAnalysis, the only faulty replacements where about string format. - They could be detected using the following grep statement: - - egrep -Ro '\{[^:}]*:[^!}]*![^}]*\}' * - - I fixed the faulty replacement with the following command: - - find ./ -name '*.py' -exec \ - sed -rie 's/\{([^:}]*):([^!}]*)!s\}/{\1!s:>\2}/g' {} \; - -commit 3afd47f54376723f3f954d56cb8d7e991b220a53 -Author: Cody -Date: Fri Jan 15 18:55:35 2016 +0000 - - Migrated `%` string formating - -commit 5437ca7865302785db1401fb22ed6a793e473511 -Merge: 7b91b2a33 e9daccb4b -Author: David Dotson -Date: Fri Jan 15 11:29:28 2016 -0700 - - Merge pull request #619 from MDAnalysis/issue-431-registerreaders - - Issue 431 registerreaders - -commit e9daccb4b56d2d7adbc9a0c721df593733a50431 -Author: Richard Gowers -Date: Fri Jan 15 09:25:20 2016 +0000 - - Docstring fixes for #431 - -commit e0235512247420d070dd4a428bbbfe832cffaacc -Author: Richard Gowers -Date: Thu Jan 14 19:29:46 2016 +0000 - - Closes Issue #620 - - Occupancies now properly written in PDB files - - Removed get_bfactors and get_occupancies methods - -commit 18a8813fbae7abfde998d7a707dee425eaecf11d -Author: Richard Gowers -Date: Thu Jan 14 19:44:50 2016 +0000 - - Fixups for #431 following review - -commit 7b91b2a33b01d7d098af2e7847d4a718f5ec8b85 -Merge: 8bb02d40e acf2425a6 -Author: David Dotson -Date: Thu Jan 14 01:40:15 2016 -0700 - - Merge pull request #613 from MDAnalysis/issue-270-topOnlySelections - - Issue 270 top only selections - -commit acf2425a63e17ce2c14f869253911188cb99dcc5 -Author: Richard Gowers -Date: Thu Jan 7 14:01:35 2016 +0000 - - Closes Issue #270 - - ag.select_atoms now doesn't require a trajectory to be loaded to perform - selections - - Refactored core/Selections module - - Extra tests for Selections - - Removed hardcoding of Selection objects - - Now all subclasses of Selection get added into language if the attribute - 'token' is defined - -commit 63e71c1615d4abd41173c2eb5c9cfd313bc9bb4c -Merge: ede0229f4 169a045f0 -Author: Richard Gowers -Date: Thu Jan 14 08:31:26 2016 +0000 - - Merge pull request #609 from MDAnalysis/issue-363-componentattrs - - Refining how Components get attribute accessors. - -commit 169a045f0f058f28506352d0f8b4cea1f083560c -Author: David Dotson -Date: Thu Jan 14 00:22:44 2016 -0700 - - Changed unnecessary list comprehensions to generator comprehensions - - This could only be done where we weren't using try-except blocks. - Perhaps we should reconsider using try-except blocks in favor of - if-statements since we have to switch to full lists in many places? - -commit d94d89798ac73811663f07a725eada228276090f -Author: Richard Gowers -Date: Wed Jan 13 12:11:02 2016 +0000 - - Rewrote coordinates/core docs - - Fixes Issue #431 - - TopologyReader, Writer and ProtoReader classes (and all subclasses) now - automatically register the class using the 'format' attribute if present. - - Writers which support writing multiple frames can declare this by - setting the 'multiframe' attribute to True - -commit 8bb02d40e4a344f1ec1495e1ccad1dd9790bf095 -Merge: 9f19607b3 df5d7a210 -Author: kain88-de -Date: Wed Jan 13 09:22:21 2016 +0100 - - Merge pull request #616 from MDAnalysis/issue-521-mol2writefix - - Issue #521 mol2writefix - -commit 42281a7cf796c91b939430c3675fcbeaedd71a64 -Author: David Dotson -Date: Tue Jan 12 23:54:18 2016 -0700 - - TransTable downconversions now use try-except blocks when possible. - - Since we want TransTable requests to be fast when using groups, since - that's where the performance benefits come in, we want these to pass - through quickly. Using try-except blocks gives greater performance for - this case at the cost of worse performance for singular item access, - which is fine. - - Also switched levels -> target_levels for TopologyAttrs. - -commit df5d7a210ba145b52c7d630de108a5ef2f716f1e -Author: Richard Gowers -Date: Tue Jan 12 22:20:46 2016 +0000 - - QC fixes - -commit 06bd71feda8ca021c5c3f08d3d3cc69a4f29bd47 -Author: Richard Gowers -Date: Tue Jan 12 13:09:32 2016 +0000 - - Fixes Issue #521 - - MOL2Reader now reads `molecule` and `substructure` into `ts.data` under - the keys `molecule` and `substructure` - - Fixed MOL2Reader not reading molecule and substructure on init. - - Fixed MOL2Writer loading the frame anew before writing (and overwriting - any changes made to the frame by the user) - - MOL2Writer no longer writes an entire trajectory using the `write` - method and instead only writes a single frame (to conform with all other - Writers) - To write an entire trajectory, use a loop - -commit 5b5278390f72e5953eab6e67929881214081299a -Author: Richard Gowers -Date: Tue Jan 12 12:29:15 2016 +0000 - - Refactored MOL2 encoding slightly - - Uses TopologyGroups better - -commit 9f19607b30caba8bf7162753c90c7e01bc40a962 -Author: Oliver Beckstein -Date: Mon Jan 11 01:02:42 2016 -0700 - - reST doc fixes - -commit 2744af369e6969a77d92320a11a1b916604edf5f -Merge: 480ab5954 71e460042 -Author: Oliver Beckstein -Date: Sat Jan 9 14:18:09 2016 -0700 - - Merge pull request #614 from MDAnalysis/Balasubra-Balasubra-Issue584 - - dynamic selections for density_from_Universe (issue #584) - -commit 71e460042e460f4e8f5f2e1fda6572a1d23491af -Author: Oliver Beckstein -Date: Sat Jan 9 12:15:46 2016 -0700 - - removed superfluous analysis.density.density_from_trajectory() - -commit 5958fa92ac0d6067d2792c34c83ad77e02a3d6de -Author: Oliver Beckstein -Date: Fri Jan 8 13:14:40 2016 -0700 - - enabled slicing of trajectories for density_from_Universe() - - - For analysis.density.density_from_Universe() - - new keywords start, stop, step - - added regression test for slicing - - added quiet (and interval) keyword in response to review by @kain88-de - - Cleaned up docs for density_from_trajectory() (just look at - the docs for density_from_Universe()) - - Note: ProgressMeter does not work well with sliced trajectories; I - left it to count relative to the total number of frames but that - can give "incomplete" (<100%) output when the last frames are not - included in the slice. - -commit 7646376fe7b6faa454cdbbdd41fa0a895ed454e6 -Author: Oliver Beckstein -Date: Fri Jan 8 11:41:51 2016 -0700 - - added test for density calculation with dynamic selections - - - Because all imports were moved to the top of density.py, there is - now a top level dependency on analysis.distances and thus on scipy; - previously, this import was only triggered if KDTree was NOT selected - for selections. However, declaring the dependencies up front avoids - later disappointments... Consequently, all density tests are now - skipped in the minimal tests - - This closes issue #584. - -commit d9c0cc8085d94861e515091ef42669c428323d7f -Author: Oliver Beckstein -Date: Fri Jan 8 11:16:52 2016 -0700 - - changed the default offset for ProgressMeter - - - changed from 0 to 1 so that ProgressMeter correctly counts when - using the new 0-based ts.frame - - adjusted the test for the defaults - -commit 1f106441518fc0cb5c966aa08463d5ec73ce91a7 -Author: Balasubra -Date: Fri Jan 8 11:12:04 2016 +0100 - - added Balasubra to authors - - - updated AUTHORS - - updated sphinx conf.py - -commit b838f8805b4ee6871e174aeedd1a0a15a4058450 -Author: Balasubra -Date: Wed Dec 30 12:38:13 2015 +0100 - - dynamic atom selections for density.density_from_Universe() - - - To update atoms selection inside density_from_Universe function: a new keyword - has been added ("update_selection"). When user set sel_update=True, then - the atomselection is updated for each frame. - - updated CHANGELOG - -commit 480ab5954ddfc36f5b9dd9fa0c393113edbcbf9b -Author: Oliver Beckstein -Date: Thu Jan 7 22:44:55 2016 -0700 - - fixed lib.util.greedy_splitext() - - - did not return the full path of the argument; the docs were a bit sparse - but it implied to be similar to os.path.splitext(), which does return - the root filename with full path - - added docs - - added test case - - updated CHANGELOG - - also cleaned up imports in test_util.py - - Note: This is not used anywhere inside the library but was added as a convenience - function for other consumers... IIRC. - -commit 0d6fbd815d894cf3e8dd1c526afbd8baff2b7e4a -Merge: 30d0766f7 3e7d847a7 -Author: Richard Gowers -Date: Thu Jan 7 20:33:27 2016 +0000 - - Merge pull request #610 from MDAnalysis/feature-helanal-tlc - - helanal cleanup - -commit 3e7d847a7cea73284ca745a0db181cc148472ac4 -Author: Oliver Beckstein -Date: Thu Jan 7 11:18:43 2016 -0700 - - helanal minor fixes as requested in review of #610 - -commit c7c8e215a751154fb55ad34d4b2841e26dbf6af5 -Author: Oliver Beckstein -Date: Thu Jan 7 01:36:23 2016 -0700 - - updated CHANGELOG with helanal changes - -commit e005d95b6ab9d0af106edb1fa2f178e0856053a1 -Author: Oliver Beckstein -Date: Wed Jan 6 23:57:08 2016 -0700 - - fixed and improved helanal_main() - - - return data as dict (instead of just logging) - - fixed missing np.mean - - use lib.mdamath were possible - - added regression test - -commit f9a61acbb57560d395468cf5c4f6ec01010f7f3c -Author: Oliver Beckstein -Date: Wed Jan 6 23:24:31 2016 -0700 - - helanal: use ProgressMeter and logging instead of print - -commit f6b576088284605c727f141e91ff686bd36da89d -Author: Oliver Beckstein -Date: Wed Jan 6 17:50:59 2016 -0700 - - minor clean-up in analysis.helanal - - - @quantifiedcode suggested: Consider simplifying bounds checks - - removed import of psyco - - replaced a "if ... pass else" with "if not (...)" - -commit acfdbb3590fe9d8ba929bda11c2e83ef860bc279 -Author: Oliver Beckstein -Date: Wed Jan 6 18:51:34 2016 -0700 - - helanal: fixes and test case - - - helanal_trajectory() was broken: fixed by using np.mean for mean - - added simple regression test: compare helanal_bending_matrix.dat for alpha - helix 8 in AdK in the test PSF/DCD (DIMS) trajectory - - cleaned up test_helanal.py - -commit ede0229f4d94065141662502f9bcdd3d1cebd827 -Author: Richard Gowers -Date: Thu Jan 7 13:23:20 2016 +0000 - - Refactored cylindrical selections - - All selections tests now pass - -commit 30d0766f731f2fc22d4f56d72271b30396efe32a -Merge: 0c80d9342 70dbfb0e6 -Author: kain88-de -Date: Thu Jan 7 11:20:50 2016 +0100 - - Merge pull request #611 from MDAnalysis/feature-remove_ezinstall - - removed easy_install/ez_setup.py from MDAnalysisTests - -commit 70dbfb0e6f6885c4f0ec0ef6c1fa8345c4657032 -Author: Oliver Beckstein -Date: Thu Jan 7 01:50:52 2016 -0700 - - removed easy_install/ez_setup.py from MDAnalysisTests - -commit afb1199829f21aee083881e1eb9429adb48c7019 -Author: David Dotson -Date: Wed Jan 6 17:10:34 2016 -0700 - - Working away at refining how Components get attribute accessors. - - Taking Masses as an example, since we already define how - `ResidueGroup.masses` and `SegmentGroup.masses` work (automatic - aggregation of components), there's no need to define the same - thing twice to make there be a `Residue.mass` and `Segment.mass` - property that gives the value for a single one of these components. - - This required making TransTable methods handle single integers, which - adds only a single if statement to methods that already had list - comprehensions anyway, so shouldn't see a performance hit. This means we - don't have to do backflips for Residues and Segments to make downward - translations work, either. - - Also mixed in here are some work on docstrings that are not yet - complete. Sorry. - -commit 455f445600a4d4c755132384504dc9b97f163bc8 -Author: Richard Gowers -Date: Wed Jan 6 21:17:00 2016 +0000 - - Fixed nucleicbackbone selection - -commit aeaceede8ecff7801e8cbe82a6eb91a6609ca1c1 -Author: Richard Gowers -Date: Wed Jan 6 20:56:10 2016 +0000 - - Fixed `same x as SEL` selections - - Now uses isclose to avoid floating point errors - -commit 4050a70097da43039bc644526b9c9a76c0fb9ea2 -Author: Richard Gowers -Date: Wed Jan 6 20:07:14 2016 +0000 - - Fixed `same fragment as` selection - -commit 2abe61d62404d12f721d5f071e0d3f195790e3c4 -Author: Richard Gowers -Date: Wed Jan 6 19:21:07 2016 +0000 - - Added fragments - - Currently universe.fragments is hardcoded, will have to fix this later - -commit 95edafcdcd96aeb2dab2a54a4adf79198e3d9185 -Author: Richard Gowers -Date: Wed Jan 6 12:43:46 2016 +0000 - - Fixes to sphlayer selection - -commit e3ad1138beb12a34c562812012f80f5f9b6dde40 -Author: Richard Gowers -Date: Wed Jan 6 12:37:35 2016 +0000 - - Fixed workings of test_atomselections - -commit 0c80d93425f847b01457e9f356d0c03e1ec19fc1 -Merge: d91e6c712 18aefe2ed -Author: Richard Gowers -Date: Wed Jan 6 09:39:58 2016 +0000 - - Merge pull request #607 from MDAnalysis/issue-606-AtomGroup_recaching - - AtomGroup timesteps now re-cached when setting positions (closes #606) - -commit 18aefe2eda128de192fe97ab0762eef79b80dfa9 -Author: Manuel Nuno Melo -Date: Tue Jan 5 15:20:00 2016 +0100 - - Removed AtomGroup.ts caching (closes #606). - -commit d91e6c712d78bee6b788b69143b0bbcf96447727 -Merge: 0371edc6d ffe725d0f -Author: kain88-de -Date: Mon Jan 4 13:45:28 2016 +0100 - - Merge pull request #605 from MDAnalysis/issue-604-basereaderimprovements - - Fixed issue with check_slice_indices and numpy ints - -commit ffe725d0f18f3e2d0a068503031d762d4b3bde48 -Author: Richard Gowers -Date: Mon Jan 4 12:05:19 2016 +0000 - - Final docstring fixes - -commit 0371edc6dd25237350a6dea1a75079f54f6496d7 -Merge: 798f3a7eb 55bc758d9 -Author: Richard Gowers -Date: Mon Jan 4 10:39:17 2016 +0000 - - Merge pull request #580 from MDAnalysis/gro-fix-truncation - - Fixing Issue#550 - -commit de6c1d9f171ed769ce7f969b31c5e71cecd41066 -Author: Richard Gowers -Date: Mon Jan 4 09:52:13 2016 +0000 - - Fixes to doc strings in coordinates/base - -commit cb2fb7e67efd82785d2d5933ec1ea450c62982b1 -Author: Richard Gowers -Date: Sat Jan 2 22:22:59 2016 +0000 - - Quantified code fixes for Issue #604 - -commit cdcbf6e4f67c7e1c14d1ba7ca51b13832a10287e -Author: Richard Gowers -Date: Sat Jan 2 21:25:39 2016 +0000 - - Fixed issue with check_slice_indices and numpy ints - - Made base.reader.check_slice_indices public (was _check_slice_indices) - - Closes Issue #604 - - refreshed some coordinates.base docs to numpy style - - Various pep8 fixes - -commit d41aa2e9be7731332c528c64088fc8e3b569259e -Author: Richard Gowers -Date: Thu Dec 31 17:20:41 2015 +0100 - - Minor fix in core.selections - -commit 261e67669b4862a9b7f48aef861fab6057b0866c -Author: Richard Gowers -Date: Thu Dec 31 17:20:32 2015 +0100 - - Pep8 fixing in test_atomselections - -commit ca2ee7020994560b61b7c174eeb8affb2fa2d1bb -Author: Richard Gowers -Date: Thu Dec 31 17:04:23 2015 +0100 - - Fixed blank ChainIDs in PrimitivePDBParser - - Previously gave empty string (''), which doesn't work. - Now gets converted to None, and then not used later - -commit 3771882d6df465a460564c71b298298a886c0e8c -Author: Richard Gowers -Date: Thu Dec 31 10:56:04 2015 +0100 - - Fixed test_atomselection test - - GRO doesn't have segids any more - -commit 7225464c0ff672cbef5b03610043cfc36d3a2dfe -Merge: 4dc231937 d3d9a0f5e -Author: Richard Gowers -Date: Thu Dec 31 09:30:30 2015 +0100 - - Merge branch 'issue-601' into issue-363 - -commit 4dc231937338f84887a050c6596604efc84e7b39 -Merge: 5b1dac5e2 4b9acb093 -Author: David Dotson -Date: Wed Dec 30 22:24:34 2015 -0700 - - Merge pull request #602 from MDAnalysis/issue-601 - - Issue 601: AtomGroup methods from TopologyAttrs (transplants) - - Closes issue #601 - - @richardjgowers has implemented a scheme needed to accommodate methods like `AtomGroup.center_of_mass` within the context of `TopologyAttr`s, and this is done by the "transplants" mechanism. Also, the `Levels` scheme has been more solidly codified as an object that defines the relationship between the atoms->residues->segments levels that is central to the new topology system. - -commit d3d9a0f5ec0821dfd535f6d10dc52174b7e2b525 -Author: Richard Gowers -Date: Wed Dec 30 17:50:28 2015 +0100 - - Fixed a few core.selection tests - - AMBER type is now different, need tests for type_indices (but need - extensible system before that) - - GRO doesn't have types by default (they were guessed) - - GRO didn't have mass and charges before either - -commit d1a63220f8e2a1685a17e1fbdd2c8a50ccf2485c -Author: Richard Gowers -Date: Wed Dec 30 17:49:05 2015 +0100 - - A few small fixes to core.selection - -commit 4b9acb093768bdbd8679116b80c9158c0c612345 -Author: Richard Gowers -Date: Wed Dec 30 13:16:38 2015 +0100 - - Updated docs for .levels - -commit 1dd2ae15828fd43b55f94ae042c3c9f09a282aeb -Author: Richard Gowers -Date: Wed Dec 30 13:09:47 2015 +0100 - - Added core.levels - - Used to handle relationships between different levels of hierarchy in - containers - -commit 275899a6acd764a018b67eb06d6dc56334b9461a -Author: Richard Gowers -Date: Wed Dec 30 11:58:03 2015 +0100 - - Moved bonded_atoms into Bonds.transplants - -commit 3611e56afc861faafec131a10e52d0d1f17a1689 -Author: Richard Gowers -Date: Tue Dec 29 12:48:08 2015 +0100 - - Added Atom.resid property - - Transplants dictionary now defines function name itself, so that - properties can be added (properties have no __name__ attribute) - -commit d62783637fdbe502c68550b8b39a60ca2edfc403 -Author: Richard Gowers -Date: Tue Dec 29 11:17:05 2015 +0100 - - Transplant logic now applies to all new TopologyAttrs - -commit f99594a770fbe0497ccda19572b870b46c874e2b -Author: Richard Gowers -Date: Tue Dec 29 11:11:05 2015 +0100 - - Added transplant mechanism (Issue #601) - - Can define a dictionary in a TopologyAttr which relates - class name to a list of methods to attach to the class. - - Internally: - All classes are held in u._classes by their name - -commit 5b1dac5e2a330d94ce9e8deaff97ea733b976f17 -Author: Richard Gowers -Date: Sun Dec 27 15:54:09 2015 +0100 - - Added missing import from core.groups - -commit b4b9790c5b97d43f539901bf5dee4697a12fa34f -Author: Richard Gowers -Date: Sat Dec 26 18:03:07 2015 +0100 - - Fixed bug in prematurely finishing PSF files - -commit 85f8cf2ec5b37d3fd84ca49a7fd0fee93a7137d8 -Author: Richard Gowers -Date: Sat Dec 26 16:35:32 2015 +0100 - - util tests now pass - - Fixed lib.mdamath.make_whole - -commit 448f665d874949da5243f4aadcff7a031af355e3 -Author: Richard Gowers -Date: Sat Dec 26 16:35:11 2015 +0100 - - Added bonded_atoms to Atom - - Fixed get_named_atom from AtomGroup - -commit 62b56a4f59b3a98231a86c2ec9ab040f56347b03 -Author: Richard Gowers -Date: Sat Dec 26 16:34:38 2015 +0100 - - Fixed components not inheriting new attributes - -commit 7dcc0d5e96884cfd6ec9e7ee11d98cc205b03fcf -Author: Richard Gowers -Date: Sat Dec 26 14:39:16 2015 +0100 - - Moved topologyobjects tests into core - -commit 2ccea8af5e513d2361f22a5323b3ccbb930c732c -Author: Richard Gowers -Date: Thu Dec 24 17:02:41 2015 +0100 - - Fixed more tests - -commit 0197caeae9edba2d199c8f90ff459592d4551f91 -Author: Richard Gowers -Date: Thu Dec 24 17:00:06 2015 +0100 - - TopologyGroup tests now pass - -commit 90ec905a1dfcf565996bcd0d144ee3ace24b17f5 -Author: Richard Gowers -Date: Thu Dec 24 14:36:54 2015 +0100 - - Added lib.util.unique_rows - -commit 2613c128f98125b635ab1ca5b12d52fd6763271f -Author: Richard Gowers -Date: Thu Dec 24 13:35:10 2015 +0100 - - Fixed ComponentBase hash to not use .index - - Added GroupBase contains (relies on .index, only Atoms have this - currently) - -commit 2390bd187fdde9fcaceecf351552c6ac5dfa0b03 -Author: Richard Gowers -Date: Tue Dec 22 07:57:33 2015 -0700 - - Reworked topoloyobjects for new topology format - -commit e8814a0302dd3ca45b5f4f9a86f650fb822dd35d -Author: Richard Gowers -Date: Tue Dec 22 07:56:22 2015 -0700 - - Moved topologyobject tests into their own file - -commit 74d48579e15b5f808dcd9021cd3a5c1b25c1f184 -Author: Richard Gowers -Date: Tue Dec 22 07:55:42 2015 -0700 - - Fixed bond attribute getter not working for single Atom - -commit 51e1720de25041b660d2eda74a35aa48490c0d36 -Author: Richard Gowers -Date: Sat Dec 19 13:58:17 2015 -0700 - - Create core subdirectory for tests - -commit 90b9b42435abd01e07fce71942944b34bd01765a -Author: Richard Gowers -Date: Sat Dec 19 13:57:59 2015 -0700 - - Fixed lammps data parsing not creating universe - -commit fb907509a68289001890e7a19fedd5f4c15c75ee -Author: Richard Gowers -Date: Sat Dec 19 13:42:58 2015 -0700 - - Updated PDBReader docs - -commit b29464f364d505d8822501dce4b8c5a477f9527e -Author: Richard Gowers -Date: Sat Dec 19 13:29:07 2015 -0700 - - Added tests for PDBQTParser - -commit 8e6012ce83ab92ad4b5e1f53aaef1dcf01012f27 -Author: Richard Gowers -Date: Sat Dec 19 13:07:58 2015 -0700 - - Removed obsolete universe reference to Parsers - -commit 441ca4475b910eb104fcd8fa3318193ebcd04ca4 -Author: Richard Gowers -Date: Sat Dec 19 12:58:12 2015 -0700 - - Moved over old PDBParser tests - -commit 3413b221a93174e0b9a4c5b0974452be9f09335c -Author: Richard Gowers -Date: Sat Dec 19 12:47:18 2015 -0700 - - Fixed bug in wrapping resids in PrimitivePDBParser - - Added support for neither chainIDS or segids in PBD file - - Added tests for PBDParser - -commit 4a942859ec2425584a81218c76d2eff74150da31 -Author: Richard Gowers -Date: Sat Dec 19 12:29:03 2015 -0700 - - Removed obsolete tests - -commit a7811afa1f600838fadb91651410969334da33c0 -Author: Richard Gowers -Date: Sat Dec 19 12:25:41 2015 -0700 - - Made dlpoly work with Universe check - -commit 18126d467406e484b771ff273d4d365a29872116 -Author: Richard Gowers -Date: Sat Dec 19 12:22:39 2015 -0700 - - Added check that Universes can be created from Parsers - -commit 14fbeabea27ebd9c7cae74108c8927067f13d847 -Author: Richard Gowers -Date: Sat Dec 19 10:34:33 2015 -0700 - - Fixed XYZParser giving 0 segments and residues - - Added tests for XYZParser - -commit d74100945cfc76c914b77d31d0993dd1611b5e95 -Author: Richard Gowers -Date: Sat Dec 19 10:25:22 2015 -0700 - - Moved across old DLPoly Parser tests - -commit 776f65b439164c16c9d3b0102e33374de1c6c290 -Author: Richard Gowers -Date: Sat Dec 19 10:14:53 2015 -0700 - - Fixed DMSParser not stripping string values - - Moved across old DMSParser tests - -commit 87eb46073a03972c38a75e029625836e787a6bf2 -Author: Richard Gowers -Date: Sat Dec 19 09:45:18 2015 -0700 - - Moved old PSFParser tests into new tests - -commit cbddde5d5ab1bd7bd160756df34d71501bf20caa -Author: Richard Gowers -Date: Sat Dec 19 09:19:01 2015 -0700 - - Removed old hoomdxml parser tests - -commit 143658ecf87d5400f6b245243038d35477ff77d8 -Author: Richard Gowers -Date: Sat Dec 19 09:18:43 2015 -0700 - - Fixed PSFParser creating wrong sized Topology - - Added tests for PSFParser - -commit 33e81392d70eb5e48ce1c5ad2b7f5c4e7ec96c96 -Author: Richard Gowers -Date: Sat Dec 19 09:10:47 2015 -0700 - - Updated docs in PrimitivePDBParser - -commit 597e1bade88eeca628f0e5bb094e8b6abb63e138 -Author: Richard Gowers -Date: Sat Dec 19 09:10:35 2015 -0700 - - Added parser tests for XPDB - -commit 992f5fa20850b68ac3606ec28dc8b7cf53b7f300 -Author: Richard Gowers -Date: Sat Dec 19 08:51:55 2015 -0700 - - Added resnum and tempfactor reading to CRDParser - - Added basic tests for CRDParser - -commit f6a65423a096e8cee88f21f2d85979a7d0e7e812 -Author: Richard Gowers -Date: Sat Dec 19 08:42:48 2015 -0700 - - Added more DLPoly topology tests - -commit e4c76a02c1464f6c116fa0f0f70947cf3c1cb428 -Author: Richard Gowers -Date: Sat Dec 19 08:42:31 2015 -0700 - - Added detail to test failure in topology/base - -commit 11ce7630efdb531e8827a3bbb77e76d1b4768f9f -Author: Richard Gowers -Date: Sat Dec 19 08:42:10 2015 -0700 - - Fixed DMS test - -commit f0a1e2db2f44c3ccbe8575b172d8819ed7a29b5c -Author: Richard Gowers -Date: Fri Dec 18 20:13:29 2015 -0700 - - Docstring and import fixes - -commit 6703726feb4c1af2bf865d0e924144590f0ca6af -Author: Richard Gowers -Date: Fri Dec 18 19:54:59 2015 -0700 - - Cleaned up some imports in TPRParser - -commit 046b09c805f062c58eb181c69fcd5074fb851b0c -Merge: 529d89157 695436c31 -Author: Richard Gowers -Date: Fri Dec 18 18:46:55 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 529d89157c1b22335bfedc7c4f26cd8fb17c01f7 -Author: Richard Gowers -Date: Fri Dec 18 17:01:18 2015 -0700 - - Rewrote PDBParser to new format - -commit b32c66ae12c433ce8a71dd9549198d4d73f8866e -Author: Richard Gowers -Date: Fri Dec 18 16:41:50 2015 -0700 - - Rewrote GMSParser to new format - -commit f778fe382736d9c39fe3bb6245d8e363a40023e5 -Author: Richard Gowers -Date: Fri Dec 18 16:23:18 2015 -0700 - - Updated CRDParser docs - -commit a4af9f1abe53b1d82a5b9f1e59d78b4e5141165c -Author: Richard Gowers -Date: Fri Dec 18 14:36:46 2015 -0700 - - DMSParser now uses ChainIDs from core - -commit c84d3e1c48a831e6ffa49005cfeed99bd6f39fed -Author: Richard Gowers -Date: Fri Dec 18 14:30:35 2015 -0700 - - Rewrote PDBQT reading - -commit ceeb16e4b7475246a00d5ddb42f7c6b0e3b53bb9 -Author: Richard Gowers -Date: Fri Dec 18 14:30:03 2015 -0700 - - Added ICodes, ChainIDs and Tempfactors Attributes - -commit 0f7d7af6a6d34725ae635fad27b635ab7872ff32 -Author: Richard Gowers -Date: Fri Dec 18 12:40:01 2015 -0700 - - Rewrote PrimitivePDBParser to new format - -commit d0cc2a29983719dc0c6c850e58e4bfc94a85b4aa -Author: Richard Gowers -Date: Fri Dec 18 12:39:49 2015 -0700 - - Removed occupancy reading from PDB reader - -commit 8443c897b45052d72efbb53b9d40b822127f82d5 -Author: Richard Gowers -Date: Fri Dec 18 12:39:32 2015 -0700 - - Fixed typoes in occupancies and bfactors attributes - -commit 56c7774a1c323b994ce3bb16258d69fd9643b6cf -Author: Richard Gowers -Date: Fri Dec 18 10:11:01 2015 -0700 - - Rewrote lammps data topology tests - -commit 24edfaa78e119f453050adc586c42c5030143d57 -Author: Richard Gowers -Date: Fri Dec 18 09:53:47 2015 -0700 - - Rewrote data parser for new Topology format - -commit a5add5fa501b4dc3e5d9a5d5ab9455f9bc6b2381 -Author: Richard Gowers -Date: Thu Dec 17 15:39:32 2015 -0700 - - Added bonds to hoomdxml parser - -commit 361d935e565d9a00448e600954fb76debb1488f8 -Author: Richard Gowers -Date: Thu Dec 17 13:04:47 2015 -0700 - - Rewrote HoomdXMLParser to new format - - Added tests for hoomdxml format - -commit ad8882c3b89703f34950c23f5b18ffa3c2db371b -Author: Richard Gowers -Date: Thu Dec 17 11:58:24 2015 -0700 - - Rewrote MOL2Parser to new format - - Added tests for MOL2Parser - -commit 359ddf501bda256772aafa370951cef769385af4 -Author: Richard Gowers -Date: Thu Dec 17 11:58:10 2015 -0700 - - Removed unused imports from GROParser - -commit aed08e8c8f625a5504931caa83152d6b382c38d8 -Author: Richard Gowers -Date: Thu Dec 17 11:13:17 2015 -0700 - - Added tests for PQRParser - -commit c8222f97a8ce17b2197adccba48340683f9ca7ea -Author: Richard Gowers -Date: Thu Dec 17 11:03:41 2015 -0700 - - Rewrote PQRParser for new Topology format - - Removed Topology stuff from PQRReader - -commit 55bc758d93bb4f8fdf9c0048dd6d9d3c5bc590e8 -Author: Tyler Reddy -Date: Thu Dec 17 16:42:59 2015 +0000 - - Moved the test for Issue#550 to its own class and improved as discussed in the PR thread. - -commit 798f3a7eb6e9a51a63da517f31a1a99316a83ee5 -Merge: 11f87078f 23302fcba -Author: Oliver Beckstein -Date: Tue Dec 15 16:31:05 2015 -0700 - - Merge pull request #593 from MDAnalysis/autofix/wrapped2_to3_fix-1 - - Fix "Explicitly number replacement fields in a format string" issue - -commit 23302fcbad80ee33b1be7e7e38e52bb9dadbb7e1 -Author: Cody -Date: Tue Dec 15 19:37:49 2015 +0000 - - Explicitely numbered replacement fields - -commit 11f87078f53ffd9b4897e1ee92edbf84176a2b23 -Merge: 2410a4996 fe5499dff -Author: Oliver Beckstein -Date: Tue Dec 15 12:34:24 2015 -0700 - - Merge pull request #591 from MDAnalysis/autofix/wrapped2_to3_fix-2 - - Fix "Consider an iterator instead of materializing the list" issue - -commit 2410a49960493f800b633e38fa51dd8ee1a3a9d6 -Merge: 526b9db1b 02e1e5201 -Author: Oliver Beckstein -Date: Tue Dec 15 12:16:32 2015 -0700 - - Merge pull request #590 from MDAnalysis/autofix/wrapped2_to3_fix-1 - - Fix "Avoid mutable default arguments" issue - -commit fe5499dff96b33f1d9b233eb434694fef95107b9 -Author: Cody -Date: Tue Dec 15 18:50:54 2015 +0000 - - Use generator expression with any/all - -commit 02e1e5201282cf833fe8023491439111c935c80f -Author: Cody -Date: Tue Dec 15 18:46:27 2015 +0000 - - Avoid mutable default arguments - -commit 695436c3180e83b822605618a7868734d7b4d17f -Merge: e8576add1 9aad28e28 -Author: Richard Gowers -Date: Mon Dec 14 23:12:36 2015 -0700 - - Merge pull request #585 from jbarnoud/tpr363 - - Adapt TPR parser as required by #363 - -commit 526b9db1b2bd923e266f8fc81ce5386195c8948c -Merge: 6c5ea32a6 c12248c7a -Author: kain88-de -Date: Mon Dec 14 23:52:32 2015 +0100 - - Merge pull request #587 from MDAnalysis/autofix/wrapped2_to3_fix-0 - - Fix "Consider dict comprehensions instead of using 'dict()'" issue - -commit 6c5ea32a6ba29b2ac895e149fa244f857d311a50 -Merge: b01f97445 11002bb33 -Author: David Dotson -Date: Mon Dec 14 15:21:26 2015 -0700 - - Merge pull request #582 from kain88-de/coveralls - - Remove vim fileencoding hint - - This is a (possibly temporary) fix to enable coverage to successfully read all our module files. This will hopefully be fixed in coverage itself; see: - - https://bitbucket.org/ned/coveragepy/issues/453/source-code-encoding-can-only-be-specified - - for the actual bug report. - -commit c12248c7a67469e33e2fa9f980978d1a7f592b12 -Author: Cody -Date: Mon Dec 14 20:41:48 2015 +0000 - - Use dict comprehension instead of dict([...]) - -commit b01f97445084323cfc66f4bb556fb721ab2c7778 -Merge: 554edc9e7 736438c50 -Author: kain88-de -Date: Mon Dec 14 15:37:38 2015 +0100 - - Merge pull request #563 from MDAnalysis/issue/544 - - test for writing DX files from density (Issue #544) - -commit 554edc9e79e43672c66f7e382c4e4cd70e7fd830 -Merge: 4a7e3cfa8 16315e1d3 -Author: kain88-de -Date: Mon Dec 14 11:32:02 2015 +0100 - - Merge pull request #586 from MDAnalysis/autofix/wrapped2_to3_fix - - Fix "Use `is` or `is not` to compare with `None`" issue - -commit 16315e1d39569ffd2de871983c60adbdef0ab7ce -Author: Cody -Date: Mon Dec 14 09:57:46 2015 +0000 - - Use `is` operator for comparing with `None` (Pep8) - -commit 98ff2712a9cc0e9bc67e6fbbd836347b9883a7ee -Author: Richard Gowers -Date: Sun Dec 13 16:37:48 2015 -0700 - - Added type_indices to TOPParser - - Added tests for TOPParser - -commit 9aad28e281fac2ec80688acf15276b22603b17e7 -Author: Jonathan Barnoud -Date: Sun Dec 13 22:20:35 2015 +0100 - - Remove unused arguments from TPRparser - - Follows advice from quantifiedcode. - -commit e4a48ee6e6021ff2e906b26b4cf3f2f3341e8dfc -Author: Jonathan Barnoud -Date: Sun Dec 13 18:56:47 2015 +0100 - - Adapt TPR parser as required by #363 - - See #572 - - Some other changes where also done: - * `MDAnalysis/core/__init__.py` import `selection` rather than - `Selection` following the module renaming in commit - 78abe4ed10f7b4eb5ab915681cada302d48c45af - * Add messages when some assertions fail in - `MDAnalysisTests/topology/base.py` - -commit 11002bb33413493c08c2996204691615058823f4 -Author: Max Linke -Date: Sat Dec 12 20:09:02 2015 +0100 - - Remove vim fileencoding hint - - This hint seems to be responsible for coveralls failing to parse the - and report and the files. - -commit e8576add198b4ccb8597bb01eb6edcb0072581c0 -Author: Richard Gowers -Date: Fri Dec 11 17:55:28 2015 -0700 - - Rewrote TOPParser to new format - -commit 025322e706f25b2fb61daf3c94f36596ae9162f2 -Author: Tyler Reddy -Date: Sat Dec 12 15:12:25 2015 +0000 - - bigbox.gro has been replaced with a compressed version of this file, which is involved in testing resolution of Issue#550. - -commit 736438c50f16200939e2e1fefa782e00a877058f -Author: Oliver Beckstein -Date: Mon Dec 7 18:25:01 2015 -0700 - - GridDataFormats >= 0.3.2 required - - - The new release 0.3.1 of GridDataFormats contains the fix for issue MDAnalysis/GridDataFormats#21 - which is needed to fix issue #544. - - The release 0.3.2 allows importing of gridData without scipy.ndimage present - (MDAnalysis/GridDataFormats#25): this allows the minimal tests to pass - -commit 4a7e3cfa89f583ceabc314420bd9c65271b3cbd7 -Merge: e354507e9 e2065be4e -Author: Richard Gowers -Date: Fri Dec 11 18:15:24 2015 -0700 - - Merge pull request #581 from MDAnalysis/recovered_develop - - Recovered develop - -commit 39b964b8174944291dd53a696cc6ea38d3c65820 -Author: Richard Gowers -Date: Fri Dec 11 14:05:34 2015 -0700 - - Added tests for dlpoly format - -commit f21502f021e53932764be06896f031b22b3c4fdb -Author: Richard Gowers -Date: Fri Dec 11 14:05:25 2015 -0700 - - Fixed universe init breaking if no segids were present - -commit e2dc19a351b2f41c15b8622ec838f95f79b8530c -Author: Richard Gowers -Date: Fri Dec 11 13:53:42 2015 -0700 - - rewrote dlpoly parsers - -commit e49fa0d0965c7752a69e4dbc912880c1cb84f613 -Author: Richard Gowers -Date: Fri Dec 11 13:45:24 2015 -0700 - - Added Parser tests for DMS - -commit e38e042fcc5797f9b592fea5f8063780e9bb0ed7 -Author: Richard Gowers -Date: Fri Dec 11 13:37:56 2015 -0700 - - Added simple base tests for Parsers - -commit 23c46f130c216e011bd8ce9884dccc559e17ab15 -Author: Tyler Reddy -Date: Fri Dec 11 17:44:15 2015 +0000 - - Added CHANGELOG entry for fix of Issue #550. - -commit ee0da3ca40f8f6777bc58c6466a0d4e14b2ecc6f -Author: Tyler Reddy -Date: Fri Dec 11 17:39:35 2015 +0000 - - MDAnalysis now truncates atom numbers when writing .gro files with more than 99,999 atoms, in a manner consistent with genbox in GROMACS 4.6.3. Note that it appears that some GROMACS utilities (i.e., trjconv) actually write 00000 instead of 0 for the 100,000th atom. Both formats can be read in by MDAnalysis and VMD, and this is (overall) an improvement that allows us to write large .gro files in a workable manner. Fixes #550. - -commit 2819903f379cfc5e3c5d5abb50dffc6ac0e5d37e -Author: Tyler Reddy -Date: Fri Dec 11 17:31:52 2015 +0000 - - Improved the test for Issue#550 to include all lines in the coordinate file. Improved the error message. - -commit 14dc5346e416ff0a9a020936831642d481554bfb -Merge: d82fd8fe0 a65f25af6 -Author: Richard Gowers -Date: Fri Dec 11 09:06:31 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit d3b6b44cefa23d8634731ef1209d6e5a5b0d8e78 -Author: Tyler Reddy -Date: Fri Dec 11 15:16:57 2015 +0000 - - Added unit test and associated data for Issue#550. - -commit a65f25af6b0805244dc9fe5173c7f5a92afc3174 -Author: David Dotson -Date: Thu Dec 10 22:20:38 2015 -0700 - - Cuts to old AtomGroup.py of things we already have moved. - - Everything left in AtomGroup.py is stuff that has yet to be adapted into - the new class structure. Some are non-trivial. - -commit d82fd8fe0f5866a3a9e4d9b30b6a13bca99ad621 -Author: Richard Gowers -Date: Thu Dec 10 22:16:15 2015 -0700 - - Added Segment.resname selection - - Fixed various selection types - -commit f02129cbbf0fd25a05294e4dd26108681fdaa4ea -Author: David Dotson -Date: Thu Dec 10 22:11:49 2015 -0700 - - Removed force, position, velocity from old Atom. - - Narrowing down the number of things left to move over to new Atom. - -commit 5bc179996cfbd240c1466dd764195673eabf5fd0 -Author: David Dotson -Date: Thu Dec 10 22:10:14 2015 -0700 - - Moved position, velocity, and force to new Atom. - -commit 9279dda50b790e03d1769957560475535c014949 -Author: David Dotson -Date: Thu Dec 10 17:27:50 2015 -0700 - - Removed implemented elements from Atom. - - Only a few things left to move. - -commit 417efa5f616b95d29a12754cdcc730ca56cf8403 -Author: David Dotson -Date: Thu Dec 10 17:24:05 2015 -0700 - - Addition for each level now defined as concatenation. - - Can add atomgroups and atoms to get atomgroups, residuegroups and - residues to get residuegroups, etc., and order is preserved. - -commit c1f38ddc05f2c5bbb3af768facef9fe373edb238 -Author: Richard Gowers -Date: Thu Dec 10 16:50:16 2015 -0700 - - Added Segment.r150 getattr - - Fixed orselection - -commit 7aad4b63a1e73f260c2a60df67b230aa5e5ec166 -Author: David Dotson -Date: Thu Dec 10 16:45:16 2015 -0700 - - Defined Group.ix for exposing indices of Group. - - Also, hacking away at addition, subtraction, etc. - -commit 9bb627b3131bcbcc50d1729024b9ca285d5b4177 -Merge: 5aac8da74 dbabdd482 -Author: Richard Gowers -Date: Thu Dec 10 16:19:17 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 5aac8da74d5ffa2f6910d3f1738582b41b4dca4c -Author: Richard Gowers -Date: Thu Dec 10 16:19:05 2015 -0700 - - Changed API again, wooo - -commit e475aeefa16613722ba19b10e86c1571ad41aedd -Author: Richard Gowers -Date: Thu Dec 10 16:16:04 2015 -0700 - - Fixed bynum - -commit 943aa04cb80584991c8ef2661cd2284a9448f244 -Author: Richard Gowers -Date: Thu Dec 10 15:51:03 2015 -0700 - - Fixed triclinic selectaround - -commit a526913bccbc77591730c276ed39b63f5001133d -Author: Oliver Beckstein -Date: Tue Dec 1 11:00:20 2015 -0700 - - test for writing DX files from density (Issue #544) - -commit 369d00bae78179c74e40681a91c5d4718113b03b -Author: Richard Gowers -Date: Thu Dec 10 14:35:27 2015 -0700 - - Fixed bonded selection - -commit dbabdd482d466e907c254a0f56296feab95bccc4 -Merge: 770c03010 5d047657e -Author: David Dotson -Date: Thu Dec 10 14:29:17 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 770c030100b2cb7f588ddecd2c6e1fe20cecf232 -Author: David Dotson -Date: Thu Dec 10 14:28:43 2015 -0700 - - Atom, Residue, Segment each have upward and downward translation properties. - -commit 5d047657ed97d8fffcb2ba96c3519323de650087 -Author: Richard Gowers -Date: Thu Dec 10 13:32:40 2015 -0700 - - Added center_of_geometry to AtomGroup - - Fixes to selections - -commit feca9ca4037b0fa49fa1fcea4ec436d8d7e583f5 -Merge: 78abe4ed1 6fff34d49 -Author: Richard Gowers -Date: Thu Dec 10 13:20:20 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - - Conflicts: - package/MDAnalysis/core/groups.py - -commit 78abe4ed10f7b4eb5ab915681cada302d48c45af -Author: Richard Gowers -Date: Wed Dec 9 15:04:31 2015 -0700 - - Selection system overhauled - -commit e2065be4ef7d143312a632e85ee618223a0c3120 -Merge: a125286c3 50101f559 -Author: Richard Gowers -Date: Thu Dec 10 11:39:14 2015 -0700 - - Merge pull request #578 from MDAnalysis/issue-576 - - Fixes Issue #576 - -commit 50101f5594bc30fe19463d8bdb81f39f41fdf18b -Author: Richard Gowers -Date: Wed Dec 9 13:51:22 2015 -0700 - - Fixes Issue #576 - - Added fix for missing libgfortran - - Tagged persistencelength scipy tests as optional - - Removed verbose from nosetests, caused travis page to be slow to use - -commit a125286c3045bc091b7e02aa57bfad4914c98067 -Merge: e354507e9 bf75c7e8e -Author: Oliver Beckstein -Date: Thu Dec 10 10:31:59 2015 -0700 - - Merge pull request #575 from sseyler/develop - - Tests for PSA now use tempdir - - Fixes Issue #557 - -commit 6fff34d49d2d4c18671bdc2c8946a6b4adc17f93 -Author: David Dotson -Date: Thu Dec 10 01:22:30 2015 -0700 - - Working on level references in Atom, Residue, Segment. - - Need to fix some low-level breakage in TransTable involving poor - handling of single values instead of arrays. - -commit 10c9af8a05ce56999bfa6afa4362ad966f525c8f -Author: David Dotson -Date: Wed Dec 9 19:26:15 2015 -0700 - - Almost there with Atom, Residue, Segment. - - Instead of building a base class with properties and then building - Atom, Residue, and Segment classes from it, we need to build each of - these classes separately since the will only expose properties at their - native level. - -commit bf75c7e8e01f64f3bc8145fcbf954290e6225058 -Author: Sean Seyler -Date: Wed Dec 9 17:27:23 2015 -0700 - - Now using tempfile.mkdtemp() and shutil to delete - -commit 692fdf0e47f634706fe337dccaf5e73bf2ac9956 -Author: Sean Seyler -Date: Wed Dec 9 17:16:34 2015 -0700 - - Fixed typo - -commit 9716b527e1aade0a946d7768614a33dedabf5538 -Author: Sean Seyler -Date: Wed Dec 9 17:14:54 2015 -0700 - - Fixed usage of tempdir - -commit a11c5615f07aed479e396534ab97ad154121d836 -Merge: c89734b66 e354507e9 -Author: Sean Seyler -Date: Wed Dec 9 16:27:12 2015 -0700 - - Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis into develop - -commit c89734b661d32345f3302b8026c799bde96d6839 -Author: Sean Seyler -Date: Wed Dec 9 16:26:27 2015 -0700 - - Using TempDir() for testing PSA - -commit 68ba615c5a94c2f61a9df6079a82293d3c873a1a -Author: David Dotson -Date: Wed Dec 9 15:25:00 2015 -0700 - - Small fixes. - -commit 7c991d403c9158e319aa96c351d763ef0fe515df -Merge: cddaf72ca cbacc03a8 -Author: David Dotson -Date: Wed Dec 9 15:09:16 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit cddaf72caebf4a6657d2012b9eacb539cf6ae528 -Author: David Dotson -Date: Wed Dec 9 15:08:52 2015 -0700 - - Moved positions, velocities, and forces into new AtomGroup. - -commit cbacc03a8cd946f56855ef40d3330a37fc049612 -Author: Richard Gowers -Date: Wed Dec 9 14:26:16 2015 -0700 - - Moved select_atoms into AtomGroupBase - -commit 00195c857f9a01f86ae49a55945c1bd1c27ea843 -Author: David Dotson -Date: Wed Dec 9 13:52:43 2015 -0700 - - Fix to GRO parser keywords to Topology. - -commit e354507e91c2f33c8dd5b659c6653c7530dfa4da -Merge: 29031fe2f 7b381aaaa -Author: Oliver Beckstein -Date: Wed Dec 9 12:25:57 2015 -0700 - - Merge pull request #528 from cyanezstange/develop - - add ZeroDivisionError exception to WaterOrientationRelaxation class - - Detailed rationale for the fix: @alejob thinks that the solution is a good option, because - the problem is generated when in time t and in time t + dt there aren't repeated molecules - (and/or when there aren't molecules in the selection), so one can't evaluate time - correlation. Usually in very small selections we have this problem that there aren't repeated - molecules in t and t + dt. With ignoring the division by zero we are just removing one point - from the mean. This final mean is one point in our output graphic. So, for instance, instead - of calculate the mean with 1000 points, we would calculate this mean with 994 points (6 zero division). - - A user shouldn't select a so small group of atoms to run this analysis, but if he decides to make it, - we have this solution. - -commit 29031fe2fde7205789efe8f44b3987a82e4036be -Merge: afb6e8d4c 5362bd568 -Author: Richard Gowers -Date: Wed Dec 9 10:08:04 2015 -0700 - - Merge pull request #460 from MDAnalysis/feature-polymers - - Feature polymers & analysis base - -commit afb6e8d4c01ec2ecd15c5d990d5808e130a184fd -Merge: 05fdf570c 94d940e30 -Author: Richard Gowers -Date: Wed Dec 9 10:05:34 2015 -0700 - - Merge pull request #573 from jbarnoud/issue-564 - - Use new-style Python classes - -commit 7b381aaaaadaf0bf51b356c3f56c802973cae837 -Author: Carlos Yañez -Date: Wed Dec 9 12:49:32 2015 -0300 - - Add comment to fix in WaterOrientationRelaxation class - -commit 94d940e304fd29a83281b7d3021a9f81adae5b88 -Author: Jonathan Barnoud -Date: Wed Dec 9 12:05:32 2015 +0100 - - Use new-style Python classes - - Fix #564 - -commit acfd15e2b680c9d0bb968bbb01f266c79f29860e -Author: David Dotson -Date: Wed Dec 9 02:13:50 2015 -0700 - - Small fixes, plus add_TopologyAttr method for Universe. - - We can now easily add TopologyAttrs to a Universe dynamically! - -commit 74e3b760c0dac8806f488c69d4e697592c5f3f5d -Merge: 440d8e1a9 d4742f3bb -Author: Richard Gowers -Date: Tue Dec 8 22:22:12 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 440d8e1a94927d508b22842d3e1007829ab84118 -Author: Richard Gowers -Date: Tue Dec 8 22:22:01 2015 -0700 - - Rewrote GMSParser to new format - - Issue #572 - -commit d4742f3bbb289b77c986153794e0b93ca1831a34 -Author: David Dotson -Date: Tue Dec 8 19:56:57 2015 -0700 - - More stuff cut from old AtomGroup. - -commit ca8c5adc1489c75a4a9762a753be0115d883ee4b -Author: David Dotson -Date: Tue Dec 8 19:04:26 2015 -0700 - - Still moving things into new Groups from old groups. - - Also some more needed touches on Atomindices, Resindices, Segindices. - Topology should now build automatically with these included. - -commit 33a18abd2be521e52de10d194b327e513841ced2 -Merge: 2531d531b f0b559830 -Author: David Dotson -Date: Tue Dec 8 18:10:21 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 2531d531bcaa35f42d48a8b5b129072a30376828 -Author: David Dotson -Date: Tue Dec 8 18:07:17 2015 -0700 - - Finished Atomindices, Resindices, Segindices. - - Also added .atoms, .residues, .segments to Groups, which are now defined - as giving Groups that are themselves *sets*: they have no repeated - elements. Without this being the case, they are not really that useful. - -commit f0b5598300f261ae7d99f2e907efcd36d34d73f9 -Author: Richard Gowers -Date: Tue Dec 8 17:36:13 2015 -0700 - - Bonds Angles and Dihedrals now work! - -commit e8fe566f822dc00db374eeb3c6facf5d89342ecf -Merge: 614038b3a c6700857b -Author: David Dotson -Date: Tue Dec 8 17:34:57 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 614038b3acdaeb6729d279fcdfcb67e4830012e1 -Author: David Dotson -Date: Tue Dec 8 17:33:38 2015 -0700 - - Hammering away on adding ad-hoc methods to AtomGroup. - - Also, implemented Atomindices, Resindices, and working on Segindices for - referencing the unique identifiers for each level. - -commit c6700857b221efce7531590e13976ada5d16b895 -Author: Richard Gowers -Date: Tue Dec 8 17:25:53 2015 -0700 - - reworking TopologyGroups - - TopologyAttribute.get_atoms get_residues and get_segments now take a - Group rather than the indices of the group - -commit 05fdf570c05daf3d46fe7e23aec61064ebe219ab -Merge: 80ec06ca5 935d36c99 -Author: kain88-de -Date: Tue Dec 8 20:10:53 2015 +0100 - - Merge pull request #570 from jbarnoud/matrix-PR - - Travis run the test in minimal and full config - -commit 935d36c990f7182b47692620e4bade6a6636680e -Author: Jonathan Barnoud -Date: Tue Dec 8 17:20:52 2015 +0100 - - Reduce the travis matrix - - Remove the build with full install and no cythonize as suggested by - @kain88-de in #570. - -commit ec83083e59dac592b41bc54f660355631d6fe5ae -Author: Jonathan Barnoud -Date: Tue Dec 8 08:56:20 2015 +0100 - - Move env section to the top of travis.yml - - This makes the file easier to understand as a reader see where the - variable come from before they are used. - -commit d6a017cdeebb172e9e85359a183135e609df0d4d -Author: Jonathan Barnoud -Date: Tue Dec 8 08:32:33 2015 +0100 - - Travis do not install cython for the minimal setup - -commit 0e21c10d76c2155411d44a17ed4f3f502681e57e -Author: Jonathan Barnoud -Date: Tue Dec 8 08:26:24 2015 +0100 - - Cleanup the build matrix - - Build the full setup with and without cythonize; build the minimal setup - only without cythonize. - -commit 90188bf9dabc088a7688b5df90ec18348d036364 -Author: Jonathan Barnoud -Date: Mon Dec 7 21:28:01 2015 +0100 - - Increase test timeout on Travis - - Tests often fail in ways that seem related to timeout issue. Indeed, - Travis can be slow sometime. This commit increases the timeout for tests - from 120 seconds to 300 seconds. - -commit 1327b5bc4bfc98eaaf04ea04c936d5bbf62a41d8 -Author: Jonathan Barnoud -Date: Mon Dec 7 19:26:54 2015 +0100 - - Travis run the test in minimal and full config - - This commit asks Travis to run the tests twice: once with all the - requirements installed (SETUP=='full'), and once with none of the - optional dependencies installed (SETUP=='minimal'). - - Note that the minimal setup, runs without the MKL as the conda mkl - package pulls scipy with it. - -commit 98f631b81754a5c3968f284411d5a40521471515 -Author: Richard Gowers -Date: Mon Dec 7 21:47:22 2015 -0700 - - Updated CRD and XYZ Parsers - -commit 80ec06ca507843b915793fab32216bb625a247d5 -Merge: e203b806a 427816042 -Author: Richard Gowers -Date: Mon Dec 7 19:34:45 2015 -0700 - - Merge pull request #568 from jbarnoud/testdep - - Skip tests if scipy or NetCDF are missing - -commit fb49cd4f8d54521f2a5c74f0a2d0ad8ac55ab8d7 -Author: Richard Gowers -Date: Mon Dec 7 17:37:27 2015 -0700 - - Added Bond topology Attrs - -commit 2c5549e525a4d7161a1dc9d7daaf416bf068c3bf -Merge: 38c4d434a ec9e53f94 -Author: Richard Gowers -Date: Mon Dec 7 16:46:07 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit e203b806ad6ef16184bc5ff44da0f9b8dfec0035 -Merge: 1a8047d29 e555a616c -Author: Richard Gowers -Date: Mon Dec 7 16:42:11 2015 -0700 - - Merge pull request #560 from kain88-de/force-cythonization - - Force recompilation of cython files - -commit 38c4d434ac0aca8731fd82bbdc998b9c916fa4fb -Author: Richard Gowers -Date: Mon Dec 7 16:40:00 2015 -0700 - - Added basic GROParser tests for new GROParser - -commit ec9e53f94528a7e35a4cf0e72e9c2d1661a9d8f5 -Author: David Dotson -Date: Mon Dec 7 16:17:15 2015 -0700 - - Todo small fix. - -commit e555a616c73bae5a64230c0fbd36f5848a102fb0 -Author: Max Linke -Date: Tue Dec 8 00:10:16 2015 +0100 - - be verbose on package installation - - we want to check if the cythonization is happening. - -commit 62b13f901b22eb3fcbfac29763fa09d33d2446ac -Author: Max Linke -Date: Tue Dec 8 00:02:05 2015 +0100 - - test cythonization and c-files - - use a matrix-build on travis now. - -commit 8c5fc19ced9bc6fbab3133f77dd1e73545d8e351 -Author: David Dotson -Date: Mon Dec 7 15:45:31 2015 -0700 - - Added todo for TopologyAttr checking. - -commit 59de74526d8d586208cd2180a2d1334b82de71f7 -Author: kain88-de -Date: Fri Dec 4 13:25:52 2015 +0100 - - Change find regex - -commit 3334a0acce42117b9156974d05f7aa32bd4a196d -Author: Max Linke -Date: Fri Dec 4 01:43:45 2015 +0100 - - Force recompilation of cython files - - touching them should be enough. - -commit db4110d8a8ed544b4359b004b267d0b3d122afeb -Author: David Dotson -Date: Mon Dec 7 15:36:53 2015 -0700 - - Added 'singular' attribute to all TopologyAttrs. - - This gives us what we need for property names in Atom, Residue, and - Segment objects. - -commit 1a8047d298e15d3d59dc0a2c14149d9aaa091e13 -Merge: 5a3d2b3c5 50f36e180 -Author: Oliver Beckstein -Date: Mon Dec 7 15:31:35 2015 -0700 - - Merge pull request #569 from kain88-de/fix-cython-modules - - Cython modules should have same name as source - -commit 50f36e18060e5f1379ad6fcc6966329a07c39f39 -Author: Max Linke -Date: Mon Dec 7 21:23:09 2015 +0100 - - Cython modules should have same name as source - - This seems to be an implicit assumption in cython. With this the import - errors about non existing init-functions in the cython modules is gone. - - Update docs as well - -commit 743d6c9091558159212cc7369a5060f893fc7db5 -Author: Richard Gowers -Date: Mon Dec 7 15:08:32 2015 -0700 - - Removed level from Groupbase - -commit 8c32ec5e0aecaa4bb400acf31b5c00863000a6b5 -Merge: 997667639 f5af13a0e -Author: David Dotson -Date: Mon Dec 7 15:01:04 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 997667639c376da3385d09402835a6647a5c8855 -Author: David Dotson -Date: Mon Dec 7 15:00:09 2015 -0700 - - Other fixes. - -commit f5af13a0e400ab79aa1d7ad60fe3ead8ba58085b -Author: Richard Gowers -Date: Mon Dec 7 14:59:00 2015 -0700 - - *GroupBases now are mixins - -commit e90ae2d321906d51fe4d40bd0de0db4d6928f877 -Merge: fb66c84a5 4519309ad -Author: Richard Gowers -Date: Mon Dec 7 14:57:35 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit fb66c84a5ca61714e46233a98759ea21309623c0 -Author: Richard Gowers -Date: Mon Dec 7 14:57:20 2015 -0700 - - Changed Topology._attrs to .attrs - -commit 4519309ad6d49c29753a37740e98564796d0b28b -Author: David Dotson -Date: Mon Dec 7 14:52:44 2015 -0700 - - Fixed copy-paste neglects. - -commit af5686de3931a60f046cc805c23da635610dd245 -Author: David Dotson -Date: Mon Dec 7 13:00:09 2015 -0700 - - Added make_group and make_levelgroup methods for Universe use. - - A Universe builds its own Group class based on what is present in the - Topology, then builds AtomGroup classes based on this base class. This - allows TopologyAttrs to be added to the Universe after-the-fact and be - propagated to all the *Group objects, even existing instances. - -commit 427816042f21739beb50186428faa4ba042d465b -Author: Jonathan Barnoud -Date: Mon Dec 7 18:59:54 2015 +0100 - - Skip tests using netcdf when netcdf is missing - -commit 6c531e254a9a964c443c7eb9cc0219426bbb24cb -Author: Jonathan Barnoud -Date: Mon Dec 7 18:52:34 2015 +0100 - - Skip the tests that use scipy if scipy is missing - - Some tests requires scipy. Scipy is an optional dependency, so it can be - missing leading to the tests to fail. - - This commit decorate the tests that need scipy with the dec.skipif - decorator. This follows the guideline discussed in #124. - -commit 04a14e77bffb8262ab75a588129e8356b5a08555 -Author: Richard Gowers -Date: Mon Dec 7 12:24:28 2015 -0700 - - Renamed Group to GroupBase etc - -commit d992b422ef32fdf47e5968f430751cb5d5ebb5e3 -Author: Richard Gowers -Date: Mon Dec 7 11:41:14 2015 -0700 - - Dynamically adding in attributes - -commit 48e5a6b121eb58a7b99489318a7c9b708e9f69a1 -Author: Richard Gowers -Date: Mon Dec 7 08:34:40 2015 -0700 - - descriptor approach to attributes - -commit dc5c8e8edb37bd058f7acd05f170d1104da8ae6d -Author: Richard Gowers -Date: Sun Dec 6 09:52:30 2015 -0700 - - Fixed coordinatefile missing in init - -commit 880547813a1cdd4bbfdea984608f00ef4c113316 -Merge: 979b47f6c 8bf26ebb3 -Author: Richard Gowers -Date: Sun Dec 6 09:28:42 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 979b47f6c367f0b545996c04a9b498a6c447a84c -Author: Richard Gowers -Date: Sat Dec 5 22:55:55 2015 -0700 - - reworked squash_by and remap id, now one function - - Added first draft of new PSFParser - - Added Segid and Atomtype topology attribute - - Added id to SegmentGroup - -commit 8bf26ebb30ebca2a33d9c86eabaa32265866fe27 -Author: David Dotson -Date: Sat Dec 5 20:54:45 2015 -0700 - - Reverted absolute imports; added getters and setters to groups. - -commit 63037c1ec38134614772438ca240e8794aaeb1c5 -Author: David Dotson -Date: Sat Dec 5 18:30:32 2015 -0700 - - Been hacking away at our new Universe, and trying to fix imports. - - Importing the module is broken at the moment, but we're getting there. - Most of what I've done here is to trim out anything that looked like it - needed major rethinking in Universe, especially the various caching it - was doing. My main goal was to cut as much as possible so we can focus - clearly on what Universe needs to do. In particular, I think Universe - should *not* store any kind of state on its own, but instead all its - state information is in its attached objects, specifically its Topology, - and trajectory Reader. We plan to rethink how bonds, angles, dihedrals - are done as well, so cut those for the moment, too. - - At the end of all this, we should have very minimal API differences. - Things that were deprecated long ago should finally disappear, I think, - to make room for clear changes we are making internally to make - MDAnalysis more internally consistent. - -commit 24a8f4d72de6b787c512fa472e96fc84083b746d -Author: David Dotson -Date: Fri Dec 4 23:55:50 2015 -0700 - - Move TransTable with Topology object. - -commit 2a674f64bb3824fdd45e13656202ae0c80ba7df0 -Author: David Dotson -Date: Fri Dec 4 23:53:02 2015 -0700 - - Tests complete for existing TopologyAttrs. - - Currently we see a failure for TestResids, because the move method for - atoms is not yet implemented in TransTable. - -commit 48eb0201cc0821a8719f8410b02b08fa49a0831d -Author: David Dotson -Date: Fri Dec 4 22:53:27 2015 -0700 - - Tests for AtomAttr, ResidueAttr, SegmentAttr complete. - -commit 13657f2e22d19416429b7133f7d5a58856bf1528 -Author: David Dotson -Date: Fri Dec 4 22:10:45 2015 -0700 - - Tests written pass. - - Now on to the rest of the TopologyAttrs. - -commit 2a714fc46f9ff9e5643a7a34982469cebca2b91d -Merge: a0a3c7d80 6042cc209 -Author: David Dotson -Date: Fri Dec 4 21:35:34 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit a0a3c7d80a6451f91ef77cfa3ee5adfcab0297c6 -Author: David Dotson -Date: Fri Dec 4 21:35:15 2015 -0700 - - Hacking away on topologyattr tests. - -commit 5a3d2b3c5be347fbbed7c759d5c0061106c02060 -Author: Oliver Beckstein -Date: Fri Dec 4 17:56:02 2015 -0700 - - fixed import naming collision in test_atomgroup (quantifiedcode) - -commit 6042cc209042b65878e20f9b98a168daad9a6d27 -Author: Richard Gowers -Date: Fri Dec 4 17:34:47 2015 -0700 - - Created new style Universe - - Currently only works loading a gro file - -commit d8ef1addf51b0ee5e8725225f60fdb7808bdf8d0 -Author: Richard Gowers -Date: Fri Dec 4 16:05:26 2015 -0700 - - Rewrote remap ids - -commit 26461a430098a6d90592f69c2a4240033fffa1fd -Author: Richard Gowers -Date: Fri Dec 4 15:45:08 2015 -0700 - - Added tests for TransTable.s2a - -commit 4806bc9feccd58c77c02cff34ed637353ca0b0d8 -Merge: d97920637 184a8bb40 -Author: Richard Gowers -Date: Fri Dec 4 15:39:27 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - - Conflicts: - testsuite/MDAnalysisTests/test_transtable.py - -commit d979206375dfd36e25cd989d21b2753af3b9dad8 -Author: Richard Gowers -Date: Fri Dec 4 15:37:18 2015 -0700 - - Removed sparse matrix implementation of TransTable - -commit 184a8bb401823342a7fb39fed3ebc2dd6595dcf7 -Author: David Dotson -Date: Fri Dec 4 15:35:13 2015 -0700 - - Filled in more of Topology test class. - - Still just a skeleton. - -commit 9cbd2733c11dd35b8dd52ab15ac5beb97207d13f -Author: David Dotson -Date: Fri Dec 4 15:09:11 2015 -0700 - - Moved some tests around for new topology objects. - -commit 85fdbef1442290c5a774166600a47fefb78b2e8a -Author: David Dotson -Date: Fri Dec 4 14:57:53 2015 -0700 - - Added placeholder __init__.py for tests/topology - -commit 890ec7afee737e6d09ceb142db6c13bfba2b3483 -Author: David Dotson -Date: Fri Dec 4 14:27:26 2015 -0700 - - Refactor of topologyattrs for less repeated code. - -commit c3ffe0739b0a41d250cdc41b365719b2de9def84 -Author: David Dotson -Date: Fri Dec 4 12:02:03 2015 -0700 - - Removed outdated notes from transtable. - -commit 533aceb2200ad20c92a2c375b6055db838f785fe -Author: David Dotson -Date: Fri Dec 4 12:01:03 2015 -0700 - - Added boilerplate to transtable. - -commit 5ea11e36fcfe2ed2549f6781a7d02c31b36a14e9 -Merge: acf686b7b e5556a19d -Author: David Dotson -Date: Fri Dec 4 10:23:37 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit acf686b7bc28b0f69080dce9d7f3d832dd33907b -Author: David Dotson -Date: Fri Dec 4 10:23:05 2015 -0700 - - Refined transtable docs. - -commit e5556a19d9da9e3f6fb13306cd00f43fe95dc911 -Merge: 88028cd2f 88c30f5c7 -Author: Richard Gowers -Date: Fri Dec 4 10:20:41 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 88028cd2fcf8f739731bb7d924d2c4386536cf14 -Author: Richard Gowers -Date: Fri Dec 4 10:08:34 2015 -0700 - - Prototype for new Groups - -commit 88c30f5c7655544d283691847a6a5963bfe5640b -Author: David Dotson -Date: Fri Dec 4 10:01:58 2015 -0700 - - Moved docstrings for TransTable methods out of Topology. - - Generally just cleaning up. - -commit b47596b69b72f5af088d4ec2b12cdb6e0dcc2dd9 -Merge: b7a143d2d dbc339987 -Author: kain88-de -Date: Fri Dec 4 13:36:20 2015 +0100 - - Merge pull request #561 from jbarnoud/issue-541 - - Fix #541 - -commit dbc33998754c838f2ea9ed551c0f607ca0d78758 -Author: Jonathan Barnoud -Date: Fri Dec 4 11:57:06 2015 +0100 - - Fix #541 - - Import `__builtin__` or `builtins` depending of the version of python. - This avoid having a misleading message about numpy missing when one - tries to install MDAnalysis under python 3. - - Whith this change, MDAnalysis can get install under python 3. Once - installed, MDAnalysis does not work, though. - -commit 8913d3d7d6db0c2bd519a8a18491bf5d580d4bb4 -Merge: 0838712b0 d5eafbe3f -Author: David Dotson -Date: Thu Dec 3 21:41:35 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 0838712b026cb4f09b6c2c5efeb1b3613c42212b -Author: David Dotson -Date: Thu Dec 3 21:35:02 2015 -0700 - - Re-added Atomnames getters for residues and segments. - - These don't make much sense for use with a number of residues/segments, - but they do make sense for single residues/segments, so we keep them - available. How they are ultimately used are up to the Universe *Group - methods anyhow. - -commit d5eafbe3f0d0768487f8dbfffe6745550a4c797d -Author: Richard Gowers -Date: Thu Dec 3 18:52:53 2015 -0700 - - More fixes for Topology - -commit 84a12c7706850906ffd6cc0868c6d0d346dc1cf6 -Author: Richard Gowers -Date: Thu Dec 3 18:41:33 2015 -0700 - - More super fixes - -commit bf0fffd5fc67e65b58e16e5b095d76d30252d04f -Merge: 8483c5b4c 977c93fe7 -Author: David Dotson -Date: Thu Dec 3 18:39:38 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 8483c5b4c7e893eac6b3903622c8ae848439201c -Author: David Dotson -Date: Thu Dec 3 18:39:23 2015 -0700 - - Stupid super fixes. - -commit 977c93fe75b5079feee2864a0fab2dee94a33f46 -Author: Richard Gowers -Date: Thu Dec 3 18:36:23 2015 -0700 - - Fixed Resnames object - - Fixed Topology signature - -commit fde2522780753b9d2b98ff55507cd7a1e45d5ecb -Merge: aafa9dd64 0f3df0b66 -Author: Richard Gowers -Date: Thu Dec 3 18:33:00 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 0f3df0b66ba684224c05c1ebdc6f86ef23ba2754 -Merge: a6657e62b 28a598178 -Author: David Dotson -Date: Thu Dec 3 18:31:16 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - - Also finished (but untested) topologyattrs needed for GRO parser at - minimum. - -commit aafa9dd6448b486da56b6964655bf711ad2b1392 -Author: Richard Gowers -Date: Thu Dec 3 18:20:19 2015 -0700 - - Added remap ids function to topology/base - - Reworked GROParser for Attribute style - -commit b7a143d2ddfd832b441c1beaf168560f0a8f65f5 -Merge: f1345fafd 64ee221b8 -Author: Oliver Beckstein -Date: Thu Dec 3 17:39:37 2015 -0700 - - Merge pull request #559 from kain88-de/cythonize - - Use cythonize to compile cython files - -commit 64ee221b8f9d24e04388e6bbdffd9251b7ec44a8 -Author: Max Linke -Date: Fri Dec 4 00:57:24 2015 +0100 - - Use cythonize to compile cython files - - I experienced some errors in the cython compilation in other branches - when I experiment and do more advanced stuff. This helps to get clean - compilations from cython. - -commit 28a5981786fe6fd8d00cea89a06f2b02138024b0 -Merge: db4779787 83e06f7f5 -Author: Richard Gowers -Date: Thu Dec 3 14:56:34 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit db47797872d09c462ac0f97d33af05d88f709c4d -Author: Richard Gowers -Date: Thu Dec 3 14:55:41 2015 -0700 - - Added tests for transtable! - -commit a6657e62b3fa85c7f46177a5e012eb7190eecfe2 -Author: David Dotson -Date: Thu Dec 3 14:54:37 2015 -0700 - - Hammering on Resids. - - Resids.set_atoms actually reassigns the atoms to different residues. At - the moment the residues must exist already in order for this to work; an - exception is raised if atoms are being assigned to non-existent - residues. This is also a slow operation, because we have to translate - the resids the atoms are being assigned to to the corresponding - resindexes, which are used to slice residue arrays. We are fine with - setting to be slow so long as getting (reading) is fast, however. - -commit 83e06f7f5a4c3d8fe957621799d09ba5d78a6036 -Merge: 738fd2a2f 30019679c -Author: David Dotson -Date: Thu Dec 3 13:52:58 2015 -0700 - - Merge branch 'issue-363' of github.com:MDAnalysis/mdanalysis into issue-363 - -commit 738fd2a2fe983c32bfc4407333e76943611d3e1f -Author: David Dotson -Date: Thu Dec 3 13:50:22 2015 -0700 - - Settled question on residue, segment non-membership. - - An atom must be a member of a residue, and a residue must be a member of - a segment. This has the consequence that there is at least 1 residue and - 1 segment in the system. We conclude that this should work fine. - -commit 30019679cba319c69ea9feb3062fccf0cd6c2c73 -Author: Richard Gowers -Date: Thu Dec 3 13:09:21 2015 -0700 - - Added the fantabulous transtable - -commit 5362bd568d08efb5334516f2b67b4dd627c36e7c -Author: Richard Gowers -Date: Thu Dec 3 09:02:38 2015 -0700 - - Finalised changes for analysis.rdf and analysis.polymer - -commit 76a0bc6cc6b192495d235ce9cd2611a0a4085362 -Author: David Dotson -Date: Wed Dec 2 23:41:06 2015 -0700 - - Hammering on Resid TopologyAttr. - - This is a bit tricky. At the moment we've decided that an atom can be a - member of one or zero residues, but this presents a problem when - building the atom membership array: what constitutes no membership? - Perhaps there should always be at least one residue and segment in any - topology (index 0 in the residue and segment tables), with every atom - belonging to this by default until switched to another? - - What problems does this solution present? - -commit ef837059b2d00a48596b3cf327e4282f5908c18e -Author: David Dotson -Date: Wed Dec 2 22:31:16 2015 -0700 - - Finished Masses TopologyAttr. - -commit f1345fafd26dbc84b316774b753ecce468179c4a -Author: Oliver Beckstein -Date: Wed Dec 2 22:16:19 2015 -0700 - - finalized fix of #556 (test failure due os.chdir/tempdir) - - - use tempdir.in_tempdir() in test_hole.py - - added Hai Nguyen to AUTHORS and sphinx/source/conf.py - (for #558) - -commit d424ccf9e4a522e756dea74839f00e7f95d9871d -Merge: c20485780 370c72138 -Author: Oliver Beckstein -Date: Wed Dec 2 22:04:35 2015 -0700 - - Merge pull request #558 from hainm/issue556 - - Fixes #556 (do not use os.chdir() but instead use tempdir context managers) - -commit 6b00adf558d068a92be6f8a886f7c7bc1a49a05f -Author: David Dotson -Date: Wed Dec 2 22:01:16 2015 -0700 - - Topology object mappings set up. - - The Topology object keeps arrays giving the mappings of atom membership - in residues, residue membership in segments, and the necessary sparse - matrices to efficiently go the other direction. We now have a set of - accessors for converting between one set of indices to another, which - will often be needed by TopologyAttr methods. - -commit 79f83847fa12454f48a950ba147ca2e5d519fd8e -Author: David Dotson -Date: Wed Dec 2 21:43:09 2015 -0700 - - Hacking away at Topology + TopologyAttrs. - -commit 370c72138f133bcf5e8f7860c547f53ebb09a081 -Author: Hai Nguyen -Date: Wed Dec 2 21:02:55 2015 -0500 - - use context - -commit 5ac4dd5eec47b2a5a7d1f9b245f5758df2fd1ad0 -Author: Hai Nguyen -Date: Wed Dec 2 19:00:16 2015 -0500 - - dirty fix for issue 556 - -commit a96314aeab41a06be985882881584944f158bb76 -Author: David Dotson -Date: Wed Dec 2 14:13:30 2015 -0700 - - Building out generic TopologyAttr. - - We want to be able to construct Topology objects with attribute - handling, such as masses, charges, resids, etc., handled by individual - TopologyAttr objects. A topology parser will parse its file, build a - number of arrays to be fed to, say, Masses, Resids, Charges objects, and - then feed these to a Topology object. The Topology object can then be - given to a Universe as the core object for accessing and modifying the - topology. All the complexity of managing the arrays that contain - topology information is encapsulated inside the Topolgy object and its - TopologyAttrs. - -commit c2048578024381890530b609ab5050f47e7527a4 -Author: Oliver Beckstein -Date: Wed Dec 2 11:26:45 2015 -0700 - - rewrote parts of NCDF float32 test - - - use explicit test for dtype - - possibly related to issue #551 - -commit c2d39e66792cb3179b6be992efe99bbac947831f -Merge: 833aa5daf 9d56a863e -Author: Carlos Yañez -Date: Wed Dec 2 10:48:38 2015 -0300 - - Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis into develop - -commit f0884b65579da8827ca2ad4643ad08e9ddb84ca7 -Author: Richard Gowers -Date: Tue Dec 1 16:44:12 2015 -0700 - - Topology object now sorts data into Levels - - Sized dict to make sure all data is of correct size - -commit bb47eba560a9ab8176df801e215cbd0a5c9141b9 -Author: Richard Gowers -Date: Tue Dec 1 16:13:20 2015 -0700 - - Added squash_by function to merge Residue attributes on a resid basis - -commit b2c8a71887add057f056d9d3f121e19e53320edc -Author: Richard Gowers -Date: Tue Dec 1 15:06:13 2015 -0700 - - First draft of newstyle parser and Topology - -commit 9d56a863eb3ba2d9b52c18358ec005a6d6f0c1de -Merge: 0c3aa90cf bb42979f5 -Author: Oliver Beckstein -Date: Tue Dec 1 14:59:19 2015 -0700 - - Merge pull request #553 from MDAnalysis/issue/552-no-analysis-tests - - include analysis tests into MDAnalysisTests - -commit bb42979f5676aae2151ebfc03a121cb2ccca8b0d -Author: Oliver Beckstein -Date: Tue Dec 1 14:31:18 2015 -0700 - - include analysis tests into MDAnalysisTests - - - needed analysis/__init__.py so that setup.py would automagically add the - package directory - - closes #552 - -commit daac9993f0a441422235d6200099baebbf8730fa -Author: Richard Gowers -Date: Mon Nov 30 14:06:53 2015 -0700 - - Added tests for AnalysisBase - -commit de72c298379210c44649d725afb02e8562f09949 -Merge: e8c755fde 0c3aa90cf -Author: Richard Gowers -Date: Mon Nov 30 13:11:23 2015 -0700 - - Merge branch 'develop' into feature-polymers - - Conflicts: - testsuite/MDAnalysisTests/datafiles.py - -commit e8c755fded638e0488e47785fcd3e6203563c440 -Author: Richard Gowers -Date: Mon Nov 30 13:03:48 2015 -0700 - - Added basic tests for InterRDF - -commit d84019f0050c562ce716c6b26974c11e82009fa9 -Author: Richard Gowers -Date: Mon Nov 30 11:37:26 2015 -0700 - - Fixes to InterRDF - -commit 0c3aa90cf0a748642a9aab5e50562ca1b9fedc18 -Merge: 82ce412a0 4fa0e6569 -Author: kain88-de -Date: Mon Nov 23 20:35:18 2015 +0100 - - Merge pull request #549 from MDAnalysis/issue-548 - - Issue 548 - -commit 4fa0e6569ee5ceb7f1d76f4cb8bf53e75dfe14a1 -Author: Richard Gowers -Date: Mon Nov 23 10:31:37 2015 -0700 - - Fixes for Issue #548 - - GROParser now doesn't read infinitely, but only the number of atoms - stated in the top of the file. - -commit 09c03f46fc64156c4c62b3795fb9dcd3137b1171 -Author: Richard Gowers -Date: Mon Nov 23 10:23:00 2015 -0700 - - Added tests for Issue #548 - -commit 82ce412a0d44c1a10ade4f698b80acb73fd31fc6 -Merge: 06ec4b64a af372016f -Author: kain88-de -Date: Thu Nov 19 19:55:10 2015 +0100 - - Merge pull request #547 from MDAnalysis/feature-betterdata - - Feature betterdata - -commit af372016f08134ea66d42cdfa3f931174bac5e74 -Author: Richard Gowers -Date: Wed Nov 18 21:35:47 2015 -0800 - - Fixed missing test files - -commit 06ec4b64a379fed89b5d6b014dc9095b826e2afe -Merge: 0995e0485 1475048f8 -Author: Oliver Beckstein -Date: Wed Nov 18 22:28:00 2015 -0700 - - Merge pull request #546 from sseyler/develop - - Added citation for PSA in docs. - - Closes Issue #545 - -commit fffb5d51fbd3a06d61adba12cd7836e229ce73d4 -Author: Richard Gowers -Date: Wed Nov 18 13:20:29 2015 -0800 - - Removed stray line - -commit 4954d80a2beb5cc30f7588614898099c7277517c -Author: Richard Gowers -Date: Wed Nov 18 13:17:14 2015 -0800 - - Finished improving lammps data parsing - -commit 8750d049b6c8ecfe2104b565f0a18004baa1a96a -Author: Richard Gowers -Date: Wed Nov 18 13:14:56 2015 -0800 - - Added tests for triclinic lammps data - -commit 2c3cb2b8cf5035be910464a1ea1f4d1191db2a03 -Author: Richard Gowers -Date: Wed Nov 18 13:12:07 2015 -0800 - - Fixed lammpsparser not liking compressed formats - -commit e54bc855370454979e42468fe873e63f20a7b8c0 -Author: Richard Gowers -Date: Wed Nov 18 12:58:43 2015 -0800 - - Added more tests for lammps topology - - Should now properly cover C++ versions of lammps data files - -commit 1475048f820962a543c125f78d45e766a625c080 -Author: Sean L. Seyler -Date: Wed Nov 18 13:22:09 2015 -0700 - - Tweak to PSA citation - -commit 3574c9c85b7aaa7d4283e93020b726303c6f7673 -Author: Richard Gowers -Date: Wed Nov 18 12:20:24 2015 -0800 - - Split lammps data tests into their own file (#466) - -commit 0d11fab37554b957068ebb8642ba61028680fd90 -Author: Sean L. Seyler -Date: Wed Nov 18 13:05:06 2015 -0700 - - Added PSA citation and DOI link to references list - -commit d459037c76fd615c0402086f6ad529c8d19048ec -Author: Richard Gowers -Date: Wed Nov 18 00:17:15 2015 -0800 - - Updated Lammps data reading - - Now should support newer formats and triclinic boxes - -commit 0995e04858047d3dfed42241cc959673c9047eb2 -Merge: c779eac63 0dac4c63c -Author: kain88-de -Date: Sun Nov 15 22:42:32 2015 +0100 - - Merge pull request #543 from MDAnalysis/issue-532 - - Issue 532 - -commit 0dac4c63cac253dbfd952f119903c1572e89eba0 -Author: Richard Gowers -Date: Fri Nov 13 15:36:30 2015 -0800 - - Fixed broken Atom add - -commit b984aa95597b65c5f5d22fdba7573ecf0b314e90 -Author: Richard Gowers -Date: Fri Nov 13 14:38:41 2015 -0800 - - Added fix for Issue #532 - - Prevents addition of AtomGroups from different Universes - -commit 51b109e10f21cc6c4cd2b6042eb0fe44324570e6 -Author: Richard Gowers -Date: Fri Nov 13 14:20:06 2015 -0800 - - Tests for Issue #532 - -commit c779eac63d741a0bb9f24af6a41640aadd42c4e0 -Merge: 20d7e7bec 30cbc1927 -Author: Richard Gowers -Date: Thu Nov 12 21:46:30 2015 -0800 - - Merge pull request #538 from MDAnalysis/issue/530 - - Issue #530: remove lib.parallel.distances - -commit 30cbc1927bfd0d4a06564b2d3ce17187edb07662 -Author: Oliver Beckstein -Date: Thu Nov 12 12:45:53 2015 -0700 - - documented selection of backend for distance calculations - - - closes issue #530. - - improved general docs for MDAnalysis.lib - -commit d399b7befcca48cf6e096ce2fd5bc39719aa936f -Author: Oliver Beckstein -Date: Thu Nov 12 10:59:06 2015 -0700 - - removed lib.parallel.distances - - - The cython/prange-based/OpenMP versions of some of the distance calculations were - slower and had fewer features than the C/OpenMP based ones that are now available - with backend="OpenMP" as implemented in PR #529 so these ones (and their tests) - are fully removed. - - removed test for deprecated core.parallel.distances - - The whole lib.parallel module was also removed because at the moment there is nothing - in it; we can revisit the discussion about organization of lib (issue #287) when - necessary. - -commit 20d7e7bec3bc8e2bc431b11d47f0d4195f038d8f -Merge: 37540592e e98720fba -Author: Oliver Beckstein -Date: Thu Nov 12 12:42:59 2015 -0700 - - Merge pull request #537 from MDAnalysis/fix-setup - - Added flag for indicating if openmp was used to Cython submodules - -commit e98720fbaebb129ec25578fde71e416cfd355d23 -Author: Richard Gowers -Date: Thu Nov 12 10:51:15 2015 -0800 - - Added test for openmp declaration - -commit 64816f0ab5f9be0fee52d7900e557f33f48268bc -Author: Richard Gowers -Date: Thu Nov 12 10:38:11 2015 -0800 - - Added flag for indicating if openmp was used to Cython submodules - -commit 37540592e1fa3edfc343dd42cb198eb3e5a6b674 -Merge: d168f86f2 4f0827fa8 -Author: Richard Gowers -Date: Thu Nov 12 09:21:23 2015 -0800 - - Merge pull request #536 from MDAnalysis/scipy-ncdf-precision - - AMBER NetCDF file writing -- enforcing float32 precision - -commit d168f86f2b429e6be24539c81a98bcb0defe6fa3 -Merge: e4d258a8c 19400a5b3 -Author: Richard Gowers -Date: Thu Nov 12 09:04:41 2015 -0800 - - Merge pull request #529 from MDAnalysis/feature-selectparallel - - enabled selecting between serial and OpenMP distance functions - -commit 4f0827fa8677bd40d3f9e9a07f4c77e30f02b5ef -Author: Tyler Reddy -Date: Thu Nov 12 15:31:01 2015 +0000 - - CHANGELOG adjusted to reflect resolutin of Issue #518. - -commit e42c9c29708f5b4f64ad8f3ff14c8053fc60b19f -Author: Tyler Reddy -Date: Thu Nov 12 13:54:50 2015 +0000 - - MDAnalysis now correctly writes float32 data for time and coordinates fields of ncdf files. Fixes #518 - -commit 9c0a40a33427329c00918f28c22e0d2ed44dbfcb -Author: Tyler Reddy -Date: Thu Nov 12 13:19:07 2015 +0000 - - Added unit tests for preservation of float32 data type in AMBER ncdf files written by MDAnalysis (for time and coordinate fields). - -commit 19400a5b338a49f87ddd88f0f43ea4540b516a14 -Author: Oliver Beckstein -Date: Wed Nov 11 17:50:12 2015 -0700 - - small modifications of distance calc backend selection - - - backend is now case-insensitive (as requested by @richardjgowers) - - missing/wrongly spelled backend now raises ValueError instead of - RuntimeError - - added tests for both - -commit 789acd9981ba7043ef59c21351208a68f2eba73a -Author: Oliver Beckstein -Date: Wed Nov 11 13:30:50 2015 -0700 - - removed c_numpy.pxd and replaced with 'cimport numpy' - - - 'cimport c_numpy; c_numpy.import_array()' replaced with - 'import numpy; cimport numpy' - - replaced ndarray.dimensions --> ndarray.shape - - re-ran cython to generate C files - -commit 34defab6ebbdfd73fd5314d52831354551242b3f -Author: Oliver Beckstein -Date: Wed Nov 11 00:35:00 2015 -0700 - - enabled selecting between serial and OpenMP distance functions - - - all functions in lib.distances acquired the backend= keyword; - - "serial" selects the standard serial C/Cython code from lib._distances; - - "OpenMP" selects the OpenMP parallelized C/Cython code from - lib._distances_openmp - - on systems without an OpenMP capable compiler, this will likely just mean - that the OpenMP versions are actually serial (the OpenMP pragma should - get ignored) --- need to be confirmed/tested - - tests in test_distances were refactored so that both serial and OpenMP - versions are tested - - the current implementation is not very pretty (see lib.distances._run()) - but will make it very easy to add additional acceleration schemes such as - CUDA or numba as long as the call signatures of the calc_* functions remain - the same. - -commit e4d258a8c98c69f74a689147cd39b701de4c41d5 -Merge: d66927039 cf9797693 -Author: Richard Gowers -Date: Wed Nov 11 09:07:40 2015 -0800 - - Merge pull request #534 from MDAnalysis/issue-533 - - Fixes incompatibility of LeafletFinder with newer numpys (closes #533) - -commit cf9797693aa1ce9a2af08e82668fa2aaa8e14647 -Author: Manuel Nuno Melo -Date: Wed Nov 11 17:35:13 2015 +0100 - - Fixes incompatibility of LeafletFinder with newer numpys (closes #533) - - Simple LeafletFinder test added, together with a water-less Martini - DPPC-CHOL bilayer gro (340KB). - -commit 833aa5dafb8863f865505991b2e1f7f11b9122a0 -Author: Carlos Yañez -Date: Tue Nov 10 16:16:55 2015 -0300 - - add ZeroDivisionError exception to WaterOrientationRelaxation class - -commit d66927039e1357da34dfc10631d66254c2c2fff7 -Merge: 946692ef7 ad41de8a8 -Author: kain88-de -Date: Tue Nov 10 09:27:26 2015 +0100 - - Merge pull request #526 from kain88-de/fix-test-bug - - Fix bug in coordinates base test - -commit ad41de8a85d37b9f8e18008b52218c0ee0c518ba -Author: Max Linke -Date: Mon Nov 9 23:16:12 2015 +0100 - - Fix bug in coordinates base test - - I didn't notice that before since we only test the xyz-reader - right now which doesn't trigger any of these bugs. - -commit 946692ef7a5fba4d7dc05cd31ff1aab6d616bfb2 -Merge: 99f2cc0ce 9ea277b2d -Author: Richard Gowers -Date: Mon Nov 9 11:40:34 2015 -0800 - - Merge pull request #524 from kain88-de/new-test - - Add new writer test - -commit 99f2cc0ce84cdcb5d4a710d1b02be184975b4c06 -Merge: b34326a32 519865428 -Author: Richard Gowers -Date: Mon Nov 9 11:39:27 2015 -0800 - - Merge pull request #525 from kain88-de/convert-dimenson-out-of-place - - change dimension in place - -commit 5198654282262c3bbc1bb2d9136615183114b577 -Author: Max Linke -Date: Mon Nov 9 18:13:54 2015 +0100 - - change dimension in place - -commit 9ea277b2d262b5ed6a309e9b808220cb1343c02b -Author: Max Linke -Date: Mon Nov 9 18:05:03 2015 +0100 - - Add new writer test - - A write shouldn't change the TimeStep object given. This is - important for formats that use different units then MDAnalysis. - -commit b34326a32514ecd408691a44c5d0455c2e27e8e4 -Merge: c675da750 3fd21044a -Author: Richard Gowers -Date: Mon Nov 9 09:58:10 2015 -0800 - - Merge pull request #523 from MDAnalysis/issue-522 - - Fixed misuse of delta arg in ChainReader and docs of MDAnalysis.Writer - -commit 3fd21044a9397f4d48851c7907599cfc1a5a63dd -Author: Manuel Nuno Melo -Date: Mon Nov 9 11:51:50 2015 +0100 - - ChainReader now properly computes times - -commit 2ace7d9c3c74108b00d3ea4254534bd1ef1e5e6d -Author: Manuel Nuno Melo -Date: Sun Nov 8 17:55:22 2015 +0100 - - Fixed misuse of delta arg in ChainReader and docs of MDAnalysis.Writer - -commit c675da750c83886eff0e393c5f4a88f5a5e75798 -Merge: 23e0f724d bc4696307 -Author: Oliver Beckstein -Date: Thu Nov 5 13:21:51 2015 -0700 - - Merge pull request #519 from MDAnalysis/issue-361 - - Added distance selection tests for triclinic boxes - -commit bc4696307df35ca15f3ee9a3529981d016f02bc5 -Merge: 6bcc93e67 23e0f724d -Author: Richard Gowers -Date: Tue Nov 3 19:37:14 2015 -0800 - - Merge branch 'develop' into issue-361 - -commit 23e0f724d8a2f6f6b6688b4f9d5fc0301bff402d -Merge: 11cf991da 270c1cf25 -Author: Richard Gowers -Date: Tue Nov 3 19:08:17 2015 -0800 - - Merge pull request #520 from MDAnalysis/travis-fix - - Fixed conda install path for travis - -commit 270c1cf25663c02325005a16afa3d8958aef0efc -Author: Richard Gowers -Date: Tue Nov 3 18:05:27 2015 -0800 - - Fixed conda install path for travis - -commit 6bcc93e673308fbf350c4ee9be1d5c50a15fec6a -Author: Richard Gowers -Date: Tue Nov 3 14:03:12 2015 -0800 - - Added distance selection tests for triclinic boxes - - Fixed slightly broken test in testdistanceselections - -commit 11cf991dacac180347975c79a03a06d7f64a874c -Merge: 35fb1b0fa 7809e1587 -Author: Richard Gowers -Date: Tue Nov 3 10:48:14 2015 -0800 - - Merge pull request #515 from kain88-de/natoms-kwarg - - Natoms kwarg - -commit 35fb1b0fa959354258f7d135443cdc067bb320bb -Merge: aac24f9b0 88f4798c5 -Author: Oliver Beckstein -Date: Tue Nov 3 11:41:53 2015 -0700 - - Merge pull request #514 from MDAnalysis/issue-362 - - updates/fixes for selections (related to #362) - - - unused code was removed - - bonded selections fully implemented - - performance improvements - -commit 7809e1587263129359c69a5426f540e7e88403f5 -Author: Max Linke -Date: Mon Nov 2 18:21:27 2015 +0100 - - Add test for container formats - - Now only some tests are allowed to skip the n_atoms argument - for writer classes. - -commit 88f4798c51c9633b167c69d1c7ae7580fe73c529 -Author: Richard Gowers -Date: Mon Nov 2 09:59:49 2015 -0800 - - Reworked spherical selections, more efficient - - Added distance selection tests for with/without PBC - - Finishes Issue #362 - -commit c1ba9d20c08475aa3594c5d1dd1dfb82785ad645 -Author: Richard Gowers -Date: Mon Nov 2 08:22:54 2015 -0800 - - Added test for byres - -commit d16c6bd3f82cfd4b37b1bce951d0ed2aa3f49583 -Author: Richard Gowers -Date: Mon Nov 2 08:17:24 2015 -0800 - - Fixed PointSelection KDTree (CNS was removed) - - Added DistanceSelection base class for distance based selections - Appropriate backend is now chosen on init, useful so we can hack in - and choose a different one for testing - - More tests for distance based selections - -commit 9f5b98afab3ace73f0075ceca744cc16e3746578 -Author: Richard Gowers -Date: Sun Nov 1 16:15:46 2015 -0800 - - Removed reprs from core/Selection - -commit 5df50ffd0bf06cde7c99d1d8c1382e91d519269c -Author: Richard Gowers -Date: Sun Nov 1 16:01:03 2015 -0800 - - Removed unused expected error from Selections - - And general code tidying - -commit 3de57fcfa61b35cb9961271ad546dc70ebd84206 -Author: Richard Gowers -Date: Sun Nov 1 15:55:29 2015 -0800 - - Added more tests for Selections - -commit 05ca00e65f15c4759eb8f995582d7d0345de3fd9 -Author: Richard Gowers -Date: Sun Nov 1 15:18:15 2015 -0800 - - Removed unused bitwise operators from Selections - -commit 4ceb1071386262743a6ed14f2aad8997fc1984c7 -Author: Richard Gowers -Date: Sun Nov 1 15:09:23 2015 -0800 - - Added warning for BondedSelection without bonds - -commit 5320fb7a5ca71f6983e5992d05916026da2603e1 -Author: Richard Gowers -Date: Sun Nov 1 14:54:17 2015 -0800 - - Added test for bonded selections - -commit 6a5e447702923ca1c0f9fafee70f72f18430e284 -Author: Richard Gowers -Date: Sun Nov 1 14:19:20 2015 -0800 - - Fixed bonded selection - -commit b4ffb7b0179f634315827a9758b3f594b87143a6 -Author: Richard Gowers -Date: Sun Nov 1 13:31:11 2015 -0800 - - removed unused associativity feature from Selection - -commit 516c8c46285f1022a66c037fa259830d96bac3db -Author: Richard Gowers -Date: Sun Nov 1 13:29:47 2015 -0800 - - Removed unused Selection.__init__ - -commit 0ad9c10f1cac75fa102f805974dd491551d1f8c8 -Author: Richard Gowers -Date: Sun Nov 1 13:24:04 2015 -0800 - - Added BONDED back into to core.Selections - - Not working yet though - - Removed dunderscores throughout core.Selections - -commit e815630314399e5d9acc82dff74cb721ae754e48 -Author: Richard Gowers -Date: Fri Oct 30 15:52:10 2015 -0700 - - Added tests for prop selection - -commit 6d389eb6e6f0edc400a9ce6cafe5491465bb9c92 -Author: Richard Gowers -Date: Fri Oct 30 15:18:14 2015 -0700 - - Removed unused CompositeSelection - -commit 7ff8710ddadeb635bc4bdbb902407690c52dc9c2 -Author: Richard Gowers -Date: Fri Oct 30 15:14:46 2015 -0700 - - Added tests for point selection - -commit dc84819d0a0667a5d4b7753cfca1b9b43901484b -Author: Richard Gowers -Date: Fri Oct 30 14:50:13 2015 -0700 - - Removed unused/orphaned code from core/Selections - - Start of Issue #362 - - Removed: - CASelection (wasn't accessible anyway?) - BondedSelection (wasn't fully implemented) - NUCLEICXSTAL (only the name existed?) - -commit aac24f9b0faa61ae085d4cc858b13a39d940d861 -Merge: 86bf68966 7172d0f57 -Author: Oliver Beckstein -Date: Fri Oct 30 13:20:59 2015 -0700 - - Merge pull request #513 from MDAnalysis/issue-512 - - Fixes Issue #512 (support handling of Timesteps without positions) - -commit 7172d0f57c15be44b0a500af0a5e6f9ef9853743 -Author: Richard Gowers -Date: Fri Oct 30 12:59:08 2015 -0700 - - More tests - - Fixed copy_slice with no positions not failing properly when given - invalid slice - -commit 3d12e60ea9ccf5f8055760d63ddfc3ceb6c8c93b -Author: Richard Gowers -Date: Fri Oct 30 11:41:04 2015 -0700 - - Fixes Issue #512 - - Added better support for Timesteps without positions - - Timestep.from_coordinates now works without positions - - Timestep.__eq__ works without positions - - Timestep.copy_slice works on Timesteps without positions - - Many more tests for Timesteps through new BaseTimestepTest - -commit 86bf68966063010e5888c3c1635819a8d87cd9ed -Merge: cf317f68b 800ea6a2d -Author: kain88-de -Date: Fri Oct 30 19:15:25 2015 +0100 - - Merge pull request #509 from MDAnalysis/tests-tidyup - - Moved Timestep tests into new structure - -commit cf317f68b9261ee0075a47c801a7e9e0f26e6c3a -Merge: 96e3ce9c2 50f699191 -Author: Richard Gowers -Date: Fri Oct 30 10:23:34 2015 -0700 - - Merge pull request #510 from kain88-de/basetest-fix - - Basetest fix - -commit 50f699191e590c5e6a607346a4f9e73bead3db75 -Author: Max Linke -Date: Fri Oct 30 07:44:09 2015 +0100 - - Change BaseReaderTest to check for TypeError - - This is the correct API used by the coordinates.base.Reader - class. - -commit 8466c64bf3b93ebfa6e14b9e506fe11a1879f776 -Author: Max Linke -Date: Fri Oct 30 07:43:20 2015 +0100 - - Raise TypeError if write is not given a Timestep - - Or the timestep can be extracted. This the same behavior as in - the base class. - -commit 800ea6a2d8f479d2cf9bbe02e1f401f1f21addb0 -Author: Richard Gowers -Date: Wed Oct 28 08:58:22 2015 -0700 - - Moved reader API tests into coordinates directory - -commit 97e16817b9853ebd8f1b9dc9a100af81fbb2e98b -Author: Richard Gowers -Date: Tue Oct 27 10:50:49 2015 -0700 - - Changed Timestep tests to use floats - -commit 092e25baf6de20913ec4c26d66f804abe98605d7 -Author: Richard Gowers -Date: Mon Oct 26 21:55:54 2015 -0700 - - Moved Timestep tests into new structure - - Coverage shouldn't change! - - Issue #466 - -commit 96e3ce9c289d784eae9ea6b0f7c70d05915cf170 -Merge: cfdf38b95 63aa6e9d4 -Author: Richard Gowers -Date: Sun Oct 25 15:59:58 2015 -0700 - - Merge pull request #474 from MDAnalysis/single-base-reader-test - - add base reader testing class - -commit 63aa6e9d450c34b76a068b2b4df6ce339e564d2b -Author: Max Linke -Date: Sun Oct 25 14:31:38 2015 +0100 - - Add assert_timestep_almost_equal - - utility function to test the equality of timesteps with limited - precisions, eq XTC and PDB. The new standard reader/writer tests now - use the timestep equality method. This makes them actually a little - easier and shorter. - -commit d207b805ebf36a614a1328ebd2e34e67e80cd0f5 -Author: Max Linke -Date: Sat Oct 24 00:18:56 2015 +0200 - - Move special coord test data to normal data-folder - - All test data live in one place and is sorted logically with the - help of the filesystem tree. It also follows the convention to have a - constant refering to the file on disk. - -commit 25693e02632455ac1cd378639d899b4e5d4026f2 -Author: Max Linke -Date: Fri Oct 23 12:42:45 2015 +0200 - - Add test files to test package. - -commit 73283f9f1f259762332d44ad08614b37a2161108 -Author: Max Linke -Date: Tue Oct 20 18:31:48 2015 +0200 - - XYZReader.writer handles n_atoms kwarg - - Now when n_atoms is not specified we assume that the same number of - atoms as in the reader should be used. This conforms to the other - standart APIs. - -commit 232ee952219d4d931b3b054c49c303ce23ab0430 -Author: Max Linke -Date: Fri Oct 23 09:33:10 2015 +0200 - - Convert XYZ-format to be tested with new test-class - - The XYZ Reader/Writer is now extensivly tested with the new base test - class for reader and writers. It also serves as an example how to add - format specific tests to these new classes. As a bonus the coverage of - the XYZ coordinate module is increased. - -commit 51c6bfad3607dd84460d11159999a1d5a1f7a6af -Author: Max Linke -Date: Fri Oct 23 09:31:05 2015 +0200 - - Add Base tests for Reader/Writer classes - - This introduces a single test class for all the different format readers - and writers. It is currently not used by any of them though. This is - done to start the unification process for testing the reader/writer - classes to be sure all follow the same API. Testing new common API's is - now also just a matter of adding it to the base class. - -commit 5efe593521be76ef238ac807d5bbd4ea5164d8a8 -Author: Richard Gowers -Date: Fri Oct 23 17:16:52 2015 -0700 - - Added analysis.rdf.InterRDF - -commit 79e0a5dd89c2503e4752e18270144df0e14b2beb -Merge: e8ca71624 cfdf38b95 -Author: Richard Gowers -Date: Fri Oct 23 16:23:30 2015 -0700 - - Merge branch 'develop' into feature-polymers - - Conflicts: - testsuite/MDAnalysisTests/test_analysis.py - -commit e8ca71624953e0d6affa04ece6a218a568e9ad71 -Author: Richard Gowers -Date: Wed Oct 7 08:42:05 2015 -0700 - - Added prepare hook to AnalysisBase - - Renamed normalise to conclude - -commit cfdf38b954fd9abdbebd6b58bcea48e730af4d50 -Merge: a222aa6d3 8de3fcebc -Author: Oliver Beckstein -Date: Thu Oct 22 14:16:28 2015 -0700 - - Merge pull request #505 from sseyler/develop - - Updated PSA module with PR citation (PLOS Comput Biol). Fixes #453. - -commit a222aa6d30c8d970b72837a9d8031e1855bf61c9 -Merge: aee590176 9b6dfd05f -Author: Richard Gowers -Date: Thu Oct 22 13:59:14 2015 -0700 - - Merge pull request #499 from MDAnalysis/issue-479 - - Issue 479 - -commit 8de3fcebce3a2762c4535fd04b786638913ed6f3 -Author: Sean L. Seyler -Date: Thu Oct 22 13:42:06 2015 -0700 - - Updated PSA citation to PR w/ DOI - -commit 962fad07711f54447b8767b6fa81ec7d21490cf9 -Author: Sean L. Seyler -Date: Thu Oct 22 13:24:37 2015 -0700 - - Changed to non-pythonic symmetric distance matrix assignment - -commit aee590176d4e6c398cd0e5fca5b68120eeea37cb -Merge: 1cda12930 58632d9ba -Author: Richard Gowers -Date: Wed Oct 21 21:26:55 2015 -0700 - - Merge pull request #501 from MDAnalysis/issue/488-amber-nc-format - - Issue/488 amber nc format - -commit 1cda12930e33b4715b93e4a35c9c16c2434a7c59 -Merge: 9fc21313e 4b39dff1f -Author: Oliver Beckstein -Date: Tue Oct 20 23:44:14 2015 -0700 - - Merge pull request #502 from MDAnalysis/feature/test-pm - - added test for log.ProgressMeter - -commit 4b39dff1f7e9baaf936def3fc0a13955bf8ab8f2 -Author: Oliver Beckstein -Date: Tue Oct 20 23:17:58 2015 -0700 - - added test for log.ProgressMeter - -commit 9b6dfd05f5e5a6bde1055299ea47e75be0e4ce7c -Author: Manuel Nuno Melo -Date: Wed Oct 21 01:58:08 2015 +0200 - - Dependency workaround more concise and less hackish - -commit 58632d9ba3dab0e5375e28534d22906b911111e3 -Author: Oliver Beckstein -Date: Tue Oct 20 11:59:49 2015 -0700 - - include forgotten Amber data files - -commit 59ad14806e4032291502e753b27247f4e1e0af0b -Author: Oliver Beckstein -Date: Mon Oct 19 07:58:08 2015 -0700 - - Amber NCDF Writer should now conform to specs (#488) - - - fixes #488 - - NCDFWriter now writes variables spatial, cell_spatial and cell_angular - with the correct values - - added additional code to the writer test that checks that - - all required dimensions and variables are written - - all dimensions have the same length as in the original trajectory - - all variables have the same values (up to prec = 5) - - needed to decrease precision from 6 to 5 - - tests pass now - - updated CHANGELOG - - Thanks to @swails for the fix. - -commit 08425d54dbabc5fdce9aff98d71a8d61d0a649a3 -Author: Oliver Beckstein -Date: Mon Oct 19 04:34:13 2015 -0700 - - Amber reader: recognize PARM7 and NC suffixes - - - PARM7 is also a common suffix for Amber parameter files, - so we auto-recognize it now - - NC was not recognized as a Amber NCDF file by the *writer*; - the reader was already working - - slightly improved the unit tests by deriving a common test and - keeping the filenames in the reference class - - use the TZ2 canonical nc trajectory to test for parm7/nc reading; - we might be able to remove the PRMncdf/NCDF one - -commit adf88d5b62f2f46fa098a02a02ad3ceaf808428f -Author: Oliver Beckstein -Date: Mon Oct 19 10:41:48 2015 +0200 - - added test Amber trajectory for #488 - - Trajectory tz2.truncoct.nc and parm7 from cpptraj test cases (GPL3) - -commit c472a14a5f1ea7a03508e6ad1a869f46d9e5c538 -Author: Oliver Beckstein -Date: Mon Oct 19 10:37:50 2015 +0200 - - moved Amber test files to datafiles/Amber - -commit 9fc21313ec019321d96d3c30dddee9162c4b82b1 -Merge: f08166167 117772598 -Author: Richard Gowers -Date: Tue Oct 20 09:31:41 2015 -0700 - - Merge pull request #500 from MDAnalysis/fix_ten2eleven - - Fix ten2eleven - -commit f081661673da0f38c41dad7ddf4d2f784479cfbd -Merge: 1bb94ffbd afdb16a76 -Author: Richard Gowers -Date: Tue Oct 20 09:27:06 2015 -0700 - - Merge pull request #496 from tylerjereddy/develop - - Remove doc/html from version control - -commit 117772598c083d11d355e38deb80a83d906ac500 -Author: Tyler Reddy -Date: Tue Oct 20 15:06:47 2015 +0100 - - Completed CHANGELOG update for recent ten2eleven changes. Fixes #470. - -commit 4e786aa1c31e2307aa196ca3a031f71f0615ab1a -Author: Tyler Reddy -Date: Tue Oct 20 15:04:14 2015 +0100 - - Added a new fixer and crude tests for conversion of numatoms argument to n_atoms argument for writer() functions. This will tolerate a variety of call signatures. - -commit 5673e8cfe98f9dec861c443e5afe0228e9785b11 -Author: Manuel Nuno Melo -Date: Tue Oct 20 14:59:32 2015 +0200 - - Fixed numpy's partial import when installing - -commit 082f02d656f1d84963f8ee5aab12fecd04664cff -Author: Tyler Reddy -Date: Tue Oct 20 12:29:04 2015 +0100 - - Added CHANGELOG entry for ten2eleven centerOfMass camelcase fix. - -commit 70fd51ba69c23dc58699a1221f1d6756adb01c82 -Author: Tyler Reddy -Date: Tue Oct 20 11:20:22 2015 +0100 - - Adjusted the camelcase fixer to account for centerOfMass, which was missing. Crude test for conversion added as well. - -commit afdb16a76396e0f5bfaab06ca788a09c2ccb915f -Merge: e6d4cb310 1bb94ffbd -Author: Tyler Reddy -Date: Tue Oct 20 10:43:10 2015 +0100 - - Resolve CHANGELOG conflict. - -commit e6d4cb310965bf52093db7d63fc56a6556d674b0 -Author: Tyler Reddy -Date: Tue Oct 20 10:08:15 2015 +0100 - - Updated CHANGELOG to reflect changes to html file version control policy. - -commit 3f642f7674fefa1e777f96a8125aa26a4208c4b3 -Author: Manuel Nuno Melo -Date: Tue Oct 20 03:10:47 2015 +0200 - - Typos - -commit 05934fec2b3cec595f521259932bcb23f87ad74d -Author: Manuel Nuno Melo -Date: Tue Oct 20 02:31:27 2015 +0200 - - Fixed setup-time dependency on numpy that broke pip installs. - - (closes #479) - -commit 1bb94ffbdd6bab91d067840898fa7ef26fcc4c74 -Merge: 9da0edf48 c063be727 -Author: Richard Gowers -Date: Mon Oct 19 08:19:49 2015 -0700 - - Merge pull request #495 from MDAnalysis/growriter-vels - - Growriter vels - -commit 9da0edf48d84578615ec5218eb6e5f1f5407366e -Merge: 19ad715d8 a65643a77 -Author: Richard Gowers -Date: Mon Oct 19 07:58:32 2015 -0700 - - Merge pull request #493 from MDAnalysis/issue-487 - - Garbage collection of universes before AtomGroup unpickling (closes #487) - -commit a2deb066f23019e0fc122c2d5822890a50eb68c2 -Author: Tyler Reddy -Date: Mon Oct 19 15:14:03 2015 +0100 - - Added doc/html/ to .gitignore. Fixes #491. - -commit f897690478d5ef7bbfc1519b066536ed525a6c11 -Author: Tyler Reddy -Date: Mon Oct 19 14:49:02 2015 +0100 - - Removed html folder from git tracking. - -commit c063be7273ab8710dbbe59639b2b745bbaa5cb1f -Author: Richard Gowers -Date: Sun Oct 18 22:53:33 2015 -0700 - - Added velocity writing to GRO format - - Fixes Issue #494 - -commit 2b83d64921e8229832f23bb32bbe42086c489f56 -Author: Richard Gowers -Date: Sun Oct 18 22:09:41 2015 -0700 - - Updated GROWriter to use .format syntax - -commit 3b4836803d156d095502fd4580cb9b042e11886e -Author: Richard Gowers -Date: Sun Oct 18 19:45:32 2015 -0700 - - Improved performance of GRO file reading - - Approx 50% faster on large GRO files (Issue #212) - -commit 19ad715d84846a120a22b1da76bd798cec9ddbf2 -Author: Oliver Beckstein -Date: Mon Oct 12 13:53:29 2015 -0700 - - fixed: docs for topologyobjects were not included - -commit a65643a7790622a013e3168a71a75f244c75b5df -Author: Manuel Nuno Melo -Date: Sun Oct 18 23:55:29 2015 +0200 - - Garbage collection of universes before AtomGroup unpickling (closes #487) - -commit c2a309ebd491c25e49bbcde05922c2e5d30c039c -Merge: f4bc620f5 e16217c5e -Author: Richard Gowers -Date: Sun Oct 18 14:10:53 2015 -0700 - - Merge pull request #492 from MDAnalysis/issue/466-testfile-reorganization - - test reorganization: analysis and coordinates - -commit e16217c5e06575d81c4dc14d6a27c6aca5b9423e -Author: Oliver Beckstein -Date: Sun Oct 18 15:19:34 2015 +0200 - - test reorganization: analysis and coordinates - - - new subdirectory analysis/ - - split the unwieldy test_analysis.py into separate - files and removed superfluous imports (and got rid of - the awful 'from numpy.tests import *': use only classes/ - functions that are actually needed) - - also moved test_mol2 and test_pdbqt to the coordinates/ - directory - - part of work on reorganizing tests #466 - - todo: fixing tempfile handling #440 - density tests #410 - issues with PSA tests (#487 and #440) - -commit f4bc620f58ada3fa2432a631022b780c15d11ee2 -Merge: 44b9a1611 e81f72b56 -Author: Oliver Beckstein -Date: Sat Oct 17 14:07:19 2015 +0200 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit 44b9a1611e5e4b89ceba8df9543b49870f636abe -Author: Oliver Beckstein -Date: Sat Oct 17 13:27:28 2015 +0200 - - virtual machine for Fedora 21 - -commit e81f72b56aca39b8ee1711ebdc406fc66bf8c435 -Merge: 5b7b6143b e265a10cf -Author: Oliver Beckstein -Date: Sat Oct 17 10:17:41 2015 +0200 - - Merge pull request #490 from MDAnalysis/issue-489 - - Fixed analysis.density requiring deprecated trajectory attributes - -commit e265a10cf0e218ecf0df2ea635c22dd912307590 -Author: Richard Gowers -Date: Fri Oct 16 14:20:45 2015 -0700 - - Fixed analysis.density requiring deprecated trajectory attributes - - Fixes #489 - -commit 5b7b6143b39bdf8c06487e1c4f96417e9fbd9b06 -Author: Richard Gowers -Date: Fri Oct 16 14:11:42 2015 -0700 - - Improved performance of lib.mdamath.make_whole slightly using sets - -commit cb772cc30cc45f38251c67c78c2217ab4275ba9c -Merge: bcaad2081 87af2cfc2 -Author: Oliver Beckstein -Date: Thu Oct 15 11:19:06 2015 +0200 - - Merge pull request #485 from kain88-de/xyzwriter - - XYZWriter should accept n_atoms - -commit 87af2cfc2e5573fb1acf7d203596dad0840250c3 -Author: Max Linke -Date: Mon Oct 12 08:18:28 2015 +0200 - - XYZWriter should accept n_atoms - - XYZWriter can now be explicitily be used as a container for different - protein models or as a trajectory for one model. This is decided by the - value of `n_atoms`. If `n_atoms is None` we assume the Writer is used as - a container for different models and as a normal trajectory otherwise. - - In addition this cleans out some PEP8 issues in the writter and replaces - the generic `*args` and `**kwargs` with explicit arguments and keyword - arguments. - -commit bcaad20818aa977082d12f4230e5ca2ba16d146b -Author: Oliver Beckstein -Date: Wed Oct 14 00:00:33 2015 +0200 - - fixed: @kain88-de was not listed as an author in the docs - -commit 7eafcdf751b5b11ffb69472598a990e6dccd0699 -Merge: 4709a97b3 031778ba2 -Author: Richard Gowers -Date: Mon Oct 12 10:38:38 2015 -0700 - - Merge pull request #482 from MDAnalysis/feature-skip_netcdf - - netCDF tests now skipped if library missing (closes #124) - -commit 031778ba25e5d065d91453ab1249e0975d4a8d5f -Author: Manuel Nuno Melo -Date: Mon Oct 12 18:45:05 2015 +0200 - - Simplified executable and module checkers. - -commit ac1f3819c96b3315dff4c3afc0dc7295f7f5dac0 -Author: Manuel Nuno Melo -Date: Sat Oct 10 23:23:53 2015 +0200 - - Removed debug output - -commit 8e4c895a018bac98a487a4f4653087e023da38c1 -Author: Manuel Nuno Melo -Date: Sat Oct 10 23:08:23 2015 +0200 - - Added netCDF pre-test check to more tests. - - Generalized the module checker code and adapted it to run at - runtime only. - -commit 1bf2db0559979e94d07c7a0d0c6ee23d5462b260 -Author: Manuel Nuno Melo -Date: Sat Oct 10 19:41:00 2015 +0200 - - netCDF tests now skipped if library missing (closes #124) - -commit 4709a97b389a141343d53f4edea1bb2a8e3af7c3 -Author: Richard Gowers -Date: Fri Oct 9 22:24:19 2015 -0700 - - Rebuilt docs - -commit fdba00dbfe0361a05ad4af3789ef6f6842a303d4 -Author: Richard Gowers -Date: Fri Oct 9 22:24:10 2015 -0700 - - Bumped version to 0.13.0 dev - -commit fb1e050f9393fdcee75c3a7b734fa86bfe5be3e4 (tag: release-0.12.1) -Merge: bd49cc9bd fdcbe8229 -Author: Richard Gowers -Date: Fri Oct 9 20:59:28 2015 -0700 - - Merge branch 'develop' into release-0.12.1rc1 - -commit fdcbe822937f95d7ee811d93726e9df46820094e -Author: Oliver Beckstein -Date: Fri Oct 9 15:05:01 2015 -0700 - - fixed numpy -> np in LeafletFinder - -commit bd49cc9bd4269df7f727e1b57214deac6fca3044 -Author: Richard Gowers -Date: Thu Oct 8 10:00:30 2015 -0700 - - Updated MANIFEST for Tests - -commit 1b738835750349898b4bd38f4cf587e6d8fc2582 -Author: Richard Gowers -Date: Thu Oct 8 09:39:28 2015 -0700 - - Docs rebuilt for 0.12.1 release - -commit 92936c7d105e60aac4fd098a929fc1e64bf27833 -Author: Richard Gowers -Date: Thu Oct 8 09:35:59 2015 -0700 - - Finalised 0.12.1 changes - -commit a6269607ffe456fc1f9f899a6a11d834d63982dd -Merge: f9eb342b9 a1ce39682 -Author: Oliver Beckstein -Date: Wed Oct 7 23:21:31 2015 -0700 - - Merge pull request #477 from MDAnalysis/issue-476 - - Issue 476 - - Fixes #476 - -commit a1ce39682885187e595a48253a96b00c31a71628 -Author: Richard Gowers -Date: Wed Oct 7 17:04:03 2015 -0700 - - Fixed topology.base.guess_atom_element raising IndexError - - Fixes #476 - -commit 547f3656920b73b781d6a69ab2ac1b33e8faba19 -Author: Richard Gowers -Date: Wed Oct 7 17:02:13 2015 -0700 - - Added tests for Issue #476 - -commit f9eb342b9365c19ec6d703e39829590ed7f7b09e -Author: Oliver Beckstein -Date: Tue Oct 6 16:43:35 2015 -0700 - - doc fix in LAMMPS DCDWriter - -commit 893f661196bc78a8a014fb068324b92b28d504b5 -Merge: 0411d1009 9dd05ccce -Author: Richard Gowers -Date: Tue Oct 6 16:07:23 2015 -0700 - - Merge pull request #472 from MDAnalysis/fix-lammps - - Fix lammps - -commit 9dd05cccebb389f2f3cc64f058b6250bf4365af4 -Author: Oliver Beckstein -Date: Tue Oct 6 14:03:12 2015 -0700 - - fixed DCDReader.dt was not in sync with Timestep.dt - -commit 2a3c00edc1781ebcfa93baf972f1365ce2b93887 -Author: Oliver Beckstein -Date: Tue Oct 6 13:47:48 2015 -0700 - - updated docs for LAMMPS trajectory reader (units) - -commit f5ad35f11e200ca0464242b5f6206278278fa969 -Author: Oliver Beckstein -Date: Tue Oct 6 11:24:15 2015 -0700 - - testing flavor of DCDReader/Writer - - Introduced an experimental class-attribute flavor for the DCDReader/DCDWriter that - helps to distinguish the CHARMM DCD code from the LAMMPS code (and later will be - useful for the NAMD DCD Reader/Writer in #359 ) - - Added tests to check that the LAMMPS DCDWriter and Reader are being used because - the last coverage report said that the LAMMPS.DCDWriter was not being covered. - -commit 15d577bdc47f5aa42d3ad7fd9ea1f0f872394300 -Author: Oliver Beckstein -Date: Tue Oct 6 03:08:01 2015 -0700 - - added tests for LAMMPS DCDWriter and exceptions in DCDReader - -commit f393a64b3df62e5bf00dfda150e53db28d8f9ca4 -Author: Oliver Beckstein -Date: Tue Oct 6 01:46:18 2015 -0700 - - fixed dt for LAMPPS DCD and setting of dt by user - - - LAMMPS default time unit is fs (for unit real, see http://lammps.sandia.gov/doc/units.html) - but we had it as ps - - Universe(..., dt=
) is working now for DCDReader (and anything derived from it such as - the LAMMPS DCDReader) - -commit 7b779518c75fb8be540bb0c5085818a0068192bd -Author: Oliver Beckstein -Date: Tue Oct 6 01:09:41 2015 -0700 - - new LAMMPS test files - - - moved all LAMMPS files into lammps/ subdirectory - - removed lammps2.data and lammps2.dcd (were not used and unknown provenance) - - added freshly generated DCD with dt=0.5 ps for testing - - added the LAMMPS input file for the new test data - - install new files (setup.py) - -commit 0411d10094ac5ecc6d82a14749043e322ee6e75d -Author: Richard Gowers -Date: Mon Oct 5 16:53:55 2015 -0700 - - Fixed up CHANGELOG chronology - -commit 68df27fa74a5e63d483b02f4ce01affb09b81901 -Merge: 8fc52ae07 b7c3522da -Author: Richard Gowers -Date: Mon Oct 5 16:51:23 2015 -0700 - - Merge pull request #471 from kain88-de/openmp-detection - - Make openmp detection work - -commit b7c3522da2471a409667e56916b7609878f66292 -Author: Max Linke -Date: Tue Oct 6 00:01:21 2015 +0200 - - Update CHANGELOG with changes in setup.py - - mainly that the setup.cfg options can also be set with environment - variables. - -commit 8fc52ae079bc85f37e6e464c0dbc267921720f6d -Author: Richard Gowers -Date: Mon Oct 5 14:37:26 2015 -0700 - - Added wheel options to setup.cfg(s) - -commit 0256699f041291646d7c033f1d5630b36c2022a7 -Author: Richard Gowers -Date: Mon Oct 5 14:37:13 2015 -0700 - - Bumped version to 0.12.1-dev - -commit 66d73c607fcbd039a99a8a739c88850f84de1330 -Author: Max Linke -Date: Mon Oct 5 10:19:35 2015 +0200 - - Make openmp detection work on debian - - This change will let the setup script correctly detect openmp - on my debian system. The thing is I have to tell the compiler - where the omp functions are defined and also link to omp. - -commit 53cdffa9f889a9fad331274b4aad1c10060d3781 -Merge: 0149cba16 2d2ae28cc -Author: Oliver Beckstein -Date: Mon Oct 5 10:32:17 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - - [no CI] - -commit 0149cba165a672872f0cbffaa8683289a9a52f73 -Author: Oliver Beckstein -Date: Mon Oct 5 09:47:25 2015 -0700 - - updated VMs - - - MDAnalysis URL in VM status message updated - git grep -l googlecode | xargs perl -wpi~ -e 's(http://mdanalysis\.googlecode\.com)(http://www.mdanalysis.org)' - - updated provide for Debian box from chef to debian (the chef box - apparently disappeared from Vagrant cloud); the debian/wheezy64 will always point to the latest - stable point release of Debian 7 (wheezy) so I also renamed the directory - -commit 2d2ae28ccb879554e4181415d38ef0f9c736f298 (tag: release-0.12.0) -Author: Richard Gowers -Date: Mon Oct 5 10:12:46 2015 -0700 - - Final fix(tm) to MANIFEST - -commit 957b263adf9fb3c882d921a69b521ad9c5895cf7 -Author: Richard Gowers -Date: Sun Oct 4 21:37:57 2015 -0700 - - Updated MANIFEST for 0.12.0 release - -commit 04b72583ae05d594e23c8542e336e0112ca520c2 -Author: Richard Gowers -Date: Sun Oct 4 18:38:17 2015 -0700 - - Rebuilt docs for 0.12.0 release - -commit 97b071f4d54c08a11cfdb0cb5bef7867b1d13fa7 -Author: Richard Gowers -Date: Sun Oct 4 18:28:50 2015 -0700 - - Bumped version to 0.12.0 - -commit e44331c6bd9675b55c9017cab3d8e81485d67f84 -Merge: f4185f657 e596de2b5 -Author: Richard Gowers -Date: Sun Oct 4 07:59:50 2015 -0700 - - Merge pull request #469 from kain88-de/test_coordinate - - Move/Split/PEP8 test_coordinates - -commit e596de2b5b06e1fb4ae0e21b1793dc0d87753719 -Author: Max Linke -Date: Sun Oct 4 13:33:42 2015 +0200 - - add tempdir install to travis and setup.py - -commit 7abd19072d7659a6a9cfca04b02b9f5d571616e0 -Author: Max Linke -Date: Sun Oct 4 13:17:07 2015 +0200 - - Use tempdir instead of tempfile - - This cleans up propberly afterwards. - -commit 84ce31e3e31db6b74d97a1efcd7a45a7d3e96e21 -Author: Max Linke -Date: Sun Oct 4 12:38:18 2015 +0200 - - Replace izip with six.moves zip - - This results in fast zip generators in python 2 and 3 - -commit 2a0470bb8cac3964cb87aa8fa0e7eff7b0c770d1 -Author: Max Linke -Date: Sun Oct 4 12:13:42 2015 +0200 - - use find_packages in setup - - Now new modules are added automatically - -commit 6fcd3c601ff0aa8a86f34db82fc717217eb69604 -Author: Max Linke -Date: Sun Oct 4 08:47:22 2015 +0200 - - Get tests running again - -commit f4185f657547ad6052812d302e14e51750b08e5e -Merge: 339c110dc b6c895f67 -Author: Oliver Beckstein -Date: Sat Oct 3 22:17:33 2015 -0700 - - Merge pull request #465 from kain88-de/setup-config - - Setup.cfg config enhancements and clean-ups. - Closes #462. - -commit d3d9ce501863a4a34d23793e9cf740e3fcd4a779 -Author: Richard Gowers -Date: Sat Oct 3 16:49:35 2015 -0700 - - Renamed skip to step (for uniformity within MDA) - - AnalysisBase now doesn't generate all frames numbers, but instead slices - the trajectory directly. - -commit 6214712362caad6cc5c35064323c5ac1a50b1422 -Author: Max Linke -Date: Sun Oct 4 00:21:24 2015 +0200 - - apply yapf with PEP8 settings - - [ci skip] - -commit 8c7dfa0812ec9098dc6b36e4a159f6172cb745ee -Author: Max Linke -Date: Sun Oct 4 00:17:46 2015 +0200 - - Split test_coordinates into different files - - Also moves it into a separate folder to keep everything tidy. - -commit b6c895f67296d38ba9faaf8af67b1a5718c68545 -Author: Max Linke -Date: Sat Oct 3 20:02:34 2015 +0200 - - Remove flake8 config - - [ci skip] - -commit 2ed613c0c23cd9249f766393ec85820feb14d626 -Author: Max Linke -Date: Sat Oct 3 19:49:03 2015 +0200 - - reorder setup() parameters - -commit 125003770207898ce3a28792de8bc94095168c35 -Author: Max Linke -Date: Sat Oct 3 19:26:22 2015 +0200 - - Use proper config wrapper class - - Have one object to read config options from various sources. This - will make it easy to add new options later on. - -commit 7c3ff3f43332c06355fa699bc13a9d6a96b72da1 -Author: Max Linke -Date: Sat Oct 3 19:11:22 2015 +0200 - - Update SUMMARY.txt - - To tell people that the full analysis sweet is not available but that - the dependencies to make them run can be installed with pip as well. - - [ci skip] - -commit 08fee3ac2236692f3233b54b7cffad20a6c21542 -Author: Max Linke -Date: Sat Oct 3 19:05:27 2015 +0200 - - Some general clean up in setup.py - -commit d4ac0a8aad8e7c57bd2002c58771015c5f5c1c3d -Author: Richard Gowers -Date: Sat Oct 3 08:50:46 2015 -0700 - - Moved _AnalysisBase to analysis.base - - Changed frames to use generator instead - -commit 5d35199ba54425ba41af854bb3b2c2cdb6ac81fd -Author: Max Linke -Date: Sat Oct 3 16:39:45 2015 +0200 - - Add Richard as maintainer and give devel list for support - -commit e7249b25bc84db79a19563569e4a6fa8fa9a9c06 -Author: Max Linke -Date: Sat Oct 3 16:34:23 2015 +0200 - - Add scipy as extra requirement agai. - -commit 1306516bf38eafdb66f7d51571792404a6676d81 -Author: Max Linke -Date: Thu Oct 1 23:13:44 2015 +0200 - - Use system installed setup_tools - - Very important for having a python 3 and 2 compatible package later. - For that to work we have to rely on the system installed packages. - -commit 8e0e8a9a339b7b4e7ebe6d2544a25411e591c49a -Author: Max Linke -Date: Thu Oct 1 23:12:24 2015 +0200 - - comment non default values - - If any one has problems with openmp or cython now he can explicitely - deactivate them in the config without much hassle - -commit b463295c861f05711c90ec005278097ded8ecbc5 -Author: Max Linke -Date: Thu Oct 1 23:12:08 2015 +0200 - - Clean up setup.py a little bit - -commit 8ee415ce648cb9b79c7da575c43319e60dd3437f -Author: Max Linke -Date: Thu Oct 1 22:51:21 2015 +0200 - - Handle extensions in own function - -commit 67f9d28432d317cb8b7d006d6a5d928f692a7209 -Author: Max Linke -Date: Thu Oct 1 22:50:54 2015 +0200 - - use configparser in setup.py - - this enables usage of setup.cfg - -commit 10914e07a7ee8b8200803f89282df41483c62771 -Author: Max Linke -Date: Thu Oct 1 21:48:52 2015 +0200 - - Introduce basic setup.cfg and parsing - -commit 339c110dca04516bdb93b84db3218eb0ea6c7607 -Merge: 54c6d2c2a 377143356 -Author: Richard Gowers -Date: Fri Oct 2 13:00:06 2015 -0700 - - Merge pull request #468 from MDAnalysis/issue-444 - - Moved many extensions files alongside the python code (Issue #444) - -commit 377143356d366b7419413d272aa4c7b12490967f -Author: Richard Gowers -Date: Fri Oct 2 09:33:59 2015 -0700 - - Moved many extensions files alongside the python code (Issue #444) - - Moved source for coordinates.dcd, lib.distances, lib.transformations, - lib.pyqcprot and coordinates.libxdrfile. - - Removed deprecated src files - - Updated c files for Cython - -commit 54c6d2c2ac68c4bc90569aa31fc886749ceb5068 -Merge: 3c5c3b640 2065c30cf -Author: Oliver Beckstein -Date: Fri Oct 2 01:32:59 2015 -0700 - - Merge pull request #467 from jbarnoud/tpr-doc - - Update the CHANGELOG and the doc to reflect #463 - -commit 2065c30cf37d2f7ca8d9844dc137198bea3e2324 -Author: Jonathan Barnoud -Date: Fri Oct 2 09:32:20 2015 +0200 - - Update the doc to reflect #463 - -commit c05ec1e676920f44804ecf5061fee92da0e7a65c -Author: Jonathan Barnoud -Date: Fri Oct 2 09:09:08 2015 +0200 - - Update CHANGELOG to reflect #463 - -commit 3c5c3b640b4293a72fd4a20e3d1b41b31cf34dda -Merge: 5a7d0e5dc ca780cedc -Author: Richard Gowers -Date: Thu Oct 1 15:29:39 2015 -0700 - - Merge pull request #463 from jbarnoud/tpr-interactions - - Treat and test all bonded interactions in the TPR parser - -commit ca780cedcc858722c5a595c9a80672627869f7c9 -Author: Jonathan Barnoud -Date: Fri Oct 2 00:11:16 2015 +0200 - - Include all TPR test files in setup.py - - Include all the files in testsuite/MDAnalysisTests/data/tprs/all_bonded/ - in the setup.py of the test suite rather than just the TPR. - - Following a suggestion from @richardjgowers - -commit e4f3483429b2104c3a9046608d872266116c70de -Author: Jonathan Barnoud -Date: Fri Oct 2 00:06:18 2015 +0200 - - Make error message clearer in tests for TPR parser - - Following a suggestion from @richardjgowers in #463 - -commit 3240a3852c1e75091783f010ef3fa11240c3c1f6 -Author: Jonathan Barnoud -Date: Thu Oct 1 13:38:40 2015 +0200 - - Test for issue #352 now pass - - Previous changes in the TPR parser should have fix issue #352. The - test_atomselections.TestSelectionsXTC.test_same_fragment test that was - known to fail pass now. This commit remove the knownfailure decorator on - this test. - -commit a2a4b8a7d10e0b587fceaf15c29ce056df372a8c -Author: Jonathan Barnoud -Date: Thu Oct 1 13:31:09 2015 +0200 - - Make the TPR parser read all bonded interactions - - Very few interactions were actually read by the TPR parser. This commit - makes the TPR parser read all bond and angle potentials. - - Constraints are counted as bonds. This should fix #222 and #352. - - Prior to this commit, a comment read: - - > this is possible a bug in gromacs, the so-named Proper Dih is actually - > Improper Dih - - I did not find other mention of thid issue, nor did I noticed it from a - basic test. Therefore, with this commit, proper dihedrals are treated as - such. This may be a mistake, though. - - Also prior to this commit, 3 body virtual sites were treated as improper - dihedral. They are not anymore. - -commit 54488a78641e45ffb148716b1658d66302a8f323 -Author: Jonathan Barnoud -Date: Thu Oct 1 13:25:43 2015 +0200 - - Add test for all Gromacs bonded interactions - - Add tests to make sure the TPR parser reads all the possible bonded - interactions that are available in Gromacs. - - The files in testsuite/MDAnalysisTests/data/tprs/all_bonded describe a - system that is supposed to contain all the bonded interactions. - - When a new bonded interaction is added to Gromacs, it should also be - added to testsuite/MDAnalysisTests/data/tprs/all_bonded/dummy.top, and - to testsuite/MDAnalysisTests/datafiles.py. Do not forget to rebuild - testsuite/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr. - -commit 38014e15ec2034efa9f840e922f5a43c8f90f1de -Author: Richard Gowers -Date: Thu Oct 1 08:52:57 2015 -0700 - - Fixes to docs on PersistenceLength - -commit abc974c4a5d01f49a7843cf52f2fb39cc0dfe0e5 -Author: Richard Gowers -Date: Thu Oct 1 08:29:52 2015 -0700 - - Fixed docstrings on blocks_of - -commit c206d6f7700f2f05b7e4f2ad4d73d97b445fd6dd -Author: Richard Gowers -Date: Thu Oct 1 08:27:54 2015 -0700 - - Fixed fit attribute shadowing fit method - -commit 5a7d0e5dc48ba8b6cd6d2f82b57bc10c47dd68f4 -Merge: 43046345c e1519b871 -Author: Richard Gowers -Date: Thu Oct 1 08:25:46 2015 -0700 - - Merge pull request #458 from jbarnoud/update-tpr - - Update TPR parser for Gromacs 5 - -commit e1519b8714a47826d6504178b6fb14cae93a7fe3 -Author: Jonathan Barnoud -Date: Thu Oct 1 10:54:56 2015 +0200 - - Update author lists and change logs - -commit f4c38301c016957d2000d3a844f10815a03b9628 -Author: Jonathan Barnoud -Date: Wed Sep 30 11:25:38 2015 +0200 - - Update the doc for pbx100 and pbx103 support - -commit c06d8e6c293be9a7986998a29967cffb2c460d69 -Author: Jonathan Barnoud -Date: Tue Sep 29 17:52:29 2015 +0200 - - Add tests for pbx100 and pbx103 - - Add Gromacs 5 run files to the TPR parser test suite. - - The new TPR files where build from the already existing one using `gmx - convert-tpr -s 2lyz_gmx_4.5.3.tpr -o 2lyz_gmx_5.0.5.tpr` following the - suggestion by Richard Gowers (@richardjgowers). - -commit 60c4a3d3c4c225c81afb3f9d8deaf71153fee88f -Author: Jonathan Barnoud -Date: Tue Sep 29 09:21:47 2015 +0200 - - Update the TPR parser for pbx100 and pbx103 - - pbx100 is the TPR format used by Gromacs 5.0.x, pbx103 is the formar for - Gromacs 5.1. This update of the parser is based on Gromacs 5.1. - - The update does not include any Gromacs 5 specific feature, it just - allows the TPR parser to read the new format the same way as the - previous ones. - -commit b29123d32c83c149f2345844c553866caacc822d -Merge: 3c0a6e960 43046345c -Author: Richard Gowers -Date: Wed Sep 30 14:01:31 2015 -0700 - - Merge branch 'develop' into feature-polymers - - Conflicts: - testsuite/MDAnalysisTests/test_analysis.py - -commit 3c0a6e960c3df49ff49ce4a6aff7897414269d19 -Author: Richard Gowers -Date: Wed Sep 30 13:57:10 2015 -0700 - - Added tests for analysis.polymer.PersistenceLength - -commit 87b320901d7d2b74706e6adda04451101d186989 -Author: Richard Gowers -Date: Wed Sep 30 12:31:07 2015 -0700 - - Added fit and plot to analysis.polymer.PersistenceLength - -commit 43046345c98a650828da2b67558e1447a7148e84 -Merge: 5b27b509b 83f4b65e4 -Author: Oliver Beckstein -Date: Tue Sep 29 13:20:15 2015 -0700 - - Merge pull request #457 from MDAnalysis/issue-454 - - Issue #454 (PrimitivePDBParser did not correctly assign resids for large (>10,000 residues) files) - -commit 83f4b65e4a4678cef3bd9f52745cbc152d4d9d94 -Author: Richard Gowers -Date: Tue Sep 29 12:40:52 2015 -0700 - - Fixes #454 - - Added detection of resids jumping downwards. - -commit 35c4302c325da10fac6c368895965e9753979a50 -Author: Richard Gowers -Date: Tue Sep 29 12:18:36 2015 -0700 - - Added test for Issue #454 - - PDBs with resids that loop over 9,999 end up with only 9,999 and - residues mixed together - -commit 5b27b509bcb60026ca6c16dd3597d038bbb5ce7e -Merge: a81187725 42607eb20 -Author: Oliver Beckstein -Date: Mon Sep 28 23:46:47 2015 -0700 - - Merge pull request #452 from MDAnalysis/issue/451 - - AtomGroup.sequence() works again for atoms. - - Close #451 - -commit 42607eb2082109d555b885cdae39350e77bc5448 -Author: Oliver Beckstein -Date: Mon Sep 28 18:49:31 2015 -0700 - - AtomGroup.sequence() works again for atoms - - - added test case - - fixes issue #451 - -commit a811877259644898d184cd5151723232aad83fbe -Author: Oliver Beckstein -Date: Mon Sep 28 18:44:23 2015 -0700 - - added semantic versioning to CHANGELOG rules - - Also bumped release number to 0.12.0-dev (instead of 0.11.1-dev) - -commit 89145e8a2704bf95d80db266d696d3f7d64d5e10 -Author: Richard Gowers -Date: Mon Sep 28 17:39:17 2015 -0700 - - Added bond length calculation - -commit 0ff135ac834fe1a85983fde0782feda06a0f0990 -Merge: 11851bf04 98fb034ad -Author: Richard Gowers -Date: Mon Sep 28 17:34:20 2015 -0700 - - Merge pull request #449 from MDAnalysis/issue-297 - - Removed weakref system from Atom.universe. - -commit 11851bf04fd248760f9e572f0873632182b8ad8d -Merge: 495ba5d02 0444b62cd -Author: Richard Gowers -Date: Mon Sep 28 17:33:24 2015 -0700 - - Merge pull request #448 from MDAnalysis/issue-446 - - Issue 446 - -commit 98fb034adb1b6b1e3b1eb1783672d9ab194397c5 -Merge: 0df8542e7 b8238e206 -Author: Richard Gowers -Date: Mon Sep 28 09:55:08 2015 -0700 - - Merge branch 'issue-297' of github.com:MDAnalysis/mdanalysis into issue-297 - -commit 0df8542e78ce3232c45c0920083e9ded8057b660 -Author: Richard Gowers -Date: Mon Sep 28 09:54:48 2015 -0700 - - AtomGroup.universe now raises NoDataError on failure - - Previous returned None - -commit b8238e206db2daeabc2e333b22d7540b7fd3a951 -Author: Manuel Nuno Melo -Date: Mon Sep 28 14:50:02 2015 +0200 - - Added AtomGroup picklability test; fixed cosmetics - -commit 0f31aa751af1a70e6c2858bf51b630e439713374 -Author: Richard Gowers -Date: Sun Sep 27 17:37:06 2015 -0700 - - Added tests for moving Universe out of scope - -commit c87c1f96c0c5ef9f603a541f5281e65ed609a1e5 -Author: Richard Gowers -Date: Sat Sep 26 17:41:08 2015 -0700 - - Removed weakref system from Atom.universe. - Atoms now hold a strong/real reference to the Universe - -commit 495ba5d0289277f1ff86f9062766f743a0199d56 -Author: Richard Gowers -Date: Sat Sep 26 10:39:12 2015 -0700 - - Removed cmp from LAMMPSParser - -commit fb05bc84519f88645a9be80e168eb5c61f6afad2 -Author: Richard Gowers -Date: Sat Sep 26 10:37:32 2015 -0700 - - Removed cmp from Atom - - replaced cmp with lt & eq - - Required for Issue #260 - -commit 7ba130eb0b3337484ea94aa009ea1eac063b351e -Author: Richard Gowers -Date: Sat Sep 26 10:25:12 2015 -0700 - - Added extra tests for Atom comparison - -commit 0444b62cd43d5d1235d031b547d9de2c3a440097 -Author: Richard Gowers -Date: Fri Sep 25 21:30:12 2015 -0700 - - Fixed Issue #446 - - Wrapped serials get set to None - - If any serials got set to None, bond parsing is bypassed - -commit 42da02636a0a1e000f7cad2bf1269747a344d913 -Author: Richard Gowers -Date: Fri Sep 25 21:15:48 2015 -0700 - - Added tests for Issue #446 - - Serials turning into '****' when going over 100k in PBD files - -commit a785e44c56c284fb48409731ec0fcdcba38aff31 -Author: Richard Gowers -Date: Thu Sep 24 15:25:20 2015 -0700 - - Improved AG IndexError message - - From: - IndexError: list index out of range - To: - IndexError: Index 758 is out of bounds for AtomGroup with size 382 - - Moves from normal Python IE to numpy like one - - Reworded a few __add__ TypeErrors - - Moved to using isinstance instead of type() == something - -commit 25ea3da8c6ae61687d2725848aff5f1fec1b14f2 -Merge: 915c0fdf1 c5ac7abf0 -Author: Oliver Beckstein -Date: Wed Sep 23 20:52:40 2015 -0700 - - Merge pull request #445 from MDAnalysis/make_whole_fix - - Make whole fix - -commit c5ac7abf0dea4bd585b18be2ae5ed5f8d98cb5bc -Author: Richard Gowers -Date: Wed Sep 23 15:44:21 2015 -0700 - - Fix for issue with lib.mdamath.make_whole - - When all bonds were short the function would return as if it had worked - even if some later checks would fail - - Reordered checks so that ALL checks are done, then the work begins - -commit bb27ff02b62deecab783f1d3d84f0ea5059e0135 -Author: Richard Gowers -Date: Wed Sep 23 15:29:59 2015 -0700 - - Added test for lib.mdamath.make_whole - -commit 915c0fdf1e452da3d29003b1403b1ce6ace49e50 -Merge: 45c56bee2 608feef30 -Author: David Dotson -Date: Mon Sep 21 16:39:33 2015 -0700 - - Merge pull request #439 from MDAnalysis/feature-fancytrajindex - - Added ability to slice Reader object using lists and arrays of integers - - Submitted by @richardjgowers. - -commit 608feef30c1198f390ecf64ddd61b92f7dddb72b -Merge: 3c86189a9 45c56bee2 -Author: Richard Gowers -Date: Tue Sep 22 00:24:17 2015 +0100 - - Merge branch 'develop' into feature-fancytrajindex - - Conflicts: - package/CHANGELOG - -commit 3c86189a978663987d3f1cfd330c05f3ee2620e7 -Author: Richard Gowers -Date: Tue Sep 22 00:15:42 2015 +0100 - - Fixed duplicate named test - -commit 45c56bee2b5d66c94f322c5caabe03412e3d973d -Author: Richard Gowers -Date: Tue Sep 22 00:14:35 2015 +0100 - - Added sseyler to CHANGELOG - -commit 58484f51a3f7145d93a350762ed7f4199e1c62bf -Merge: 4a3f08c27 2ae4ae626 -Author: Richard Gowers -Date: Mon Sep 21 19:06:06 2015 -0400 - - Merge pull request #438 from sseyler/develop - - Updated PSA module - -commit 4a3f08c277f6810dd4681230bdfe3c0fe2b07b70 -Merge: ef3f62e1d e045b6686 -Author: Richard Gowers -Date: Mon Sep 21 18:48:58 2015 -0400 - - Merge pull request #442 from MDAnalysis/fix-coverage - - Fixed converagerc for coverage 4.0 - -commit e045b6686c19cbc6923bf3ccf76ecea2c690fdaf -Author: Richard Gowers -Date: Mon Sep 21 23:30:50 2015 +0100 - - Fixed converagerc for coverage 4.0 - -commit 2ae4ae62626cfe25ce61e70f0df4cf23a5f78395 -Author: Sean L. Seyler -Date: Mon Sep 21 11:52:51 2015 -0700 - - Added note directives to docs for getter methods (where analyses must be performed prior) in PSAnalysis - -commit 0ef949cdb336776288ee8b8e5bd6c5f05c79c2d8 -Author: Sean L. Seyler -Date: Mon Sep 21 11:00:04 2015 -0700 - - psa_pairs, nearest_neighbors, hausdorff_pairs are properties whose corresponding instance variables (_psa_pairs, _NN, and _HP) are now removed from the API - -commit 83b6d982f9e7ad592183720e808637406fb10c2f -Author: Sean L. Seyler -Date: Mon Sep 21 10:47:58 2015 -0700 - - Updated documentation for psa_pairs, nearest_neighbors, hausdorff_pairs properties in PSAnalysis - -commit 2c3ad5aa371020cdeb6099fa619b501d034e8efc -Author: Sean L. Seyler -Date: Mon Sep 21 09:53:13 2015 -0700 - - Made 'get_psa_pairs' a property - -commit b0374da7ed4e6d891183aea2e6e22394c15745a3 -Author: Sean L. Seyler -Date: Fri Sep 18 18:43:17 2015 -0700 - - Instances of PSA --> PSAnalysis - -commit 65834165a897100c6734607af20cc9b56f5c6aad -Author: Sean L. Seyler -Date: Fri Sep 18 18:41:10 2015 -0700 - - Added note about PSA --> PSAnalysis in CHANGELOG - -commit e2b99d8bf5d7bd070b8be7df88d3885db243ebb4 -Author: Sean L. Seyler -Date: Fri Sep 18 18:38:23 2015 -0700 - - 'PSA' now 'PSAnalysis' (less namespace confusion); added import for psa.py in test_analysis.py - -commit c9132364f1620e9e36aef9c67819fbd6a279746a -Author: Sean L. Seyler -Date: Fri Sep 18 18:29:15 2015 -0700 - - Updated CHANGELOG for PSA tests and new AdK DIMS DCD test file - -commit 9cc3e4d13b8397b3b47ad863bf92c69c95c42408 -Author: Sean L. Seyler -Date: Fri Sep 18 18:23:22 2015 -0700 - - Added seaborn to 'extras_require' in setup.py, try/except for seaborn imports in PSA plotting methods - -commit e029273cf93bf009d9c3c3ce9c2f1e24250871b8 -Author: Sean L. Seyler -Date: Fri Sep 18 18:09:43 2015 -0700 - - Added back DCD2 to datafiles - -commit 673fbebcc187884c1c76ffd18b4cf7e1c1fdc66d -Author: Sean L. Seyler -Date: Fri Sep 18 17:58:22 2015 -0700 - - PSA.HP/PSA.NN now properties, fixed NN plot method - -commit 8a23524075fa4b0acf385be473c3a8a68da78896 -Author: Sean L. Seyler -Date: Fri Sep 18 17:22:55 2015 -0700 - - Revert "Added DCD2 (DIMS AdK transition) to datafiles" - - This reverts commit a68bf3a47296ae247594d8a2642aa90ddc67b5a1. - -commit 3492ae6caf6319ab0b677e8974fdb834013a8104 -Author: Sean L. Seyler -Date: Fri Sep 18 15:16:06 2015 -0700 - - Added basic tests for PSA - -commit 4a5caf6c955fe1fe8c997fb23a7e14b2f833be58 -Author: Sean L. Seyler -Date: Fri Sep 18 15:14:22 2015 -0700 - - Minor tweaks to nearest neighbor plotting method - -commit 8e5520030581929fb52349bb58a9c3160077c668 -Author: Richard Gowers -Date: Fri Sep 18 07:36:31 2015 +0100 - - Added more tests for Reading fancy indexing - -commit a68bf3a47296ae247594d8a2642aa90ddc67b5a1 -Author: Sean L. Seyler -Date: Thu Sep 17 15:26:46 2015 -0700 - - Added DCD2 (DIMS AdK transition) to datafiles - -commit 3af46b27fda68ea25ca93053c2c5c28bcebd5381 -Author: Sean L. Seyler -Date: Thu Sep 17 15:21:44 2015 -0700 - - Added new DIMS AdK trajectory to test data - -commit 3bb5ec65190955dd0fb0830ddacb2eb026e03928 -Author: Sean L. Seyler -Date: Thu Sep 17 15:20:57 2015 -0700 - - Added enhancements to PSA in CHANGELOG - -commit f1cecf5e20ed7f15264fbe16abfd69a08e9e60de -Author: Richard Gowers -Date: Thu Sep 17 12:23:28 2015 +0100 - - Added ability to slice Reader object using lists and arrays of integers - (Issue #437) - - Added tests - -commit bc13c0245bc5e927f2137393c00fc95075557bb9 -Merge: 5a2f6bad2 ef3f62e1d -Author: Sean L. Seyler -Date: Wed Sep 16 15:20:47 2015 -0700 - - Fixed psa.py conflicts (numpy --> np) - -commit 5a2f6bad2c9ca375c51e82f9868bfb81ca909f36 -Author: Sean L. Seyler -Date: Wed Sep 16 15:11:37 2015 -0700 - - PSA updated: new metrics, Hausdorff/nearest neigh analysis and plotting, additional functions/features - -commit ef3f62e1d31b19e84e35362fc874fe88b73e0db3 -Merge: d4351b135 6ef55d9c9 -Author: Oliver Beckstein -Date: Tue Sep 15 22:31:14 2015 -0700 - - Merge pull request #436 from MDAnalysis/feature-topologycoordinates - - Removed _topology_coordinates_readers dict from coordinates - -commit 6ef55d9c96a3a691f903495e8780fdf8c367bc09 -Author: Richard Gowers -Date: Tue Sep 15 08:26:46 2015 +0100 - - Removed _topology_coordinates_readers dict from coordinates - - Previously this dict listed all formats that could act as both - coordinate and topology files. A more logical way to do this check - is to instead just see if the format is in both the coordinate - and parser dicts. - - This means if someone adds a Topology parser for a previously only - coordinate format, that it would get picked up automatically, rather - than having to declare it as being able to do both. - -commit d4351b1353a7ab6f98f7a8cf43b21b39dde9afb7 -Merge: 9c7b9270f 04d0ec72b -Author: Richard Gowers -Date: Mon Sep 14 23:39:16 2015 +0200 - - Merge pull request #435 from dotsdl/issue-434 - - Fixes #434: trying to write empty AtomGroup gives clear message. - -commit 04d0ec72b2f022ab0e50bd0351ec3b1e7643055a -Author: David Dotson -Date: Mon Sep 14 11:31:47 2015 -0700 - - Added change to changelog. - -commit 9c7b9270f05c7103610935eca8d5a3b8ba2e37fa -Author: Oliver Beckstein -Date: Mon Sep 14 10:14:37 2015 -0700 - - README: changed Google Group badges - - [ci skip] - -commit d4bc077a7b4852e328c5c9b8386dccfa052d6ca0 -Author: David Dotson -Date: Sun Sep 13 17:47:02 2015 -0700 - - Fixes #434: trying to write empty AtomGroup gives clear message. - - Also added an explicit test that writing an AtomGroup with no atoms - raises on IndexError. - -commit c3f3a63d800e8d75904ca76217a47741e58edaa9 -Merge: 80bc2a2a9 30a4c1d43 -Author: Oliver Beckstein -Date: Sat Sep 12 17:20:20 2015 -0700 - - Merge pull request #433 from MDAnalysis/issue/386 - - automatic doc deployment (closes #386) - -commit 30a4c1d43c0fb082cb3b495edb645a208401834b -Author: Oliver Beckstein -Date: Sat Sep 12 15:20:18 2015 -0700 - - doc deployment: only fetch shallow doc branch for speed-up - - - in deploy: only fetch a shallow copy of the doc branch to speed up the - process - - fetch a shallow copy of gh-pages; with newer git version >=1.9 we can also - to push to the branch - - renamed branch variable to GH_DOC_BRANCH - - the submitting user is now called TravisCI because I could not figure out - how to include spaces in global envvars in travis.yml (despite trying to - backslash-escape or use of double quotation marks) - -commit 007c85935a79f68267614187c36535da41049f9e -Author: Oliver Beckstein -Date: Sat Sep 12 14:19:28 2015 -0700 - - doc deployment: only run if first job - - - use subshells when using cd (otherwise deploy script is not found) - and should make the travis process more robust - - only run doc deployment if we are the first job in the build matrix (from - @bguiz , see https://github.com/steveklabnik/automatically_update_github_pages_with_travis_example/issues/5) - - configure almost everything through env vars in .travis.yml - -commit 80bc2a2a9cc826627eca2691e425c284fb76269f -Author: Oliver Beckstein -Date: Sat Sep 12 14:19:28 2015 -0700 - - doc deployment: added travis build_ext step - - As suggested by @kain88-de in #386, we let travis also build the libraries in place - (with "python setup.py build_ext --inplace") so that sphinx can properly import - the local build of MDAnalysis. - - Manually tested but needs to be run on travis on the develop branch to check - that it performs as it should. - -commit 04b7a208ace659209f2f6c4cbe6287d1d90e4eab -Merge: df0a40e05 af0ce2294 -Author: Richard Gowers -Date: Sat Sep 12 11:35:03 2015 +0100 - - Merge pull request #428 from MDAnalysis/feature-XYZimprovements - - Added frame seeking to XYZReader - -commit af0ce2294e42d01004d405a2193159117bb2f95e -Merge: b7a549e78 df0a40e05 -Author: Richard Gowers -Date: Sat Sep 12 10:31:02 2015 +0100 - - Merge branch 'develop' into feature-XYZimprovements - - Conflicts: - package/CHANGELOG - package/MDAnalysis/coordinates/XYZ.py - -commit df0a40e054e7ad54631a3704ece7c129fdb30d02 -Merge: f6a8bb057 4488c598b -Author: Richard Gowers -Date: Sat Sep 12 10:26:30 2015 +0100 - - Merge pull request #432 from MDAnalysis/extra-occupancy - - Extra occupancy tweaks - -commit 4488c598b39e1606f41a2bf7bf8beea6052fb054 -Author: Richard Gowers -Date: Sat Sep 12 10:05:42 2015 +0100 - - Added set_occupancies - -commit 8874af690323c301a6abaa6f1928d3c6c49f2266 -Author: Richard Gowers -Date: Sat Sep 12 09:38:46 2015 +0100 - - Changed AtomGroup.occupancy to occupancies - - Added ability to set occupancy from AtomGroup - -commit f6a8bb057bd786ea9c2d503ef8c541ffd807522e -Merge: 0a81b3f39 6c94fc841 -Author: Richard Gowers -Date: Sat Sep 12 09:07:26 2015 +0100 - - Merge pull request #425 from kain88-de/pdb-reading - - PDB reading - -commit 0a81b3f39e6ea7e32343d80618827af0c7c2db40 -Merge: f8bdc8065 29d9e8935 -Author: Richard Gowers -Date: Sat Sep 12 09:04:55 2015 +0100 - - Merge pull request #430 from MDAnalysis/issue/386 - - Issue/386 - -commit 29d9e89353380979e399d40b99ddd5fa4098d515 -Author: Oliver Beckstein -Date: Fri Sep 11 16:59:17 2015 -0700 - - README: updated doc badges - - - use color scheme with custom badges - - added badge for developer docs at new URL - - shortened names (Documentation to docs) - - docs: latest ---> release docs - docs: development ---> autogenerated docs of develop branch - -commit f4bbc95a7d854cffeecd5c5e923ff1601826eeab -Author: Oliver Beckstein -Date: Fri Sep 11 16:43:23 2015 -0700 - - automatic develop doc deployment (#386) - - - build and deploy development docs from Travis-CI - - see https://github.com/MDAnalysis/mdanalysis/issues/386 for details - - closes Issue #386 - - NOTE: The development docs are now visible at http://www.mdanalysis.org/mdanalysis/ - (so various URLs and forwarding for devdocs.mdanalysis.org need to be - changed) - -commit 6c94fc8415b49ff95acc3c807763faf94563c92b -Author: Max Linke -Date: Fri Sep 11 22:57:53 2015 +0200 - - Add changes to changelog - -commit 734b25961944d1c02f5579bccd3e7335a77436e2 -Author: Max Linke -Date: Fri Sep 11 22:51:22 2015 +0200 - - Use numpy style doc strings - - awesome that we can use them now. - -commit 4bdfa3d5d83f4753cbad379de86e48880e10d5fc -Author: Max Linke -Date: Fri Sep 11 19:11:57 2015 +0200 - - Add test for occupancy field - -commit 890c4ceff0fa561014eea441ba0dff9ca143b0ed -Author: Max Linke -Date: Fri Sep 11 18:27:51 2015 +0200 - - Add occupancy information to Atom/AtomGroup - -commit b7a549e7836ceae8d734e362142b6d9031904e11 -Author: Richard Gowers -Date: Fri Sep 11 19:46:24 2015 +0100 - - Fixed Compressed test - -commit f8bdc80656da45c2b35ba052b4ad3ab1104a7503 -Merge: c12ec883b 526139054 -Author: Richard Gowers -Date: Fri Sep 11 19:45:03 2015 +0100 - - Merge pull request #423 from kain88-de/docs - - Proof that numpy-style docs can be used with normal ReST - -commit b7a7a07142b11db9aee87dc98ed7670c35965b02 -Author: Richard Gowers -Date: Fri Sep 11 19:24:53 2015 +0100 - - Added frame seeking to XYZReader - -commit 1bb22bd3c60775c8459ddb7d66b7eb11538ca3e7 -Author: Max Linke -Date: Thu Sep 10 07:46:05 2015 +0200 - - Default to occupancy=1 if not given in PDB - - This is the most permissive default I can think of. Imagine someone has - a pdb like this. - - ATOM 1 CA LYS A 1 111 123 124 .5 - ATOM 1 CA VAL A 1 111 123 124 .5 - ATOM 2 CA ALA A 2 111 123 125 - ATOM 3 CA CYS A 3 9 9 9 .9 - ATOM 3 CA LYS A 3 9 9 9 .1 - - What should be the occupancy of the alanine? In the most probable cause - the author of the PDB thought it should be one. The occupancies are - afterwards added to the timestep object. - - This also fixes another issue we might have had with the old code. It - was possible to have less occupancy values then atoms in a universe. - That should have triggered an error. - -commit 6bf36fdb7bccb53f374ab3a77d6fdcf4dd8e703b -Author: Richard -Date: Fri Sep 11 14:07:35 2015 +0100 - - WIP Polymer analysis - -commit 4ebc66e91f51b50eb1097d789e7cf601c4a47b59 -Author: Richard -Date: Fri Sep 11 12:37:08 2015 +0100 - - Added lib.util.blocks_of - -commit 526139054f3b0d9d1cae7066a4f6c8ee6a3b89d6 -Author: Max Linke -Date: Wed Sep 9 21:24:34 2015 +0200 - - Activate sphinx.ext.napoleon for numpy-style docs - - This also changes one of the docs strings to demonstrate that - normal ReST files and the numpy-style can live side by side. - - [skip ci] - -commit c12ec883b5501f081c2df6af1823d25d82e50503 -Author: Oliver Beckstein -Date: Wed Sep 9 17:48:07 2015 -0700 - - use links through mdanalysis.org - - - Changed links for developer group and docs to use the *.mdanalysis.org forwards. - - Added links to trajectory and topology formats. - -commit 6bf440ebb77ba7fe6efe952e4b59687a680ea6fc -Author: Max Linke -Date: Wed Sep 9 22:33:05 2015 +0200 - - Fix missing occupancy in PrimitivePDBReader - - PrimitivePDBReader is now permissive about missing occupancies. - -commit de7b4e1ca2e4d50d44ab93f00f8af7a8fd3a0a90 -Author: Max Linke -Date: Wed Sep 9 22:29:22 2015 +0200 - - Add failing test to read PDB trajectory - - If occupancy aren't present the current primitive PDBreader is - failing. - -commit e99650e725bf27ff70254c1e99a08bc14ee2bf33 -Author: Max Linke -Date: Wed Sep 9 21:23:55 2015 +0200 - - Use current branch to build docs - - Please never change this again. It makes sure that 'make html' just - works and does what you think it will do. - -commit 48a4641c7805a6e1221d13eb46eef7cc63b2a945 -Merge: f9cfb6155 c2dfd613a -Author: Richard Gowers -Date: Tue Sep 8 19:45:24 2015 +0100 - - Merge pull request #421 from kain88-de/numpy-to-np - - Use numpy with abreviation np consistently - -commit c2dfd613a31ef75280acbb069e40c5f18c21e39d -Author: Max Linke -Date: Tue Sep 8 20:23:27 2015 +0200 - - Fix 'from numpy import ...' - - No numpy function is imported into the global namespace - -commit ef3fa2301f6436c3af03faa9106fe44787ad1aec -Author: Max Linke -Date: Tue Sep 8 18:02:41 2015 +0200 - - Use numpy with abreviation np consistently - - Fix #392 - -commit f9cfb61559e54a0f46322d3ca444775442c68376 -Author: Richard Gowers -Date: Tue Sep 8 10:14:44 2015 +0100 - - Added small example to Readme - -commit 6b64424b83667d243a9b4bf8264b2c730fce1bf5 -Author: Richard Gowers -Date: Tue Sep 8 09:43:24 2015 +0100 - - Added docs link to README - -commit 0cebefab580d401595528f98ca830cb8b976e787 -Author: Richard Gowers -Date: Mon Sep 7 20:44:27 2015 +0100 - - Bumped version to 0.11.1-dev - -commit de97ccc10ecade5e6b255c644c83327f8eaf2d4c (tag: release-0.11.0) -Author: Richard Gowers -Date: Mon Sep 7 12:15:56 2015 +0100 - - Rebuilt docs for 0.11.0 release - -commit 75452427a773f55e21e443e5ab39b808c75359fb -Author: Richard Gowers -Date: Mon Sep 7 11:59:30 2015 +0100 - - Updated version number to 0.11.0 - -commit 5313e06affca233528e8fd152c66129095f93797 -Author: Richard Gowers -Date: Mon Sep 7 10:36:56 2015 +0100 - - Finalised CHANGELOG for 0.11.0 - -commit d1ed4b1333b0c1d5982bd864dff84343c9ff518f -Merge: 8fedf34ab 5807229bb -Author: Richard Gowers -Date: Sun Sep 6 12:56:17 2015 +0100 - - Merge pull request #417 from MDAnalysis/exclude_migration - - Excluded migration from coverage - -commit 5807229bbf3ff033fdfb83fb2d0bb2ceaef9ac33 -Author: Richard Gowers -Date: Sun Sep 6 12:44:32 2015 +0100 - - Excluded migration from coverage - -commit 8fedf34ab966af75eacb419a1e63da0b71ea76d7 -Author: Richard Gowers -Date: Sun Sep 6 10:18:00 2015 +0100 - - Added notes to CHANGELOG on how to survive API changes (#415) - -commit b5451462bee9fd7586f6fb7fece3f39867fa7165 -Author: Richard Gowers -Date: Sun Sep 6 10:04:18 2015 +0100 - - Tidying changelog for Issue #415 - -commit d23e7c0018c1dcbd697195b83465f92054334679 -Merge: d37794f12 a2e4e20b7 -Author: Richard Gowers -Date: Sun Sep 6 08:44:38 2015 +0100 - - Merge pull request #416 from dotsdl/doc-scan-0.11.0 - - Fixed documentation for AtomGroup in light of 0.11.0 changes. - -commit a2e4e20b78745d40df555af8ecb70c61d5a5c193 -Author: David Dotson -Date: Sat Sep 5 23:14:38 2015 -0700 - - Fixed documentation for AtomGroup in light of 0.11.0 changes. - - Updated AtomGroup docs to refer to properties for setters and to also - use the new (plural) setter names. Also updated alignment analysis doc - to use AtomGroup.positions instead of AtomGroup.coordinates(). - -commit d37794f1222e8627f0aae69aacb88756377ddcc8 -Merge: cdd3f80c1 394b7896c -Author: Oliver Beckstein -Date: Sat Sep 5 16:58:50 2015 -0700 - - Merge pull request #413 from MDAnalysis/feature-merged-ten2eleven - - Feature merged ten2eleven: migration from 0.10 to 0.11 with MDAnalysis.ten2eleven() - - Closes #377. - - We still need docs #381 (specifically [Migrating MDAnalysis code with ten2eleven.py](/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py)) but we can tackle this better with `ten2eleven` in place. - - I will consider this merge to close #377 even though we have not full resolved `.frames` handling. If anything major comes up, we will re-open #377. - -commit cdd3f80c127fa74351934d38b1d393f8ed2b9006 -Merge: dbd7cc66e 1a6f76926 -Author: Oliver Beckstein -Date: Sat Sep 5 16:47:54 2015 -0700 - - Merge pull request #414 from MDAnalysis/issue249 - - Merge now merges bonded topology - -commit 1a6f76926a5178283e3e624e2e0d3bf57e9f0a1c -Author: Richard Gowers -Date: Sat Sep 5 18:16:43 2015 +0100 - - Merge now merges bonded topology - - Fixes issue #249 - -commit 394b7896c5c66b63281ca13d0601ad4f73021062 -Author: Richard Gowers -Date: Sat Sep 5 10:24:11 2015 +0100 - - Moved ten2eleven fixes to inside package - - Added migration.ten2eleven.ten2eleven function - -commit 88ac3960f5b1437d5b7e72b50a829d1ef485812c -Author: Tyler Reddy -Date: Fri Sep 4 16:38:38 2015 +0100 - - Updates to .frame fixers and test code. - -commit 674c99277cc2574160c83e489b0b0f6a129fa52b -Merge: dbd7cc66e ccef352dd -Author: Richard Gowers -Date: Fri Sep 4 16:21:38 2015 +0100 - - Merge branch 'ten2eleven-master' into develop - -commit dbd7cc66edc3ce9ea584464d0bc9a0c97d64ada9 -Merge: 06fbc36d0 ca4545637 -Author: Richard Gowers -Date: Fri Sep 4 14:44:18 2015 +0100 - - Merge pull request #409 from MDAnalysis/TG_fixes - - Some fixes for TopologyGroup - -commit ca45456378ea4bac7f8c8d9c8e1dcf5ed39835b5 -Author: Richard Gowers -Date: Fri Sep 4 14:01:52 2015 +0100 - - Some fixes for TopologyGroup - -commit ccef352dd9f56c3bc6ef017eacd36efbdef25d6a -Merge: 30ab3dbae 3b67793ac -Author: Tyler Reddy -Date: Fri Sep 4 11:30:28 2015 +0100 - - Richard's extra align_principalAxis camelcase fix. - -commit 30ab3dbae7e15411e7de4db5de355832c778cb61 -Author: Tyler Reddy -Date: Fri Sep 4 11:28:25 2015 +0100 - - Initial efforts to place warning comments before .frame lines. Still needs work to deal with parentheses in prefix, etc. - -commit 3b67793ac1cf45749a1d850f03dc3fa38c189775 -Merge: 63541a47d 08f46bff0 -Author: Tyler Reddy -Date: Fri Sep 4 11:26:07 2015 +0100 - - Merge pull request #1 from richardjgowers/master - - Fixes for a missed camelcase - -commit 08f46bff0a17c0bff2ad38187282c4321531a262 -Author: Richard Gowers -Date: Fri Sep 4 10:47:24 2015 +0100 - - Test for align_principalAxis - -commit 145f31fbc324cd05fd0aebeaaf609bf424c19092 -Author: Richard Gowers -Date: Fri Sep 4 10:42:31 2015 +0100 - - Fix for align_principalAxis - -commit 06fbc36d02bc2d08ba3efc40a660f9de831bce99 -Merge: e044ddd1b ed319124d -Author: Richard Gowers -Date: Fri Sep 4 10:37:53 2015 +0100 - - Merge pull request #408 from MDAnalysis/missedcamelcase - - Missed camelCase fix - -commit ed319124d9e2976e9489c8fd24bed1ff47c2e42c -Author: Richard Gowers -Date: Fri Sep 4 10:22:18 2015 +0100 - - Missed camelCase fix - - Issue #389 - -commit 63541a47de3240255717f6be8cce8e451daf1664 -Author: Tyler Reddy -Date: Wed Sep 2 12:22:25 2015 +0100 - - Adjusted agsetterpluralization fixer to handle more pathological test case that was causing issues in the unit tests. - -commit cb213597a0eafa7e5ff8e5093d9fb228a9df3c2e -Author: Tyler Reddy -Date: Wed Sep 2 11:10:33 2015 +0100 - - Added new fixer for atomgroup method set_plural conversions along with some crude tests. - -commit e044ddd1b24c40072527789805884e53d0a6a5b8 -Merge: 0019fe9bf 7cdff97a9 -Author: Richard Gowers -Date: Mon Aug 31 20:17:37 2015 +0100 - - Merge pull request #406 from dotsdl/issue-385 - - Fixes issue #385 - -commit 7cdff97a913cb9b2da2ecaba6f46ed91ecb8bdf9 -Author: David Dotson -Date: Mon Aug 31 10:32:30 2015 -0700 - - Added deprecation warnings to use of old singular setters for AtomGroups - -commit 1c6fcfa68c1699111477ab3734c7b5a2f675440c -Author: David Dotson -Date: Fri Aug 28 23:34:42 2015 -0700 - - Fixes issue #385 - - AtomGroups now return arrays of length equal to the AtomGroup when calling - properties like `resids`, `resnames`, and `resnums`. Likewise, - ResidueGroups return arrays of length equal to the ResidueGroup when - calling `segids`. - - Adjustments were made to fix issues with stale ResidueGroup and - SegmentGroup cacheing in light of these changes, and these happned to - fix some lonstanding known errors in the tests. Not all cacheing issues - were solved; these will have to wait for the AtomGroup overhaul in the - next release cycle. - - Changed property setters in AtomGroups with names like `set_` - to use the plural form to directly match the names of the properties - they correspond to. - - Also added two spaces between many test classes to improve readability. - Couldn't resist. - -commit 0019fe9bfe63fd0b04b5f5862aaf571599877d79 -Merge: c457cfc48 6d8a712d1 -Author: Richard Gowers -Date: Mon Aug 31 13:12:07 2015 +0100 - - Merge pull request #407 from MDAnalysis/Issue397 - - Fixes Issue397 - -commit 6d8a712d108737d236805f6e8f7f7aa675968cd7 -Author: Richard Gowers -Date: Mon Aug 31 12:27:34 2015 +0100 - - Fixed circular reference to reader causing memleak - -commit e059ad9037369dd114e0d6c6ba6cf34e1eab16c9 -Author: Richard Gowers -Date: Mon Aug 31 12:08:56 2015 +0100 - - Fixed failing test - - Rewrote tests for Timestep copying - - Fixed XTC/TRR rewinding on calculating dt - -commit c457cfc4864922b9e704124e1393a21d4ec07c6d -Merge: 030227fe8 ddd287b80 -Author: Richard Gowers -Date: Sat Aug 29 12:42:31 2015 +0100 - - Merge pull request #405 from MDAnalysis/tidyup - - Tidyup - -commit ddd287b80485fae19dc52c366818caa87d477411 -Author: Richard Gowers -Date: Sat Aug 29 11:57:36 2015 +0100 - - Replaced dunderscore trajectory from Universe - -commit 04ed9685edb43ea7805d54ca8f7e69330ff55bbb -Author: Richard Gowers -Date: Sat Aug 29 11:56:02 2015 +0100 - - Tidied some imports in lib/util - -commit 8fe58a896e2e2a813b91d4406a55b2f662f6541f -Author: Tyler Reddy -Date: Fri Aug 28 16:14:54 2015 +0100 - - Added new fixer and associated test code for MDA 0.11 calc_torsions() -> calc_dihedrals() conversion. - -commit 320c3d9bdf1cbed1498d4546a15430800e146b9d -Author: Tyler Reddy -Date: Fri Aug 28 15:45:51 2015 +0100 - - Added new fixer for torsion to dihedral class name changes along with a set of simple tests. - -commit 030227fe812482165ba2ccc21e74a5b8b5a9b4e2 -Merge: 248b48959 5a1f046bd -Author: Oliver Beckstein -Date: Fri Aug 28 01:46:56 2015 -0700 - - Merge pull request #403 from MDAnalysis/issue-336 - - Fixes Issue 336 - -commit 2070abff18b4e13ed4c7ee37343df7b4ca578c75 -Author: khuston -Date: Thu Aug 27 15:58:27 2015 -0400 - - Reader _get_dt method, causes problems - -commit 5a1f046bda621657fbb2d56543e5b18a6551bb69 -Author: Richard Gowers -Date: Thu Aug 27 14:44:24 2015 +0100 - - Added Error tests - -commit 6d9d0fb252f00d001189d383a2845ca9a46dcc3d -Author: Richard Gowers -Date: Thu Aug 27 12:44:32 2015 +0100 - - Added compressed filename checks to get_reader - -commit 4f26066629a5536f19d2a8bec39b7506dc23a5a4 -Author: Richard Gowers -Date: Thu Aug 27 12:38:53 2015 +0100 - - Updated changelog - - Removed knownfailure - -commit 331f6f408feda09eca574ac7d3a90e4385e6db5a -Author: Richard Gowers -Date: Thu Aug 27 12:21:43 2015 +0100 - - Fixed ChainReader and format kwarg - -commit 89eebd35c217d749b271467cbb7eae77b8d1e3b1 -Author: Tyler Reddy -Date: Thu Aug 27 12:12:34 2015 +0100 - - Added a fixer and corresponding test code for conversion of numframes to n_frames in MDA 0.11 release. - -commit 5d3498130f3c064761b1196e5c1d4507c8bb2afc -Author: khuston -Date: Wed Aug 26 16:07:35 2015 -0400 - - Fixes for Issue #397 - - When each trajectory reader initializes, it creates a Timestep which is - an attribute of the Reader. In __init__() for the XDR and TRZ readers, - the Timestep's dt attribute was not set. In __init__() for the DCD reader, - delta conversion was calculated without regard to value of self.units. - DLPoly also gave a testing error because units['time'] was undefined. - - After fixing the above, the @known_failure decorator was removed from - test_dt. - -commit 290b531c2933ae495f7b28f717aa12e9ce424fa6 -Author: Richard Gowers -Date: Wed Aug 26 21:10:19 2015 +0100 - - Fixed failing test - -commit 13bac79278ede566de2e7b8220650290784c3395 -Author: Richard Gowers -Date: Wed Aug 26 20:46:38 2015 +0100 - - Added .gz to tests - -commit 19f87ddb96684d1e29c6136e604e1432998f2cf3 -Author: Richard Gowers -Date: Wed Aug 26 18:03:44 2015 +0100 - - WIP Issue #336 - -commit 248b489595fd83c05f309689f9b890aa2c6a9971 -Merge: d0fea1af8 80078feaa -Author: Richard Gowers -Date: Mon Aug 24 23:13:36 2015 +0100 - - Merge pull request #395 from kain88-de/sklearn-kdtree - - WIP: Sklearn kdtree - -commit 80078feaaf715f1efb8c86d9837d45138ae2f04b -Author: Max Linke -Date: Mon Aug 24 23:06:33 2015 +0200 - - Fix circular import. - - The problem here is that an import statement actually EXECUTES all the - code that is defined inside of the modules __init__.py. The problem now - is that the lib module was loaded before the execptions were loaded, - note that lib/__init__.py now loads `NeighborSearch.py` which in return - loads `AtomGroup.py` which loads `SelectionError` which is defined later - int the top `__init__.py`. This means we have a circular import and - everything just stops working. By importing the exeptions first - everything will work fine. - -commit 3023fa996eadb710497fdc32e845f4756a2e726b -Author: Max Linke -Date: Mon Aug 24 22:39:38 2015 +0200 - - Update sphinx documentation that KDTree is removed - - I also added a page for the new NeighborSearch module - -commit c3f375d8fe7d0528814508832f2b5b0e3286dfa3 -Author: Max Linke -Date: Mon Aug 24 14:14:57 2015 +0200 - - Add more documentation for NeighborSearch - - [ci skip] - -commit 8fdd717f54887aabbe88895d92fafffee7f9497c -Author: Max Linke -Date: Mon Aug 24 14:01:41 2015 +0200 - - Add NeighborSearch to lib init - - [ci skip] - -commit e93f249f0f043d2c3789627ddb48e114576d7233 -Author: Max Linke -Date: Sun Aug 23 20:29:59 2015 +0200 - - Wrong import in test_pdbqt.py - -commit 318c20aadabe9d41327a0ee7016c36528eaf883d -Author: Max Linke -Date: Sun Aug 23 09:22:01 2015 +0200 - - Add KDTree removal to CHANGELOG - -commit 975b4b2b40daef7e753924098ad6710fe244a9f7 -Author: Max Linke -Date: Sun Aug 23 09:13:50 2015 +0200 - - Add doc-string for AtomNeighborSearch - -commit ed81f174975982bea6a47b537f35b927dda6a152 -Author: Max Linke -Date: Sun Aug 23 08:52:59 2015 +0200 - - Add MDAnalysis.KDTree again - - Explain that the KDTRee has been removed and that this now only - loads the NeighborSearch package. - -commit 7ed58b88d718141c4b43b5e3567037965b03e327 -Author: Max Linke -Date: Mon Aug 17 07:51:04 2015 +0200 - - Use Bio.KDTree for selections - - This way the KDTree removal doesn't require any new dependencies. - -commit 885fa28432af9147062d16d268f9f561ab0a4708 -Author: Max Linke -Date: Mon Aug 17 07:41:31 2015 +0200 - - Switch to BioPython KDTree in AtomNeighborSearch - -commit f6e13066e878b4b1dfb8d90bd0aa4581592d0d14 -Author: Max Linke -Date: Sun Aug 16 18:24:30 2015 +0200 - - Use new AtomNeighborSearch in pdbqt test - -commit 91a17892dbe043e5e8e8953b4c8b9e7a4d027c7b -Author: Max Linke -Date: Sun Aug 16 18:22:53 2015 +0200 - - Use new AtomNeighborSearch in hbond_analysis - - PEP8-tify the functions I touched as well. - -commit 5291c974bef51a141403e899a1f83117d4c3cda5 -Author: Max Linke -Date: Sun Aug 16 17:47:32 2015 +0200 - - Re add AtomNeighborsearch class - - This is a refactored implementation of this class based on using the - sklearn KDTree. The search_all method is currently not implemented. The - tests aren't currently passing that will be fixed in later commits. - -commit d22da537e22a9a68d1799ba8318431bb14a0f2c0 -Author: Max Linke -Date: Sun Aug 9 16:46:23 2015 +0200 - - Remove KDTree module - - This removes all appearences of the KDTree Module and it's - Neighbor classes as well. I will reimplement the AtomNeighbor - class again later. - -commit 33fd5335c0328a6a7e105294a05d60184035a198 -Author: Max Linke -Date: Sun Aug 9 16:22:00 2015 +0200 - - port sphericalzoneselection for new KDTree - -commit ad3b14ef1e00f08d70ac1863da71067e29c777c9 -Author: Max Linke -Date: Sun Aug 9 16:19:10 2015 +0200 - - Port Sphericallayer selection for new KDTree - - Continue to get rid of the old KDTree module - -commit caf13f0214ee41480a3ab550424507fadcd0afa7 -Author: Max Linke -Date: Sun Aug 9 14:11:52 2015 +0200 - - Use scikit-learn KDTree in around selection - - We switch from the old copied and here maintained Biopython version of - KDTree to the scikit-learn. For one this will result in a speed increase - and secondly it will allow us to remove the old python 3 incompatible - SWIG module. Plus less code to test and maintain. - - For spherical selections the tests fail right now because they are not - ported yet. - -commit d0fea1af8c7a4399a4fa92e4f6aa7c7da501c6cb -Merge: 103f922c1 0b3712098 -Author: Richard Gowers -Date: Sun Aug 23 10:58:46 2015 +0100 - - Merge pull request #400 from MDAnalysis/issue-396 - - Issue 396 - -commit 0b37120989856cf07e69b0486839e824ed154bbc -Author: Richard Gowers -Date: Sun Aug 23 09:48:49 2015 +0100 - - Fixes for Issue #396 - -commit 06e2f8835b7250e32de6e062e8a83d391e56fc31 -Author: Richard Gowers -Date: Sun Aug 23 09:12:17 2015 +0100 - - Added tests for Issue #396 - -commit ef5ad0de6e59b819ac2ea51ca074e5a71f40c97f -Author: Tyler Reddy -Date: Sat Aug 22 17:01:09 2015 -0300 - - Added new fixer for various camelcase conversions in MDAnalysis 0.11, along with some simple test cases. - -commit 103f922c18d9dabb51ef5918dc6563bd3fed2ecf -Merge: a298fd686 ca72ee95d -Author: Richard Gowers -Date: Sat Aug 22 11:28:51 2015 +0100 - - Merge pull request #399 from MDAnalysis/feature-camelCaseApocalypse - - Fixes Issue #389 - -commit ca72ee95d6d6366b584da4b0bd48bfe9d1310c37 -Author: Richard Gowers -Date: Sat Aug 22 11:05:07 2015 +0100 - - Fixup of last - -commit 223e381968a54f14669debd9ac6bafb616642338 -Author: Richard Gowers -Date: Sat Aug 22 11:00:41 2015 +0100 - - Fixes Issue #389 - - Got rid of camelCase in core/AtomGroup and lib/distances - -commit 7de8cb2772664a83f47ae28599dfd3e4df860bef -Author: Tyler Reddy -Date: Thu Aug 20 17:08:03 2015 -0300 - - New fixer dealing with torsion to dihedral conversions (Issue#373) involving AtomGroup / atom / universe. Crude examples for testing also added. - -commit 15f4b39230232ce6e4ed7fe85b08cee7b07d199b -Author: Tyler Reddy -Date: Thu Aug 20 16:17:05 2015 -0300 - - Incorporated new fixer covering part of the changes introduced by Issue#373 -- methods to properties returning an object. Crude test examples also updated. - -commit a298fd68679e024492c754883eb15ea8d42760d3 -Author: Richard Gowers -Date: Thu Aug 20 12:55:02 2015 +0100 - - Added doc update to renaming of calc_torsions - - Added deprecated version for backwards compat. - -commit dd9fbdc9947e564d2b519bf64afd8a0c8a6db381 -Merge: 96f813a14 b9dc1f99d -Author: Oliver Beckstein -Date: Wed Aug 19 17:21:28 2015 -0700 - - Merge pull request #398 from khuston/TestTimeUnits - - Added test_dt to TestTimestepInterface and added @known_failure - - The test is needed to address issue #397 - -commit b9dc1f99df1fbbc842aaa6776d9db3f65fb57955 -Author: Kyle J. Huston -Date: Wed Aug 19 13:46:53 2015 -0400 - - Added test_dt to TestTimestepInterface and added @known_failure decorator - -commit 3be2479d7858ac674c612764f33b8625a5372a5d -Author: Tyler Reddy -Date: Fri Aug 14 17:33:20 2015 -0300 - - Fixed docstrings for fixes now that copying to standard library dir is no longer needed. - -commit 5bb869eed5f39c5b0033b20c2bb5d5d14cce9a22 -Author: Tyler Reddy -Date: Fri Aug 14 15:50:28 2015 -0300 - - New ten2eleven.py module to run MDA 0.10 to 0.11 conversions directly on the command line without copying modules elsewhere. New fixes package directory for holding the fixes. - -commit 3a16ced6b346500bdfcfcbb182edcf4e6740754c -Author: Tyler Reddy -Date: Fri Aug 14 14:39:05 2015 -0300 - - Added new fixer for MDAnalysis module displacements in 0.11. Passes for new tests added, though I presume this won't tolerate importing MDAnalysis as MDA, etc. - -commit e84bc324af2516446ac984a9e60819ef41260261 -Author: Tyler Reddy -Date: Thu Aug 13 19:05:32 2015 -0300 - - New fixer added to deal with atomgroup count methods changing from camelcase to new property names. Added corresponding test code lines.. - -commit 6b2215fefea734ddeaacd2f9ce18456b4a0634d7 -Author: Tyler Reddy -Date: Thu Aug 13 18:43:11 2015 -0300 - - Added new fixer for converting atomgroup methods to properties. Updated the test file to contain suitable test cases. - -commit 7f8a0e3b40f84011527cb5423e41d09195a01c78 -Author: Tyler Reddy -Date: Thu Aug 13 14:52:05 2015 -0300 - - Added a crude fixer for selectatoms change in MDA 0.11 and a corresponding simple test file. - -commit 96f813a14289f711a5144477f56268689420d6bb -Author: David Dotson -Date: Mon Aug 10 22:15:36 2015 -0700 - - updated CHANGELOG entry for #376 - -commit 90f8581c9eef33ac5c81cfc23c52f69dadf12685 -Author: Oliver Beckstein -Date: Sun Aug 9 23:49:27 2015 -0700 - - regenerated html docs with sphinx (big API changes) - - This update to the docs encompasses a large number of changes that - break the API compared to 0.10.0, including many changes in the interface - to AtomGroup, trajectory readers, and Timestep. - - For further details see the wiki page - http://wiki.mdanalysis.org/MDAnalysis-0.11-unifying-release-user-guide - -commit 80bc3899f632a449b777062b06cb8fc38b43bc4f -Author: Oliver Beckstein -Date: Mon Aug 10 00:13:58 2015 -0700 - - added docs for Hoomd XML topology parser - -commit 5b223670b3ae5d76709c84282e5a6b2bc7391f31 -Author: Oliver Beckstein -Date: Sun Aug 9 23:43:17 2015 -0700 - - reST fixes (version, AtomGroup, topology, helanal) - -commit df74125e6b6d43e3e1adff7650db6bb93f31bd49 -Author: Oliver Beckstein -Date: Sun Aug 9 17:47:43 2015 -0700 - - regenerated distances_parallel.c - - core.distances moved to lib.distances and apparently that had not been - picked up in the C-code yet; related to #287 - -commit 0b971567f5c2f73ee00f53fbe013bdaf7a9fce69 -Author: Oliver Beckstein -Date: Sun Aug 9 17:45:15 2015 -0700 - - maintainer scripts updates - - - adjusted run_tests.sh to use mda_nosetests and use parallel testing - by default (new argument -n NPROC) - - removed run_nosetest_coverage.sh because we get this nicely with travis-ci/coveralls - and the script in its current form seemed broken - -commit 1c57d4a60f0d7add83f8c091f15278305c849ecd -Merge: df56711f9 0cdeed9b1 -Author: Oliver Beckstein -Date: Sun Aug 9 17:10:25 2015 -0700 - - Merge pull request #394 from MDAnalysis/feature-global_keyword - - Added 'global' selction keyword (closes #268) and deprecation warning for 'fullgroup'. - -commit df56711f9450b262c098edcd832e0d5ebd4c310c -Author: Oliver Beckstein -Date: Sun Aug 9 16:58:58 2015 -0700 - - test_topology: fixed deprecated import from core.distances --> lib.distances - -commit 0cdeed9b1fa1cfeffb2110b734afee275b267642 -Author: Manuel Nuno Melo -Date: Mon Aug 10 01:54:57 2015 +0200 - - Updated the CHANGELOG. - -commit 2559f6013c573ddec23668473b4da241cc800260 -Merge: b15647bcb 2734036df -Author: Oliver Beckstein -Date: Sun Aug 9 16:45:10 2015 -0700 - - Merge branch 'PR/388' into develop - -commit 2734036df7cef4c71c1c641c07db9e67874e9bbb -Merge: 97b6dd4d5 b15647bcb -Author: Oliver Beckstein -Date: Sun Aug 9 16:44:50 2015 -0700 - - resolved conflicts when merging PR #388 - -commit 6a24aa0036cd371e012c9e725b62ba0a43b3afce -Author: Manuel Nuno Melo -Date: Mon Aug 10 00:33:01 2015 +0200 - - Switched 'fullgroup' deprecation method to class decoration. - -commit 19ea07b7aa9c212d464f89c5c93184dee52e3cb9 -Author: Manuel Nuno Melo -Date: Sat Jul 11 17:56:15 2015 +0200 - - Added 'global' selction keyword (closes #268) and deprecation warning for 'fullgroup'. - -commit b15647bcbccb9c90aafbe347f922c5e53212fd35 -Merge: c08fa10ef a42f9f2f7 -Author: Oliver Beckstein -Date: Sun Aug 9 00:29:36 2015 -0700 - - Merge pull request #391 from MDAnalysis/feature-LOUDDEPRECATION - - Feature louddeprecation - -commit a42f9f2f7fac55f8d52b0cc9fd42ac407cda9809 -Author: Richard Gowers -Date: Sat Aug 8 16:26:30 2015 +0100 - - Updated CHANGELOG - -commit f1024c10415785d84263a7afb49b9278e58e21e6 -Author: Richard Gowers -Date: Sat Aug 8 16:24:53 2015 +0100 - - Updated tests following selectAtoms deprecation - -commit ac6595db08b9a6b9b4d41186bebf2088f5fb11fe -Author: Richard Gowers -Date: Sat Aug 8 16:23:29 2015 +0100 - - Made DeprecationWarnings always loud - - Deprecated AtomGroup.selectAtoms in favour of select_atoms - -commit 97b6dd4d5a474f0f235c91c90fcab99234933c89 -Author: Richard Gowers -Date: Sat Aug 8 09:26:39 2015 +0100 - - Removed duplicate file - -commit c08fa10ef6c73d538daff2ba19527c039cd3fb2a -Merge: cea16be07 be942b269 -Author: Richard Gowers -Date: Sat Aug 8 09:24:52 2015 +0100 - - Merge pull request #390 from MDAnalysis/issue/366 - - fixed spurious test failures in Timestep API tests - -commit be942b269cec125a9d1c38b9b2e505ed04e6a7dc -Author: Oliver Beckstein -Date: Fri Aug 7 17:52:58 2015 -0700 - - fixed spurious test failures in Timestep API tests - - - replaced assert_equal(ts1, ts2) with assert_(ts1 == ts2) and - also assert_not_equal() with assert_( != ) - - fixes #366 - - tests in test_timestep_api.TestTimestepEquality failed on Mac OS X 10.6.8 - python 2.7, numpy 1.8.1, nose 1.3.7 but passed in Travis CI and Linux; - the fix makes them pass everywhere - -commit daa6fa4adafac8635b0f7a5945b5ac6e621a8d8d -Author: Richard Gowers -Date: Fri Aug 7 13:51:01 2015 +0100 - - Doc fixup - -commit 991a3403e4da237d3b17c50800fcc0ef428d69c9 -Author: Richard Gowers -Date: Fri Aug 7 01:28:37 2015 +0100 - - Changes for Issue #373 - -commit cea16be07a17a652ea76d5e478e29b92905c5e84 -Merge: e799580bb e833ad4ca -Author: Richard Gowers -Date: Fri Aug 7 11:06:07 2015 +0100 - - Merge pull request #387 from MDAnalysis/issue-376 - - Change usage of numberOfAtoms to n_atoms (same for residues, segments); change usage of numframes to n_frames - -commit e833ad4caabab447b094701e62538eddeb8af606 -Author: David Dotson -Date: Fri Aug 7 00:17:13 2015 -0700 - - Added corresponding changes for n_... to c sources. - - Also, tests appear to pass! - -commit 82a821bab5b7fb414adf6a08dc4c242950769d25 -Author: David Dotson -Date: Thu Aug 6 23:33:12 2015 -0700 - - Switched to n_atoms, n_residues, n_segments, n_frames. - - To make access to the number of atoms, residues, or segments in an - atomgroup easier, we include convenience properties for getting at these - values. Now, instead of ``ag.numberOfAtoms()``, one need only call - ``ag.n_atoms``. Likewise for number of residues and segments. Note that - these methods aren't completely necessary since AtomGroups, - ResidueGroups, and SegmentGroups have a ``__len__`` method, but - they are useful for introspection. - - For consistency, we have also changed ``trajectory.numframes`` to - ``trajectory.n_frames``. - - Have yet to update sphinx docs or tests. That's next. - -commit e799580bb1f217ba9ef226e63536fa68828e4291 -Author: Gorman Stock -Date: Thu Aug 6 13:40:17 2015 -0700 - - HOLE: fixes that CPOINT was ignored - - - fixes #384 - - CPOINT is now properly written to the HOLE input file - (instead of CVECT in place of CPOINT) - - also removed superflupus newlines in inp file - - added Gorman Stock to AUTHORS etc - - updated CHANGELOG - -commit bd3b41cfd0012b7e84a5ae9ce42194bd797401d4 -Author: Oliver Beckstein -Date: Thu Aug 6 13:11:42 2015 -0700 - - hole module: update URLs to Oliver Smarts new site: http://www.smartsci.uk/hole/ - -commit 4c8191adf36b3dcf7f89d5617140a8220d4a7c30 -Merge: fda6c2030 2033232b1 -Author: Oliver Beckstein -Date: Thu Aug 6 12:47:18 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit fda6c203033e4161d6edc13f42fec527613fdc11 -Author: Oliver Beckstein -Date: Thu Aug 6 12:47:09 2015 -0700 - - primitive test for lib.log start_logging()/stop_logging() - -commit 0d72817a909ffed1d9b7ea12e43acc7e361c1870 -Author: Oliver Beckstein -Date: Thu Aug 6 12:42:10 2015 -0700 - - moved __version__ to MDAnalysis.version - - - new module MDAnalysis.version at toplevel to avoid circular imports from - lib.log; also allows us to add more fancy version functions - there - - added docs that explain semantic versioning - - logger reads the version from MDAnalysis.version.__version__; - fixed start_logging() and stop_logging(), which broke after the - move to lib.log - - use toplevel import of __version__ so that everything else - still works - - added test cases to test_meta - - modified the maintainer/change_release.sh script - so that it runs sed on version.py - -commit 2033232b1e272b96947856761e8710121ecffb4c -Author: Richard Gowers -Date: Thu Aug 6 09:32:41 2015 +0100 - - Changed Python requirement in setup to 2.7 - - Added Max to 0.11.0 authors - -commit c3aa3f6be77a509b852c4f6820c85f5746f6b347 -Merge: d043dd117 827296ce4 -Author: Richard Gowers -Date: Wed Aug 5 13:12:22 2015 +0100 - - Merge pull request #379 from kain88-de/dcd-new-removal - - Replace new with types - -commit 827296ce49e1c708483a130d113cce585471786d -Author: Max Linke -Date: Wed Aug 5 13:51:04 2015 +0200 - - Replace new with types - - new is decreated since 2.6. Types is supported up to 3.5. - Even though this works we should rewrite the dcdmodule functions - to be pure functions. This way of adding methods to a class - seems hacky to me. - -commit d043dd1172d6a7b87c60d8f819281dea240aaaec -Merge: c79efaa2a 14efd69cd -Author: Richard Gowers -Date: Wed Aug 5 08:54:03 2015 +0100 - - Merge pull request #375 from kain88-de/cython-contact-map - - WIP: Cython port of contact map functions - -commit 14efd69cd3ce46cc533310c2f1c5532dab2ee4e4 -Author: Max Linke -Date: Tue Aug 4 19:48:54 2015 +0200 - - update doc file for analysis.distances - -commit 4c34d7ec1ab80d3da01e1e0aab898c0fd3b9f588 -Author: Max Linke -Date: Tue Aug 4 19:48:06 2015 +0200 - - Update CHANGELOG - -commit 3d2c416e87920f3ea24ad67d9a389b627db93ef3 -Author: Max Linke -Date: Tue Aug 4 11:52:13 2015 +0200 - - Update docstring of contact_matrix - -commit f74f0b882d3279a520b696d059302aa11a417473 -Author: Max Linke -Date: Tue Aug 4 11:35:58 2015 +0200 - - Add author/changelog information - -commit 484e0a6109b86a297e0055f97c21403910b6d1c1 -Author: Max Linke -Date: Tue Aug 4 11:27:55 2015 +0200 - - Handle PBC correctly for contact-matrix sparse - - Now also points that are several images apart are handled correctly. All - tests are passing. - -commit ebfd790e9f569c12663231fd1b208a84a6f7fcb6 -Author: Max Linke -Date: Tue Aug 4 11:12:01 2015 +0200 - - Add test for general pbc conditions in contact-matrix - - Two points with PBC can be further apart then one image. The test now - checks that as well. The numpy pbc function already passes this. The - sparse version still assumes that a point is maximally in a neighboring - image. - -commit ac0acb00b3f8102f184c91fa24a581c672fcb25d -Author: Max Linke -Date: Tue Aug 4 09:31:20 2015 +0200 - - Clean up contact-matrix cython code. - - I reordered some variable assigment and calculate the squares directely - instead of using `pow`. This can lead to performance improvements on - some platforms. - -commit b26a60281cb531d99b525ee00a0bedb5b2c61237 -Author: Max Linke -Date: Tue Aug 4 09:24:37 2015 +0200 - - Refactor contact-matrix tests - - The refactored tests don't depend on any external test-data anymore. - This has two nice effects. Giving the coordinates explicitely makes it - easy to see where a contact is and the tests now run over a 100 times - faster. Plus everything looks a lot more cleaned up. - -commit b106b6abe5f32b4a9228aa92bb6b30e222f04197 -Author: Max Linke -Date: Tue Aug 4 07:56:03 2015 +0200 - - Diagonal elements in contact-matrix are always true - - This makes the behavior consistent regardless of the chosen return type. - -commit cf7a0d46e3f1b8791743e9458d5fcd4c856d44ba -Author: Max Linke -Date: Tue Aug 4 07:31:56 2015 +0200 - - Remove progressbar for sparse contact-matrix - -commit 026f7fc52af53e73af49be2efa049f99497dd6cc -Author: Max Linke -Date: Tue Aug 4 07:26:01 2015 +0200 - - Use symmetry in contact-matrix calculation. - - Only calculate the distances for the upper triangle contact matrix. The - other entries are already determined through the symmetry. This also - sets the contacts along the diagonal automatically to true.This should - save about half of the operations. - -commit c79efaa2a5fbfd3c22162cd998083c4faa16972c -Merge: bd5f77546 2c4909933 -Author: Oliver Beckstein -Date: Mon Aug 3 16:15:22 2015 -0700 - - Merge pull request #374 from MDAnalysis/feature-atomgroup_properties - - Feature atomgroup properties - -commit 2b928353e4300bee17bc10f1b4646c0936b01ca8 -Author: Max Linke -Date: Mon Aug 3 15:15:59 2015 +0200 - - Port contact_matrix_pbc to cython - - Simple port. I'm currently not using any of the helper functions defined - in calc_distances.h - -commit 9fac3a19e0e9bac2d1767ae9b569b0d9e27b421e -Author: Max Linke -Date: Mon Aug 3 15:15:07 2015 +0200 - - Add sparse PBC test for contact-matrix - -commit 949ccea0a188b92315ace6ddc163d2cdac7895b4 -Author: Max Linke -Date: Mon Aug 3 13:20:52 2015 +0200 - - Use correct axis in contact_matrix_no_pbc - - Due to a typo I calculated the distance between points on different axes - instead of on the same one. - -commit af65ed5f9113865b9455180e02d038d6dc485664 -Author: Max Linke -Date: Sun Aug 2 23:25:32 2015 +0200 - - Add test for contac-matrix with pbc - - The test are currently only run for the dense arrays. - -commit 841be3db1ce7d274208abb488167bcd49c65d6c5 -Author: Max Linke -Date: Thu Jul 30 16:58:16 2015 +0200 - - Port contact_matrix_no_pbc to cython - - Simple Cython implementation. Instead of the other functions in - distances.pyx I have used pure cython for clarity. The loop is converted - to pure C except for saving the sparse matrix element. - -commit 2c490993360a987e7f4a5a234c9466f4cb704c35 -Author: Richard Gowers -Date: Thu Jul 30 13:38:48 2015 +0100 - - Renamed atom.number to atom.index - -commit 25e209f366c5a99e75cdbaeee2670c88052f5896 -Author: Richard Gowers -Date: Thu Jul 30 00:07:54 2015 +0100 - - Updated tests for new properties - -commit 28bcf0130d629dbaeda39c361b4df800085b0810 -Author: Richard Gowers -Date: Wed Jul 29 23:57:43 2015 +0100 - - Doc update to AtomGroup - -commit ff821bd1e8121f412c3951869e602038f8957525 -Author: Richard Gowers -Date: Wed Jul 29 23:55:06 2015 +0100 - - Changed AtomGroup methods to properties - - Implementation of Issue #372 - -commit bd5f775466ec767087bcbfdfa474e36d8dde3dd7 -Author: Richard Gowers -Date: Mon Jul 27 22:44:55 2015 +0100 - - More tests - - For Issue #363 - -commit 2a830bf2472d8b5b48575c2f34cd5266a7d13609 -Merge: ce8657d1d b1165fe65 -Author: Oliver Beckstein -Date: Sun Jul 26 18:54:03 2015 -0600 - - Merge pull request #367 from MDAnalysis/parallel-test - - Fixes parallel builds in travis. nose>=1.3.7 now required. - -commit b1165fe65c2faa03f1859a133c460ec4be5a3f3c -Author: Manuel Nuno Melo -Date: Sun Jul 26 14:22:02 2015 +0200 - - Everything now expects nose>=1.3.7. - -commit e9929f50c6b3f1a68d4ea7530e3301e0f16901c3 -Author: Manuel Nuno Melo -Date: Sun Jul 26 02:22:19 2015 +0200 - - Updated the nose>=1.3.7 requirement in setup.py too. - -commit b76d506fc3d637c674d959ab99fd31bce5755b56 -Author: Manuel Nuno Melo -Date: Sun Jul 26 01:09:13 2015 +0200 - - Fixes parallel builds in travis. nose>=1.3.7 now required. - -commit ce8657d1d2c04ded14e5603e72e52e5d473b9602 -Author: Tyler Reddy -Date: Sat Jul 25 15:04:19 2015 +0100 - - MDAnalysis.analysis.distances.contact_matrix docstring has been updated to reflect the data type of the input and the details of the operation of the progress meter. - -commit 58975636091533a5fdba86dd25263561ebf08d9f -Author: Oliver Beckstein -Date: Fri Jul 24 00:06:09 2015 -0700 - - more reST fix (in qcprot) - -commit 33ad0916e1963c1fa1a77545c3beae075c8bcac3 -Author: Oliver Beckstein -Date: Fri Jul 24 00:01:51 2015 -0700 - - rebuilt docs with sphinx - -commit 9b2817d8843b9842ceceb4e6dfbe60c52467277d -Author: Oliver Beckstein -Date: Fri Jul 24 00:01:19 2015 -0700 - - reST fixes - -commit c11f5734b6cb36878e9836794fc8fda6b9e8d43f -Author: Oliver Beckstein -Date: Thu Jul 23 16:07:23 2015 -0700 - - moved core.qcprot to lib.qcprot - - - addendum to Issue #287 - - added stub so that until 1.0, core.qcprot will still work but emit - a deprecation warning - - adjusted test_qcp - - adjusted links in docs - -commit 35476b1671dd5608b59aec672046576bb255b2df -Author: Oliver Beckstein -Date: Thu Jul 23 15:44:32 2015 -0700 - - added import stub core.parallel - - - parallel moved to lib.parallel (issue #287) - - import stub to be removed in release 1.0 - -commit a3bd9af3cca5bfadc77ae504d577a7f87ced7448 -Author: Oliver Beckstein -Date: Thu Jul 23 15:22:09 2015 -0700 - - test that deprecated old module imports are still working - - - These imports should work until release 1.0. - - See issue #287 for details. - -commit 1474a2aa67ba52acb275f6e2c2b849f46861dbdd -Author: Richard -Date: Wed Jul 22 12:22:48 2015 +0100 - - Fixup of last - -commit a5ecea11a270eaa114db81b3c317ccaf2a83b4a8 -Author: Richard -Date: Wed Jul 22 11:12:01 2015 +0100 - - Fixed usage of format kwarg with Readers - - Fixed single file Universe with Reader as kwarg - - Closes #364 - -commit 71a4aa286572b25181581511f02b58b2c2a8cc68 -Author: Richard Gowers -Date: Tue Jul 21 18:10:22 2015 -0700 - - updated Trajectory API history - -commit d4be14803aeecdad19a6e8220ac31575a4afa878 -Author: Oliver Beckstein -Date: Tue Jul 21 17:32:42 2015 -0700 - - regenerated online docs with sphinx - - (see also #350) - -commit 6fea232010833556357da89064ccf48db46f4070 -Author: Richard Gowers -Date: Tue Jul 21 21:52:05 2015 +0100 - - Doc fixup - -commit 5bdbb47b809d2b593225bbb1866577203fa84673 -Author: David Dotson -Date: Tue Jul 21 11:43:01 2015 -0700 - - Closes Issue 310: Fixed doc mentions of 1-based frames to 0-based. - -commit 44e2fa55f239bfc59661df83c0db654d1fc9a72f -Merge: 7f78d4eef c2c8dfe96 -Author: Richard Gowers -Date: Mon Jul 20 20:09:11 2015 +0100 - - Merge pull request #358 from MDAnalysis/feature-triclinic_dimensions - - Added triclinic_dimensions to timestep - -commit c2c8dfe968946d55289677462f0329bb60cac709 -Author: Richard Gowers -Date: Sun Jul 19 22:22:12 2015 +0100 - - Added triclinic_dimensions to timestep - -commit 7f78d4eef9c8799bbdeeb4d69252db41ed3f699c -Merge: 4688e49f9 4b3e50b45 -Author: Richard Gowers -Date: Sun Jul 19 19:59:45 2015 +0100 - - Merge pull request #357 from MDAnalysis/feature-readercleanup - - Feature readercleanup - -commit 4b3e50b45038fbe6f9068bb7a5f105f6af8daa39 -Author: Richard Gowers -Date: Sun Jul 19 19:40:32 2015 +0100 - - Final changes following review - -commit 552d67d421a7e9cdb3f811b72c59296a51e65295 -Author: Richard Gowers -Date: Sun Jul 19 17:45:56 2015 +0100 - - Added use of time_offset and dt to tests - -commit 0e364610daaac4d9efc4d2b3e0bae9443cbf0a54 -Author: Richard Gowers -Date: Sun Jul 19 16:40:18 2015 +0100 - - Updated Reader API - - fixed, skip_timestep, periodic, skip and delta no longer required for - Readers (Issue #350) - - All writers now refer to time between steps as "dt" (was previously - delta in XTC, TRR and NCDF Writers) (Issue #206) - - Timesteps now have a default dt of 1.0 ps (and issue warning when using - this) - - Timestep attribute time now tries to return data['time'] first, then dt - * frame, using the default value of 1.0 ps if necessary. (Issue #308) - -commit 4688e49f9be7fb829317b873a6478b1c19209a03 -Author: Isaac Virshup -Date: Fri Jul 17 14:40:40 2015 -0400 - - docs for new Jmol selection writer - - - Updated AtomGroup.write() docstring to reflect addition of new writer. - - files for online docs - - CHANGELOG entry - - added name to AUTHORS and conf.py - - closes #356 - -commit 4e6a04bbf65746acc6b0bcc2bf67994801ffbbb5 -Author: Isaac Virshup -Date: Fri Jul 17 13:03:54 2015 -0400 - - Added tests for Jmol selection writer. - -commit 592403b62d484dd4e804f2412622c4eb9c8251de -Author: Isaac Virshup -Date: Thu Jul 16 14:25:33 2015 -0400 - - Added SelectionWriter for Jmol. - -commit 1106ba29e3c8564b96af66269380191a5ebba431 -Merge: 354aae793 606454db8 -Author: Oliver Beckstein -Date: Sat Jul 18 01:20:54 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit 354aae79382fcc4e9071d3ab6ee3b21f7bd703a8 -Author: Oliver Beckstein -Date: Sat Jul 18 01:18:08 2015 -0700 - - test for all selection writers (closes issue #353) - - - shortened selection to be able to keep the fixtures reasonably small - - added tests for Charmm, PyMOL and VMD writer - -commit 606454db838168010f3edabf3a653bc36795b4b6 -Author: Richard Gowers -Date: Sat Jul 18 09:03:13 2015 +0100 - - Updated distance calculation docs - -commit 59c3ebd2224e3e286a9f492ff399b2b9d1e3a762 -Merge: 9ca6ee688 27d10b065 -Author: David Dotson -Date: Sat Jul 18 00:44:56 2015 -0700 - - Merge pull request #355 from MDAnalysis/feature-make_whole - - Added function lib.mdamath.make_whole - -commit 9ca6ee688e075b94e3fb75261b571db932d2c093 -Author: Oliver Beckstein -Date: Sat Jul 18 00:39:57 2015 -0700 - - analysis.nuclinfo fix and more tests - - - fixed missing import (from new mdamath move); in fact prefixed every mdamath - function with mdamath instead of top level import - - added a few more tests - -commit 27d10b0651ad03da2839a8e8731431f2254a7f57 -Author: Richard Gowers -Date: Fri Jul 17 18:50:32 2015 +0100 - - Final updates to make_whole following review - -commit fe00c53d58c56233cad1e7626e73c61918af2c18 -Author: Richard -Date: Thu Jul 16 14:27:51 2015 +0100 - - Added function lib.mdamath.make_whole - -commit 45f9c9e0808db321a131f2a1b57a34329bf1986d -Author: Richard -Date: Thu Jul 16 10:59:44 2015 +0100 - - Moved mathematical functions from lib.util to lib.mdamath - -commit d93d357f2e7ed149ae3be311aaf729c6b24b60cb -Merge: 2f5cdcd0c 73c03cdbe -Author: Oliver Beckstein -Date: Wed Jul 15 16:32:53 2015 -0700 - - Merge pull request #354 from MDAnalysis/feature-testselectionwriters - - MDAnalysis.selection testing (partially addresses #353) - -commit 73c03cdbe3bbc7df1701ab13da4d565888988854 -Author: Oliver Beckstein -Date: Wed Jul 15 16:06:58 2015 -0700 - - MDAnalysis.selection testing (partially addresses #353) - - - test_selections.py is now used for testing selection writers - - added example test for Gromacs NDX file writer - - selection writers can now write to streams (uses util.openany()) - but format recognition does not work yet with bzipped of gzipped - files - -commit 2f5cdcd0c8f1651aa77675474ee3cf526840ccc8 -Merge: c3333ce4e 6313163bf -Author: Oliver Beckstein -Date: Wed Jul 15 12:51:31 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit c3333ce4e10027b87ada98c53fcdb947875c4037 -Author: Oliver Beckstein -Date: Wed Jul 15 12:50:30 2015 -0700 - - tests: renamed test_selections --> test_atomselections - - We need tests for the MDAnalysis.selection module (see issue #353) and once we do this - we can use the name test_selections.py for those tests. - -commit 6313163bfc9c6e465f079e7b6ae844ae4188e223 -Author: Richard -Date: Wed Jul 15 16:53:16 2015 +0100 - - Marked test as knownfailure - - Caused by Issue #352 - -commit 38c08f830b42c8655ecaeaa1c80f05c627a37cb4 -Author: Richard -Date: Wed Jul 15 16:23:20 2015 +0100 - - Fix for TPRParser - - Closes Issue #351 - -commit 6e89d46f9d8fe76f25bcdbaca34b13562aba991a -Author: Richard Gowers -Date: Wed Jul 15 09:16:12 2015 +0100 - - Updated coordinates docs - -commit d79d4620d598868c7cc306b38b1e9301aed0a01d -Author: Richard Gowers -Date: Mon Jul 13 21:16:59 2015 +0100 - - Updates to Timestep API docs - -commit ef886c3bf8d0072dc69589eb674fe143675eea0f -Author: Richard Gowers -Date: Mon Jul 13 21:01:03 2015 +0100 - - Updated outdated topology docs - -commit 700a7a57ea7cbba425a5a24d8a8dcf8eb7442a51 -Merge: 6275409a4 185a0845a -Author: Richard Gowers -Date: Mon Jul 13 20:46:09 2015 +0100 - - Merge pull request #349 from MDAnalysis/feature-timesteptimes - - Feature timesteptimes - -commit 185a0845a12b0294fe600b7b32bcfc8dc6c555ea -Author: Richard -Date: Mon Jul 13 15:46:32 2015 +0100 - - Closes Issues #306 and #307 - - Added init to base.Reader to try and homogenise Readers. - -commit ebf05d438ed1e6980007715725a8fd0cdea8e385 -Author: Richard -Date: Mon Jul 13 13:36:13 2015 +0100 - - Added dt and time_offset to Timestep API - - Fixed TRR.Timestep not passing along kwargs - -commit 6275409a4fb9d7808a3a1893d71a74976e54aa45 -Author: Richard Gowers -Date: Sun Jul 12 21:01:15 2015 +0100 - - Rebuilt docs - -commit 4c960f59a41dd7afbb275c7a8c04d3290ecbb6c6 -Author: Richard Gowers -Date: Sun Jul 12 12:30:00 2015 +0100 - - Docs updates for Timestep - -commit ded57cd5efd4c293e6c18dd18a5179f89ae35d27 -Merge: 0aa31f875 7c9c3049f -Author: Oliver Beckstein -Date: Sat Jul 11 14:44:34 2015 -0700 - - Merge pull request #346 from MDAnalysis/issue-250 - - closes Issue #250 and Issue #213 - - (just docs need to be update) - -commit 7c9c3049f907a440c38b8e976001b365feddd046 -Author: Richard Gowers -Date: Sat Jul 11 22:22:02 2015 +0100 - - Extra tests for from_coordinates Timestep constructor - -commit 33be12120fe21cfd1a6cf77b69cf5a864c92828a -Merge: e74822f2b 0aa31f875 -Author: Richard Gowers -Date: Sat Jul 11 17:48:17 2015 +0100 - - Merge branch 'develop' into issue-250 - - Conflicts: - testsuite/MDAnalysisTests/test_atomgroup.py - -commit e74822f2b0e5cf05efcc88344caac0df8fbc3991 -Author: Richard Gowers -Date: Sat Jul 11 11:44:55 2015 +0100 - - Work on Issue #213 - - Timesteps can now allocate velocities and forces - - Access to data in Timesteps is now done through the properties - .positions, .velocities and .forces. These will raise - NoDataError if the data isn't present - - Extra tests for TRR functionality - -commit 3b95cb970f103039de098e747cfb4fe983499929 -Author: Richard Gowers -Date: Thu Jul 9 10:05:38 2015 +0100 - - Finished work on Issue #250 - - All timesteps now use has_positions, has_velocities - and has_forces flags. - - TRR uses these flags to manage when data is missing - -commit 0aa31f87578ad535ca6373141da7521a004d9916 -Merge: 99999391f 1bb0bf5e4 -Author: Richard Gowers -Date: Fri Jul 10 19:13:48 2015 +0100 - - Merge branch 'feature-newtestrun' into develop - - Conflicts: - .travis.yml - -commit 1bb0bf5e4798bac00fcc14844e77ef2d3ff8fe66 -Author: Manuel Nuno Melo -Date: Fri Jul 10 18:13:23 2015 +0200 - - Coverage now works with the new test system - - Banned MDAnalysis imports from MDAnalysisTests.__init__.py (closes #344) - Cleaned up (commented out) some debigging print statements in tests. - New test file test_meta.py, for setup- and testing-related tests. - -commit 99999391fc89a90515f594fd1cb79023acad508c -Merge: 076cebc47 07e3e5668 -Author: Richard Gowers -Date: Fri Jul 10 14:24:45 2015 +0100 - - Merge pull request #343 from MDAnalysis/feature-buildmatrix - - Feature buildmatrix - -commit cef7ac9518fd8c3f71007b0ada5373e99c0eb1b9 -Author: Manuel Nuno Melo -Date: Fri Jul 10 12:01:03 2015 +0200 - - Checking travis' nose version. - -commit 07e3e5668cef9b81893823e7a275259d79873b0e -Author: Richard Gowers -Date: Fri Jul 10 09:40:14 2015 +0100 - - Updated travis to use container based system - -commit c84eacf0f1e0a4f20cae41ed001b74aec24cff5c -Author: Richard Gowers -Date: Thu Jul 9 11:50:57 2015 +0100 - - Added new memleak testing to travis testing - - Travis build now contains 2 jobs - - full unit test with memleak testing (in parallel) - - full unit test with coverage - -commit 263bcc8eeb2d185e57901167a6ee1e7926c4768d -Author: Manuel Nuno Melo -Date: Fri Jul 10 01:24:16 2015 +0200 - - Increasing nose's version to try to definitely solve the coverage problem - -commit 30b11a047ff8508a984c7f2895a8480c446aa0f1 -Author: Manuel Nuno Melo -Date: Thu Jul 9 17:52:28 2015 +0200 - - Fixes nose call that caused coverage misreporting (#341) - -commit 71409701b00ad8e53220e44e4ee7b10b49beffa6 -Author: Richard Gowers -Date: Thu Jul 9 11:50:57 2015 +0100 - - Trying new nosetests - -commit 076cebc47d9152e3871d37847017c27f8ebfa102 -Author: Richard Gowers -Date: Thu Jul 9 08:49:53 2015 +0100 - - removed references to 2.6 in travis - -commit 650d8d90eb9bc3f4059a0626ea350af3647dc548 -Merge: 520ed5add d1480cf5f -Author: Richard Gowers -Date: Thu Jul 9 08:44:03 2015 +0100 - - Merge branch 'develop' into issue-250 - - Conflicts: - package/MDAnalysis/coordinates/DCD.py - -commit 520ed5addde5ff05652da6face6642933c01bdab -Author: Richard Gowers -Date: Fri Jul 3 12:05:23 2015 +0100 - - More of Issue #250 - - In general, moved to relative import style across coordinates modules - - Timesteps now read their native frame into "_frame". - This replaces what was "step" in some Readers. - - Timestep.data dictionary added for formats with nonstandard data for - their Timestep. - - Writing a Timestep with XTC/TRR Writer no longer modifies the Timestep - passed - -commit d1480cf5f66459851c5d92d9e9c07bdd54900a24 -Merge: 6a1a0049d 4a2836483 -Author: Oliver Beckstein -Date: Wed Jul 8 19:26:25 2015 -0700 - - Merge pull request #340 from MDAnalysis/feature-TestOverhaul - - Overhaul of the test subsystem. - -commit 4a2836483bd790de74543cdac80afb07caf4e081 -Author: Manuel Nuno Melo -Date: Thu Jul 9 03:54:57 2015 +0200 - - Fixed treatment of "label" argument. Cleaned up. - -commit 77d3b041d5b3321622387273e56f60f8722381f7 -Author: Manuel Nuno Melo -Date: Thu Jul 9 03:37:12 2015 +0200 - - Addressed comments on PR #340 - -commit 9bad485c6a2860800ec46585f0396dedcb133ed9 -Author: Manuel Nuno Melo -Date: Thu Jul 9 03:09:15 2015 +0200 - - Fixed wrong knownfailure import - -commit db492724bff6878830b6f7bee857f1477cb473e1 -Author: Manuel Nuno Melo -Date: Wed Jun 24 02:41:41 2015 +0200 - - Overhaul of the test subsystem. - - Implements nose plugins, as a submodule (closes #331). - - Available plugins are: memleak testing, stderr capturing - (for quieter test runs), and proper knownfailure implementation. - - The test function is no longer imported from numpy. We - roll our own that registers our external plugins. - - Behavior was kept regarding parallel testing, labels, and invocation - from the command line. stdout and stderr suppression was made default. - - Running nosetests from the command line bypasses our test function, - and plugins aren't loaded. Plugin-dependent code (the knownfailure - decorator, for instance) is aware of this and behaves accordingly. - - A command-line script mda_nosetests was added to the suite that acts - as a replacement for the nosetests command, but is plugin-friendly. - - Knownfailure usage was corrected (closes #338). - - (Replaces pull request #326) - -commit 6a1a0049d5acefcb1a45112315ac9173cf6ad058 -Merge: df7627352 50b443430 -Author: Richard Gowers -Date: Thu Jul 9 00:07:13 2015 +0100 - - Merge pull request #339 from MDAnalysis/feature-distancesmove - - Feature distancesmove - -commit 50b4434309a737f9ab9306e0a9b6174fc9000460 -Author: Richard Gowers -Date: Wed Jul 8 23:32:48 2015 +0100 - - Added docs for new module - -commit 933510779bd1b7037595e4de0d45a3f71268439a -Author: Richard Gowers -Date: Wed Jul 8 23:25:18 2015 +0100 - - Doc changes for core.distances move - -commit 61d4aa820cdb014cc669a0149175ad29e78cbc9b -Author: Richard Gowers -Date: Wed Jul 8 23:20:21 2015 +0100 - - Code changes for moving core.distances to lib.distances - -commit df7627352540a60ed96f779ef7dcac7fade062ba -Merge: 0842afabb 699876d2c -Author: Oliver Beckstein -Date: Wed Jul 8 14:12:20 2015 -0700 - - Merge pull request #335 from khuston/HoomdXMLParser - - HoomdXMLParser - -commit 699876d2cb884d38d1969b03ed51f5b920545356 -Author: khuston -Date: Wed Jul 1 10:15:54 2015 -0400 - - Compressed xml test data, amended docs - - altloc -> PDB_full - Improved handling of missing data - Amended comment text for missing mass/charge in HoomdXMLParser.py - Removed import of guess_atom_charge - Added HoomdXML bond and angle recognition. Added CHANGELOG and AUTHORS entires, removed [#a]_ from HoomdXMLParser docs, added xml datafile to setup.py in testsuite - Added HoomdXML dihedral and improper reading - made doc changes - Compression support in xml top reader, compressed xml data file, added comma to list in testesuite/setup.py - -commit 0842afabb2e08628f8f2096b2cd5615b27c3d631 -Author: Richard -Date: Mon Jul 6 11:43:32 2015 +0100 - - Small tidy up to coordinates/DCD - - Also moved to strictly relative imports (Py3k compat) - -commit fcccca7bfe3c68dc696f751bfa2d917939a834dd -Merge: 74aad51dc b23dae59b -Author: Oliver Beckstein -Date: Thu Jul 2 01:45:29 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit 74aad51dc7586a28b5bd0273ce8b635c1a3e4b99 -Author: Oliver Beckstein -Date: Thu Jul 2 01:45:22 2015 -0700 - - rebuilt html docs with sphinx - - In particular, cleaned up files for modules that were moved (log, units) - or added new ones (exceptions) - -commit c99fecedee3bef5415aa89e917b0695d873b8542 -Author: Oliver Beckstein -Date: Thu Jul 2 01:38:09 2015 -0700 - - more relative imports (minor) - -commit b23dae59b8ee157eedb7e33dc22fd9fa1eb20507 -Author: Richard Gowers -Date: Thu Jul 2 08:39:28 2015 +0100 - - Start of Timestep API solidification (Issue #250) - - Readers now always always return ts.frame = 0 on first frame. - - Fixed INPCRD and DLPoly Config giving -1 as first frame (should be 0) - -commit f3f2a97a46a8473fb9157381a15ecc126777f37e -Author: khuston -Date: Wed Jul 1 10:01:23 2015 -0400 - - Added HoomdXMLParser and basic test - -commit d0bec3d356bb910c67b5de5895bcb17c5606b5c4 -Merge: 71a3e6786 6ead85ac9 -Author: Oliver Beckstein -Date: Mon Jun 29 20:08:49 2015 -0700 - - Merge pull request #334 from MDAnalysis/issues/332 - - fixed parsing of PDB header data for PrimitivePDBReader (closes #332) - -commit 6ead85ac966d9dab008036ded9f5c65fa24e69ab -Author: Oliver Beckstein -Date: Mon Jun 29 19:01:47 2015 -0700 - - fixed parsing of PDB header data for PrimitivePDBReader (closes #332) - -commit 71a3e67860c1cd9937d477205756c30b432043f2 -Author: Oliver Beckstein -Date: Mon Jun 29 17:40:54 2015 -0700 - - docs: purged last remnants of Google Code links - - - replaced with links to new home page or github issue tracker or wiki - - use issues.mdanalysis.org, docs.mdanalysis.org, wiki.mdanalysis.org - (which all redirect to the proper places on github and pythonhosted.org) - -commit 1b775d1702679fdf5bb81159077dc65060243070 -Author: Richard Gowers -Date: Fri Jun 26 09:35:18 2015 +0100 - - Moved core.units to MDAnalysis.units - - Part of #287 - -commit b9ba4ad6dc6a1988f6dbd36a9e0b831d541b8329 -Author: Richard Gowers -Date: Fri Jun 26 09:17:58 2015 +0100 - - Moved core.units to MDAnalysis.units - - Part of #287 - -commit bc3fea07038de4a03e6e14664af3a39c443150ca -Author: Richard Gowers -Date: Fri Jun 26 08:59:04 2015 +0100 - - Moved exceptions into their own file - - Still imported into top namespace so no real change - -commit 0a6b404e884899df4dd82ce7fb754e6de0ac06b0 -Author: Richard Gowers -Date: Fri Jun 26 08:34:10 2015 +0100 - - Moved core.log to lib.log - - Part of #287 - -commit 09bb5115347095902e3612195e2968bd8722a15a -Merge: 38d03cd5f 7536bb864 -Author: Oliver Beckstein -Date: Thu Jun 25 21:07:58 2015 -0700 - - Merge pull request #330 from MDAnalysis/feature-utilmove - - Moved core.util to lib.util - -commit 7536bb86455c91f520ba46caa78b47af1e57befa -Author: Richard Gowers -Date: Thu Jun 25 22:35:36 2015 +0100 - - Moved core.util to lib.util - -commit 38d03cd5fb6e0090af59aefb728ecb286ed178c7 -Merge: 49b1eacee 4f5a0d93c -Author: Oliver Beckstein -Date: Thu Jun 25 13:29:15 2015 -0700 - - Merge pull request #327 from cyanezstange/develop - - fixed "division by zero" bug in analysis.waterdynamics - -commit 49b1eaceedbc7abcce95e64d5296394e403f1535 -Author: Oliver Beckstein -Date: Thu Jun 25 10:43:56 2015 -0700 - - updated __all__ in analysis/__init__ (related to #328) - -commit 4f5a0d93cd293c8b83def9da7db792a79fe490b4 -Merge: 07ee64d19 7069b716f -Author: cyanezstange -Date: Thu Jun 25 14:41:19 2015 -0300 - - Merge pull request #2 from cyanezstange/patch-1 - - Add new author. - -commit 7069b716fb30689cdb07e1173337433332dc9e9d -Author: cyanezstange -Date: Thu Jun 25 14:37:34 2015 -0300 - - Add new author. - -commit 07ee64d193511c786abd5dc8172b8ca8995e68cb -Merge: 5dcf427ad 22cd0b81c -Author: cyanezstange -Date: Thu Jun 25 14:34:51 2015 -0300 - - Merge pull request #1 from alejob/patch-1 - - Update waterdynamics.py - -commit 22cd0b81c87edea0ab65ab71a6d68396d0f2c808 -Author: Alejandro Bernardin -Date: Thu Jun 25 11:57:47 2015 -0300 - - Update waterdynamics.py - - Orthography correction - -commit 6c7e7b394bbf5b02db61bfdde7c87677faf2f007 -Author: Alejandro Bernardin -Date: Thu Jun 25 11:52:38 2015 -0300 - - Update waterdynamics.py - - Bug fix commented - -commit 5dcf427ad85cafcb84f2901ee629302473563bde -Author: Carlos Yañez -Date: Wed Jun 24 14:22:54 2015 -0300 - - Fixed bug and added DivisionByZero exception in analysis/waterdinamics.py in SurvivalProbability class. - -commit 32d98f0d4f950f83beca0d5b985052c66cfeeaed -Author: Oliver Beckstein -Date: Tue Jun 23 12:08:49 2015 -0700 - - rebuilt html docs with sphinx - -commit b6cdd0a12f55186f6607bca91a735acb05d95cc4 -Author: Oliver Beckstein -Date: Tue Jun 23 12:25:07 2015 -0700 - - docs: new References page - - - decluttered top page by moving growing list of citations for included - algorithms to the new References page - - added waterdynamics citation to the list (Araya-Secchi et al, BJ 2014) - - In the future, add new citations to references.rst - -commit ffe3724bfee7d10ef583e2c7c57f9d99a72687ff -Author: Oliver Beckstein -Date: Tue Jun 23 12:08:30 2015 -0700 - - fixed reST/LaTeX in PSA (closes #325) - -commit d480d3bcb8fcd487c63f75871654e386f40e33b8 -Author: Oliver Beckstein -Date: Tue Jun 23 03:22:29 2015 -0700 - - regenerated html docs for 0.11.0-devel - - - moved KDTree and core.transformations to lib - - includes reST fixes from preceding commit - -commit 4a3bdd15d0f4e199dca11100fe8f65ab03161cfa -Author: Oliver Beckstein -Date: Tue Jun 23 03:17:46 2015 -0700 - - reST fixes throughout - - - added DL_POLY to start doc page - - removed duplicate replacement rules in PSA - - fixed table markup of topology readers - - fixed KDTree and transformations new location in lib - - ... other stuff - -commit 21d48ccf4c939586c72d4de9c5e3a03e87dabd7b -Author: Oliver Beckstein -Date: Tue Jun 23 02:54:10 2015 -0700 - - test_imports: test each test_*.py file individually - - - use test generator - - cleaned out pretty much all other imports but us os.path for path manipulation - - added linenumber to error message for easier debugging - Note that only the first relative import triggers a FAIL. - -commit dc8e276e3810d9e0f66cc70f66f698d5cf4a971d -Author: Oliver Beckstein -Date: Tue Jun 23 02:11:10 2015 -0700 - - require numpy >= 1.5 (to streamline tests) - - Removed relative (for our tests illegal) imports of _assert ("from . import _assert") - and in the process removed our definition of assert_ because it is - available in at least numpy >= 1.5; because that release of numpy is actually already - ancient, I just bumped our requirement for numpy to 1.5 or higher. - - Also fixed the initial import check for MDAnalysis and separated it from the version - check (which could have given cryptic error messages). - -commit 77b4b527ca2f1831a64fce44bda0825d5c708b7b -Author: Richard -Date: Tue Jun 23 09:43:31 2015 +0100 - - Touched up SingleFrameReader tests - - Removed IOBase.close_trajectory (deprecated since 0.8) - -commit 44a72e785a0736189b9e785db50170aa6e016895 -Merge: be7924056 aaab2dfb3 -Author: Oliver Beckstein -Date: Mon Jun 22 18:07:51 2015 -0700 - - Merge pull request #324 from MDAnalysis/issue323 - - Tests can now detect memleaks on a test-by-test basis (closes #323) - -commit aaab2dfb378afc99d78943519f3bc3c14ef46b58 -Author: Manuel Nuno Melo -Date: Tue Jun 23 01:31:13 2015 +0200 - - Leak detection now works even if the offending objects aren't deleted in tearDown - -commit be79240566fe9b3f7b3b7e187fa7699f2e1eb9f2 -Author: Richard -Date: Mon Jun 22 14:57:43 2015 +0100 - - Added tests for deleting topology from Universe - -commit ac6c3b2740590cfd1ee3ebb20fe24755bcf19959 -Author: Richard -Date: Mon Jun 22 14:50:52 2015 +0100 - - Excluded test files from coverage - -commit bac72911d83fe7ece05a4570fa349c8c8f1935e3 -Merge: 280e313a5 c8fa3c9b3 -Author: Richard Gowers -Date: Mon Jun 22 14:46:03 2015 +0100 - - Merge pull request #322 from MDAnalysis/issue-310-fin - - Closes Issue #310 - -commit 412584c8a3febb43c50aa346209f46e94c54290f -Author: Manuel Nuno Melo -Date: Mon Jun 22 14:18:31 2015 +0200 - - Tests can now detect memleaks on a test-by-test basis (closes #323) - -commit c8fa3c9b328ab3928f3eef57a7e0eef18d0de224 -Merge: 80591565c 280e313a5 -Author: Richard -Date: Mon Jun 22 13:54:06 2015 +0100 - - Merge branch 'develop' into issue-310-fin - - Conflicts: - package/MDAnalysis/coordinates/base.py - -commit 80591565caab2fa394f84a9c7e395f7033f3f30f -Author: Richard -Date: Mon Jun 22 12:43:59 2015 +0100 - - Fixed up XYZReaderAsTopology test - -commit 280e313a560aeada9ec8ae923617b5a7e1b057fe -Merge: 685b8d831 19c2b7cb6 -Author: Richard Gowers -Date: Mon Jun 22 11:23:12 2015 +0100 - - Merge pull request #321 from MDAnalysis/feature-pickleAtomGroup - - Lightweight serialization of AtomGroups by reutilization of built Universes - -commit 19c2b7cb66936e529f67225be60685594565cfb6 -Author: Manuel Nuno Melo -Date: Mon Jun 22 11:30:54 2015 +0200 - - Addressed comments on pull-request #321 - - Added the possibility to explicitly name Universes - to target AtomGroup unpickling. - - Improved overall documentation on this. - - Removed memleak test that prevents parallel testing. - - Made MDAnalysisTests import or define assert_ at the - module level, preventing code triplication. - -commit 84e3882825ea6a9586f93a788c7f2460e6eb185e -Author: David Dotson -Date: Tue Jun 16 15:03:40 2015 -0700 - - Closes Issue #310 - - *Special thanks to @richardjgowers for lots of work on troublesome - Readers.* - - Went through each Reader class; changed frame to 0-based. - - Fixed tests relating to 0 based frame numbering - - Added 0 based frames to DCD - - Modified tests for DCDs. - - Added 0-based frame tests to DMS, GMS test classes. - - Added new tests for MOL2 reader checking frame indexing. - - Finished tests for XYZ reader frames indices. - - Fixed TRZ Reader frame numbering. TRZReader now reports Time from - Timestep not based on dt * frame. - - Fixed MOL2 reader 0-based numbering. Now reuses Timesteps (like other - Readers) Now has _reopen method which "rewinds" the frame - numbering - - The helanal analysis could use a redesign, but in the meantime fixed to - ensure that it works as expected regarding trajectory times. - - Fixed test_reader_api tests to work with 0-based frames. - - Updated Reader API checks for 0 based operation - - Fixed XYZReader not rewinding properly on checking numframes - - Added final .. versionchanged directives to classes, module docs - - Fixed 2.6 XYZReader - -commit 685b8d8310311bf8f83e191ee0874a47947b255d -Author: Richard Gowers -Date: Sun Jun 21 18:09:58 2015 +0100 - - Added DLPoly test files to MDAnalysisTest setup - -commit 9d831e6cb6ba854b59d63460aff12e89b6f2dac2 -Author: Manuel Nuno Melo -Date: Thu Jun 4 02:51:42 2015 +0200 - - Lightweight serialization of AtomGroups by reutilization of built Universes - - AtomGroups can now be pickled/unpickled (closes #293) - A weakref system was implemented so that Universes can have a __del__ - method without memleaking (closes #297) - ChainReaders no longer leak (and also no longer have a __del__ method) - (closes #312) - Tests now specifically look for uncollectable objects at the end. Breaks - parallelization, though. - -commit 74699a9eedb71312b542a86e437a8ff0662bac5c -Merge: feb7b2e3f 363b05b57 -Author: Richard Gowers -Date: Sat Jun 20 16:08:50 2015 +0100 - - Merge pull request #320 from MDAnalysis/feature-transformationsmove - - Move core.transformations to lib.transformations - -commit 363b05b5732a2f7df45b5767d60dabba6fc48967 -Author: Richard Gowers -Date: Sat Jun 20 15:17:03 2015 +0100 - - Move core.transformations to lib.transformations - - Part of Issue #287 - -commit feb7b2e3f1790cdc009b0ef61bd5c47d6a694a19 -Author: Richard Gowers -Date: Sat Jun 20 09:12:13 2015 +0100 - - Added more tests for core.util - - Fixed convert_aa_code not raising error properly - -commit 4696809ce77eaae4367efbefb846b0af93c2981d -Author: Oliver Beckstein -Date: Fri Jun 19 17:14:22 2015 -0700 - - KD-Tree: added/fixed tests and minor upgrades in package - - - fixed failing test: we cannot "from MDAnalysis.KDTree import NeighborSearch" - because that KDTree.py is not a module anymore but just a stub until MDAnalysis.KDTree - is fully removed in 1.0. (Use MDAnalysis.lib.KDTree instead.) - - moved Thomas Hamelryck's original testing code from the module to the test_kdtree - and turned it into proper unit tests - - minor python updates in the KDTree module: - - make everything new-style classes - - use relative imports - -commit 1e1e9b99174878c7debf72472ad84548785e7776 -Merge: 53ce9b151 67e7e5cc9 -Author: Oliver Beckstein -Date: Fri Jun 19 13:39:45 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit 53ce9b151c8f39927841c2c486a35479d2d48242 -Author: Oliver Beckstein -Date: Fri Jun 19 13:39:15 2015 -0700 - - minimal tests for KDTree - - - turned rudimentary test that was removed in #318 (related to - #287) into a unit test - - also test for the stub module MDAnalysis.KDTree (only remove - for 1.0) - -commit 67e7e5cc98e866779a78be617a022dc061ffbd33 -Author: Richard Gowers -Date: Fri Jun 19 17:11:57 2015 +0100 - - Fixed XYZ format acting as standalone topology & coordinates - -commit 2c4c1fe70c5bbb709d557d06fc398d8282fc55bd -Merge: 90f41d2e0 e722ceecc -Author: Oliver Beckstein -Date: Fri Jun 19 08:53:48 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit e722ceecc393a2f9d566e9ebfb68157bd8b82564 -Author: Richard Gowers -Date: Fri Jun 19 16:21:02 2015 +0100 - - Removed Python 2.6 travis temporarily - - So #312 isn't quite as annoying for everyone - -commit cf6c6907650a0414b48622d021a3af2f2c48577f -Merge: fbceab411 a7533f70c -Author: Richard Gowers -Date: Fri Jun 19 16:18:50 2015 +0100 - - Merge pull request #318 from MDAnalysis/feature-Issue287 - - Moved MDAnalysis.KDTree to MDAnalysis.lib.KDTree - -commit a7533f70cba56bccf553af6a3a36c57704181d98 -Merge: 8a46174c4 fbceab411 -Author: Richard Gowers -Date: Fri Jun 19 15:10:28 2015 +0100 - - Merge branch 'develop' into feature-Issue287 - - Conflicts: - package/CHANGELOG - -commit 8a46174c4dbc2c8fef3ab72a557a17c86fd1f39c -Author: Richard Gowers -Date: Fri Jun 19 15:08:50 2015 +0100 - - Changes to KDTree move, following review - -commit 90f41d2e0de4db8be5b654fd56cb5556dd851160 -Merge: d75929957 fbceab411 -Author: Oliver Beckstein -Date: Tue Jun 16 23:54:56 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit d75929957015ae2a719891856047e59eeff9c03b -Author: Oliver Beckstein -Date: Tue Jun 16 15:40:25 2015 -0700 - - whitespace formatting - -commit fbceab4113d599ccdf3cf337bd7401c018577fb4 -Merge: 67b3a26b4 993ee1926 -Author: Oliver Beckstein -Date: Tue Jun 16 14:57:34 2015 -0700 - - Merge pull request #317 from MDAnalysis/feature-unified_iter - - Cleaned up Reader classes - -commit 8aa711e1d24dbd45d422b979e86a099602315250 -Author: Richard Gowers -Date: Tue Jun 16 16:05:42 2015 +0100 - - Moved MDAnalysis.KDTree to MDAnalysis.lib.KDTree - - Part of Issue #287 - -commit 993ee1926432af6ee8bd2d07df760512680af701 -Author: Richard Gowers -Date: Tue Jun 16 10:35:33 2015 +0100 - - Cleaned up Reader classes - - Removed custom __iter__ from all but xdrfile (XTC & TRR) - - Removed many custom _sliced_iter implementations, can use base version - - base.Reader now has __iter__ method - - base.Reader rewind now doesn't require seeking access, instead - reopens and calls next - -commit 67b3a26b4842060363d20c1947f0c962faea485e -Author: Oliver Beckstein -Date: Tue Jun 16 01:54:54 2015 -0700 - - README: fixed link/text in footnote - -commit d421e8b34e743acb2c4864f7d6937dff1ebab25d -Merge: 2da4b76ac 4fa5ea893 -Author: Oliver Beckstein -Date: Mon Jun 15 23:04:34 2015 -0700 - - Merge pull request #316 from MDAnalysis/feature-hbonds - - HydrogenBondAnalysis: small improvements - -commit 4fa5ea8935fd5449ca7de861d49e02cb642a9c95 -Author: Oliver Beckstein -Date: Mon Jun 15 22:27:13 2015 -0700 - - HydrogenBondAnalysis: small improvements - - - generate_table(): do not build recarray but just dtype array and removed superfluous code - - added tests for generate_table() - - import itertools at module level instead multiple times in methods - -commit 2da4b76aca4c27d35d00cf9291c02894adf7c958 -Author: Oliver Beckstein -Date: Mon Jun 15 17:22:33 2015 -0700 - - README: badges for google groups - - - Custom badges from http://shields.io - - also added links to docs for analysis and visualization modules - -commit 72fe0c1bb1624ff37dec75a2048f3f58218a1766 -Merge: 1e8246621 4a96fdf7b -Author: Oliver Beckstein -Date: Mon Jun 15 16:59:40 2015 -0700 - - Merge pull request #313 from dotsdl/bugfix-ProgressMeter - - Bugfix to ProgressMeter. - -commit 4a96fdf7bc5e154c301053af59929e439f464e52 -Author: David Dotson -Date: Mon Jun 15 15:50:36 2015 -0700 - - Bugfix to ProgressMeter. - - ProgressMeter would only output progress if the frame number coincided - with the given *interval*; when doing frame steps other than 1, this - often meant seeing no output at all. The behavior has been modified to - output only every *interval* number of calls to - :meth:`ProgressMeter.update`. - -commit 1e8246621380ab7305f9cfbf5532339f568500ce -Merge: 3a1b23def 0d6b32d73 -Author: Oliver Beckstein -Date: Mon Jun 15 16:15:39 2015 -0700 - - Merge pull request #305 from dotsdl/issue-288 - - Issue #288: Basic RMSF analysis - -commit 0d6b32d735dd8dc5a1dbf10af89d953214c49166 -Author: David Dotson -Date: Thu Jun 11 17:49:22 2015 -0700 - - Added RMSF analysis class analysis.rms.RMSF (closes Issue #288) - - The RMSF class takes an atomgroup as input and then iterates through - that atomgroup's parent universe's trajectory (start, stop, step - supported). It obtains an RMSF for each atom in the atomgroup, - calculated across the iterated frames. The RMSF class features an - API similar to the RMSD class. At present it performs no fitting, - however, using only the atom coordinates as-is. - - Added tests, including test rmsf pickled numpy array. - - Added 'quiet' keyword to RMSF class. This is informally a standard - keyword for making these things suppress output. - -commit 3a1b23def48760363123872d96ebcc9884c87c52 -Author: Richard -Date: Mon Jun 15 13:31:08 2015 +0100 - - Added verbose to travis to debug #312 - -commit 2e5a8214df845351ed2a55a16114728549d72b04 -Merge: 07f87997b d63b0f588 -Author: Richard Gowers -Date: Mon Jun 15 13:27:00 2015 +0100 - - Merge pull request #311 from MDAnalysis/feature-trzboxfix - - Feature trzboxfix - -commit d63b0f588ea780917fa468889016f674238df8d5 -Merge: 4dd444745 07f87997b -Author: Richard -Date: Mon Jun 15 12:41:26 2015 +0100 - - Merge branch 'develop' into feature-trzboxfix - - Conflicts: - package/CHANGELOG - -commit 4dd4447454a44450cd3f38e164850a0a414673bf -Author: Richard -Date: Mon Jun 15 12:40:08 2015 +0100 - - More tests for TRZ - -commit 07f87997b4529f9c40d1edd331864bbb0ba6b636 -Author: Tyler Reddy -Date: Mon Jun 15 11:40:32 2015 +0100 - - Updated CHANGELOG to reflect resolution of Issue #189. - -commit c074991e067af25f3a2b3d6c7a44218d48761bc7 -Author: Tyler Reddy -Date: Mon Jun 15 11:31:30 2015 +0100 - - -added new test_imports.py module to enforce the ban on relative imports in unit testing modules (Issue #189) - -manually repaired unit testing modules caught by above unit testing of import statements - -commit d3f506b236cae21dae5999829837e75a318d5b85 -Merge: fd50fb757 18b2983bc -Author: Richard -Date: Mon Jun 15 11:12:08 2015 +0100 - - Merge branch 'develop' into feature-trzboxfix - - Conflicts: - package/MDAnalysis/coordinates/TRZ.py - -commit fd50fb75732f4e7505e5f662d18df7e882e613ea -Author: Richard -Date: Mon Jun 15 11:06:37 2015 +0100 - - Fixes for TRZWriter when handling non TRZ Timestep - - Fixes Issue #302 - -commit d77bd8403116fbdecb3dd4d184bbcabe20cd0cd8 -Author: Tyler Reddy -Date: Sun Jun 14 18:57:37 2015 +0100 - - -adjusted test_analysis.py to replace a relative import with an absolute import so that both nosetests test_analysis:Test_Helanal and nosetests test_analysis.py:Test_Helanal call signatures work - -commit 18b2983bc22e32d5f4de0ffa24ad339c930cafa7 -Merge: cafb7ecc9 760eeb46b -Author: Richard Gowers -Date: Sat Jun 13 19:50:01 2015 +0100 - - Merge pull request #294 from richardjgowers/feature-newtimestepconstructor - - Reworked coordinates.base.Timestep construction - -commit 760eeb46b99a40de3eca6d9b9a680ba19330a19b -Merge: 4d630e88f cafb7ecc9 -Author: Richard Gowers -Date: Sat Jun 13 18:06:40 2015 +0100 - - Merge branch 'develop' into feature-newtimestepconstructor - - Conflicts: - package/CHANGELOG - -commit cafb7ecc938fe8a96a9a7102613c17e896c1ef18 -Author: Oliver Beckstein -Date: Fri Jun 12 12:09:00 2015 -0700 - - use pythonic check for empty atomgroups - - See Issue #304 for background. - -commit c3124c0f24a99b5cefa63e0ddcd043ece5b12718 -Merge: 36ecc1db8 e9c013fd2 -Author: Richard -Date: Fri Jun 12 09:41:00 2015 +0100 - - Merge branch 'develop' into feature-trzboxfix - -commit e9c013fd2d04d03fdcf0ec3eaab96975af32559a -Author: Richard -Date: Fri Jun 12 09:04:11 2015 +0100 - - Added tests for Issue #304 - - No changes needed to pass - -commit e9daa846acedfbb0c2477ce1063cde792b67526c -Merge: bf50264d4 8be82f660 -Author: Oliver Beckstein -Date: Fri Jun 12 00:04:20 2015 -0700 - - Merge pull request #303 from MDAnalysis/feature-issue296 - - HydrogenBondAnalysis checks selections (fixes #296) - -commit 8be82f660f42d803278e44bba0ce67f269249341 -Author: Oliver Beckstein -Date: Thu Jun 11 23:33:40 2015 -0700 - - distances.contact_matrix() minor improvements - - - the sparse routine now properly honors the quiet=True keyword - (needed to include it into the weave C-code as integer value) - - use quite=True in tests to suppress the status output - - changed old 'suppress_progmet' keyword to 'quiet' - -commit 2d11f4eb1ee6b30438e9c47dbf758392df2f105b -Author: Oliver Beckstein -Date: Thu Jun 11 22:59:40 2015 -0700 - - waterdynamics cosmetic improvements - - - Added quiet=True to tests (and as default in HydrogenBondLifetimes._HBA(). - - Also maded all waterdynamics classes new-style classes and a little bit of formatting - (but not anywhere near PEP8 yet) - -commit fef6b8987882a45bd2177d14625efb4052859b9a -Author: Oliver Beckstein -Date: Thu Jun 11 22:22:04 2015 -0700 - - HydrogenBondAnalysis allows frames without donors/acceptors - - If the initial sanity checks are passed then run() should go through the - whole trajectory and simply ignore frames where it cannot find donors - or acceptors. The assumption is that with dynamically updated selections, - some frames simply might not contain appropriate atom groups. - - Check the warnings (in particular SelectionWarning). - -commit a8cf18321b89500654e076bef2535c68edd0b6ea -Author: Oliver Beckstein -Date: Thu Jun 11 21:51:29 2015 -0700 - - HydrogenBondAnalysis test improvements - - - added quiet keyword to run() so that progress output is suppressed during test - - made the generator method safer by executing the manual tearDown in a finally - clause - - fixed the fail condition for the boring test runOK() (must raise AssertionError, - returning False still counts as passing) - -commit 7078b8b13a19737723a303938bbfad08019d725b -Author: Oliver Beckstein -Date: Thu Jun 11 18:43:02 2015 -0700 - - HydrogenBondAnalysis checks selections (fixes #296) - -commit 36ecc1db8a5ddc1c3773854ca5a299a811f9f313 -Author: Richard Gowers -Date: Thu Jun 11 18:10:35 2015 +0100 - - Fix for TRZWriter issue - -commit 4d630e88f722442ffe507117d36bb9d1490fe471 -Author: Richard -Date: Thu Jun 11 12:27:36 2015 +0100 - - More docs to squash - -commit 0e27adc930b139540c068e93ac8fa0f08a28b3ca -Merge: 85f7b7d41 bf50264d4 -Author: Richard -Date: Thu Jun 11 11:55:21 2015 +0100 - - Merge branch 'develop' into feature-newtimestepconstructor - - Conflicts: - package/CHANGELOG - -commit 85f7b7d41289a948e53a3d685ed1a6ee52ed0218 -Author: Richard -Date: Thu Jun 11 08:46:45 2015 +0100 - - More docs, what fun! - -commit bf50264d426e1305be7daec73178d40198e5d6a6 -Author: Oliver Beckstein -Date: Wed Jun 10 15:32:56 2015 -0700 - - cleanup in AUTHOR and CHANGELOG files - - - added dotsdl to AUTHORS (was forgotten since 0.9.0) - sorry - - synced AUTHORS between package and testsuite - - package/CHANGELOG: merged 0.10.1 and 0.11.0 entries into 0.11.0 - - testsuite/CHANGELOG: retroactivelu added entry for 0.7.5 - -commit 94d8fda30964459f2d207f8a704d302726e06277 -Merge: eea8478ab 61070c11a -Author: Oliver Beckstein -Date: Wed Jun 10 15:11:11 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit 61070c11a55ec802e61599e7eeb2287f63724a50 -Merge: ef107d549 eacddb5ed -Author: Oliver Beckstein -Date: Wed Jun 10 13:45:04 2015 -0700 - - Merge pull request #300 from alejob/develop - - New module to analyze water dynamics. - - See: - - Araya-Secchi, R., Tomas Perez-Acle, Seung-gu Kang, Tien Huynh, Alejandro Bernardin, - Yerko Escalona, Jose-Antonio Garate, Agustin D. Martinez, - Isaac E. Garcia, Juan C. Saez, Ruhong Zhou (2014). Characterization of a novel water pocket - inside the human Cx26 hemichannel structure. Biophysical Journal, 107(3), 599-612. - -commit 4a3ed3e1f5e7f0880ef84945e69842bede2d773c -Author: Richard Gowers -Date: Wed Jun 10 21:01:25 2015 +0100 - - Will squash - - Removed FormatError completely. - -commit eacddb5edf728cca77feebfe63776fb930a37b99 -Author: Alejandro Bernardin -Date: Wed Jun 10 16:21:48 2015 -0300 - - Added version information and CHANGELOG update. - -commit ba7ddc07f448d8a2c32c69c4e9a1eeeb961161e4 -Merge: 21895ef66 ef107d549 -Author: Richard -Date: Tue Jun 9 11:09:24 2015 +0100 - - Merge branch 'develop' into feature-newtimestepconstructor - - Conflicts: - package/CHANGELOG - testsuite/MDAnalysisTests/test_coordinates.py - -commit eea8478abc14407c83daaea53424b86988e1aef4 -Merge: d2f6900c3 ef107d549 -Author: Oliver Beckstein -Date: Wed Jun 10 08:46:32 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit b27bcda3227074378c1c26f18e6b586f21d7c0bd -Author: Alejandro Bernardin -Date: Tue Jun 9 16:37:18 2015 -0300 - - Solved merge conflict. - -commit 2a745e6c2398b1163a63044a2dfeb183bddc582f -Merge: ef107d549 79038a727 -Author: Alejandro Bernardin -Date: Tue Jun 9 15:50:08 2015 -0300 - - Merge branch 'feature-watdyn' into develop - - Conflicts: - testsuite/MDAnalysisTests/datafiles.py - testsuite/MDAnalysisTests/test_analysis.py - -commit 79038a727bdcc2f6d8d72cddb7f270335a88208c -Author: Alejandro Bernardin -Date: Tue Jun 9 15:15:21 2015 -0300 - - Added corrected suggestions in #295. - Documentation fixed and updated. - -commit ef107d54995093e826a980b717c1d03d8d64034f -Author: Richard Gowers -Date: Mon Jun 8 12:45:28 2015 +0100 - - Update README.rst - -commit 8b6c0514f07b9663d2a16785bdcb573deb86d312 -Merge: 60cfb5a7b d2c7d5fc9 -Author: Richard Gowers -Date: Mon Jun 8 12:01:41 2015 +0100 - - Merge pull request #299 from MDAnalysis/feature-dlpolyreader - - Adding support for ascii DL_Poly format things - -commit d2c7d5fc9e09d2aac432a0c61f0af14839fdb2f0 -Author: Richard -Date: Mon Jun 8 11:05:17 2015 +0100 - - Updated topology docs - -commit ea4749b66a2bcd72f5344b9b312d1aa07b3210bb -Author: Richard -Date: Mon Jun 8 11:02:41 2015 +0100 - - pep8 pass - -commit 10667881c9661b8a05ca7a1b121964f3bb607df3 -Author: Richard -Date: Mon Jun 8 10:55:28 2015 +0100 - - Added frame seeking to HISTORY reader - - Finishes support for DL_Poly ascii formats #298 - -commit 3cb7145ce1425474efe5417b3ef868285815aed7 -Author: Richard Gowers -Date: Mon Jun 8 09:03:32 2015 +0100 - - TEST ALL THE THINGS - - For DL_Poly - -commit 9dcc7c3e02af2e9a0b1f730aff23222a10f5d5d7 -Author: Richard -Date: Sun Jun 7 18:20:37 2015 +0100 - - Added DL_Poly History reader and parser - -commit 4455e7dd4cada54c904f4134d4d5058f45e14cc6 -Author: Richard Gowers -Date: Sat Jun 6 21:19:37 2015 +0100 - - Fixed missing docs for DLPolyParser - -commit e299f1fc5d596a4427dc8b6f131e28d8fdd652ea -Author: Richard Gowers -Date: Sat Jun 6 21:13:48 2015 +0100 - - Added DL_Poly CONFIG parser - - Starts Issue #298 - -commit 21895ef66d59a6aa55bdb9996201f7bb3d0514b2 -Author: Richard -Date: Wed Jun 3 13:01:50 2015 +0100 - - Temporarily adding verbose to travis - -commit 35ffd18abe9147900418a9bbbec93c36394d404f -Author: Alejandro Bernardin -Date: Tue Jun 2 14:41:28 2015 -0300 - - New module to analize water dynamics. - This module have five new analysis methods: - Hydrogen Bond Lifetime (HBL) - Water Orientation Relaxation (WOR) - Angular Distribution (AD) - Mean Square Displacement (MSD) - Surivival Probability (SP) - -commit d78cdb0a97b9df7323354c0ae67ef9d03ce769e6 -Author: Richard -Date: Tue Jun 2 13:16:24 2015 +0100 - - Start of doc update - -commit 1c15903c5230ab12e934558db2911f609a8023a6 -Merge: ef342a8eb 60cfb5a7b -Author: Richard -Date: Tue Jun 2 12:50:57 2015 +0100 - - Merge branch 'develop' into feature-newtimestepconstructor - -commit ef342a8ebbd8eaf1e428184fae8637dec944db88 -Author: Richard -Date: Tue Jun 2 11:52:27 2015 +0100 - - Fixup - -commit aae0e6a595f3d2c58a6c4a23fb3c8babdfe8ffa8 -Author: Richard -Date: Tue Jun 2 11:46:10 2015 +0100 - - Added eq to base.Timestep - - Fixed bug in TRR force setting - - Tests! - -commit 8026e6c743adae62dece1bd88842ddb391f23b1d -Author: Richard Gowers -Date: Fri May 29 10:42:19 2015 +0100 - - Changed Timestep constructor to only accept integer argument - (defines size of Timestep) - - base.Timestep can now have velocities and forces through - keywords 'velocities' and 'forces' [False by default] - - Added alternate constructors to Timestep - - from_timestep(other_timestep) - - Allows construction of a Timestep from another Timestep of different type - - from_coordinates(pos, velocities=None, forces=None) - - Allows construction from set of existing coordinates - - All other Timesteps updated to reflect new capabilities of base.Timestep - - Still TODO: - Docs! - Travis check - Sanity check! - -commit 60cfb5a7bc0024794e0bd0495740ad2f3e596103 -Author: Sébastien Buchoux -Date: Mon Jun 1 18:58:07 2015 +0200 - - Version changed to 0.11.0 and doc regenerated - -commit 06c93bc0f6e664232e6ccbe401efc2ae02167e32 (tag: release-0.10.0) -Author: Sébastien Buchoux -Date: Mon Jun 1 18:40:01 2015 +0200 - - Version changed to 0.10.0, date on CHANGELOG fixed and documentation regenerated - -commit 56f75a7df6fa41524274b47dd06e275e6b2e14d1 -Author: Richard Gowers -Date: Fri May 29 09:15:09 2015 +0100 - - Split out Timestep tests into own file - -commit 36153870e89923d400a4afe08cc3a1d5d08a7ff0 -Merge: 37602a6cc 147309d02 -Author: Oliver Beckstein -Date: Wed May 27 12:18:20 2015 -0700 - - Merge pull request #291 from MDAnalysis/orbeckst-patch-1 - - README.rst: footnote on coverage - -commit 147309d0247ffff6f88eee09492bfe7f92baa33b -Author: Oliver Beckstein -Date: Wed May 27 12:17:08 2015 -0700 - - README.rst: footnote on coverage - -commit 37602a6ccc96137cefb555c8d7da18f8fe440a84 -Merge: 4fff0794f 0ae5394d9 -Author: Richard Gowers -Date: Wed May 27 19:55:36 2015 +0100 - - Merge pull request #290 from MDAnalysis/feature-booleanindexing - - Added indexing of *Groups via boolean arrays - -commit 0ae5394d975b99137027c6b71a6b4cdf0990a017 -Author: Richard Gowers -Date: Wed May 27 18:48:32 2015 +0100 - - Added indexing of *Groups via boolean arrays - - Closes Issue #282 - -commit 4fff0794f02b949752de50cf761423377ab5df6e -Author: Richard -Date: Wed May 27 08:23:22 2015 +0100 - - Tagged some obsolete parts of LAMMPSParser as no cover - - Removed set workaround from Selection and KDTree/NeighbourSearch - -commit fc47f0952925539c176bb35a687b156a873a5ae6 -Author: Richard -Date: Wed May 27 08:17:20 2015 +0100 - - Excluded visualizations from code coverage - - Finishes #286 - -commit 70eb2903c518bd1a20eff307b38cb53a41562072 -Author: Richard -Date: Wed May 27 08:15:45 2015 +0100 - - Finished finishing transformations tests - -commit dc155a529ad1140a5bdc5cc3f4a9116732e4f4e4 -Merge: 696c9919e 92800c5ed -Author: Richard Gowers -Date: Tue May 26 21:51:55 2015 +0100 - - Merge pull request #289 from MDAnalysis/feature-transform_tests - - Finished writing tests for core.transformations - -commit 92800c5ed553ec155278301b2d0aeef89d84bc94 -Author: Richard Gowers -Date: Tue May 26 21:05:05 2015 +0100 - - Finished writing tests for core.transformations - -commit 696c9919e7ea0e908cee01871970175877c2114c -Author: Richard -Date: Tue May 26 12:36:38 2015 +0100 - - Fixes for 2.6 compat - -commit 6bd2b6bc6acd757f41d71684578f7b984a8b724f -Author: Richard -Date: Tue May 26 11:49:43 2015 +0100 - - More tests for core.transformations - -commit 00b00dca8faa27f8a92dec0893cf512fcb0b9ad0 -Author: Richard -Date: Mon May 18 10:52:09 2015 +0100 - - Started translating core.transformations doctests into unit tests - -commit 40ac1dce55bccfb8eb794dd7d4f998f0cd341eb2 -Author: Richard Gowers -Date: Tue May 26 08:47:33 2015 +0100 - - Removed some unused tpr utils from coverage scope - -commit d2f6900c3e68dbfc23769c190021e77c96fb195f -Author: Oliver Beckstein -Date: Mon May 25 22:51:37 2015 -0700 - - fixed requirement for numpy (>=1.4.0) in setup.py - -commit af18501f432d01e02c6ab6230d4f62c0964cbf83 -Author: Richard Gowers -Date: Mon May 25 22:23:01 2015 +0100 - - Removed analysis from coverage report - -commit fafb7b291fc2a89000f79bdbc43047ada073aeb7 -Merge: ae2f747aa 417d5de25 -Author: Richard Gowers -Date: Sat May 23 20:17:20 2015 +0100 - - Merge pull request #285 from sseyler/develop - - Removed superfluous scipy import from psa module - -commit 417d5de259a518a5cb674f4224b70709507f46af -Author: Sean Seyler -Date: Sat May 23 11:33:52 2015 -0700 - - Removed superfluous scipy import from psa module. - -commit ae2f747aab15a2bcd4297552c1a758ed18712020 -Author: Oliver Beckstein -Date: Fri May 22 12:27:25 2015 -0700 - - online docs regenerated - -commit c707706e5b3d14161413609be1ea7d96b7c556be -Author: Oliver Beckstein -Date: Fri May 22 12:27:09 2015 -0700 - - more reST fixes in analysis.psa - -commit eea3d60843e4c078b70d392333987bc6de681a91 -Merge: 87d362544 1687fc5d7 -Author: Oliver Beckstein -Date: Fri May 22 12:19:06 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit 87d362544f98faf3eae9780f9d3c2129eb4c952d -Author: Oliver Beckstein -Date: Fri May 22 12:13:43 2015 -0700 - - regenerated online docs with sphinx - -commit 135dc550d8befb54a5091433a74795287693fec2 -Author: Richard Gowers -Date: Sat May 16 23:06:28 2015 +0100 - - Added MDAnalysis.lib._distances_openmp - -commit 57eebe16919c618ba480e0e10b5f83e9f302acfc -Author: Richard -Date: Fri May 22 10:16:06 2015 +0100 - - Updated travis to only run coverage report on 2.7 job - - Closes #284 - -commit cd5583b4cc787697230608451a4119de3760ccb5 -Author: Oliver Beckstein -Date: Fri May 22 12:12:33 2015 -0700 - - reST fixes (align and psa) and CHANGELOG fix - -commit 129497ef832c5198c269133c55485cdb9f8df882 -Merge: 128d611c8 0dee7a533 -Author: Oliver Beckstein -Date: Fri May 22 11:50:37 2015 -0700 - - Merge branch 'develop' into gh-pages - -commit 1687fc5d73dbfa9bdaf1ea82346b19847a573ee9 -Merge: 0a1a26831 b584b3784 -Author: Richard Gowers -Date: Fri May 22 11:43:37 2015 +0100 - - Merge pull request #283 from MDAnalysis/feature-openmpdistances - - Feature openmpdistances - -commit 0a1a2683119236935e4f107218d607fa003429ca -Author: Richard -Date: Fri May 22 10:16:06 2015 +0100 - - Updated travis to only run coverage report on 2.7 job - - Closes #284 - -commit 0dee7a5332e0e3995ba9f9cf05e7da3e07b71319 -Author: Sean L. Seyler -Date: Thu May 21 17:30:41 2015 -0700 - - added sseyler to AUTHORS and updated CHANGELOG - -commit 3f320d3fcbc1a0b5161c4083fcc216b37ee81357 -Merge: bc3db2cd3 797712d4d -Author: Oliver Beckstein -Date: Thu May 21 17:26:55 2015 -0700 - - Merge pull request #281 from sseyler/psa - - Path Similarity Analysis module - -commit 797712d4d20907256e727550ac9de502bf8e7e08 -Author: Sean L. Seyler -Date: Thu May 21 17:12:14 2015 -0700 - - Generated Sphinx docs for psa - -commit 7a26ab166bbfd91b31d4870c87bb7a4751396b95 -Author: Sean L. Seyler -Date: Thu May 21 16:39:12 2015 -0700 - - Added PSA module, updates to sphinx RSTs (not compiled). - -commit bc3db2cd3122080e3425d5a580f67e41afa8ca1a -Merge: 987a41205 04a8f70d8 -Author: Oliver Beckstein -Date: Wed May 20 18:59:00 2015 -0700 - - Merge branch 'feature-improvedPDB' into develop - - Closes #280 - -commit 04a8f70d82a9dc07fc2c17dcb29b0416586fe9ba -Merge: 1d86042a6 987a41205 -Author: Oliver Beckstein -Date: Wed May 20 18:58:35 2015 -0700 - - merged develop (fixed CHANGELOG conflicts) - -commit 987a4120552ebf58a4e8490dcb63bbf4321099cf -Author: Oliver Beckstein -Date: Wed May 20 18:05:58 2015 -0700 - - fixes/enhancements for analysis.align - - - Last commit broke tests for test_modelling and TestAlign: pass again - ALL HAIL TRAVIS-CI - - explicitly use analysis.rms.rmsd because rmsd() is not directly in the - align namespace anymore - - fixes for align.get_matching_residues() - - only try heuristic if number of atoms does not match - - more diagnostics (code is ugly but more useful output) - - strict kwarg properly passed through - -commit 1d86042a6fbd04465679009fcba74e0add3cafd4 -Author: Richard Gowers -Date: Wed May 20 21:36:19 2015 +0100 - - Final fixes - -commit 8250a838d32c65afd6bfbc3e7819f37f2f52d3ef -Merge: e53bc0926 3c7fe4fc8 -Author: Oliver Beckstein -Date: Wed May 20 12:38:57 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit e53bc0926983748d49a5412f8947b942512c9e74 -Author: Oliver Beckstein -Date: Wed May 20 12:35:30 2015 -0700 - - Structural superpositions (analysis.align) can use incomplete matches - - - changed check_matches() to get_matching_atoms(), which tries to get - a subset of matching atoms in two selection groups - - using partial matches is now the default; use kw strict=True to get - the old behvior whereby a single mismatch atom will throw a selection - error. The new behavior is much more convenient. - - logger output contains details on mismatches - - needed to increase numpy version requiremen from 1.0.3 to 1.4 in order - to use numpy.in1d() - -commit 846f7a7a61e403fd8d049081c53887c767962378 -Author: Oliver Beckstein -Date: Wed May 20 10:50:46 2015 -0700 - - MDAnalysis.align: submodules are not automatically imported anymore - - Import any submodule manually that you need. - -commit b561151fd9886df988695e6b3708b699320d1cde -Author: Oliver Beckstein -Date: Wed May 20 10:38:38 2015 -0700 - - bumped release to 0.10.0-dev - -commit 0048b0a08e930ba524e92a8de147fbd791959900 -Author: Richard Gowers -Date: Wed May 20 10:10:09 2015 +0100 - - Improved PDB performance (Issue #212) - - Changed PrimitivePDBParser - - Now is a proper parser, rather than relying on Reader. - - Improved PrimitivePDBReader - - Now requires the numatoms keyword - - Removed "get_bfactors", was deprecated since 0.80 - - Iterating through PrimitivePDBReader now changes the same Timestep in - place, previously returned a different Timestep object for each frame. - This matches the behaviour of other Readers. - - Updated tests because of this behaviour - -commit 3c7fe4fc84f732e7230f11338929e9625b2b649d -Author: Oliver Beckstein -Date: Wed May 20 00:13:57 2015 -0700 - - README: changed travis-ci coverall badges - - - travis-ci: now https://travis-ci.org/MDAnalysis/mdanalysis - - coverall: now https://coveralls.io/r/MDAnalysis/mdanalysis?branch=develop (but not active yet) - -commit 4345e164a7fe886149bcfbceeb999a6a1f5db474 -Merge: e5c059e72 69cfb1535 -Author: Richard Gowers -Date: Tue May 19 22:46:56 2015 +0100 - - Merge pull request #278 from richardjgowers/develop - - Added travis and coveralls - -commit e5c059e72100eddc5437ad5b3dd9004cadc0b526 -Author: Oliver Beckstein -Date: Tue May 19 14:33:18 2015 -0700 - - TestTopologyObjects: reduced test precision from 4 to 3 decimals - - - closes #271 - - tests pass locally (need to check on another machine such as i686 from the original - report in #271) - - added note to methods that calculate torsions, impropers and angles that - the precision is not more than 4 decimals and is only tested to 3 decimals - - not sure where we are really loosing the precision (probably simply for cases - that are almost degenerate to start with as in the test case for the improper - which has an angle of -3.7 degrees) but for analysis tasks this still seems to be - acceptable precision - - see #271 for further discussion - -commit 69cfb15359f714a6ebc8b746246e7b3e041b4054 -Author: Richard -Date: Tue May 19 11:27:59 2015 +0100 - - Added travis tests for 2.6 - - Removed dict comprehensions - - Python 2.6 formatting fixes ({0} not {}) - -commit 28261dc2055d1c0f6f971b04ae2fa54ee2d59618 -Author: Richard -Date: Mon May 18 10:32:30 2015 +0100 - - Added travis and coveralls - -commit af862dfdec7421cd299d8091cde023f19e55f027 -Author: Richard -Date: Tue May 19 11:50:03 2015 +0100 - - Removed dict comprehensions - - For 2.6 compatibility. - -commit b584b378462416e2881047d8aa8bb4e0f1aeede2 -Merge: 62a54ef78 e77de5cac -Author: Richard Gowers -Date: Mon May 18 20:29:12 2015 +0100 - - Merge branch 'develop' into feature-openmpdistances - -commit e77de5cac3aa95e2282d6560a7328295def22fa7 -Author: Richard -Date: Mon May 18 11:21:51 2015 +0100 - - Fixed core/distances - -commit 40404f579d0803d2da5e25843a6543de159a1c0c -Author: Richard -Date: Sun May 17 18:07:40 2015 +0100 - - Fixed empty Universe not having topology dict - - Partially related to #249 - -commit 62a54ef78d2195028fde93790af59a209f3d212f -Author: Richard Gowers -Date: Sat May 16 23:06:28 2015 +0100 - - Added MDAnalysis.lib._distances_openmp - -commit cea341f86c1ae0b847f8b40e433516f375324d02 -Author: Richard -Date: Fri May 15 18:16:12 2015 +0100 - - Minor fixes to some docs - -commit 29df17b56e46ce64a94e44699920ece0db9addb2 -Author: Richard -Date: Fri May 15 18:09:28 2015 +0100 - - Doc & pep8 fixup for core.distances - -commit bb7f382bf998b0d7358fccc0a13111469c465207 -Author: Richard -Date: Fri May 15 15:00:42 2015 +0100 - - Added MDAnalysis.lib module - - lib._distances now has zero error checking wrapper around C math - routines - - core.distances is now pure python module which calls lib._distances - -commit 9b1f0e900c7b00537ec8ba31262c021521b923b0 -Author: Manuel Nuno Melo -Date: Thu May 14 15:36:47 2015 +0200 - - Minor cosmetic cleaning - -commit 26a20bfac364a29f51102a9e9abd61449d2848a3 -Merge: 6736ddb0d 82c65572c -Author: Manuel Nuno Melo -Date: Thu May 14 15:29:55 2015 +0200 - - Merge branch 'fixed_cyzone' into develop - -commit 82c65572c353b568f64f63e8a6a7e26dad2109b8 -Author: Manuel Nuno Melo -Date: Thu May 14 15:16:44 2015 +0200 - - Cylinder selections now work from AtomGroup instances and honor PBC. - - Overhaul of cylinder selections for PBC compliance, AtomGroup - compatibility (Fixes #274), and speed (~2x speedup). - - Cylinder selections now relative to the selection's CoG also in z. - Documentation updated. - - bynum selections also modified to work from AtomGroup instances - (Fixes #275). - -commit 6736ddb0dee82f62784bb00c8b81b20d0164afcd -Author: Richard Gowers -Date: Tue May 12 23:08:41 2015 +0100 - - Fixes Issue #273 - - Removed separate dict of permissive readers - -commit 0d1220f8a9a32cf78cae923dc3e1c0007fd31647 -Author: Oliver Beckstein -Date: Mon May 11 10:48:53 2015 -0700 - - better error messages for topology and coordinate formats (Issue #266) - - - closes #266 - - TypeError more verbose for both topology and coordinate format - detection: mentions keywords to Universe() and added URLs to - documentation (at http://docs.mdanalysis.org) for the file - format (because the format strings are not really self explanatory...) - -commit e72df36f713639e676507d9bcaf6402aa06a4e0a -Merge: 7d288d9c1 e57d9e8e2 -Author: Oliver Beckstein -Date: Mon May 11 09:03:39 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit e57d9e8e21c0d3e6f98758d1215a9365b72e8b60 -Merge: 1438f5965 c648075a9 -Author: Richard Gowers -Date: Thu May 7 20:45:09 2015 +0100 - - Merge pull request #269 from MDAnalysis/feature-readercleanup - - Cleanup of base.Reader - -commit c648075a97e9b2b499e245c80e3f5e95fdb01896 -Author: Richard Gowers -Date: Thu May 7 20:43:42 2015 +0100 - - Finished coordinates tidy up - -commit 1438f5965cab0dffb74d161be5b1ad26c2441c3b -Author: Richard Gowers -Date: Wed May 6 00:21:40 2015 +0100 - - Fixed MDAnalysisTest not installing inpcrd data - -commit 45bb4ee9748483f8c686a2aa6d1a5a77f6f352e2 -Author: Richard Gowers -Date: Tue May 5 11:24:46 2015 +0100 - - Cleaned up coordinates/PDB - - Removed obsolete Timestep class - - Changed PDBReader to subclass SingleFrameReader - - Cleaned up multiframe Readers - - Moved Reader API tests into own file. - -commit bd13e24e70b8a66160806b752fb5bf6bdf912e3c -Author: Richard Gowers -Date: Mon May 4 21:14:08 2015 +0100 - - Updated INPCRDReader to SingleFrameReader style - -commit 2f76d65bd89e17cbf5c19aa9ab38deda67ce52b2 -Merge: b9f12ce97 b2d70dd26 -Author: Oliver Beckstein -Date: Fri May 1 17:38:50 2015 -0700 - - Merge pull request #267 from MDAnalysis/feature-singleframereader - - Added SingleFrameReader. - - Good clean up effort – nice when the line count goes _down_ while readability and maintainability goes _up_! - -commit b9f12ce97c235252737eecfee967357bc7dbec30 -Merge: 1f330d14b 7d2e276cd -Author: Oliver Beckstein -Date: Fri May 1 17:31:20 2015 -0700 - - Merge pull request #265 from MDAnalysis/feature-AmberCRDReader - - Added (another) Amber coordinate reader. - - Thanks @richardjgowers ! - -commit 7d2e276cda3e67ae5fc948746c5b05a82801896b -Author: Richard -Date: Fri May 1 15:27:35 2015 +0100 - - Fixed failure when time not present in INPReader - -commit b2d70dd269af23a44c3d4d949a06c588cf145ee4 -Author: Richard -Date: Fri May 1 15:25:46 2015 +0100 - - Added SingleFrameReader - - Acts as base class for Readers which only have a single frame - Should help reduce amount of boilerplate. - - Removed some Timesteps which are now obsolete because base.Timestep - handles dimensions - * CRD.Timestep - * LAMMPS.DATATimestep - * PDBQT.Timestep - - Added tests for coordinates.base.SingleFrameReader which ensure that - the new reader strictly follows the API (and therefore all subclasses - do) - -commit 4b657e149030941244234036908bb69b116ebe85 -Author: Richard Gowers -Date: Fri May 1 10:11:05 2015 +0100 - - Updated CHANGELOG - -commit 8848fd06060850fe7a749870b1d08391248a68fa -Author: Richard Gowers -Date: Fri May 1 09:57:26 2015 +0100 - - Added (another) Amber coordinate reader - - Now reads formats 'inpcrd' and 'restrt' (Issue #262) - -commit 7d288d9c1eeeb2b98eeb37e3ea1a805bdf8627c3 -Merge: c4de5de32 1f330d14b -Author: Oliver Beckstein -Date: Wed Apr 29 14:07:57 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit 1f330d14b88cec568e364e6f2113b81c23d92765 -Author: Manuel Nuno Melo -Date: Wed Apr 29 12:57:41 2015 +0200 - - Added docs for the 'same ... as' selection keyword - - Also improved performance on 'same residue/segment/fragment searches. - Added the optional flag 'expected=True' to SelectionParser.__error to - allow for more meaningful error messages. - -commit c4de5de328a7e949706118cb7d2b179a7eeb0b04 -Merge: 3e02ee9f7 566f3ee30 -Author: Oliver Beckstein -Date: Tue Apr 28 21:51:50 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit 566f3ee30aa5753554472cf8154c7c05393fdcff -Author: Caio S. Souza -Date: Wed Apr 29 02:49:02 2015 +0200 - - Added the 'same ... as' selection keyword (Fixes #217) - -commit 3e02ee9f75a82d030b74e422bcd466e6ef67981d -Author: Manuel Nuno Melo -Date: Wed Apr 29 02:49:02 2015 +0200 - - Added the 'same ... as' selection keyword (Fixes #217) - -commit 83503283403d390e5f4b16f14984ca0d6cc45ef0 -Merge: 625b0765f 855c36366 -Author: Richard -Date: Tue Apr 28 09:24:53 2015 +0100 - - Merge branch 'feature-netCDF_Forces' into develop - - Closes #257 - Closes #259 - -commit 855c36366d8367abcf3669fe9453f83771d3b9dd -Author: Richard -Date: Tue Apr 28 09:24:37 2015 +0100 - - Bumped version number - -commit b2109345d3633471478b6e62baf957b9c28a617a -Merge: c5ca8b6e4 625b0765f -Author: Richard -Date: Tue Apr 28 09:21:39 2015 +0100 - - Merge branch 'develop' into feature-netCDF_Forces - - Conflicts: - package/CHANGELOG - -commit 625b0765f6493f98ba1bb0d40a56a08d0db57d31 -Author: Jan Domanski -Date: Mon Apr 27 17:54:10 2015 -0400 - - Partially resolves #222 - - still no tests, likely still broken for more complex cases - -commit c5ca8b6e4a93dde4e341114a41a45930dc89432c -Author: Richard Gowers -Date: Sat Apr 25 11:39:46 2015 +0100 - - Added tests for NCDFReader. Finished Issue #257 - - Thanks to Albert Solernou for the Amber trajectories. - - Added ability to write velocities and forces to ncdf trajectories. - -commit bb010e7939e1ecb83b32fec8fe1121838cd3f1f3 -Author: Jan Domanski -Date: Fri Apr 24 15:44:12 2015 -0400 - - MOL2Writer - add limitations and examples to documentation - - resolves #227 - - incorporated suggestion from @richardjgowers - -commit ec77b3c4119bc62f1483a5e06470242fe976f236 -Merge: f53e05438 660115cbc -Author: Richard Gowers -Date: Tue Apr 21 09:03:32 2015 +0100 - - Merge branch 'feature-autobonds' into develop - -commit 660115cbc93887c970ef642e49ff29242c103b83 -Merge: ada5de0cf f53e05438 -Author: Richard Gowers -Date: Tue Apr 21 09:03:16 2015 +0100 - - Merge branch 'develop' into feature-autobonds - - Conflicts: - package/CHANGELOG - -commit ada5de0cf7303a752948d79b580c4e2fa41d62df -Author: Richard Gowers -Date: Tue Apr 21 08:59:02 2015 +0100 - - Added guess_bonds to Universe and AtomGroup (Issue #245) - - Adds ability to guess_bonds on Universe creation and on an AtomGroup - basis - -commit df95ff6ca9add274161bc671590a0eedad45d87f -Author: Richard Gowers -Date: Mon Apr 20 21:53:58 2015 +0100 - - Added force reading to Amber netCDF4 reader - - Start of issue #257 - - Added new force units to core.flags 'kcal/(mol*A)' - Added conversion for 'kcal/(mol*A)' => 'kJ/(mol*A)' - -commit f53e0543889c620ccd5e3bdbd21257c5592a9494 -Author: Sébastien Buchoux -Date: Mon Apr 20 17:18:12 2015 +0200 - - Added Tyler back to the 0.9.2 entry of the Changelog - -commit dc7831e7dc28397e6212bf6ad3d1bacee63c016a -Merge: e1f7a924e 603f76836 -Author: Sébastien Buchoux -Date: Mon Apr 20 17:09:43 2015 +0200 - - Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis into develop - - Conflicts: - package/CHANGELOG - -commit e1f7a924e9391b1008cad06c1ef65742b9c95637 -Author: Sébastien Buchoux -Date: Mon Apr 20 17:04:02 2015 +0200 - - Version updated to 0.9.3-dev and doc regenerated - -commit 603f768363a9cb44606720fc37d492dc31883665 -Author: Tyler Reddy -Date: Mon Apr 20 15:42:26 2015 +0100 - - Updated CHANGELOG to reflect resolution of Issue 256. - -commit 1f8e35fac6fd69a2f82d868b465096247c55b248 (tag: release-0.9.2) -Author: Sébastien Buchoux -Date: Mon Apr 20 16:26:15 2015 +0200 - - Version number set to 0.9.2, date in CHANGELOG updated and Documentation regenerated - -commit 01f3a9cde1c5ac53da3eef8ccd093cfdfe9ee1e1 -Author: Tyler Reddy -Date: Sun Apr 19 21:19:19 2015 +0100 - - test_selections.py tests updated to properly close trajectory objects (was causing unit tests to fail on some systems due to open file descriptor limit) - -commit 30a1d5cb4023c5f6eb90fdb30dde33193180138b -Merge: f8edb8aa7 42872762d -Author: Oliver Beckstein -Date: Thu Apr 16 16:58:44 2015 -0700 - - Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop - -commit f8edb8aa7b88fc1867a6583939a23d935ed3990a -Author: Oliver Beckstein -Date: Thu Apr 16 11:02:48 2015 -0700 - - AtomGroup instant selectors now raise AttributeError (Issue #220) - - - fixes issue #220 - - AtomGroup instant selectors now raise AttributeError and not SelectionError - - Note: using string indexing like AtomGroup['C'] will still raise SelectionError - if there is no atom 'C' in the group). AtomGroup.C will now raise AttributeError. - We could make the former raise KeyError instead of SelectionError but that seems - less than a problem than the common case in interactive use where mistyping an - attribute or method name gave the cryptic SelectionError - - The current implementation just uses another level of indirection and introduces - the method AtomGroup._get_named_atom(name). - - unit test included (check that non-existent attribute raises AttributeError) - -commit 42872762d5b617c46bccaf7deeb5b5675e35584f -Merge: 37d4fdbc9 c9cc016ab -Author: Richard Gowers -Date: Sun Apr 12 20:12:35 2015 +0100 - - Merge pull request #246 from MDAnalysis/feature-wrap - - Added wrap method to AtomGroup Fixes #190 - -commit c9cc016ab31b72ba370bee2938e18d9506244401 -Author: Richard Gowers -Date: Sun Apr 12 20:11:03 2015 +0100 - - Fixes to documentation - -commit 88e7694d7cb06e5e3d143ad972f9fea9f65b1bb9 -Author: Richard Gowers -Date: Fri Apr 10 12:33:24 2015 +0100 - - Added wrap method to AtomGroup - - Wrap allows the centers of groups of atoms to be - moved within the primary unit cell without breaking up the group. - (Fixes Issue #190) - - Added bonds to TRZ psf file so fragments can be made. - -commit 37d4fdbc984d8e1504695403c7aa55c542856031 -Author: Richard -Date: Thu Apr 9 10:17:48 2015 +0100 - - Tidying of topology related things - - Changed Universe._psf to Universe._topology - - topology.base.TopologyReader now has keyword 'universe' which - gets saved as self._u. This is then passed to Atoms on creation. - - Atoms can now be passed their Universe as kwarg. - - All '_things' renamed to 'things' in Universe._topology. - - Renamed __is_guessed to _is_guessed in Bond (death to double - underscores) - - Added absolute_import from future to all topology modules (Issues #132 #216) - - Updated tests to reflect new names - -commit 128d611c8f534b171d27a9804ebeb846c9aded3c -Author: Oliver Beckstein -Date: Thu Apr 9 01:31:51 2015 -0700 - - Added .nojekyll file to disable Jekyll - - Otherwise, the site appears without css because Jekyll ignores - all directories and files starting with underscore, whereas sphinx - uses underscore diretories. See also: - - - https://github.com/blog/572-bypassing-jekyll-on-github-pages - - https://help.github.com/articles/files-that-start-with-an-underscore-are-missing/ - -commit 9f7711ad93cd7f25786b05c1a2ae41128a36ed1c -Author: Oliver Beckstein -Date: Thu Apr 9 01:13:46 2015 -0700 - - regenerated online docs (now with new URLs) - -commit 3ed4450f7cbeb0318be49e6370dc2982496994f3 -Author: Oliver Beckstein -Date: Thu Apr 9 01:22:42 2015 -0700 - - changed URLs in sphinx docs from Google Code to GitHub - -commit 9ead510e8240accd9852f218366f2d07940d9cff -Author: Oliver Beckstein -Date: Thu Apr 9 00:40:28 2015 -0700 - - fixed imports in TPR parser - - - use explicit relative imports (PEP8) - - broke a cyclic import by moving the un-used do_inputrec() function - from tpr.settings to tpr.utils. (No idea why this might have worked previously...) - - small TPR parser doc cleanups - -commit dde819af267a77fd347043f92d5175fba4b7daee -Author: Oliver Beckstein -Date: Wed Apr 8 18:37:39 2015 -0700 - - more Google Code link cleanup - - - README and INSTALL - - also changed links for netcdf4, which moved to GitHub - - fixes issue #240 - -commit 2a0fb78af38e8831c0de600eb7e5a9a780d8a32d -Author: Tyler Reddy -Date: Wed Apr 8 15:20:27 2015 +0100 - - -updated wiki links in .py files to reflect move to github - -commit f3c4b33334d2e20b63710bbd36c0c681cf51db63 -Author: Tyler Reddy -Date: Wed Apr 8 15:09:37 2015 +0100 - - -updated links to issue attachments after move to github -- these still seem to depend on google in some way though. - -commit 507fa305551119d9ad317fbc577f3cf87b60821d -Author: Tyler Reddy -Date: Wed Apr 8 15:01:06 2015 +0100 - - -replaced old issue links with new github issue links (except for attachment links) in .py files in MDA project - -commit 1d4e8bca12dffc6fca1e7b76dffa9531f9162e09 -Author: Tyler Reddy -Date: Wed Apr 8 12:57:23 2015 +0100 - - -replaced the old MDAnalysis webpage URL with the new (post-github) webpage URL in all MDA package files ending in .py - -commit 21225ce79955881c904fb8ae2fcbd657930f6578 -Author: Oliver Beckstein -Date: Tue Apr 7 18:40:41 2015 -0700 - - move to GitHub: updated top level information - - - setup.py (metadata) - - README, INSTALL, SUMMARY.txt - - CHANGELOG - - removed upload scripts for googlecode - -commit bd147eef87ac01b6dcd3c66be2d419d9d1ff0e25 -Author: Oliver Beckstein -Date: Tue Apr 7 18:17:24 2015 -0700 - - removed applications - - - RotamerConvolveMD now lives in its own repository at - https://github.com/MDAnalysis/RotamerConvolveMD - - see https://github.com/MDAnalysis/mdanalysis/wiki/Splitting-off-RotamerConvolveMD - for details of the procedure - - applications or tools get their own repository and team under github.com/MDAnalysis - -commit 26ca924d0b8d6a5eeb687fb71645a9e2878c37e7 -Author: Richard Gowers -Date: Tue Apr 7 02:28:32 2015 +0100 - - Fixed up docs on new Atom methods - -commit 0765aec7601b7fb9a5a988045162c5a2a8663a79 -Author: Richard Gowers -Date: Tue Apr 7 02:09:58 2015 +0100 - - Atoms can now set/get force & velocity - - Fixes #221 - -commit 9dc9c0e8c94c004e25b58268239c23c48929d82c -Merge: 957796622 b893bf55a -Author: Oliver Beckstein -Date: Fri Apr 3 18:30:38 2015 -0700 - - Merge branch 'master' into develop - -commit b893bf55a2f5e15ef237c15026f2cd14586aaf76 -Author: Oliver Beckstein -Date: Fri Apr 3 18:30:18 2015 -0700 - - updated top-level README (and added top level LICENSE) - -commit 95779662217f00b6e8881bd6d8de82bd7e03559d -Author: Oliver Beckstein -Date: Fri Apr 3 18:28:34 2015 -0700 - - updated top-level README - -commit 61b23db47569ca3715aca3b187f8fe888e5178a7 -Author: Oliver Beckstein -Date: Sat Mar 28 22:07:30 2015 -0700 - - regenerated html docs with sphinx - -commit 3ab7d34d71826b50d485fdb2d97ebb169472e113 -Author: Oliver Beckstein -Date: Sat Mar 28 22:01:44 2015 -0700 - - topology docs clean-up/extension - - - manually listed classes for each topology parser - - added docs for the tpr parser support module - - added docs for topology.base - - updated topology format table (readers that can provide - topology AND coordinates) - -commit 0fce20953c1ec87cdd7798c7ab468d2471316a40 -Author: Richard -Date: Sat Mar 28 08:35:45 2015 +0000 - - Fixed Documentational for recent changes - - Fixes Issue 230 - - rst stubs added for - GAMESS coordinate & topology readers - MOL2 coordinate & topology readers - LAMMPS topology reader - XYZ topology reader - - Fixed errors in rst for xPDB - - Fixed up DCD markup - -commit 3800a84b36d95128a951f7ffbcf533a1c320f445 -Author: Oliver Beckstein -Date: Fri Mar 27 17:33:21 2015 -0700 - - added Alex Nesterenko (comconadin) to CHANGELOG and sphinx docs - - - author contribution of comcodin1 to 0.9.1 was omitted: apologies - - minor reformatting of CHANGELOG - - added Alex to sphinx html docs - - updated year to 2015 in sphinx docs (for copyright etc) - -commit 1763454685714e7ffd968bb3571ade68b490a630 -Author: Sébastien Buchoux -Date: Fri Mar 27 22:49:07 2015 +0100 - - version changed to 0.9.2-dev. Documentation regenerated accordingly - -commit 1f1b48f3d9a4382483d8376542194e2e7f092e03 (tag: release-0.9.1) -Author: Sébastien Buchoux -Date: Fri Mar 27 21:29:28 2015 +0100 - - Version changed to 0.9.1 and doc regenerated - -commit 03305b24e9a05dbadcc1d49d89c29d57403c3ec8 -Author: Oliver Beckstein -Date: Thu Mar 26 16:20:29 2015 -0700 - - TestGMSReader: fixed error (gms.gz data files were not included) - -commit ed244dde7c0ac62a5568b18d2a0d6cfa1c480db2 -Merge: 4b6ef9ddf b4a70b5ab -Author: Richard -Date: Thu Mar 26 17:16:56 2015 +0000 - - Merge branch 'feature-GAMESS_Reader' into develop - - Fixes Issue 228 - -commit b4a70b5ab7949db545855d6db7f5d60d686475cb -Author: comcon1 -Date: Tue Mar 24 18:30:12 2015 +0300 - - Many different code corrections according to code review (on Issue 228). Inculding: testsuites for topology reader were added. testsuites for topology reader were modified. - -commit feff64a5db8de7da4134d968b04645410d34de5e -Author: comcon1 -Date: Tue Mar 24 18:28:16 2015 +0300 - - XYZ files removed from data-for-tests because Topology reader for GAMESS files was added - -commit 4b6ef9ddf29e85a385d1017f0b8b33ff41cbf536 -Author: Manuel Nuno Melo -Date: Mon Mar 23 21:18:21 2015 +0100 - - Removed reference to MDAnalysis.builder from setup.py - -commit 2cc54050d77ba0fafe46897283d06e0d7d1da176 -Author: Manuel Nuno Melo -Date: Mon Mar 23 20:57:52 2015 +0100 - - Updated the UnitTests pertaining to Issue 224. - - Setter tests are now more stringent and run on all Timesteps. - - Optional "mightpass" flag added to the knownfailure decorator - as the setter tests pass on some (TRR) but not all Timesteps. - -commit 3a9fd6af11a60e1b5ed5c93744eb20e4c156683c -Author: Oliver Beckstein -Date: Sun Mar 22 17:14:50 2015 -0700 - - updated .gitignore - - - ignore files from nosetest/coverage - - ignore cached Gromacs trajectory offsets (generated when - the unit tests are run in the MDAnalysisTests directory) - -commit 5603471eb812a791282036af97bf15904f5fca3f -Author: Oliver Beckstein -Date: Sun Mar 22 17:07:44 2015 -0700 - - removed undocumented MDAnalysis.builder module - -commit b5efcf0ca5ae148e8348f4e6ef6ee5954457ea60 -Author: Richard -Date: Sun Mar 22 22:42:40 2015 +0000 - - fixed cached decorator breaking function docs - -commit 708f3ad8b555ade35c78b3d90f2b3200cece8e36 -Author: comcon1 -Date: Fri Mar 20 19:06:57 2015 +0300 - - Simple TestCase for GMSReader with data files was added. - -commit 43df53c3d6577d4ae3e148fb6e94145246dd0156 -Author: comcon1 -Date: Fri Mar 20 19:06:30 2015 +0300 - - GAMESS output reader feature added. - -commit 685bb52bdbc2cae87be0934158461e66a6283e29 -Author: Richard -Date: Thu Mar 19 18:39:37 2015 +0000 - - Fixed an incorrect requirement for hbond autocorrel tool - - Also touched up docs for it. - -commit e0585ae964ddb01b893ddd30a8e67c0577cbc9b4 -Author: Richard -Date: Thu Mar 19 15:05:29 2015 +0000 - - Added ability to read XYZ files without topology file - - Added XYZParser, just reads the atom labels. - - Removed XYZ.Timestep, was identical to base.Timestep - - Fixed up coordinate and topology documentation - -commit ef89319c8222b9ad92705f3e6553fcb0b2cf571c -Author: Oliver Beckstein -Date: Tue Mar 17 11:41:30 2015 -0700 - - changed "if ts == None" to "if ts is None" (for consistency) - - Note that this is a purely cosmetic change because ts is not an array - and there is no danger of the comparison being wrong in the future. - (Also some whitespace changes.) - -commit 2495473b783dff7a4c083d1e05e0635d6a3adbf2 -Author: Oliver Beckstein -Date: Tue Mar 17 11:38:03 2015 -0700 - - fixed comparisons of array to None in distances_parallel - - FutureWarning: comparison to `None` will result in an elementwise object comparison in the future. - (came up in the test MDAnalysisTests/test_parallel.py:94) - -commit 9b6f0511da14cb7bb5300130f1226880ea572f20 -Merge: 8f4d1bfa4 121a42a27 -Author: Manuel Nuno Melo -Date: Tue Mar 17 14:48:19 2015 +0100 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - - Conflicts: - package/CHANGELOG - -commit 8f4d1bfa4e054f0d178185e4727e29c51b8b68a3 -Author: Manuel Nuno Melo -Date: Tue Mar 17 14:46:10 2015 +0100 - - Fixed TRR coordinate access via _y and _z (Issue 224) - -commit 121a42a272eb5ff4a525d019df20c031ec7c7fe0 -Author: Sébastien Buchoux -Date: Tue Mar 17 13:55:49 2015 +0100 - - version updated to 1.0.0-dev and doc regenerated accordingly - -commit aed54ddbef8b818dcfa7a15934014f1e3c412612 -Merge: 5a45de19b 128a5c1e1 -Author: Sébastien Buchoux -Date: Tue Mar 17 13:43:23 2015 +0100 - - Merge tag 'release-0.9.0' into develop - -commit 128a5c1e1d51d8b7b0532bd07abdfb12e7641318 (tag: release-0.9.0, upstream/release-0.9.0) -Author: Sébastien Buchoux -Date: Tue Mar 17 11:54:06 2015 +0100 - - Documentation regenerated - -commit ceefe7516d4b1328be72e62b71b0c0a1a4577579 -Author: Sébastien Buchoux -Date: Tue Mar 17 11:53:13 2015 +0100 - - removed duplicated testcase in test_util and fixed potential segfaulting test - -commit d59c895fc9d27e173aa0e6811978c04bdcee59f1 -Author: Sébastien Buchoux -Date: Tue Mar 17 10:58:36 2015 +0100 - - Shebang lines fixed - -commit b5581dc841fbcb34d83d1aae3ee77c155fca7a8a -Author: Oliver Beckstein -Date: Fri Mar 13 17:04:02 2015 -0700 - - fixed failing tests in test_modelling - - - test_capping_file and test_capping_inmemory failed with a dimensions error - - fixed by using new canonical way to directly assign to Timestep.dimensions in the - capping() function - - also fixed capping() in the examples/example_cap_peptide/capping.py - script - - All UnitTests pass now (or skip). - -commit a1063ee2c5a3b96b8c41c0beb19f0b68b4b2c9ef -Author: Richard -Date: Fri Mar 13 12:11:37 2015 +0000 - - Fixed DMSTimestep initial unitcell being wrong - - Fixed test_dimensions test for DMS - - Fixed unitcell setting for base.Timestep - -commit 1c8cf3db5a355170a4f67178f507bf69253c404d -Author: Richard -Date: Fri Mar 13 11:27:15 2015 +0000 - - Removed incorrect test - - base.Timestep now has blank unitcell (ie np.zeros(6)) by default - -commit 5a45de19b328bb119da448a716abc4ef0668243e -Author: Sébastien Buchoux -Date: Tue Mar 17 10:58:36 2015 +0100 - - Shebang lines fixed - -commit 5e98c08d0695e78e98e1ef2cc255bc875df38e8b -Author: Oliver Beckstein -Date: Fri Mar 13 17:04:02 2015 -0700 - - fixed failing tests in test_modelling - - - test_capping_file and test_capping_inmemory failed with a dimensions error - - fixed by using new canonical way to directly assign to Timestep.dimensions in the - capping() function - - also fixed capping() in the examples/example_cap_peptide/capping.py - script - - All UnitTests pass now (or skip). - -commit 6dd4ca9e8d42157fdb2d4a5325d8feee1e5e64c8 -Author: Richard -Date: Fri Mar 13 12:11:37 2015 +0000 - - Fixed DMSTimestep initial unitcell being wrong - - Fixed test_dimensions test for DMS - - Fixed unitcell setting for base.Timestep - -commit bf511f51c60a8f4ffbddfebfe7242712986f7f74 -Author: Richard -Date: Fri Mar 13 11:27:15 2015 +0000 - - Removed incorrect test - - base.Timestep now has blank unitcell (ie np.zeros(6)) by default - -commit 3a72b875aaaabf9ae15c0776a62639b01f573814 -Author: Sébastien Buchoux -Date: Fri Mar 13 09:52:10 2015 +0100 - - Changelog update with a release date - -commit 03975aa053bd8631c06af00c790049c241c3a906 -Author: Sébastien Buchoux -Date: Fri Mar 13 09:49:26 2015 +0100 - - Version changed to 0.9.0 and Documentation regenerated accordingly - -commit 69b0099e0ce1d7edadefecd80c7a9c6c5fbd2436 -Author: Sébastien Buchoux -Date: Fri Mar 13 09:29:50 2015 +0100 - - Removed offset files in testsuite to avoid side effects from the - modification of the trajectories ctime without actual modifications of the - files (as ctimes are not guaranteed to be preserved during installation) - -commit 912e92a97de5a0624ea6706fe24462ce3491aa89 -Author: Oliver Beckstein -Date: Thu Mar 12 16:58:34 2015 -0700 - - alternative square MDAnalysis logo (for GitHub) - -commit a3edee5ff4942e7e1abf8ff966b119eb8445fe96 -Merge: b1f046a64 fe9d9900e -Author: Oliver Beckstein -Date: Thu Mar 12 14:20:28 2015 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit b1f046a640d307801f9cd4bd34bfdc385d57ebf5 -Author: Oliver Beckstein -Date: Thu Mar 12 14:18:45 2015 -0700 - - regenerated html docs - -commit 4788ecc8a7a6abf9503db9a91d99de211c981daf -Author: Oliver Beckstein -Date: Thu Mar 12 13:52:23 2015 -0700 - - corrected version: 0.9.0-dev (used to be 0.8.2-dev) - - - previously everything was 0.8.2-dev but we had decided to go from 0.8.1 to 0.9.0 - (see also the discussion on SemanticVersioning) - - preliminary docs will now have the correct version included as well (together - with the recently updated versionchanged reST directives) - - updated CHANGELOG - -commit dd4a5abab898ee73b86b2d521b3866a98d231b38 -Author: Oliver Beckstein -Date: Thu Mar 12 13:41:41 2015 -0700 - - reST docs: integrated xdrfile and restructured coordinates section - -commit 489765f91c42cb19be58ea64c04eeee0932e0cc3 -Author: Oliver Beckstein -Date: Thu Mar 12 12:41:23 2015 -0700 - - reST fixes in the doc strings - - - changed all 0.8.2 to 0.9.0 (in the doc strings only) - - fixed some "versionchanged" directives (no blank line between - the reST directive and the text, see - http://sphinx-doc.org/markup/para.html#directive-versionchanged ) - - headings in coordinates.xdrfile - -commit fe9d9900e99ce1f96b8dbc9db633e5e4f866b3ba -Author: Richard -Date: Thu Mar 12 18:39:51 2015 +0000 - - Rewrote AtomGroup.momentOfInertia - - Approx 50x faster. - -commit dec267ddb824f6f2de541dc38c2b27e34ba3d0d8 -Author: Oliver Beckstein -Date: Thu Mar 12 11:05:11 2015 -0700 - - maintainer script for coverage reporting - - The coverage html report is occasionally pushed to - http://wiki.mdanalysis.googlecode.com/git/pages/quality_control/cover/index.html - but we'd really like this to be automated (Issue 134). - -commit e98a82fbd816b93a06efcb21434d6ac7ed88f02d -Author: Oliver Beckstein -Date: Wed Mar 11 17:14:12 2015 -0700 - - fixed a FutureWarning: comparison to `None` will result in an elementwise object comparison in the future. - -commit 0dc7c6a17b55cc27da3d31e8c613f79ead081986 -Author: Richard -Date: Fri Mar 6 00:25:10 2015 +0000 - - Fixed GROParser not stripping atom and residue names - -commit 4b395f4c815f46f2ecd3ac207ea8141f58e363e4 -Merge: 512855d56 c7c417d00 -Author: Richard -Date: Fri Mar 6 00:23:47 2015 +0000 - - Merge branch 'feature-persistentoffsets' into develop - -commit c7c417d00645f35409decfda36d94b945d337b7e -Author: David Dotson -Date: Thu Mar 5 00:04:51 2015 -0700 - - Fixes Issue 208 - - Added more error handling/reporting to persistent offsets. - - Moved XTCReader and TRRReader offset tests to separate classes. - - Since we need to copy the trajectories to a temporary directory to - ensure the offsets are generated, including the offset tests in with the - other XTCReader and TRRReader tests would have made all of them slower. - To mitigate this I moved all the offset tests to their own test classes. - I also broke the tests up into smaller, more isolated pieces. - -commit 512855d560c90845a2784c2e3433aaf46d0e186e -Merge: 50b05f40f effea4869 -Author: Oliver Beckstein -Date: Thu Mar 5 17:56:20 2015 -0600 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 50b05f40f3220b78ca13cf8f38963c8bb5f92805 -Author: Oliver Beckstein -Date: Sat Feb 21 22:59:24 2015 -0700 - - new AtomGroup.sequence to extract sequence information - - - makes it easy to get a sequence of a protein or any selection - - return Bio python SeqRecord, Seq or just a string - - raises ValueError if a residue is not recognized (only handles - the standard residues defined in core.util) - - tests added - -commit effea48690cd6982865662e8375a40bf87adeadc -Author: Richard -Date: Thu Mar 5 22:39:27 2015 +0000 - - Slight performance tweak to guess_atom_element - -commit b6832d683e188e06b0a665226d8e7e39e89ef06f -Author: Richard -Date: Thu Mar 5 22:33:34 2015 +0000 - - GROParser performance update - - Also fixed potential bug where 5 character resname and atomname could - not be split - -commit 04f5132c52745ec7ef34c3531ea8c4e1349a1b77 -Author: Richard -Date: Sun Mar 1 00:34:18 2015 +0000 - - Improved performance of creating residuegroup from AG - - Added use of sets in creating residue and segment groups from AtomGroup - -commit 09b18ed324670ffe0dc2402011b7826cca009dbe -Author: David Dotson -Date: Tue Jan 27 17:01:39 2015 -0700 - - XTC and TRR files now write offsets to disk. - - It is a common problem that if one has large XTC or TRR files, it can - take a long time to get the number of frames when loading these as - coordinates of a universe. Getting the number of frames is necessary for - the chain reader upfront, so when loading multiple XTC or TRR files this - may mean a substantial wait before the universe is ready for use. - - When the number of frames is obtained, an index of the trajectory file - giving the offsets of its frames is also stored. This allows for quick - random access through the trajectory thereafter. Until now, this index - is lost when python session ends. Now, these offsets are stored as - (small) hidden pickle files in the same directory as the trajectories - with names ``._offsets.pkl``. - - When a universe is loaded with XTC or TRR files, the TrjReader tries to - load these offsets. If they are present, it then checks the ctime of the - trajectory file against that stored in the offset file. If they match, - the offsets are applied. Otherwise, they are ignored and eventually - overwritten when numframes is called. - - Updated unit tests to reflect changes to offsets. - - Added exception for storing xdrfile offsets. - - This elegantly handles cases for which offsets cannot be automatically - stored in the same directory as the trajectory (due to permissions, for - example). - - Added additional checks to ensure offsets are not stale. - - In addition to ctime, the size of the trajectory file is also stored - with the offsets. On load the size and ctime of the trajectory file is - compared to these stored values. - - Following load of the offsets, the last frame of the trajectory is - loaded. If this fails, then the offsets are dropped so they will be - regenerated. This is a final sanity check that the offsets aren't wrong. - - Tests passing for xdrfile persistent offsets. - - New tests added to ensure that offsets aren't used when stale. - -commit 2fc9a84fd5abef9774cadf80805189f3de38dca0 -Author: Oliver Beckstein -Date: Thu Feb 19 18:35:01 2015 -0700 - - Contact analysis: can use centroids of selected atoms per residue (closes Issue 169) - -commit 994e77d7a20ba3e1c02ad85a71572847e83cc1af -Author: Bala Subramanian -Date: Thu Feb 19 12:11:30 2015 -0700 - - added custom selection to ContactAnalysis (closes Issue 169) - - - q1-q2 contact analysis can use other atoms than CA with the new - selection keyword - - default remains CA - - NOTE: would need to implement using centroids for e.g. sidechains to - to make it more useful - -commit ff5c5d02ea5c6cb49c265ca73b2506f2f7bf4b70 -Merge: 99714410e 26be6b89e -Author: Oliver Beckstein -Date: Thu Feb 19 17:56:40 2015 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 99714410e30e3075371b19a4a819c9e233ac47f6 -Author: Oliver Beckstein -Date: Thu Feb 19 17:51:06 2015 -0700 - - new feature AtomGroup.split(level): list of AtomGroups, one for each level of the hierarchy - - - level = 'atom', 'residue', 'segment' - - purpose: simplify working e.g. with the sidechain atoms in each residue - - tests added - -commit 26be6b89e2940411d8a523b2ca2f852a1183a1c9 -Merge: 199d6bf54 dfe1c1bca -Author: Richard -Date: Thu Feb 19 19:57:51 2015 +0000 - - Merge remote-tracking branch 'origin/feature-atompartners' into develop - - Fixes Issue 219 - -commit 199d6bf54d6c72eb538ce42942fd2cdffd07a24a -Merge: c58c80f71 e6fc3b20d -Author: Richard -Date: Thu Feb 19 19:21:59 2015 +0000 - - Merge branch 'feature-customreaders' into develop - - Fixes Issue 198 - -commit e6fc3b20ddd7ff40e2384410ea960d783b51feba -Author: Richard -Date: Wed Feb 18 12:11:04 2015 +0000 - - Can supply trajectory and topology readers as kwargs for Universe - - "format=" and "topology_format=" can now be passed a subclass of - coordinates.base.Reader and topology.base.TopologyReader respectively to - define a reader for the input. - - This allows users to "inject" custom reader classes into MDAnalysis - without having to compile from source. - - Added absolute_import from future to core.AtomGroup, removed implicit - imports. (py3k) - Moved imports to top of module where possible (pep8) - - Tidied Universe __init__ slightly - -commit c58c80f71f1b4544639584178cc3a4757d9e84c9 -Author: Oliver Beckstein -Date: Wed Feb 18 00:38:14 2015 -0700 - - regenerated html docs (for updated DCD docs) - -commit 2ebcae2369a4d0d4ec36ff6cbdd180e68ced909a -Author: Oliver Beckstein -Date: Tue Oct 21 17:32:15 2014 -0700 - - correct reading/writing of DCD unit cell information (fixes Issue 187) - - ATTENTION: Prior to this fix, triclinic box handling was BROKEN for DCDs. Orthorhombic boxes were ok because the order - of the angles did not matter. - - - in combination with the fixed DCD C code, the unit cell information is extracted from the DCD as - [A,gamma,B,beta,alpha,C] and presented in the canonical format as [A,B,C,alpha,beta,gamma]. - (The changes in dcd.c were modelled after the 2013 version of the VMD molfile plugin.) - - the DCDReader heuristically guesses if new-style (at least CHARMM c36b) box matrix information is supplied - and then converts on the fly to the [A,B,C,alpha,beta,gamma] format - - the DCDWriter *always* writes writes [A,gamma,B,beta,alpha,C] (in fact, the underlying C code in DCD.c, which is based - on the VMD DCD molfile plugin) writes the angle cosines instead of the angles but it takes [A,gamma,B,beta,alpha,C] - as its input); the DCDWriter will not write box matrix to a DCD: this is not supported at the moment. - - NOTE: Therefore, if one reads a DCD and then writes it with MDAnalysis, it might not be identical because the unit cell - information might have been converted from box matrix to lengths/angle cosines. This DCD file might then - not be readable in CHARMM any more. - - - added test cases for reading/writing triclinic boxes (files from the Issue 187 report; - thanks to caioubiounb for providing a set of NAMD files) - - updated docs (lots of notes and links to Issue 187) - - For further details and background see Issue 187. - -commit b3c6b475f7f1f0dc55dfb3e5e93d9707aa7276f6 -Author: Oliver Beckstein -Date: Tue Feb 17 14:39:17 2015 -0700 - - regenerated docs (lots of reST changes in core.units) - -commit 0fdf484f7a30491e0bca2d639c1263b42f6fcf34 -Author: Oliver Beckstein -Date: Tue Feb 17 13:25:20 2015 -0700 - - core.units: added docs and some cleanup + more tests - - - table with base docs - - added some MathJax - - store calorie as constants['calorie'] (+ test) - - more force conversions + tests - - use nosetest generators to make each assert an individual test - -commit 87a1dba04bc9285587757ddf27dba054edb76ebd -Author: Oliver Beckstein -Date: Tue Feb 17 10:58:33 2015 -0700 - - rebuilt docs with sphinx (to check Issue 182) - -commit 90ff75379f94a70f6640db90e7f22a0b168d558e -Author: Oliver Beckstein -Date: Tue Feb 17 10:57:44 2015 -0700 - - units: move from __future__ import AFTER the module doc string. - - Otherwise the doc string is not recognized and sphinx complains about a missing title. - Alternatively one can assign to __doc__ but I found this uglier than making the - import the first code statement after the doc string. - -commit 3d9b19ffb7a3ca182dcbecd95a63f0a6c18a413e -Author: Tyler Reddy -Date: Tue Feb 17 09:03:33 2015 -0800 - - Sphinx conf.py now specifies secure https mathjax_path. Rebuilt html docs. Should resolve Issue 182. - -commit dfe1c1bca441edddd75451351394d2a0d3a89468 -Author: Richard -Date: Tue Feb 17 11:04:56 2015 +0000 - - New property on Atom, partners - - Returns a list of the Atoms that the Atom is bonded to. - - Basically a shortcut to: - - a = u.atoms[0] - - bonded_to_a = [b.partner(a) for b in a.bonds] - -commit 61438a03f14e076363d779ebf12d29ed19188fa1 -Author: Sébastien Buchoux -Date: Tue Feb 17 11:09:37 2015 +0100 - - Added support for both Unicode and UTF8-encoded version of Angtrom symbol - -commit 61a03b2869f8616bc5d7d531c084506ec83c8560 -Author: Sébastien Buchoux -Date: Tue Feb 17 08:58:56 2015 +0100 - - Corrected Emacs and Vim mode lines - -commit d4cd7d9d18b61cf981d9888d10022674b32105f9 -Merge: 1174293c9 d9438954d -Author: Oliver Beckstein -Date: Mon Feb 16 11:38:47 2015 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 1174293c96920776df61529b32ae7a114980d00c -Author: Oliver Beckstein -Date: Mon Feb 16 11:38:43 2015 -0700 - - fixed UTF-8 Angstrom symbol in core.units - -commit d9438954d52d412784fe29b947f0fbc93b40ec9e -Author: Richard -Date: Mon Feb 16 11:35:28 2015 +0000 - - Reworked AtomGroup & Topology repr methods - - Should outwardly be the same, internally it's easier to see what gets - printed on repr calls. - - Removed calling self.__class__.__name__ to find name as each subclass - redefines __repr__ anyway. - -commit 41aee008faba0e8a44e845d4be43dcb5356c141e -Author: Oliver Beckstein -Date: Sun Feb 15 23:04:59 2015 -0700 - - core.units: additional docs (tiny changes in constants) and more tests - - - The last commit changed the values of N_Avogadro and elementray_charge; the - changes were tiny (new CODATA 2010 values vs whatever else we had before). - Added proper versionchanged notes. - - Use units.constants everywhere instead of either hard coded elementary charge - or units.N_Avogadro (deprecated) - - Added tests for unit.constants to detect ANY future changes. - - NOTE: Whenever a unit is added to units.constants you also MUST add a - corresponding entry to test_units:TestConstants.constants_reference ! - -commit 2e6686733be068a724016de676c0f1c3ce6da23e -Author: Sébastien Buchoux -Date: Sun Feb 15 20:20:29 2015 +0100 - - Corrected setup.py - -commit d477d58d9558c04fdaa93c948d7f187db8ed4144 -Author: Sébastien Buchoux -Date: Sun Feb 15 09:53:15 2015 +0100 - - Corrected non-working lipid order example - -commit 9098e46848b0af27f1d9f901abcd81a387a249be -Author: Sébastien Buchoux -Date: Sat Feb 14 10:02:21 2015 +0100 - - Code "PEP8-fied" - - Copyright header updated to 2015 - -commit e61eebbf1845e90834540d5be8433bcef26b6c22 -Author: Oliver Beckstein -Date: Thu Feb 12 22:28:31 2015 -0700 - - added energy units and conversion (fixes Issue 214) - -commit e01b6ec13ea39429e614d5c5f9445014a03df1f1 -Author: Rich -Date: Mon Feb 9 14:59:00 2015 +0000 - - Tagged tests from Issue 202 as known failures for now - -commit c8bde94ab285e677630d764d49035afbdbbb44a0 -Author: Richard -Date: Wed Feb 4 19:08:45 2015 +0000 - - Changed topology reading to be class based - - Fixes Issue 210 - - New class topology.base.TopologyReader, subclasses IObase. - Initialised with filename. - - All previous parse functions now wrapped inside subclass of - TopologyReader. - - Selecting topology reader simplified. - Previously 3 dicts of parsers existed, now single dict with a few ifs - for the various PDB options. - - Mixin tests for all parsers, must conform to API. - - Topology Readers can now raise either IOError or ValueError, IOError - being for more file access based mess ups, ValueError for when things - have been read but just don't work. - - Most topology reader namespaces tidied to only feature classes. - - LAMMPS DATA coordinate reader now uses the class based topology reader - - TPR: - * move everything into inside TPRParser class - * removed callable version of this module - - CRD: - * Tidied slightly - * Removed creation of blank attributes in structure dict (not - required) - - DMS: - * Removed creation of blank attributes in structure dict (not - required) - - GRO: - * Tidied slightly, removed some unnecessary parsing - * Removed creation of blank attributes in structure dict (not - required) - - MOL2: - * Removed unused import - * No longer creates unnecessary structures. - These were used when it directly created the Bond objects. - - PDB: - * Removed parsing occupancy (later unused) - * Removed unnecessary suffix check - - TOP: - * Removed parsing skipped sections - - PSF - * Refactored - -commit bb6998840394bff02dcec89bf71df6a65429868b -Author: Richard -Date: Mon Feb 2 23:52:06 2015 +0000 - - Tidying of coordinate modules - - LAMMPS Data reader - * removed unused check in frame reading. - * Improved test coverage - - TRZ Reader - * Simplified things slightly, removed the numatoms calculation - - TRJ Reader - * Removed numatoms calculation, reader requires this to initialise. - * Remove duplicate len method - -commit 9fa476c2ed8edf75da87261fdd9e93b3a786e007 -Author: Richard -Date: Mon Feb 2 11:50:48 2015 +0000 - - Fixed TRZ reader not iterating properly - -commit 852ebaeedc7567ee85e24cce639e63e651ccd380 -Author: Richard -Date: Mon Feb 2 11:48:02 2015 +0000 - - Removed unnecessary if in atomgroup_intersection - -commit 9ab177abf9ef2beaa4bd81179269512e73a4d0b6 -Merge: 759b06b4d ab943cab1 -Author: Oliver Beckstein -Date: Sun Feb 1 12:11:54 2015 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 759b06b4d695f9cb3570e1bed66704c89b7817ff -Author: Oliver Beckstein -Date: Sun Feb 1 12:05:12 2015 -0700 - - Fixes Issue 199: FutureWarning from numpy in pyqcprot - - - "FutureWarning: comparison to `None` will result in an elementwise object comparison in the future." - was raised by pyqcprot.CalcRMSDRotationalMatrix() (and possibly also - pyqcprot.InnerProduct()) because arrays were compared to None with - the "==" operator instead of using "is None" or "is not None" - - comparison of arrays to None is now handled correctly - - manually checked against numpy 1.9.1; note that I was not able - to write correct test cases that check for the warning (see - http://bugs.python.org/issue21724 for notes on why this is - difficult) - - background on the FutureWarning itself: - http://comments.gmane.org/gmane.comp.python.numeric.general/58863 - -commit ab943cab119d467b0889917fc88cd28c2e3229eb -Author: Richard -Date: Sun Jan 25 11:23:40 2015 +0000 - - Added "cached" decorator (Issue 207) - - cached decorator automates the use of cache within classes. - - Usage: - - [@property] - can work with cached too - @cached('_cache key') - def function(self, *args, **kwargs): - # This code defines how to calculate the property - # it will only be ran on the first call of it however - # otherwise a cached value (stored under '_cache key') will - # be returned. - - Ie a class method call can become cached by adding a decorator with - single argument which is the key name it will be stored under. - - Requires the class to have a cache dict called "_cache", no error - checking for this. - - Added @cached to AtomGroup, Universe and TopologyGroup - - Changed "__cache" to "_cache". No reason to use name mangling here. - - Old tests updated to not expect name mangling. - - Added unit tests for cached decorator. - - Bonds/angles/torsions/impropers set methods now use _fill_cache over direct dict access - - Added deleter methods to Universe bonds/angles/torsions/impropers - -commit d2e255c6b29fd1dba2361ecccce77d9e05cb4082 -Author: Richard -Date: Thu Jan 22 19:35:09 2015 +0000 - - Docs rebuilt to include new hbonds submodule - -commit eaa6c2940cc27c83c85b84020086d12dc9befc2b -Author: Richard -Date: Wed Apr 23 12:01:43 2014 +0100 - - Added HydrogenBondAutoCorrel (Issue191) - - Allows the calculation of hydrogen bond lifetimes via their - time auto correlation function. - - Added analysis.hbonds submodule - - Renamed hbonds.py to hbond_analysis.py to avoid confusion - - analysis.hbonds submodule contains: - * HydrogenBondAnalysis - * HydrogenBondAutoCorrel - - Updated sphinx to be aware of new hbonds submodule - - Renamed hbonds.rst to hbond_analysis.rst to match source. - -commit 9091cfdfe3e9b4c278a415539de28fe9c0968e6a -Author: Oliver Beckstein -Date: Wed Jan 21 17:01:30 2015 -0700 - - maintainer/install_all.sh: added -u option for user installation - -commit 6d5b87ae9c8de38cb6a956ab8b4a01c564ce526a -Merge: b3d781e9b 51f6826de -Author: Oliver Beckstein -Date: Tue Jan 20 18:05:38 2015 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit b3d781e9b0955b783b557120fa091d867b1cebd6 -Author: Oliver Beckstein -Date: Tue Jan 20 18:05:18 2015 -0700 - - testing unitcell dimensions with PDBReader - - - Biopython PDB reader does not parse CRYST1 - - our primitive PDB reader should work (and the test needs to pass) - - added non-zero CRYST1 to the smaller test PDB for easier testing - -commit cfdcdee4d5584f76890789cc204678d00db6a154 -Author: Oliver Beckstein -Date: Tue Jan 20 17:31:23 2015 -0700 - - fixed DMS Timestep: unitcell now initialized with 0s instead of Nones - - UnitTest MDAnalysisTests.test_coordinates.TestDMSTimestep:test_repr passes again - -commit 51f6826de7d207aa386d0bc33cb60cde335eb73f -Author: Richard -Date: Tue Jan 20 23:16:38 2015 +0000 - - Updates to TRZ Reader - - Now can read forces. - -commit 4f20078ce5783ff034b678da78aa43dd4187550f -Author: Oliver Beckstein -Date: Fri Aug 8 18:10:18 2014 -0700 - - DCDWriter workaround: new kwarg dt to set time between frames in ps - - NOTE: Currently, the DCDWriter breaks the docs of - Writer() which state that "delta is given in ps" - whereas the DCDWriter expects AKMA. Until we clean - up the mess (see Issue 206), the dt keyword can - be used as a workaround. - -commit 5a3ae862457923a11e43a1768f7bea9a17d339e5 -Author: Oliver Beckstein -Date: Thu Jan 15 18:14:47 2015 -0700 - - regenerated html docs - -commit 39e911ff05f6a67012245a0a937cac818844894d -Author: Oliver Beckstein -Date: Tue Jul 1 15:24:18 2014 -0700 - - elements table: additional name guesses (inspired by PROPKA) - -commit 50d65c001c605b26ced1a01ab8ae8c3ac1cc4433 -Author: Oliver Beckstein -Date: Thu Jan 15 17:22:45 2015 -0700 - - streamIO docs and CHANGELOG entry - -commit ac0763221ca1f651a38b9a1bab151c143a40beaa -Author: Oliver Beckstein -Date: Thu Jan 15 16:37:33 2015 -0700 - - UnitTests for streamIO functionality - -commit 0a0b3b4b13739deed42121b64ac677993de655a9 -Author: Oliver Beckstein -Date: Mon Jun 9 13:43:34 2014 -0700 - - streams for coordinate topology readers and writers (streamIO) - - - new util.isstream() function with test case: - Utility function to check if something is a filename or a proper stream. Useful for - enhancements so that we can pass stream objects around instead of filenames. - - - util.NamedStream with test case: - wrapper class around a stream (eg cStringIO or file) that also provides a (fake) - filename. Can be used to be dropped in the place of filename if the underlying - code uses openany(). Will not work with C-code that does its own fopen(). - - - new MDAnalysis.StreamWarning (used in NamedStream) - - - util.filename(): can deal with NamedStream - - - util.anyopen(): changed return values (INCOMPATIBLE TO PREVIOUS) - - To streamline the use of anyopen() the function now returns only - the stream instead of a tuple (stream, filename) as before. - - This will BREAK OLD CODE although the impact is probably small - as the function was not used widely and within in MDAnalysis was - only called wrapped in openany() (pre 0.8.2). - - - using util.openany() or util.anyopen() instead of open()/file() in - any Python-based coordinate and topology IO (excludes DCD, XTC/TRR, - netcdf): can use compressed files automagically - - - with stream-enabled open functions it is possible to use streams in - many places by simply providing util.NamedStream (which can wrap - a cStringIO buffer or a urllib2.urlopen instance) - - EXPERIMENTAL feature; wrap a stream into util.NamedStream and - construct a Universe from the stream. - - Available for: - * PSF - * PDB (only primitive PDB reader, not the Biopython one) - * CRD - * PQR - * PDBQT - * GRO - * MOL2 - * XYZ - -commit ddb57592252642d483d418b94debb6c47af6e5f4 -Author: Oliver Beckstein -Date: Wed Jan 14 18:28:01 2015 -0700 - - added unitcell to ALL Timesteps - - - need unitcell even if format does not define it: otherwise writing - to formats with unitcell breaks - - added Timestep._init_unitcell() to Trajectory API: hook that is run by the - default __init__ (but can/should be overridden or not used at all if __init__ is - overriden as done for AMBER and GROMACS readers) - - added dummy timesteps to XYZ, MOL2, CRD - - test_coordinates:TestDCDWriter passes again - -commit a6f17fab167d20fc81a33dbf5f4b86f500beba6e -Author: Oliver Beckstein -Date: Wed Jan 14 17:20:22 2015 -0700 - - TestDCDWriter.test_with_statement(): more specific except clause - - Catching ANY exception masked other problems. Now only catch - AttributeError which we take to mean that we are missing the - __exit__() method of the context manager protocol. - -commit ce1cb9487b1c5b0a086650bdd42829bf41f99e74 -Author: Oliver Beckstein -Date: Tue Jan 13 18:09:43 2015 -0700 - - added PQRWriter and PQRReader update - - - write whitespace formatted PQR files - - test cases (old and new tests pass) - - PQRReader reads chainID (if present) and uses it as the segid - (previously always used 'SYSTEM' even if chainid was present) - - refactored topology.PQR into a PQRParser class (and a legacy - parse() function) - -commit c856979156470e9dea83367e6b414ce537837cf5 -Merge: a6c31a883 00952ec92 -Author: Oliver Beckstein -Date: Tue Jan 13 15:39:33 2015 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 00952ec921d9f35b0af24eaf5f1b4f3c29e7f359 -Author: Richard -Date: Sun Jan 11 13:10:19 2015 +0000 - - Fixes Issue203 - - Added GRO and DMS dimensions change support. - -commit 4d52ef7491f011fa0af78a71efd04e658420c4d0 -Author: Richard -Date: Sat Jan 10 12:28:21 2015 +0000 - - Timestep dimension setting - - Added ability to define Timestep dimensions for formats: - * DCD - * LAMMPS - * LAMMPSData - * PDB - * PDBQT - * TRJ - * TRZ - * TRR - * XTC - - Can also set dimensions from - * Universe.dimensions - * AtomGroup.dimensions - - Added unit testing for ALL Timestep classes. - -commit 39502ec1e86cc35eb6f81cce60ff05c0f82cd490 -Author: Rich Gowers -Date: Fri Jan 9 12:01:52 2015 +0000 - - Topology system update - - Atoms no longer store lists of B/A/T/I. These are instead stored inside - a dictionary on the Universe. Atoms have property that looks up this - dict. - - u.bonds/angles/torsions/impropers now settable property. Set with a - list of tuples of indices [(0, 1), (1, 2), ...]. - Note that this will (currently) overwrite the previous TopologyGroup. - - This should now allow Universe topology to be populated using: - u.bonds = guess_bonds(u.atoms, u.atoms.positions) - u.angles = guess_angles(u.bonds) - u.torsions = guess_torsions(u.angles) - - Tests for all of above. - -commit a6c31a883b692bf618b9919ccf233c8fda098fc9 -Author: Oliver Beckstein -Date: Wed Jan 7 16:54:13 2015 -0700 - - docs: fixed generated links in selections docs - -commit a193ab802d47fb48cbb12b9051e4c57f3e5ae12e -Author: Richard -Date: Wed Jan 7 23:33:09 2015 +0000 - - Fixes Issue193 - - Now atoms can be given in any order and the correct number of Residue - will be found. - -commit 5e28702d034578c1f55f52ef719b49a036c82afd -Author: Richard -Date: Wed Jan 7 18:58:42 2015 +0000 - - Unit test for Issue 193 - -commit 0228236f780c2defb2f33d87e0da88a8c7bee177 -Author: Richard -Date: Tue Jan 6 22:25:08 2015 +0000 - - Fixes for Issue 201 - - Simplified AtomGroup len & iter - - Simplified Group getitem access - - Now uses unified __getitem__ across all subclasses - - Simplified getattr slightly - - And test cases - -commit 2dee1737384d5ef493c0f1c9141611d5f242eb50 -Merge: a364eefc8 8f5c3f7be -Author: Richard -Date: Tue Dec 16 00:30:45 2014 +0000 - - Merge branch 'feature_wrap' into develop - -commit 8f5c3f7befecda143636d6d3885c046be7bd4383 -Author: Richard -Date: Wed Dec 3 16:41:04 2014 +0000 - - Fragments - - Added _clear_caches and _fill_cache methods to Universe. - These function identically to the same named methods on AtomGroup. - Test cases for these. - - Added fragments. These are single continuously bonded groups of atoms. - Atom.fragment returns the fragment the Atom is in. - AtomGroup.fragments returns a list of all fragments that atoms from this - AG are in. - Universe.fragments is a list of all fragments in the entire Universe. - These are all lazily built and cached. - Test cases for this too. - -commit a364eefc8642560a95d314364f010feb9a523682 -Author: Richard -Date: Sun Dec 7 20:33:26 2014 +0000 - - Fixes to lammps data parser - - Fixed comments breaking the parser - - Changed mini data test to check for comments in lines - -commit ee2f377d9f65f453dceb734fc6082ccf22093ade -Merge: 0fd450972 c5316bbd1 -Author: Oliver Beckstein -Date: Thu Dec 4 22:54:43 2014 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit c5316bbd1cad793256c6eaecb2ecb8b6145d1864 -Author: Richard -Date: Thu Dec 4 22:53:13 2014 +0000 - - Fixes for Lammps data parser - - Lammps data files no longer require all fields in header if they are 0 - anyway. - - Mass in lammps data will default to 0 if mass section not present - - Added Timestep for lammps data so dimensions will work. - -commit 0fd450972068e0c60be7e0f55d63141d62ff9386 -Author: Oliver Beckstein -Date: Wed Dec 3 16:47:21 2014 -0700 - - tests: include missing test files into package (data/mol2/, data/capping/, LAMMPS DATA) - -commit 370150b6caf60b7e3fcbe18a4206bab42acab9c5 -Author: Oliver Beckstein -Date: Wed Dec 3 15:03:09 2014 -0700 - - cython-generated files regenerated - - (triggered by the change in header in the comments; no functional changes) - -commit 8f8c1eeece08e65f26ce90082f4db61fed5e730e -Author: Oliver Beckstein -Date: Wed Dec 3 15:02:11 2014 -0700 - - maintainer/run_tests.sh: added options and logging to file by default - -commit 9c90d7554939b33694207b11fb1a6470ed413586 -Author: Oliver Beckstein -Date: Wed Dec 3 00:51:13 2014 -0700 - - small changes in LAMMPSParser - - - use util.openany() to read compressed DATA files - - added docs - - renamed the deprecated LAMMPSData to LAMMPSDataConverter - -commit 544bf598ce8aa680773ebf05cdb94951db533807 -Author: Oliver Beckstein -Date: Wed Dec 3 00:49:41 2014 -0700 - - added new test case for LAMMPS DATA file - - - small (mini) data file with 1 atom (derived from datatest.data) - - orthorhombic box with 3 distinct box lengths so that unit tests for dimensions - will be unambiguous - - refactored LammpsData_Coord test to use fixtures - - Note: The tests for dimensions fail at the moment because of current work on Issue 179 - and in particular Issue 187 in commit cad2cf955e0c. - -commit 8fdeab5b6f93cfabe59eb06b1603b611dbd1b452 -Author: Oliver Beckstein -Date: Tue Dec 2 23:23:43 2014 -0700 - - updated copyright/author header in comments of source files - - - bumped last year to 2014 - - for contributors see now file AUTHORS instead of website - -commit b6f08a8570a7a234666d92dcee56b55370df218e -Author: Oliver Beckstein -Date: Tue Dec 2 22:34:21 2014 -0700 - - UTF-8 encoding (PEP 263) where necessary - - - made all emacs-style lines uniform: encoding: utf-8 --> coding: utf-8 - - added vim fileencoding setting in addition to emacs style ones - - can have the angstrom symbol in strings - -commit 0157526aa0b878f14484776b7d69630001009dbe -Author: Oliver Beckstein -Date: Tue Dec 2 21:56:53 2014 -0700 - - update CHANGELOG (Issue 184 fixed) - -commit 2b7ac7dc1def6c2321ceb45bbfb9e12ad2f1eb00 -Merge: 0f8e5390b 66605cfd3 -Author: Oliver Beckstein -Date: Tue Dec 2 21:29:14 2014 -0700 - - Merge branch 'alfred532008-tpr' into Issue/184 - -commit 0f8e5390b93cc57b48fb7a2c204a295466546ea3 -Author: Oliver Beckstein -Date: Tue Dec 2 11:48:03 2014 -0700 - - Vagrant/VirtualBox virtual machine: Debian 7.6 Wheezy - - (Full feature MDAnalysis including netCDF.) - -commit 936a16f40625296cb4ef0d3f620c8a628235480a -Author: Oliver Beckstein -Date: Mon Dec 1 13:13:44 2014 -0700 - - leaflet finder: more control over sparse vs full - -commit a68d0e65fada802b2673355a153d55e5515f16d9 -Merge: f99af326e bb9e34d14 -Author: Oliver Beckstein -Date: Mon Dec 1 13:16:56 2014 -0700 - - merged (only white space in commented out debug logging in topology/LAMMPSParser.py - -commit 66605cfd3b6c36e3b4d283635e22d5347ed0de66 -Author: Zhuyi Xue -Date: Fri Nov 21 12:02:11 2014 -0800 - - added test case TPR455Double - -commit 664e55aec4d2749206897a7e6e5c708adecbc538 -Author: Zhuyi Xue -Date: Fri Nov 21 11:44:10 2014 -0800 - - changed unpack_float to unpack_real in tpr/setting.py and tpr/utils.py - -commit b2bdb24b738468ca71d2e43d0fefd87253f861a2 -Author: Zhuyi Xue -Date: Fri Nov 21 11:43:15 2014 -0800 - - added define_unpack_real, which defines a data.define_unpack_real method based on the gromacs precision of the tpr file - -commit dfdbbc410f4a35aece87cec3ff70f61ddd4034e8 -Author: Zhuyi Xue -Date: Fri Nov 21 11:16:23 2014 -0800 - - improved log_header - -commit bb9e34d147a13e6d14fe61a5f3944b4771fe8d86 -Author: Rich Gowers -Date: Wed Nov 19 12:35:19 2014 +0000 - - Unit tests for new issue - - Failure details: - - - Setting resnums from AtomGroup doesnt work, atoms keep their original - number - - - Setting a single resname for the whole AtomGroup works - - - Setting sequence of resnames for AtomGroup, only the first name is - returned - - This is all caused by the way that residues are built - -commit fce34b756c2782f828b618e9b46beaefac379db0 -Author: Rich Gowers -Date: Thu Nov 13 13:52:54 2014 +0000 - - Improving test coverage for MDA.core.AtomGroup, current at ~92% - - Fixed bug with adding AtomGroup to Atom - - Added a version of adk.psf without topology information for tests - - Fixed: - - Atoms now have "None" as Universe on creation, so they properly - report - their lack of Universe later. - - As Universe can now be made with no args, IndexError on init couldn't - be hit, fixed this so correct error message is reached. - - ** Cache rebuild changes: - - Avoided code duplication by redoing how cache rebuild is done. Eg to - rework how residues are built, the code is only found in one place. - - Added bonds/angles/torsions/impropers to cache rebuild. - - Merged ag.write_selection with ag.write - ag.write_selection marked for deprecation - - write (and write_selection) needs unit tests to check selections output - Selections in general still need tests too though! - - ** Removed parser specific errors: - - Removed TOPParserError, PSFParserError and PDBParserError, replaced all - this with ValueError. These did nothing except make it hard to catch - errors. - - Universe building will now catch these parsing errors properly. - - ** Topology tests - - Too much logging seemed to make the LAMMPS unit tests run very slow. - I'm guessing nose was capturing as it went, it was logging every line. - - Caught an exception in guess_format better - - ** AtomGroup bugs - - Setting segment id fixed - - segment.id assignment should now work - - Fixed phi/psi/omega/chi1 failed selections - - selectAtoms doesn't raise errors, causing the try/except blocks in - phi/psi/chi1/omega selections to not work any more. Instead these were - returning AtomGroups with 2/3 atoms (instead of correct 4) - - Fixed by checking size of AG prior to return. - - ** AtomGroup caching atoms now variable - - AtomGroup._atomcache_size variable allows the size of AtomGroup which - causes Atoms to be cached to be defined - -commit f99af326edddb7d1f384892c4cc636ce00ea3d91 -Author: Oliver Beckstein -Date: Sat Oct 18 01:21:03 2014 -0700 - - deprecated topology.LAMMPS.LAMMPSData (now that we have proper Data parsing) - -commit 569edaccb871d1d7de4b57fce877f45cc84dca35 -Merge: a8ed84cf5 c5182f1ae -Author: Oliver Beckstein -Date: Fri Oct 17 12:08:30 2014 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit a8ed84cf527e31d18c9f042c1d35a1943c6651f4 -Author: Oliver Beckstein -Date: Fri Oct 17 12:07:17 2014 -0700 - - Vagrant/VirtualBox virtual machines with full feature MDAnalysis - - - Ubuntu 14.04 - - Ubuntu 12.04 - -commit c5182f1ae14ef659b45d7fb83d87936511d92008 -Author: Richard -Date: Sat Oct 4 20:11:52 2014 +0100 - - Unit tests for DATA stuff - -commit 8ee2f3bc5574cff61d3b1adf67ff1a83ddd02d98 -Author: Richard -Date: Tue Sep 30 14:05:44 2014 +0100 - - Added support for LAMMPS data files. - - These can be used as either topology information for trajectories, or - to read a single frame on their own (similar to .gro files) - - Fixes Issue 139 - -commit d4607f817d017c43b5149889e44f6f05fe84db2f -Author: Oliver Beckstein -Date: Wed Sep 24 10:47:51 2014 -0700 - - added rotation_matrix() to docs in analysis.align - -commit f5834233b704e57325a2b132aa4ff08e06227938 -Author: Richard -Date: Thu Sep 18 09:12:32 2014 +0100 - - TRJ Reader Fix - - Fixes Issue 195 - - _read_trj_numframes calculated linesPerFrame wrong, - so got numframes wrong too - - __iter__ and __len__ methods didn't load first frame again, - but instead just reopened file at start - -commit 4ae9f7a51d493184aa56a114d0a4029f2f1e8ae8 -Author: Richard -Date: Sat Aug 30 12:14:35 2014 +0100 - - Reworked Topology system - - - Topology information is now loaded lazily into the Universe. - Can force universe to preload everything with u.load_topology() - - - AtomGroups now have lazily built .bonds .angles .torsions & .impropers attributes - - - TopologyDict (.bondDict etc) removed from AtomGroups in favor of new system. - - - TopologyGroup now supports selecting all of a given bond type through - the .selectBonds method - - - Can select all bonds from a TopologyGroup which are in an AtomGroup with the - .atomgroup_intersection() method. - This also accepts the 'strict' keyword to force all members of all bonds within - the returned TopologyGroup to feature in the queried AtomGroup. - - Changes to some Parsers to homogenise ._psf outputs. - - - Changed DMS and MOL2 parser to no longer create - Bond instances into their parsing return, but instead - create tuple of atom numbers in line with other parsers. - - - Added _bondorder to u._psf. - Parsers that want to add 'order' to bonds use this dictionary to do that - All parsers now strictly pass a tuple of length 2 tuples to define bonds - - Created TopologyObject. Analogous to Atom object, smallest unit of Topology. - - - Bonds Angles Torsions now subclass this. - - Added Improper_Torsions - - All TopologyObjects now use .atoms instead of .atom1 etc, - This might break old code that looks for bond.atom1 for instance, - use bond[0] in this case - - All TopologyObjects work nicely with __eq__ __contains__ etc - - Added lt and gt methods to TopologyObject. - This now allows lists of them to be sorted(), - TopologyGroup now sorts its input. - This makes slicing work nicer, as order is more logical between - different groups. - - Improved guess_bonds, now scales O(n) wrt memory. - Added guess_angles, guess_torsions, guess_improper_torsions - - Added lots of unit tests for topology, ~90% coverage. - -commit 7b091abe188bdafbc1b26e6750e575f3abf2af94 -Author: Tyler Reddy -Date: Tue Jul 22 18:10:07 2014 +0100 - - CHANGELOG updated to reflect changes to helanal docs. - -commit 033b67d7ebd71f318e23d3a5d43586daf69dd4e0 -Author: Tyler Reddy -Date: Tue Jul 22 18:02:07 2014 +0100 - - -MDAnalysis.analysis.helanal.helanal_trajectory docstring modifications: - -the begin and finish arguments now also specify that the units are in picoseconds, which is useful information and serves to remind the user that these are times and not frame numbers - -now includes information about FinishTimeException, which is raised when the finish time precedes the start time of the trajectory (or its current time stamp) - -selective update of this particular html file in the development docs - - -general documentation changes: - -I've disabled import mocking on MDAnalysis for the sphinx build process as we are no longer working toward readthedocs rendering (and this interferes with the standard html build procedure if not disabled)) - -commit cad2cf955e0c6e1c06686665b655a69dafd194ef -Author: Oliver Beckstein -Date: Tue Jul 8 19:12:55 2014 -0700 - - WIP: Issue 187 - - - made CHARMM DCD time step and changed the order of unitcell information - (swapped alpha and gamma) - - base.Timestep is now really a baseclass (dimensions is not implemented) - -commit ff0e5d01cdc5a47b5cc90ac128e2aa590bbaebbc -Author: Tyler Reddy -Date: Tue Jul 8 19:58:10 2014 +0100 - - -resolves Issue 188 regarding Helanal Finish argument: - -new unit test for fix: basically raise an Exception to indicate that Finish time specified by user is before the trajectory start time - -commit 0c839ddad75cc10385a1c506d3420e11d5deefb7 -Author: Oliver Beckstein -Date: Mon Jun 9 12:01:12 2014 -0700 - - newer version of fastio.h (1.20 from 2009) - - See Issue 150. File provided by ing.chris. - -commit b3d88bb0f1804c2a04adecf504fbcd18022a9f71 -Author: Oliver Beckstein -Date: Thu Jul 3 22:09:08 2014 -0700 - - changes to IOError error codes for Windows compatibility (see Issue 150) - - - XTC/TRR reader raise IOError with errorcode EIO (instead of - ENODATA) when the last frame is reached and EBADF (instead of - EFAULT) for any other issues (partially addresses Issue 150, - Windows compatibility) - - added UnitTests - -commit d4f7749a3b3c77238b01f88d9ca54c3165c5d04a -Author: Zhuyi Xue (Mac OS) -Date: Thu Jun 19 13:11:10 2014 -0700 - - extract fep_state for fver >= 79 instead of fver > 79 - -commit 07bdf3eebf3f665a33ac2e3c7d06bd4083632802 -Author: Zhuyi Xue (Mac OS) -Date: Thu Jun 19 13:10:33 2014 -0700 - - updated do_iparams in utils.py for additional function types in gromacs-4.6.x - -commit ef365fc3b3db4381ce7012adbf0a3fa742d92033 -Merge: 01fa5b47b 3d2439938 -Author: Oliver Beckstein -Date: Wed Jun 18 16:39:16 2014 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 01fa5b47bbf65d363f04267ab0ca88ab0fcf0792 -Author: Joe Jordan -Date: Wed Jun 18 16:34:46 2014 -0700 - - HBond analysis: new distance_type keyword (closes Issue 185) - - - can use the heavy atom D-A distance instead of the hydrogen - H-A distance - - default is H-A (as previously) - - added simple test case - - added Joe Jordan as a contributor (code is based on his - patch) - -commit 3d24399381b3e29f57c898d6b8b0b8fd1702cc61 -Author: Tyler Reddy -Date: Wed Jun 11 15:30:28 2014 +0100 - - Attempting to improve MDAnalysis readthedocs behaviour based on Mock imports for C-dependencies described here: http://read-the-docs.readthedocs.org/en/latest/faq.html - -commit 55460633d1bf941b500b3df7b90c80d26cdcf088 -Author: Oliver Beckstein -Date: Thu Jun 5 23:55:43 2014 -0700 - - fixed setup.py: correctly parse cython strings - - (Reported by Eric Lang) - -commit 2d301d961b15e633ac7e0b8327ed80fcb6920896 -Author: Oliver Beckstein -Date: Mon May 26 14:13:57 2014 -0700 - - rebuilt html docs - -commit c76e0b948298a59052614ec7a956e99d1b48624f -Author: Oliver Beckstein -Date: Mon May 26 14:08:40 2014 -0700 - - docs: second example for Merge() - -commit 8e5bc9feb6b989c5349e53f161e1a64c314023a1 -Author: Oliver Beckstein -Date: Mon May 26 13:57:20 2014 -0700 - - fixed residues/segments in Merge() - - AtomGroup.Merge() did not update references to universes in residues and - segments so that one cannot renumber segments or residues. Fixed and - added UnitTests. - -commit 89c9a68b397f549bf48b19d4dabc9b258668ab09 -Author: Oliver Beckstein -Date: Mon May 26 11:51:55 2014 -0700 - - regenerated docs with sphinx - -commit 2ec07b0459e1f7a5852880f11cf55ea35a20c53c -Author: Oliver Beckstein -Date: Mon May 26 10:48:45 2014 -0700 - - reST doc additions for Atom and AtomGroup - - - altLoc, bonds, angles, dihedrals had not been documented for - 0.8.1 - - Merge() had not been documented (Issue 157) - - minor reST fixes (eg in math code); note that I cannot get - the autodoc sphinx for :func:`list` working - -commit d55c082a44bc59f0f032cc793cdd2c556a1c0899 -Author: Jan Domanski -Date: Wed Apr 16 19:14:32 2014 +0100 - - New feature: support PDB altloc records (Issue 170) - - - read and write PDB's containing altlocs (tested), - - support for 'altloc' atomsel, see docs, - - Tests are based on a simple PDB with some altloc records - - check sum atom counts for the 'altloc' selection string, - - check bonds, when guessing bonds from PDB, - - check if output written has same number of atoms as original. - -commit 018e0fd6f96be2cb4fa8ff56a07211450e4ad769 -Author: Jan Domanski -Date: Sun Apr 20 01:07:45 2014 +0200 - - New feature: capping proteins - - An example script is added showing how MDAnalysis can be used to modify a - simple peptide and add terminal caps to it. The peptide is AAQAA3 and the - caps are ACE and NMA. - - Tests descriptions: - - check if cap resids were changed correctly, - - check number of atoms after capping (compare to maestro output), - - check if box dimensions were changed. - -commit f1136283f57ee7319a03e83d9019feebae8a20f8 -Author: Jan Domanski -Date: Sun Apr 20 00:31:06 2014 +0200 - - New feature: MOL2 format support - - MOL2 molecular structure format, developed by Trips, - is used to store structures of small molecules and proteins. - - Mol2 files can have multiple blocks, with different number of atoms, - much like MAE files. This is not supported. Similarly to PDB reader, - only multi-molecule mol2 files with the same number of atoms are supported. - - - Basic unit testing, tests for corrupt mol2 files. Added support for atom selections, - - Added example to the Mol2 reader docs, - - Mol2Parser is a class, - - Parser errors are just exceptions. - -commit 9cc9df15829405baefe197193089d1d3a986e1c6 -Merge: 4bb36e64e bb6e7cd51 -Author: Oliver Beckstein -Date: Tue Apr 15 01:20:34 2014 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 4bb36e64e8d182226c9303777a166bdb56d08b34 -Author: Oliver Beckstein -Date: Tue Apr 15 01:06:23 2014 -0700 - - __getstate__() and __setstate__() raise an NotImplementedError for Universe and AtomGroup - - * Before they were silently accepted on pickling and a cryptic - "TypeError: AtomGroup is not callable" was raised (see also - Issue 173 for detailed explanation). - - Arguably this should be fixed properly (see Issue 173) but - hopefully this quick patch here should at least make the error - clearer. - * added UnitTest - -commit bb6e7cd51b59572e85e57e493c7a2371d921f79d -Author: Rich -Date: Mon Apr 14 18:20:47 2014 +0100 - - Upgrades to TRZReader, much faster now - - Added dedicated seek method to TRZReader; - - skipped frames will no longer be read into Timestep - - "backwards" skips do not require reopening file - - Numframes method reworked, now works on basis of filesize rather than - reading entire trajectory - -commit bcbed160c26c16b669e176c69418c3af1bc0adeb -Author: Oliver Beckstein -Date: Thu Apr 10 18:32:55 2014 -0700 - - XYZWriter added - - - write simple XYZ trajectories (no comment line) - - updated docs - - added UnitTests - -commit 177d5e956b08e0851a73d4bb06d60c010755f722 -Author: Oliver Beckstein -Date: Thu Apr 10 15:30:02 2014 -0700 - - bumped release to 0.8.2-dev - - (Also corrected the 0.8.1 release date in CHANGELOG) - -commit 7c0559aa852083e67a96bbbdb244ddf18d5c2f90 -Author: Tyler Reddy -Date: Mon Apr 7 18:59:04 2014 +0100 - - CHANGELOG updated for recent 2D streamplot module adjustment. - -commit b2ba39ffe529dac54cb06c17550ad1f93a4972ca -Author: Tyler Reddy -Date: Fri Apr 4 18:28:55 2014 +0100 - - MDAnalysis.visualization.streamlines adjusted in the following ways: - -suppression of all print statements via their deletion from source code - -the module no longer depends on the deprecated matplotlib.nxutils module and the replacement (matplotlib.path) has been benchmarked as ~equivalent using %timeit in IPython for a real-use biomolecular test case - -commit 23b85331ecb91fd5a64a1b10b61ef046ef430944 -Author: Rich -Date: Thu Apr 3 11:03:19 2014 +0100 - - Fixed up issue172 fix - -commit 627e3578a696cb05ffbce0bba7eaea6dec1e43d8 -Merge: 34f925beb d48b1149f -Author: Rich -Date: Thu Apr 3 10:45:58 2014 +0100 - - Merge branch 'develop' into issue/172 - -commit d48b1149f52d9ea803acc26b913c97c5c58e8166 -Author: Oliver Beckstein -Date: Wed Apr 2 18:25:06 2014 -0700 - - meta data updates - - - added release date to CHANGELOG - - removed google code download from SUMMARY (and also from google code - home page --- see Issue 155) - - adjusted the ordering of names in the sphinx copyright line (see comment) - -commit 1e17fa62feff31559dc2c6817b8c94d51628cdf5 (tag: release-0.8.1) -Author: Sébastien Buchoux -Date: Tue Apr 1 15:42:01 2014 +0200 - - Documentation regenerated and version changed to 0.8.1 - -commit 719e468488d7c66f3bebd2e556fcd6773a730553 -Author: Manuel Nuno Melo -Date: Sat Mar 29 03:52:31 2014 +0100 - - issubclass vs. isinstance fix (Issue 176) - -commit 1d4c5997908010097cac4626ca26b70105c8ca63 -Merge: 257b2aa1a ddf5b1d3a -Author: Manuel Nuno Melo -Date: Sat Mar 29 02:54:50 2014 +0100 - - Merge branch 'NamedSel' into develop - -commit ddf5b1d3a46557c77f874b3286433773617f9093 -Author: Manuel Nuno Melo -Date: Fri Mar 28 00:03:06 2014 +0100 - - Named groups in selections now accepted (Issue 174) - - LeafletFinder takes both AtomGroups and string selections (Issue 175) - asUniverse now works with subclasses of MDAnalysis.Universe (Issue 176) - -commit 34f925bebd9d116e43b6ed221336378274b90635 -Author: Rich -Date: Thu Mar 27 17:29:36 2014 +0000 - - PBC for angle and torsion calculations (fixes Issue 172) - - Test cases for Issue 172 - - Added box option to calc_angles and calc_torsions in core.distances - Using this option ensures that the vectors between atoms adhere to minimum image convention - - Added pbc flag to angles and torsions methods for TopologyGroup - This will pass box information to cython functions - -commit 257b2aa1a1f074e11966be2ec30f16966b093d11 -Author: Tyler Reddy -Date: Tue Mar 18 15:05:11 2014 +0000 - - -updated docstring for MDAnalysis.visualization.streamlines_3D to include an example using the new coordinate boundary arguments - -attempting a selective docs rebuild that only commits the modified pages/ images rather than full commit / push of mostly unchanged html pages - -commit 457bf8e8ac15ea148987a04cacacf7476b7dff9c -Author: Tyler Reddy -Date: Tue Mar 18 14:47:11 2014 +0000 - - MDAnalysis.visualization.streamlines_3D adjusted in the following ways: - -the assessment of proper grid cube geometries is now less sensitive to floating point equality failure (assertion is now from numpy.testing.assert_almost_equal rather than a conventional equality test) - -print statements for debug / progress monitoring have been suppressed (mostly deleted from source code) - -the generate_streamlines_3d() function now accepts x,y,z Cartesian coordinate limits for the analysis instead of automatically calculating the limits of the system; this change is largely motivated by increased consistency with the 2D version of the code in MDAnalysis.visualization.streamlines.generate_streamlines() - -commit c37ca714a12f4f435e83e0c494a3b21508c4e519 -Author: Oliver Beckstein -Date: Thu Mar 13 15:46:27 2014 -0700 - - removed toplevel matplotlib imports - - - removed matplotlib and pyplot imports from hole and x3dna - - not needed and make the module fail when matplotlib not available - - do local imports in plotting functions (so we can run analysis anywhere - and only need matplotlib at the actual plotting stage) - -commit d79ca74731e661825d412b86f7f674a3075c3650 -Author: Tyler Reddy -Date: Thu Feb 27 15:53:52 2014 +0000 - - -MDAnalysis.visualization namespace properly labelled as experimental in the CHANGELOG and Matthieu Chavent credited in authors list for most recent set of changes - -Matthieu Chavent added to AUTHORS file and to authors list in documentation conf.py file - -Changed the citation format for Chavent, Reddy et al. (2014) for consistency with MDA formatting standards - -Python assertion statements in the 2D / 3D streamplot modules have been removed in cases where they perform type checking on user input, but they remain for algorithm-level integrity checks (i.e., expected array shapes at different stages) - -The 2D streamplot code now raises a more useful ImportError message when a user does not have matplotlib installed - -commit 7bf16765d759ee6fd44666b15d4af8522e07ce00 -Author: Tyler Reddy -Date: Mon Feb 24 12:39:49 2014 +0000 - - Rebuilt docs to include new MDAnalysis.visualization modules - -commit 2eabfad7a49f2ae95fb9203fbb7cf5bdde699b3b -Author: Tyler Reddy -Date: Mon Feb 24 12:23:25 2014 +0000 - - -incorporation of the new MDAnalysis.visualization.streamlines_3D module and associated documentation - -commit 25afe787986af4ab58a4e6ed86f8d64134128f7c -Author: Tyler Reddy -Date: Sun Feb 23 17:21:32 2014 +0000 - - work on (sphinx) documentation for 2D streamplot visualization code: - -mdanalysis/package/doc/sphinx/source/index.rst adjusted to include entry for visualization modules - -new visualization_modules.rst entry and package/doc/sphinx/source/documentation_pages/visualization/streamlines.rst for pulling in 2D streamplot documentation automatically - -major improvements to the documentation in and related to MDAnalysis.visualization.streamlines, including an inline example of usage / output plot - -commit 54b2860e881cc2fe7b5e52b763dbd3f7c326f258 -Author: Tyler Reddy -Date: Sun Feb 23 09:12:52 2014 +0000 - - MDAnalysis.visualization.streamlines adjusted in the following ways: - -an ImportError with appropriate message should now be raised when a non-standard dependency of this module is not available (rather than a print statement only) - -the only non-standard (i.e., outside of regular MDAnalysis) module requirement has been simplified to matplotlib.nxutils, and ideally this requirement will eventually be removed because it is a deprecated module of matplotlib (and also an analytical rather than plotting use of matplotlib) - -the standard dependencies (MDAnalysis, multiprocessing, numpy, scipy) are now imported in separate statements for improved dependency sanity - -a substantial amount of extraneous debugging code has been removed (although a bit more clean-up could likely still be done) - -the placeholder main() function has been renamed to generate_streamlines() and the workflow may eventually be adjusted (perhaps encapsulated in a class) - -commit e2dabb0a76957824411524f5d1f105192b443913 -Author: Tyler Reddy -Date: Sat Feb 22 19:07:41 2014 +0000 - - MDAnalysis now correctly initializes the namespace for MDAnalysis.visualization. The 2D streamplot code in MDAnalysis.visualization.streamlines has been added and appears to function properly. - -commit 64c6ebaaa2e16f534013a7eb9a420bda29235f84 -Author: Tyler Reddy -Date: Sat Feb 22 18:01:54 2014 +0000 - - Addition of new MDAnalysis.visualization.streamlines namespace. - -commit bd35685e54f5d5224ac454757d5a620749cf0dbb -Author: Oliver Beckstein -Date: Thu Feb 13 22:57:01 2014 -0700 - - minor doc fix for XTC - -commit c49143709855dd2a1d57af491d25bbb2a2a26fa0 -Author: Alejandro Bernardin -Date: Thu Feb 13 17:15:58 2014 -0300 - - Conflicts in documentation solved (Revision f69f2dbd1bd7) - -commit 5eb989986d11a96d083db0f822abe0880f1d33f3 -Author: Manuel Nuno Melo -Date: Thu Feb 13 12:11:16 2014 +0100 - - TRR doc minor cleanup. - -commit 96859f6e368a7d7db75c696d4dec1e25d34b1d32 -Author: Oliver Beckstein -Date: Thu Feb 13 02:16:44 2014 -0700 - - cleaned up docs for XTC and TRR - - - removed double occurences in TRR and XTC docs by explicitly - listing the classes to be documented - - minor fixes in TRR, XTC, xdrfile docs (e.g. moving some change notes - into the full docs) - -commit 48d106ff894713e2c0c3879d81c343c8683cb49a -Author: Oliver Beckstein -Date: Thu Feb 13 02:09:24 2014 -0700 - - libxdrfile2 docs: added all exdr symbols - -commit d20554a6173d6e05d78bdc53ad4549669eeef3aa -Author: Richard -Date: Wed Feb 12 17:07:14 2014 +0000 - - Doc update - - Topology, core.distances and TRZ docs updated - -commit a7249de1484efab039ddb365d1606d6334e96560 -Author: Manuel Nuno Melo -Date: Wed Feb 12 16:43:59 2014 +0100 - - libxdrfile2,XTC,TRR doc update and cleanup. - -commit 94fed0d4e7f5772818a73c525d901bfafd96f115 -Author: Manuel Nuno Melo -Date: Wed Feb 12 13:51:57 2014 +0100 - - XTC/TRR-related doc update and cleanup. - -commit 7de22de5dbfaf1c1119e5c643cc596f74321ce6c -Author: Oliver Beckstein -Date: Tue Feb 11 16:00:03 2014 -0700 - - reST fixes in analysis.density - -commit 8c7dc343d315a932d3d2688ebe9d0b2824a4ab49 -Author: Sébastien Buchoux -Date: Tue Feb 11 22:07:29 2014 +0100 - - Doc regenerated. libxdrfile2 generated doc files added to git - -commit 3e9feb05398fecb8081b7f1bb39ff50f4bf5440f -Author: Sébastien Buchoux -Date: Tue Feb 11 22:00:28 2014 +0100 - - Version bumped to 0.8.1rc1 - -commit e07ff2b0bcb3189f5e913542ea04cc1b4855f361 -Author: Alejandro Bernardin -Date: Tue Feb 11 12:53:14 2014 -0300 - - Some corrections to documentations files. - -commit 2ad3e7f21c236a2538f222460ea0482c4be3ef1b -Author: Oliver Beckstein -Date: Thu Feb 6 16:28:43 2014 -0700 - - changed name of flag 'convert_gromacs_lengths' to 'convert_lengths' - - This change can POTENTIALLY BREAK OLD CODE (in the unlikely event - that someone actually changed this flag). - - We are using this flag in all writers/readers that deal with conversion - between native and MDAnalysis length units so it should not sound specific. - - (Also cleaned up a few commented out lines in the test cases; just note - that in the test cases we CANNOT change the flags because it breaks - parallel tests.) - -commit de467cca0931fdaa364dc00b34db116fbfb404ad -Author: Oliver Beckstein -Date: Thu Feb 6 16:03:10 2014 -0700 - - MDAnalysis.analysis.rms.rmsd(): new center keyword - - one can immediately calculate the minimum rmsd of two rigid-body superimposed - structures; center removes the translation, the QCP algorithm implicitly - carries out the rotation while calculating the RMSD - -commit 53ed8c0ff14f86da2f992b757bc63179d251d7a2 -Author: Richard -Date: Tue Feb 4 21:29:14 2014 +0000 - - Added copy_slice(slice) method to base.Timestep (Fixes Issue 163) - - This method creates a new Timestep which has all header information and a portion (defined by slice) - of the per atom information. - - AtomGroup.ts attribute now uses this copy_slice method to make its Timestep. - - In turn, Writers should now recieve this partial Timestep when writing an - AtomGroup. This means the result of Write(AtomGroup) should feature all - information that was possible to include. (Fixes Issue 163) - - Unit tests for: - - AtomGroup.ts attribute - - Writing a partial Timestep - - Creating a partial Timestep for all formats - -commit 510db464e390bce8bfbdd47efdc56c7160ce48d3 -Author: richardjgowers -Date: Thu Jan 16 15:17:54 2014 +0000 - - TRZReader upgrade - - Changed TRZ reader to use np.fromfile instead of struct.unpack, is now not terribly slow - Added arbitrary slicing to TRZReader class - - Added unit tests for TRZWriter. - -commit 1c81d7717018a738f43dbf8c06d256d7d9b3dbf7 -Author: Oliver Beckstein -Date: Tue Feb 4 12:04:08 2014 -0700 - - added maintainer/install_all.sh for quick installation - -commit 044b513061a9f25324ccf5e2341e168c5025c383 -Merge: a42d48891 2d5a068c8 -Author: Oliver Beckstein -Date: Tue Feb 4 12:02:54 2014 -0700 - - Merge remote-tracking branch 'richardjgowers2/TScopy' into develop - -commit 2d5a068c8747fb948f40cd41e79b99fe515a99b0 -Author: Richard -Date: Tue Feb 4 10:28:07 2014 +0000 - - Fixed Timesteps not copying correctly (fixes Issue 164) - -commit 69ebc6c3682d08a8775797628f49811ef37ff67d -Author: Richard -Date: Sun Feb 2 14:44:30 2014 +0000 - - Made unit tests for Issue 164, Timestep.copy() not functioning properly - -commit a42d48891c9586a07440bffb7565c83994852931 -Author: Oliver Beckstein -Date: Mon Feb 3 10:13:51 2014 -0700 - - reST fix - -commit 5f9b2f2716bb8c9218e3d4144e614cae9c7145d7 -Author: Oliver Beckstein -Date: Mon Feb 3 10:01:34 2014 -0700 - - reduced prec from 5 to 3 in TestPBCFlag - - Some sub-tests failed on Mac OS X due to precision. At reduced precision theses tests pass. - -commit dceb7c7816d4e38f7f4b9b19588165d16f68a930 -Author: Oliver Beckstein -Date: Sun Feb 2 17:54:10 2014 -0700 - - AtomGroup.bond(): renamed keyword minimage to pbc for consistency - - All other methods that take periodicity into account are taking the pbc=True keyword. - Bond used minimage=True for the same purpose. Even though the underlying approach is - different (using packIntoBox() vs code directly available to distance_array()) from - a users point of view the behavior is the same and therefore should use the same - keywords. (Also, bond(minimage) was only introduced in 0.8 so this is unlikely to break - any existing code. - -commit 31d83bb105649d16e777b11704fa4d1b7be1411b -Author: Oliver Beckstein -Date: Sun Feb 2 17:01:24 2014 -0700 - - minor reST cleanup in AtomGroup - -commit 62b8bdcb722232e0a28869c1fd206789af2934f4 -Merge: a955578e9 517bfa44e -Author: Oliver Beckstein -Date: Sun Feb 2 16:31:20 2014 -0700 - - Merge remote-tracking branch 'richardjgowers2/issue156' into Issue/156 - -commit 517bfa44edfbd03c5fee1680f06973792f3a99f8 -Author: Richard -Date: Mon Jan 27 21:33:47 2014 +0000 - - Added 'use_pbc' flag to core.flags this toggles the pbc flag in AtomGroup - methods. - - Added unit tests for pbc modifications to AtomGroup methods. - - Updated CHANGELOG - -commit ae1b14ceda80d99008d59f49be44eac7cbd9148d -Author: Richard -Date: Sun Jan 26 22:28:36 2014 +0000 - - Added applyPBC(coords, box) function to core.distances. This moves all - atoms within the primary unit cell as defined by box. Will work with - both triclinic and orthogonal boxes. - - calc_bonds in core.distances now allows triclinic boxes to be used - when calculating minimum image convention. - - AtomGroup.packintobox() renamed to packIntoBox for consistency - - packIntoBox() now has inplace flag which works similarly to - coordinates.core.convert_to_native(). True changes the coordinates - whereas False just returns them - - AtomGroup.bond() now has minimage flag. If true will account for minimum - image when calculating bond distance. - - Lots of AtomGroup methods now have a pbc flag. If true, this will move - atoms within the primary unit cell before the rest of the calculation. - This is false by default, so default behaviour has not changed. - Affected methods: - centerOfGeometry - centerOfMass - radiusOfGyration - shapeParameter - aspehericity - momentOfInertia - bbox - bsphere - principalAxes - -commit a955578e9c3dc4c87486048f7ed95f589de6bfbd -Author: Manuel Nuno Melo -Date: Sun Jan 26 17:42:48 2014 +0100 - - Update of TRR I/O doc and improved error-checking. - -commit 30e29e0d4f050d605d695b0fd1f74af5fd6c076f -Merge: e649a9582 e67ce35b6 -Author: Manuel Nuno Melo -Date: Sun Jan 26 01:04:08 2014 +0100 - - Merge branch 'XDRclean' into develop - Merged and finished converting the code to use libxdrfile2 - -commit e67ce35b66606bdfe7c60ba3c9b26707eeac5ebe -Author: Manuel Nuno Melo -Date: Sat Jan 25 04:13:29 2014 +0100 - - Adaptation/renaming to libxdrfile2 - -commit e649a95825cc8091de86141c8da6ae94fc6daa3c (tag: release-0.8.0) -Author: Manuel Nuno Melo -Date: Sat Jan 25 04:35:55 2014 +0100 - - TRR documentation update - -commit dc6e0a667be07157bad5c5a2fd107997ca4b8e64 -Author: Manuel Nuno Melo -Date: Fri Jan 24 22:16:25 2014 +0100 - - TRR Timestep constructor now accepts has_x, has_v and has_f - Added **kwargs to Timestep constructors that didn't have them already - -commit 58d676bbe9518740b70a7b2a96af66ad7e916c64 -Author: Manuel Nuno Melo -Date: Wed Jan 22 00:15:33 2014 +0100 - - Cleaned up TRR I/O property-control code - -commit a72168f48c89ab9ef1e5b3d7a884a317d058a007 -Author: Manuel Nuno Melo -Date: Sun Jan 19 06:35:20 2014 +0100 - - TRR I/O fully aware of missing coord/vel/force information (Issue 162) - Exceptions are raised on access of missing data. - -commit f71164eef7cf122020337c9c592f933f1b552abe -Merge: e262263c2 796c56edb -Author: Oliver Beckstein -Date: Mon Jan 20 01:25:50 2014 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit e262263c2c1f84a440125cc38c6cb1c66c83645a -Author: Oliver Beckstein -Date: Mon Jan 20 01:25:34 2014 -0700 - - improved HBonds docs - -commit e75d86916f1c596ad8aacbfb01cc72b1c84e9513 -Author: Manuel Nuno Melo -Date: Thu Jan 16 05:20:15 2014 +0100 - - libxdrfile2.0 license modified to GPL. Minor cleaning. - -commit 6cc7b1755a8ff72114941f0ef46ed2293c993876 -Author: Manuel Nuno Melo -Date: Tue Jan 14 15:38:53 2014 +0100 - - XDR-related cleanup and unit tests. Large file indexing now ok in 32bit. - -commit 796c56edb168495d19c8b7475944b9eba6c0ceee -Author: Manuel Nuno Melo -Date: Thu Jan 16 02:53:18 2014 +0100 - - Fix default creation of writer from XTC/TRR TrjReader. Fixed docs. - -commit aa544f563ab68fbc20cf8934e0f9aadda491833b (tag: RotamerConvolveMD-1.0) -Author: Oliver Beckstein -Date: Wed Jan 15 14:50:44 2014 -0700 - - application RotamerConvolveMD: write licence when starting up - -commit d2ee47f62aaba2146b7441ad8f7f351b7da595ae -Author: Oliver Beckstein -Date: Wed Jan 15 14:45:08 2014 -0700 - - application RotamerConvolve: 1.0 release - - - update reference to the final published paper - - bumped release to 1.0 - -commit 002ced05fe72c5b0dee7445a7b0741a4918687e6 -Author: Manuel Nuno Melo -Date: Wed Jan 15 21:37:57 2014 +0100 - - fixed XDR writer incorrect use of delta parameter (Issue 154) - -commit e6b7061637fdfaf58880febae91085f5a225346a -Author: Oliver Beckstein -Date: Tue Jan 14 14:09:46 2014 -0700 - - provide assert_allclose() from numpy 1.6.1 numpy.testing.utils - - Required for the tests in test_parallel.py with numpy 1.3... 1.4.1 (and perhaps up to 1.6?) - -commit 256f32c2c6a0df3e71e924fe69c94db4ea770eb1 -Author: Alejandro Bernardin -Date: Tue Jan 14 18:32:36 2014 -0300 - - Fixed compatibility with Python2.6. Positional argument specifiers - can't be omitted in Python2.6. - -commit f69f2dbd1bd76d35c9452fe783b78e1d870496bf -Merge: 75779f12a 11c1fd94e -Author: Alejandro Bernardin -Date: Tue Jan 14 18:15:36 2014 -0300 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - - merge origin/develop develop - - Conflicts: - package/MDAnalysis/analysis/x3dna.py - -commit 11c1fd94e190c5c5ddc13f49c9893a84f8d9b373 -Author: Alejandro Bernardin -Date: Tue Jan 14 11:40:52 2014 -0700 - - fixed Python 2.6 incompatibility in topology.Bond.__eq__() - -commit 93c45e6dcdfc1c89a514594ef8e396c3cc0efcc2 -Author: Tyler Reddy -Date: Fri Jan 10 16:56:05 2014 +0000 - - Resolves Issue 161 (trajectory slicing is now possible in MDAnalysis.analysis.contacts.ContactAnalysis1.run() method) - -commit a5626591be5fd1c93d784029cfc648e746c380e4 -Author: Oliver Beckstein -Date: Tue Jan 7 16:57:46 2014 -0700 - - fixed another velocity test - -commit 42a5735ba49f65a3999ecf6772df8a7e56fe83d6 -Author: Oliver Beckstein -Date: Tue Jan 7 14:45:42 2014 -0700 - - added new authors to online docs - - - Richard J Gowers, Lennard van der Feltz and Alejandro Bernardin were - added to the authors list in sphinx/source/conf.py - - corrected Alejandro Bernardin's handle in CHANGELOG - -commit 98aa7d5528ac5182e4d30038094e9bfce93129e9 -Author: Oliver Beckstein -Date: Tue Jan 7 11:52:26 2014 -0700 - - deprecations in AtomGroup: AtomGroup.velocities is now an attribute - - - AtomGroup.velocities() (as a method) had been deprecated for 0.8. It has - now become a (managed) attribute. - - Change your code - - ag.velocities() ---> ag.velocities - - - Note that you can also assign velocities directly to ag.velocities. - - Test cases were changed accordingly. - - Removed deprecation warning for AtomGroup.bfactors: we will let it - remain an attribute (instead of switching it back to a method). - -commit 6ed015c6491b0fb7e9acfacea49f6e5ce17c17b1 (tag: release-0.8.0rc4) -Author: Sébastien Buchoux -Date: Tue Dec 31 18:04:06 2013 +0100 - - Version updated to 0.8.0rc4. Doc regenerated - -commit 2a0b4a462265e5be83954255a9018615d14b8680 -Merge: 06384636e cda661674 -Author: Sébastien Buchoux -Date: Tue Dec 31 17:48:04 2013 +0100 - - Merge remote-tracking branch 'richard/develop' into develop - - Conflicts: - package/MDAnalysis/topology/core.py - -commit 06384636ea5e841565cf0a9dcd636138b3c56bd2 -Author: Sébastien Buchoux -Date: Tue Dec 31 17:33:24 2013 +0100 - - Duplicated line in selections.rst removed - -commit da6d78ffc3cf25273c941be5d154d33d917fc3fd -Author: Sébastien Buchoux -Date: Tue Dec 31 17:29:21 2013 +0100 - - topology/core.py fixed, updated to Py3K convention and cleaned to avoid cyclic imports - -commit cda66167479e8e02b60e457586f7f4c443b77f04 -Author: richardjgowers -Date: Tue Dec 31 10:37:09 2013 +0000 - - Robust bond identity tests - - Added contains super function to Bond Angle Torsions classes - - Changed bond/angle/torsion identity unit tests to be order insensitive - -commit cc4aad65e04f556310e3e525bf3b76b9b713ea8a -Author: Oliver Beckstein -Date: Mon Dec 30 18:49:06 2013 -0700 - - TestPSF_bonds.test_bonds_identity(): changed test - - The ordering of bonds appears to change; when I ran it, what used to be - bonds[0] in the original test case is now bonds[3]. This was changed - but we should look into a more robust test case. - -commit 2620a49a3230715bbbc9b58a362514f5b60fe337 -Author: Oliver Beckstein -Date: Mon Dec 30 18:41:57 2013 -0700 - - Bond: fixed: repr failed if no coordinates available - -commit ff1fc01b45c34f650f405e1d48fbc7194fd75f82 -Author: richardjgowers -Date: Mon Dec 30 17:29:02 2013 -0700 - - UnitTests for TopologyDict functionality - - (orbeckst: broke a few tests into smaller tests) - -commit 074ba807e25834c5157a0e0ec11e2a00f14c0c65 -Author: Oliver Beckstein -Date: Mon Dec 30 17:13:55 2013 -0700 - - Revert "PSF Parser Fix" (not needed because atom numbering was fixed) - - This reverts commit 4a1d06f6bc8d8ac3fbfb1170db8e8b5a971b14fe because - commit 8b5a8e9c7b13a68f1046467e87d5a298b5c9f4a3 changed the numbering - of bonds so that the new TopologyDict code should be working again. - - The UnitTests introduced in 4a1d06f6bc8d8ac3fbfb1170db8e8b5a971b14fe - are added back in the next commit. - -commit 26b13dcc28e3e6fd271a32183280879c7cca376d -Merge: 102cbec76 5f12ae537 -Author: Oliver Beckstein -Date: Mon Dec 30 17:37:14 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 102cbec764ef2f27ed88ab054e732e4b83481c0e -Author: Sébastien Buchoux -Date: Mon Dec 30 18:19:42 2013 +0100 - - Version bumped to 0.8.0rc3. Doc fixed and regenerated - -commit 93da921b05132c42e2286b9c584a318ee01f8e22 -Author: richardjgowers -Date: Mon Dec 30 13:15:30 2013 +0000 - - PSF Parser Fix - - Fixed PSF Parser shifting to 0 based indices when reading bond info - this shift was already happening in Universe building. - - Added unit tests for PSF parsing bonds - - Added unit tests for TopologyGroup and TopologyDict classes - -commit 06a2888974672e89bc69ec4d568e0fab166dac35 -Author: Oliver Beckstein -Date: Mon Dec 30 16:56:36 2013 -0700 - - test cases for 0-based Atom.number (PSF, TPR, TOP, PDB) - - - simple test_atom_number to check that the first atom has - number 0 and the last one numberOfAtoms() - 1 - - added test for PDB - -commit 0b35c6e972390fff28dd6910ed688ec44c9aa8fa -Author: Oliver Beckstein -Date: Mon Dec 30 16:22:44 2013 -0700 - - Bonds: changed to using 0-based atom indices (PDB, guess_bonds()) - - Atoms are identified by Atom.number. The bond connectivity code related - to PDB files and bond guessing used a 1-based index. See also - http://code.google.com/p/mdanalysis/wiki/TopologyDataStructures - - - That was changed by using Atom.number where possible instead of generated indices from - enumerate(). - - Universe._init_bonds(): use 0-based index! (see Issue 160) - - Replaced expensive list comprehensions by generator expressions when - possible. - - Added a few docs. - - UnitTests pass. - -commit 83b2b9e0a3a0e9c297a5e3b4e1ee751090d4ae5e -Author: Oliver Beckstein -Date: Mon Dec 30 15:26:02 2013 -0700 - - Bonds and bond guessing: non-breaking changes - - - made Bond.is_guessed a managed attribute (removed get_is_guessed() and - set_is_guessed()) - - added __eq__ special method to Bond so that one can compare if two - bonds are the same (should work across Universes because atom numbers - are compared) - - added some docs - - white space formatting changes (sorry -- my emacs enforces the standards - set in the header of each file) - - For additional notes on Bonds see http://code.google.com/p/mdanalysis/wiki/TopologyDataStructures#Bonds - -commit 8fe79c912b40f3344381bd5917c3b10a387ae734 -Author: Oliver Beckstein -Date: Mon Dec 30 15:25:24 2013 -0700 - - fixed logging in TPRParser - -commit 75779f12a69ea77ba0dbc9e2e902275d487c2350 -Author: Alejandro Bernardin -Date: Mon Dec 30 18:54:26 2013 -0300 - - Some corrections to documentation files. - -commit 5f12ae537be7cd6258cc5a45cf61665ed3111f20 (tag: release-0.8.0rc3) -Author: Sébastien Buchoux -Date: Mon Dec 30 18:19:42 2013 +0100 - - Version bumped to 0.8.0rc3. Doc fixed and regenerated - -commit 4a1d06f6bc8d8ac3fbfb1170db8e8b5a971b14fe -Author: richardjgowers -Date: Mon Dec 30 13:15:30 2013 +0000 - - PSF Parser Fix - - Fixed PSF Parser shifting to 0 based indices when reading bond info - this shift was already happening in Universe building. - - Added unit tests for PSF parsing bonds - - Added unit tests for TopologyGroup and TopologyDict classes - -commit 8afdeda5d3f00d6294dec828849db3af3bcee3a0 -Author: Sébastien Buchoux -Date: Sun Dec 29 23:01:29 2013 +0100 - - "a1, a2 = self.atoms[i],self.atoms[j]" changed back to "a1, a2 = self.atoms[i-1],self.atoms[j-1]" - -commit d8a503a7eefd5f5a8447eab9565bf8be3fed215a -Merge: 12e11a2de c69201809 -Author: Sébastien Buchoux -Date: Sun Dec 29 21:53:23 2013 +0100 - - Merge remote-tracking branch 'richard/triclinic' into develop - -commit c69201809c6f7aff63c73c891d087e96bc6bfb94 -Author: richardjgowers -Date: Sun Dec 29 19:19:24 2013 +0000 - - Small fix with missing import - -commit 12e11a2de8c82802bc040f1e258eb989109697b7 -Author: richardjgowers -Date: Sun Dec 29 19:17:51 2013 +0000 - - Doc update - - Docs docs docs - -commit 17a2d6852a1a93411a2621d670f7c7fd44431e2d -Merge: ee8cbda17 72c1c5129 -Author: richardjgowers -Date: Sun Dec 29 19:12:46 2013 +0000 - - Merge branch 'develop' into topologydicts - - Merged topologydicts with 0.8rc2 - -commit ee8cbda171aa4f2eec2a07e2c66c3e343ab9be28 -Author: richardjgowers -Date: Sun Dec 29 10:36:32 2013 +0000 - - Update to Top - - Updated doc strings - Added more unit tests - -commit 72c1c51293424768136976339b20b97cc9807dbb -Author: Sébastien Buchoux -Date: Sat Dec 28 10:45:59 2013 +0100 - - Version number changed to 0.8.0rc2 - -commit 478630212e2be6efe011cda6363dfa56a867b3dc -Merge: 666ca37e0 42a105f90 -Author: Sébastien Buchoux -Date: Sat Dec 28 09:57:46 2013 +0100 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 42a105f909729a63fe08640fa50122eef546a0c9 -Author: Oliver Beckstein -Date: Fri Dec 27 17:06:37 2013 -0700 - - minor changes in tests - - - only check for executable 'clustalw2' (which is the default for - the fasta2select() function) - - removed comments about slicing of ChainReader: given that this - seems to be working nowadays no need to keep the commented out - knownfailure. I think it started working once we derived all - trajectory readers from Reader and also made sure that DCD and - Gromacs formats can deal with slices - -commit 3791f1dd811a2efbec560bb55dd73b6e612b8ca2 -Author: Oliver Beckstein -Date: Fri Dec 27 14:32:35 2013 -0700 - - changed how we handle knownfailure tests due to missing executable - - - HOLE test: test_analysis.TestHoleModule.test_hole_module_fd_closure(): replaced - the knownfailure() decorator from a27e92637544a86af0a181e4544f418a438a356 - with the numpy decorator - - @dec.skipif(executable_not_found_runtime("hole")) - - because the @knownfailure(msg, OSError) decorator even skipped the test if the - HOLE binary was available. This makes use of the new executable_not_found_runtime() - helper factory function. - - Also skip this test if we cannot set the rlimits with another skipif() that - looks at the helper function rlimits_missing(). - - - protected test_analysis.TestAlignmentProcessing.test_fastta2select_ClustalW() - with a check that the ClustalW binary can be found. - - - added a factory function executable_not_found_runtime() that can be used with the - numpy test decorator skipif(): - - @dec.skipif(executable_not_found_runtime("binary_name"), msg="skip test because binary_name not available") - def test_something(self, ...) - - It uses the new helper executable_not_found(). - - If someone has a better grip on decorators than I then they might be able to roll skipif() - and (executable_not_found_runtime() together in another decorator such as "skipifnoexe()". - -commit 666ca37e08a04760eedebc9a4398af8f5b68f24d -Author: Sébastien Buchoux -Date: Mon Dec 23 22:44:53 2013 +0100 - - PDB.py fixed according to discussion on commit b6fff8dbc113 - -commit d7912a095fc931c890801cc31f0b526ab090419c -Author: Sébastien Buchoux -Date: Mon Dec 23 15:38:57 2013 +0100 - - libxdr interface modified to avoid 64-bit portability issues - -commit 362ef51dbab04578e012fa933be896d3b5b68ee7 -Author: Sébastien Buchoux -Date: Mon Dec 23 10:58:42 2013 +0100 - - Documentation regenerated - -commit 8112be9de81c9cd1e00088f0595c537219ae20b4 -Author: Sébastien Buchoux -Date: Mon Dec 23 10:26:42 2013 +0100 - - release number changed to 0.8.0rc1 - -commit ea2233ed5718bfaf5d88f1718147cf9e3e0a4f78 -Author: Sébastien Buchoux -Date: Sun Dec 22 23:16:25 2013 +0100 - - Added another PBC distance test for triclinic box - -commit a27e92637544a86af0a181e4544f418a438a356b -Author: Sébastien Buchoux -Date: Sun Dec 22 22:33:06 2013 +0100 - - HOLE test skipped instead of raising warning when HOLE is not found - -commit 511bc6a7a8bf2d99c6c5bb1ae30b0a7f66016b2e -Author: Sébastien Buchoux -Date: Sun Dec 22 22:19:37 2013 +0100 - - Added test system for triclinic box distances - -commit 43e745c09c87a1fb4af425502e1a265329263dfb -Merge: 8cc6ec19b 3685f5c03 -Author: Sébastien Buchoux -Date: Sun Dec 22 19:19:23 2013 +0100 - - Merge branch 'feature-triclinic' into develop - -commit 8cc6ec19bbe94a74112157c2a1c4f877ad9dbc58 -Merge: c121b7473 07cf0a783 -Author: Sébastien Buchoux -Date: Sun Dec 22 18:44:34 2013 +0100 - - Corrections made by Alejandro merged - -commit c121b7473c315dfd6be292925ec794b27ff37132 -Author: Alejandro Bernardin -Date: Fri Dec 6 16:28:05 2013 -0300 - - added extensions to Selection Commands - - - added new geometrics selections: - sphlayer: spherical layer - sphzone: spherical zone - cylayer: cylindrical layer - cyzone: cylindrical zone - - functionality extension to geometric selection "prop". Now it is - possible to operate with the members of the inequation. It uses - the numpy function eval() - - added selections tests: sphlayer, sphzone, cylayer, cyzone, around and prop - - CHANGELOG and AUTHORS modified - - added documentation to new selections - -commit b6fff8dbc11343b857e8e9bc65ec10699b0ad02f -Author: Sébastien Buchoux -Date: Sun Dec 22 13:20:18 2013 +0100 - - Fixed regression in PDB.py introduced by commit cf13de7d55c3 - -commit 07cf0a7836c3dac289de4f89aab453e2f65a10f9 -Author: Alejandro Bernardin -Date: Fri Dec 20 14:43:01 2013 -0300 - - added extensions to Selection Commands - - - added new geometrics selections: - sphlayer: spherical layer - sphzone: spherical zone - cylayer: cylindrical layer - cyzone: cylindrical zone - - added selections tests: sphlayer, sphzone, cylayer, cyzone, around and prop - - CHANGELOG and AUTHORS modified - - added documentation to new selections - -commit f7a7b5fef106c1e3108e495e04f4418eeb99743f -Author: Joshua Adelman -Date: Tue Dec 17 20:46:50 2013 -0500 - - Modified analysis.rms.rmsd docstring to clarify important elements of the algorithm - -commit 0b7ac40eaaeaa9ece1a802d40b0b975ee26d788d -Author: Oliver Beckstein -Date: Mon Dec 16 15:04:07 2013 -0700 - - util.convert_aa_code() recognizes non-standard residue names such as HSE, GLUH, GLH, ... - - - added hard-coded list of canonical and non-standard resnames (3 and 4 letter) - - added test cases - (not for all of them) - - note that we should really have one common table for convert_aa_code() and the protein selection class - -commit cf13de7d55c3fa5e326026ee5f40a02383462d0c -Author: Lennard van der Feltz -Date: Mon Dec 16 11:42:03 2013 -0700 - - fixed: PDB with blank lines gave IndexError (fixes Issue 158) - -commit 073b075dd3ec980eacd7920c3ea747cfe5ed18ca -Author: Sébastien Buchoux -Date: Mon Dec 16 17:55:17 2013 +0100 - - Known failures implemented by hand since nosetest don't use the numpy ones - TestCoordinates modified accordingly - -commit 514cb44f64d5fa0bf86d9fe243e4c1729da38b31 -Author: Sébastien Buchoux -Date: Mon Dec 16 16:58:24 2013 +0100 - - .trz file added to testsuite/setup.py - -commit f4c91b354e7bb8f8d9c0ede5a41853fba341a076 -Author: Sébastien Buchoux -Date: Mon Dec 16 16:50:14 2013 +0100 - - Added data/merge pdbs to setup.py - -commit 4890fd563a6ecfe8022b948aa757ee94772d323b -Author: Sébastien Buchoux -Date: Mon Dec 16 16:49:17 2013 +0100 - - Test for HOLE changed form error to warning when HOLE binaray is not there - -commit a11ce7659d845e4225da4764a4c5411e36146863 -Merge: ce6047684 5d590fa70 -Author: Sébastien Buchoux -Date: Mon Dec 16 16:22:48 2013 +0100 - - Merge branch 'fix-tpr-IO' into develop - -commit ce604768487489e8463f86b4d5f0bf7ba4688a25 -Author: Sébastien Buchoux -Date: Mon Dec 16 16:22:21 2013 +0100 - - .idea and *.egg added to .gitignore - -commit 5d590fa70629a9952a32b23ad631d4d7e79dbb52 -Author: Sébastien Buchoux -Date: Mon Dec 16 16:20:57 2013 +0100 - - Warning commented out in PSFParser - -commit d7b0f3a50a6e434a86f75c4976cb77fe23b6b6b6 -Author: Sébastien Buchoux -Date: Mon Dec 16 16:17:46 2013 +0100 - - - DMS testfile added to testsuite setup.py - - DMSParser fixed so it raises an IOError when file not found - -commit 2c97b9d7e7832033f402d43a48bca7711f7b71d5 -Author: Sébastien Buchoux -Date: Mon Dec 16 16:15:16 2013 +0100 - - AtomGroup.py fixed to allow topology file to be loaded without coordinates - -commit 07a93b56e1b4e6c223c742551c9773bc6d4b6cc3 -Author: Sébastien Buchoux -Date: Mon Dec 16 15:05:09 2013 +0100 - - Added tpr files located in testsuite data subfolder - -commit fafb7d7931440cfd0bc7ddf3173f186ad2412af7 -Author: Alejandro Bernardin -Date: Fri Dec 6 16:28:05 2013 -0300 - - added extensions to Selection Commands - - - added new geometrics selections: - sphlayer: spherical layer - sphzone: spherical zone - cylayer: cylindrical layer - cyzone: cylindrical zone - - functionality extension to geometric selection "prop". Now it is - possible to operate with the members of the inequation. It uses - the numpy function eval() - - added selections tests: sphlayer, sphzone, cylayer, cyzone, around and prop - - CHANGELOG and AUTHORS modified - - added documentation to new selections - -commit 3685f5c031ab8ea85c016bab7713be44a6fe4676 -Author: richardjgowers -Date: Sat Nov 23 12:17:30 2013 +0000 - - Triclinic minimum image convention - - Added option for triclinic boxes in self_distance_array and - distance_array. - - Added new functions in core.distances transform_StoR and - transform_RtoS, transforms to and from fractional coordinates. - - Added cython functions to calculate all of above. - - Added test cases for all of above. - -commit dd808b288abf0e8b5f9c67400b2270840c1a9387 -Author: richardjgowers -Date: Sun Nov 17 14:17:37 2013 +0000 - - Documentation - - Html doc update - -commit 077c188b5b76428a0710b7c8d56bed23df62d01c -Author: richardjgowers -Date: Sat Nov 16 20:56:48 2013 +0000 - - Doc strings and tidying - - Added lots of documentation and tidied things. - -commit 615f1a75a170be85989488f5f7d076c1e7b7539d -Author: richardjgowers -Date: Mon Nov 11 20:12:48 2013 +0000 - - Added unit tests for new cython distance modules - (calc_bonds, calc_angles and calc_torsions) - -commit 5bd25e7e1ae874e8080ba6f7700647e0c3253d4b -Author: richardjgowers -Date: Sun Nov 10 23:04:22 2013 +0000 - - Cython analysis work - - Adding type checking to calc_angles and calc_torsions - - Changed calc_angle and calc_torsion to use atan2 rather than acos. - -commit e4f0cee2276883554c4b3c1c17bb1fa7480543a7 -Merge: b63866642 a666fdf76 -Author: Oliver Beckstein -Date: Sun Nov 10 15:21:57 2013 -0700 - - merged feature-xpdb (extended PDB) into develop (closes Issue 159) - -commit a666fdf762ad00a54a55fbf844d1b9dfa4973974 -Author: Alejandro Bernardin -Date: Wed Nov 6 16:20:17 2013 -0300 - - extended format PDB reader test case - - - added a five digit resid file - - added a test to the XPDB format - -commit 8feb35d493722cf2cfc1edea57080abdf98c9d61 -Author: Oliver Beckstein -Date: Mon Sep 2 09:51:52 2013 -0700 - - extended format PDB reader - - - can read 5-digit resid (to be compatible with eg VMD/NAMD) by reusing the insertChar field - in the PDB format - - reorganized PrimitivePDBParser as a class to make it reusable; still not pretty but this is how we - could organize the topology parsers in the future - - reused PrimitivePDBReader and only added one if...else that checks the format and if it is - the extended format XPDB it will read a 5-digit resid: that made it easy to subclass - ExtendedPDBReader(PrimitivePDBReader). - - added ExtendedPDBParser.py - - added docs and CHANGELOG entry for non-standard extended PDB format (XPDB) - -commit edd5c9c9c590aa02efed68eb3fd4ee1a53fc68f1 -Author: richardjgowers -Date: Thu Nov 7 21:25:26 2013 +0000 - - Added calc_angles and calc_torsions to core.distances - These are cython implementations of mass angle/torsion calculation - - Topology groups can now be added to eachother and retain order - - TopologyGroup now has .bonds() .angles() and .torsions() methods - which are shortcuts to using the cython implementations. - -commit 364440a1c4e46f755c65c583b46a763b1ef79a9e -Author: richardjgowers -Date: Wed Nov 6 11:28:39 2013 +0000 - - More work on topologyDicts and topologyGroups - - Added Torsion and Angle class to topology.core, currently just stubs - that hold 4 or 3 Atom objects respectively. - - Added .torsions and .angles attribute to atoms. Populated when - universe starts, these are lists of all torsions and angles that - a particular atom has, similar to the existing .bond attribute. - - topologyDict can now read bonds angles or torsions. - - topologyDicts now store Atom objects not just numbers of atoms. - - atomGroup.selectBonds() can now select angles and torsions. - -commit d18ceeb14d2b7eaef4174551f068765c20ee2ffe -Author: richardjgowers -Date: Sun Nov 3 15:30:47 2013 +0000 - - Fixed bad commit - - Fixed error with previous commit - -commit 9a8d2e2eb7112288deeeb01e610e559b30e58fe3 -Author: richardjgowers -Date: Sun Nov 3 15:25:14 2013 +0000 - - topologyGroup created - - Added a new class, topologyGroup, which is a container for atomGroups - A bond topologyGroup has 2 atomGroups, corresponding to each atom - of a bond, angles will have 3 atomGroups etc - ag.selectBonds now returns topologyGroups - - Added cython method in distances bond_distance which returns the - distance between each pair in two lists of coordinates - ie - r_ij1 = (r_i1, r_j1) - r_ij2 = (r_i2, r_j2) - -commit 7dd804de21345ace786812de79ed15ed73d313c6 -Author: richardjgowers -Date: Sat Nov 2 20:29:47 2013 +0000 - - topologyDict created - - Created topologyDict in topology.core. Takes a list of groups of atoms, - (representing bonds/angles etc) and creates a dictionary of the - different types of bonds, and the members of each group. - - Added bondLists() method to atomGroups, creates a topologyDict of the - bonds in the current atomGroup. - - ag.selectBonds() can then return lists of atomGroups of the bonds - -commit b638666423827417c7c0b5e6ee685630aa4d3d80 -Author: Jan Domanski -Date: Thu Oct 31 22:57:59 2013 +0000 - - New feature: merge AtomGroups together giving a new Universe - - - Merge two or more AtomGroups into a new Universe, - - use MDAnalysis.Merge(gr1, gr2, ...) - - - possible to use a single AtomGroup, if atoms were - re-ordered for example, - - support for an empty universe, u = Universe(), - - - add basic test class, - - add other tests, make sure that merge doesn't messup the origin - universes from which the input AtomGroups come, - - test write out of merged pdb file, - - CHANGELOG modified - -commit 56b1273d0842ea82340d7de84e36f997ec8324bf -Author: Jan Domanski -Date: Thu Oct 31 18:11:56 2013 +0000 - - Added VdW radius for phosphorus - - - corrected the fix for the presence of an atom radius - -commit ae71b70a47094aa7643300d46c89a70ee3d92250 -Author: Oliver Beckstein -Date: Tue Oct 29 11:50:21 2013 -0700 - - application RotamerConvolveMD: added paper citation - - - paper accepted: doi:10.1016/j.jmb.2013.10.024 - - added parts of README to docs in __init__ - - updated Stelz paper with doi - -commit 5e84d12d132db7c306a90dac59d937fc44b39b1d -Author: Oliver Beckstein -Date: Tue Oct 29 10:40:37 2013 -0700 - - closes Issue 153: AtomGroup.packintobox() merged - - - updated CHANGELOG - - updated packinbox() reST docs - - removed superfluous return statement - -commit b582036dd402b43c9eea05765a5c1cd3c5dcb1d4 -Author: richardjgowers -Date: Thu Aug 22 14:31:32 2013 +0100 - - Added packintobox method for atom groups. - Shifts all atoms so they lie between 0 and box length - Added unit tests to test this - -commit e74236a1549372b3eb177f83f9bf820755bfab08 -Author: Oliver Beckstein -Date: Thu Oct 24 15:07:48 2013 -0700 - - Trajectory API: improved reST docs - -commit d35e7c3f76d6232864e86c9d09ccc9109a74eced -Author: Oliver Beckstein -Date: Thu Oct 24 14:43:19 2013 -0700 - - TRR writer: fixed writing of forces (without unit conversion) - -commit 91f383cc66d1f5f48b4c01ea7bc43d8f842a95c2 -Author: Oliver Beckstein -Date: Sun Oct 13 23:59:37 2013 -0700 - - added googlecode_upload.py to the maintainer tools (will work until 15 Jan 2015) - -commit da309d5893aa6db4d2c11c2c47569b43a316d70a -Author: Oliver Beckstein -Date: Sun Oct 13 22:46:55 2013 -0700 - - apps: RotamerConvolveMD renamed package and downgraded version to 1.0-rc1 - - - renamed Python package from rotamers to rotcon - - rotamers was not a very unique name space whereas rotcon is (rotcon python only gives 58 google hits). - - also changed the docs a little bit where necessary. - - - changed version to 1.0-rc1 (release candidate 1) - - make it final release after some more testing - - add full citation to 1.0 when JMB paper is published - -commit 7353f28c42a73dc48bf6708634c903f3933c3ddd -Merge: cadd70eef bc0a3b3f1 -Author: Oliver Beckstein -Date: Sun Oct 13 22:41:20 2013 -0700 - - Merge branch 'applications' into develop - -commit bc0a3b3f195737dd31b8216e66601e844b482352 -Author: Oliver Beckstein -Date: Sun Oct 13 22:40:55 2013 -0700 - - apps: added URL http://code.google.com/p/mdanalysis/wiki/Applications to README - -commit ced2aa262bd025592d06c204ceb1301a467a3565 -Author: Oliver Beckstein -Date: Thu May 16 16:14:11 2013 +0200 - - applications library - - The applications/ directory contains self-contained Python packages - that make use of MDAnalysis as their primary dependency. Each package - should be installable on its own but make use of dependency mechanisms - to automatically install MDAnalysis (and other required packages). - - The idea is that an interested use can easily install a particular - application without having to worry too much about MDAnalysis itself. - - See the toplevel README.txt for more details. - -commit cadd70eef06435f9822dca7b34cb41179a8fe8ab -Author: Oliver Beckstein -Date: Sun Oct 6 21:25:47 2013 -0700 - - MDAnalysis application: RotamerConvolveMD package - - Converted Phil's original script into a standard python package: - - - library manages rotamer libraries; at the moment only Jeschke's MTSL - rotamer library R1A 298K is included - - convole does the fitting - - script that uses MDAnalysis to fit the rotamers - - added GPL v2+ licence (both for code and MTSL library) - - added docs (README) - - Below are notes on the various parts of the conversion process - in which as simple script was inflated into a whole package - (with the idea that this would make it easier to add new rotamer - libraries and also use it as a library in other applications) - - - heavily modified the covolve-mtss script - - - moved script code into a if __name__ == "__main__" block - - added copyright and authorship - - changed the calling signature of script: provide topology and - trajectory or multiple trajectories as arguments; removed the - --pdbfile argument (needs MDAnalysis 0.8 for concatenating - multiple trj files on the fly) - - use quiet option to suppress output from rms_fit_trj() - (needs MDAnalysis 0.8) - - new option to specify the rotamer library directory - - use logging - - updated example with new option and README insted of the - shell script - - - for the future: combined rotamer lib into TRR - - Coordinates are kept in framse and the occupancy of each rotamer in the lambda (Timestep.lmbda) - - not used yet but see code in the data directory - - - Split into a package and a small script, convolve-mtss-rotamers.py - - - created the rotamers package with rotamers.library and rotamer.convolve - - rotamers.library is responsible for loading rotamer libraries; at the - moment, only 'MTSSL 298K' is available but more can be added - - library files live in the data/ directory and are installed with - the package. New library metadat must be added to rotamers.library.LIBRARIES - - rotamers.convolve contains most of the original code but packaged as - a class RotamerDistance - - added copyright blurb and info messages - - tested (see doc/example/README) and get same result as before - - - setuptools installable package - - - plot distribution - - - added MDAnalysis>0.7.7 to requirements - - NOTE: uses features that are currently in the 0.8-dev development version - - - added installation instructions - - - reorganized example and wrote primitive shell test script - - - changed library: Only prepend [0] to weights and not [0,0] - - - The first frame of the rotamer library trajectory is (apparently) - just a (ideal?) structure; rotamers start at the second frame. - -commit 183a490cdc58214e12f168944061cde3a5289dd1 -Author: Phil Fowler -Date: Sun Oct 6 21:18:00 2013 -0700 - - MDAnalysis application: convolve-mtss-rotatmers - - - original files (script + rotamers) - - includes Gunnar Jeschke's rotamers for MTSS at 298 K - - basic README - -commit e32e5e61f6e9b3ccf302e16109fe56e4d77d778d -Author: Oliver Beckstein -Date: Sat Aug 31 13:57:23 2013 -0700 - - fixed: XTC/TRR reader failed on Python 2.6 - - Checking for UTF filenames introduced a test for python major version. - sys.version_info.major only exists for Py >= 2.7 so for compatibility - we need to use sys.version_info[0]. - - Changed all occurences in the package and tests. - -commit feb07226f516d9f9ba900c7c278d615bf27fb2b1 -Author: Oliver Beckstein -Date: Thu Aug 22 19:11:43 2013 -0700 - - H-bonding analysis now defaults to updating selections each time step (fixes Issue 138) - - The old behavior leads to unexpected behavior in conjunction with the pre-filtering - optimization. Documentation has been added and CHANGELOG updated. - -commit e05d87cafa8fd2beb28ccf79fc1a0915b52d045a -Author: Oliver Beckstein -Date: Thu Aug 22 18:48:37 2013 -0700 - - touched up docs in TRZ reader - -commit f8f99b814f46ae7ed200c0b7e16e4e8cb9be2891 -Author: richardjgowers -Date: Mon Aug 19 15:06:21 2013 +0100 - - Made changes based on code review. - Added much more data into custom timestep, - and appropriate unit tests for this. - Finished documentation for TRZ format - -commit d7ca9f4978b4824f1f944d3ea8d27dd341145507 -Author: richardjgowers -Date: Fri Aug 16 11:55:19 2013 +0100 - - Added documentation to all TRZ related stuff. - - Signed-off-by: Rich - -commit 9db11c7f2dd3572993e3e7fe63477b0bbff7d322 -Author: Rich -Date: Thu Aug 15 12:50:21 2013 +0100 - - Added the TRZReader into coordinates, can now read .trz files. - - Added testcases for this too and added name to AUTHORS. - - Signed-off-by: Rich - -commit 8fc2f2a715d2c1bd46b953927937907316073df0 -Author: Oliver Beckstein -Date: Sat Aug 10 00:16:07 2013 -0700 - - analysis.align.rms_fit_trj: new quiet kwarg to suppress most status/error output - -commit 89fc2ae83ed4ad64e2fb11579c99117c17e0630e -Merge: d1b4430d5 939e4988b -Author: Oliver Beckstein -Date: Fri Aug 9 23:24:47 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit d1b4430d5c2ce56dd3d1cd6f6b36d89e8b3beaea -Author: Oliver Beckstein -Date: Fri Aug 9 23:21:59 2013 -0700 - - Universe can load multiple trajectories from positional args - - - Can load multiple trajectories as Universe(topology, traj2, traj2, - ...) in addition to providing all trajectories as a list, - i.e. Universe(topology, [traj1, traj2, ...]) - - UnitTest added - -commit 939e4988b0c2a24f60f9cc9d84f634997ea85dc4 -Author: Elizabeth Denning -Date: Fri Aug 9 18:05:20 2013 -0700 - - corrected directionality for pseudo_dihe_baseflip in nuclinfo - -commit 8a7ad02e00776f3cc882008282498c386008c89c -Author: Elizabeth Denning -Date: Fri Aug 9 11:50:41 2013 -0700 - - updated nuclinfo - -commit 8fd85c1284739a82a1ec1d696f78dfa9b4e284b7 -Author: Elizabeth Denning -Date: Fri Aug 9 11:30:16 2013 -0700 - - updated test_nuclinfo to reflect segid selection option - -commit 0ff2cf980004de3120d81cae6ca0abf3e2dd0a04 -Author: Elizabeth Denning -Date: Fri Aug 9 11:29:44 2013 -0700 - - fixed major_pair issue in nuclinfo - -commit 5fff0f48feb67ef32e232e7af2bf6f78a47f2fe7 -Author: Oliver Beckstein -Date: Wed Aug 7 14:14:09 2013 -0700 - - AUTHORS: Joshua Adelman should also appear under contributors - -commit 8c74659ec5525b9ef850114a38f9fb702a062355 -Merge: 10b8e9816 03c87d1ac -Author: Oliver Beckstein -Date: Wed Aug 7 11:38:28 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 10b8e9816c4b439ed1b8a37c65ed30172e09ef6e -Author: Oliver Beckstein -Date: Wed Aug 7 11:36:41 2013 -0700 - - analysis.align.rms_fit_trj(): added force keyword to control trajectory clobbering - - The default is force=True (the previous behaviour): just overwrite an - existing trajectory. With force=False you get a warning and the function returns. - -commit 03c87d1ac750289478d9004d5f61b2f48f02c96b -Author: Oliver Beckstein -Date: Wed Aug 7 09:37:03 2013 -0700 - - spelt out rmcgibbo as Robert McGibbon - -commit 22b33e812c4526a7c6bface7c5c83fd85939ce27 -Author: rmcgibbo -Date: Tue Aug 6 15:28:51 2013 -0700 - - detect OpenMP-capable compiler during setup (fixes Issue 145) - - The cython-produced c code guards all of its openmp pragmas and - function calls with #ifdef _OPENMP - e.g https://code.google.com/p/mdanalysis/source/browse/package/src/numtools/distances_parallel.c#2603), - which is set only when -fopenmp is passed as a flag to the compiler. - So it's fine to compile the "parallel cython" code on compilers that - don't support openmp -- if its not available or you don't pass -fopenmp, - you will just get a serial version. - - The key is to dynamically detect the compiler capabilities. - The attached patch file detects whether the compiler supports openmp, - and inserts the -fopenmp. Some compilers also require linking against - libgomp, so it's good to check for that too. - -commit 385a5a7a36e70aae1b64ca12d8bec90323661a63 -Merge: 846f450f2 3f7d5300d -Author: Oliver Beckstein -Date: Tue Aug 6 11:21:30 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 3f7d5300d730328fb826ebe8252cea4954c4f583 -Author: Oliver Beckstein -Date: Tue Aug 6 10:57:55 2013 -0700 - - Fixed PBC in parallel distance array (closes Issue 151) - - - translated rmcgibbo's fix to the parallel cython code - - added the PBC2 test to test_parallel.py - - use atol=1e-6 for all parallel tests (the PBC ones fail with - atol=0 or atol=1e-8) - - replaced simple assert with assert_almost_equal for the standard - distance array test PBC2 - - added rmcgibbo to AUTHORS (and Contributors) - - updated CHANGELOG - -commit 36f4829a7752e1a07a6b83f1700bfa32f0f9ef90 -Author: rmcgibbo -Date: Mon Aug 5 23:34:56 2013 -0700 - - Fixes Issue 151 (distance array did not properly observe PBC) - -commit 1de49eec3252602b2a534e11845dc770614a012c -Author: Oliver Beckstein -Date: Mon Aug 5 23:17:12 2013 -0700 - - regenerated htnl docs with sphinx (x3dna added) - -commit 52d291558bbf64c489b31ff72c9612a3d42da455 -Author: Oliver Beckstein -Date: Mon Aug 5 23:10:29 2013 -0700 - - added X3DNA to reST docs (+ minor docs adjustments) - -commit ec35cea0ec91e824e628459defc42004ce70487b -Merge: 940f3ca47 93c7a0c98 -Author: Oliver Beckstein -Date: Mon Aug 5 22:19:17 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 93c7a0c9851353895df8fd91767fb7dcda9f36eb -Merge: 699775efa 406400da9 -Author: Elizabeth Denning -Date: Mon Aug 5 22:13:27 2013 -0700 - - updates to selections and test_selections - -commit 699775efaf41aec8ed6f7066df9f34d22f0726ad -Author: Elizabeth Denning -Date: Mon Aug 5 22:01:51 2013 -0700 - - updates to the x3dna plugin and nucl acid analysis - -commit 846f450f2d89e87280035ed50896b4e20221efac -Author: Oliver Beckstein -Date: Mon Aug 5 18:14:42 2013 -0700 - - MDAnalyis.analysis.align.rms_fit_trj(): minor usability improvements - - - added kwargs to manipulate the output trajectory - - returns filename (useful when it is auto-generated) - -commit 406400da9dd73aee825e348c8d6e5b24fa921b26 -Author: Oliver Beckstein -Date: Mon Aug 5 17:43:50 2013 -0700 - - nucleic selections enhanced - - - added the common Gromacs nucleic acid residue names DA, DT, DC, DG, DU to - the standard nucleic selection - - added test cases for nucleic, nucleicbackbone, nucleicsugar, nucleicbase - - minor code cleanup - -commit 940f3ca4713b4b5aaf00620eb4c7e4d9a2caee43 -Author: Oliver Beckstein -Date: Sat Aug 3 13:55:13 2013 -0700 - - setup.py: test_suite = "MDAnalysisTests" - - This is supposed to enable 'python setup.py test' although for some reason - this leads to ~80 tests failing. If I am running these tests manually with - nosetest -v test_coordinates.py then all is fine. - -commit 300033863d0be838c855146904e8f8c827a2dd1e -Author: Oliver Beckstein -Date: Fri Aug 2 19:05:50 2013 -0700 - - fixed memory blowup in the unit tests (introduced in commit 1e05654b23e2) - - Running the unit tests (specifically, test_coordinates.py) would consume ~8 GB - of memory because the memory for the created universes was not freed (despite - the tearDown methods: apparently something kept a reference to the universe alive - and garbage collecting could not kick in). The culprit turned out to be a a - __del__() method that I had added to Universe "just to make sure that trajectories - are closed". Somehow this method kept a universe alive in a TestCase. The - Universe.__del__ method was removed and the test cases all run fine (and consume - about 800 MB in total). - -commit fe3aba244023935842c9b13903363486fd481fb9 -Author: Oliver Beckstein -Date: Fri Aug 2 18:15:29 2013 -0700 - - tests: add tearDown to multi PDB reader test case - -commit 1e05654b23e2395586072ca3986b43d87e7bede1 -Author: Oliver Beckstein -Date: Fri Aug 2 14:24:47 2013 -0700 - - discontinued support for Python 2.5 (Issue 130) - - - changed check in setup.py to fail for python < 2.6 - - updated docs - - removed from__future__ import with_statement from code - - use with_statement much more liberally (although this would have also - worked in 2.5) - - in the spirit of using with and context managers I maded all trajectory - readers and writers context managers that can be used in with statements. - This is implemented in the IOBase class so it automatically applies to all - Readers/Writers. Just make sure that you have a valid close() method. - Updated the trajectory API. - -commit cd9a044d4e49d827bd01bcb673845ffec492239e -Author: Oliver Beckstein -Date: Mon Jul 29 13:27:02 2013 -0700 - - methods of AtomGroup return NumPy arrays - - - resnums, resids, segid, names, resnames will now return - numpy.ndarray instead of lists; this is consistent with many - other methods such as charges, radii, indices that already returned - arrays - - added unit tests for types and values (and also added tests for - a few more methods that were missing) - - updated CHANGELOG - -commit 1c6af5856fcbc7cb96bcd8f534af8cebdf1146b6 -Merge: 4e47be6c5 bd9254f71 -Author: Oliver Beckstein -Date: Mon Jul 29 10:56:43 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit bd9254f7187d4cae3c2c6680c8d8df7f8180e843 -Author: Oliver Beckstein -Date: Thu Jul 25 11:09:23 2013 -0700 - - updated to setuptools 0.9.6 - - (see also Issue 125) - - Downloaded the boot strap loader: - wget --no-check-certificate https://bitbucket.org/pypa/setuptools/downloads/ez_setup.py - -commit 4e47be6c52886ebc7b8de1355d37ca9cb9bce059 -Author: Oliver Beckstein -Date: Tue Jul 23 09:49:17 2013 -0700 - - bumped release to 0.8.0-dev (in sync with CHANGELOG) - -commit a564df308f42ed7f2db2172e1518b865980bc561 -Author: Oliver Beckstein -Date: Tue Jul 23 09:48:32 2013 -0700 - - maintainer/change_release.sh: can deal with either -dev or -devel release suffix - -commit ad9b79d35bed0bbb94f63f4a1e95bec72b5f84d7 -Author: Elizabeth Denning -Date: Fri Jul 19 14:17:27 2013 -0700 - - fixed x3dna trj bug - -commit 028674d8ee3651d11975247225376a1ad3954479 -Author: Elizabeth Denning -Date: Fri Jul 19 14:07:59 2013 -0700 - - fixed bug in x3dna trj analysis - -commit 074d3492a36dfb58b82f378d9036586bd51229fa -Author: Oliver Beckstein -Date: Thu Jul 18 12:12:42 2013 -0700 - - Slicing of ResidueGroup and SegmentGroup produces the same groups (fixes Issue 135 and 148) - - - ResidueGroup and SegmentGroup will produce ResidueGroup/SegmentGroup - - Residue will produce AtomGroup - - Segment will produce ResidueGroup - - unified the __getitem__ method between AtomGroup, ResidueGroup, SegmentGroup, and - use slightly modified code for Residue and Segment. - - advanced slicing (like numpy) is enabled, i.e. you can do ResidueGroup[[2,5,6,9]]. - - added test cases - - updated CHANGELOG - - fixes Issue 135 (see comments there) and Issue 148 - - NOTE: This change has the potential to break code that somehow relies on slices being - lists; see Issue 135 for discussion. The impact in real life is probably small, - though. - -commit 712c7c658ca82c36eeb0df49f8521755490b9430 -Author: Oliver Beckstein -Date: Tue Jul 16 18:55:17 2013 -0700 - - improved manipulating of topology information - - - changing resid (set_resid()) or segid (set_segid()) changes the - topology - - - lists of resids/segids can be assigned to groups - of objects: AtomGroup.set_resid([34, 34, 34, 35, 35]) will *split* - the atoms into two residues numbered 34 and 35; - ResidueGroup.set_resid([33, 34, 34, 35]) will *merge* the two - residues numbered 34 into one. - - - added topology.core.build_residues() to rebuild list of residues - from changed Atoms - - - split initialization of Universe into methods (looked cleaner) - - - added __cache manipulation methods to AtomGroup (important for - propagating changes in Atoms and Residues) - - - various clean ups in AtomGroup.py - - - added unit tests (AtomGroup.set_resid, set_segid, also ResidueGroup - and SegmentGroup); not all setters are tested at the moment but - all the ones that change topology (set_resid, set_segid) and one - example for just changing attributes (set_mass) - - - added docs, updated CHANGELOG - -commit 1ce9fffdfb9bc2e17e54fe84b21032220ba7ca9e -Author: Oliver Beckstein -Date: Wed Jul 17 09:10:36 2013 -0700 - - UnitTests for dihedral angle: decreased precision - - The omega test gives slightly different values in the 3rd decimal on different architectures. - To avoid spurious failures I decreased the precision of all dihedral tests to 2 decimals. - -commit ad8e5aaa40c02243b8c4f39d9757b3e3b957d74b -Merge: c8b6ef668 a5f9288b7 -Author: Oliver Beckstein -Date: Wed Jul 17 08:53:24 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit f4c324742e10e944ddbb0f0cf6d7681a4aa76ba7 -Merge: 5e6830f76 a5f9288b7 -Author: Elizabeth Denning -Date: Mon Jul 15 14:26:28 2013 -0700 - - merged CHANGELOG - -commit 5e6830f763fa7a9fe8bcd5a02f4b3a9b18902e27 -Author: Elizabeth Denning -Date: Mon Jul 15 14:22:41 2013 -0700 - - initial x3dna plugin - -commit c0ae391e0a063e3a4d1b35ae162213a9fe725347 -Merge: 956422ddf 43d0db12f -Author: Elizabeth Denning -Date: Mon Jul 15 14:21:55 2013 -0700 - - updated nuclic acid selections and nuclinfo - -commit a5f9288b7e59b86e0231c1511423d25a8f7bea7a -Author: Oliver Beckstein -Date: Thu Jul 11 22:37:34 2013 -0700 - - fixes Issue 143: alignto() now checks that the two selections describe the same atoms - - - Created a new function check_same_atoms() from the code in rms_fit_trj() that is - used by both alignto() and rms_fit_trj(). - - Added UnitTest. - - Added docs. - -commit 5a0eb5c3642dfae352b09a22a8cbe19be80425cb -Author: Oliver Beckstein -Date: Thu Jul 11 21:55:41 2013 -0700 - - increased required Biopython version to 1.59 (Issue 147) - - Reportedly, Bio.PDB.StructureBuilder.StructureBuilder was not found with 1.58. - Versions 1.59 and 1.61 are known to work. - -commit 70824b4751a0a1dae2cfde550b5de3fe23a14d8b -Author: Oliver Beckstein -Date: Thu Jun 27 13:12:52 2013 -0700 - - doc improvements in MDAnalysis.analysis.distances; also use logging - -commit 7271e520ff1f3dd9a13900b80059e112a1a20fa3 -Author: Oliver Beckstein -Date: Wed Jun 26 11:21:08 2013 -0700 - - docs: fixed broken links to CHARMM docs - - (Thanks to Alejandro Bernardin for reporting.) - -commit 98d4aa0fbcaabe540a94ffa872eb65d18cb0628a -Author: Oliver Beckstein -Date: Wed Jun 26 11:09:47 2013 -0700 - - regenerated html docs with sphinx - -commit 16b34c5b74d6d63745a439ea485d6dac89107baf -Author: Oliver Beckstein -Date: Wed Jun 26 11:01:29 2013 -0700 - - doc updates (reST) - - - re-added Zhuyi Xue to authors list in sphinx/conf.py (a merge - removed him) - - use nice mathJax for describing dipole timeseries (also in response - to a recent discussion on the list, https://groups.google.com/d/msg/mdnalysis-discussion/CgZoQol8Rak/JJVh7pMpA28J ) - - use mathJax for some docs in util, changed a "versionadded 0.7.8" to 0.8 - -commit 6758f84e752d92d6e908d7a9acd2e11cc6d4cce0 -Author: Sébastien Buchoux -Date: Wed Jun 26 18:16:20 2013 +0200 - - setup.py scripts updated to include TPR parsing machinery and testsuites/data - -commit db0e89dde496472d4ab168042adb57f36951a910 -Merge: 6247a2b43 eb27af245 -Author: Sébastien Buchoux -Date: Wed Jun 26 17:57:33 2013 +0200 - - feature-xtc merged into develop - -commit eb27af24534c1ecaa3449d55706d6eee8bdd9ee5 -Merge: cc52c5311 2450fd554 -Author: Sébastien Buchoux -Date: Wed Jun 26 17:51:35 2013 +0200 - - fixes issue 146 - -commit cc52c5311a010eb2eeb15ad0ba52c2bd3399cc6d -Author: Sébastien Buchoux -Date: Wed Jun 26 11:11:31 2013 +0200 - - Added: Exception is raised if XTC/TRR traj filesize is too big for xdrfile lib - -commit 6247a2b43ff408b3e5a426e12f15412be4ce9a7a -Author: Oliver Beckstein -Date: Sun Jun 9 22:58:21 2013 -0700 - - RMSD analysis: added computation of additional groups - - - MDAnalysis.analysis.rms.RMSD enhancement - - can compute additional RMSDs after superposition on the primary selection - - example script examples/rmsd_groups.py with output added - - docs with shorter example script - -commit d7336b942c9170833093137b2d0770341607d205 -Merge: f671817a3 19007de4f -Author: Oliver Beckstein -Date: Wed May 29 16:22:47 2013 -0700 - - Merge branch 'pyTPRparser' into develop - - Updated AUTHORS and CHANGELOG and made sure that the author list - and year in the sphinx docs (conf.py) are correct - -commit 19007de4fd5ba7f555bd0bdfaf0dc8877ee25482 -Author: Oliver Beckstein -Date: Wed May 29 12:14:44 2013 -0700 - - TPRparser: store bonds as list of tuples, not list of lists. - - - updated TPRparser so that it stores bonds, angles, dihedrals, impropers as lists of - tuples (consistent with the code changes for Issue 23 and how it is done in the PSFparser); - this is required to make the TPRparser work with the current development version - - added Developer Notes to the topology parser docs, outlining the current format for the - structure dictionary. - -commit ec362ecce249d59345fd4a18c1d8cf79cc76f11d -Author: Oliver Beckstein -Date: Wed May 29 12:14:22 2013 -0700 - - TPRparser: collected supported versions in tuple setting.SUPPORTED_VERSIONS and added docs - -commit a1d650d3e16fc21a2ce96d0160204ae39b73a990 -Merge: 7131d6e8f b90925b5e -Author: Oliver Beckstein -Date: Wed May 29 12:16:33 2013 -0700 - - Merge remote-tracking branch 'alfred532008/tprparser' into pyTPRparser - -commit b90925b5ef25b770414f002b19ebfe986209d44d -Author: Zhuyi Xue (Mac OS) -Date: Wed May 29 14:17:20 2013 -0400 - - fixed a typo in TPRParser.py: fer_err => fver_err - -commit 7131d6e8fe1b5493c8d56b710f79bc635ad724cf -Author: Oliver Beckstein -Date: Wed May 29 10:13:20 2013 -0700 - - Closes Issue 2: TPRParser for Gromacs 4.0 - 4.6.1 - - Consolidated the table of supported versions (version and generation in a single - table because at the moment they are in sync; maybe change later). - - Updated CHANGELOG. - -commit aff64aa87a6cdabe3fe2add2dba2a7555752c3f1 -Merge: ed3654e9b 4b859d043 -Author: Oliver Beckstein -Date: Wed May 29 09:59:23 2013 -0700 - - Merge remote-tracking branch 'alfred532008/tprparser' into pyTPRparser - -commit f671817a3a2f11219c28727ce444480f4dd35394 -Author: Jan Domanski -Date: Sun May 26 13:51:20 2013 -0400 - - Fixed Issue 144 PrimitivePDBWriter bug - - - AtomGroup rotate() method modified positions stored in - the AtomGroup object.universe.trajectory.ts._pos, - - AtomGroup write() method was using the coordinates copied - to instantiate the AtomGroup, stored in object.ts._pos, - - To correct that, in the write() method use - object.universe.trajectory.ts._pos, - -commit 4b859d0439d1c37149e9f4ddb2d5bc42fa79eec4 -Author: Zhuyi Xue (Mac OS) -Date: Sun May 26 13:24:45 2013 -0400 - - fixed testcases from 4.6 and 4.6.1 - -commit c070e4cc7ea646cdb7755938ee94e5c227a2e859 -Author: Zhuyi Xue (Mac OS) -Date: Sun May 26 13:13:47 2013 -0400 - - added ab42_gmx_4.6.tpr as a testcase - also updated corresponding info in - testsuite/MDAnalysisTests/datafiles.py - testsuite/MDAnalysisTests/test_tprparser.py - -commit cdd5a618ff56675753747793dea62f716d7a2e5a -Author: Zhuyi Xue (Mac OS) -Date: Sun May 26 13:13:19 2013 -0400 - - ignored lele* file in .gitignore - -commit 1fc95494a80ba38de51d1744fd411bf7badc0973 -Author: Zhuyi Xue (Mac OS) -Date: Sun May 26 13:11:13 2013 -0400 - - Increased speed more than twice - by separating namedtuple calls from tpr/utils.py into tpr/obj.py, especially - Atom in do_atom function. - -commit b53ac5fcc8466cf68b3f4cf65663b9c96d10cccb -Author: Zhuyi Xue (Mac OS) -Date: Sun May 26 12:51:37 2013 -0400 - - tprparser works now for gromacs-4.6 and gromacs-4.6.1 - 1. updated read_tpxheader functino since the tpx header format has changed - 2. updated variables in tpr/setting.py - 3. updated docstring in TPRParser.py - -commit 2606a4f55b73e6ebc52d35b97fbd0df99b4c42be -Author: Zhuyi Xue (Mac OS) -Date: Tue May 21 16:55:56 2013 -0400 - - added data/tprs/ab42_gmx_4.6.1.tpr; prepared the test - -commit 0f427d626d5f13d8b7fdc023433f44cba9036f74 -Author: Manuel Nuno Melo -Date: Mon May 13 03:37:47 2013 +0200 - - Fixed memory deallocation: under certain conditions the offset array could be freed more than once. - -commit ff55b4fd974f79f7456e9d43367bf3bccc4878cb -Author: Manuel Nuno Melo -Date: Sun May 12 03:15:38 2013 +0200 - - Implemented TrjReader functions save_offsets and load_offsets - -commit 887ccee74cabe4fccfef71816be70863154ffda4 -Author: Jan Domanski -Date: Sat May 11 17:26:03 2013 -0400 - - Closing fixes to Issue 23: guessing bonds - - - Moved vdwradii to topology.core and remove the factor of - 10 multiplication (converting to Angstroms) - - Use self_distance_array and appropriate indexing, rather than - computing a full distance-matrix - -commit 3c9ae52e59f647b9ea1908697dae0afcc5fba62c (tag: pre-sub-trr) -Merge: 2450fd554 373b1abb9 -Author: Oliver Beckstein -Date: Sat May 11 12:45:04 2013 -0700 - - closes Issue 23: bond information can be guessed for a PDB - - - use Universe(PDB, permissive=True, bonds=True) - - list of radii currently only contains hard-coded values for - C, F, H, N, O, S (in guess_bonds() --- from Gromacs) - - code might still be slow and could be optimized - -commit 373b1abb9cc53064f8b14dd698e3432ca8930508 -Author: Jan Domanski -Date: Sat May 11 10:15:14 2013 -0400 - - Extending the bond-guessing - - - PrimitivePDBParser can now tolerate TER records in PDBs, in the - context of bonds, - - The bonds can be written out to a PDB, either only the ones - originally defined in CONECT records, or all (including those - guessed internally in MDAnalysis) - -commit 2450fd5543ee1ee0e701a74814736e60d7c3f2bc -Author: Oliver Beckstein -Date: Fri May 3 15:00:11 2013 -0700 - - updated CHANGELOG with Danny Parton's fixes - -commit 6f9cdc4607540d07365281972cc2653cf9ef4de3 -Author: Oliver Beckstein -Date: Thu May 2 10:01:07 2013 -0700 - - removed MDAnalysis.util (was not used) - -commit 4800dcf97c0e84dc875ee00e2ced0d283ab6976f -Author: Oliver Beckstein -Date: Thu May 2 12:25:24 2013 -0700 - - simple convert_float() function and math docs added to util.py - -commit dd2ea3b0fe34484c744c24c2121adebae17ba93b -Author: Oliver Beckstein -Date: Thu May 2 10:00:36 2013 -0700 - - moved util.LAMPPSParser to topology - - - native parser() not written yet - - LAMMPSData can be used to extract PSF and PDB - - This code worked for older (2007) LAMMPS data files but has not been maintained - since. - - TODO - - add parser() so that LAMMPS data files can be used as a topology (and structure - file) - - check if it works with current data file format - -commit c8b6ef66870f0e735ba4a6ab027216f55d97ca6f -Merge: d4797b2de 9fbf128d6 -Author: Oliver Beckstein -Date: Thu May 2 11:59:45 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 6111be98e1dde697373cb20d758fa5e13331c229 -Author: Manuel Nuno Melo -Date: Sat Apr 27 03:06:03 2013 +0200 - - Fixes error introduced by a different return tuple by libxdrfile.read_trr - -commit 2cb77bc33c3cbdf043f3c08451a8b75bc833f9a6 -Merge: 3fba12a9a 9fbf128d6 -Author: Oliver Beckstein -Date: Thu Apr 25 21:55:32 2013 -0700 - - Merge branch 'develop' into feature-xtcindex - -commit 9fbf128d6f82dc3f658d36be1d13e7aba47c37f2 -Author: Oliver Beckstein -Date: Thu Apr 25 18:37:49 2013 -0700 - - immediately close fd from tempfile.mkstemp() - - All instances in the main code base of tempfile.mkstemp() were checked in - because we only create an empty file to be overwritten by other code we - can immediately close the file instead of wasting open file descriptors. - -commit 6a51af3434bee35632745db2ca3c4dfca100321e -Author: Oliver Beckstein -Date: Thu Apr 25 18:33:44 2013 -0700 - - test cases: close fd for any tempfile.mkstemp - - Tempfiles are only created to be overwritten; hence we can immediately - close the file descriptors. - -commit d524b7e47e5b90abb22eb3a1954ba6003fb52eda -Author: Oliver Beckstein -Date: Thu Apr 25 18:20:56 2013 -0700 - - Issue 129: improved fix - - - close file right after it has been opened: we only need an empty file - to overwrite - - shortened the time for the test to fail to 2s and to pass to 10s by - internally manipulating the resource limit for open files - (see http://docs.python.org/2/library/resource.html) - -commit 3fba12a9a727e28817a04df731a5ed2f8f1618fc -Merge: 4153b52a3 9fc92b290 -Author: Oliver Beckstein -Date: Thu Apr 25 16:57:11 2013 -0700 - - merged develop into feature branch - -commit 4153b52a344a5506bd15574764a4bb9b94223334 -Merge: c3ec76257 de4474895 -Author: Oliver Beckstein -Date: Thu Apr 25 16:55:00 2013 -0700 - - merged Manel's updates - -commit 9fc92b29035cccf96b20243a48e5644fb2d143b9 -Merge: 59560c2ed 3198250f7 -Author: Tyler Reddy -Date: Thu Apr 25 17:03:00 2013 +0100 - - Resolving CHANGELOG conflict. - -commit 59560c2ed969699bb8aa307cf1d684a5c6096757 -Author: Tyler Reddy -Date: Thu Apr 25 16:48:27 2013 +0100 - - Resolved issue 129 with unit test included. hole.py analysis module was missing os.close() call on temporary PDB file descriptors. - -commit de447489597ee5738331e56cadffb146fcc8c17e -Author: Manuel Nuno Melo -Date: Thu Apr 25 05:39:49 2013 +0200 - - Now complies with all libxdr-related unit tests. - - Implemented the same indexing procedure for TRR trajectories. - - Instead of copying, indices are now passed as a pointer to a - PyArray_SimpleNewFromData, with care to implement a memory deallocator. - - Reverse iteration for XTC/TRR is working, so that test has been enabled. - - Fixed an unreported bug with TRR parsing where coordinates/velocities/forces - get wrongly scaled if they're not present every frame. - -commit d4797b2dee808fec008a57ccbb5145d0c694cdf7 -Merge: 420f0352a 3198250f7 -Author: Oliver Beckstein -Date: Wed Apr 24 14:33:52 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit c3ec762574b5309f80c4d5994d30b14b6d8e6bef -Author: Oliver Beckstein -Date: Wed Apr 24 10:44:55 2013 -0700 - - updated CHANGELOG with xtc index enhacement and added Manuel Nuno Melo to author lists - -commit 1440a833207c2bededbea6fd1d81c33d4c41a755 -Merge: 3198250f7 c5f5f9acf -Author: Oliver Beckstein -Date: Wed Apr 24 10:35:53 2013 -0700 - - Merge remote-tracking branch 'manuelxtc/master' into feature-xtcindex - -commit 3198250f79f65965ee10252fd5a205ec543b9578 -Author: Xavier Deupi -Date: Wed Apr 24 09:50:46 2013 -0700 - - Fixes Issue 133: helanal: additional output of local bend and unit twist angles - - - changes in helanal.py (took code from Issue 133) - - added Xavier Deupi to all author lists - -commit 4ba9dbdeb75dc5aa12d23f7cca7ced40e6519815 -Author: Oliver Beckstein -Date: Wed Apr 24 09:38:54 2013 -0700 - - sphinx: added intersphinx links and more extensions - - - intersphinx links for matplotlib and networkx - - mathjax extension so that we can use beuatifully typeset maths - - viewcode extension to directly show source code - -commit c5f5f9acf665647372593ceef6cf09a526552af2 -Author: Manuel Nuno Melo -Date: Wed Apr 24 14:31:37 2013 +0200 - - Cleaned debug prints - -commit ac5422b8add4043deb85b2d0bf6b0bfcb8a4187d -Author: Manuel Nuno Melo -Date: Wed Apr 24 14:01:43 2013 +0200 - - Adds XTC seeking/indexing capabilities - -commit 956422ddf8dde9ba60344d1923f43874f5f512c5 -Author: Elizabeth Denning -Date: Fri Apr 19 17:34:58 2013 -0700 - - updated nuclicinfo for selection-specific functions and Selections to remove NucleicXtal - -commit 44b88ee41a0727f51c26082d063dfcdd95dbb31b -Author: Zhuyi Xue (Mac OS) -Date: Wed Apr 17 20:35:27 2013 -0400 - - trim comments in TPRParser.py - -commit 85fe3f47fee9b665c82444515c82318f9ed1d8bc -Author: Zhuyi Xue (Mac OS) -Date: Wed Apr 17 20:29:33 2013 -0400 - - removed redundant lines in tpr/utils.py - - - removed class definition of NotImplementedError since it's built-in - - remove "from MDAnalysis.topology.core import guess_atom_type" since it's not used in utils.py - -commit ed3654e9b447586352826f6b982da6fc84d8da48 -Author: Oliver Beckstein -Date: Tue Apr 16 22:26:45 2013 -0700 - - added Zhuyi Xue to the authors in the reST docs - -commit cdbcd138e0f2abc47f8721bb32c57ff4869617b9 -Author: Oliver Beckstein -Date: Tue Apr 16 21:10:59 2013 -0700 - - TPRReader: fixed failure if angles could not be found - -commit 4ec3120c4b6269ec35160e5cbaed46aeb8653778 -Author: Oliver Beckstein -Date: Tue Apr 16 21:03:31 2013 -0700 - - rebuilt docs (added TPRParser) - -commit 2e40ab1e431c3ac06029a6d96b40b31acafbb00c -Author: Oliver Beckstein -Date: Tue Apr 16 20:39:12 2013 -0700 - - TPRparser reorganization and integration - - - made the tpr_*.py helper modules a separate sub-module - topology.tpr (adjusted all imports) - - raise ValueError if the header cannot be parsed - - use logging instead of print - - range -> xrange - - added documentation (inside TPRParser and in the - reST docs); updated the table of supported - topology formats - - added standard copyright header comment block (with - explicit authorship/copyright of Zhuyi Xue) - -commit b1bf7aa7760343336409effcdf47ece3aa342dce -Merge: fac7796b0 43d0db12f -Author: Oliver Beckstein -Date: Thu Apr 11 18:58:30 2013 -0700 - - merged developed into pyTPRparser feature branch - -commit 43d0db12f95830f85e6cbe84ff0dbeea6fe5f59b -Author: Daniel L. Parton -Date: Thu Apr 11 18:43:14 2013 -0400 - - Fixed array comparison bug in helanal - -commit 4ae13ac2d28bd6e49c7ce764014bf621ef5615f1 -Author: Oliver Beckstein -Date: Tue Apr 9 22:48:40 2013 -0700 - - ChainReader: can fake a time with delta keyword - - If the keyword delta is supplied, the ChainReader will return the number - of current frames times delta in the attribute time. This is a hack and - we should really implement a proper calculation of the time from the - individual trajectories but this workaround allows using the ChainReader - in some cases where getting some/any time information is needed. - -commit 46f29f98da528022f7d32105263a6fbfd5059529 -Author: Oliver Beckstein -Date: Tue Apr 9 22:37:30 2013 -0700 - - HOLE analysis: cpoint keyword can now select HOLE's own algorithm - - If set to ``True`` then *cpoint* is guessed as the - :meth:`~MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry` of - the *selection* from the first frame of the trajectory. - - If *cpoint* is not set or set to ``None`` then HOLE guesses it - with its own algorithm (for each individual frame). [``None``] - -commit fd434698bc619a27a789921624578cf72a3cae84 -Author: Oliver Beckstein -Date: Tue Apr 9 22:35:32 2013 -0700 - - updated links in SUMMARY.txt (PyPi) - - The PyPi summary had severely outdated links to the old docs on SVN: - Changed to point to the docs in the master branch. (Maybe that will - help to purge hits to the SVN docs on google...) - -commit 420f0352aa4dfe423e0061fb2eb99818abc454ed -Merge: 402a9a8bc de88e958c -Author: Oliver Beckstein -Date: Tue Feb 26 14:59:49 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 402a9a8bca46757fd6357aa0d5849495b49a598b -Author: Oliver Beckstein -Date: Tue Feb 26 14:59:36 2013 -0700 - - HOLE analysis: added min_radius() method and made y-label of 3D plot configurable - -commit de88e958c44b61255be1da6b82dfaebb4b74da2d -Author: Daniel L. Parton -Date: Sun Feb 24 17:57:38 2013 -0500 - - Fixed bug in rms.py - - - rms.RMSD.run gave incorrect results if ref_frame != 0 - -commit aa87e2b6c692c03c6994ef1ab64b7aa1d287be5b -Author: Daniel L. Parton -Date: Sun Feb 24 00:16:17 2013 -0500 - - PrimitivePDBReader - fixed bug related to 1-based frame indexing, which had broken multi-model PDB parsing - -commit 0a621945a248bacfab224b5fc6a8b71e543fc70e -Author: Jan Domanski -Date: Tue Feb 19 20:47:52 2013 -0500 - - DMSReader - fixed a 'dictionary' typo, replaced with 'dict' - -commit a5d674e6788c62a168bf14330d7086daea35a652 -Author: Oliver Beckstein -Date: Thu Feb 7 18:04:05 2013 -0700 - - regenerated docs (fixed Issue 127, DMS parser, TRR parser sub argument) - -commit c2f5b25774c03ebc001674a09ca3021408867ca4 -Author: Oliver Beckstein -Date: Thu Feb 7 17:14:32 2013 -0700 - - added boilerplate docs for DMS coordinate and topology reader - -commit 9d0585fc1d8d992f52d0d2850b9735b0e9235daa -Merge: 577bb55f5 2bf6e69c6 -Author: Oliver Beckstein -Date: Thu Feb 7 17:01:49 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 577bb55f580bc41d77a8115a288def2198d8ea7a -Author: Jan Domanski -Date: Sat Feb 2 22:48:04 2013 -0500 - - DMSReader for topology and coordinates - - - added CHANGELOG and __init__.py trivia, - - python 2.5 compatibility - -commit 83d837106a17d6a869aff3428e9de42c781225bc -Author: andy.somogyi -Date: Fri Feb 1 12:07:39 2013 -0500 - - merge feature-trr-sub branch, adds 'sub' arg to TRRReader - -commit 8433d134993508125edb9900fdb80fc5c9731385 -Author: Oliver Beckstein -Date: Thu Feb 7 16:36:37 2013 -0700 - - fixed Issue 126: corrected links to examples - - - Links point to the browsable source in the git master branch - - added a few more internal links to modules and corrected one link - - also removed spurious doc for class Timeseries.PrincipalAxis - (which had been removed previously) - -commit 612c547144f28731bfeb8d9a1473746f1f6ff823 -Author: Jan Domanski -Date: Sun Jan 20 21:29:24 2013 -0500 - - DMSReader for topology and coordinates - - - only read support, via sqlite3, - - reads coordinates, velocities and bonds only, - - added sanity tests (number of atoms and bonds), - - added atomselection tests (name, resname, segid). - -commit 2bf6e69c624911e638f734934b6264d2a9133b9f -Author: Jan Domanski -Date: Sat Feb 2 22:48:04 2013 -0500 - - DMSReader for topology and coordinates - - - added CHANGELOG and __init__.py trivia, - - python 2.5 compatibility - -commit 477236ba11a888c479af5704608d1049e9e7f725 -Author: andy.somogyi -Date: Fri Feb 1 12:07:39 2013 -0500 - - merge feature-trr-sub branch, adds 'sub' arg to TRRReader - -commit 431582a69ad0bf8ebcc46cdf9fbd266d0fb6c90b -Merge: 65b4af27b bebea4a81 -Author: Oliver Beckstein -Date: Tue Jan 29 18:51:58 2013 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 65b4af27bed7980c3223be6b58a13169fc541cb0 -Author: Oliver Beckstein -Date: Tue Jan 29 14:24:28 2013 -0700 - - removed non-functional Timeseries.PrincipleAxis - - Also improved the reST docs in Timeseries with links and - updated some of the usage information. - -commit 38136b444b1c40a601ddd8e06a097a6089a94ec2 -Author: Oliver Beckstein -Date: Tue Jan 29 14:17:29 2013 -0700 - - improved documentation for WaterDipole time series - - - see https://groups.google.com/d/topic/mdnalysis-discussion/gGf1Sa0Lwmc/discussion - - no code changes, only indentation and documentation - -commit 3ff668d05dda4388291f5df0328ed5ce8f2f4df7 -Author: Oliver Beckstein -Date: Sun Jan 20 20:36:30 2013 -0700 - - MDAnalysis.analysis.density: updated docs - - - The bin size delta is fixed (and is NOT adjusted), see core.util.fixedwidth_bins - - minor adjustments in the docs - -commit bebea4a817b18ea7004703d50ee13559f737d57b -Author: Jan Domanski -Date: Sun Jan 20 21:29:24 2013 -0500 - - DMSReader for topology and coordinates - - - only read support, via sqlite3, - - reads coordinates, velocities and bonds only, - - added sanity tests (number of atoms and bonds), - - added atomselection tests (name, resname, segid). - -commit a88b91f4947c0091cb01b6a2955d92ba95933a4d -Author: Oliver Beckstein -Date: Fri Jan 18 18:50:38 2013 -0700 - - dihedral calculation as separate function - - - removed dihedral_orig() and made dihedral_numpy() --> dihedral() - (as we should have done for 0.7.3 or whatever the comments said...) - - actual calculation of a dihedral angle was moved into - util.dihedral() and a simple test case added - - advantage: less clutter in Atomgroup module and we can have a - specific unit test - -commit fac7796b04952655b448d24a37b6ccc8f63fc27a -Merge: f14fbb2e3 826fa8a96 -Author: Oliver Beckstein -Date: Fri Jan 11 10:03:54 2013 -0700 - - Merge remote-tracking branch 'alfred532008/tprparser' into pyTPRparser - - Pull request from Zhuyi on 2013-01-11: - - I just fixed a bug found by one of my colleagues in the tpr_utils.py. - shown in https://code.google.com/r/alfred532008-mdanalysis-tprreader/source/list?name=tprparser - -commit 826fa8a9638197f0275f299a38b9c9be22ea4367 -Author: Zhuyi Xue (Mac OS) -Date: Fri Jan 11 11:51:06 2013 -0500 - - fixed a bug in tpr_utils.py: data.unpack => data.unpack_float - -commit f14fbb2e3b011e29c9827a62c6eff49d5f8bb2df -Merge: 881b9133d a8bbf7caf -Author: Oliver Beckstein -Date: Wed Jan 2 20:48:55 2013 -0700 - - updated CHANGELOG - - moved experimental pyTPRparser into the 0.8 section - -commit a8bbf7caf094b0932825b00bcbf016b6981a50e1 -Author: Sébastien Buchoux -Date: Wed Jan 2 11:01:28 2013 +0100 - - version number changed to 0.7.8-dev - -commit 881b9133dbb7604e26602c09959fe2492432fcb6 -Merge: d177a8dd9 004bcbcb1 -Author: Oliver Beckstein -Date: Mon Dec 31 17:48:21 2012 -0700 - - Merge branch 'develop' into pyTPRparser - - Brought pyTPRparser branch in sync with the 0.7.7 release. - -commit faf262f3bf0b9e862dbffd1a4aac04ac032f764e (upstream/release-0.7.7) -Author: Sébastien Buchoux -Date: Mon Dec 24 20:21:03 2012 +0100 - - Version number change to '0.7.7' - Documentation regenerated - sebastien.buchoux added to contributors in CHANGELOG - -commit ad076bbb9639083648c736df203ef3076320a880 -Author: Sébastien Buchoux -Date: Thu Dec 20 18:53:20 2012 +0100 - - Version number bumped to 0.7.7-rc1 - -commit 004bcbcb17fe73b0d4b5d5643f79e70b148a302f -Author: Sébastien Buchoux -Date: Thu Dec 20 22:00:09 2012 +0100 - - Updated MANIFEST.in to include scripts/ - -commit dcd3dbc2d7907ab04c3dd125b63a600d81281611 -Author: Sébastien Buchoux -Date: Thu Dec 20 16:50:06 2012 +0100 - - Fixed run_tests script - -commit 05a9d47874edba2de428764e33d779403f4eed91 -Merge: 6d5f1afed cdaeb609a -Author: Sébastien Buchoux -Date: Thu Dec 20 16:47:07 2012 +0100 - - Merge branch 'code-cleaning' into develop - -commit cdaeb609a04d17bab278109380866cb066db0544 -Author: Sébastien Buchoux -Date: Thu Dec 20 14:10:06 2012 +0100 - - A few errors in code corrected - -commit d177a8dd9d7f4a2f99334b360719066d07f84d2a -Merge: 5a0d89c87 6d5f1afed -Author: Oliver Beckstein -Date: Wed Dec 19 09:58:33 2012 -0700 - - merged develop into pyTPRparser - - (note that the bondlist code was removed) - -commit 5a0d89c8755993bddd0dbf3429f2b0e6d819663b -Author: Oliver Beckstein -Date: Mon Dec 10 21:46:52 2012 -0700 - - Revert "Issue 23: generate bond list when using a PDB instead of a PSF" - - Removed the bondlist feature from the pyTPRparser branch so that it is easier to merge with develop. - Once the bondlist gets fully implemented we can easily merge develop again. - -commit 6d5f1afed9a9858a819e84ecd2bbf6d52e7d5d20 -Author: Sébastien Buchoux -Date: Wed Dec 19 11:27:31 2012 +0100 - - Empty commit to save state before psfgen addition - -commit dd3345ea7768c62ef1b59e7387e8ddb6fd31c48b -Author: Oliver Beckstein -Date: Tue Dec 18 13:39:36 2012 -0700 - - updated authors/copyright in README - -commit 50e6f5a36595bbfe05f09804cd5d9dea9dd0fee7 -Author: Oliver Beckstein -Date: Tue Dec 18 12:39:13 2012 -0700 - - fixes Issue 122 by making netCDF4 an optional dependency - - netcdf4 python requires both HDF5 and netcdf, which can be difficult - to compile. MDAnalysis only needs netcdf for the AMBER ncdf Reader/Writer - so we make this dependency optional and later raise a error if the user - tries to read/write a ncdf trajectory. This approach makes MDAnalysis - compile out of the box on most machines but imposes a post-installation - burden on AMBER users. - - - netCDF4 can be automatically installed with - - cd MDAnalysis-0.7.7 - easy_install --user . MDAnalysis[AMBER] - - (i.e. netCDF4 has become a extra_requires package, tagged with 'AMBER') - - the AMBER ncdf reader/writer will raise an ImportError with links to the wiki page - https://code.google.com/p/mdanalysis/wiki/netcdf to help people install the required - packages. MDAnalysis.core.TRJ will also log a message at level DEBUG whenever it is - loaded. - - TODO: make setup.py accept options to make netCDF4 a hard requirement so that one - does not need to invoke easy_install. - - updated CHANGELOG - -commit 431d037df1801027b1495b3eb839801f786d7e31 -Author: Oliver Beckstein -Date: Fri Dec 14 17:08:02 2012 -0700 - - logger reports MDAnalysis version when starting - -commit 050d4ab0f1583658b1a272bb018ae09434811401 -Merge: 09458b2ab 76e776b98 -Author: Oliver Beckstein -Date: Fri Dec 14 10:49:06 2012 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 09458b2abae1d5418d9585368a40f32105e1929b -Merge: 8d8a89a1e f07e1d3b1 -Author: Oliver Beckstein -Date: Fri Dec 14 10:48:46 2012 -0700 - - Merge branch 'xdrfile_update' into develop - -commit f07e1d3b176ab73fbb5f2ccae462c79a2b05d902 -Author: Oliver Beckstein -Date: Fri Dec 14 10:26:03 2012 -0700 - - libxdrfile: updated to 1.1.1 - - Selectively applied patches from git://git.gromacs.org/libxdrfile.git - that improve compilation with C++. This should not change functionality. - - Updated docs (and regenerated swig wrapper). - -commit 54ed4b38b20351fd3c51c93854d334fb8aa70d03 -Author: David van der Spoel -Date: Fri Oct 8 13:55:34 2010 +0200 - - Fixed bug 582 for compilation with C++ and additional fixes for compilation with c++. - - Merged selected patches from git://git.gromacs.org/libxdrfile.git - - Added fixes for compilation with c++. - 93678df8253f938b1dff811e938a9ce5eef665c3 - - Fixed bug 582 for compilation with C++. - 887ed8f3a801a36f9b8717aff0abf29c80394330 - -commit 8d8a89a1ea7aa4601b03968d895a51b8763eeb90 -Author: Oliver Beckstein -Date: Fri Dec 14 10:12:02 2012 -0700 - - LeafletFinder: use asUniverse() - -commit 4104e5a64ffcf32a07a2dbbb829573a4e7f15e64 -Author: Oliver Beckstein -Date: Fri Dec 14 10:11:27 2012 -0700 - - updated sphinx conf - -commit 76e776b98c6a4df1937aec3bd4900447f1c26c14 -Author: Oliver Beckstein -Date: Thu Dec 13 09:35:31 2012 -0700 - - fixed force conversion (from commit ca3a3f62347e6b154ca167211a92b0db533b6d2b) - - The conversion from kJ/(mol*A) to kJ/(mol*nm) requires multiplication by 10, not division. D'oh. - -commit 1c85077ff7cff75cb7e07b888b446c185574b2f3 -Author: Oliver Beckstein -Date: Wed Dec 12 19:16:00 2012 -0700 - - fixed Issue 121: PSFParser raised IndexError for missing SEGID - - - added hack so that an empty SEGID is set to SYSTEM - - note that there is currently no way that we can detect if a NAMD/VMD format - PSF file (which is space separated) is missing a SEGID - -commit fdb8acdb6ff7f4bcbf03c5acef7ea48fc91e41bd -Author: Oliver Beckstein -Date: Mon Dec 10 21:46:52 2012 -0700 - - Revert "Issue 23: generate bond list when using a PDB instead of a PSF" - - The patch is not fully tested and might break the PDB writer - code. I'm removing it from the develop branch but maintain it - in the bondlist branch. - - This reverts commit ef59286a296e7d933281bfdad044fe108b8eb0d9. - -commit dd1624a6ae997bd1cc5d0794c0342a0f95c5e0cb -Author: Oliver Beckstein -Date: Mon Dec 10 21:39:10 2012 -0700 - - updated CHANGELOG - -commit ca3a3f62347e6b154ca167211a92b0db533b6d2b -Author: Oliver Beckstein -Date: Mon Dec 10 15:16:31 2012 -0700 - - forces: unit conversion and test case - - - added entries for 'force' to the units conversion machinery - - added from/to native conversion for forces to the TRRReader and Writer - - added test case: short TRR for cobrotoxin in water (OPLS-AA); the TRR - contains positions, velocities, and forces - - renamed test_velocities.py -> test_velocities_forces.py - -commit 3cdab9a5b33fc6cec022aae58376f30317aa691b -Author: andy.somogyi -Date: Thu Dec 6 16:07:10 2012 -0500 - - added elements to mass table - -commit cd19ce0b72ec7b931a4cbbace4770f467b0d5e34 -Author: andy.somogyi -Date: Thu Aug 16 14:34:52 2012 -0400 - - added force methods / properties to AtomGroup - -commit 1294a3f45c800d3aa65e139c8455b39a4c084dfb -Author: Oliver Beckstein -Date: Mon Dec 3 14:29:04 2012 -0700 - - reST update: changed 'versionadded:: 0.8' to 0.7.7 - - The next release will be 0.7.7 and not 0.8 so I adjusted the reST - doc strings accordingly: - - git grep -l '\.\. versionadded:: 0\.8' | xargs -I FILE sed -i~ '/\.\. versionadded:: 0\.8/s/0\.8/0.7.7/' FILE - -commit b1596bc3678f94cfccb7db3041b8b1b59d0745b3 -Merge: 396662696 94db576e1 -Author: Oliver Beckstein -Date: Mon Dec 3 13:48:09 2012 -0700 - - Merge branch 'develop' into pyTPRparser - -commit 396662696e51e5322bb977fb048e0c007df2acea -Merge: ed7ccab5c 6b788feeb -Author: Oliver Beckstein -Date: Mon Dec 3 13:45:35 2012 -0700 - - Merge remote-tracking branch 'alfred532008/tprparser' into pyTPRparser - -commit 94db576e19b574cdc30b99cedc2d4e32fcda3b4e -Merge: ffa309f40 ef59286a2 -Author: Oliver Beckstein -Date: Mon Dec 3 13:44:30 2012 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 6b788feeb8366d8e0bef4fa22b8603d1e2a873d8 -Author: Zhuyi Xue (Mac OS) -Date: Sun Dec 2 09:43:34 2012 -0500 - - added comments in test_tprparser.py to make it easier to understand - - improved comments in TPRParser.py and tpr_utils.py. - -commit 8ff69a194b6462dc4724134c492a9030d9b74cc0 -Author: Zhuyi Xue (Mac OS) -Date: Fri Nov 30 23:55:01 2012 -0500 - - sparated tpr testing from test_topology.py to test_tprparser.py - -commit 87db7c4eb951f74ccc1f2dc4f045ff4adfd9d852 -Author: Zhuyi Xue (Mac OS) -Date: Fri Nov 30 16:05:46 2012 -0500 - - removed gmxv73.tpr; added different version of tpr files; added test for v73 - and v58, both works. - -commit 4cb40cf3cea953b7f7c43dc2b28a520567df6546 -Author: Zhuyi Xue (Mac OS) -Date: Fri Nov 30 16:05:27 2012 -0500 - - added print_header function in TPRParser.py to print out tpr header info when - parsing. - - This is handy to take a look at the gromacs version, tpx version and tpx - generation. - -commit b753342642b1dff158dac047a5a341382b2ce1e5 -Author: Zhuyi Xue (Mac OS) -Date: Fri Nov 30 15:44:20 2012 -0500 - - TPRParser.py is working for tpr version 73 - -commit f443cc8044fc09806f0969ebb4d06b60aa23822f -Author: Zhuyi Xue (Mac OS) -Date: Sun Nov 25 22:51:31 2012 -0500 - - moved most functions in TPRParser.py to tpr_utils.py to make the parsing work - flow more obvious. - -commit ef59286a296e7d933281bfdad044fe108b8eb0d9 -Author: Jan Domanski -Date: Sat Dec 1 18:02:28 2012 -0500 - - Issue 23: generate bond list when using a PDB instead of a PSF - - - bonds are guessed basing on distances between atom pairs, - - VdW radii of atoms are taken from GROMACS vdwradii.dat file, - - fudge factor is changed from 0.6 (VMD) to 0.7 to make it all - work (VMD likely has a slightly different VdW radii table), - - added a basic sanity check based on the pdb/psf pair available - in the test suite. - -commit 60da00bff6baae9fa45d85f7414924cb83f4864f -Author: Zhuyi Xue (Mac OS) -Date: Sun Nov 25 22:50:41 2012 -0500 - - added gmxv73.tpr - -commit ffa309f4015f1f1454eff51ef1469f0b0c4b6129 -Author: Oliver Beckstein -Date: Thu Nov 22 09:38:05 2012 -0700 - - added comments to examples/potential_profile.py - -commit 31df9717b9df01a0339438aef6077a58732add66 -Author: Oliver Beckstein -Date: Mon Nov 19 11:29:27 2012 -0700 - - CHANGELOG: heading for 0.7.7, added link to Issue 120 - -commit ed7ccab5c420e8421c8565a82ad7a3c7b8f5980f -Author: Oliver Beckstein -Date: Mon Nov 19 11:10:29 2012 -0700 - - added Zhuyi Xue to CHANGELOG and AUTHORS - -commit e9af2c46765cdbd11525eaef5c8aba4fb54479dd -Author: Zhuyi Xue (Mac OS) -Date: Sun Nov 18 22:43:10 2012 -0500 - - added testcase: TestTPRv58 in test_topology.py - -commit e3f59628aa565cef855a91a93b7c51f60699312a -Author: Zhuyi Xue (Mac OS) -Date: Sun Nov 18 21:49:03 2012 -0500 - - added 'TPRParser' to __all__ in MDAnalysis/topology/__init__.py - -commit 9f05abec38e9aefa119bb904337cc119b5c7a910 -Author: Zhuyi Xue (Mac OS) -Date: Thu Nov 15 19:36:31 2012 -0500 - - imporoved segment naming to make it more general - -commit f591d5942fb99c8e5f6107f522fc261a4b139820 -Author: Zhuyi Xue (Mac OS) -Date: Thu Nov 15 18:29:57 2012 -0500 - - added TPR support to MDAnalysis/topology/__init__.py - -commit a8c920be0cd98f360e926ac40ddbb163de70f8f6 -Author: Zhuyi Xue (Mac OS) -Date: Thu Nov 15 18:28:56 2012 -0500 - - written TPRParser.py for tpx version 58 - -commit 06cd49d5192de25e9c9431b11c95c44cc8fabb70 -Author: Oliver Beckstein -Date: Thu Nov 1 18:30:15 2012 -0700 - - regenerated online docs - -commit a1cff5a64dd7df22e5e3303c2d06263051791d91 -Author: Oliver Beckstein -Date: Thu Nov 1 18:29:53 2012 -0700 - - doc fixes (Dima2004 reference) - -commit 553b355d48a8794cb31facbfcced2578f0a3adaf -Author: Oliver Beckstein -Date: Thu Nov 1 17:25:45 2012 -0700 - - parallel distance array - - - updated docs (can use orthorhombic box) - - checked test cases - - rebuilt c file with cython - -commit 7cced8939e806de7ed29728c594473756dd2b6d7 -Author: Oliver Beckstein -Date: Fri Oct 19 16:13:36 2012 -0700 - - fixed: helanal analysis was missing import statement - - (Thanks to David Dotson.) - -commit 1433d0ac4a1588123040ed4aa31be3e42056b0d4 -Author: Oliver Beckstein -Date: Mon Oct 15 15:20:01 2012 -0700 - - added test case for DCDWriter unitcell fix (and updated CHANGELOG) - -commit 07a1f30b52c4838eaa1abf71cb6ffebfc08c8a09 -Author: Naveen Michaud-Agrawal -Date: Mon Oct 15 15:02:48 2012 -0700 - - fixes DCD writer: wrote wrong unitcell - - See https://groups.google.com/d/topic/mdnalysis-discussion/67O3YogdWLo/discussion - -commit 6f593c09ce3d486d3584c0f2daeb5f13ebafe22f -Author: Elizabeth Denning -Date: Fri Sep 21 11:33:42 2012 -0700 - - updated nucleic acid selection definitions - -commit 4a0b2e5f7fc0517c03dc8832cc92e9a7ba430498 -Author: Oliver Beckstein -Date: Mon Sep 3 11:54:20 2012 -0700 - - fixes Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup) - - - AMBER Timestep class had a wrong check on input coordinate/velocity arrays - (would work with velocities but not without) - - added test case - -commit e15fb06e844ca9a1093e13c09d8611c5d6620a46 -Author: Oliver Beckstein -Date: Mon Sep 3 10:54:42 2012 -0700 - - fixes Issue 117 - - - added explicit casts to step, time, and lambda before handing over to - the swiged XDR library - - added test cases - - updated CHANGELOG - -commit 63d571ca27533764c8d2c84fb1fa62ffa510c69b -Author: Oliver Beckstein -Date: Wed Aug 29 18:42:25 2012 -0700 - - asphericity() and shapeParameter() additions - - - added simple test cases (need to be checked for correctness) - - replaced range --> xrange - - added citation to doc string - - added entry to CHANGELOG - - added Joshua Phillips to contributors in AUTHORS and the docs - -commit e792b024158e13855cc62970ae0c54f29f9d7f18 -Author: Joshua L. Phillips -Date: Wed Aug 29 11:49:06 2012 -0600 - - Added shapeParameter and asphericity calculations to AtomGroup.py. - - Citation: - Dima, R. I., & Thirumalai, D. (2004). Asymmetry in the shapes of - folded and denatured states of proteins. The Journal of Physical - Chemistry B, 108(21), 6564-6570. doi:10.1021/jp037128y - -commit 06f592c099eb7cd7104059eba685b43354ea2315 -Author: Jan Domanski -Date: Mon Aug 6 21:37:22 2012 -0400 - - Issue 80: Parallel distance matrix computation using Cython (closing) - - - cython parallel distances now has the same signature as - core.distances.distance_array, - - complete tests with random inputs (including box and a defined - result array), for serial and parallel cython codes. - -commit 642a6cebdad2efea1f5166de22f9c92f7817d4d5 -Author: Oliver Beckstein -Date: Sat Aug 4 11:51:45 2012 -0700 - - Nuclinfo test fixes - - - decreased precision from 7 to 4 for torsion test (failed otherwise) - - renamed TestNucl --> TestNuclinfo - -commit e11b6d2d887c1b975c82d62017cf2a8f1a2b868f -Merge: 700421475 d326bca81 -Author: Oliver Beckstein -Date: Sat Aug 4 10:48:25 2012 -0700 - - Issue 76: integrated jjlights03's patch - - - Merge remote-tracking branch 'jinju/develop' into develop - - integrated test case into test_coordinates - - added entries to AUTHORS and CHANGELOG (and sphinx) - -commit d326bca814bd842022e0a8dd79ce270b0894eab8 -Merge: 57887a701 b91013f7b -Author: Jinju Lu -Date: Fri Jul 20 23:05:52 2012 -0700 - - Merge branch 'Issue/76' into develop - -commit b91013f7b740eb1f1fae7c5b17fb10220523b6a8 -Author: Jinju Lu -Date: Fri Jul 20 23:02:06 2012 -0700 - - Issue 76: chainreader format - -commit 700421475140f74f8adf684615f022319f73a692 -Author: Oliver Beckstein -Date: Thu Jul 19 10:37:00 2012 -0700 - - regenerated online docs - -commit e469b9b3cf4e6c5c675b6aa62b27547263f16e50 -Author: Oliver Beckstein -Date: Thu Jul 19 09:36:43 2012 -0700 - - reST docs: better referencing of QCP in rms and align - -commit 57887a70156cfccd33694f7eff68048c1a836ec7 -Merge: f060ed300 3e46aa08b -Author: Oliver Beckstein -Date: Wed Jul 18 17:43:23 2012 -0700 - - Merge branch 'Lukas/HOLE' into develop - - MDAnalysis.analysis.hole: classes to run HOLE on single PDBs - or trajectories (any Universe). Requires a local copy of the - HOLE2 (v2.2) software, which used to be available from - http://hole.biop.ox.ac.uk/hole but is un-available at the moment. - -commit 3e46aa08b241426bbe86d1fcb2ef476bbf11de03 -Author: Oliver Beckstein -Date: Wed Jul 18 17:42:32 2012 -0700 - - regenerated html docs (HOLE, RMS, parallel added) - -commit aac158fbc8dceeb5031a8befa1b7463c67c0a8d2 -Author: Oliver Beckstein -Date: Wed Jul 18 17:39:01 2012 -0700 - - docs for HOLE, RMS, parallel - -commit 94553068e318dfa57791c81ab5a58e52210d4eef -Merge: 61c831644 f060ed300 -Author: Oliver Beckstein -Date: Tue Jul 17 16:14:22 2012 -0700 - - Merge branch 'develop' into Lukas/HOLE - -commit f060ed3003b1af34c4fb3a2f47793972074314c0 -Author: Oliver Beckstein -Date: Tue Jul 17 14:13:54 2012 -0700 - - parallel distance_array (Issue 80) in core.parallel.distances - - - moved analysis.cython.distances to core.parallel.distances: - core.parallel can become a module for parallel versions of algorithms; - eventually we can add flags to core.flags so that the user can determine - if parallel versions should be used. - - fixed the check for cython 0.16 in setup.py - - moved the test cases to new test_parallel.py - - added some docs and updated CHANGELOG - -commit 61c8316449ac5c590d826abef848a668f795cd6a -Author: Oliver Beckstein -Date: Tue Jul 17 11:45:47 2012 -0700 - - New RMS analysis module - - - rmsd calculations (as opposed to fitting) are in the new - MDAnalysis.analysis.rms module - - analysis class RMSD for standard RMSD over a trajectory; - can be enhanced to do trajectory-vs-trajectory - - moved some stuff from MDAnalyis.analysis.align to rms; rms - is supposed to become more central than align (i.e. align imports - rms but rms should not import align) - - enhanced the ProgressMeter class to easily add arbitrary variables - to the output (use for the RMSD analysis class) - - added docs - -commit 4381bbc9bcbf2e190e618a9290a7ce1bc5b3ee7c -Author: Oliver Beckstein -Date: Tue Jul 17 11:43:30 2012 -0700 - - HOLEtraj: can read orderparameters from file or sequence - - - more flexibility in passing orderparameters into the hole - analysis - - renamed the processing function from _read_orderparameters() - to _process_orderparameters() - - more docs on using HOLE + orderparameters (references new - analysis.rms module already) - -commit 0f81a6ff86b708e7f6022fcc6045f01bc34998e9 -Author: Oliver Beckstein -Date: Mon Jul 16 10:03:59 2012 -0700 - - hole: can save profiles as pickle - - - renamed PlotHOLE to BaseHOLE as a general base class - (still somewhat messy) - - add save() to BaseHOLE - - added docs - -commit 390b6e838ebf87967bc8f2a78574e73c39c24e0f -Author: Jan Domanski -Date: Sat Jul 14 23:04:51 2012 -0400 - - Issue 80: Parallel distance matrix computation using Cython - - - serial and parallel (cython.parallel) implementation of - the distance matrix computation in - MDAnalysis.analysis.cython.distances, - - the serial code is slightly slower than MDAnalysis.core.distances, - - the parallel code beats the serial C version from - MDAnalysis.core.distances.distance_array but is only a starter - and improvement is possible, - - added tests to compare the output from the cython distance_array*() - calls to the existing C implementation; with randomized input. - -commit 86f7c4c057c7868f283114228666d9c8a68cbbf4 -Author: Oliver Beckstein -Date: Thu Jul 12 10:25:54 2012 -0700 - - HOLE analysis: HOLEtraj can take any MDAnalysis universe - - - HOLE: does a simple run with hole - - HOLEtraj: splits a trajectory into individual PDBs and - calls HOLE on each one. Also allows associating each frame - with an arbitrary order parameter. - - moved plotting code into a base class (could be cleaned up - but sort of works for both simple HOLE and HOLEtraj with - orderparameters) - - added docs and example - -commit 1a38e4b53ee78392f4d1101fe9ef944072b157d7 -Author: Oliver Beckstein -Date: Fri Jun 29 11:40:46 2012 -0700 - - HOLE analysis: better error check and streamlined code - - - check for ERROR in output (and return 255) - - new MDAnalysis ApplicationError exception - - use common kwarg preprocessing for HOLE.plot() and HOLE.plot3D() - -commit d52d0110d582800d00a70c3f257ba251092d40b7 -Author: Oliver Beckstein -Date: Sat Jun 23 11:52:03 2012 -0400 - - HOLE analysis: 2D and 3D plot of profile families - -commit 009fb406529000ab3c9e05178678e93e5e3958fb -Author: Oliver Beckstein -Date: Mon Feb 20 00:59:03 2012 -0700 - - HOLE analysis - - - simple HOLE run works - - parsing output file into dict of recarrays working - - added test file gA (but no tests yet) - -commit bc3d6806514fe1657cb89d31b6e76ae7924f9908 -Author: Oliver Beckstein -Date: Mon Feb 20 00:43:41 2012 -0700 - - new utility functions which() and realpath() - -commit 5cc5d7032ed753f7023e458bb7a1f01659337586 -Author: Oliver Beckstein -Date: Sun Feb 19 00:09:24 2012 -0700 - - HOLE analysis - - Original file hole_read_13-11-11_4Oli.py provided by Lukas Stelzl - on 2011-11-13; used as a starting point. - -commit b523653315d657bd4b55b451d0b7f657a199412b -Author: Oliver Beckstein -Date: Sat Jul 14 15:56:53 2012 -0700 - - adjusted GRO velocity test case for fixed Issue 115 - -commit daafe4c95080a1777489f2221fb32943c396fd11 -Author: Oliver Beckstein -Date: Fri Jul 13 17:42:40 2012 -0700 - - disabled Bio.PDB warnings in PDBReader - - Bio.PDB.PDBExceptions.PDBConstructionWarning related to missing elements are now filtered. - Note that this applies to any code running in the Python interpreter as we are using - warnings.filterwarnings() - -commit e4fa96d26c998e68365866eb66f701211aa2bbed -Merge: f4184ea39 4c9f18de2 -Author: Daniel Parton -Date: Thu Jul 12 11:13:57 2012 -0500 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit f4184ea39fc8b3aee282d6e35a4b7f591f17a453 -Author: Daniel Parton -Date: Thu Jul 12 01:02:06 2012 -0500 - - Updated CHANGELOG - -commit b5f1f843627044fd635370a700fbfe636d0696ba -Author: Daniel Parton -Date: Thu Jul 12 00:53:19 2012 -0500 - - Fix for Issue 115 - GRO file column width - -commit 365d54cdcb9bf812a3b83c11ebc84274deec3619 (tag: release-0.7.6) -Merge: 93808b3cf e2b95225f -Author: Sébastien Buchoux -Date: Wed Jul 4 21:15:39 2012 +0200 - - Merge branch 'release-0.7.6' - -commit 4c9f18de29cb795c70da4da78c93fcc48b3551da -Merge: c6063110f e2b95225f -Author: Sébastien Buchoux -Date: Wed Jul 4 21:15:09 2012 +0200 - - Merge branch 'release-0.7.6' into develop - -commit e2b95225fb6bdf3b42e862b660206340796e10ad -Author: Sébastien Buchoux -Date: Wed Jul 4 21:14:44 2012 +0200 - - removed '(in development)' inside CHANGELOG - -commit 93808b3cf1b81d0512c228eb50eb361a73c05744 -Merge: 82391208d ae2fe774e -Author: Sébastien Buchoux -Date: Wed Jul 4 10:53:46 2012 +0200 - - Merge branch 'release-0.7.6' - -commit c6063110f9fb41c698b3008b8574a3a429616cb9 -Merge: 999aca63d ae2fe774e -Author: Sébastien Buchoux -Date: Wed Jul 4 10:50:52 2012 +0200 - - Merge branch 'release-0.7.6' into develop - -commit ae2fe774ead5b3aa9a29215a0fb5495875acef65 -Author: Sébastien Buchoux -Date: Wed Jul 4 10:08:15 2012 +0200 - - Documation regenerated - -commit 8ca4bd26ae802aac5ab2c57755bd205e0391bcac -Author: Oliver Beckstein -Date: Tue Jul 3 19:29:07 2012 -0700 - - HydrogenBond analysis: fixes and tests (Issue 103) - - - Replaced the old (fairly useless) test for analysis.hbonds.HydrogenBondingAnalysis - with a small one of an ideal alpha helix with a central proline (script to build - it in MODELLER is included in the maintainer/scripts dir for reference). - The test only looks at a single frame but at least we know exactly what we should - get. In the future we will need more tests, including a small trajectory. - - Added code to remove duplicates from the HBonding analysis (e.g. for the test helix - with 8 hbonds the old code would always get 16); the old behaviour can be forced with - h.run(remove_duplicates=False) - - Added/improved docs. - -commit 999aca63d3f0302b232122d660a4dade2aa7ce90 -Author: Sébastien Buchoux -Date: Tue Jun 26 21:55:01 2012 +0200 - - version bumped to 0.7.7-devel - -commit 6ba466714ffa366fdf277330d034446a9cee37c3 -Author: Sébastien Buchoux -Date: Tue Jun 26 17:43:39 2012 +0200 - - MANIFEST.in files corrected - -commit 9161c1aa74418b11875297564d5d25ebd2ed49db -Author: Sébastien Buchoux -Date: Tue Jun 26 11:37:23 2012 +0200 - - MDAnalysisTests.egg-info added to .gitignore - -commit fdb8809ce3365c1f1149f07ebfc6529b790949d6 -Author: Sébastien Buchoux -Date: Tue Jun 26 11:24:46 2012 +0200 - - HTML doc regenerated doc + corrected a few mistakes. - -commit ee773d02ac59946f1f4fe78ca79015a594550f9b -Author: Sébastien Buchoux -Date: Tue Jun 26 09:11:22 2012 +0200 - - version number changed to 0.7.6 - -commit 6a764636f62467f95de789f9ebd9ead69491a796 -Author: Oliver Beckstein -Date: Sun Jun 17 20:37:19 2012 -0700 - - fixes Issue 113 (ClustalW would not be run in align.fasta2select()) - - Replaced outdated Biopython constructs with more recent ones (see - http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc76) but - now requires Biopython >= 1.51). - - Added new keyword arguments to fasta2select(): clustalw to provide - the path to the ClustalW binary and alnfilename for a custom filename - for the alignment. - - Added test case (but this will fail if ClustalW 2 has not been installed; - clustalw2 can be downloaded from http://www.clustal.org/clustal2/ ) - -commit 435430e64caf7b9c9d4c5d86baa85f441561edbd -Author: Oliver Beckstein -Date: Sat Jun 16 18:12:35 2012 -0700 - - fixes Issue 111 (qcprot would sometimes return NAN) - - joshu.adelman ported a fix in Dougla Theobalds original code: - - Ok, figured out the problem. It was fixed in the most recent - version of Doug Theobald's qcp code, and had to do with small - floating point erros that sometimes resulted in negative numbers - where there shouldn't have been any. - -commit d4610a5cd438945a75dc73d63f2f6df9c20605ec -Author: Oliver Beckstein -Date: Tue Jun 12 01:19:30 2012 -0700 - - hbonds: fixed NH1NH2 --> NH1, NH2 - - This had been fixed previously but apparently re-introduced through some merges. - -commit 4339386da04c659ed96baca58eede776ba54b5ed -Author: Oliver Beckstein -Date: Fri Jun 8 11:31:01 2012 -0700 - - fixed type selection - - In some cases the 'type NAME' or 'type NUM' atom selection would fail with a - TypeError because some topology readers would read atom types as integers. - Atom.type was changed so that the type is always converted to a string and a - number of additional test cases were added to test_selections.py. - (Also reformatted TOPParser.py while I was looking at it, only white space) - -commit 48d78c16c05ae3570412fe2e9ae4df0f06470c7b -Merge: 2f2f6f011 35b8c7659 -Author: Oliver Beckstein -Date: Thu Jun 7 18:51:11 2012 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 35b8c76594f251bcdc6a3ec73af9ed1261454ed1 -Merge: fe1683fdb 91ff4159b -Author: Oliver Beckstein -Date: Thu Jun 7 18:47:17 2012 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit fe1683fdb5686375bea30ebf56f0c193a91899cc -Author: Oliver Beckstein -Date: Thu Jun 7 18:46:18 2012 -0700 - - added docs to TOPParser - -commit 91ff4159b55cf4a4235039d9c1eaaccec5f1cfba -Author: Elizabeth Denning -Date: Thu Jun 7 18:37:42 2012 -0700 - - fixed for nuclinfo docs and testcases - -commit 2f2f6f011eb6a5d77b293bfe29b1400f8a159095 -Merge: 1bd901d71 bfd9d363f -Author: Oliver Beckstein -Date: Thu Jun 7 18:08:26 2012 -0700 - - merged origin/develop into local develop - -commit 1bd901d7175954b193c7947dde963f02a53961ab -Author: Oliver Beckstein -Date: Thu Jun 7 18:01:45 2012 -0700 - - fixes Issue 112 (alig.fasta2select used outdated Biopython) - - - added test case based on francesco.oteri's issue report and test input - - updated code that used very old Biopython constructs - - MDAnalysis will now require Biopython >= 1.51 (from 2010), which - should not be a problem for most people - -commit bfd9d363f758ebffb43eb1879324170e5fcb213e -Author: Elizabeth Denning -Date: Thu Jun 7 18:01:14 2012 -0700 - - additional nuclinfo testcase - -commit bbe4dcf8e52213bac86c9187aa394f380989b182 -Author: Elizabeth Denning -Date: Wed Jun 6 20:40:09 2012 -0700 - - Fixed Amber TOPParser for both 10 and 12 formats - - Fixes Issue 100 - -commit 7d8246788583f644e5a4422f96b7c9da54a7e8d7 -Merge: ab1b66b37 e7371cdda -Author: Elizabeth Denning -Date: Wed Jun 6 20:23:17 2012 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit ab1b66b37abfd8e05e6e049add7de9b05dd96371 -Author: Elizabeth Denning -Date: Wed Jun 6 20:20:46 2012 -0700 - - updated nuclinfo - -commit e7371cdda27c1dc08fba32f7840a783343bbde81 -Author: Oliver Beckstein -Date: Wed Jun 6 10:10:58 2012 -0700 - - initial test case for Issue 100 - - Reading of AMBER12 prmtop currently fails because a new FLAG was added to the file format. - The newly added test just checks that the example topology file anti.top (provided by - zhuhongaaa in the report for Issue 100) can be read. - -commit 35118f6dab8cb774c28fb8aaeefcaa5db3bb2abc -Author: Oliver Beckstein -Date: Tue Jun 5 16:37:46 2012 -0700 - - removed experimental moveto() method from CHANGELOG (should have done this previously...) - -commit a66a34bf24a80ebab047da8a3e548db410a4238b -Author: denniej0 -Date: Tue Jun 5 11:39:06 2012 -0700 - - addition of nucleic acid analysis - -commit f5786ebecb27e2c8894c981a9cedc404b73f021b -Author: Oliver Beckstein -Date: Mon Jun 4 19:47:37 2012 -0700 - - updated CHANGELOG - -commit 5d67a2b093beb5b68dbe8cb9f4159298d52c7cb3 -Author: Oliver Beckstein -Date: Mon Jun 4 19:08:34 2012 -0700 - - single frame reader fixes - - - the Timestep.frame is a frame number, and the first frame in a trajectory - has frame number 1 - - changed all single frame readers so that this is always true (and adjusted test - cases) and explicitly documented in the Trajectory API - - single frame readers can all cope with simple slicing - - reading beyond the first frame raises IOError - - indexing beyond first frame raises IndexError - but standard iteration such as trj[:] or even trj[-1::1] should - work - - permissive=False was ignored and the Biopython reader was not selected: - fixed - - cleaned up single frame readers (eg removed methods that are inherited - from base.Reader) - - ChainReader: uses the new slicing methods from base.Reader - -commit 963ad0bf1c01ba7c2b98dd3ffb66c11614bc6a64 -Author: Oliver Beckstein -Date: Mon Jun 4 17:58:02 2012 -0700 - - PrimitivePDBReader: fixed: __getitem__ and __iter__ returned None for single frame - -commit 1de7eaf9eb0be931fbc0d7289ad69ca54b71f43f -Merge: 6298104f3 0d129b486 -Author: Oliver Beckstein -Date: Mon Jun 4 17:25:51 2012 -0700 - - Merge Lukas Grossar's HydrogenBondAnalysis (Issue 103) - - - closes Issue 103 - - Merged branch 'Issue/103/develop' into develop (including - additions to trajectory slicing) - -commit 0d129b486d11f382ada5af4ab22b037eaa4a58ac -Author: Oliver Beckstein -Date: Mon Jun 4 17:21:30 2012 -0700 - - HbondAnalysis: use new standard slicing - -commit 6033416eb982efcb479d68d620b39539f3a1971b -Author: Oliver Beckstein -Date: Mon Jun 4 17:02:00 2012 -0700 - - Trajectory API: partial implementation of Reader.__getitem__() - - Added implementation of __getitem__() to base.Reader that - - returns the Reader.__iter__() (always implemented!) if one slices for the - whole trajectory - - calls Reader._read_frame(frame) otherwise, which is supposed to raise - a TypeError if it is not fully implemented - - added test cases (some fail at the moment but I will address these cases - in another commit, hopefully leading to a more streamlined interface) - - added the TypeError requirement to the Trajectory API - -commit 6298104f3372a22af2735a3d767c195614d74873 -Author: Oliver Beckstein -Date: Mon Jun 4 15:53:55 2012 -0700 - - notes on netcdf installation and projected release date for 0.7.6 - -commit f1b64de3ff6a1a880f80a831d59b7f36fb7f80f7 -Merge: 9ccc54413 98d55e07a -Author: Oliver Beckstein -Date: Sun Jun 3 14:20:08 2012 -0700 - - Merged Lukas Grossar's HbondAnalysis improvements (fixes issue 103) - - - Merge branch 'develop' of https://code.google.com/r/lukasgrossar-mdanalysis-glycam into Issue/103/develop - - resolved conflicts - -commit 17b28b17027a0ab8a952e13fdb411d92b4b5e585 -Merge: 8aa93bae0 b92cad39a -Author: Tyler Reddy -Date: Sun Jun 3 17:15:48 2012 +0100 - - Dealing with CHANGELOG conflict resolution. - -commit 8aa93bae09f8739bec48f5f316216ddbfe5d4178 -Author: Tyler Reddy -Date: Sun Jun 3 16:59:40 2012 +0100 - - Velocities may now be accessed from GRO files as AtomGroup.velocities() or Atom.velocity ; A velocity unit test was included with this commit to verify that both the AtomGroup and Atom-specific velocity reading functionalities are preserved for GRO files. This implementation uses the ts._velocities attribute. Addresses Issue 102. - -commit b92cad39a65a8b34620854383b11618a5ae01262 -Author: Oliver Beckstein -Date: Fri Jun 1 15:22:47 2012 -0700 - - removed test for moveto() - -commit ca96458ed7c56324d0eb3d5e612658ed3277a515 -Author: Oliver Beckstein -Date: Fri Jun 1 15:13:07 2012 -0700 - - regenerated online docs (removed moveto() and generally nicer) - -commit f3ae14664de6cfaffdd452572999f43dd6e7e093 -Author: Oliver Beckstein -Date: Fri Jun 1 15:11:13 2012 -0700 - - removed experimental AtomGroup.moveto() - - The moveto() method was identical to the new set_positions() - method and hence superfluous. - - Also polished the reST docs for the new getters/setters. - -commit ce5a6580c93466922791e9ef735035f9c2745d5b -Author: Oliver Beckstein -Date: Fri Jun 1 14:31:56 2012 -0700 - - regenerated online docs (changes in AtomGroup) - -commit d5d6df4ad1140332b53d7bae66358179d4dff7fe -Author: Oliver Beckstein -Date: Fri Jun 1 14:17:34 2012 -0700 - - positions/velocities in AtomGroup: docs, tests - - - fully integrated Andy Somogyi's changes and added more docs, including - versionadded/changed and deprecation notes; used aliasing instead of - methods for coordinates(). - - added a few more test cases for individual components (positions, - set_positions(), get_positions()) - - added get_velocities() and set_velocities() + tests; note that - AtomGroup.velocities() is currently a method but in 0.8 we want to make - it an attribute so that it works like AtomGroup.positions - - added Andy to contributors (AUTHORS, sphinx docs and web site) - -commit 80fd2c3aaac2af2b2b18e8bc3b684e44eee1b875 -Author: andy.somogyi -Date: Thu May 31 15:46:35 2012 -0400 - - added unit tests for Atom.position and AtomGroup.positions - -commit 14e523e3dfca02688ee7c2bd6afa7abad85929d1 -Author: andy.somogyi -Date: Thu May 31 13:40:50 2012 -0400 - - updated position property - -commit e0f7a07a120721a41fc0825a2656c97718849c82 -Author: Oliver Beckstein -Date: Thu May 31 11:18:11 2012 -0700 - - use null-vectors for non-periodic/empty unit cells in Gromacs trajectories - -commit d25969ac6bcf2d773345970e876571e88db964f2 -Author: Oliver Beckstein -Date: Thu May 31 11:16:09 2012 -0700 - - fixes Issue 101 - -commit e81a933636e5031fea790fad0d142d0c15f8c87c -Author: Oliver Beckstein -Date: Thu May 31 11:03:33 2012 -0700 - - UnitTests for Issue 101 - - - test fail for writing TRR from single frame universes (GRO, PDB, CRD) - - DCDWriter and XTCWriter work (although the latter does not catch a - division by zero in the unitcell computation for a non-periodic - input such as the CRD system) - -commit e58958cbaa26298ee1ac76950f16ede8349bd6da -Author: Oliver Beckstein -Date: Wed May 30 18:38:35 2012 -0700 - - minor fixes for PrimitivePDBWriter - - - properly write END record - - AtomGroup.write(): select the frame writer and make sure that - it gets closed; this method is only supposed to be used for - writing single frames - - remarks are line wrapped in the PDB file - -commit daa117fc9351b187bf34ea9170b1965ad841cdad -Merge: cc73f72f1 8a710815a -Author: Oliver Beckstein -Date: Wed May 30 16:31:00 2012 -0700 - - Merge branch 'Issue/107' into develop - -commit 8a710815ac8554a8e05743ed4742515a1c875dfa -Author: Oliver Beckstein -Date: Wed May 30 16:22:35 2012 -0700 - - fixes Issue 107: read NAMD/VMD space separated PSF files - - NAMD/VMD uses their own "PSF" file format, which is space separated and not - fixed column (as the original CHARMM/XPLOR specification). Such files - would lead to a ValueError in the PSF reader. They are produced when very - long atom type names (from CGENFF in conjunction with the XPLOR alphanumeric - atom types) are used. - - The PSF parser was changed to explicitly use a detected format (CHARMM standard - or EXT) or NAMD. From VMD 1.9.1 the VMD psfpluging adds the flag "NAMD" to the - PSF header so we can detect the format as usual. Older files are precariously - detected: We assume standard format (or EXT if the EXT flag was found). The - first ValueError triggers a switch to the NAMD format for the rest of the file. - A warning is issued (and logged if logging is enabled). - - Logging was added to the PSFParser and a new warning, FileFormatWarning created. - - The test case for the namd_cgenff example files now passes. - -commit fe7292d8fafb5d63ee8d137ee79b2fe6479187dd -Author: Oliver Beckstein -Date: Wed May 30 14:30:06 2012 -0700 - - data files and test case for Issue 107 - - NAMD/VMD-style PSFs are not always handled well, at least in this issue reported - when CGENFF atom types (longer than allowed by standard PSF format!) are used. - - Added fixtures (provided by JiyongPark.77) and a test case that produces the described failure. - - Re-roganized the topology tests and made them more modular. Added a test for the - standard CHARMM PSF format. - -commit cc73f72f1c0098fcc949ff27fb7330e282ae8fdd -Author: Oliver Beckstein -Date: Wed May 30 10:05:43 2012 -0700 - - NCDFReader (Issue 109): load coordinates right away - - fixed: NCDFReader started out with empty coordinates and required a next() or - NCDFReader[0] to read the first data frame. - - Added testcases (which also cover the TRJReader). - -commit 5f8b06c39787b039382f7e8023fa575935a84a3f -Author: Oliver Beckstein -Date: Wed May 30 09:42:13 2012 -0700 - - deleted testsuite/MDAnalysisTests.egg-info - - The egg-info directory is a temporary directory that we ignore; not sure why it was checked in. - -commit a81dcdb72f3df090e858fb235d3d4a1a1bca2889 -Author: Oliver Beckstein -Date: Wed May 30 09:40:17 2012 -0700 - - forgot to include the test cases for Issue 109 in package - -commit 3c68292ef6c800036f72d43ca07cf60638dd9a5e -Author: Oliver Beckstein -Date: Tue May 29 19:27:14 2012 -0700 - - Empty AtomGroup allowed (Issue 12) - - Creating an empty AtomGroup with AtomGroup([]) or a selectAtoms("resname NONE") will - not any longer raise a NoDataError. User code should check the length of the resulting - AtomGroup: len(ag) == 0 if they want to detect that a selection did not find anything. - - CAUTION: This change might break code that relies on NoDataError being raised. - -commit 58730f88bf6505ea8e8762bc63efc4c64c421ce6 -Author: Oliver Beckstein -Date: Tue May 29 18:15:39 2012 -0700 - - regenerated online docs (new AMBER readers, omitted LAMMPS R/W, pdb extensions) - -commit 0bd5b1afc7fe2f42f13e989c48e29bd8a3ffd561 -Author: Oliver Beckstein -Date: Tue May 29 18:14:03 2012 -0700 - - documentation fixes and small things in the AMBER NCDF Reader/Writer - -commit 50c3f6213db0afa66ea4844f543196d837483a0a -Merge: 557491b30 c44d84485 -Author: Oliver Beckstein -Date: Tue May 29 17:07:00 2012 -0700 - - Merge branch 'Issue/109' into develop - -commit c44d84485cf7f9cacc1138f02d183b4f2c34dae0 -Author: Oliver Beckstein -Date: Tue May 29 16:54:49 2012 -0700 - - NetCDFWriter working (closes Issue 109) - - The AMBER NetCDFWriter can deal with coordinates and velocities. Test cases have been - added (e.g. writing a Gromacs TRR file with velocities to the AMBER NetCDF format). - - Updated the INSTALL instructions: the netcdf4-python library is required (currently - added to the requirements in setup.py). If this turns out to be a pain for most people - then we should make it truely optional. The coordinates.TRJ module is set up to complain - if netcdf4 cannot be imported and issues a warning that no NetCDF support will be available - (but your code will simply crash with an ImportError at some point if you try to use - NCDFReader or NCDFWriter). - - Consider this EXPERIMENTAL because I don't have enough test cases; we're now waiting - for user feedback. - -commit 86b41e2306c3ac4d43153f5f5b42c4246b2a40e9 -Author: Oliver Beckstein -Date: Sun May 27 21:18:53 2012 -0700 - - NetCDFReader working (Issue 109) - - - reads example trajectory - - should be able to deal with velocities and the saved time for each frame - but this could not be tested with the example trajectory - - testcases added for NCDFReader - - Note that the reader opens the trajectory before setting up the Timestep - instance in order to find out if space for velocities needs to be allocated. - The Timestep class has an optional keyword flag to add velocities. This is - experimental; it should not break the existing Trajectory API but this - particular feature might be subject to change. - -commit 557491b30b113fe9821f689b5bff9367d92fc6af -Author: Oliver Beckstein -Date: Sun May 27 17:40:33 2012 -0700 - - fixed test case test_atomgroup:TestWritePDB.test_write_universe - - The fixes for Issue 109 make it mandatory that a PDB writer obtained - with Writer() is properly close()'d. If this is not done then the test - case reads an incomplete file as not all contents are flushed to disk - immediately. - -commit eb213a2c8f79810ad5f13a648c74664f39cd8307 -Author: Oliver Beckstein -Date: Fri May 25 18:41:26 2012 -0700 - - test AMBER trajectories for Issue 109 - - Files supplied by bala.biophysics (originally named - TEST.prmtop, TEST.TRAJ, and TEST.NCDF) - - Amber supports MD trajectories to be written in binary netcdf format. Using such netcdf is less consuming and hence a support for file format would be a good addition to MDAnalysis. - - Herewith a test amber top, ascii (.TRAJ) and netcdf (.NCDF) are attached. - -commit 2d2427efbd4af7a34595dd1656d249e423c9f3e4 -Author: Oliver Beckstein -Date: Tue May 22 16:49:38 2012 -0700 - - fixes Issue 105: MultiPDB support and writing of single PDB frames - - - Issue 105 fixed (can write single frames from a trajectory to - a PDB file) - - added multiframe keyword support to select a trajectory writer when - also a single frame writer exists (currently only relevant for the - permissive ("primitive") PDBWriter) - - changed behaviour of PrimitivePDBWriter so that it behaves like the - other writers, i.e. no automatic writing of trajectories; use the - write_all_timesteps() method for that - - added convenience class MultiPDBWriter (which sets multiframe = True - as default) and registered that one in the _trajectory_writers registry - - added full slicing support to the PrimitivePDBReader (but performance - could be improved, see comments in PDB.py) - - fixed some minor formatting issues in REMARK, TITLE and HEADER records - - more docs and examples for PDB writing; added notes to the trajectory - API; added docs for pdb.extensions - - added test cases and split the PDB reading/writing tests into tests - for the single frame writer and the multiframe versions - -commit 98d55e07af48de6eb13223f645656530079134f2 -Author: Lukas Grossar -Date: Mon May 21 15:30:18 2012 +0200 - - analysis/hbonds.py - - always initialize the dicts in _update_selection_{1,2} as empty to - avoid problems in _donor_lookup_table_{byindex,byres} - -commit 3fbb15c63e85b8f36259ef48d2d17c6a6894e55c -Author: Lukas Grossar -Date: Mon May 21 14:07:52 2012 +0200 - - analysis.hbonds.py - - slicing doesn't work for XYZ files, so I needed to comment it - -commit d97c7df0c7a91d21452dc9c142395ea93107531f -Author: Lukas Grossar -Date: Mon May 21 09:35:12 2012 +0200 - - analysis/hbonds.py - - renamed count_by_type_correlation --> timesteps_by_type - -commit 9ccc544135a634a9b43b64a786ec584ac05aa83b -Merge: 77594ec91 04bbe28ad -Author: Oliver Beckstein -Date: Fri May 18 15:40:26 2012 -0700 - - Merge remote-tracking branch 'lukasgrossar/develop' into Issue/103/develop - -commit 77594ec914de2ac4bef0a7d65da6c463d859472e -Author: Oliver Beckstein -Date: Fri May 18 15:35:11 2012 -0700 - - hbonds: removed doubled r_cov and doc improvements - -commit 04bbe28ad4b1f63a3214518919ae1c39ba218723 -Author: Lukas Grossar -Date: Thu May 10 16:48:10 2012 +0200 - - analysis/hbonds.py - - fixed a merge error - - changed implementation of count_by_type_correlation to match - count_by_type - -commit a847635edc3ce8c6eb36659dc35457622442415a -Author: Oliver Beckstein -Date: Mon May 7 23:24:10 2012 -0700 - - hbond analysis: use tuples directly as keys - - The code for count_by_type and count_by_type_correlation can be simplified - by using the key tuple directly as a key. - -commit 0f2d36e9e2e208c1a2f669bf0efce46b7fb295f9 -Author: Oliver Beckstein -Date: Mon May 7 23:09:13 2012 -0700 - - hbond analysis: fixes and new feature: start:stop:step - - - can give start:stop:step for trajectory (NOTE: ProgressMeter - incorrect for non-default start/stop) - - fixed: donor heavy atom names in count_* methods - - tightened up code for count_by_time() --- the previous version did not - work for me and only gave lots of (0,0) records... - -commit 2e59a03263b97bd5b223135462abc59fa49314f9 -Author: Oliver Beckstein -Date: Mon May 7 19:20:33 2012 -0700 - - HBond analysis enhancements (H-detection and count_by_type_*) - - - use r_cov for the "distance" H-bond detection algorithm (removed - the cutoff keyword with the default value 1.58). Now both detection - algorithms should always find the same hydrogens (for good PSF). - - patched the donor heavy atom names in to the output of - count_by_type and and count_by_type_correlation; this is a bit of - a hack, which uses the new _donor_lookup_table_byindex() to - find the heavy atom that a hydrogen belonged to. Currently only working - for static selections. - - updated the docs in various places - -commit dccc66892361b3dc5f9987a295a015f46cca4297 -Merge: 1b5b8e45b 24171ce8b -Author: Oliver Beckstein -Date: Mon May 7 17:15:21 2012 -0700 - - Merge branch 'develop' into Issue/103/develop - -commit 24171ce8b0ce44a19a185e19982380f7c937060e -Author: Oliver Beckstein -Date: Mon May 7 17:13:45 2012 -0700 - - fixed NameError in AtomGroup.__contains__ - - "Atom in AtomGroup" would raise a - NameError: global name atoms is not defined - -commit 1b5b8e45b04c3ef7efc66b8503f0743c37042f05 -Merge: c401ddd63 d564da1b4 -Author: Oliver Beckstein -Date: Mon May 7 14:24:32 2012 -0700 - - merged orbeckst/hbonds into Lukas Grossars development branch - - Conflicts were only formatting and documentation text. Also - updated some of the docs. - -commit c401ddd63a515869628176d7a98f3542876f1110 -Author: Lukas Grossar -Date: Fri May 4 14:26:58 2012 +0200 - - added count_by_type and count_by_type_correlation to analysis/hbonds.py - -commit da8e05bbee50e7c9fb29c4bafe8e13f5a2dbac69 -Author: Oliver Beckstein -Date: Thu May 3 16:22:18 2012 -0700 - - fixed Universe.load_new() raised a NameError - - - missed an import statement: added - - added test cases - - Thanks to Jiyong for reporting it on the mailinglist! - -commit 936af568923003cadb896d3eccae48314a909e5a -Author: Lukas Grossar -Date: Thu May 3 16:11:43 2012 +0200 - - implemented count_by_time in HydrogenBondAnalysis - -commit 178af90c92cfc989ecc3d5b57b20e797599bee95 -Author: Oliver Beckstein -Date: Tue May 1 13:31:01 2012 -0700 - - fixes for PDB and GRO writer - - - PrimitivePDBWriter: special segid SYSTEM is translated to empty - chainID - - added documentation explaining that PrimitivePBDWriter writes - CHARMM/NAMD-style PDBs and not strict PDB v3.2 - - GROWriter: enforce maximum resname and atomname length of 5 chars - - See also discussion https://groups.google.com/forum/?fromgroups#!topic/mdnalysis-discussion/qnRKXBcr6c4 - -commit 4e59491eaa74576ca5c393f85cfa7e7cbeba9d53 -Author: Lukas Grossar -Date: Thu Apr 26 18:07:02 2012 +0200 - - patch for the heuristic H-detection - * _get_bonded_hydrogens_list() was changed so that any hydrogens found - also have to be within a maximum distance of the donor - * the maximum distance is stored in the defaultdict HydrogenBondAnalysis.r_cov; - covalent H-donor distances are hard coded for N, O, S, P; anything else gets - a default value of 1.5 A. - - NOTE: test case still broken - -commit 4e440ebafbede6d46828ff04ffe372c422cce327 -Author: Oliver Beckstein -Date: Tue Apr 24 10:00:54 2012 -0700 - - removed CHO and EAM for resnames recognized as protein - -commit d564da1b48cd8919b31b731720a632f0a610d373 -Author: Oliver Beckstein -Date: Fri Apr 20 11:16:59 2012 -0700 - - hydrogen bond analysis: Lukas Grossar's patches for the heuristic H-detection - - * _get_bonded_hydrogens_list() was changed so that any hydrogens found - also have to be within a maximum distance of the donor - * the maximum distance is stored in the defaultdict HydrogenBondAnalysis.r_cov; - covalent H-donor distances are hard coded for N, O, S, P; anything else gets - a default value of 1.5 A. - * updated the authors list for hbonds.py with Lukas Grossar's and my name - * patches used (for reference): - - 0001-_get_bonded_hydrogens_list-now-also-takes-distance-t.patch - - 0002-constructed-a-dict-to-take-different-covalent-radii-.patch - - NOTE: test case still broken - -commit 1127d73e551e5ac0791644b2d6c69a33ab974896 -Author: Lukas Grossar -Date: Thu Apr 19 14:53:55 2012 +0200 - - removed some wrong atom types from DEFAULT_ACCEPTORS - -commit 2747eafe44e6c17efd8502dc6107765873090e6b -Author: Lukas Grossar -Date: Thu Apr 19 12:37:41 2012 +0200 - - added changes to accomodate the switch to multiple available force fields - -commit 92d1ae942a1d0954fc4cf3e33801cc1c81f760ef -Author: Lukas Grossar -Date: Wed Apr 11 16:41:20 2012 +0200 - - Built table with values for GLYCAM06 force field, DEFAULT_... tuples not yet updated - -commit 7af7fc40b5cfd1d3a460f2ceb7df2a8dfab0c60c -Merge: 696ccd55f d565fb8bf -Author: Lukas Grossar -Date: Tue Apr 10 12:41:25 2012 +0200 - - merged with d565fb8bf98f of orbeckst/hbonds - -commit 696ccd55fa69432ff9c0645c7b4471e6ab1b1ded -Merge: 1c1a7e5f7 8e3a4102a -Author: Lukas Grossar -Date: Fri Apr 6 18:02:17 2012 +0200 - - merged mdanalysis/develop - -commit 1c1a7e5f706fc0d424eda579e7a8b5fdd1b96ca3 -Author: Lukas Grossar -Date: Fri Apr 6 17:15:57 2012 +0200 - - analysis/hbonds.py: changed DEFAULT_DONORS and DEFAULT_ACCEPTORS to a dict, to allow switching to different forcefields - -commit c61e39f197f452ddbc227f1be71065d05ed9865d -Merge: e4ddfea42 82391208d -Author: Lukas Grossar -Date: Wed Apr 4 10:20:44 2012 +0200 - - Merge remote-tracking branch 'mdanalysis/master' - -commit d565fb8bf98f05ea91853191ac73597263a9ca16 -Author: Oliver Beckstein -Date: Sun Mar 25 15:12:10 2012 -0700 - - HBond analysis: better detection of bonded hydrogens - - - new keyword: detect_hydrogens to switch between the new distance-based - selection algorithm ("distance") and the previous list-based one - ("heuristic") - - fixed: hydrogens were not found when the name started with a number - such as "1HE12" "2HD22" - - TODO: testcases broken - -commit 8e3a4102ab7259a3ecdb64fc6b6c6fe2178b795d -Merge: c25ea38a8 1a44a237f -Author: Oliver Beckstein -Date: Sat Mar 24 19:17:29 2012 -0700 - - Merge branch 'orbeckst/hbonds' into develop - -commit 1a44a237fde424c1804040de3e14f8fcd45cfc99 -Author: Oliver Beckstein -Date: Sat Mar 24 19:09:41 2012 -0700 - - hbond analysis: possibly fixed bug and added ProgressMeter - - - generate_table() would sometimes loose data and put the last few frames - at the beginning of the table: rewrote the loop, which is hopefully - a bit more robust and added an assertion - - added progress output for the run() method (using log.ProgressMeter); - incurs a start-up penalty for trajectories that don't store the total - number of frames - - added constructor verbose keyword (which sets the verbose attribute): - only if HydrogenBondAnalysis.verbose == True will we write per-frame - debugging messages to the log file (through the standard logging mechanism). - By default, verbose = False (this is different from the situation before - where debug messages would always be enabled but because this can create - a huge log file the new default is to not to enable it) - -commit 8dcc038578e471383d2e0a05d8c2bbab602a2aaf -Author: Oliver Beckstein -Date: Sat Mar 24 19:04:43 2012 -0700 - - ProgressMeter: fixed docs - -commit c25ea38a8335668c729b95bc79a9832e3239cb98 -Author: Oliver Beckstein -Date: Fri Mar 23 23:21:59 2012 +0000 - - HydrogenBondAnalysis.run(): do not return results anymore - - HB results can be enormously big. By never returning them we can save a - bit of memory and it is much less hassle when doing work interactively - in IPython. The results are (as previously) available as the attribute - HydrogenBondAnalysis.timeseries. - -commit 2d46c0e18183f98955a3111c14715083fa64c739 -Author: Oliver Beckstein -Date: Fri Mar 23 16:00:57 2012 -0700 - - resphinxed docs - -commit 88bc68f73f11a263d648fc5a157ac2a27a6eb62b -Author: Oliver Beckstein -Date: Fri Mar 23 15:29:21 2012 -0700 - - HydrogenBondAnalysis: fixed acceptors, doc improvements - - - Acceptors 'NH1', 'NH2' were not recognised (was read as 'NH1NH2') - so previous results were incomplete. - - adjusted test case so that it passes - - added more docs (reST) - - use sets when adding custom acceptors/donors to weed out duplicates - - added a few more logger.debug statements - -commit 6220bcd291d9d3003372820be53223c123f79600 -Author: Oliver Beckstein -Date: Sat Mar 10 16:24:45 2012 -0700 - - minor fixes to coordinates code and docs - - - Trajectory API: replaced stray close_trajectory() with close() - - reformatted some code in DCD.py and base.py and added docs - - fixed typos: premissive=True --> permissive=True in test_coordinates.py - and compacted a little bit (e.g. we only need two temp files - in TestPrimitivePDBWriter) - -commit f53cff4f87159413fc2fea40ab16ef91336532f4 -Merge: d3f7100e6 a8a280c5f -Author: Jan Domanski -Date: Sat Mar 10 14:53:19 2012 -0500 - - Merge branch 'Issue/99/pdb-writer' into develop - -commit a8a280c5fa90764e4eb5d3515abcf62957ab8d4a -Author: Jan Domanski -Date: Sat Mar 10 14:42:12 2012 -0500 - - fixes issue #99 Infinite loop when writing single frame - - - there might still be some confusion : - u.trajectory[0] may give u.trajectory.frame = 1 or 0, should start/stop/step flags be applied on the list or the trajectory.frame level? - - added a test case - -commit d3f7100e6c09fa905d3e107d701876e81c179d6a -Merge: 81160173c b4cd3b232 -Author: Oliver Beckstein -Date: Wed Mar 7 22:40:15 2012 -0700 - - Merge branch 'develop' of https://code.google.com/p/mdanalysis into develop - -commit 81160173cc8bae7a46e1b8626e6cd741352afb01 -Author: Oliver Beckstein -Date: Wed Mar 7 22:34:56 2012 -0700 - - new AtomGroup.moveto() method (+test) - -commit b4cd3b232f990bb1bc52a30db10eb0b950deda85 -Author: Sébastien Buchoux -Date: Wed Feb 29 10:11:46 2012 +0100 - - Added: test running script - -commit 58f1ba99b7980ff29b821a9e857db1e65108316d -Author: Sébastien Buchoux -Date: Wed Feb 29 09:44:39 2012 +0100 - - Version bumped to 0.7.6-devel - maintainer/change_release.sh fixed - -commit a4d50aec4ad705e3d43af2388252ce269ee8f0d8 -Author: Oliver Beckstein -Date: Tue Feb 28 01:29:14 2012 +0000 - - fixed: hbond analysis generate_table() - - Would fail if no data in a frame due to uninitialised variable cursor - -commit 0c2a7074137a01aef506160cd2f33b2411d950dc -Author: Oliver Beckstein -Date: Tue Feb 28 02:24:04 2012 +0000 - - fixed maintainer/change_release.sh - - - regex did not find hotfix releases - - look for sed that understands extended regular expressions - - works on Mac OS X, please check on Linux - - make .bak files (and ignore them in git) - -commit e4ddfea421ac2dc04dcb6afa64f57076042ea368 -Author: Lukas Grossar -Date: Fri Feb 24 14:05:55 2012 +0100 - - hbonds.py: _get_bonded_hydrogens now also takes distance to donor atom into account to avoid choosing hydrogens that are close by by index, but not bonded - -commit 7ee2d25c3d9ead2346221215092b7005abb36f87 -Author: Oliver Beckstein -Date: Mon Feb 20 16:22:05 2012 -0700 - - updated Ben Hall's analysis packages - - - updated email address - - added author information to reST in gnm.py - -commit 82391208d365dbe193f582fb109a69f093fd56e4 -Author: Oliver Beckstein -Date: Fri Feb 17 16:51:19 2012 -0700 - - regenerated HTML (online) docs - - Includes better documentation for AtomGroup (e.g. AtomGroup.indices()) and Timestep. - -commit 262a933557dfc28cd718cb17a1efb204ebe72099 -Merge: d2523b1d7 7387d8e5d -Author: Oliver Beckstein -Date: Fri Feb 17 16:47:05 2012 -0700 - - Merge branch 'master' of https://code.google.com/p/mdanalysis - -commit d2523b1d7a2ce12b1253001134c3d119dd6c8bb7 -Author: Oliver Beckstein -Date: Fri Feb 17 14:46:40 2012 -0700 - - improved docs for AtomGroup and Timestep - - Added doc strings to a number of important methods in AtomGroup (in particular, - indices() which until now was effectively undocumented and lead to a question - by PBurns on the mailing list. Documented individual attributes through the - sphinx mechanism and removed ad-hoc docs from class doc strings. - - Also added documentation for a number of important attributes of Timestep. - -commit 7387d8e5de9c6ec68becbbbacc3cad0442c126a2 (tag: release-0.7.5.1) -Author: Sébastien Buchoux -Date: Thu Feb 16 15:55:37 2012 +0100 - - MANIFEST.in corrected in testsuite to include license and related files - -commit 2c4dcde2b8059b8659b59dbb3069216e7589bbee -Merge: 740db3d31 fb9ba38d5 -Author: Sébastien Buchoux -Date: Thu Feb 16 15:29:44 2012 +0100 - - Merge branch 'master' of https://code.google.com/p/mdanalysis - -commit 740db3d3136ca37e77af6155ee87e0b44a345d8b -Merge: a8627514d 2787fb06c -Author: Sébastien Buchoux -Date: Wed Feb 15 23:11:54 2012 +0100 - - fixes issue #95 - -commit 20568775df14ba78190f9a15181efc95b398c6e0 -Author: Oliver Beckstein -Date: Wed Feb 15 23:34:28 2012 -0700 - - updated coordinate module docs - - - TRR can handle velocities, and Timestep can have _velocities - - various smaller fixes and updates that probably should have - been done ages ago - -commit fb9ba38d50f11e38cb63f93b2ba228939c1d1a86 -Merge: a8627514d 2787fb06c -Author: Sébastien Buchoux -Date: Wed Feb 15 23:11:54 2012 +0100 - - fixes issue #95 - -commit 2787fb06ca790531d9727939735625f0c0d89fd4 -Author: Sébastien Buchoux -Date: Wed Feb 15 23:06:20 2012 +0100 - - MDAnalysisTests.egg_info added - -commit b5f587f89edda07f259140c466710f5e4ea6f449 -Author: Sébastien Buchoux -Date: Wed Feb 15 23:03:58 2012 +0100 - - C files regenerated - -commit 948d06d9ed08441fb62729897c78e4044361ddfe -Author: Sébastien Buchoux -Date: Wed Feb 15 23:03:07 2012 +0100 - - Version number changed back to 0.7.5.1 - -commit 450ad43b77914a26897956383c038f1e8e89acef -Author: Sébastien Buchoux -Date: Wed Feb 15 22:58:58 2012 +0100 - - doc/sphinx/source/logos/LICENSE deleted to avoid lintian warnings. - doc/sphinx/source/logos/AUTHORS was already fixed to include link to CC - License text - -commit 9d515b33180bf7409b92581e3c41f562e585ac0a -Author: Sébastien Buchoux -Date: Wed Feb 15 22:52:53 2012 +0100 - - A few changes in sphinx configuration to make it more close to - the default configuration. - doc/Makefile fixed so "make clean" actually cleans something - -commit 359cae028ae6aa596f97640311324aa2d70ad824 -Author: Sébastien Buchoux -Date: Wed Feb 15 22:44:19 2012 +0100 - - delaunay stuff deleted - -commit a8627514d5dc7e3848a5b5b91528bf88f1d49d13 -Author: Oliver Beckstein -Date: Sun Feb 12 21:35:18 2012 -0700 - - maintainer scripts - -commit e686a9f57006278384a9ac403eee3a01a0d34425 -Author: Oliver Beckstein -Date: Sun Feb 12 14:41:35 2012 -0700 - - testsuite: prepared setup.py for PyPI - - MDAnalysisTests 0.7.5 is now on PyPI: - http://pypi.python.org/pypi/MDAnalysisTests - and hence can be installed using the standard - easy_install or pip mechanisms. See - http://code.google.com/p/mdanalysis/wiki/MDAnalysisTests - -commit b2589df86b513250e07de7ae92828057d4ad4d72 -Author: Oliver Beckstein -Date: Sun Feb 12 14:15:58 2012 -0700 - - regenerated online docs (includes MDAnalysis.analysis.gnm) - -commit ed23f7d1fa0fe2df5b9707000122a6f2503ddb0a -Author: Oliver Beckstein -Date: Sun Feb 12 14:12:11 2012 -0700 - - doc improvements (GNM and Universe) - - - should have been in 0.7.5 - - added docs for Ben Hall's GNM analysis module (including - reference); also added the citation to the home page to "included - algorithms"; it has been in the README since the code was added - - updated docs for Universe (can use mult-PDB and note on guessing - atom attributes) - -commit 54d8b900db527a018ad6e8bf1df07cdfeb530770 -Author: Oliver Beckstein -Date: Sun Feb 12 01:10:49 2012 -0700 - - bumped release to 0.7.6-devel - -commit c453b4004d35423b9ecccbffd3a96c1f7ccee8b3 -Merge: e29e04943 02319baf8 -Author: Oliver Beckstein -Date: Sun Feb 12 01:02:37 2012 -0700 - - Merge branch 'build' - -commit e29e0494393ecedb63f5d5218aec84aa2297b4e2 -Author: Oliver Beckstein -Date: Sun Feb 12 00:26:53 2012 -0700 - - updated PyPI summary with MDAnalysisTests - -commit e52b313495af066f70c83c439b0d1d9da40747f2 (tag: release-0.7.5) -Author: Oliver Beckstein -Date: Sat Feb 11 18:09:53 2012 -0700 - - online docs for release 0.7.5 - -commit 633c090278a63925a22cd8066731dc97fc4ae64b -Author: Oliver Beckstein -Date: Sat Feb 11 17:50:32 2012 -0700 - - updated metadata for release 0.7.5 - - - release 0.7.5 for MDAnalysis and MDAnalysisTests; - docs is now using MDAnalysis.__version__ to automatically - determine the release that the docs are generate for - - MDAnalysis and MDAnalysisTests MUST have the same - release number; this is enforced by comparing the __version__ - data and encouraged through appropriate dependencies in the setup.py - files of MDAnalysis (package) and MDAnalysisTests (testsuite) - - updated authors in AUTHORS and the sphinx docs - - updated CHANGELOG - - updated various INSTALL and README files (especially with reference - to MDAnalysisTests) and fixed links pointing to the old docs on - the SVN repository (which still exists) - - removed unused setup_develop.py from MANIFEST.in - -commit c598b2ec1d600d245cbbc4c5f565fd287927e5a2 -Author: Oliver Beckstein -Date: Sat Feb 11 14:46:04 2012 -0700 - - Fixed potential issues in XTC,TRR,GRO,PDB writers (when convert_units=False) - - When convert_units == False we need to make sure that we still assign - the positions to a temp variable that is used by the writer. - - Added new warning category ConversionWarning that can be used to - alert the user that there might be problems with the (lack of) - conversion between units. - - (Also beautified some of the doc strings in the PrimitivePDBWriter) - -commit 092647cacbc90e2e84e5497eecaf6b06212734be -Author: Oliver Beckstein -Date: Sat Feb 11 13:34:53 2012 -0700 - - TRR velocity fix - - If you had set flags['convert_gromacs_lengths'] = False then - the TRRWriter would have set all your velocities to 0 before - writing... just got the indentation level wrong. - -commit f766ecdf894d695291de92cce61f1d9fa43a31fc -Author: Oliver Beckstein -Date: Sat Feb 11 03:44:48 2012 -0700 - - fixed path to online docs in doc/README - -commit b92ba10be51d9aa7d440aaa51f98f691bef07566 -Author: Oliver Beckstein -Date: Sat Feb 11 03:41:14 2012 -0700 - - regenerated online docs - -commit 4be4cb5612a616657f4670e50db30d505beb1a5e -Author: Oliver Beckstein -Date: Sat Feb 11 03:22:59 2012 -0700 - - Fixes Issue 91: Reading/Writing of TRR velocities - - - TRR Timesteps always had the raw velocities in ts._velocities; - these are now fully integrated into MDAnalyis - - velocities are subject to unit conversion; the base unit for - speed in MDAnalysis is Angstrom/ps. - - NEW attribute Atom.velocity --- velocity of the atom - - NEW method AtomGroup.velocities() --- velocities of all atoms - - Timestep._velocities --- raw array of velocities (after unit - conversion) - - Velocities can be written to a TRR file (and are automatically - converted to the Gromacs native unit of nm/ps) - - added unit tests - - NOTE: universe.trajectory[frame][i] (which is Timestep[i]) continues to - only return the coordinates of the atom with index i as it - would likely break existing scripts if we returned anything else. - Furthermore, Universe.coord[i] (which is again just Timestep[i]) - should continue to only provide coordinates). - -commit 009098cc1d972b619f5403d2102a30a764ed8b2f -Author: Oliver Beckstein -Date: Sat Feb 11 01:45:56 2012 -0700 - - changed generic Exceptions to specific ones in DCD module - -commit 8a0de3967d47f2521350ccc457e74d9da9c46f1f -Author: Oliver Beckstein -Date: Sat Feb 11 01:45:06 2012 -0700 - - Writers do not modify coordinates in place anymore - - Writers for formats where the native units are different from MDAnalysis used - to convert the coordinates and time in place (faster and saves memory). However, - this will lead to problems if the timestep is analysed AFTER it was written - to disk. Even though no Issue has been filed, this was corrected as it is - very unintuitive behavior and could lead to very weird bugs. If performance - is a issue please file a bug report. - - The convert_to/from_native() methods were changed to - 1) accept a inplace=True|False keyword; the default (as before) is - True so that operations are in place - 2) if no conversion takes place then we do not even perform the - multiplication by 1 and just return the reference to the input - (even if inplace=False) - -commit 02319baf8ebb951c62ff368eafc2384e124b479d -Author: Oliver Beckstein -Date: Sat Feb 11 01:45:56 2012 -0700 - - changed generic Exceptions to specific ones in DCD module - -commit ecfd6e4be47750b05033cfcfe898330e44e8ff11 -Author: Oliver Beckstein -Date: Sat Feb 11 01:45:06 2012 -0700 - - Writers do not modify coordinates in place anymore - - Writers for formats where the native units are different from MDAnalysis used - to convert the coordinates and time in place (faster and saves memory). However, - this will lead to problems if the timestep is analysed AFTER it was written - to disk. Even though no Issue has been filed, this was corrected as it is - very unintuitive behavior and could lead to very weird bugs. If performance - is a issue please file a bug report. - - The convert_to/from_native() methods were changed to - 1) accept a inplace=True|False keyword; the default (as before) is - True so that operations are in place - 2) if no conversion takes place then we do not even perform the - multiplication by 1 and just return the reference to the input - (even if inplace=False) - -commit 0c9cf4612e4ec889c34d8ac2d441a93386672efd -Author: Oliver Beckstein -Date: Fri Feb 3 12:49:44 2012 -0700 - - new builder module: helper for creating CHARMM-ready structures - -commit c7fa3aacefd8edb77e4874408d777352c39e8453 -Author: Oliver Beckstein -Date: Thu Feb 2 23:27:14 2012 -0700 - - misspelt Lukas Grossar's name in his handle --- sorry - -commit 239140871ed8b602425d726386cc9c6db4e2674d -Author: Lukas Grossar -Date: Thu Jan 26 17:04:52 2012 +0100 - - Issue 92: fixes/enhancements in relation to GLYCAM - - Patches provided by Lukas Grosser (lukasgrosser) via clone; see Issue 92 - for details (pull request). All changes were merged and rebased into a - single commit. (orbeckst) - - - analysis/hbonds.py: - - fixed a bug when calling save_table - - Added default values DEFAULT_{ACCEPTORS,DONORS} - to hbonds.py - - coordinates/XYZ.py: can set timestep value - - core/util.py: changed RegEx to detect GLYCAM style residue names - adjustments to work with ALL GLYCAM_06 residue names - - tests for XYZReader still pass (orbeckst) - - added Lukas Grosser to AUTHORS and CHANGELOG - -commit bf98edd60d2ec42a9371a268009953430537c2c4 -Author: Lukas Grossar -Date: Mon Jan 30 14:11:14 2012 +0100 - - Final changes before giving out pull request: - core/util.py: adjustments to work with ALL GLYCAM_06 residue names - analysis/hbonds.py: reverted DEFAULT_{ACCEPTORS,DONORS} to original - -commit 61b469179fb8df72fadb39b892199303136151f7 -Author: Lukas Grossar -Date: Mon Jan 30 13:33:42 2012 +0100 - - Added further defaule values to hbonds.py and fixed minor errors in XYZ.py - -commit 9fcfe41253e45999b3e1cf1a8b69fed7c720e3a6 -Author: Lukas Grossar -Date: Fri Jan 27 14:52:05 2012 +0100 - - Small adjustments to get it working. - analysis/hbonds.py: fixed a bug when calling save_table - coordinates/XYZ.py: added two dummy variables - core/util.py: changed RegEx to detect GLYCAM style residue names - -commit b059c46af4ea5649f20ef70c2cd328958284dcdc -Author: Lukas Grossar -Date: Thu Jan 26 17:04:52 2012 +0100 - - small changes to start testing - -commit ec26dd0362665bb84ad8cd0b7ad90a1479cbe214 -Author: Oliver Beckstein -Date: Tue Jan 10 20:12:02 2012 -0700 - - fixed writing of element column in PrimitivePDBWriter - - - the writer failed to write the element for almost all atoms except - hydrogens (this was due to stripping white space and then the name - could not be guessed...) - - related: for guessing we now give precendence to NE -> N and HE -> H; - previously these atom names were interpreted as Neon and Helium. Until - the guesser takes more information into account than just the name - we'll rather cater to the protein crowd than the noble gas simulators; - I think CA is also one of those cases... - - added test cases for elements (in particular NE and HE) - -commit 6479badd02d5863bed6731c0eb65ae4bb4343e4c -Author: Oliver Beckstein -Date: Tue Jan 10 19:04:05 2012 -0700 - - fixes in PrimitivePDBWriter and PrimitivePDBReader - - - failed if PDB had a MODEL 0 entry (for instance, written by Gromacs - 'trjconv -dump NNN -o output.pdb'): fixed by setting model_offset (default -1) - to 0 if a MODEL number of 0 is read. Not very robust implementation but - probably better than before. - - multi PDB reader: read CRYST1 unitcell for each step (i.e. each MODEL); not - fully tested, feedback welcome - - added a few comments and generally removed whitespace to make the code more compact - - use isintance(obj, other) instead of type(obj) == type(other) comparison (ensures - that inheritance is properly taken into account) - - changed some generic Exception to TypeError, ValueError or AssertionError - -commit 30e21da161dcbb2ad43f0b459279f1519e8bd623 -Author: Oliver Beckstein -Date: Wed Dec 21 14:19:23 2011 -0700 - - Issue 87: moved UnitTest code from package to testsuite - - - closes Issue 87 - - left stub code so that MDAnalysis.tests.test() works (if MDAnalysisTests is installed) - and also any of the examples that use 'from MDAnalysis.tests.datafiles import *' - - initial tests appear to pass but some more checking might be required - - adjusted release of tests to 0.7.5 and modified the setup.py files accordingly - -commit b26bbffe6bcc820dd4981c39b5dea4f86771c9d9 -Author: Oliver Beckstein -Date: Wed Dec 21 09:35:53 2011 -0700 - - Issue 87: testsuite along package - -commit 966c8c2c27a2af4258faeaff961c866bedffc001 -Author: Oliver Beckstein -Date: Wed Dec 21 09:25:54 2011 -0700 - - Issue 87: moved master into package/ dir - -commit 166bb87041356291040e2bc5e0c43e71b1e3a472 -Author: Oliver Beckstein -Date: Mon Dec 19 16:33:15 2011 -0700 - - generate more docs for parents of AtomGroup - -commit de451c8024314616bc0d1b922778fc89d396104d -Author: Oliver Beckstein -Date: Sun Dec 18 18:08:47 2011 -0700 - - ignore files from builds and some generated example data - -commit d84fe099b572631a395a148cdadc1552088e655f -Author: Jan Domanski -Date: Wed Dec 14 21:38:55 2011 -0500 - - Minor fixes in PrimitivePDB reader/writer - - - The REMARK field is parsed correctly, - - check if Reader generated bonds, before attempting to added them to Universe.bonds . - -commit ce1508d14c67b3f297f711d48d1e9a00276283b6 -Author: Jan Domanski -Date: Tue Dec 13 22:15:56 2011 -0500 - - Issue 77: adding tests, extending the functionality - - Unit tests cover only: - - mulitframe pdb read: check if the number of frames is correct, check if all the frames contain the desired number of atoms, - - multiframe pdb write: with start, step attributes, from a selected AtomGroup: check the number of frames, check if each frame contains the desired number of atoms. - - check the Universe object _psf attribute '_bond' entry; a known output is provided to compare agains. - No actual coordinate check is performed; some of the tests should be moved from PrimitivePDBWriter to the Reader. - - closes Issue 77 - -commit 89c98347427ff71243f2f81c51fd9696d78515b2 -Author: Ben Hall -Date: Mon Dec 12 14:54:28 2011 +0000 - - Added - *docstrings - *way to treat non protein groups for CA based GNM - *alternative to CA based GNM, using 4.5 A closest atom contacts - -commit 9b322ca29c469023a81edcce779500cae4a4a4a1 -Author: Ben Hall -Date: Mon Dec 12 09:44:33 2011 +0000 - - Example script for using GNM analysis - -commit 0b8348d28ed3659b40aa365c1030d9cd2dae3fdf -Merge: 9a91cf074 6d5800f05 -Author: Sébastien Buchoux -Date: Sun Dec 11 22:32:27 2011 +0100 - - Closes issue 85. - -commit 6d5800f059ced84dd2546bdc6d3677f56f89a251 -Merge: 9a91cf074 1aec10a7a -Author: Sébastien Buchoux -Date: Sun Dec 11 22:18:59 2011 +0100 - - Merge branch 'setup-merge' into develop - -commit 1aec10a7a1ceeeead23e5a073716d313bcdef9ea -Author: Sébastien Buchoux -Date: Sun Dec 11 22:12:22 2011 +0100 - - setup.py modified to use Cython if present. setup_developer.py deleted - -commit 9a91cf074be5dd048c614a713bf188be2a0ca747 -Author: Sébastien Buchoux -Date: Sun Dec 11 11:45:54 2011 +0100 - - __version__ attribute added to MDAnalysis/__init__.py - -commit 495c1c242876398a9c96ea66fe6cbc6b29ec8698 -Author: Oliver Beckstein -Date: Thu Dec 8 12:20:16 2011 -0500 - - metadata for Ben Hall's GNM trajectory analysis - - - added citation information to README - - updated CHANGELOG with note, referencing Issue 90 - -commit 39223ab2b6d5b80a1b0ad51849989987d0dca5af -Merge: e5e942ac3 3f5a1b7d6 -Author: Ben Hall -Date: Thu Dec 8 09:22:58 2011 +0000 - - Merge branch 'master' of https://code.google.com/p/mdanalysis - -commit 3f5a1b7d6c3f597841c2ddb7f3b533d90f02acd8 -Author: Oliver Beckstein -Date: Tue Dec 6 13:29:37 2011 -0500 - - added AUTHORs to Copyright note and formatted citations uniformly - -commit d4c8e037ec1cc0816e2c6c96187c599f9145e661 -Author: Oliver Beckstein -Date: Mon Dec 5 15:38:48 2011 -0500 - - minor updates to AUTHORS (utf-8) and INSTALL - -commit e5e942ac3e09ac13d631a94fba985967dff92b32 -Author: Ben Hall -Date: Mon Dec 5 10:06:51 2011 +0000 - - GNM trajectory analysis tool - Please cite Hall et al JACS 2007 http://dx.doi.org/10.1021/ja071797y - benjamin.a.hall@ucl.ac.uk - -commit f7b4fd5e1551e2feba14953c6b9b407f2d5574b2 -Author: Oliver Beckstein -Date: Wed Nov 30 13:47:13 2011 -0500 - - fixed/improved docs - - - logger and ProgressMeter - - notes on topology_format and format keywords to Universe - -commit 175008441ffa14ce77f00712d5fb2227c9bb3e09 -Author: Jan Domanski -Date: Tue Nov 29 22:21:55 2011 -0500 - - Fixed: testest broken by the new PrimitivePDB Reader and Writer - - Lost the bonds records for the time being - they will be probably put inside the universe.psf in the future. - -commit df1cdbfea6c7b1f2045000b39f0d9a221276f464 -Author: Jan Domanski -Date: Mon Nov 28 22:52:23 2011 -0500 - - fixed LAMMPS - PDB merge confict - -commit a7de6ce0ec8a6a9da27eb4fdf41587d142615cb4 -Author: Jan Domanski -Date: Mon Nov 28 22:33:10 2011 -0500 - - Experimental PrimitivePDBReader/Writer: Support for r/w of multiframe PDB files - - Summary - PDB files with multiple MODEL entries can be read in: coordinates for the first frame are stored, for the reminder the starting line is stored, which allows the PDB file to be read when a particular frame is called for. No checking is done if the PDB changes in between frame reads (file is not locked), only integrity check is the atom number (shouldn't change between the frames). This is in disagreement with the API which uses file locks extensively. Writing of a selection of atoms and/or frames is also supported. - - TODOs - - Unit tests are lacking, - - The type checking performed at many stanges (Universe vs AtomGroup) is unnecessary and not elegant; this will get improved, - -commit 74e446fbcadc22fb7964828b9033a92f82ca23ef -Author: Jan Domanski -Date: Sat Nov 26 22:37:23 2011 -0500 - - Enhancements to PrimitivePdbReader and PrimitivePdbWriter - - - parse new records in PDBs: CONECT, REMARK (improved), COMPND and HEADER; support both reading and writing, - - connect records are now stored inside Universe, as an attribute `bonds` alongside `atoms`, - - selectAtoms has no effect on bonds; to subset of bonds will not be selected, and when writing the AtomGroup to pdb, all original bonds will be written out, - -commit 8a0849632059e804f8bbd9727a18f51969aff090 -Author: Oliver Beckstein -Date: Mon Nov 28 18:28:03 2011 +0000 - - experimental support for a special LAMMPS DCD Reder/Writer (Issue 84) - - - use format="LAMMPS" with Universe or Reader for default timeunit - pico seconds (ps) - - Writer not tested - - can use keywords timeunit and lengthunit with Universe (passed through - the Reader/Writer) - - added time unit 'fs' to units - - added LAMMPS DCD to CHANGELOG - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@925 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f219f93ac5bab4c3b78558faed2c7126f1229991 -Author: Oliver Beckstein -Date: Mon Nov 28 17:21:33 2011 +0000 - - AtomGroup set_NAME() methods for residues also modify residues - - New AtomGroup._set_residues() method that is called to change - underlying Residue instances when any of the AtomGroup.set_NAME() - methods are called that change residue attributes. This is a bit - of a hack. In particular, changing the resid should really rebuild - all residues. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@924 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 24d80008e012bcb4b5706fdef706b6a98fcea035 -Author: Oliver Beckstein -Date: Mon Nov 28 03:47:25 2011 +0000 - - example output from native contact analysis - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@923 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2cdb8f753a33d7e20f103b71157f9381d4154b18 -Author: Oliver Beckstein -Date: Mon Nov 28 03:47:20 2011 +0000 - - unified caches in AtomGroup - - Instead of multiple _cache_NAME attributes we just have __cache[NAME]. - This makes it a little bit easier to keep track of the different - caches and manage them. - - The set_NAME methods are now making sure to clear the corresponding - cache(s) so that changes are correctly reflected in the topology. - - All test pass. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@922 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0e78d845f90c49c6a644deaf6c07c988c7f90db6 -Author: Oliver Beckstein -Date: Mon Nov 28 03:47:16 2011 +0000 - - hbond analysis test update - - r905 fixed a serious oversight in the list of acceptors but the test case had not been updated - and thus failed. Note that this test case only tests that we get the previous results, the - results have not been verified independently. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@921 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f12cc49476b9ec1d59d51ecc0fea7634020601fe -Author: Oliver Beckstein -Date: Mon Nov 28 03:47:11 2011 +0000 - - added fs as a time unit and minor fix in flags - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@920 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 009600be71a852dbd29225a9c7ab76470b1bd975 -Author: Sebastien Buchoux -Date: Fri Nov 18 21:16:15 2011 +0000 - - A few modifications made to INSTALL to reflect Debian support. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@919 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ff9470f1dbeb76726ba7f10b3e89277cc26bef8f -Author: Oliver Beckstein -Date: Wed Nov 16 16:44:23 2011 +0000 - - fixed bug in core.util.iterable(): failed on unicode - - The function wrongly detected unicode strings as "iterable" even though we - explicitly do not want this to be the case. As a consequence, the trajectory - reader detection would fail to detect this as a single file, hand it over to - ChainReader, and then fail with a "Runtime warning: maximum recursion depth - exceede". - - Fixed and added test cases. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@917 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 33caccf8c225b45fd5da9c0bd07953d6b58cd214 -Author: Oliver Beckstein -Date: Mon Nov 14 15:39:08 2011 +0000 - - fixed Issue 82: support files for online docs are now included in the source distribution - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@916 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 739cf761b9abb05445a9862e6b8bf9fb71f98dce -Author: Oliver Beckstein -Date: Fri Nov 4 22:21:09 2011 +0000 - - fixed Issue 81: ChainReader CRD bug (Timestep problem) - - ChainReader trajectory built from CRD contained garbage coordinates. This - was really due to the fact that when building a Timestep from a coordinate - array we did not enforce float32 type. This was fixed for base.Timestep and - and xdrfile.base.Timestep and a test case was added. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@914 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f2205eead58ab0f58e67bee50ae7e0c41591dd19 -Author: Oliver Beckstein -Date: Wed Oct 26 16:31:00 2011 +0000 - - updated html docs with contact analysis example - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@913 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a6d015644224e74741c64a85309470ef71f137d2 -Author: Oliver Beckstein -Date: Wed Oct 26 16:30:52 2011 +0000 - - contact analysis: additional example and cleaned up docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@912 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit bd1b1cac97f25d9db063dd8d4ef1909356cb2fe4 -Author: Oliver Beckstein -Date: Tue Oct 11 18:08:27 2011 +0000 - - fixed: SUMMARY.txt was not distributed with source dist - - Would lead to failure to build from the source tar file. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@911 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f3f698fd913443a1aa4b7b61153d90eb5171d6a1 -Author: Oliver Beckstein -Date: Tue Oct 11 18:01:37 2011 +0000 - - new chi1_selection() method for Residues - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@910 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6ec77eef3f5e52658626a2f05d6b33c8cdff9cfe -Author: Oliver Beckstein -Date: Tue Oct 11 18:01:27 2011 +0000 - - fixed(?): util.angle() would sometimes produce nan - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@909 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 396b6dc5a4d16be56261a597699eeaa593d404f2 -Author: Oliver Beckstein -Date: Wed Oct 5 23:12:17 2011 +0000 - - regenerated online docs (0.7.5-devel) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@908 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f41558fc34f813f91463cd27131ba95df38cad7d -Author: Oliver Beckstein -Date: Wed Oct 5 23:10:43 2011 +0000 - - reST fixes (mainly ..note formatting) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@907 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 134951b82d84cf7269f8efc49bcf600342056841 -Author: Oliver Beckstein -Date: Wed Oct 5 23:10:12 2011 +0000 - - Issue 79: recipe for making PCA TRRs from arrays - - Ramon Crehuet's recipe from Issue 79 and the mailing list, - slightly commented and some missing context added. - (If there are problems, re-open Issue 79.) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@906 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6cf1f6e3cda6edb5d05910d19cccedab43dd7e32 -Author: Oliver Beckstein -Date: Wed Oct 5 21:27:25 2011 +0000 - - fixed HydrogenBondingAnalysis backbone donor list - - had 'C' but should have been 'O' (this was supposed to be fixed - with r849 in 0.7.4 but a typo crept in). - - WARNING: analysis with the broken version might have produced - partially wrong/incomplete results! - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@905 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8bc9e923c1f2408ddaf50904f449f14177d93b47 -Author: Oliver Beckstein -Date: Mon Oct 3 23:13:35 2011 +0000 - - updated CHANGELOG with changes so far - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@904 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5fee8376d013839270714a5a6027288d43668b07 -Author: Oliver Beckstein -Date: Mon Oct 3 23:13:26 2011 +0000 - - improved writing of trajectories - - * new method OtherWriter() for trajectory readers to generate a - writer for any format that has been initialised for the common - basic values - * added testcases for OtherWriter() - * FIXED: analysis.align.rms_fit_traj(): can output fitted trajectory to any - supported format not just the input format - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@903 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit cbec9fe5b6d373a202a6ea359f5384477fd844a9 -Author: Oliver Beckstein -Date: Sat Oct 1 00:22:09 2011 +0000 - - fixed: ProgressMeter - - The default format string was missing a format specifier. Also - fixed the docs. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@902 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c8022abbc59f91023520989eaf785037883b8ac8 -Author: Oliver Beckstein -Date: Sat Oct 1 00:22:01 2011 +0000 - - fixed: ResidueGroup and SegmentGroup indexing - - - The type check rejected numpy.int64, which lead to rather irritating - NotImplementedErrors when attempting to use indices from numpy arrays. - Fixed by using the same numpy.dtype(type(item)) == numpy.dtype(int) - kludge that we have been using for AtomGroup... maybe this can - be written in a nicer way. - - Also changed the exception to TypeError. - - tests still pass - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@901 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3c339ed193ab44e10c43280a2ba5103d6f934352 -Author: Oliver Beckstein -Date: Sat Oct 1 00:21:52 2011 +0000 - - new distances.between() function (EXPERIMENTAL) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@900 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b901dfc49d1ad31b4466bf033a962511006b536c -Author: Oliver Beckstein -Date: Wed Sep 28 20:54:59 2011 +0000 - - upgraded some analysis depedencies to be installed right away - - A number of packages that are used in the MDAnalysis.analysis module have been moved - into the setuptools requirement section so that they are immediately installed when - MDAnalysis is installed so that users can immediately access most of the functionality. - All these packages are available from PyPi and are typically Python-only or are known - to install via setuptools without problems in general. - More complicated packages (more elaborate compilation, use of optimised libraries) are - left in the optional section because it is assumed that the user will install them - through a package management system or manually. These packages are at the moment - * matplotlib - * scipy - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@899 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 75da459fd3ea257631e0839811527c29e31d6775 -Author: Oliver Beckstein -Date: Wed Sep 28 20:54:53 2011 +0000 - - updated PyPI metadata and summary - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@898 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 30f480f5e7e8107a8aa2278b50e04949e5dbf70d -Author: Oliver Beckstein -Date: Wed Sep 14 20:15:03 2011 +0000 - - merged changes for PyPI submission into master - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@891 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e36836e69e93a7a977fcee7015d154dc74d626b1 -Author: Oliver Beckstein -Date: Wed Sep 14 20:14:57 2011 +0000 - - test dependencies in dedicated setuptools variables - - (see e.g. http://parijatmishra.wordpress.com/2008/10/08/python-packaging-setuptools-and-eggs/ - for notes) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@890 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit abfa65e2f629f05b28b33e35155d2d5ed4459352 -Author: Oliver Beckstein -Date: Wed Sep 7 22:34:53 2011 +0000 - - started development: bumped version to 0.7.5-devel - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@877 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 82013d0553607df28057ffdc676f4a38a714b52e -Author: Oliver Beckstein -Date: Wed Sep 7 22:32:57 2011 +0000 - - online docs for 0.7.4 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@876 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9163e911bd047fc8b0953d5693d8e22e303c43b2 -Author: Oliver Beckstein -Date: Wed Sep 7 22:32:44 2011 +0000 - - release 0.7.4 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@875 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0fb11f43328eff208f4353f5e0d927c62b949ef4 -Author: Oliver Beckstein -Date: Wed Sep 7 20:23:13 2011 +0000 - - removed trajectory test data (Issue 28) - - - all data moved into MDAnalysisTestData - (new branch in svn:branches/MDAnalysisTestData, branch point is r860) - - UnitTests will not work unless the datafiles are installed separately. - One MUST install MDAnalysisTestData first. All examples should work as - previously (once MDAnalysisTestData is installed) because MDAnalysis.tests.datafiles - transparently imports the file names from MDAnalysisTestData.datafiles. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@866 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 407a2e5066bbaee6b1b49ef0239be370166474e3 -Author: Oliver Beckstein -Date: Wed Sep 7 18:02:12 2011 +0000 - - minor fixes - - - fixed error message in FixedColumnEntry - - use os.extsep instead of '.' - - white spacing formatting (automatic) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@861 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f875567d0564f37beb0fc16baa9ec88c5543b340 -Author: Oliver Beckstein -Date: Mon Aug 29 02:10:59 2011 +0000 - - regenerated html docs (new setters and resnum) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@858 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b73133eaa527f421550b570205f0e21f7a245a1d -Author: Oliver Beckstein -Date: Mon Aug 29 02:10:51 2011 +0000 - - new attribute 'resnum' for Atom and Residue - - The resnum attribute can be used to store the canonical residue number - as used, for instance, in the original PDB structure. At the moment - there is no automated way to assign these resnums and by default the - resnum is set to the resid. - - In core.Selections, the ranged selections ResidueIDSelection, ResnumSelection, - and ByresSelection are now derived from a base class _RangedSelection and - also processed together. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@857 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b8ca8093604906beecad328645ddb28ece608d8b -Author: Oliver Beckstein -Date: Mon Aug 29 02:10:44 2011 +0000 - - new set_*() methods for AtomGroup (EXPERIMENTAL) - - - set_segid() sets the segid for all atoms in AtomGroup; this allows - labeling of e.g. chains after loading a universe. Also updates - the segment objects and segid instant selectors - - other setters such as set_resname() or set_resid() only change - the attribute of the atoms (which works for atom selections) but - does not generate new Residue objects or merges old ones - - settable atom attributes: - name, resid, resname, segid, mass, type, charge, radius, bfactor - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@856 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3dea3dbf023499b2078fd6f59af9fbe3fff9f0fe -Author: Oliver Beckstein -Date: Tue Aug 23 00:15:45 2011 +0000 - - alignto(): preserve atom order in input AtomGroups - - - for select == None or select == "all" no further - selections are applied, thus preserving the ordering - of the mobile and reference AtomGroup - - allows construction of complicated correspondences via - AtomGroups - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@855 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6d7eacc9034efd1c9639bd4aa8272d0fabb4ce3e -Author: Oliver Beckstein -Date: Tue Aug 23 00:15:38 2011 +0000 - - fixed: alignto() and rms_fit_trj() selection - - order of mobile and reference selection was reversed when supplied - as a tuple (sel1, sel2) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@854 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 54fc0002ba6e86f5491538b7b127fbc7472cb9c7 -Author: Oliver Beckstein -Date: Tue Aug 23 00:15:31 2011 +0000 - - added simple test case for distance_array - - - analytical test case - - without AND with PBC (orthrhombic cell); needed because we had no - meaningful test case for distance_array() with PBC - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@853 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 28ae7b42ca61953e732646f91d6c5d81afb29cee -Author: Oliver Beckstein -Date: Tue Aug 23 00:15:22 2011 +0000 - - replaced progress_meter() with class ProgressMeter - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@852 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b34f8b9bbd16ee348f3fde7f7a7eb53f5eb1eee0 -Author: Oliver Beckstein -Date: Tue Aug 23 00:15:13 2011 +0000 - - moved echo() and progress_meter() to core.log - - - minor cleanup and consolidation of functions useful - for logging into the MDAnalysis.core.log module. Removed - analysis.util and changed imports accordingly. - - test_analysis passes - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@851 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5282576dc7a9cb076e5f14f59a64f3c915f184e1 -Author: Oliver Beckstein -Date: Wed Aug 10 22:27:50 2011 +0000 - - regenerated online docs (mainly for hbonds update) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@850 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d0e633eb266252a3158f6d0d72487a07bd0a3d34 -Author: Oliver Beckstein -Date: Wed Aug 10 22:27:37 2011 +0000 - - hydrogen bonding analysis: changes to atom list an - - - fixed one entry in the list of acceptors: CO --> O - This should capture many more backbone bonds than before. - - added more docs - - checked donors/acceptors against CHARMM 27 and the OPLS/AA topology - in Gromacs 4.5.3: we have everything - - one additional acceptor: Methionine SD: It was in the list before but - is not listed as anacceptor in CHARMM 27. I added a reference for - evidence of H-bonding of Met. - - added simple regression test for HydrogenBondingAnalysis - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@849 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 46814de4de48e71b164a018bdca0379729c8fec3 -Author: Oliver Beckstein -Date: Wed Aug 10 19:02:18 2011 +0000 - - regenerated online docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@848 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 64fe87cfa5bfe2fe7742415e36f66264e6739d6f -Author: Oliver Beckstein -Date: Wed Aug 10 19:02:07 2011 +0000 - - hbonds: still return timeseries from run() and fixed reST - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@847 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d4b4f571dab6efb93405e001984307cbf726cf6d -Author: Oliver Beckstein -Date: Wed Aug 10 18:58:30 2011 +0000 - - regenerated online docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@846 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e896e0b156201e91d7b92f5f475cd1e238b5a332 -Author: Oliver Beckstein -Date: Wed Aug 10 14:23:55 2011 +0000 - - hbonds: fixed bugs in save() - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@845 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 44fc96570357961b5e6f1b588a943c797e2a82ad -Author: Oliver Beckstein -Date: Tue Aug 9 22:31:26 2011 +0000 - - hbonds: fixed failure to import warnings - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@844 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e3334a71ec1f84009c9615cce7efc36f5c5db76f -Author: Oliver Beckstein -Date: Tue Aug 9 22:02:28 2011 +0000 - - hbond analysis: added additional method generate_table() - - - generate_table() repackages timeseries into a numpy.recarray, which is more suitable for - SQL-like processing - - save_table() simply pickles the recarray - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@843 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit bc277e2285d550194aa8afcf6679e06d620c3a96 -Author: Oliver Beckstein -Date: Tue Aug 9 22:02:21 2011 +0000 - - added parse_residue() to util - - - quick hack to parse typical residue description strings such as - "K300:HZ1" to ("LYS", 300, "HZ1") - - taken from GromacsWrapper gromacs.cbook.IndexBuilder and gromacs.util - - added quick test case - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@842 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1ddf707fb2feb1caed46fb0e40e02554854bdf0e -Author: Oliver Beckstein -Date: Tue Aug 9 22:02:10 2011 +0000 - - hbonds: use norm() and angle() from core.util - - - unified use of geometry calculations by using core.util functions - - added simple test cases for geometry functions - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@841 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7052c1a5cf0393b0c76188d4c968916f92d9e685 -Author: Oliver Beckstein -Date: Tue Aug 9 22:02:02 2011 +0000 - - hbond analysis: updated docs for output format - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@840 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a2961b0771ed8dce0b492534eacc4bedf621c473 -Author: Oliver Beckstein -Date: Fri Aug 5 19:43:46 2011 +0000 - - jandom was forgotten as a author of 0.7.4 in CHANGELOG - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@836 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 81cef48b3c6ab5b0a5c5729c1526e87b804d560a -Author: Oliver Beckstein -Date: Fri Aug 5 19:43:33 2011 +0000 - - streamlined AtomGroup.dihedral_numpy() - - - made code simpler - - moved angle(), normal() and stp() into core.util - - passes UnitTests - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@835 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit cf49068d5c981cd15b1fbabf6617c914476ac593 -Author: Jan Domanski -Date: Fri Aug 5 19:01:05 2011 +0000 - - fix for Issue 48 (sparse contact_matrix in distances.py) - - The sparse_contact matrix method, from distances.py, has been changed from - pure python. For large systems (CG bilayers with ~30k lipid atoms) the - calculation of the contact matrix with pure python code took too long. - - Solution was written using python.scipy.weave module, which allows - compilation and execution of c code (stored as a string inside python - script). - - Added a test case, after manually inspecting the data. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@833 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5b4883baf2f4bf8239417ca9b885f30f59675d8d -Author: Oliver Beckstein -Date: Fri Jul 29 04:18:52 2011 +0000 - - regenerated online docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@830 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c6249a82a7bdab4e07667e1ce5c18cb464395437 -Author: Oliver Beckstein -Date: Fri Jul 29 04:18:44 2011 +0000 - - hbond analysis: minor changes and docs - - - moved DEFAULT values for atom names into class - - added a bit more documentation and links (table of atom names) - - use None as default value for donors and acceptors instead of an empty list - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@829 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 170457886bdbcfc291cb4a42164a9e8e1707c8ac -Author: Oliver Beckstein -Date: Fri Jul 29 04:18:34 2011 +0000 - - fix for Issue 75 (HydrogenBondingAnalysis) - - - author: dcaplan - - provides additional keywords donors and acceptors to define additional atom - names for H-bonding analysis - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@828 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b2d6ea7905a937dd7606e59df5dced24dd299fae -Author: Oliver Beckstein -Date: Fri Jul 29 04:17:42 2011 +0000 - - regenerated online docs with improvements in intro (links) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@827 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8a515c74e4427624ad2fc2461aea00225b9562d7 -Author: Oliver Beckstein -Date: Fri Jul 29 04:17:34 2011 +0000 - - reST: some link fixing in intro - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@826 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 94f4e4046c550e34416ba1eca9240f7e45d67912 -Author: Oliver Beckstein -Date: Wed Jul 20 15:34:36 2011 +0000 - - regenerated online docs - - - updated citation - - had added some docs of interest to developers (ChainReader) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@825 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 268c33daf1cfcbae700e9c2e16c845c66402394a -Author: Oliver Beckstein -Date: Mon Jul 18 18:41:50 2011 +0000 - - chain reader: added frame indexing - - - Can use 0-based frame indexing to jump to a frame in a chained - trajectory (uses the underlying trajectory readers and bisecting - to find the appropriate trajectory so it should be fast even when - joining a few 1000 single frame PDBs or CRDs). - - Enabled test cases. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@823 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 90b1ddf21252effe60778c1c180090d67a868ecb -Author: Oliver Beckstein -Date: Mon Jul 18 18:41:38 2011 +0000 - - INSTALL: fixed requirements and added help - - first sentence wrongly stated that cython was still required - - added links to web site and mailing list - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@822 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fba02f016170e9ed49644630126a404d006e301b -Author: Oliver Beckstein -Date: Tue Jun 14 11:36:02 2011 +0000 - - fixed: stop_logging() - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@818 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2e79cb4031a3d8679a486ac5d310f6698f93a821 -Author: Oliver Beckstein -Date: Fri Jun 3 11:00:37 2011 +0000 - - full paper citation - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@817 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1ddf95c786a2664da43c3a5152e3d1aa5c40c3b2 -Author: Oliver Beckstein -Date: Thu Jun 2 16:50:11 2011 +0000 - - fix for Issue 74 (htaoyu1): AMBER TOP parser failure and related changes - - - ceil() function had been ommitted (fixed); required - adjustment of the loops; - - cleaned up (removed unused code) - - optimized a little bit - - added simple test case (althouh the test case does not - really check for this particular error, only makes sure - that the current PRM is properly read) - - minor cleanup in PSFParser and util.FORTRANReader - - also made ceil more explicit in PSFParser - - removed unecessary code from PSFParser - - util.FORTRANReader.parse_FORTRAN_format(): changed behaviour: - always raises a ValueError if the format descriptor is not - recognised - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@816 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1a7a236d034aefac03bb78fc7e0398b9e4ba5f1d -Author: Oliver Beckstein -Date: Wed May 25 11:05:37 2011 +0000 - - regenerated online html docs (0.7.4-devel + density) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@813 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8149a38b338bc6976fe5f10578e36a006a22d1a3 -Author: Oliver Beckstein -Date: Wed May 25 11:05:26 2011 +0000 - - small improvements in Density docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@812 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f6f7ce1d26fd656c9af617d5e6ddc1050d5ce993 -Author: Oliver Beckstein -Date: Tue May 24 20:03:19 2011 +0000 - - fixed: XTC and TRRReader would fail to obtain an appropriate Writer - - The Writer() method of a Reader should return a working writer of - the same format. This was not working properly for XTC and especially - TRR (discovered by Lukas Stelzl --- thanks!) - - - Fixed the Timestep object for TRR and XTC: only accept ndarrays - with format (natoms, 3) (XTC or TRR) or (natoms, 3*3) (TRR) - - for TRR arrays without forces and velocities, we now add empty - arrays (not really used elsewhere at the moment) - - various smaller fixes related to selecting the correct writer - (the XDR Reader base class has got a new class attribute _Writer - which needs to be set to the appropriate Writer class); also - fixed missing/non-existent keywords - - added proper test cases - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@811 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2dd048fd19ae9256ffb26a95e5a449aaa87acaf0 -Author: Oliver Beckstein -Date: Tue May 24 19:59:00 2011 +0000 - - fixed exception message for coordinate format guessing and minor doc typo - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@810 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e771e626a0d3b9549ed72bcdb9408f1fe4687d16 -Author: Oliver Beckstein -Date: Tue May 24 17:57:21 2011 +0000 - - fixed: rmsd_fit_trj() failed to write a XTC file - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@809 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit dd8932d46ea03563ac3d68a074079160b147b289 -Author: Oliver Beckstein -Date: Tue May 24 17:42:44 2011 +0000 - - updated classifier keywords - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@808 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 55e0d16e9be3695ff8dad12bb16c25e11d408241 -Author: Oliver Beckstein -Date: Mon May 23 20:26:09 2011 +0000 - - CHANGELOG: updated with coordinate_format -> format - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@807 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e199fea281519ff706e5931f69b70da660559e29 -Author: Oliver Beckstein -Date: Mon May 23 18:09:14 2011 +0000 - - keywords for format specification - - - changed coordinate_format to format (to make the most likely use case - simpler) - - hacked in the logic that uses either topology_format or format appropriately - when loading a coordinate file that also serves as topology - - removed small sanity check from the GROParser: it looked for the file - extension and raised an error of it was not .gro: with the format keyword - this check would raise an error if the user had changed the extension of - an otherwise valid gro file - - Issues: - - does not work with the chained reader (i.e. [file1.dcd, file2.dcd, file3.xtc, file4.gro] as coordinates) - - you will get a variety of odd errors when specifying the wrong format - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@806 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ae97e37f70b77a806b0f837181c5d592049d6c00 -Author: Oliver Beckstein -Date: Mon May 23 17:30:25 2011 +0000 - - specify file formats when building the Universe - - Universe() got new keywords topology_format and coordinate_format to allow - the user to specify the file formats instead of deriving it from the - extensions (does not work with "chained" files at the moment) - (Suggested by Michael Lerner.) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@805 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 906a91f633dcab1adae637d0ad6a2dd9271b66f9 -Author: Oliver Beckstein -Date: Sat May 21 23:44:00 2011 +0000 - - bumped release to 0.7.4-devel - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@798 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4855f14c8729b7578eb85421389973b0c7f63bef -Author: Oliver Beckstein -Date: Sat May 21 23:43:52 2011 +0000 - - added forgotten CHANGELOG entry (from the Release073 wiki notes) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@797 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 13c108b1b0911b2f93f9d52be01d543465bdb85a -Author: Oliver Beckstein -Date: Sat May 21 23:25:24 2011 +0000 - - release 0.7.3 (only changed release number and CHANGELOG) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@793 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0fd173b8fd46a3051f1ffdb980feeeb40050580d -Author: Oliver Beckstein -Date: Fri May 20 17:59:31 2011 +0000 - - regenerated online docs with sphinx (changes to align examples) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@792 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 84b2be3bff691629107afdbdf11d95e3e0ef624c -Author: Oliver Beckstein -Date: Fri May 20 17:58:24 2011 +0000 - - fixed mass weighted RMSD fitting - - weights were not calculated properly or it was not documented that they - need to be relative to the mean; added code so that the user can simply - provide an array of masses and the weights are computed - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@791 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0410f40af4a7ed9118cc7441f51ea9fda4bf84dd -Author: Oliver Beckstein -Date: Fri May 20 17:30:21 2011 +0000 - - removed core.rms_fitting - - The old rms_fitting module has been superceded by the qcprot module. - Feedback from the mailinglist indicated that this module is not used - anymore - http://groups.google.com/group/mdnalysis-discussion/browse_thread/thread/b120747ffccfc340 - Because this is the only module that requires LAPACK (which can be a pain - to install) we are removing the whole module ahead of schedule (originally - the removal was planned for release 0.8) to immediately improve installation. - - Examples were updated accordingly: rmsd.py shows how to just calculate the - RMSD over a trajectory, rmsfit.py the trajectory fitting; rmsfit_alignment.py - was removed because all functionality is MDAnalysis.analysis.align. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@790 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7c84c951c628003af2c14c96751f94105598885e -Author: Oliver Beckstein -Date: Fri May 20 17:30:12 2011 +0000 - - enabled mass-weighted fitting in rms_fit_trj() - - (not sure why this was still set to Not Implemented, probably oversight) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@789 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b414093dbb60b7df3488f1d97f190d0098363317 -Author: Oliver Beckstein -Date: Wed May 18 21:40:19 2011 +0000 - - setup: removed un-used fast_numeric_include from transformations.c - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@784 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3f88313bdc1d5787c107f50c0eaf94b1f543d555 -Author: Oliver Beckstein -Date: Wed May 18 16:39:20 2011 +0000 - - regenerated online docs 0.7.3 with sphinx - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@783 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit bb193dfbec7efa4286448b7e68e8bfac491fc287 -Author: Oliver Beckstein -Date: Wed May 18 16:39:09 2011 +0000 - - added improper() with test case; more reST fixes - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@782 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c4b1728c79b32edd6ed9cc890745da4fec49d8dc -Author: Oliver Beckstein -Date: Wed May 18 16:39:01 2011 +0000 - - reST doc fixes and updates - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@781 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a8bab4554c3271745829df389e092093fd70f277 -Author: Oliver Beckstein -Date: Wed May 18 02:55:48 2011 +0000 - - new AtomGroup methods bond() and angle() - - - calculate more standard geometric descriptors for groups of special size - 2 and 3 - - added test cases for bond and angle (checked with VMD) - - TODO: improper - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@780 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c2dc848a01ee173047e75818ef41345d367da717 -Author: Oliver Beckstein -Date: Wed May 18 02:55:34 2011 +0000 - - dihedral() function - - - added back numpy version as dihedral_numpy() and return - degrees not radians - - rename non-numpy to dihedral_orig() - - use dihedral() to switch between versions --- will be switched to - numpy version once this works as expected (and is confirmed to - work) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@779 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit eeb44e25261dcc0a7bc6c0ebbc83f496c0c828f5 -Author: Oliver Beckstein -Date: Wed May 18 01:48:59 2011 +0000 - - old dihedral() function - - - fixed indentation - - changed test case: dihedral() returns degrees - - unit test for AtomGroup passes - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@778 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f48a746e8b23a137f7c3b28a7dc71abffe37ae70 -Author: Elizabeth Denning -Date: Wed May 18 01:19:13 2011 +0000 - - dihedral orig - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@777 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c21e1147f02fb473e3410ac8600cf18c5796188f -Author: Elizabeth Denning -Date: Tue May 17 21:42:36 2011 +0000 - - fixed dihedral function in AtomGroup - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@776 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e347580c143d13e90bfb9bf47b897d5a3c700653 -Author: Oliver Beckstein -Date: Wed May 11 12:49:51 2011 +0000 - - generated online docs with new layout (sphinxdoc) and logo - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@775 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d1b37bb073e74d597e17b86eb8765c1a668bc277 -Author: Oliver Beckstein -Date: Wed May 11 12:48:58 2011 +0000 - - MDAnalysis with new logo: rebranded docs - - - added Christian Beckstein's winning logo (licence: cc-by-nd) - - added CB to AUTHORS and full LICENCE and AUTHOR information - in logo directory - - generated 200x150px and favicon (32bit, 32x32) in Gimp - (favicon is cut of the graphic) - - 127x55 is for the googlecode web site - - derivatives are licenced under same conditions (we have - a licence from Chris Beckstein to create derivative works) - - use sphinxdoc theme for docs which is almost the right colour - schema for the logo - - reduced depth of toc to 1 and added Contents heading to the - rst files at level 2: less cluttered and with new theme the - docs look much cleaner and sleaker - - added some refs etc to KD-tree - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@774 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ead81796457f8f2ff3b52d75ddefcc312cecc866 -Author: Oliver Beckstein -Date: Mon May 2 15:43:09 2011 +0000 - - AtomGroup.dihedral(): use faster numpy functions to calculate dihedral; added test cases for dihedral() and the phi()/psi()/omega() selection methods - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@772 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e56a2a6e93782120a0dfc79f2cf1bfb9b700af96 -Author: Oliver Beckstein -Date: Mon May 2 14:37:54 2011 +0000 - - added method AtomGroup.bsphere() - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@771 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a25173d1f216b4f24b2280c186c5f4c75d1f7cf3 -Author: Oliver Beckstein -Date: Mon May 2 14:37:47 2011 +0000 - - fixed: AtomGroup.bbox() - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@770 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 843848731d0047ea2177ef5c8af55abc33837786 -Author: Oliver Beckstein -Date: Sat Apr 30 17:27:51 2011 +0000 - - MDAnalysis.analysis.distances.dist() for computing distances between matching atoms in two groups - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@768 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit be2381a51b34dec910e7b9841f243192cdfd33b2 -Author: Oliver Beckstein -Date: Thu Apr 28 00:12:28 2011 +0000 - - regenerated online docs (H-bonding analysis and PDBQT format) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@764 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 33ab4080640bda6cee3e2a7e1d90e4bce748d215 -Author: Oliver Beckstein -Date: Thu Apr 28 00:12:10 2011 +0000 - - integrated docs for David Caplan's hbonds analysis module into online docs - added h-bonding analysis to CHANGELOG and David Caplan to AUTHORS - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@763 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 956f4feb61153b6aefb7ec4407c3c7802bbf4456 -Author: Oliver Beckstein -Date: Thu Apr 28 00:12:00 2011 +0000 - - added tweaks to David Caplans hbond.py to make it work with Gromacs waters - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@762 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 95f61edf17e4fe30c2336ed4725b9f6f151976d3 -Author: Oliver Beckstein -Date: Thu Apr 28 00:11:49 2011 +0000 - - David Caplan's hydrogen bond analysis - - add http://github.com/davecap/labwork/raw/master/mdanalysis/hbonds.py - - currently GPL3 so we cannot use it - - added to init - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@761 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 147d013b69fe852585f0151ad33e1f99ee2e70bd -Author: Oliver Beckstein -Date: Wed Apr 27 20:22:20 2011 +0000 - - docs for PDBQST format integrated into online docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@759 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit aae1ef933ae76666a7fd8f4ed5c586f6c20b9559 -Author: Oliver Beckstein -Date: Wed Apr 27 20:21:58 2011 +0000 - - PQDBQT: use Atom.charge for partial charges and Atom.type for atomtype - - removed partialCharge and element attributes from Atom - - minor comments and streamlining - - adjusted format description to match PDBQT - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@758 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 684b281ce6d7e7c2f94cfeb1fa6beb36fd2fd51f -Author: Oliver Beckstein -Date: Wed Apr 27 20:21:52 2011 +0000 - - added test for writing PDBQT files - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@757 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3ab420246c90fb8cc6925e226cb4b2a2508fd29a -Author: Oliver Beckstein -Date: Wed Apr 27 20:21:44 2011 +0000 - - PDBQT small changes - - fixed PDBQT test case; passes now sensibly - - added docs - - removed commented out Bio.PDB stuff in PDBQT.py (not needed) - - updated CHANGELOG and AUTHORS with Paul Rigor's contribution - - added PDBQT to the list of supported formats - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@756 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2af90585799c9d3512847a793c965dc661311809 -Author: Oliver Beckstein -Date: Wed Apr 27 20:21:30 2011 +0000 - - PDBQT support (Paul Rigor http://www.ics.uci.edu/~prigor ) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@755 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a0548a9fa6480e4a9f693fe4efa3ecbae854eb94 -Author: Oliver Beckstein -Date: Sat Apr 23 20:10:45 2011 +0000 - - regenerated online docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@754 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 58572f982cf9459e9fa4e923a602cebf0df4983c -Author: Oliver Beckstein -Date: Sat Apr 23 20:09:48 2011 +0000 - - updated MDAnalysis paper citation: published online http://dx.doi.org/10.1002/jcc.21787 ; also added HELANAL citation and made everything look similar to the googlecode home page - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@753 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2627b536cf2cdc7a8ec1a8c97ce4d20389eb1b24 -Author: Oliver Beckstein -Date: Wed Apr 20 21:19:22 2011 +0000 - - example updates: fixed normalization in radial_distribution_function.py and redrew figures - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@750 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8b0721178dd6a86acd6f733429eb3672a8588d07 -Author: Oliver Beckstein -Date: Wed Apr 20 20:30:34 2011 +0000 - - updated a number of examples - - write figures to ./figures subdirectory - - write data to ./output - - added example output and figures for blocks.py, backbone_dihedrals.py, - radial_distribution_function.py - - fixed/update a number of examples - - blocks.py: block averaging (see example in the paper) - - radial_distribution_function.py: g(r); this is the optimized version - (see paper) with correct normalisation - - backbone_dihedral.py: example for Timeseries.Collection and use of the - new special Residue.phi_selection() and Residue.psi_selection() methods - for the common backbone dihedrals; script is now ran on the DIMS AdK - trajectory and produces a figure - - TODO: other scripts - - made all scripts executable - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@749 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8caec3ce32df124449112082df8c4281f502bcd2 -Author: Oliver Beckstein -Date: Wed Apr 20 20:30:24 2011 +0000 - - coordinates: use close() throughout instead of deprecated close_trajectory() - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@748 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3a7fe45dd3fc13e6d39352c557722e070ea8d791 -Author: Oliver Beckstein -Date: Wed Apr 20 20:30:00 2011 +0000 - - fixed Issue 70 (instant selection of atoms in residues that are also termini) - - removed caching of atoms in Residue - - decreases performance (probably) but at least returns correct selections - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@747 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c1758c61cad95b4e5350936ca53c1ccc74b448c5 -Author: Oliver Beckstein -Date: Wed Apr 20 20:29:40 2011 +0000 - - regenerated online docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@746 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7e42c6ed0d06cf44877460df56e002aad9b14f9a -Author: Oliver Beckstein -Date: Wed Apr 20 20:29:31 2011 +0000 - - online docs: link to Selection exporters from start page and made exporter table clearer - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@745 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e2ee557fb32c5fbc458bc8e91f47c8a44d99f5f2 -Author: Oliver Beckstein -Date: Wed Apr 20 20:29:24 2011 +0000 - - new attribute Timestep.volume: unit cell volume (+test cases) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@744 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ae0b88dae56efab53cdf35f70913712ceffe4682 -Author: Oliver Beckstein -Date: Wed Apr 20 20:29:16 2011 +0000 - - notes on using Apple gcc and possible problems running examples from source dir (thanks to Justin Lemkul for the tips) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@743 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b559fe382b530c300c02b9fcc2c9c17dd6987877 -Author: Oliver Beckstein -Date: Tue Apr 19 20:06:30 2011 +0000 - - regenerated online docs with new docs on selection exporters - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@740 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ea0e3d1aa35216d00d505bf15978a07827774f78 -Author: Oliver Beckstein -Date: Tue Apr 19 20:06:12 2011 +0000 - - integrated and expanded documentation on selection exporters - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@739 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 894f85e0641337539ece43d6ce286f50df17059e -Author: Oliver Beckstein -Date: Tue Apr 19 20:06:03 2011 +0000 - - LeafletFinder: removed deprecated atoms() method and some reST fixes - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@738 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 616dc4ed66adbc954476eb5f9848f28d98410989 -Author: Oliver Beckstein -Date: Mon Apr 18 02:44:00 2011 +0000 - - regenerated docs (after helanal reST fixes) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@737 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8da7bedc9c0b0494724b8281844e5000bc1cdecf -Author: Oliver Beckstein -Date: Mon Apr 18 02:43:50 2011 +0000 - - fixed reST in helanal.py - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@736 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ec5546ea09b972ac0a914fafade179bac4739657 -Author: Oliver Beckstein -Date: Mon Apr 18 02:32:36 2011 +0000 - - regenerated online docs (includes HELANAL) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@735 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1000dd5d60157247793518bcb4f43868bb20b97f -Author: Oliver Beckstein -Date: Mon Apr 18 02:30:52 2011 +0000 - - HELANAL helix analysis (integrated Ben Hall's Python implementation) - - Ben's code is licensed under the GPL v2+ - - http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html - - reference: Bansal M, Kumar S, Velavan R., HELANAL - A program to - characterise helix geometry in proteins. J Biomol Struct Dyn. 2000 17(5):811-9. - - requires universe and start and stop residue of the helix to be analyzed, - write a number of output files - - not fully tested! - - numpified, removed support code for vector handling and trajectory I/O - (now all done with numpy or MDAnalysis), added docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@734 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6ee0d03cffce47186e7f0668d83d67606218259f -Author: Oliver Beckstein -Date: Mon Apr 18 02:30:38 2011 +0000 - - new attributes for universe.trajectory: frame and time - - report the frame number and time of the current time step - - single frame formats return frame = 0 and time = 0.0 - - added test cases - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@733 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6cf3507db2243edd0c90472ba273d6b4f9dd3571 -Author: Oliver Beckstein -Date: Mon Apr 18 02:30:29 2011 +0000 - - replaced uses of CartesianToolkit with numpy (untested) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@732 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d9b741c1a529002faff683e012b49cf76cabf709 -Author: Oliver Beckstein -Date: Mon Apr 18 02:30:17 2011 +0000 - - added original HELANAL (Python) code by Benjamin Hall - - LICENCE: not free, DO NOT DISTRIBUTE yet - - not integrated, this is the code as provided by Ben - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@731 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1adeb82b2cce4ea089d78fc43016d2c7187d95ca -Author: Oliver Beckstein -Date: Sun Apr 17 19:36:26 2011 +0000 - - CRDReader streamlined and improved - - fixed default unit as Angstrom, but that did not - have any influence on the behaviour so far) - - added official CRD format to the comments for future reference - - improved robustness of EXT detection by using a staged detection of - lines (continue blocks) and checking length of fields - - added additional sanity check on the number of atoms (which we can - get from the CRD header) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@730 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 67e1102b48b9def91c1012649089241daff1bcd3 -Author: Oliver Beckstein -Date: Sun Apr 17 19:36:19 2011 +0000 - - fixed: units.py must be in UTF-8 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@729 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 87977a395605663ef3d3772f4298b3b84b2f8e75 -Author: Oliver Beckstein -Date: Sun Apr 17 14:28:19 2011 +0000 - - added comment and formatting header to files (Issue 68 and Issue 69) - - name, url, copyright and licence (GPL v2+); Issue 68 - - citation information (need to update once full citation available) - - modelines for emacs and vim to ensure that no TABs are use (Issue 69) - - might have to take a closer look at the licences of the bundled packages - and customize their comment headers - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@728 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0114e6a8e6fc346265f8ca230a1020cb78684a61 -Author: Oliver Beckstein -Date: Sun Apr 17 14:27:27 2011 +0000 - - converted all TABs to spaces (Issue 69) - - used emacs 'untabify' on all files; see - http://code.google.com/p/mdanalysis/issues/detail?id=69#c1 - - unit tests pass - - TODO: add marker lines for editors (do this together with a - fix for Issue 68) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@727 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 46cc00dd3eddf8eb30f609d655c25cce630cfc37 -Author: Oliver Beckstein -Date: Sun Apr 10 13:05:51 2011 +0000 - - changed legal coordinate values for GRO and PDB - - limits -999.9995/9999.9995 - - changed the actual check to min < x <= max (see Issue 57 comment #7) - - tests: the min test is ok, the max test relies on <= and somehow does not - sharply discriminate; e.g. for GRO 9999.9996 passes and for PDB 9999.9951 - passes. Not sure what's going on but I made the tests a little bit weaker - (PDB: 9999.996, GRO: 9999.999). In practice it probably won't matter... - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@724 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3ace9d4e5fc0033ef26f0c293430bed2284a8d1c -Author: Oliver Beckstein -Date: Sun Apr 10 12:20:57 2011 +0000 - - test case for writing GRO files and optimization of fixes for Issue 57 - - testing for writing GRO and limits ( -999.994 nm < x < 9999.994 nm ) - - sharpened test for PDB limits ( -999.994 A < x < 9999.994 A); note units A vs nm - - conceivably we could include the boundaries into the legal values (they still round down); - if we do then we need to adjust the tests - - legal coordinates check for GRO: moved out to before the file is even opened so we can get - rid of removing the opened file - - GRO writer: use "with open() as ..." instead of "try: ... finally: close()" - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@723 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f0b2076b47ffe2bec2e9e64de2757f27a38b4477 -Author: Oliver Beckstein -Date: Sun Apr 10 12:20:45 2011 +0000 - - patch 57b by jandom: completes the fix of Issue 57 (coordinate checking of GRO/PDB writers) - - From http://manual.gromacs.org/current/online/gro.html - - position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places) - - velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4 decimal places) - Does that mean a max values of 9999.999/-999.999 for coords and same for velocities, but with the decimal moved a digit to left? - - added validation for gro writing, moved the coordinate checking method to parent writer class. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@722 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f28ec8b49d4b3b02667b6e6d00327d584b73879c -Author: Oliver Beckstein -Date: Sat Apr 9 22:34:26 2011 +0000 - - updated CHANGELOG with recent 0.7.3 changes - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@721 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 241afbf437d58e8dc6d0bdef98fb601a4d74270f -Author: Oliver Beckstein -Date: Sat Apr 9 22:34:19 2011 +0000 - - relaxed test for MDAnalysis.analysis.align.rmsd: rmsd(A,B) == rmsd(B,A) only - has to be equal to 5 decimals (jandom reported some spurious test failures in Issue 57) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@720 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d1ffce7ae86796c879808357833bbb1a4e194654 -Author: Oliver Beckstein -Date: Sat Apr 9 22:34:12 2011 +0000 - - fixed Issue 57: optimized patch and added test case - - moved the coordinate check out of the loop and test the whole coordinate array in one - go (better performance but error reporting is worse because we do not report the offending - atom anymore) - - remove the opened PDB file before raising the ValueError - - added test case (should have had one for PrimitivePDBWriter anyway...) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@719 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0d37e3cf1d8daf7c7c78e74e4a74bf267ec5820d -Author: Oliver Beckstein -Date: Sat Apr 9 22:34:05 2011 +0000 - - patch for Issue 57 by jandom - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@718 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ca30f661e1b2e7eeb0b15d3b8f1315ceff3bd95b -Author: Oliver Beckstein -Date: Sat Apr 9 22:33:59 2011 +0000 - - comment on benchmarking sqrt(dot(v,v)) vs numpy.linalg.norm (first one is 3x faster) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@717 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5d27868d6d17f764eaf01d18a2aaa7e31eff5b53 -Author: Oliver Beckstein -Date: Fri Apr 1 00:01:54 2011 +0000 - - regenerated docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@713 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fdf23da42bb7ab9767adc1142ed3a4ca6ec2d01b -Author: Oliver Beckstein -Date: Thu Mar 31 23:58:33 2011 +0000 - - alignto() and rms_fit_trj(): changed keyword 'select' default from 'backbone' to 'all' because this leads to less confusion, especially when the mobile and ref groups are already appropriately chosen - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@712 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1af849bc50a0cd91ca3bd9e92733dabe2c30a31d -Author: Oliver Beckstein -Date: Thu Mar 31 23:46:55 2011 +0000 - - FIXED: alignto() raises KeyError: 'target' - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@711 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f9f75fcd1588eb83ffefe1f02e8de106cfd50da3 -Author: Oliver Beckstein -Date: Thu Mar 31 23:19:19 2011 +0000 - - regenerated online docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@710 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e50d42242335d08325c777064fa0f14b5ea4001a -Author: Oliver Beckstein -Date: Thu Mar 31 23:19:03 2011 +0000 - - better docs for logging - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@709 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 16efded960bf48f9876fdb9fe4f4f181f4c0fd06 -Author: Oliver Beckstein -Date: Thu Mar 31 16:14:16 2011 +0000 - - fixed: mime type of new html online docs was not text/html - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@708 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0747737016a678b91ee70b293b02e8ad770034f1 -Author: Oliver Beckstein -Date: Thu Mar 31 16:08:47 2011 +0000 - - regenerated online docs with TRR/XTC additions - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@707 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 615227f00cfbc57a3b521f63f48a3fe72d00553d -Author: Oliver Beckstein -Date: Thu Mar 31 16:08:22 2011 +0000 - - added documentation for Gromacs TRR and XTC format and libxdrfile - - new reST docs - - also fixed documentation for Writer() (was still the DCD one) - - sanitized argument processing of xdrfile.core.TrjReader.Writer() (most of the DCD arguments - are not used by XTC/TRR) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@706 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3189b2b51dad4ddda4f58f8506c7154e9d60ab02 -Author: Oliver Beckstein -Date: Thu Mar 31 16:08:08 2011 +0000 - - bumped release to 0.7.3-devel - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@705 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit bd402abea945764c3d0395b58f2f740341c04960 -Author: Oliver Beckstein -Date: Thu Mar 31 12:07:09 2011 +0000 - - online documentation for Release 0.7.2 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@699 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f089d8f3f9b2e5d7aa4928f628612b9bf86b4672 -Author: Oliver Beckstein -Date: Thu Mar 31 12:06:52 2011 +0000 - - release 0.7.2 - - bumped release - - fixed documentation (made all headings start with text, not a module name) - - added documentation to the topology module - - bumped developer release to 0.7.3-devel - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@698 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7fc2d6f1693bedc4cba749c41f18ac296a8e0822 -Author: Oliver Beckstein -Date: Thu Mar 31 10:46:47 2011 +0000 - - internally rewired guess_atom_type() to use guess_atom_element() and changed docs accordingly - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@697 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ad586dcdb6dced2e0c4aedf37e9b55b4a8e48e6c -Author: Oliver Beckstein -Date: Thu Mar 31 10:46:40 2011 +0000 - - fixed: CRDWriter tests failed because of a bug in the use of the with statement - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@696 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e3db494ff94eac11901812713b1854db1966c109 -Author: Oliver Beckstein -Date: Thu Mar 31 00:39:10 2011 +0000 - - CHANGELOG: white space fixes (note: do not edit CHANGELOG through the gcode web interface because whitespace is messed up) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@694 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e95a78f22c2cf02b03478e2149dfda5a5d1f3aa4 -Author: Oliver Beckstein -Date: Thu Mar 31 00:25:02 2011 +0000 - - added improved masses and atomtypes detection and white space fixes throughout - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@693 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4d43e920b189a54760ec50fabb5fbf9a98174f98 -Author: Oliver Beckstein -Date: Wed Mar 30 18:13:44 2011 +0000 - - regenerate online docs (updated Trajectory API and align) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@691 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit db97ed4b92af55537a5d617f7764ddc6924eb256 -Author: Oliver Beckstein -Date: Wed Mar 30 18:12:41 2011 +0000 - - analysis.align: streamlined rms_fit_trj() and alignto(); use common 'select' interface - - consistent usage of 'mobile' and 'reference' set - - fasta2select() returns dict with 'mobile' and 'reference' keys (MIGHT BREAK OLD - CODE ... but I don't think anyone used this) - - the common select code _process_selection() has a hack to accept the old - 'target' key instead of 'mobile' until 0.8 - - test cases: added unit test for rmsd() and had to adjust the value for - the rms_fit_trj() test case (not really sure why but at least it's consistent - with what VMD shows) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@690 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 20253fa44cd28e04ac7bbd137a95cbbba0d9c7bd -Author: Oliver Beckstein -Date: Wed Mar 30 18:12:33 2011 +0000 - - TrajectoryReader gained new Writer() method that returns an appropriate TrajectoryWriter for the read trajectory - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@689 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit bf53397df083ce7dfd852d9711156bf1bf94ce79 -Author: Oliver Beckstein -Date: Wed Mar 30 18:12:27 2011 +0000 - - minor align docs (rms_fit_trj() is now pretty fast) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@688 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 12f3fec349e602ec834f76e76ba2cbf263f4cf65 -Author: Oliver Beckstein -Date: Thu Mar 24 00:34:57 2011 +0000 - - regenerated online docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@686 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit acdb227db350b9b940498f5bf7fc6c9ff954e262 -Author: Oliver Beckstein -Date: Thu Mar 24 00:34:45 2011 +0000 - - improved docs for align - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@685 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d71a51491b23274cb920bd5f44cb98e5aaf6f98b -Author: Oliver Beckstein -Date: Wed Mar 23 14:11:29 2011 +0000 - - regenerated online docs (new analysis.align docs) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@684 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 596b8eff163cbb8ddde1a766fe75653aaad14d52 -Author: Oliver Beckstein -Date: Wed Mar 23 14:09:56 2011 +0000 - - align module improvements - - alignto(): added subselection to transform arbitrary AtomGroups - - much more exhaustive documentation (including step-by-step tutorial) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@683 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3b16db1a269ac63b9ace230b52506bf0749d24bf -Author: Oliver Beckstein -Date: Wed Mar 23 03:38:52 2011 +0000 - - fixed Issue 59 (naveen.michaudagrawal) -- DCDWriter now checks input coordinate array for continguousness - - Because DCD's store the data in fortran format, ie a single timestep is (x,x,x,..., y,y,y..., z,z,z...) and through the magic of numpy arrays that's usually transparently handled. - - The DCD writer is a bit brain dead when it comes to writing a trajectory. When I wrote the c interface to dcd writer I just took the ts._x, ts._y, ts._z arrays and assumed they were contiguous. However, the xtc data comes as (x,y,z, x,y,z, ...) and so the individual coordinate arrays are discontiguous in memory. So the easy solution is to check the flags argument of the _x, _y, _z arrays in DCDWriter and make a copy if they aren't contiguous. - - - added new unit test (passes with Naveen's patch) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@682 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c919b8dcfb9d324db9a13823b50aa53be8937dce -Author: Oliver Beckstein -Date: Wed Mar 23 03:38:44 2011 +0000 - - minor doc improvements - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@681 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9a368a6ac41d963c6659ce3829df5325c668d960 -Author: Oliver Beckstein -Date: Wed Mar 23 03:04:00 2011 +0000 - - regenerated online docs http://mdanalysis.googlecode.com/svn/trunk/doc/html/index.html again - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@680 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit dba11341e3f60f9588675839633808a79bb9c213 -Author: Oliver Beckstein -Date: Wed Mar 23 03:03:50 2011 +0000 - - alignto(): doc update - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@679 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 59aa167d3bad139645c126b51cd504b293f6b7da -Author: Oliver Beckstein -Date: Wed Mar 23 02:56:24 2011 +0000 - - regenerated online docs http://mdanalysis.googlecode.com/svn/trunk/doc/html/index.html - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@678 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 319ca59ae334657df40419531df9225efe85b0f3 -Author: Oliver Beckstein -Date: Wed Mar 23 02:56:11 2011 +0000 - - spatial alignment convenience functions added to analysis.align: - - rotation_matrix(a,b, weights=None) to get the matrix for b = R.a - - alignto(mobile, ref, select="backbone", mass_weighted=False) to align the Universe of the mobile - AtomGroup - - rmsd() is now using qcprot - - rms_fit_trj() minor optimizations (preallocate R) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@677 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 818a0600f613939cba66c984dae6902c3996c92c -Author: Oliver Beckstein -Date: Wed Mar 23 02:56:03 2011 +0000 - - _angle(v1,v2) should not return nan - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@676 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1d180488ed162647e915f144d5aa55135b9e0d04 -Author: Oliver Beckstein -Date: Wed Mar 23 02:55:55 2011 +0000 - - added many more residue names from Amber and OPLS/AA to be recognised as protein - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@675 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8ac5acd5f6b2773a418ed5bb679a489985f6c1df -Author: Oliver Beckstein -Date: Mon Mar 21 18:13:38 2011 +0000 - - regenerated online docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@674 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1a318b584441950c16b54265797914bf45c97813 -Author: Oliver Beckstein -Date: Mon Mar 21 18:13:26 2011 +0000 - - minor reST fixes in doc (more to do... volunteers, anyone?) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@673 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9ecb534cc42e0041d7677d7e10399d5142d8d11f -Author: Oliver Beckstein -Date: Mon Mar 21 18:12:57 2011 +0000 - - new attributes for Atom: radius and bfactor - - enhanced Atom object with the radius value (read by the PQR reader) and - added radii() to AtomGroup; this should make it easier to handle PQR files - - changed the way that B-factors were stored: they are now also store with - each individual Atom. For compatibility with the old behaviour, AtomGroup.bfactors - is still a (managed) attribute but this will likely be changed to a method in - the 0.8 release to have a more uniform interface - - Fixed a bug with the Bio.PDB reader: in the absence of a segid in the file it - would throw an error - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@672 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a6487d99b4093b3f7766c951bae35d793bd202d4 -Author: Oliver Beckstein -Date: Mon Mar 21 00:48:08 2011 +0000 - - regenerated online docs with new topology reader docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@671 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3f58920c00889570fde30c9e3389fab8c1cd2896 -Author: Oliver Beckstein -Date: Mon Mar 21 00:47:42 2011 +0000 - - added reST docs for topology modules, including the hard-coded tables - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@670 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 61add54bc08706609fd2492d56ecefa0a3024f62 -Author: Oliver Beckstein -Date: Sat Mar 19 05:00:51 2011 +0000 - - topology: moved atom types and masses into separate tables - - new topology.tables module (can be later expanded to read tables from files) - - added more masses and atom types (using CHARMM top_all27 and Gromacs atommass.dat) - - added unit tests for masses (note: atomtype/masses test cases are incomplete... TODO)- new functions: get_atom_mass() and guess_atom_element() that do not do much yet - but will allow finer grained control later - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@669 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 58644ccfdb46e1279a79669e8ef9074c43230f6e -Author: Oliver Beckstein -Date: Sat Mar 19 05:00:34 2011 +0000 - - guess_atom_types(): added more ions (mostly GROMOS) and unit test - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@668 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 44eb889232c87ea7d7618efeea8e1e7a07b44686 -Author: Oliver Beckstein -Date: Sat Mar 19 05:00:19 2011 +0000 - - fixed: PDB writer would fail if atom type was an integer - - use new guess_atom_element() which right now just does the same as guess_atom_type() - to always guess the element from the atomname - - improved guess_atom_type() by also checking for names that start with numbers - such as some hydrogen atoms - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@667 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 71a286b565b0c4317a636deeb34d549b676829a7 -Author: Oliver Beckstein -Date: Thu Mar 17 13:42:17 2011 +0000 - - fixed XTC/TRR testcase: fix for Issue 64 broke dt and totaltime - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@666 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1afa771b25e894180ba29367feffdb3a380e9704 -Author: Oliver Beckstein -Date: Thu Mar 17 12:54:07 2011 +0000 - - fixed AdK testcase: dt and totaltime was broken by fix for Issue 64 - - dt is not rounded anymore, hence dt is reported as 0.99999 and not 1.0 - - use assert_almost_equal() in test case - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@664 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fa564fe637d48e26a2ab209bfa556aceb61e12b8 -Author: Oliver Beckstein -Date: Thu Mar 17 12:44:57 2011 +0000 - - MANIFEST fixes: add *.c files to distribution, also make sure that the html docs are included; + some cleanup - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@663 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 86cf7d9cdece5e156ac18f4dce2ce35447536af6 -Author: Oliver Beckstein -Date: Thu Mar 17 00:15:21 2011 +0000 - - fixed Issue 66: supply generated C files so that only developers need Cython - - provide generated C files - - provide simple setup.py (for users) and setup_developers.py - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@662 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3ac43e7e29e035fe54d6171b43f351221fd20ba2 -Author: Oliver Beckstein -Date: Wed Mar 16 23:33:42 2011 +0000 - - fixed: minimum requirment is Python 2.5 - - check in setup.py - - explicitly say in CHANGELOG that we need Python 2.5 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@661 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 154f362207c740a04bfbcc5001021924c7e638dc -Author: Oliver Beckstein -Date: Wed Mar 16 23:02:29 2011 +0000 - - fixed: Python >=2.5 required (with statement is used) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@659 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ca81a4d51f755c6a7f1e6ee9714a4b13fac466cb -Author: Oliver Beckstein -Date: Fri Mar 11 03:24:13 2011 +0000 - - synced CHANGELOG with http://code.google.com/p/mdanalysis/w/edit/ReleaseNotes072 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@656 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 23a1bb7bc6e742c4934337883f49fbf9ab42a89b -Author: Oliver Beckstein -Date: Fri Mar 11 01:52:59 2011 +0000 - - Support for PDBs with 4 character resnames and segID output when writing (PrimitivePDBWriter) - (Issue 63, patch by dcaplan) - - When I try to read and write PDBs with 4 character resnames used in NAMD/VMD I end up with an improperly formatted PDB file. This is also an issue with segIDs not being written. - - I've made a quick patch where I add support for 4 character resnames and change the format string for the output to write the segID. I also added very simple support for better guessing of atom types since the function guess_atom_type was just returning 0. - - I'm still not sure about how to deal with the 2 types of format strings for writing PDBs. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@655 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b946c380056b2738667ea6fef5920bb40fbf7d5d -Author: Oliver Beckstein -Date: Wed Mar 9 20:06:32 2011 +0000 - - Issue 64 fixed: universe.trajectory.delta values are rounded when read from the dcd header file - (This used to be rounded to 4 decimals but people suggested that the full - precision would be better.) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@654 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f74ffcb49af16ab99bad37c21a6cbb06bba4985e -Author: Oliver Beckstein -Date: Tue Feb 15 14:57:09 2011 +0000 - - rebuilt online docs (0.7.2 with fix for point selection) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@651 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit cfd2e95ccae2bcb4ae62597a83a006a47bff8035 -Author: Oliver Beckstein -Date: Tue Feb 15 14:56:56 2011 +0000 - - fixed Online Doc for point selection (reported by Joe) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@650 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 88356e8fc398ab67328ed1006022380ecd5b181b -Author: Oliver Beckstein -Date: Mon Feb 14 19:31:17 2011 +0000 - - density: corrected docs for density units (and added better error message) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@649 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 61bfdfe325fb62546627aefd7fb151f2a16e93a2 -Author: Oliver Beckstein -Date: Mon Feb 14 19:31:00 2011 +0000 - - density: use PrimitivePDBReader to get PDB (can do B-factors and does not break as easily) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@648 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a7fbe07c7b99ab04169551f18a38a4eed11fd314 -Author: Oliver Beckstein -Date: Mon Feb 14 19:30:52 2011 +0000 - - new method bbox() for AtomGroup: calculates the orthorhombic bounding box - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@647 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e3c57639773e2268ddf86de2f6204c7bf27d6bd0 -Author: Oliver Beckstein -Date: Mon Feb 14 13:53:20 2011 +0000 - - PrimitivePDBWriter writes chainID (from 1st letter of segid) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@646 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 014e7ef83edcaee4b419f21fd545d1ed5d99d45c -Author: Oliver Beckstein -Date: Mon Feb 14 12:06:52 2011 +0000 - - fixed problems with reading an processing triclinic unitcells - - Issue 60: fixed reading of CRYST1 (was completely messed up) - - Issue 61: order of angles was wrong when converting from a box vectors representation to - box lengths, angles; see e.g. http://en.wikipedia.org/wiki/Lattice_constant - for definitions - - Issue 34: revisited old bug and changed test case so that it would catch angle mix up that was - overlooked in the previous fix - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@645 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 36e42bc5b4e628027795b122843d1633379633b0 -Author: Oliver Beckstein -Date: Sat Feb 12 21:09:58 2011 +0000 - - updated deprecated usage in potential profile example (and added note that the example requires user editing) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@644 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 08610ac6c0d3f6dcfb0a15e204cd912dd5992871 -Author: Oliver Beckstein -Date: Sat Feb 12 20:55:16 2011 +0000 - - regenerated online docs (0.7.2 with MDAnalysis citation) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@643 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit db3bd0ba96a2bf5321e6ce434948840f4806da45 -Author: Oliver Beckstein -Date: Sat Feb 12 20:54:52 2011 +0000 - - added accepted MDAnalysis paper as citation - - in README, online docs and init - - also updated the examples section in the overview - - also ask users to cite the Theobald articles for the QCP rotation code - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@642 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1764edddfe80eefdc98a2cd0ae9dcfb28ad4abd9 -Author: Oliver Beckstein -Date: Sat Feb 12 20:54:39 2011 +0000 - - copied QCP rotation example to examples directory - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@641 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4a73b46ec1db7d566883641c96b43a508c9fc05b -Author: Oliver Beckstein -Date: Wed Feb 9 22:44:28 2011 +0000 - - Segment.id is an alias for Segment.name (to make the interface more consistent) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@640 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f150c0042ba766c64f9b88b86bfb8f145a810100 -Author: Oliver Beckstein -Date: Wed Feb 9 22:44:18 2011 +0000 - - PDB topology parser: use chain as segment id if no other segid defined in the file - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@639 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8f2c67b048c1c6a937fefc0bbabd3de0f3f74db2 -Author: Oliver Beckstein -Date: Tue Feb 8 12:13:55 2011 +0000 - - bumped version to 0.7.2-devel for developing - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@637 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit da035486f59220d9b618b0475403da4386ce43a8 -Author: Oliver Beckstein -Date: Tue Feb 8 11:59:59 2011 +0000 - - prepared 0.7.1 release - - bumped version to 0.7.1 - - updated README with various package licences - - updated contacts - - removed doc/DevelopmentBranch.txt (outdated) and - added short README to point user to docs - - fixed: pqr must be included in test cases - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@633 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e6a43acf57b256dafbdb4337472ff1f5d7c3719a -Author: Oliver Beckstein -Date: Mon Feb 7 03:38:50 2011 +0000 - - regenerated online docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@630 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6adfc95ee02751e39c1bf7e5b9d935c4ecfb0b40 -Author: Oliver Beckstein -Date: Mon Feb 7 03:38:29 2011 +0000 - - simple example for block averaging - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@629 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ae0d4f56ecf6096e3526287837b914d0e835af01 -Author: Oliver Beckstein -Date: Mon Feb 7 03:38:19 2011 +0000 - - updated units docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@628 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 22eb49febe0ea9bccc2ddeb519b70a46933a2dc1 -Author: Oliver Beckstein -Date: Mon Feb 7 03:38:05 2011 +0000 - - density: new density_from_PDB() function - (uses BFactorDensityCreator to make a density from crystal waters; - checked with 1IFC.) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@627 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e37557f6c8eb4b117282183290281d4a5d79d337 -Author: Oliver Beckstein -Date: Sun Feb 6 14:52:29 2011 +0000 - - regenerated online docs (coordinates) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@626 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b60c129c8e3f1c4260b308fc5f881a6379b5b35a -Author: Oliver Beckstein -Date: Sun Feb 6 14:52:13 2011 +0000 - - docs on iteration and slices in the Trajectory API - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@625 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fbe6c827a6f5003a4d8ae6db8e362f6222ce725a -Author: Oliver Beckstein -Date: Sun Feb 6 14:30:23 2011 +0000 - - regenerated docs: added table of supported coordinate formats - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@624 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit dc58ca82f176655453a8a327508b38b3f158c7fa -Author: Oliver Beckstein -Date: Sun Feb 6 14:30:02 2011 +0000 - - docs: added table of all supported coordinate formats and linked it from top page - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@623 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4c664d4b714514c77da7991c289389d1e35d966d -Author: Oliver Beckstein -Date: Sun Feb 6 00:12:15 2011 +0000 - - regenerated online docs (PQR and TRJ added) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@622 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e9a355661b04f6d9d525776b71d9aca2ff0fcdcc -Author: Oliver Beckstein -Date: Sun Feb 6 00:11:50 2011 +0000 - - added PQR and Amber TRJ docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@621 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 94c09f1eb0821e03855ce8b2d889d36590782cd3 -Author: Oliver Beckstein -Date: Sat Feb 5 23:04:26 2011 +0000 - - added PQR support - - - can read a minimum topology and/or coordinates from a whitespace separated - PQR file as described at http://www.poissonboltzmann.org/file-formats/biomolecular-struc - - added testcase (input generated with - 'pdb2pqr --ff=charmm --whitespace adk_open.pdb adk_open.pqr') - - Note: Reading of compressed pqrs as topologies is not supported yet. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@619 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d26b36871960649861c8b13b2c72a1d0d22029eb -Author: Oliver Beckstein -Date: Sat Feb 5 22:59:01 2011 +0000 - - Amber top parser: convert charge to MDAnalysis base unit e - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@618 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 399eff18938bd99e8fe2c1568bfebfba02510eaa -Author: Elizabeth Denning -Date: Fri Feb 4 01:28:47 2011 +0000 - - CHANGELOG AMBER - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@617 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 60f478b373874df987f593639e84eb41d7d3a9c6 -Author: Oliver Beckstein -Date: Wed Feb 2 14:37:14 2011 +0000 - - test_atomgroup.py: added assert_() that is missing in numpy 1.2 and earlier: lead to 4 failed tests - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@616 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a21bf731471d77197f03e59c3d537d3b2bfd945d -Author: Oliver Beckstein -Date: Wed Feb 2 13:06:18 2011 +0000 - - PBC Amber test cases - - PBC Amber trajectory (provided by Ranjit Vijayan) - - various fixes to bugs uncovered by testcases - - added functionality to the FORTRANReader class - - more Amber formatted TRJ tests - - example conversion Amber -> DCD - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@615 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a263b1115778357ff89bf3f9446987f086d46720 -Author: Oliver Beckstein -Date: Wed Feb 2 12:59:15 2011 +0000 - - protein selections: added ACE and NME (Amber termini) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@614 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 11eca030fe74beba26bd028e497e2f61c197173a -Author: Oliver Beckstein -Date: Tue Feb 1 17:40:49 2011 +0000 - - added testcase for Amber TRJ (thanks to Ranjit Vijayan!) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@613 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b2c933b22ee5b91e784225fb5887513ce337f77e -Author: Oliver Beckstein -Date: Tue Feb 1 17:09:12 2011 +0000 - - work on Amber TRJ format - - enhanced the Trajectory API: readers must be able to accept (and - ignore) any keywords. This is necessary to pass the number of atoms - to the Amber TRJ reader, which needs it - - updated all readers to accept **kwargs if they hadn't done so already - - made the TRJReader work with or without box in the trajectory - (reads the first frame and looks for box information - - documented the quirks of the TRJ reader - - Amber TRJ reader can also read compressed files - - introduced a registry for formats that can do compressed files - (MDAnalysis.coordinates._compressed_formats) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@612 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 559c64de7e980f28bf945ce2d1e5867307b1cdce -Author: Oliver Beckstein -Date: Tue Feb 1 17:09:04 2011 +0000 - - added HIE residue (Amber) to protein selections and updated some docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@611 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c2dd67297b4f9d1e154af7cc48356ef5e9b562f6 -Author: Oliver Beckstein -Date: Tue Feb 1 04:35:39 2011 +0000 - - docs again (small issue in analysis.align and set all svn properties on docs) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@607 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 01cef05c0242d2e6f5284779bd27e4d0f4d7cf1f -Author: Oliver Beckstein -Date: Tue Feb 1 04:19:56 2011 +0000 - - generated docs with sphinx (includes QCP rotation and distances module (which had been missing)) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@606 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d353a88d76ecd1516ea8e1c8d8a0bdedeb970d70 -Author: Oliver Beckstein -Date: Tue Feb 1 04:19:23 2011 +0000 - - docs for qcprot (and also distances) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@605 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6b16151846711a3a7dbf43706b8c0b6710d21121 -Author: Oliver Beckstein -Date: Tue Feb 1 04:18:18 2011 +0000 - - fast RMSD aligner, based on Douglas Theobald's QCP method - - contributed by Joshua Adelman from his pyqcprot package - https://github.com/synapticarbors/pyqcprot - - new module: core.qcprot - - used as a drop-in replacement for core.rms_fitting.rms_rotation_matrix(); - rms_rotation_matrix() is deprecated and scheduled for removal in 0.8 - - added test case for qcprot (using Josh's example.py) - - analysis.align.rms_fit_trj() got additional functionality (thanks to - qcprot): - - can do mass-weighted RMSD fit with new mass_weighted=True keyword - - can write the RMSD timeseries to a text file (rmsdfile keyword) - - ATTENTION: qcprot uses cython so we - - dropped pyrex - - use cython (works without any code changes, at least cython 0.14) - - updated docs (but still need to do website) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@604 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f66c5ab3d06a75430506a667d4f2f2ad476b5389 -Author: Oliver Beckstein -Date: Fri Jan 28 17:21:31 2011 +0000 - - density: friendly error message if GridDataFormats are not installed - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@602 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 818886210551a7deb3bb15008bf32b4ff73c4bfb -Author: Oliver Beckstein -Date: Fri Jan 28 17:09:29 2011 +0000 - - regenerated 0.7.1 docs with new density analysis module - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@601 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4e42355c5c16f9b73098d3484890aef85650fc1b -Author: Oliver Beckstein -Date: Fri Jan 28 17:09:12 2011 +0000 - - density module - - generate volumetric data from trajectories - - Density class and density_from_* functions for water/protein/... densities - - originally from hops.sitemaps - - added docs - - added a few custom Exceptions and Warnings at top level - - improved docs for units (which are central to the Density class) - - uses GridDataFormats from https://github.com/orbeckst/GridDataFormats - (added as a requirement for the analysis module in setup.py; can be downloaded - from PyPi) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@600 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6fcb061f7b582bceb154f8040f4ca60f44eaf61b -Author: Oliver Beckstein -Date: Fri Jan 28 17:09:03 2011 +0000 - - added online docs to CHANGELOG (Tyler) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@599 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1fff1b008fd725a8ad2efee046af16c9fbf22751 -Author: Oliver Beckstein -Date: Fri Jan 28 10:56:48 2011 +0000 - - fixed Issue 58 (analysis.align.rms_fit_try) - - messed up a horrible if/elif construct - - fix reported by Joshua Adelman - - added unit test (and marked as slow) - - updated CHANGELOG - NOTE: The rms_fit_trj() function should be rewritten for - - speed - - better handling of trajectory formats - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@598 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6975481ba0e485620b48853f02bb766661eefec9 -Author: Oliver Beckstein -Date: Fri Jan 28 10:56:42 2011 +0000 - - fixed: some tests did not remove temporary files - - added forgotten import os so that files get properly unlinked - - problem was silently ignored because I had put it in an indiscriminate - try...except: pass block... d'oh - - now only pass if os.unlink(temp) produces OSError; otherwise raise - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@597 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a5355588d3530c174f46d4c037cb475f11fe0994 -Author: Oliver Beckstein -Date: Tue Jan 25 11:30:03 2011 +0000 - - updated CHANGELOG and bumped numpy version requirement to 1.0.3 (histogramming code??) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@593 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8014ed78bd268c49a6483152f29aaf8c6e1e94da -Author: Elizabeth Denning -Date: Mon Jan 24 02:50:21 2011 +0000 - - Amber support - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@587 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit dd94415396036287d512dc4953435a6847b3b944 -Author: Oliver Beckstein -Date: Wed Jan 19 10:22:50 2011 +0000 - - new example: monitor multimeric state of helical TM peptides (Jan Domanski) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@586 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 535cabd7092cf185d88f626bfc485e79ac374063 -Author: Oliver Beckstein -Date: Mon Jan 10 19:47:20 2011 +0000 - - regenerated sphinx docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@584 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c691a1d87572712b9cd0e3875ab4342d69e024e3 -Author: Oliver Beckstein -Date: Mon Jan 10 19:47:06 2011 +0000 - - updated/beautified docs - - added Trajectory API - - added intro to core - - wenth through DCD and XYZ - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@583 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c15845cd008a99fd71ea2064dd5fc8ec1de9c936 -Author: Oliver Beckstein -Date: Mon Jan 10 19:46:26 2011 +0000 - - regenerated docs (now show that they are for 0.7.1) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@582 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 464f2d63384a7cbb472fb03615b59e0e1ad95741 -Author: Oliver Beckstein -Date: Mon Jan 10 19:46:17 2011 +0000 - - bumped docs version info to 0.7.1 and added docs (invisible) to functions in AG.dihedral() - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@581 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 85e93997eecc75af76a06ad1c982cdfcb5230794 -Author: Oliver Beckstein -Date: Mon Jan 10 19:46:10 2011 +0000 - - transformation improvements - - added align_principalAxis() method to AtomGroup - - added two helpers to transformations - - added transform(4x4matrix) to AtomGroup - - also made AtomGroup.dihedral() raise ValueError if the group has not - 4 members. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@580 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 70c1dd83a7b10c3564f1689ee687d84d72b25119 -Author: Oliver Beckstein -Date: Mon Jan 10 15:16:22 2011 +0000 - - regenerate docs (make html) with sphinx 1.05 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@579 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7ad7cd99150e1da0a338a33dbd5d613d5cf264ad -Author: Oliver Beckstein -Date: Mon Jan 10 15:16:09 2011 +0000 - - docs fixes (see Paul Rigor's email and Comment 5 in Issue 26 (http://code.google.com/p/mdanalysis/issues/detail?id=26#c5)) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@578 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5dcee4abce19e9721f3b408b9a842c03e00c774c -Author: Oliver Beckstein -Date: Wed Jan 5 19:49:11 2011 +0000 - - added mime types for serving docs from googlecode, see Issue 44 - - svn propset -R svn:mime-type text/css `find . -name "*.css"` - svn propset -R svn:mime-type text/javascript `find . -name "*.js"` - svn propset -R svn:mime-type text/html `find . -name "*.html"` - svn propset -R svn:mime-type image/png `find . -name "*.png"` - svn propset -R svn:mime-type image/gif `find . -name "*.gif"` - svn propset -R svn:mime-type image/jpeg `find . -name "*.jpg"` - svn propset -R svn:mime-type image/tiff `find . -name "*.tif"` - - Note that these properties can only be set with the subversion client and not git-svn. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@571 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit bf16cd7d34de2b1e4f8767a674f3b217d62a9d10 -Author: Oliver Beckstein -Date: Wed Jan 5 19:21:16 2011 +0000 - - generated docs with sphinx - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@570 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 49e815e7d6e760401d0cdaf9ed700a3b3383e5a2 -Author: Oliver Beckstein -Date: Fri Dec 17 15:26:11 2010 +0000 - - FIXED: Issue 53 (ChainedReader failed when accessing dt) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@569 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1ca2520ad7697aed46bd3653badc5b0af8a2d4ff -Author: Oliver Beckstein -Date: Fri Dec 17 15:25:59 2010 +0000 - - enabled inter-sphinx links to numpy and scipy - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@568 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit cd442619e1dc76190da240d63d46ddef138c5297 -Author: Oliver Beckstein -Date: Fri Dec 17 15:22:00 2010 +0000 - - Writer class: fixed repr even if no numatoms provided - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@567 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 43be61e9178c1cd14f110d13e5f56182ca9e5332 -Author: Tyler Je Reddy -Date: Thu Nov 18 15:42:05 2010 +0000 - - Sphinx source updated to include documentation from modules in: - MDAnalysis/KDTree (except for the CKDTree module which has no docstrings) - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@565 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e1f4c1422545f8a9050701ad7ed222575cee9782 -Author: Tyler Je Reddy -Date: Sun Nov 7 19:18:58 2010 +0000 - - The Makefile in /doc/sphinx/ has been modified to put all output in the doc/html/ folder. Simply use the command: 'make html'. - Newly included sphinx .rst documentation (source only, not including built html): - -modules in /MDAnalysis/core/ - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@563 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 653ee5d5cd0ea7ef7d956d6f25ed0ab27dee0126 -Author: Tyler Je Reddy -Date: Sat Nov 6 01:47:36 2010 +0000 - - -Sphinx .rst source changes in this commit, but not supplying the built html - -not everything is formatted/fully consistent but at least we are grabbing more docs - -a few syntax warning do pop up during the build by they are not exceptions and allow the index file to be made - - Sphinx documentation additions: - -modules (except TRR.py and XTC.py which don't seem to have docs but import from elsewhere) in MDAnalysis.coordinates (trying to use a similar doc organization as MDAnalysis.analysis) - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@555 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 22a353d4401a3bf3557bd8e81e56e3a15ec33a7d -Author: Elizabeth Denning -Date: Fri Nov 5 21:00:44 2010 +0000 - - dihedral analysis for AtomGroupmust use a hard-specific selection to get correct dihedral value - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@554 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4a637c235039fabf79c7d25087d6568af20f3cb6 -Author: Oliver Beckstein -Date: Fri Nov 5 04:15:54 2010 +0000 - - documentation enhancements and configuration changes - - added overview (not finished) and page on selections (goes beyond the current - online docs and includes the docs on instant selectors) - - maded analysis modules separate pages (otherwise the analysis page becomes very - long and cluttered) - - renamed the top level file to index because that makes it easier to serve it - via apache - - configuration file changes - - bumped version/release - - put authors in one variable and also added Joe - - removed most of the special sphinx modules, only kept autodoc and intersphinx, - add the others peicewise when needed (also might help to reduce weird sphinx - errors) - - added links for intersphinx (but commented out during development because - loading the objects.inv always takes a while) - - removed all path fiddling; simply use full import names in docs. This works well - but keep in mind that this obtains the docs from imported modules; works best - with developer installation (i.e. "python setup.py develop") - - "make html" works fine for me - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@553 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4af4a348c13db21648a27526c2936e9f3b9a73e6 -Author: Elizabeth Denning -Date: Thu Nov 4 00:22:01 2010 +0000 - - selection update for nucleicxstal 0.7.1 only - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@552 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4784f04e815d763ee9fd276ce6171b68b2599e43 -Author: Oliver Beckstein -Date: Wed Nov 3 23:39:44 2010 +0000 - - contacts: can write figures by suppling filename and more docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@551 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 094b90a178422c4854ceed79e75350b7e41b429b -Author: Oliver Beckstein -Date: Wed Nov 3 22:24:57 2010 +0000 - - added Joe Goose to AUTHORS and documented fix of Issue 51 in CHANGELOG - (picked from the 0.7.0 release branch) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@549 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5fc635e39d3a60f8fc4cac5a0513a8fdfef0905e -Author: Joseph Goose -Date: Wed Nov 3 21:11:09 2010 +0000 - - Fix for issue 51: bolean correction from and to or for various flot32/64 checks etc. - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@546 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c1a04e4dc667b0b1f69062cd001a53ee313f2825 -Author: Oliver Beckstein -Date: Wed Nov 3 20:10:50 2010 +0000 - - contact analsysis: added docs and matrix plotting - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@545 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit aec43106ccc2d3dd3073294bed9171625c0ea25a -Author: Oliver Beckstein -Date: Wed Nov 3 18:45:56 2010 +0000 - - fixed: tests for crd files would fail (added crds to setup.py distribution) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@544 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3ce00985a31457069de0be391b330892747fb0b7 -Author: Oliver Beckstein -Date: Wed Nov 3 18:40:40 2010 +0000 - - upgraded ez_setup.py to 0.6c11 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@542 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c47fadb8f868ec21a419ef40227a02f940cb580b -Author: Oliver Beckstein -Date: Wed Nov 3 18:40:35 2010 +0000 - - new COntactAnalysis1 class - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@541 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2e778c03e0beee8bc3f08a98010999806546bbab -Author: Oliver Beckstein -Date: Wed Nov 3 18:40:28 2010 +0000 - - names() for AG - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@540 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 97e5ab69613a35c5a64d86a7999727accbf5752f -Author: Oliver Beckstein -Date: Wed Nov 3 12:46:17 2010 +0000 - - fixed race conditions in test suite - - any tests that relied on values of the internal flags have been - changed so that they set behaviour through keyword arguments instead - of manipulating flags - - affects gromacs conversion of length (GRO, XTC, TRR) with the convert_gromacs_length - flag and the use of the permissive PDB reader (permissive_pdb_reader flag) - - tests could fail when they were performed in parallel and different test threads - changed the global flags - - added a fes tests to check for the default values but DO NOT USE THE FLAGS during - testing - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@536 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0d30f46803ae14e8a5efe537f6ea3bbe89bbd5f7 -Author: Oliver Beckstein -Date: Tue Nov 2 12:46:44 2010 +0000 - - started 0.7.1 development - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@535 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9dd0cc767a302e7c653775fcbeb11758c80f7aa7 -Author: Oliver Beckstein -Date: Mon Nov 1 22:10:16 2010 +0000 - - updated CHANGELOG with denniej's CRD additions (from http://code.google.com/p/mdanalysis/wiki/ReleaseNotes070 ) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@531 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7129ae7044d8008992cfff36a551a1119d2920e3 -Author: Oliver Beckstein -Date: Mon Nov 1 22:10:11 2010 +0000 - - use PrimitivePDBReader as default PDB reader - - Bio.PDB's reader can drop atoms when they have the same name - in a residue (which happens for systems generated from MD simulations) - The PrimitivePDBReader copes just fine with thos cases (but does - not handle esoteric PDB features such as alternative atoms and - insertion codes that are not needed for handling MD simulation data). - - The default behaviour of MDAnalysis can be set through the flag - MDAnalysis.core.flag['permissive_pdb_reader'] - The default is True. - - One can always manually select the PDB reader by providing the - permissive keyword to Universe; e.g. Universe(...,permissive=False) - will read the input file with the Bio.PDB reader. This might be - useful when processing true Protein Databank PDB files. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@530 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6ff313f30307f7f4809147cdf4a938e4fb5f7bfd -Author: Oliver Beckstein -Date: Sun Oct 31 00:29:34 2010 +0000 - - Frame writer can take a Universe (fixes one half of Issue 49) - - added universe attribute to Universe - - altered GRO, CRD, and PrimitivePDB writer so that they can - deal with a Universe as argument (just get the coordinates from - the atoms instead of the 'selection' --- no performance penalty, - just making use of the improved hierarchy and the fact that - .atoms is now a true AtomGroup) - - added test case (passes) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@528 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2edbb9139d1320fc8868e9ce54c78562924b943e -Author: Oliver Beckstein -Date: Sun Oct 31 00:29:24 2010 +0000 - - test datafiles: fixed import list CRD_small -> CRD - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@527 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b869469932edd2085081e2cd8fb0d6f61e5c3097 -Author: Oliver Beckstein -Date: Sun Oct 31 00:29:18 2010 +0000 - - Trajectory API: clarified use of Writer write() method in response to Issue 49 - - no code changes, only docs - - Trajectory writers can take a Timestep as a rgument to write() - - Frame writers only take a AtomGroup or a Universe for write() - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@526 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 76033057a7e2c2cc1480489cc65a42ab456270ee -Author: Oliver Beckstein -Date: Sat Oct 30 23:05:37 2010 +0000 - - coordinate tests: make sure that for Gromacs tests the conversion flag is set correctly - - set core.flags[convert_gromacs_lengths] explicitly in setUp - - encountered failures (possibly when running multiple tests with --processes=8) which - came about because the conversion flag was set to False even though it should have - been True - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@525 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit adc66cac090996661f8c91373547a0bb230de873 -Author: Oliver Beckstein -Date: Sat Oct 30 13:03:50 2010 +0000 - - updated TODO: removed fixed stuff, added new ideas - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@521 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4bb7156039693cd78df851b7eb16191fb427ca48 -Author: Oliver Beckstein -Date: Sat Oct 30 13:03:41 2010 +0000 - - added CRD parser for quick and dirty topology building from CHARMM card coordinate file - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@520 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8bfa301cfb62748a81023f26309a7d9ffe8d1bb9 -Author: Oliver Beckstein -Date: Sat Oct 30 13:03:32 2010 +0000 - - tests: made coordinates test work consistently, also for crd - - changed precisions to match the file format (e.g. 3 for pdb and 5 - for crd); otherwise the tests do not pass consistently) - - new crd file that matches the small pdb so that we can use the same - tester class - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@519 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b37a7b582fee1a830c1f0d5281fd4f6aeb1b3556 -Author: Oliver Beckstein -Date: Sat Oct 30 13:03:25 2010 +0000 - - CHARMM CRD format: fixed a few inconsistencies in the Writer - - TotRes is really 5 digits wide (not 4); - - x,y,z are 10 wide (not 9) - - should have been not really a problem because we had simply padded the - fields so everything was in the right colum; technically, one could have had problems for totres > 9999 - and coordinates >99999.999 - - make sure to strip to larger values when writing extended format - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@518 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7554fb49d27ab12a47faf7afd447a6fc34ba05d5 -Author: Oliver Beckstein -Date: Sat Oct 30 13:03:15 2010 +0000 - - rc3 with CRD reader (CRD PSF parser still missing and leads to unit test errors) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@517 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4edd6be7a75902d616a66dabe35ddb634d43e964 -Author: Elizabeth Denning -Date: Thu Oct 28 20:41:57 2010 +0000 - - CRD Reader and Writer now in both standard and extended formats - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@515 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 691d22f75838eb226c45a2e42d91d02ae43423e2 -Author: Elizabeth Denning -Date: Thu Oct 28 09:12:12 2010 +0000 - - CRD reader and test case - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@514 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4419adf52349a0312a49cf49de7d9b8e472df963 -Author: Oliver Beckstein -Date: Wed Oct 27 10:27:36 2010 +0000 - - Trajectory API: added totaltime attribute to base.Reader - - totaltime = dt * numframes - - added test cases - - made DCDReader error messages slightly more verbose - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@512 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9b963c68ab018253f40f70c067467dfc5e70e87c -Author: Oliver Beckstein -Date: Wed Oct 27 10:27:16 2010 +0000 - - FIXED Issue 50: can write DCDs again - - only minor things needed to correct this - - also removed deprecated dcdfilename attribute - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@511 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 52f1642a2856a4adea458958391f5be0bc5e2af3 -Author: Oliver Beckstein -Date: Wed Oct 27 10:27:05 2010 +0000 - - fixed: stop_logging() - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@510 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 48f2fb203f1b8fd3f101dc429d30bc789c2634ee -Author: Oliver Beckstein -Date: Mon Oct 25 12:58:33 2010 +0000 - - analysis.align: quick hacks to make it work again - - must use an atom selection for the writer (workaround for Issue 49 when writing to a PDB or GRO) - - added tol_mass parameter to avoid raising an exception for small mass differences (e.g. when - one structure is defined via a psf and the other via a pdb with atom mass heuristics) - - fixed the progress counter (maybe use analysis.util.progress_meter instead?) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@509 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0a7324849bb9bd9e95809e5d1b7dce8b0cddc42e -Author: Oliver Beckstein -Date: Mon Oct 25 12:27:35 2010 +0000 - - added start_logging() and stop_logging() functions to top level - - simple setup for a default logger - - must be manually activated or a script must setup its own logger (see docs) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@508 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b417d5da375c73bc2ec25181cfaab0f58416374d -Author: Oliver Beckstein -Date: Sun Oct 24 00:01:03 2010 +0000 - - minor omissions fixed - - CHANGELOG: oops, AtomGroup._atoms is still here and really necessary - - setup.py: added scipy as a requirement for analysis (needed for - sparse matrix in contact_matrix()) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@507 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 207223f9656f72fa49b809559471e1b03d0adcd9 -Author: Oliver Beckstein -Date: Sun Oct 24 00:00:54 2010 +0000 - - release candidate 1 for 0.7.0 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@506 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1307d9df1646ef02ac25f01d267f2a4d32990294 -Author: Oliver Beckstein -Date: Wed Oct 20 13:55:22 2010 +0000 - - transformations: removed print() function (not needed and introduces backwards incomaptibilities) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@501 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fba0d9879a68b16b4207acf3dcabd4e4bb3618c5 -Author: Oliver Beckstein -Date: Wed Oct 20 10:39:30 2010 +0000 - - completed FIX of Issue 45 - - delete universes in tearDown() AND any references held in other data structures - - reduced the maximum memory footprint to <512MB (roughly) of one test process - - tests run faster again (with --processes=2 I get 109s on my MacBook Pro 2-core for ~170 tests - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@500 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6a8f62ef6927a1c2b6424d117bbe5c16f8053ac3 -Author: Oliver Beckstein -Date: Wed Oct 20 00:03:32 2010 +0000 - - test cases: addressing Issue 45: deleting universes in test cases (in tearDown) to reduce memory footprint --- needs to be tested - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@499 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit aed58812854316ad4fd3b80e1986246a57c59777 -Author: Oliver Beckstein -Date: Wed Oct 20 00:03:18 2010 +0000 - - AtomGroup: indexing reworked; implemented advanced slicing (Issue 36) - - indexing of AtomGroup now always behaves like a list: integer --> Atom, slice --> AtomGroup, list/array --> AtomGroup (NEW, fixes Issue 36) - - added test cases and modified older test cases (basically, atoms[:] cannot - be used to test for equality as it is now a AtomGroup; use ._atoms. - - updated CHANGELOG (reorganized with a big AtomGroup section) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@498 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fbc514981307a349dc07d23dc36a64ad7b12d9d6 -Author: Oliver Beckstein -Date: Tue Oct 19 21:22:18 2010 +0000 - - leaflets: new example (center of planar membrane and approximate thickness) - - new script membrane-parameters.py - - updated membrane-composition.py (atoms -> groups avoids deprecation warning); - better default selection - - more docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@497 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 261691788ef1c6077c9b8118e92e6a12e1c34ee4 -Author: Oliver Beckstein -Date: Tue Oct 19 20:34:31 2010 +0000 - - Trajectory API: use close() to close the trajectory - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@496 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4249e9520de7c726ba4effc8a172b6ee892d98cd -Author: Oliver Beckstein -Date: Tue Oct 19 20:34:10 2010 +0000 - - simple example for using rotateby(): build the MthK tetramer (sort of...) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@495 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e80811b66c1f9b0290d1e809cbfe4232e6232838 -Author: Oliver Beckstein -Date: Tue Oct 19 20:33:56 2010 +0000 - - LeafletFinder: use groups() instead of deprecated atoms() - - atoms() method clashes conceptually with the atoms attribute of an AtomGroup - - will be removed for 0.7.0 final (added deprecation warning) - - separate group() function (like old atoms()) - - and better docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@494 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8c994aae474a9d0d94fdcb7aaec3b463ce38b6fc -Author: Danny Parton -Date: Mon Oct 18 13:46:22 2010 +0000 - - Fix of "point" selections in atomSelect. Corrected docstring and converted coordinate arrays to dtype=float32 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@493 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d3ceb6a653ec60f8df3d90278d523e54dd14c6ec -Author: Oliver Beckstein -Date: Fri Oct 15 12:51:45 2010 +0000 - - FIXED: Concantenated selections (for dih) were broken with the new AtomGroup.atoms attribute - - make sure to get atoms from AtomGroup._atoms - - added test case! - - cleaned up AtomGroup docs - - fixed some test cases that got broken, too - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@492 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ae4f2a39711baee1f5d25ea893369bfeda072a30 -Author: Oliver Beckstein -Date: Fri Oct 15 12:50:06 2010 +0000 - - removed undocumented HBond setup (working on it on local branch) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@491 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2c26403e5dc472a2b06051ff70bd1b185d482a0c -Author: Oliver Beckstein -Date: Fri Oct 15 12:49:53 2010 +0000 - - updated CHANGELOG with hierarchy improvements - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@490 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d099b49b62f923b41dcafbbf9495979846635d33 -Author: Oliver Beckstein -Date: Fri Oct 15 01:45:46 2010 +0000 - - hierarchy made more consistent: AtomGroup.atoms is now a AtomGroup - - AtomGroup.atoms is managed attribute - - atom list (immutable, the old AG.atoms) is now AG._atoms - - reSTified docs - - use @property where possible in AtomGroup.py - - adjusetd AG testcase - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@489 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3689a065ca9ac1140f173a5759a5297130f2dc5b -Author: Oliver Beckstein -Date: Fri Oct 15 01:45:31 2010 +0000 - - New SegmentGroup; residues and segments attributes return the corresponding group - - improves the uniformity for access to the hierarchy - - added new warning SelectionWarning - - added docs and explained Universe > Segment >Residue > Atom hierarchy - - added testcases for Atom and the hierarch attributes - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@488 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 11d0e8e130ab8d7133f892427a84db380fc2b0bf -Author: Oliver Beckstein -Date: Tue Oct 12 20:43:25 2010 +0000 - - forgot to check in 2nd half of fix for Issue 27 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@487 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7053bf82941b361e0750fd0f868a4280dc694754 -Author: Oliver Beckstein -Date: Tue Oct 12 20:20:12 2010 +0000 - - Possibly FIXED Issue 27 (at least on Mac OS X 10.6) - This bug is of little consequence to the user because the DCD _dcd_header() - function was only implemented for debugging purposes and never documented; - it should not be used in code. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@486 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 54c592ffd7b508bf8eb72a26a05750fa05349e31 -Author: Oliver Beckstein -Date: Tue Oct 12 20:20:01 2010 +0000 - - CHANGELOG updating and polishing - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@485 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 37506636e3d0dd6231feae8fc3c93a491290a641 -Author: Danny Parton -Date: Tue Oct 12 17:42:34 2010 +0000 - - Fix of leaflet.py - AtomGroup must be imported from MDAnalysis.core - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@484 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3811c87768ff466fe7aa1ef5e63db439529e3f3b -Author: Danny Parton -Date: Tue Oct 12 14:29:30 2010 +0000 - - Test case for contact_matrix. Updated CHANGELOG - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@483 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 570d557a125b9d0cc54adadad67fbfb4de39bf3d -Author: Danny Parton -Date: Tue Oct 12 12:55:38 2010 +0000 - - Merge branch 'cmatrix' - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@482 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1d9fd027adc4ac1aea75461be70d32a721f5776a -Author: Oliver Beckstein -Date: Tue Oct 12 01:10:24 2010 +0000 - - fixes to distances test so that it runs with deprecated code removed - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@481 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit aa1f7e4847ce70600e48a00099edef9305be5c7a -Author: Oliver Beckstein -Date: Tue Oct 12 00:59:39 2010 +0000 - - removed ALL deprecated and legacy code: OLD CODE MIGHT BREAK - - AtomGroup._atoms removed - - AtomGroup.principleAxes (Issue 33) - - DCD.DCDReader.dcd_header() and DCD.DCDWriter.dcd_header() - (use _dcd_header()) - - Universe.dcd (and Universe.xtc, Universe.trr...) --- from - now on only Universe.trajectory is supported. - WILL BREAK LEGACY CODE! - - removed the following packages from top-level MDAnalysis - name space: - - AtomGroup, Selection: import them from MDAnalysis.core if - really needed (e.g. 'import MDAnalysis.core.AtomGroup') - - distances, rms_fitting: 'import MDAnalysis.analysis.distances' - or 'import MDAnalysis.analysis.align.rms_fitting' (the - actual modules still live in MDAnalysis.core but they - might get moved in the future and bundled with - transformations) - - 'from MDAnalysis import *' will only get ['Timeseries', - 'Universe', 'asUniverse', 'Writer', 'collection'] - - removed copy flag from distance_array and self_distance_array: - setting it to False would always give wrong results so there was - no good reason keeping it around (also removed the test cases with - known failures) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@480 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1e4529205fe95587c035b60fe768b1a934fdf377 -Author: Oliver Beckstein -Date: Tue Oct 12 00:59:26 2010 +0000 - - minor changes to tests of fixed issues (added issue attribs and changed text) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@479 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4e727ff5328c77681404e2170cbf9fb97be9b561 -Author: Oliver Beckstein -Date: Mon Oct 11 22:06:46 2010 +0000 - - FIXED Issue 47 (attribute residue selection from segname now always returns a ResidueGroup) - - changes old undocumented behaviour and MIGHT BREAK CODE - - also documented the Segment.r selection but made it 1-based - (makes more sense from the user point of view as all structures/topologies start - numbering at 1 and not at 0 - - updated CHANGELOG - - tests pass (including the one for Issue 47) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@478 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5c097836be42a463cbecf332664d7f3a83e64f19 -Author: Oliver Beckstein -Date: Mon Oct 11 21:03:42 2010 +0000 - - added tests for Issue 46 and Issue 47 - - Issue 46 passes (except for CRD because CRD Reader is missing, see Issue 40) - - Issue 47 fails (because no solution is implemented yet) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@477 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d13722c88e51fba47aa232494c9aee2c668289f4 -Author: Oliver Beckstein -Date: Mon Oct 11 20:30:34 2010 +0000 - - fixes for writing selections - - fixed test for selection writin, which gave a false positive - - fixed GROWriter - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@476 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f9450759a3a6aaa752633da76baf0bd29f550242 -Author: Oliver Beckstein -Date: Mon Oct 11 17:08:29 2010 +0000 - - FIXED Issue 46: failed to write Segment, Residue, ResidueGroup - - need to make sure to access the underlying list of atoms - - also fixed an unreported issue in the CRDWriter, which wrote the wrong number of - atoms for a selection - - simplified code in CRDWriter - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@475 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 06ecf2ece8748ce6577e3e0fa07ec5718a18bfe2 -Author: Oliver Beckstein -Date: Mon Oct 11 15:24:23 2010 +0000 - - new exception NoDataError - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@474 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d85833d15e882d063bb6b28fecd9ceafaa2b57b2 -Author: Oliver Beckstein -Date: Mon Oct 11 15:24:14 2010 +0000 - - FIXED: test_write_selection: Test writing CA atoms to external file. - (I had forgotten to add blanket kwargs to the GRO reader, which is required so that one can pass - numatoms=None as required by the revised Trajectory API.) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@473 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fa52c1b1af5d1b486f26fe3c95f5af18da523055 -Author: Oliver Beckstein -Date: Mon Oct 11 15:23:56 2010 +0000 - - AtomGroup gained residues and segments attributes - - managed attributes (cached) that contain the full list of residue and - segment objects that make up the AtomGroup - - use residues and segments to simplify or implement the resids(), resnames(), - numberOf...() methods - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@472 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 47670d719b178fa2af6960803adf32f86b1f2f38 -Author: Oliver Beckstein -Date: Mon Oct 11 15:23:48 2010 +0000 - - added special selections for phi, psi, and omega dihedrals to Residue class - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@471 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e4dd298fd862d4a75aaad039c794db7d99b5dabf -Author: Oliver Beckstein -Date: Mon Oct 11 15:23:42 2010 +0000 - - added transformations and improved trajectory writing to CHANGELOG - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@470 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 529a2bf6296977236183a982197d646ffc4d6bc0 -Author: Oliver Beckstein -Date: Mon Oct 11 02:02:51 2010 +0000 - - added centroid() to AtomGroup and Atom - - synonym for centerOfGeometry() and pos - - allows using Atoms instead of AtomGroups in the translate() and rotateby() - methods - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@469 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c47b518c8cf8d948649c1c0cd9dab26713ec6484 -Author: Oliver Beckstein -Date: Mon Oct 11 02:02:27 2010 +0000 - - rotateby() method for AtomGroup and use of AtomGroups instead of arrays - - uses transformations to compute the transformation matrix - - allows use of AtomGroups to specify axis and point or absolute - cartesian coordinates - - allow AtomGroup tuple for translate() - - fixed (?) rotate() -- not sure if it properly updated _pos - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@468 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4cd5c780dbd3c9eef8b50ec98b2281562b00922c -Author: Oliver Beckstein -Date: Mon Oct 11 02:02:09 2010 +0000 - - added transformations module - - transformations.py and transformations.py are Copyright Christoph Gohlke, - published under the Revised BSD Licence (GPC compatible) - - obtained from http://www.lfd.uci.edu/~gohlke/ - - This is a bit overkill but we might be able to use more of these functions - for homogeneous coordinates later for more model building; see - http://en.wikipedia.org/wiki/Homogeneous_coordinates and - http://en.wikipedia.org/wiki/Transformation_matrix for an introduction - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@467 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 42e557f9284cb164038b717adde0f3e9354b0e0a -Author: Oliver Beckstein -Date: Mon Oct 11 02:01:52 2010 +0000 - - AtomGroup can be translated and rotated - - added translate() and rotate() methods to AtomGroup - - this will go into 0.7 so I bumped version to 0.7.0-devel - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@466 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 518ca5d5f5daa47fa5d97b8c0f15098b87f6333c -Author: Oliver Beckstein -Date: Mon Oct 11 02:01:36 2010 +0000 - - writing of selections to trajectories - - Writer class gained new high-level write() method which can take - either a Timestep, a Universe, or a AtomGroup. The atoms contained in - the argument are written as the next frame to the trajectory. - - AtomGroup gained the "ts" property, which builds a Timestep on the fly - only containing the coordinates of the atoms in the group. frame and - unitcell are copied from the parent trajectory. - - At the top level, import the coordinates.core.writer() factory function - as Writer to make it clearer for the user that it provides a Writer() - class instance. - - updated Trajectory API (and all writer classes) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@465 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f10048037e5bcb98612b6fad9292d7d8d05182de -Author: Oliver Beckstein -Date: Mon Oct 11 02:01:22 2010 +0000 - - reader() and writer() factory functions - - coordinates.core.reader() returns the appropriate Reader instance for filename - - coordinates.core.writer(filename, numatoms) gets a Writer instance; kwargs - are passed on to the actual Writer class - - updated docs - - removed get_writer_for from the general import statements in favour of - writer() - - added docs - - tests seem to pass - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@464 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 34cd627e36e9dcd105e40fd890ae3490f557993c -Author: Oliver Beckstein -Date: Mon Oct 4 02:26:57 2010 +0000 - - nativecontacts example - - added example script that makes the figure (works for me) - - contacts.py: removed deprecated usage for Universe and added load() method - to simply read an existing contacts file - - added and improved docs - - added q1-q2 figure for DIMS AdK - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@463 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e38e52a93d4564bca511314783811a138dccd098 -Author: Oliver Beckstein -Date: Mon Oct 4 02:26:49 2010 +0000 - - backported log for 0.6.4.1 to CHANGELOG and added Tyler for fix of Issue 43 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@462 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 319e53c4f0c1b7cae8e95e547fa7520903ed7ca5 -Author: Tyler Je Reddy -Date: Sun Oct 3 17:28:45 2010 +0000 - - Summary: patch to resolve issue 43--whitespace is no longer required around the parentheses in selectAtoms strings. In module MDAnalysis/core/Selection.py and class SelectionParser, the method parse(self,selectstr) now adds bounding whitespace around the input string so the parser can handle a lack of whitespace. Method __consume_token(self) in the same class has also been streamlined to incorporate the built-in pop() method rather than the more verbose alternative in place. The changes pass the unit test introduced in r456 and the enhancement has been added to the CHANGELOG. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@457 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6ee42c375eb0ae40cb5c8eb2486e287c19f0848c -Author: Oliver Beckstein -Date: Sat Oct 2 23:51:23 2010 +0000 - - additional testcases - - added testcases for selections (but need more) - NOTE: testcase for Issue 43 (parenthesis without spaces) will currently throw and ERROR - until Issue 43 is fixed - - added initial testcases for important methods of AtomGroup - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@456 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d6e790cd36e99870f56f6b54c9554937ff53a446 -Author: Oliver Beckstein -Date: Thu Sep 30 21:11:25 2010 +0000 - - added Tyler to AUTHORS - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@455 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fe4650739317a5f6e3f84fbfe9c4df1e31c5c620 -Author: Tyler Je Reddy -Date: Wed Sep 29 08:25:26 2010 +0000 - - generated html docs from reST sources via sphinx - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@454 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fd8866de92e627d58856895b43e35e254ac7815d -Author: Tyler Je Reddy -Date: Wed Sep 29 08:24:25 2010 +0000 - - sphinx sources for docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@453 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2e9b8651b65f59c96fe7cf3686e4776c2f824a48 -Author: Tyler Je Reddy -Date: Wed Sep 29 08:00:17 2010 +0000 - - The docstrings for the four analysis modules located in MDAnalysis/analysis/ have been modified to a reasonably consistent reStructuredText format to produce readable html pages (under doc/html/) built from the Sphinx source (at doc/sphinx/). The file doc/index.html has been removed as this was an old build for the MDAnalysis website. Docstring changes to distances.pyx were necessary as some objects were imported from this module by analysis/distances.py. - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@452 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 560ca41f6d909391f33604d6d3d753bbcec48ff4 -Author: Oliver Beckstein -Date: Sun Sep 19 16:06:33 2010 +0000 - - FIXED Issue 41: with statement not recognized in PDB.py under python 2.5 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@437 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1986ac1e15038e20e6ccd2ae5b716cbbb8bceb53 -Author: Oliver Beckstein -Date: Thu Sep 16 11:04:37 2010 +0000 - - release 0.6.4 (no code changes relative to 0.6.4-rc1, only docs) -- updated docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@436 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fa19a403f430badbc0bf50192d9e7573a58e0a12 -Author: Oliver Beckstein -Date: Thu Sep 16 11:04:31 2010 +0000 - - 0.6.4 release --- final adjustments (including using canonical GROWriter) - - release set to 0.6.4 - - removed original GROWriter and replaced with GROWriterStandard (should be invisible to most - users because GROWriter could only be used explicitly anyway). - The olf GROWriter functionality of writing the whole universe can be simply obtained by passing - the universe's universe.atoms AtomGroup to the write() method - - cherry-picked from 0.6.4 branch and adjusted - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@435 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ca5d4472c4897136ee842e02b28e6caf67061769 -Author: Oliver Beckstein -Date: Fri Sep 10 16:17:30 2010 +0000 - - added Dannys AtomGroup enhancements to CHANGELOG (sort of backport from the 0.6.4 branch) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@425 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7510d9aa2e11e832f12c9114ea3763e3dd3345b8 -Author: Oliver Beckstein -Date: Fri Sep 10 14:28:24 2010 +0000 - - renamed bilayer analysis script to adhere to common scheme membrane-XXX.py - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@422 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5afb44ad7d168de2fa86a29770208c15900394d5 -Author: Oliver Beckstein -Date: Fri Sep 10 14:24:23 2010 +0000 - - new LeafletFinder example: membrane composition - - added memanal-composition.py - - cleaned up leaflet.py example (use class from module) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@421 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 52728c8b4dc7c8d1546123e5014ffdd4eaba5402 -Author: Oliver Beckstein -Date: Fri Sep 10 14:24:17 2010 +0000 - - make AtomGroup.coordinates() return an array of type numpy.float32 by default - - distance array needs float32 and when interfacing with I/O this is also - how coordinates are stored so it makes sense to enforce it at this - crucial entry point - - LeafletFinder would raise an error when building the adjacency matrix - because the array returned by coordinates() was float64 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@420 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit cddddc7fb0adf3e0ae3a112a1e66f9585d887e7f -Author: Danny Parton -Date: Fri Sep 10 13:17:48 2010 +0000 - - Merge branch 'printres' - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@419 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 21e43b3a427606ef20186f62cde9a018e213f53b -Author: Danny Parton -Date: Fri Sep 10 13:17:34 2010 +0000 - - Merge branch 'printres' - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@418 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b8dc525b99b9bb97149df4accec6429347ce618f -Author: Oliver Beckstein -Date: Sat Sep 4 16:41:56 2010 +0000 - - selection writing improved - - cleaned up AtomGroup.write() by using the coordinates.get_writer_for() - function (the standard way to do this nowadays) - - added test case - - note that get_writer_for() and get_reader_for() are now imported into - MDAnalysis.coordinates - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@417 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 738b306f1655c6de54c42ea7a5b9eb1d21a6bf75 -Author: Oliver Beckstein -Date: Sat Sep 4 01:16:49 2010 +0000 - - GRO writer: cleaned up and write output within try/finally - - put all output formatting strings into class-level dict to make things easier - to change - - write file in a safe manner, i.e. always close it via finally clause - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@416 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b57f768dde361944e3ef255e97dc053503fb8284 -Author: Oliver Beckstein -Date: Sat Sep 4 01:16:42 2010 +0000 - - FIXED: AtomGroup.write() failed because it was using lower case file format strings (which were changed in r409) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@415 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 13e7f7d6db622c4063c607e857deeb050f97386b -Author: Oliver Beckstein -Date: Mon Aug 30 08:41:11 2010 +0000 - - chain reader added (Issue 39) - - universe can read a list of files and concatenate them transparently - on the fly: u = Universe(PSF, [DCD_1, DCD_2, ...]) - - only basic Trajectory API implemented (no indexing/slicing!) - - can mix any formats (!) - - added simple test case - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@414 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3f7c650f489c562c8cde00c3b14481314446d995 -Author: Oliver Beckstein -Date: Wed Aug 25 03:53:38 2010 +0000 - - topology parsing: file format identifier is now UPPER case - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@413 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit cf5b272c0b050c532efa40fea2a5695b96d866f9 -Author: Oliver Beckstein -Date: Wed Aug 25 01:56:34 2010 +0000 - - Primitive PDB parser that reads simple PDB without a fuzz - - added PrimitivePDBReader and parser which just stupidly - read a well-formatted pdb file without raising a stink if the resids - are oddly numbered or multiple atom names occur in the same residue - - added permissive=False (default) flag to Universe; True switches on - the primitive readers (right now, only PDB has this distinction) - - moved the guess_atom_type/mass/charge functions from PDB into topology.core - - added permissive keyword arg to the get_parser_for() and get_reader_for() - functions - - added a second dictionary each for the permissive parsers and readers (a bit - of an ugly hack...) - - added unit tests for the primitive PDBReader/parser (and all pass) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@412 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2c5c85f8d48669a73e8fb45d748804ae0424470b -Author: Oliver Beckstein -Date: Sun Aug 22 06:36:38 2010 +0000 - - dcd-to-xtc conversion working - - added example script dcd2xtc.py - - hacked a few fixes into the xdr writer to substitute missing parameters - (maybe need to do something similar of dcd writer...) - - not well tested - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@411 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d014d41f6b3df95cb04903d84744a27111ff1ae8 -Author: Oliver Beckstein -Date: Sun Aug 22 05:31:25 2010 +0000 - - FIXED Issue 37: simulation box were not converted - - added coordinates.core.triclinic_box() and triclinic_vectors() to handle conversion - - added function convert_dimensions_to_unitcell() to Writers - and added to the requirements of the Trajectory API - - GROWriter: introduced a temporary GROWriterStandard class which will replace the current - GROWriter (which got a DeprecationWarning) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@410 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 12d816e6e3f15611d3a74bd787342c91abc35e9a -Author: Oliver Beckstein -Date: Sun Aug 22 05:31:17 2010 +0000 - - Trajectory API: format is now UPPERCASE - - the format specifier has been changed to the upper case extension (to be - consistent in naming) - - added single frame writers to API definition - - new get_writer_for() convenience function - - refactored check for compressed file formats into check_compressed_format() - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@409 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2727bf7634c09bbb8ab7f3a2754b794cc390e17b -Author: Oliver Beckstein -Date: Sun Aug 22 05:31:06 2010 +0000 - - created MDAnalysis.analysis.distances which simply imports from core.distances - - distances are useful analysis functions so most people would expect them under analysis - - distances are also used for selections so that is why we keep them in core - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@408 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2fe94c30627e9ba4dd2671b11837d7a44b2ed359 -Author: Oliver Beckstein -Date: Tue Aug 3 18:22:21 2010 +0000 - - added Danny's GRO writer to CHANGELOG before this is forgotten - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@407 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 91ac199bec94ddb4fa19a051c37214b27fabc342 -Author: Oliver Beckstein -Date: Tue Aug 3 18:13:03 2010 +0000 - - FIXED Issue 38: XTC writer broken - - fix provided by Danny Parton - - added unit test (passes) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@406 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1939985533aed12ba231ab6294043dbcb6b39fbc -Author: Danny Parton -Date: Thu Jul 22 13:09:38 2010 +0000 - - Added GROWriter - writes from either a Universe or AtomGroup - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@405 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit dccf3cb131bb580b7e229052611afc355a1ca7ce -Author: Oliver Beckstein -Date: Thu Jul 8 11:52:40 2010 +0000 - - Universe and load_new: cleanly load universe from a sole pdb or gro but nothing else - - load_new: returns file format and filename or None if no input file (for building - psf-only universes) - - load_new: raises TypeError if no reader for the format can be found - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@404 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3ee5997f38181a34b107c6822cdcc9f57c458922 -Author: Oliver Beckstein -Date: Thu Jul 8 11:45:21 2010 +0000 - - bumped version to 0.6.4-devel and updated CHANGELOG from the release - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@403 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fbc7f2409ad8338b8cc4baf0212aa68bb2be4618 -Author: Oliver Beckstein -Date: Thu Jul 8 09:17:42 2010 +0000 - - fixed: AUTHORS file was not included in distribution - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@388 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5deb87c56c3070538a958abde64c34a0db0b9c50 -Author: Philip Fowler -Date: Thu Jul 8 08:02:10 2010 +0000 - - forgot to svn add testfiles and added comments to tests/__init__.py - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@387 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7e5d433bf50ede21e07928c34f1364d947daf6b1 -Author: Philip Fowler -Date: Thu Jul 8 07:47:47 2010 +0000 - - altered XYZReader class to not use format; also added unit tests for simple and compressed XYZ files - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@386 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit cbe504208e266ae7547a0003d7c57bfc042df470 -Author: Oliver Beckstein -Date: Tue Jul 6 22:36:20 2010 +0000 - - Trajectory API: optional attribute 'compressed' defined and streamlined guess_format() by introducing get_ext() - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@382 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2730208cf884a03e30c588fb38702c1305739582 -Author: Oliver Beckstein -Date: Tue Jul 6 22:36:14 2010 +0000 - - standard documentation update - - added Phil Fowler as author - - reformatting and update of the README, with links to the wiki - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@381 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b577010b4b88c24b02382649fa5909a898f81978 -Author: Oliver Beckstein -Date: Tue Jul 6 22:36:09 2010 +0000 - - minor doc improvements - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@380 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a439462768647633fd3e37a54888eba2211433ca -Author: Philip Fowler -Date: Tue Jul 6 12:50:07 2010 +0000 - - added basic XYZ trajectory reader with compression support. See coordinates/XYZ.py for more details - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@374 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6f0c871c8659b3d0cc439b6b4f60d3f441d26035 -Author: Elizabeth Denning -Date: Mon Jul 5 18:19:26 2010 +0000 - - updated scripts in examples - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@373 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4e5b30326b690a3822d23afe5ab7789b90d78098 -Author: Elizabeth Denning -Date: Mon Jul 5 18:15:05 2010 +0000 - - fixed backbone_dihedral in examples - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@372 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 147b5215a73ba3affb97dda838a43b3b484845e4 -Author: Oliver Beckstein -Date: Wed Jun 30 16:45:47 2010 +0000 - - reduced precision for distance tests from default to 5 decimals so that they also pass on 32 bit - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@357 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 96d649cc452fdb36b96a8422aac98c2a5b024232 -Author: Oliver Beckstein -Date: Wed Jun 30 15:01:04 2010 +0000 - - FIXED: adk_oplsaa.gro test file was not included and some tests failed if done from a non-developer install - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@356 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ad58cedb36a971d27384ad432d64873ab08afaf1 -Author: Oliver Beckstein -Date: Wed Jun 30 14:02:46 2010 +0000 - - added AUTHORS file - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@352 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6f0c4db4aaa792a6018956f6760f2da248970fb6 -Author: Oliver Beckstein -Date: Wed Jun 30 02:19:18 2010 +0000 - - GRO reader: fix of fix .. should have run the tests after r341 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@343 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7d963e30035aca9ebe051283b991f09687af1fbc -Author: Oliver Beckstein -Date: Wed Jun 30 02:19:11 2010 +0000 - - added dt managed attribute to all Readers - - computes time between frames in ps - - round to 4 decimals to get nice and tidy numbers (the unit conversion - can introduce some small and spurious numerical contamination) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@342 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 73771308aecceaa6c66cad3df2ac442bcfccbbac -Author: Oliver Beckstein -Date: Wed Jun 30 01:57:19 2010 +0000 - - GRO reader: fixed case with only 3 entries for the unitcell - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@341 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3b2d102071c7ee6a8c6501e09bb54c2d15ef1a34 -Author: Oliver Beckstein -Date: Wed Jun 30 01:31:16 2010 +0000 - - GRO reader: unitcell and unit conversion - - added unit conversion so that the GROReader behaves like all the other readers: it - automatically converts the distances to Angstroem - - read unitcell (according to the file format specs); requires special Timestep - class with the appropriate dimensions property to do the conversion - - added some docs to the trajectory API to better explain what is expected of - Timesteps (this was not properly documented) - - added more test cases for GRO (note that the precision for comparisons goes down - to a single decimal in some cases, eg when subtracting positions!) - - minor clean up in various readers: removed explicit setting of the units attribute: this - is a class attribute and set in the class declaration; no need to set it again in __init__. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@340 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 71ab28d00e30ea921e36d3ecf2404b591e900bab -Author: Oliver Beckstein -Date: Wed Jun 30 01:31:10 2010 +0000 - - use attribute "issue" to mark tests relating to recorded problems so that we can run them separately - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@339 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1ea6c00e48ab1db6a4e0044f7acd5f72b9d4e750 -Author: Oliver Beckstein -Date: Wed Jun 30 01:31:02 2010 +0000 - - FIXED Issue 34: fixed unitcell for XTC/TRR - - box vectors were extracted wrongly - - moved rad2deg, _angle, _veclength into coordinates.core (for further use) - - added test case - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@338 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 30997e17cedf1481a448bd72404a83720da1d24a -Author: Oliver Beckstein -Date: Tue Jun 29 19:12:10 2010 +0000 - - additional tests for coordinate readers - - more GRO tests; coordinates and distances fail at the moment because the GRO reader - does not convert units (TO BE FIXED) - - more tests for PDB files - - use GRO parser for the XTC and TRR tests instead of PDB (a bit faster and more native) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@337 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit bb2971682d520836239f8a0ed8f9eed16119c11c -Author: Danny Parton -Date: Tue Jun 29 11:08:01 2010 +0000 - - Added working GROReader and TestGROReader, and fixed Timestep.numatoms issue - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@336 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 87cd8dd8bc98acc71fb8f98118186953c49cf24a -Author: Oliver Beckstein -Date: Tue Jun 29 10:18:40 2010 +0000 - - FIXED Issue 33: principleAxes() return values are confusing - - new principalAxes() method (correct name, too, as a bonus) that returns - the three eigenvectors directly and does not require unpacking - - kept old method bu deprecated it - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@335 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit daa6a4e4759d7bd195d6539a5ef35b456989607a -Author: Oliver Beckstein -Date: Mon Jun 28 20:13:00 2010 +0000 - - parser/coordinate entry points: FIXED: would not allow building of psf-only universe - (but now issue a warning) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@334 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 71c4b8c0095004d53666077d76e11ea06899b8e0 -Author: Oliver Beckstein -Date: Mon Jun 28 19:54:43 2010 +0000 - - unified parser/coordinate reader entry points - - use a two-stage process to clean up the messy loading in Universe - 1. determine file type with a "guess_format()" function (currently will - simply look at the file extension) - 2. look up known file formats (in the sub-modules' top level there are - approriate dictionaries that connect format to the appropriate reader) - 3. return the appropriate parser (get_parser_for()) or reader (get_reader_for()) - 4. load - - add new formats to - topology._topology_parsers - coordinates._trajectory_reader - - PDBParser: made the first failure for wrong extension more general, but we should not - really get there anymore because we use guess_format/get_parser_for - - updated CHANGELOG - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@333 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 36834403d2e492478ac41826994735d7a4ca98fa -Author: Oliver Beckstein -Date: Fri Jun 25 14:29:16 2010 +0000 - - FIXED: trajectory IObase.convert_time_from_native() did the opposite - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@332 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c3822a22ccb3dc2ccb28697d3ca83fbe3847105e -Author: Oliver Beckstein -Date: Fri Jun 25 01:52:07 2010 +0000 - - trajectory reader improvements: slices - - XTC/TRR reader can do simple slices by sequential iteration - - moved some functionality from DCDReader into the base class TrjReader - - added explicitly required methods to TrjReader (cf Trajectory API) - mostly with NotImplementedError - - enabled reverse iteration for the DCDReader (but disabled for XTC/TRR - because it would require re-seeking every single frame from the beginning) - - UnitTests for slices - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@330 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a111720e160eba419da5427434aec9ca2e681d1e -Author: Oliver Beckstein -Date: Fri Jun 25 01:52:00 2010 +0000 - - analysis contacts: dcd --> trajectory (although will break for XTC at the moment if no reference structures supplied) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@329 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 22959c7b9b892ad55f138658a383262339fe8962 -Author: Elizabeth Denning -Date: Wed Jun 23 20:26:24 2010 +0000 - - fixed rms_fitting bug - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@326 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fc2a737fe6b0af019e4fbf1ad65afefd85a7ae07 -Author: Elizabeth Denning -Date: Wed Jun 23 14:58:19 2010 +0000 - - PSFParser to allow for EXT formatted PSF and selection updates to allow for nucleic acid xstal structure resname codes - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@325 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit aae63052dfb54959e8200065408240c466df9f18 -Author: Oliver Beckstein -Date: Fri Jun 18 00:37:39 2010 +0000 - - Universe init - - commented out debugging messages when building topology - - changed vanilla exceptions to either NotImplementedError or ValueError (until - we define better custom exceptions) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@324 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d78b52d6a2878f54af93de26fc3bebf60fa2c0e8 -Author: Oliver Beckstein -Date: Fri Jun 18 00:37:33 2010 +0000 - - analysis module: added rms fitting (with optionally selection derived - from a sequence alignment) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@323 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4aaeaaebf0a0f598f3a629d48f02bfb1350c05b0 -Author: Oliver Beckstein -Date: Thu Jun 17 17:30:48 2010 +0000 - - example scripts improvements and additions - - added examples for simple and fancy rms fitting - - added graph for the simple fitting - - fixed: filename for g(r) example - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@322 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3f067a63788d49036588f96612616fd0f1c5e4bf -Author: Oliver Beckstein -Date: Thu Jun 17 17:30:41 2010 +0000 - - moved SelectionError into top level - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@321 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 59e188c59b3259bdcaa2d58f1a9feab9d8461fed -Author: Oliver Beckstein -Date: Thu Jun 17 00:35:03 2010 +0000 - - added testcase for Issue 32 (empty dcd segfault Universe) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@320 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e24330f134f3776ead948001fd62954300fabdc5 -Author: Oliver Beckstein -Date: Thu Jun 17 00:19:18 2010 +0000 - - Issue #32: sort of fixed (check if a DCD has size 0 and raise IOError, instead of segfaulting - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@319 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8fa51e02bed1ab9e8473ebeb3bfc5fd4cb19061d -Author: Danny Parton -Date: Wed Jun 16 14:56:46 2010 +0000 - - GROParser added. GROReader to follow. - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@318 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 652fec1a3cc71ec6f3a8b95912d7019943603ced -Author: Oliver Beckstein -Date: Thu May 27 15:19:01 2010 +0000 - - reST docs for top __init__ & canonical licence blurb header - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@313 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 521e328d11904b8d61bc4411a248b22f2bba132e -Author: Oliver Beckstein -Date: Thu May 27 15:18:50 2010 +0000 - - changed minimum requirement to python 2.4 - (Most of MDAnalysis probably still works on 2.3 but we have not tested it - and there is also new code that uses with_statement, set, etc.) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@312 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ff38143a76771b5facc169075675aef1a0af951a -Author: Oliver Beckstein -Date: Thu May 27 12:03:24 2010 +0000 - - reST docs for top __init__ & canonical licence blurb header - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@308 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ceca35138be0ab4062ddf6a8943577aa2ca99abd -Author: Oliver Beckstein -Date: Thu May 27 12:03:11 2010 +0000 - - contacts analysis: working and added reST docs - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@307 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c2ef173a0e3e1f38be5c54f18e0577d7af460ad6 -Author: Oliver Beckstein -Date: Thu May 27 12:02:57 2010 +0000 - - asUniverse() convenience method added to unify input - - useful for analysis input: either take a universe, a single - filename (PDB), or a tuple (topology,trajectory) and return - a universe - - imported at top level (SUBJECT TO CHANGE!) - - also more reST doc for AtomGroup - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@306 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 787a5a74ef4c582765fc92814e1de05082b79f2c -Author: Oliver Beckstein -Date: Thu May 27 12:02:32 2010 +0000 - - additional requirements (I thought this was added already but must have lost it) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@305 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 32679eee65932b850584d95cfaa168b4cbc6fdd7 -Author: Oliver Beckstein -Date: Thu May 27 12:02:16 2010 +0000 - - analysis: added native contacts analysis (from AdK/lib/python/AdK/contacts.py) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@304 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e7e20e466c1b9ee9732a27a62fea8fe248ca3bca -Author: Oliver Beckstein -Date: Thu May 27 00:37:07 2010 +0000 - - selection writer for VMD, PyMol, CHARMM, Gromacs working - - use get_writer() to encapsulate the choosing of an appropriate writer - based on filename or default format (should be implemented similarly for - the single frame writers) and corresponding changes in AtomGroup class - - write comments (or not, if commentfmt is None) - - can write a preamble comment - - use the selection writer for LeafletFinder instead of the simple - VMD writer - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@303 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 748085508cb9b3c2dc863b3d97a37412f356739d -Author: Oliver Beckstein -Date: Thu May 27 00:36:49 2010 +0000 - - Merge branch 'topic/examples' - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@302 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 67565233be4bba255e5ae0fdb33784d6a6020aa5 -Author: Oliver Beckstein -Date: Thu May 27 00:36:38 2010 +0000 - - provide assert_() in case numpy is <1.3 so that some of the tests pass - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@301 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9b802c7b3574b55ef9e905ec9a6d11ba6042f583 -Author: Oliver Beckstein -Date: Thu May 27 00:36:27 2010 +0000 - - minor doc fixes - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@300 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1fc9243928147c992bef7a6315ee3b0de6deb6ed -Author: Elizabeth Denning -Date: Tue May 25 23:12:49 2010 +0000 - - principleAxes fix and additional nucleic acid selections - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@294 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6541096bd69db3d2e2fc8d6f8722bd98bc460f8f -Author: Oliver Beckstein -Date: Fri May 21 17:19:17 2010 +0000 - - pruned some top-level imports (especially rms_fitting); probably breaks some 0.5.x scripts - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@271 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ffa040857355f15806f0f28183d05d1057649890 -Author: Oliver Beckstein -Date: Fri May 21 17:19:10 2010 +0000 - - setup.py improvements - - better waning if numpy not found (which we need even for RUNNING setup.py!) - - added setuptools dependencies for numpy (moot...) and nose (as a tests option) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@270 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e8ccb168c95d2c2d272a6523b1f6514e024a21b0 -Author: Oliver Beckstein -Date: Fri May 21 17:19:00 2010 +0000 - - FIXED Issue 16: can easy_install from tar file but at the prices of copying c_numpy.pxd into each subdirectory; easy_install breaks if these are symbolic or hard links - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@269 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4c5ced765a365a6d68bdd085c85de005268b9a95 -Author: Oliver Beckstein -Date: Fri May 21 17:18:50 2010 +0000 - - KDTree: fixed compiler warning: comparison between signed and unsigned integer expressions - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@268 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9ec242327482b0e7f823bdbbef237c0a7e7d104c -Author: Oliver Beckstein -Date: Fri May 21 17:18:42 2010 +0000 - - updated libxdrfile AUTHORS (OB messed with the original files...) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@267 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 575da3ccd34990c77b47066d1346caed8ccda6d6 -Author: Oliver Beckstein -Date: Wed May 5 22:08:45 2010 +0000 - - updated CHANGELOG with units - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@264 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d93d7b23fda87a628fa689e3fcce07683c71feb5 -Author: Oliver Beckstein -Date: Wed May 5 22:08:37 2010 +0000 - - units and unit conversion added - - simple conversion facility for units (length, time) in core.units (taken from my hop package) - - flag[convert_gromacs_lengths] is set to True: the XTC and TRR reader (tested) and writer (untested) - automatically convert to the base units - - define MDAnalysis base units as ps and Angstrom (in flags[]) - - added test cases (all pass) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@263 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 52a3d0ddea10cbaad2831d606ee905fe62306716 -Author: Oliver Beckstein -Date: Wed May 5 22:08:28 2010 +0000 - - trajectory API: derive from base classes - - base classes for Reader, Writer, Timestep in coordinates.base: all other Reader/Writer - derive from them; the API is not full spelled out in the base classes, though: see - the comments in the code and the description in the module doc string - - added units to all Readers/Writers (purely informative at the moment); note - that we write Angstrom - - added format attribute to all classes - - moved DCD.Timestep to base - - note: DCDReader and DCDWriter have become new-style classes (inherit from base.Reader <- object...) - - moved some common methods into the base classes (eg __del__, __len__, __repr__) but not the full - API - - CRDWriter: reorganized so that write() opens and closes the file, similar as PDBWriter; - also made all the individual writing methods private - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@262 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1d76f09a136b8a9e37137ef0915819d61c3e275f -Author: Oliver Beckstein -Date: Wed May 5 22:08:20 2010 +0000 - - trajectory API: additions - - delta and skip_timestep added (compute for XDR trj, hard-code for - single frame formats, read as usual from DCD header) - - units: describe the length and time units used (for possible - later automatic conversions) - - deprecated DCDReader.dcd_header(): not part of API and not really - supported for XDR; also broken, see Issue 27 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@261 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b1eace6610abb4788cbab97b174b3937bab83645 -Author: Oliver Beckstein -Date: Wed May 5 03:04:20 2010 +0000 - - added numframes to TrjReader as a cached attribute - - can get numframes for XTC/TRR but takes a long time when accessed the first time - - added test cases - - broke correl test case into individual test cases - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@257 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6ba94a7499bbb8e3fb5c86ceb4ed63faee109ca9 -Author: Oliver Beckstein -Date: Wed May 5 03:04:10 2010 +0000 - - libxdr: added function to count the number of frames in a trajectory - - read_xtc_numframes() and read_trr_numframes() do the brain-damaged thing and - iterate through all frames; in particular for trr one should be able to do better - - maybe cache the frame offsets and in this way implement random access (LOOS seems to be doing - something like this) - - added a few simple test cases - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@256 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 24827d9162f213b87a4590abc2646d1a43b3c03e -Author: Oliver Beckstein -Date: Sat May 1 20:37:07 2010 +0000 - - unittests: new tests for distance_array() and self_distance_array() - - added distance array tests, including known failures with copy=False - - classified the XTC/TRR tests as slow - - updated docs on testing considerably - - moved filenames needed for all unittests into separate module - NOTE: test target values were obtaine on my Macbook running python 2.6, OS X 10.6.3, this version of MDAnalysis; the should probably be checked against independent evidence such as VMD measure(). - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@254 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5a667880d6d03aaa463b33b40674b1a79f4c9956 -Author: Oliver Beckstein -Date: Sat May 1 20:37:02 2010 +0000 - - self_distance_array() docs: clarified input/output requirements (different from distance_array()! - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@253 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit cb62c94b999f7a30da86687a2beb0852f29be284 -Author: Oliver Beckstein -Date: Sat May 1 20:36:57 2010 +0000 - - fixed syntax error in test cases (lost the commit somewhere...) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@252 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5cc4ef5ac0b4a47677734e294946916b63ffc856 -Author: Oliver Beckstein -Date: Sat May 1 20:36:51 2010 +0000 - - bumped release but include devel - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@251 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 94995d302e627043c69220c257100232a6b3f5e8 -Author: Oliver Beckstein -Date: Sat May 1 05:27:11 2010 +0000 - - notes on what to do when unittests are not running - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@246 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c5b7c4a27cb3b571c7d57ce773bec1d195d34687 -Author: Oliver Beckstein -Date: Sat May 1 05:27:04 2010 +0000 - - Gromacs trajectories fixes and improvements - FIXED: trr/xtc tests failed (on Mac OS X) when MDAnalysis was properly installed as a egg directory but not as a developer install: - forgot to include the trr and xtc files in the package - learned that xdrfile_open() segfaults (at least Mac OS X) if there is no file: added additional check to prevent that - Gromacs XDR reader now behave like DCDReader: (1) raise IOError when done; (2) continue raising with repeated next() - for some reason, TRR files can (always??) return status exdrINT at end of file; catch this in _read_next_timestep() - regenerated swig files from libxdrfile.i (only minor doc things) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@245 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit cadb75b8d46cf1ebb9e9067d04d1b7a78fe9ce5f -Author: Oliver Beckstein -Date: Sat May 1 03:57:38 2010 +0000 - - reSTified docs and added stub for flag to convert Gromacs nm to A - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@242 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ef40fc00b2433998d7e6810852831bd1c3ffd0bd -Author: Oliver Beckstein -Date: Fri Apr 30 22:08:33 2010 +0000 - - added patches that were lost in the last orbeckst -> trunk merge - - crucial fix of old pyrex loops in src/dcd/dcdtimeseries.pyx - - experimental HBond.py re-added - - fixed date in CHANGELOG... - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@236 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f196e19f6f27bd598cccf20e5ba43036ce7fcfd5 -Author: Oliver Beckstein -Date: Fri Apr 30 21:42:55 2010 +0000 - - Merge branch 'orbeckst' - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@235 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 81ed2283bfddbc3ea7d7313954a4f09fb92c2131 -Author: Oliver Beckstein -Date: Mon Apr 26 15:16:28 2010 +0000 - - FIXES Issue #22 (Universe.dimensions broken) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@208 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 96b2148bd12c8f26d106b481dd3a368bfa7201df -Author: Oliver Beckstein -Date: Mon Apr 26 15:16:22 2010 +0000 - - updated INSTALL: easy_install is mostly working - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@207 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d06aa63fb36f45798a00661596d284978c3810a6 -Author: Oliver Beckstein -Date: Thu Apr 8 16:59:48 2010 +0000 - - FIXED: problem in PDB.PDBWriter; also bumped version as we are working towards 0.6.1 - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@188 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0adf5d2fc5765d10eec978686c510f550a4159d7 -Author: Oliver Beckstein -Date: Tue Apr 6 18:47:50 2010 +0000 - - removed empty python dir (should have done this with the 0.6.0 release) - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@187 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 01369f414451c9328e4dbdca043570dbcda5c758 -Author: Oliver Beckstein -Date: Tue Apr 6 18:35:43 2010 +0000 - - reverted pyrex for-loop syntax to be compatible with old pyrex 9.6.x - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@186 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5b1fe771e852d077a68981f5a671bc9739993197 -Author: Oliver Beckstein -Date: Thu Apr 1 22:01:45 2010 +0000 - - Merge branch 'rel-0.6.0' - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@182 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4dc0d3d9eecc6608944a83385cf6c92a3efa5ca5 -Author: Oliver Beckstein -Date: Sat Aug 23 00:36:29 2008 +0000 - - Release 0.5.1: bugfixes and some enhancements that accrued over the last few months (see CHANGELOG for details). - - LICENSE was updated with the UIUC Open Source License (catdcd code) - - updated email addresses etc in README - - updated TODO (distance_array bug fixed) - - added keyword expansion for some of the doc files so that Id lines are - properly shown - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@108 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2a09f624073d29212061406e0b0da15bd762b12b -Author: Oliver Beckstein -Date: Tue Jul 15 16:04:08 2008 +0000 - - Only provide setup.cfg.template and let the user copy and modify it. This is better because otherwise local modifications mess up svn. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@106 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 37c0aa037a6e53b669144f77527645a032e2dd6b -Author: Oliver Beckstein -Date: Tue Jul 1 21:52:54 2008 +0000 - - Moved the distance array workaround into the function itself: we - simply copy the arrays ourselves and all seems to be fine. For daring - souls we provide copy=False and disclaim all responsibility. - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@105 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 63e9b86c4b1efa1a5bb67eea83138f708ad0f33e -Author: Oliver Beckstein -Date: Sun Jun 22 04:07:02 2008 +0000 - - * new water dipole correl time series: calculates the vector of - the dipole moment of a rigid 3-site water model - * sanitized formatting of correl.h (sorry) - * started using specific Exceptions instead of the generic one - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@104 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d70bb1c5229a5cf1b19c0aa65a3a443d2c893b68 -Author: Oliver Beckstein -Date: Sun Jun 22 03:59:51 2008 +0000 - - fixed: exception did not display psf file name - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@103 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 57a2bbb840a61e598e4cebab94ba94f766da4256 -Author: Oliver Beckstein -Date: Sun May 18 13:21:30 2008 +0000 - - Universe now knows the filename of the psf file it was built from; dcd - and pdb instances also have the filename attribute. - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@102 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0e1f31ad39c64827bb3b2348430f41fa203461d7 -Author: Oliver Beckstein -Date: Sun May 18 13:19:06 2008 +0000 - - Added ID keyword - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@101 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2fb5875cd2f7147911ba99fcf3577033514e132d -Author: Oliver Beckstein -Date: Thu Feb 28 02:45:34 2008 +0000 - - Fixed: check for dcd extension always failed - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@100 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0c907a8b8511f4c8904e6e8f2ded5a22796d934a -Author: Oliver Beckstein -Date: Thu Feb 28 02:35:29 2008 +0000 - - Universe: Convenience functionality for interactive work: if the dcd - argument has a extension 'pdb' then we try to load it as a pdb. The - dcd exception handling is not robust enough yet (e.g. segmentation - faults occur when accessing self.dcd after erroneously loading a dcd) - so we cannot do a simple try: load_dcd() ... except IOError. - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@99 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b0b650e5832817b05c38fb3f79d9f4d00a55e52f -Author: Oliver Beckstein -Date: Thu Feb 28 02:32:18 2008 +0000 - - streamlined - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@98 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4bbbabfbae7c5a80a1aa723b9d6ce0f54fdfb5c2 -Author: Oliver Beckstein -Date: Mon Feb 25 02:07:17 2008 +0000 - - Added Ben's authorship. - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@97 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit bf338f56af24ad8acfdf33623d94b6361b0bc240 -Author: Oliver Beckstein -Date: Mon Feb 25 00:43:35 2008 +0000 - - Issue #6: "accessing coordinate functions of universe segments fails" - was caused by my previous skipping of the check for an empty - AtomGroup. - Reverted to previous version. - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@96 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 85b6118870378e83eb81681f5853bc3e06fadb07 -Author: Oliver Beckstein -Date: Wed Feb 20 17:26:10 2008 +0000 - - House keeping: - - added generated files to svn:ignore - - added a little bit to TODO and made sure that it gets into the tar ball - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@95 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 49099c9e5f0c53b1e76929f41b899e50860b17d1 -Author: Oliver Beckstein -Date: Wed Feb 20 17:19:37 2008 +0000 - - Allow an empty AtomGroup (removed the check for length < 1) - so that one can have intermediate selections that don't select - anything. This can be useful in 'or'ed selections. - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@94 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1a7b735df2c518090deeae5d27df4442645101d7 -Author: Oliver Beckstein -Date: Wed Feb 20 17:13:24 2008 +0000 - - new attribute 'filename' (just initializes to 'dcdfilename') (also - previously added to the PDBReader class): By having a common API for - PDBReader and DCDReader on can more easily write code that can - transparently use either. - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@93 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4a76baee3b588b07eac464c57fd9fb7c388805c5 -Author: Oliver Beckstein -Date: Wed Feb 20 17:10:46 2008 +0000 - - added reference in docs - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@92 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 67d7a1aed61677ab5424d76aaeeb077b4286a300 -Author: Naveen Michaud-Agrawal -Date: Mon Feb 11 18:23:23 2008 +0000 - - numpy.array only makes a copy if you force it. This should fix the problem with AtomGroup.coordinates() function and distance_array - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@89 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b53c031e623b49e32bd9f43441016de01130cb62 -Author: Oliver Beckstein -Date: Sun Feb 10 23:59:51 2008 +0000 - - Added bfactors property to the AtomGroup. It is only set when the - structure is loaded from a PDB file. The bfactors array itself is an - attribute of the Universe (because it makes no sense to attach it to - the time step as it is only defined for a single frame) and handled as - a managed attribute in AtomGroups. (Change where bfactors[] resides?) - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@88 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 792533c46d37b35e895e0f6b58f50a47bd69a2ba -Author: Oliver Beckstein -Date: Sun Feb 10 23:55:26 2008 +0000 - - * primitive PDB writer: only works if structure was read as a pdb. It - simply replaces the pdb coordinates with the time step coordinates. - For something more complicated we should have segment and residue - lists in MDAnalysis (perhaps save them when reading the psf). - * added filename attribute to both DCDReader and PDBReader to make it - easier to write unified code. The other important methods and - attributes are already identically named. - - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@87 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3e4db218f059db7ae4a7ac72a73225bd83bafbc8 -Author: Oliver Beckstein -Date: Fri Feb 1 22:51:16 2008 +0000 - - Make PointSelection use the periodic flag in the same way as AroundSelection; even if it's no working properly at least it's consistent. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@86 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fb1c908a146487163507e388d6387bc804530a5a -Author: Oliver Beckstein -Date: Thu Jan 31 11:53:36 2008 +0000 - - Release tar ball. - - Change version to 0.5.0 (.0 signifies alpha status; later use a1, a2, b1, b2 - after the patch version) - - Added MANIFEST.in to include doc files and all the necessary header files as they are - not automatically picked up by distutils (apparently, a bug: 'getting C library - sources currently broken--no get_source_files() method in build_clib.py') - Also need to pick up all pyrex files and the docs - - Revamped docs a little bit. - - NOTE: python setup.py install --prefix=mydir is not working properly; it still - tries to install something in the site-wide dir - Added links to googlecode and a template for acknowledgements. - - Tested the sdist and managed to compile bot on MAc OS X and Linux (CentOS 4.2 with - modern numpy (> 1.0.3)) - - updated CHANGELOG - This corresponds to r94 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@82 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f76af6194d95e4fc2914423c66fa4f21b978cc30 -Author: Oliver Beckstein -Date: Thu Jan 31 11:53:27 2008 +0000 - - updated version to 0.5-rc1 in order to put a tar ball up on google code - This corresponds to r93 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@81 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 78e0581b4d80cb93a5a6fb57f8b3ed04e3490ebb -Author: Oliver Beckstein -Date: Thu Jan 31 11:53:20 2008 +0000 - - updated Naveen's email address and google code url - This corresponds to r92 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@80 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9109d325ed1295e44040d9a07a1ac5363fd70fea -Author: Oliver Beckstein -Date: Thu Jan 31 11:53:13 2008 +0000 - - reformatted and moved some functions out of the class. Working but need to integrate into the standard MDAnalysis frame work - This corresponds to r91 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@79 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit af20b16e024963db53841463d22ca4f6221bf778 -Author: Oliver Beckstein -Date: Thu Jan 31 11:53:05 2008 +0000 - - python xtc reader by Benjamin Hall (originally named xtcio.py). Used under GPL 3. - This corresponds to r90 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@78 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit cfd0d8c7de3b6bb169d17d5ffc4429cd023bd896 -Author: Oliver Beckstein -Date: Thu Jan 31 11:52:56 2008 +0000 - - - distance_array bug: need to copy() to get a contigious array - - AROUND selection: if periodic = False then do not use minimum image - convention when looking for neighbours. The default is now True to - get the behaviour from previous version of MDAnalysis. - Note: I'm not sure if the AROUND selection is working properly at - all. It didn't work for me before and it needs to be tested - again. - - This corresponds to r89 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@77 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c770738521ea4e70e1de7ff63f48cf71e967b517 -Author: Oliver Beckstein -Date: Thu Jan 31 11:52:49 2008 +0000 - - Under certain circumstances, numframes is not (yet) defined and then - repr throws an exception so I removed numframes from the - representation. - - This corresponds to r88 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@76 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit d39995059c5dda8c940690650825aece54d3962e -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:52:42 2008 +0000 - - Coordinates now returns a brand new array - doesn't break any of the numtools c functions that don't check for contiguity - long term we should fix the c functions to work properly with non-contiguous arrays - This corresponds to r87 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@75 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit eee8a6924cc77be4817212aac97b0f27548eb416 -Author: Elizabeth Denning -Date: Thu Jan 31 11:52:35 2008 +0000 - - LAMMPSParser: proper psf formatting - This corresponds to r86 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@74 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c315dc41cb646c93991b11db77e544c190734b7f -Author: Elizabeth Denning -Date: Thu Jan 31 11:52:26 2008 +0000 - - LAMMPSParser: one version of the LAMMPSParser that may be useful for MDAnalysis - This corresponds to r85 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@73 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9868860c76efac194dcb0c05f95901fd7bf06519 -Author: Elizabeth Denning -Date: Thu Jan 31 11:52:17 2008 +0000 - - fixed charge parser - This corresponds to r84 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@72 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 1e9e46f806efb957018527deea3c987479218856 -Author: Oliver Beckstein -Date: Thu Jan 31 11:52:10 2008 +0000 - - only doc changes - - This corresponds to r83 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@71 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a016ec6c41337cd49073d7c800963b65c094a4c7 -Author: Elizabeth Denning -Date: Thu Jan 31 11:52:03 2008 +0000 - - updated LAMMPSParser for version 81 - This corresponds to r82 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@70 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f7faed3f277df893e2389e344393bbfb0f2972f8 -Author: Oliver Beckstein -Date: Thu Jan 31 11:51:56 2008 +0000 - - fixed: typo (lead to NameError: results) - This corresponds to r81 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@69 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5fe135270dcbdb8691b0c78b49f6da05f6a5c02e -Author: Oliver Beckstein -Date: Thu Jan 31 11:51:49 2008 +0000 - - fixed sanity check on result (seg faulted before) - - This corresponds to r80 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@68 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a56824492f6b8c83ee60b38b6efcaf5a094bb4e1 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:51:33 2008 +0000 - - Stupid difference in numpy.nonzero between versions of numpy - later versions return a tuple - This corresponds to r77 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@67 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 617c3f2c534c7f3372d8aff7d13832b340b80319 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:51:26 2008 +0000 - - Fixed coordinate based selections on AtomGroups - This corresponds to r76 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@66 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c4d8fc2f074a98e6bf3d545822bb005d6fa1d521 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:51:19 2008 +0000 - - Forgot to actually parse the 'all' token in selections - This corresponds to r75 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@65 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6b80874ac8a897db77c02d29a00f5fbfd8529d8a -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:51:11 2008 +0000 - - Now rms_fitting can compile with both OS X VecLib and Intel MKL without changing headers - This corresponds to r74 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@64 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 85ea1bd1f2194b86eb33750817a3ed7470769f4b -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:51:04 2008 +0000 - - Subselections on AtomGroup; also incorporated 'all' selection - This corresponds to r73 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@63 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5d616667cef24c59350bdde11d550b464dd18e96 -Author: Oliver Beckstein -Date: Thu Jan 31 11:50:57 2008 +0000 - - fixed: AROUND selection (Naveen) - This corresponds to r72 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@62 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit cb29d568d0d6bad454f1133e58f597aed5454239 -Author: Oliver Beckstein -Date: Thu Jan 31 11:50:50 2008 +0000 - - Can calculate the distance array without minimum image by setting bpx=None. - This makes sense when working on RMS-fitted trajectories which do not obey the - original PBC any more. This code avoids having to use a stupid hack like - box = 2*box and is perhaps 25% faster by leaving out minimage() - This corresponds to r71 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@61 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8a26aa3fda587f01e235ba60a4310f1fbf951f40 -Author: Oliver Beckstein -Date: Thu Jan 31 11:50:42 2008 +0000 - - Re-added HSE,HSD, etc by merge -r65:63 (somehow got lost). - - This corresponds to r70 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@60 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ff9792d93c56566915328cc4c8cbbbe1e9b6a664 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:50:35 2008 +0000 - - Added doc string to RMS fitting code - This corresponds to r69 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@59 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 803b03d888a20091dc1895f8b778aca55121ae57 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:50:28 2008 +0000 - - Fixed a typo in name of function in DCD class - This corresponds to r68 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@58 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9e0e37b125d8c5d29a6b2a246808f04a6b8de8bc -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:50:21 2008 +0000 - - Fixed some bugs with equality testing using == instead of 'is', also added potential_profile example - This corresponds to r67 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@57 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 51319af027ec3ac458bcc9114efceefc52a665e5 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:50:13 2008 +0000 - - Documentation for the atomSelection function - also added Point selection to select atoms around a point, optimized around,point and property selections - This corresponds to r66 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@56 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 18f927d68f01e78cdfe8aa7480f471d9909f5dc4 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:50:04 2008 +0000 - - Added doc strings to most of the python code - This corresponds to r65 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@55 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 071b3c15be598385ab8639d2fa73a86e00e5d099 -Author: Oliver Beckstein -Date: Thu Jan 31 11:49:54 2008 +0000 - - fixed: centerOfMass(), centerOfGeometry(), radiusOfGyration() were broken because numpy.sum() now HAS to include the axis - This corresponds to r64 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@54 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 18ec2db9837a57002a0138d4ee02fa60bfe69133 -Author: Oliver Beckstein -Date: Thu Jan 31 11:49:47 2008 +0000 - - fixed protein selection: Charmm Histidine residues were left out of the protein selection - This corresponds to r63 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@53 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8cfd13016f6d2e85f13326eeec08b4d04c5432ec -Author: Oliver Beckstein -Date: Thu Jan 31 11:49:34 2008 +0000 - - Universe can read a structure from a PDB file - * added PDB module; the reader is attempting to fake the DCDReader - * PDB uses BioPython - * added pdb managed attribute to Universe class. - - This corresponds to r61 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@52 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5b5e019a69ca8e9e945a5405c6c0355cb04082fd -Author: Oliver Beckstein -Date: Thu Jan 31 11:49:27 2008 +0000 - - use standard distutils instead of numpy's version (otherwise it won't build,at least on OS X with python 2.4.3 and numpy 1.0.3.1 - This corresponds to r60 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@51 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4e539e446f8bba26b9124f4a2252d1a1c45ae1e0 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:49:20 2008 +0000 - - Fixed documentation - This corresponds to r59 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@50 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a5aaa2f30aa1e019a4bb7648059c078905d67efe -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:49:13 2008 +0000 - - Documentation for release - This corresponds to r58 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@49 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 25e196761c2727b800deb8151ed86ab3ef44df48 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:49:05 2008 +0000 - - Ready for distribution - This corresponds to r57 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@48 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a49584c5772fb566edc9377a37d0116854e89022 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:48:51 2008 +0000 - - Fixed some timeseries bugs - upgraded to work with numpy. Now individual timeseries objects can be treated like numpy arrays - This corresponds to r56 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@47 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fe5e1f34e0dc8a502e2d6f0062ea59c70e4e26b5 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:48:44 2008 +0000 - - Some more odd cases for indexing a trajectory - This corresponds to r55 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@46 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 25c9ed31932ab5f51ff5fb39150dd073bf016d32 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:48:36 2008 +0000 - - Disabled delaunay library for now - until I can resolve compilation issues with different platforms - This corresponds to r54 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@45 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4ee5bb43455b9d0703321a22b99b2dedfd969629 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:48:29 2008 +0000 - - Cleanup of code and minor bug fixes related to esoteric indexing of trajectories - This corresponds to r53 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@44 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0bd1bdf5a4a25fc7034ce626bb6ff4cb31c3c8da -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:48:18 2008 +0000 - - Tidied up the AtomGroup class and fixed a few minor bugs - This corresponds to r52 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@43 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9199c09bebb31581f1bb1f1222350d7e534a0240 -Author: Oliver Beckstein -Date: Thu Jan 31 11:48:11 2008 +0000 - - fixed: Bug in psf parser would not read charges correctly. Eg 0.900000E-01 would be read as 0.9 and not lead to an exception. This means that anything done with MDAnalysis and charge analysis in the past needs to be rechecked. I referencedd the Charmm source code for the authoritative PSF format. - This corresponds to r51 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@42 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit e76542dea177e6d72eb6f9233a471d63e375cac2 -Author: Oliver Beckstein -Date: Thu Jan 31 11:48:04 2008 +0000 - - use numpy.linalg (with old Numeric LinearAlgebra it does not work anymore) - This corresponds to r50 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@41 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ab34cb38f649ac5907352423e5d2e99477599de9 -Author: Oliver Beckstein -Date: Thu Jan 31 11:47:57 2008 +0000 - - * in comments: changes to make it compile on Mac OS X 10.3.9 without intel compiler and libs. The current version still compiles as before with intel. - * added the numpy includes to rms fitting as well (otherwise it failed for me) - This corresponds to r49 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@40 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2a8e613da429182276eda7eb14f3c26886bd0cb7 -Author: Oliver Beckstein -Date: Thu Jan 31 11:47:50 2008 +0000 - - added prototype because compiler complained - This corresponds to r48 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@39 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a55e6bdc161763b1faebae101ba9403165ad6ee8 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:47:43 2008 +0000 - - Small bug in distances helper code - This corresponds to r47 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@38 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 20d0a9b12c0d80c69c41a7a110a5f3cb6c94f563 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:47:35 2008 +0000 - - Finally - MDAnalysis has been updated to use numpy. Have fun! - - - This corresponds to r46 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@37 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0b6c4cb9dc8fe4c1444dfcda56c8817ee1bd3c15 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:47:20 2008 +0000 - - Fixed PSF parsing when number of residues is greater than 10000 - This corresponds to r45 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@36 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 14cf0e54a9093f23a6f00e4c2d11a899dce75de6 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:47:13 2008 +0000 - - Small psf parsing bug when there are 0 entries for a particular potential term - This corresponds to r44 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@35 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 4084aae0977682f1004aef328a385cab6fe36b3d -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:47:06 2008 +0000 - - Fixed delaunay tetrahedronalization - This corresponds to r43 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@34 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 5f7dffac0b1503b66a9ff9a4517544602df12548 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:46:58 2008 +0000 - - Updated schlitter example to automatically remove translational and rotational degrees of freedom - This corresponds to r42 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@33 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f8b71739bc20df43657d50a0735dc579f1f7a515 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:46:51 2008 +0000 - - RMS fitting to a reference set of coordinates - now compiles with Intel's MKL library - This corresponds to r41 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@32 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit efdd5e1a5826f177be1c49d059d1f7265f60e4b5 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:46:43 2008 +0000 - - AtomGroup.atoms is now a proper attribute - deprecated '_atoms' access - This corresponds to r40 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@31 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 3599d77ab889aea96150f05a2ddeac733a1a56bd -Author: Elizabeth Denning -Date: Thu Jan 31 11:46:34 2008 +0000 - - new schlitter calculation that uses the determinant - This corresponds to r39 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@30 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 87eccb896010d39f2c3a27ecf57a6c4e263f2257 -Author: Elizabeth Denning -Date: Thu Jan 31 11:46:27 2008 +0000 - - deleting - This corresponds to r38 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@29 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7408b1e5f6095551d737b02969a2c307e90d7c5f -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:46:19 2008 +0000 - - Cleanup of c source code directory - removed some modules that are no longer necessary - This corresponds to r37 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@28 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c9a78429889d6fc86ef5868bcf653f55d1b21432 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:46:02 2008 +0000 - - Updated examples to use new 'dcd' attribute - This corresponds to r36 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@27 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8c989bec501b970c4d33554921ab715d07513c68 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:45:54 2008 +0000 - - Deprecated the ugly '_dcd' reference usage in Universe, use 'dcd' from now on - This corresponds to r35 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@26 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 7335792f837264bab4c048ed2867eb1c22a9db9c -Author: Elizabeth Denning -Date: Thu Jan 31 11:45:47 2008 +0000 - - alternative Schlitter code that calculates entropy using the determinant - This corresponds to r34 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@25 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 6ea6e66a02664a383546660d2f6f120c2ca937fa -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:45:40 2008 +0000 - - Pass in preformed array to distance functions - usefull for repeated calls with the same sets of atom groups - This corresponds to r33 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@24 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit a656bf58a903b8d4d8368943097927363c831d0e -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:45:33 2008 +0000 - - Added a self_distance function to compute distances within a group of atoms - returns a linear array which corresponds to the upper triangular distance matrix - This corresponds to r32 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@23 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 565ae2c3486578acad8181c47f5fd7948c4738a8 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:45:26 2008 +0000 - - Some changes to Timeseries objects for pretty printing - This corresponds to r26 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@22 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 97817bcd81fa63f4afe5c7ceacf7135be52748c3 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:45:17 2008 +0000 - - Changes to Timeseries so reference individual timeseries - This corresponds to r25 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@21 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c421884c2ec9009397a3889778d43a3ea3a390be -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:45:09 2008 +0000 - - Import common objects into base namespace, also fixed some things in AtomGroup.py - This corresponds to r24 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@20 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit b3f6a4ee0951056ccdbb68de85a9ff7970904336 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:45:02 2008 +0000 - - Fixed Timeseries so that you can pass in an AtomGroup - This corresponds to r23 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@19 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit c88e3fe409dc18276848247043f29f353274f1b2 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:44:55 2008 +0000 - - Fixed a bug I must have introduced when trying to make PSF reading faster by preallocating the bond, angle, etc lists, but I was only including the last item that was read in each line - also disabled building of bondlists on each atom for the Bond selection, since noone's using it and it really slows down reading a psf - This corresponds to r22 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@18 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 23194312889992a1fc2a5ec0b196681cfc74855b -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:44:48 2008 +0000 - - Why was I ever returning a copy of the timestep when using the indexing notation on the dcd reader? Who knows what I was thinkingsvn status - This corresponds to r21 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@17 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9200719c0d79a53fddf3cfa1d25ce7384653009e -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:44:41 2008 +0000 - - Fixed a bug in the DCD reader when jumping to the beginning of the trajectory and there are fixed atoms - This corresponds to r20 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@16 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit f4fc049e6031ef8490ded8746457a22ae4628112 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:44:34 2008 +0000 - - Stupid bug in the calculation of CenterOfMass for Timeseries (in correl.h) - This corresponds to r19 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@15 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit fd540ca83f91ab7f578a02a399b3d5204b6c7d93 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:44:27 2008 +0000 - - Fixed a bug with loading new dcds into a universe, where each atom would refer to a previous dcd's timestep object - This corresponds to r18 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@14 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 17ad3fecab28f74c1020978661a5ce1f4243f230 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:44:20 2008 +0000 - - PSFParser now gracefully handles psf files that only contain NATOM fields - This corresponds to r17 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@13 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 52933eaf991d15277f1c00e24caeac4b4fa1dcaf -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:44:13 2008 +0000 - - For the Atom timeseries, can now pass in a list of atoms - This corresponds to r16 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@12 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 8c90d030b8fc8bcd1dce5851405534590a7a3938 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:44:06 2008 +0000 - - Added frame range to DCD::correl - This corresponds to r14 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@11 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 44ded8ba456c844f878109a15bc3cae6c7392761 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:43:57 2008 +0000 - - Calculate distance matrix between two sets of atoms - This corresponds to r13 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@10 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 9152cf3754a7075faa63a78347f32ba783ac6dde -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:43:47 2008 +0000 - - Anastasia's change to load more than one dcd file (for split trajectories) - This corresponds to r12 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@9 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ba342c11e99a3afbc40cdbcc03bd6df90db92b63 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:43:39 2008 +0000 - - Added auxiliary data to correl function (to do mass weighting, for example) - This corresponds to r11 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@8 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 0d324fcdfdb75e258fa76669e6e7e0cc0ea6ec23 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:43:31 2008 +0000 - - Bug dcd correl functions when running on 64 bit machines - This corresponds to r10 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@7 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit bffbfe2c34272ad41943d92c6e92e4954aea11b4 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:43:23 2008 +0000 - - MDAnalysis - added a center of geometry timeseries - This corresponds to r9 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@6 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 86f4d4b56656ee051cbbff29726f7cde0ae3ac1e -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:43:15 2008 +0000 - - MDAnalysis - added momentOfInertia call - This corresponds to r8 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@5 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 50d16d939cf67fb25e95db5b01f85e2587f14f6e -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:43:08 2008 +0000 - - AtomGroup - bug in __getitem__ for ResidueGroup - This corresponds to r7 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@4 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit 2a8eb95c4c157c01d1e70cc0487af31e63ab32a9 -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:43:01 2008 +0000 - - MDAnalysis - bug with dcd slices - This corresponds to r6 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@3 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit eaccb2eb8c2cbb640a4f731b5dda163732d727ac -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:42:54 2008 +0000 - - Added some example usages to MDAnalysis - This corresponds to r5 in /code/MDAnalysis. - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@2 dcee7792-c13e-0410-88f5-272e5f544b36 - -commit ac235b9b094ef3a0f2003467fcb70dc69d96ed9e -Author: Naveen Michaud-Agrawal -Date: Thu Jan 31 11:42:33 2008 +0000 - - initial import - - git-svn-id: https://mdanalysis.googlecode.com/svn/trunk@1 dcee7792-c13e-0410-88f5-272e5f544b36 diff --git a/package/MDAnalysis/analysis/encore/clustering/affinityprop.c b/package/MDAnalysis/analysis/encore/clustering/affinityprop.c deleted file mode 100644 index 8ead646491f..00000000000 --- a/package/MDAnalysis/analysis/encore/clustering/affinityprop.c +++ /dev/null @@ -1,8714 +0,0 @@ -/* Generated by Cython 0.29.33 */ - -/* BEGIN: Cython Metadata -{ - "distutils": { - "depends": [ - "C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include\\numpy\\arrayobject.h", - "C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include\\numpy\\arrayscalars.h", - "C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include\\numpy\\ndarrayobject.h", - 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#undef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 0 - #undef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 0 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #undef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 0 - #undef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 0 - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 - #endif -#elif defined(PYSTON_VERSION) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 1 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #undef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 0 - #undef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 0 - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 - #endif -#elif defined(PY_NOGIL) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 1 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #ifndef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 1 - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 1 - #endif - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 -#else - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 1 - #define CYTHON_COMPILING_IN_NOGIL 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #elif !defined(CYTHON_USE_PYTYPE_LOOKUP) - #define CYTHON_USE_PYTYPE_LOOKUP 1 - #endif - #if PY_MAJOR_VERSION < 3 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #elif !defined(CYTHON_USE_PYLONG_INTERNALS) - #define CYTHON_USE_PYLONG_INTERNALS 1 - #endif - #ifndef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 1 - #endif - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #elif !defined(CYTHON_USE_UNICODE_WRITER) - #define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #elif !defined(CYTHON_FAST_THREAD_STATE) - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000) - #endif - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000) - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) - #endif - #ifndef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1) - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #elif !defined(CYTHON_USE_EXC_INFO_STACK) - #define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3) - #endif - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 - #endif -#endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #if PY_MAJOR_VERSION < 3 - #include "longintrepr.h" - #endif - #undef SHIFT - #undef BASE - #undef MASK - #ifdef SIZEOF_VOID_P - enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) }; - #endif -#endif -#ifndef __has_attribute - #define __has_attribute(x) 0 -#endif -#ifndef __has_cpp_attribute - #define __has_cpp_attribute(x) 0 -#endif -#ifndef CYTHON_RESTRICT - #if defined(__GNUC__) - #define CYTHON_RESTRICT __restrict__ - #elif defined(_MSC_VER) && _MSC_VER >= 1400 - #define CYTHON_RESTRICT __restrict - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_RESTRICT restrict - #else - #define CYTHON_RESTRICT - #endif -#endif -#ifndef CYTHON_UNUSED -# if defined(__GNUC__) -# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -#endif -#ifndef CYTHON_MAYBE_UNUSED_VAR -# if defined(__cplusplus) - template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } -# else -# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) -# endif -#endif -#ifndef CYTHON_NCP_UNUSED -# if CYTHON_COMPILING_IN_CPYTHON -# define CYTHON_NCP_UNUSED -# else -# define CYTHON_NCP_UNUSED CYTHON_UNUSED -# endif -#endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) -#ifdef _MSC_VER - #ifndef _MSC_STDINT_H_ - #if _MSC_VER < 1300 - typedef unsigned char uint8_t; - typedef unsigned int uint32_t; - #else - typedef unsigned __int8 uint8_t; - typedef unsigned __int32 uint32_t; - #endif - #endif -#else - #include -#endif -#ifndef CYTHON_FALLTHROUGH - #if defined(__cplusplus) && __cplusplus >= 201103L - #if __has_cpp_attribute(fallthrough) - #define CYTHON_FALLTHROUGH [[fallthrough]] - #elif __has_cpp_attribute(clang::fallthrough) - #define CYTHON_FALLTHROUGH [[clang::fallthrough]] - #elif __has_cpp_attribute(gnu::fallthrough) - #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] - #endif - #endif - #ifndef CYTHON_FALLTHROUGH - #if __has_attribute(fallthrough) - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - #else - #define CYTHON_FALLTHROUGH - #endif - #endif - #if defined(__clang__ ) && defined(__apple_build_version__) - #if __apple_build_version__ < 7000000 - #undef CYTHON_FALLTHROUGH - #define CYTHON_FALLTHROUGH - #endif - #endif -#endif - -#ifndef CYTHON_INLINE - #if defined(__clang__) - #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) - #elif defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline - #else - #define CYTHON_INLINE - #endif -#endif - -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - if (type) { - PyErr_Restore(type, value, traceback); - } - return co; - } -#else - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_STACKLESS - #define METH_STACKLESS 0 -#endif -#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) - #ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - #endif - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); - typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast - #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1 - #define PyMem_RawMalloc(n) PyMem_Malloc(n) - #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) - #define PyMem_RawFree(p) PyMem_Free(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#elif PY_VERSION_HEX >= 0x03060000 - #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() -#elif PY_VERSION_HEX >= 0x03000000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#else - #define __Pyx_PyThreadState_Current _PyThreadState_Current -#endif -#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) -#include "pythread.h" -#define Py_tss_NEEDS_INIT 0 -typedef int Py_tss_t; -static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { - *key = PyThread_create_key(); - return 0; -} -static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { - Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); - *key = Py_tss_NEEDS_INIT; - return key; -} -static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { - PyObject_Free(key); -} -static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { - return *key != Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { - PyThread_delete_key(*key); - *key = Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { - return PyThread_set_key_value(*key, value); -} -static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { - return PyThread_get_key_value(*key); -} -#endif -#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) -#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) -#else -#define __Pyx_PyDict_NewPresized(n) PyDict_New() -#endif -#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION - #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) -#else - #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS -#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) -#else -#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_READY(op) (0) - #else - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #endif - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) - #else - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) - #endif - #endif -#else - #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 - #define __Pyx_PyUnicode_READY(op) (0) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) - #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) - #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) - #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) -#endif -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) -#else - #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ - PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) -#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? 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"" : "s", num_found); -} - -/* RaiseDoubleKeywords */ -static void __Pyx_RaiseDoubleKeywordsError( - const char* func_name, - PyObject* kw_name) -{ - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION >= 3 - "%s() got multiple values for keyword argument '%U'", func_name, kw_name); - #else - "%s() got multiple values for keyword argument '%s'", func_name, - PyString_AsString(kw_name)); - #endif -} - -/* ParseKeywords */ -static int __Pyx_ParseOptionalKeywords( - PyObject *kwds, - PyObject **argnames[], - PyObject *kwds2, - PyObject *values[], - Py_ssize_t num_pos_args, - const char* function_name) -{ - PyObject *key = 0, *value = 0; - Py_ssize_t pos = 0; - PyObject*** name; - PyObject*** first_kw_arg = argnames + num_pos_args; - while (PyDict_Next(kwds, &pos, &key, &value)) { - name = first_kw_arg; - while (*name && (**name != key)) name++; - if (*name) { - values[name-argnames] = value; - continue; - } - name = first_kw_arg; - #if PY_MAJOR_VERSION < 3 - if (likely(PyString_Check(key))) { - while (*name) { - if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) - && _PyString_Eq(**name, key)) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - if ((**argname == key) || ( - (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) - && _PyString_Eq(**argname, key))) { - goto arg_passed_twice; - } - argname++; - } - } - } else - #endif - if (likely(PyUnicode_Check(key))) { - while (*name) { - int cmp = (**name == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**name, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - int cmp = (**argname == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**argname, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) goto arg_passed_twice; - argname++; - } - } - } else - goto invalid_keyword_type; - if (kwds2) { - if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; - } else { - goto invalid_keyword; - } - } - return 0; -arg_passed_twice: - __Pyx_RaiseDoubleKeywordsError(function_name, key); - goto bad; -invalid_keyword_type: - PyErr_Format(PyExc_TypeError, - "%.200s() keywords must be strings", function_name); - goto bad; -invalid_keyword: - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION < 3 - "%.200s() got an unexpected keyword argument '%.200s'", - function_name, PyString_AsString(key)); - #else - "%s() got an unexpected keyword argument '%U'", - function_name, key); - #endif -bad: - return -1; -} - -/* PyCFunctionFastCall */ -#if CYTHON_FAST_PYCCALL -static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) { - PyCFunctionObject *func = (PyCFunctionObject*)func_obj; - PyCFunction meth = PyCFunction_GET_FUNCTION(func); - PyObject *self = PyCFunction_GET_SELF(func); - int flags = PyCFunction_GET_FLAGS(func); - assert(PyCFunction_Check(func)); - assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))); - assert(nargs >= 0); - assert(nargs == 0 || args != NULL); - /* _PyCFunction_FastCallDict() must not be called with an exception set, - because it may clear it (directly or indirectly) and so the - caller loses its exception */ - assert(!PyErr_Occurred()); - if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) { - return (*((__Pyx_PyCFunctionFastWithKeywords)(void*)meth)) (self, args, nargs, NULL); - } else { - return (*((__Pyx_PyCFunctionFast)(void*)meth)) (self, args, nargs); - } -} -#endif - -/* PyFunctionFastCall */ -#if CYTHON_FAST_PYCALL -static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, - PyObject *globals) { - PyFrameObject *f; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject **fastlocals; - Py_ssize_t i; - PyObject *result; - assert(globals != NULL); - /* XXX Perhaps we should create a specialized - PyFrame_New() that doesn't take locals, but does - take builtins without sanity checking them. - */ - assert(tstate != NULL); - f = PyFrame_New(tstate, co, globals, NULL); - if (f == NULL) { - return NULL; - } - fastlocals = __Pyx_PyFrame_GetLocalsplus(f); - for (i = 0; i < na; i++) { - Py_INCREF(*args); - fastlocals[i] = *args++; - } - result = PyEval_EvalFrameEx(f,0); - ++tstate->recursion_depth; - Py_DECREF(f); - --tstate->recursion_depth; - return result; -} -#if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { - PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); - PyObject *globals = PyFunction_GET_GLOBALS(func); - PyObject *argdefs = PyFunction_GET_DEFAULTS(func); - PyObject *closure; -#if PY_MAJOR_VERSION >= 3 - PyObject *kwdefs; -#endif - PyObject *kwtuple, **k; - PyObject **d; - Py_ssize_t nd; - Py_ssize_t nk; - PyObject *result; - assert(kwargs == NULL || PyDict_Check(kwargs)); - nk = kwargs ? PyDict_Size(kwargs) : 0; - if (Py_EnterRecursiveCall((char*)" while calling a Python object")) { - return NULL; - } - if ( -#if PY_MAJOR_VERSION >= 3 - co->co_kwonlyargcount == 0 && -#endif - likely(kwargs == NULL || nk == 0) && - co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { - if (argdefs == NULL && co->co_argcount == nargs) { - result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); - goto done; - } - else if (nargs == 0 && argdefs != NULL - && co->co_argcount == Py_SIZE(argdefs)) { - /* function called with no arguments, but all parameters have - a default value: use default values as arguments .*/ - args = &PyTuple_GET_ITEM(argdefs, 0); - result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); - goto done; - } - } - if (kwargs != NULL) { - Py_ssize_t pos, i; - kwtuple = PyTuple_New(2 * nk); - if (kwtuple == NULL) { - result = NULL; - goto done; - } - k = &PyTuple_GET_ITEM(kwtuple, 0); - pos = i = 0; - while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { - Py_INCREF(k[i]); - Py_INCREF(k[i+1]); - i += 2; - } - nk = i / 2; - } - else { - kwtuple = NULL; - k = NULL; - } - closure = PyFunction_GET_CLOSURE(func); -#if PY_MAJOR_VERSION >= 3 - kwdefs = PyFunction_GET_KW_DEFAULTS(func); -#endif - if (argdefs != NULL) { - d = &PyTuple_GET_ITEM(argdefs, 0); - nd = Py_SIZE(argdefs); - } - else { - d = NULL; - nd = 0; - } -#if PY_MAJOR_VERSION >= 3 - result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, kwdefs, closure); -#else - result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, closure); -#endif - Py_XDECREF(kwtuple); -done: - Py_LeaveRecursiveCall(); - return result; -} -#endif -#endif - -/* PyObjectCall */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { - PyObject *result; - ternaryfunc call = Py_TYPE(func)->tp_call; - if (unlikely(!call)) - return PyObject_Call(func, arg, kw); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = (*call)(func, arg, kw); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallMethO */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { - PyObject *self, *result; - PyCFunction cfunc; - cfunc = PyCFunction_GET_FUNCTION(func); - self = PyCFunction_GET_SELF(func); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = cfunc(self, arg); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallOneArg */ -#if CYTHON_COMPILING_IN_CPYTHON -static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_New(1); - if (unlikely(!args)) return NULL; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif - if (likely(PyCFunction_Check(func))) { - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (__Pyx_PyFastCFunction_Check(func)) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } - } - return __Pyx__PyObject_CallOneArg(func, arg); -} -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -#endif - -/* GetItemInt */ -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { - PyObject *r; - if (!j) return NULL; - r = PyObject_GetItem(o, j); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyList_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyTuple_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } - else if (PyTuple_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } else { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_item)) { - if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { - Py_ssize_t l = m->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return NULL; - PyErr_Clear(); - } - } - return m->sq_item(o, i); - } - } -#else - if (is_list || PySequence_Check(o)) { - return PySequence_GetItem(o, i); - } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -} - -/* ObjectGetItem */ -#if CYTHON_USE_TYPE_SLOTS -static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { - PyObject *runerr = NULL; - Py_ssize_t key_value; - PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; - if (unlikely(!(m && m->sq_item))) { - PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); - return NULL; - } - key_value = __Pyx_PyIndex_AsSsize_t(index); - if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { - return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); - } - if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { - PyErr_Clear(); - PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); - } - return NULL; -} -static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { - PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; - if (likely(m && m->mp_subscript)) { - return m->mp_subscript(obj, key); - } - return __Pyx_PyObject_GetIndex(obj, key); -} -#endif - -/* GetTopmostException */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* PyErrFetchRestore */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -} -#endif - -/* RaiseException */ -#if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* PyDictVersioning */ -#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; -} -static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) { - PyObject **dictptr = NULL; - Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset; - if (offset) { -#if CYTHON_COMPILING_IN_CPYTHON - dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj); -#else - dictptr = _PyObject_GetDictPtr(obj); -#endif - } - return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; -} -static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) - return 0; - return obj_dict_version == __Pyx_get_object_dict_version(obj); -} -#endif - -/* GetModuleGlobalName */ -#if CYTHON_USE_DICT_VERSIONS -static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value) -#else -static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name) -#endif -{ - PyObject *result; -#if !CYTHON_AVOID_BORROWED_REFS -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 - result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } else if (unlikely(PyErr_Occurred())) { - return NULL; - } -#else - result = PyDict_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } -#endif -#else - result = PyObject_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } - PyErr_Clear(); -#endif - return __Pyx_GetBuiltinName(name); -} - -/* PyObjectCall2Args */ -static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { - PyObject *args, *result = NULL; - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyFunction_FastCall(function, args, 2); - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyCFunction_FastCall(function, args, 2); - } - #endif - args = PyTuple_New(2); - if (unlikely(!args)) goto done; - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 0, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 1, arg2); - Py_INCREF(function); - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); -done: - return result; -} - -/* ExtTypeTest */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(__Pyx_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* IsLittleEndian */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) -{ - union { - uint32_t u32; - uint8_t u8[4]; - } S; - S.u32 = 0x01020304; - return S.u8[0] == 4; -} - -/* BufferFormatCheck */ -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type) { - stack[0].field = &ctx->root; - stack[0].parent_offset = 0; - ctx->root.type = type; - ctx->root.name = "buffer dtype"; - ctx->root.offset = 0; - ctx->head = stack; - ctx->head->field = &ctx->root; - ctx->fmt_offset = 0; - ctx->head->parent_offset = 0; - ctx->new_packmode = '@'; - ctx->enc_packmode = '@'; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->is_complex = 0; - ctx->is_valid_array = 0; - ctx->struct_alignment = 0; - while (type->typegroup == 'S') { - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = 0; - type = type->fields->type; - } -} -static int __Pyx_BufFmt_ParseNumber(const char** ts) { - int count; - const char* t = *ts; - if (*t < '0' || *t > '9') { - return -1; - } else { - count = *t++ - '0'; - while (*t >= '0' && *t <= '9') { - count *= 10; - count += *t++ - '0'; - } - } - *ts = t; - return count; -} -static int __Pyx_BufFmt_ExpectNumber(const char **ts) { - int number = __Pyx_BufFmt_ParseNumber(ts); - if (number == -1) - PyErr_Format(PyExc_ValueError,\ - "Does not understand character buffer dtype format string ('%c')", **ts); - return number; -} -static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { - PyErr_Format(PyExc_ValueError, - "Unexpected format string character: '%c'", ch); -} -static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { - switch (ch) { - case '?': return "'bool'"; - case 'c': return "'char'"; - case 'b': return "'signed char'"; - case 'B': return "'unsigned char'"; - case 'h': return "'short'"; - case 'H': return "'unsigned short'"; - case 'i': return "'int'"; - case 'I': return "'unsigned int'"; - case 'l': return "'long'"; - case 'L': return "'unsigned long'"; - case 'q': return "'long long'"; - case 'Q': return "'unsigned long long'"; - case 'f': return (is_complex ? "'complex float'" : "'float'"); - case 'd': return (is_complex ? "'complex double'" : "'double'"); - case 'g': return (is_complex ? "'complex long double'" : "'long double'"); - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - case 's': case 'p': return "a string"; - case 0: return "end"; - default: return "unparseable format string"; - } -} -static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return 2; - case 'i': case 'I': case 'l': case 'L': return 4; - case 'q': case 'Q': return 8; - case 'f': return (is_complex ? 8 : 4); - case 'd': return (is_complex ? 16 : 8); - case 'g': { - PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); - return 0; - } - case 'O': case 'P': return sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(short); - case 'i': case 'I': return sizeof(int); - case 'l': case 'L': return sizeof(long); - #ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(PY_LONG_LONG); - #endif - case 'f': return sizeof(float) * (is_complex ? 2 : 1); - case 'd': return sizeof(double) * (is_complex ? 2 : 1); - case 'g': return sizeof(long double) * (is_complex ? 2 : 1); - case 'O': case 'P': return sizeof(void*); - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -typedef struct { char c; short x; } __Pyx_st_short; -typedef struct { char c; int x; } __Pyx_st_int; -typedef struct { char c; long x; } __Pyx_st_long; -typedef struct { char c; float x; } __Pyx_st_float; -typedef struct { char c; double x; } __Pyx_st_double; -typedef struct { char c; long double x; } __Pyx_st_longdouble; -typedef struct { char c; void *x; } __Pyx_st_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_st_float) - sizeof(float); - case 'd': return sizeof(__Pyx_st_double) - sizeof(double); - case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -/* These are for computing the padding at the end of the struct to align - on the first member of the struct. This will probably the same as above, - but we don't have any guarantees. - */ -typedef struct { short x; char c; } __Pyx_pad_short; -typedef struct { int x; char c; } __Pyx_pad_int; -typedef struct { long x; char c; } __Pyx_pad_long; -typedef struct { float x; char c; } __Pyx_pad_float; -typedef struct { double x; char c; } __Pyx_pad_double; -typedef struct { long double x; char c; } __Pyx_pad_longdouble; -typedef struct { void *x; char c; } __Pyx_pad_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); - case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); - case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { - switch (ch) { - case 'c': - return 'H'; - case 'b': case 'h': case 'i': - case 'l': case 'q': case 's': case 'p': - return 'I'; - case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': - return 'U'; - case 'f': case 'd': case 'g': - return (is_complex ? 'C' : 'R'); - case 'O': - return 'O'; - case 'P': - return 'P'; - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { - if (ctx->head == NULL || ctx->head->field == &ctx->root) { - const char* expected; - const char* quote; - if (ctx->head == NULL) { - expected = "end"; - quote = ""; - } else { - expected = ctx->head->field->type->name; - quote = "'"; - } - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected %s%s%s but got %s", - quote, expected, quote, - __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); - } else { - __Pyx_StructField* field = ctx->head->field; - __Pyx_StructField* parent = (ctx->head - 1)->field; - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", - field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), - parent->type->name, field->name); - } -} -static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { - char group; - size_t size, offset, arraysize = 1; - if (ctx->enc_type == 0) return 0; - if (ctx->head->field->type->arraysize[0]) { - int i, ndim = 0; - if (ctx->enc_type == 's' || ctx->enc_type == 'p') { - ctx->is_valid_array = ctx->head->field->type->ndim == 1; - ndim = 1; - if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { - PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %zu", - ctx->head->field->type->arraysize[0], ctx->enc_count); - return -1; - } - } - if (!ctx->is_valid_array) { - PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", - ctx->head->field->type->ndim, ndim); - return -1; - } - for (i = 0; i < ctx->head->field->type->ndim; i++) { - arraysize *= ctx->head->field->type->arraysize[i]; - } - ctx->is_valid_array = 0; - ctx->enc_count = 1; - } - group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); - do { - __Pyx_StructField* field = ctx->head->field; - __Pyx_TypeInfo* type = field->type; - if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { - size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); - } else { - size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); - } - if (ctx->enc_packmode == '@') { - size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); - size_t align_mod_offset; - if (align_at == 0) return -1; - align_mod_offset = ctx->fmt_offset % align_at; - if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; - if (ctx->struct_alignment == 0) - ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, - ctx->is_complex); - } - if (type->size != size || type->typegroup != group) { - if (type->typegroup == 'C' && type->fields != NULL) { - size_t parent_offset = ctx->head->parent_offset + field->offset; - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = parent_offset; - continue; - } - if ((type->typegroup == 'H' || group == 'H') && type->size == size) { - } else { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - } - offset = ctx->head->parent_offset + field->offset; - if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; - } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } - } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; -} -static PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number, ndim; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ndim = ctx->head->field->type->ndim; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; - } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; - } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; - } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; -} -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; - } - break; - case '}': - { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } - } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; - } - CYTHON_FALLTHROUGH; - case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && - (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - CYTHON_FALLTHROUGH; - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: - { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; - } - } - } -} - -/* BufferGetAndValidate */ - static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { - if (unlikely(info->buf == NULL)) return; - if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; - __Pyx_ReleaseBuffer(info); -} -static void __Pyx_ZeroBuffer(Py_buffer* buf) { - buf->buf = NULL; - buf->obj = NULL; - buf->strides = __Pyx_zeros; - buf->shape = __Pyx_zeros; - buf->suboffsets = __Pyx_minusones; -} -static int __Pyx__GetBufferAndValidate( - Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, - int nd, int cast, __Pyx_BufFmt_StackElem* stack) -{ - buf->buf = NULL; - if (unlikely(__Pyx_GetBuffer(obj, buf, flags) == -1)) { - __Pyx_ZeroBuffer(buf); - return -1; - } - if (unlikely(buf->ndim != nd)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - nd, buf->ndim); - goto fail; - } - if (!cast) { - __Pyx_BufFmt_Context ctx; - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; - } - if (unlikely((size_t)buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", - buf->itemsize, (buf->itemsize > 1) ? "s" : "", - dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; - return 0; -fail:; - __Pyx_SafeReleaseBuffer(buf); - return -1; -} - -/* PyIntCompare */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED long inplace) { - if (op1 == op2) { - Py_RETURN_TRUE; - } - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - const long b = intval; - long a = PyInt_AS_LONG(op1); - if (a == b) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - int unequal; - unsigned long uintval; - Py_ssize_t size = Py_SIZE(op1); - const digit* digits = ((PyLongObject*)op1)->ob_digit; - if (intval == 0) { - if (size == 0) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } else if (intval < 0) { - if (size >= 0) - Py_RETURN_FALSE; - intval = -intval; - size = -size; - } else { - if (size <= 0) - Py_RETURN_FALSE; - } - uintval = (unsigned long) intval; -#if PyLong_SHIFT * 4 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 4)) { - unequal = (size != 5) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[4] != ((uintval >> (4 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif -#if PyLong_SHIFT * 3 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 3)) { - unequal = (size != 4) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif -#if PyLong_SHIFT * 2 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 2)) { - unequal = (size != 3) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif -#if PyLong_SHIFT * 1 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 1)) { - unequal = (size != 2) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif - unequal = (size != 1) || (((unsigned long) digits[0]) != (uintval & (unsigned long) PyLong_MASK)); - if (unequal == 0) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - if ((double)a == (double)b) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } - return ( - PyObject_RichCompare(op1, op2, Py_EQ)); -} - -/* PyObjectFormat */ - #if CYTHON_USE_UNICODE_WRITER -static PyObject* __Pyx_PyObject_Format(PyObject* obj, PyObject* format_spec) { - int ret; - _PyUnicodeWriter writer; - if (likely(PyFloat_CheckExact(obj))) { -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x03040000 - _PyUnicodeWriter_Init(&writer, 0); -#else - _PyUnicodeWriter_Init(&writer); -#endif - ret = _PyFloat_FormatAdvancedWriter( - &writer, - obj, - format_spec, 0, PyUnicode_GET_LENGTH(format_spec)); - } else if (likely(PyLong_CheckExact(obj))) { -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x03040000 - _PyUnicodeWriter_Init(&writer, 0); -#else - _PyUnicodeWriter_Init(&writer); -#endif - ret = _PyLong_FormatAdvancedWriter( - &writer, - obj, - format_spec, 0, PyUnicode_GET_LENGTH(format_spec)); - } else { - return PyObject_Format(obj, format_spec); - } - if (unlikely(ret == -1)) { - _PyUnicodeWriter_Dealloc(&writer); - return NULL; - } - return _PyUnicodeWriter_Finish(&writer); -} -#endif - -/* PyObjectFormatAndDecref */ - static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatSimpleAndDecref(PyObject* s, PyObject* f) { - if (unlikely(!s)) return NULL; - if (likely(PyUnicode_CheckExact(s))) return s; - #if PY_MAJOR_VERSION < 3 - if (likely(PyString_CheckExact(s))) { - PyObject *result = PyUnicode_FromEncodedObject(s, NULL, "strict"); - Py_DECREF(s); - return result; - } - #endif - return __Pyx_PyObject_FormatAndDecref(s, f); -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatAndDecref(PyObject* s, PyObject* f) { - PyObject *result = PyObject_Format(s, f); - Py_DECREF(s); - return result; -} - -/* JoinPyUnicode */ - static PyObject* __Pyx_PyUnicode_Join(PyObject* value_tuple, Py_ssize_t value_count, Py_ssize_t result_ulength, - CYTHON_UNUSED Py_UCS4 max_char) { -#if CYTHON_USE_UNICODE_INTERNALS && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - PyObject *result_uval; - int result_ukind; - Py_ssize_t i, char_pos; - void *result_udata; -#if CYTHON_PEP393_ENABLED - result_uval = PyUnicode_New(result_ulength, max_char); - if (unlikely(!result_uval)) return NULL; - result_ukind = (max_char <= 255) ? PyUnicode_1BYTE_KIND : (max_char <= 65535) ? PyUnicode_2BYTE_KIND : PyUnicode_4BYTE_KIND; - result_udata = PyUnicode_DATA(result_uval); -#else - result_uval = PyUnicode_FromUnicode(NULL, result_ulength); - if (unlikely(!result_uval)) return NULL; - result_ukind = sizeof(Py_UNICODE); - result_udata = PyUnicode_AS_UNICODE(result_uval); -#endif - char_pos = 0; - for (i=0; i < value_count; i++) { - int ukind; - Py_ssize_t ulength; - void *udata; - PyObject *uval = PyTuple_GET_ITEM(value_tuple, i); - if (unlikely(__Pyx_PyUnicode_READY(uval))) - goto bad; - ulength = __Pyx_PyUnicode_GET_LENGTH(uval); - if (unlikely(!ulength)) - continue; - if (unlikely(char_pos + ulength < 0)) - goto overflow; - ukind = __Pyx_PyUnicode_KIND(uval); - udata = __Pyx_PyUnicode_DATA(uval); - if (!CYTHON_PEP393_ENABLED || ukind == result_ukind) { - memcpy((char *)result_udata + char_pos * result_ukind, udata, (size_t) (ulength * result_ukind)); - } else { - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030300F0 || defined(_PyUnicode_FastCopyCharacters) - _PyUnicode_FastCopyCharacters(result_uval, char_pos, uval, 0, ulength); - #else - Py_ssize_t j; - for (j=0; j < ulength; j++) { - Py_UCS4 uchar = __Pyx_PyUnicode_READ(ukind, udata, j); - __Pyx_PyUnicode_WRITE(result_ukind, result_udata, char_pos+j, uchar); - } - #endif - } - char_pos += ulength; - } - return result_uval; -overflow: - PyErr_SetString(PyExc_OverflowError, "join() result is too long for a Python string"); -bad: - Py_DECREF(result_uval); - return NULL; -#else - result_ulength++; - value_count++; - return PyUnicode_Join(__pyx_empty_unicode, value_tuple); -#endif -} - -/* Import */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* BufferFallbackError */ - static void __Pyx_RaiseBufferFallbackError(void) { - PyErr_SetString(PyExc_ValueError, - "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); -} - -/* PyErrExceptionMatches */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* GetException */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* ImportFrom */ - static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { - PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); - if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_Format(PyExc_ImportError, - #if PY_MAJOR_VERSION < 3 - "cannot import name %.230s", PyString_AS_STRING(name)); - #else - "cannot import name %S", name); - #endif - } - return value; -} - -/* CLineInTraceback */ - #ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ - #include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - if ((0)) {} - view->obj = NULL; - Py_DECREF(obj); -} -#endif - - - /* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* FastTypeChecks */ - #if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; - if (a == b) - return 1; - } - return b == &PyBaseObject_Type; -} -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { - PyObject *mro; - if (a == b) return 1; - mro = a->tp_mro; - if (likely(mro)) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(mro); - for (i = 0; i < n; i++) { - if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) - return 1; - } - return 0; - } - return __Pyx_InBases(a, b); -} -#if PY_MAJOR_VERSION == 2 -static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { - PyObject *exception, *value, *tb; - int res; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&exception, &value, &tb); - res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - if (!res) { - res = PyObject_IsSubclass(err, exc_type2); - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - } - __Pyx_ErrRestore(exception, value, tb); - return res; -} -#else -static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { - int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; - if (!res) { - res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); - } - return res; -} -#endif -static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - assert(PyExceptionClass_Check(exc_type)); - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; i '9'); - break; - } - if (rt_from_call[i] != ctversion[i]) { - same = 0; - break; - } - } - if (!same) { - char rtversion[5] = {'\0'}; - char message[200]; - for (i=0; i<4; ++i) { - if (rt_from_call[i] == '.') { - if (found_dot) break; - found_dot = 1; - } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') { - break; - } - rtversion[i] = rt_from_call[i]; - } - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* InitStrings */ - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - if (PyObject_Hash(*t->p) == -1) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT -#if !CYTHON_PEP393_ENABLED -static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); - return NULL; - } - } - } -#endif - *length = PyBytes_GET_SIZE(defenc); - return defenc_c; -} -#else -static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (likely(PyUnicode_IS_ASCII(o))) { - *length = PyUnicode_GET_LENGTH(o); - return PyUnicode_AsUTF8(o); - } else { - PyUnicode_AsASCIIString(o); - return NULL; - } -#else - return PyUnicode_AsUTF8AndSize(o, length); -#endif -} -#endif -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { - return __Pyx_PyUnicode_AsStringAndSize(o, length); - } else -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - if (PyByteArray_Check(o)) { - *length = PyByteArray_GET_SIZE(o); - return PyByteArray_AS_STRING(o); - } else -#endif - { - char* result; - int r = PyBytes_AsStringAndSize(o, &result, length); - if (unlikely(r < 0)) { - return NULL; - } else { - return result; - } - } -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - int is_true = x == Py_True; - if (is_true | (x == Py_False) | (x == Py_None)) return is_true; - else return PyObject_IsTrue(x); -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) { - int retval; - if (unlikely(!x)) return -1; - retval = __Pyx_PyObject_IsTrue(x); - Py_DECREF(x); - return retval; -} -static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { -#if PY_MAJOR_VERSION >= 3 - if (PyLong_Check(result)) { - if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, - "__int__ returned non-int (type %.200s). " - "The ability to return an instance of a strict subclass of int " - "is deprecated, and may be removed in a future version of Python.", - Py_TYPE(result)->tp_name)) { - Py_DECREF(result); - return NULL; - } - return result; - } -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - type_name, type_name, Py_TYPE(result)->tp_name); - Py_DECREF(result); - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS - PyNumberMethods *m; -#endif - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x) || PyLong_Check(x))) -#else - if (likely(PyLong_Check(x))) -#endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS - m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = m->nb_int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = m->nb_long(x); - } - #else - if (likely(m && m->nb_int)) { - name = "int"; - res = m->nb_int(x); - } - #endif -#else - if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) { - res = PyNumber_Int(x); - } -#endif - if (likely(res)) { -#if PY_MAJOR_VERSION < 3 - if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) { -#else - if (unlikely(!PyLong_CheckExact(res))) { -#endif - return __Pyx_PyNumber_IntOrLongWrongResultType(res, name); - } - } - else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_TypeError, - "an integer is required"); - } - return res; -} -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { - Py_ssize_t ival; - PyObject *x; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(b); - } -#endif - if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - 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} - break; - case -4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - } - } - #endif - return PyLong_AsSsize_t(b); - } - x = PyNumber_Index(b); - if (!x) return -1; - ival = PyInt_AsSsize_t(x); - Py_DECREF(x); - return ival; -} -static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) { - if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) { - return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o); -#if PY_MAJOR_VERSION < 3 - } else if (likely(PyInt_CheckExact(o))) { - return PyInt_AS_LONG(o); -#endif - } else { - Py_ssize_t ival; - PyObject *x; - x = PyNumber_Index(o); - if (!x) return -1; - ival = PyInt_AsLong(x); - Py_DECREF(x); - return ival; - } -} -static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) { - return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False); -} -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { - 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#else - typedef unsigned __int8 uint8_t; - typedef unsigned __int32 uint32_t; - #endif - #endif -#else - #include -#endif -#ifndef CYTHON_FALLTHROUGH - #if defined(__cplusplus) && __cplusplus >= 201103L - #if __has_cpp_attribute(fallthrough) - #define CYTHON_FALLTHROUGH [[fallthrough]] - #elif __has_cpp_attribute(clang::fallthrough) - #define CYTHON_FALLTHROUGH [[clang::fallthrough]] - #elif __has_cpp_attribute(gnu::fallthrough) - #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] - #endif - #endif - #ifndef CYTHON_FALLTHROUGH - #if __has_attribute(fallthrough) - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - #else - #define CYTHON_FALLTHROUGH - #endif - #endif - #if defined(__clang__ ) && defined(__apple_build_version__) - #if __apple_build_version__ < 7000000 - #undef CYTHON_FALLTHROUGH - #define CYTHON_FALLTHROUGH - #endif - #endif -#endif - -#ifndef CYTHON_INLINE - #if defined(__clang__) - #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) - #elif defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline - #else - #define CYTHON_INLINE - #endif -#endif - -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - if (type) { - PyErr_Restore(type, value, traceback); - } - return co; - } -#else - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - 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#define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1 - #define PyMem_RawMalloc(n) PyMem_Malloc(n) - #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) - #define PyMem_RawFree(p) PyMem_Free(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#elif PY_VERSION_HEX >= 0x03060000 - #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() -#elif PY_VERSION_HEX >= 0x03000000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#else - #define __Pyx_PyThreadState_Current _PyThreadState_Current -#endif -#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) -#include "pythread.h" -#define Py_tss_NEEDS_INIT 0 -typedef int Py_tss_t; -static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { - 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PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) - #endif - #endif -#else - #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 - #define __Pyx_PyUnicode_READY(op) (0) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) - #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) - #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) - #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) -#endif -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) -#else - #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ - PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) -#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) -#if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) -#else - #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) -#endif -#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII) - #define PyObject_ASCII(o) PyObject_Repr(o) -#endif -#if PY_MAJOR_VERSION >= 3 - #define PyBaseString_Type PyUnicode_Type - #define PyStringObject PyUnicodeObject - #define PyString_Type PyUnicode_Type - #define PyString_Check PyUnicode_Check - #define PyString_CheckExact PyUnicode_CheckExact -#ifndef PyObject_Unicode - #define PyObject_Unicode PyObject_Str -#endif -#endif -#if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) - #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) -#else - #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) - #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) -#endif -#ifndef PySet_CheckExact - #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) -#endif -#if PY_VERSION_HEX >= 0x030900A4 - #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt) - #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size) -#else - #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt) - #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size) -#endif -#if CYTHON_ASSUME_SAFE_MACROS - #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) -#else - #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq) -#endif -#if PY_MAJOR_VERSION >= 3 - #define PyIntObject PyLongObject - #define PyInt_Type PyLong_Type - #define PyInt_Check(op) PyLong_Check(op) - #define PyInt_CheckExact(op) PyLong_CheckExact(op) - #define PyInt_FromString PyLong_FromString - #define PyInt_FromUnicode PyLong_FromUnicode - #define PyInt_FromLong PyLong_FromLong - #define PyInt_FromSize_t PyLong_FromSize_t - #define PyInt_FromSsize_t PyLong_FromSsize_t - #define PyInt_AsLong PyLong_AsLong - #define PyInt_AS_LONG PyLong_AS_LONG - #define PyInt_AsSsize_t PyLong_AsSsize_t - #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask - #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask - #define PyNumber_Int PyNumber_Long -#endif -#if PY_MAJOR_VERSION >= 3 - #define PyBoolObject PyLongObject -#endif -#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY - #ifndef PyUnicode_InternFromString - #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) - #endif -#endif -#if PY_VERSION_HEX < 0x030200A4 - typedef long Py_hash_t; - #define __Pyx_PyInt_FromHash_t PyInt_FromLong - #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsHash_t -#else - #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t - #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsSsize_t -#endif -#if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyMethod_New(func, self, klass) ((self) ? ((void)(klass), PyMethod_New(func, self)) : __Pyx_NewRef(func)) -#else - #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) -#endif -#if CYTHON_USE_ASYNC_SLOTS - #if PY_VERSION_HEX >= 0x030500B1 - #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods - #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) - #else - #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) - #endif -#else - #define __Pyx_PyType_AsAsync(obj) NULL -#endif -#ifndef __Pyx_PyAsyncMethodsStruct - typedef struct { - unaryfunc am_await; - unaryfunc am_aiter; - unaryfunc am_anext; - } __Pyx_PyAsyncMethodsStruct; -#endif - -#if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS) - #if !defined(_USE_MATH_DEFINES) - #define _USE_MATH_DEFINES - #endif -#endif -#include -#ifdef NAN -#define __PYX_NAN() ((float) NAN) -#else -static CYTHON_INLINE float __PYX_NAN() { - float value; - memset(&value, 0xFF, sizeof(value)); - return value; -} -#endif -#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL) -#define __Pyx_truncl trunc -#else -#define __Pyx_truncl truncl -#endif - -#define __PYX_MARK_ERR_POS(f_index, lineno) \ - { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; } -#define __PYX_ERR(f_index, lineno, Ln_error) \ - { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; } - -#ifndef __PYX_EXTERN_C - #ifdef __cplusplus - #define __PYX_EXTERN_C extern "C" - #else - #define __PYX_EXTERN_C extern - #endif -#endif - -#define __PYX_HAVE__MDAnalysis__analysis__encore__cutils -#define __PYX_HAVE_API__MDAnalysis__analysis__encore__cutils -/* Early includes */ -#include -#include -#include "numpy/arrayobject.h" -#include "numpy/ndarrayobject.h" -#include "numpy/ndarraytypes.h" -#include "numpy/arrayscalars.h" -#include "numpy/ufuncobject.h" - - /* NumPy API declarations from "numpy/__init__.pxd" */ - -#include -#ifdef _OPENMP -#include -#endif /* _OPENMP */ - -#if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS) -#define CYTHON_WITHOUT_ASSERTIONS -#endif - -typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding; - const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; - -#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 -#define __PYX_DEFAULT_STRING_ENCODING_IS_UTF8 0 -#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT (PY_MAJOR_VERSION >= 3 && __PYX_DEFAULT_STRING_ENCODING_IS_UTF8) -#define __PYX_DEFAULT_STRING_ENCODING "" -#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString -#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize -#define __Pyx_uchar_cast(c) ((unsigned char)c) -#define __Pyx_long_cast(x) ((long)x) -#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ - (sizeof(type) < sizeof(Py_ssize_t)) ||\ - (sizeof(type) > sizeof(Py_ssize_t) &&\ - likely(v < (type)PY_SSIZE_T_MAX ||\ - v == (type)PY_SSIZE_T_MAX) &&\ - (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ - v == (type)PY_SSIZE_T_MIN))) ||\ - (sizeof(type) == sizeof(Py_ssize_t) &&\ - (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ - v == (type)PY_SSIZE_T_MAX))) ) -static CYTHON_INLINE int __Pyx_is_valid_index(Py_ssize_t i, Py_ssize_t limit) { - return (size_t) i < (size_t) limit; -} -#if defined (__cplusplus) && __cplusplus >= 201103L - #include - #define __Pyx_sst_abs(value) std::abs(value) -#elif SIZEOF_INT >= SIZEOF_SIZE_T - #define __Pyx_sst_abs(value) abs(value) -#elif SIZEOF_LONG >= SIZEOF_SIZE_T - #define __Pyx_sst_abs(value) labs(value) -#elif defined (_MSC_VER) - #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value)) -#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define __Pyx_sst_abs(value) llabs(value) -#elif defined (__GNUC__) - #define __Pyx_sst_abs(value) __builtin_llabs(value) -#else - #define __Pyx_sst_abs(value) ((value<0) ? -value : value) -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); -#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) -#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) -#define __Pyx_PyBytes_FromString PyBytes_FromString -#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); -#if PY_MAJOR_VERSION < 3 - #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString - #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize -#else - #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString - #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize -#endif -#define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) -#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) -#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) -#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) -#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) -static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { - const Py_UNICODE *u_end = u; - while (*u_end++) ; - return (size_t)(u_end - u - 1); -} -#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) -#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode -#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode -#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) -#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*); -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); -#define __Pyx_PySequence_Tuple(obj)\ - (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj)) -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); -static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*); -#if CYTHON_ASSUME_SAFE_MACROS -#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) -#else -#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) -#endif -#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) -#else -#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) -#endif -#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII -static int __Pyx_sys_getdefaultencoding_not_ascii; -static int __Pyx_init_sys_getdefaultencoding_params(void) { - PyObject* sys; - PyObject* default_encoding = NULL; - PyObject* ascii_chars_u = NULL; - PyObject* ascii_chars_b = NULL; - const char* default_encoding_c; - sys = PyImport_ImportModule("sys"); - if (!sys) goto bad; - default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); - Py_DECREF(sys); - if (!default_encoding) goto bad; - default_encoding_c = PyBytes_AsString(default_encoding); - if (!default_encoding_c) goto bad; - if (strcmp(default_encoding_c, "ascii") == 0) { - __Pyx_sys_getdefaultencoding_not_ascii = 0; - } else { - char ascii_chars[128]; - int c; - for (c = 0; c < 128; c++) { - ascii_chars[c] = c; - } - __Pyx_sys_getdefaultencoding_not_ascii = 1; - ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); - if (!ascii_chars_u) goto bad; - ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); - if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { - PyErr_Format( - PyExc_ValueError, - "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", - default_encoding_c); - goto bad; - } - Py_DECREF(ascii_chars_u); - Py_DECREF(ascii_chars_b); - } - Py_DECREF(default_encoding); - return 0; -bad: - Py_XDECREF(default_encoding); - Py_XDECREF(ascii_chars_u); 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"'complex long double'" : "'long double'"); - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - case 's': case 'p': return "a string"; - case 0: return "end"; - default: return "unparseable format string"; - } -} -static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return 2; - case 'i': case 'I': case 'l': case 'L': return 4; - case 'q': case 'Q': return 8; - case 'f': return (is_complex ? 8 : 4); - case 'd': return (is_complex ? 16 : 8); - case 'g': { - PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); - return 0; - } - case 'O': case 'P': return sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(short); - case 'i': case 'I': return sizeof(int); - case 'l': case 'L': return sizeof(long); - #ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(PY_LONG_LONG); - #endif - case 'f': return sizeof(float) * (is_complex ? 2 : 1); - case 'd': return sizeof(double) * (is_complex ? 2 : 1); - case 'g': return sizeof(long double) * (is_complex ? 2 : 1); - case 'O': case 'P': return sizeof(void*); - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -typedef struct { char c; short x; } __Pyx_st_short; -typedef struct { char c; int x; } __Pyx_st_int; -typedef struct { char c; long x; } __Pyx_st_long; -typedef struct { char c; float x; } __Pyx_st_float; -typedef struct { char c; double x; } __Pyx_st_double; -typedef struct { char c; long double x; } __Pyx_st_longdouble; -typedef struct { char c; void *x; } __Pyx_st_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_st_float) - sizeof(float); - case 'd': return sizeof(__Pyx_st_double) - sizeof(double); - case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -/* These are for computing the padding at the end of the struct to align - on the first member of the struct. This will probably the same as above, - but we don't have any guarantees. - */ -typedef struct { short x; char c; } __Pyx_pad_short; -typedef struct { int x; char c; } __Pyx_pad_int; -typedef struct { long x; char c; } __Pyx_pad_long; -typedef struct { float x; char c; } __Pyx_pad_float; -typedef struct { double x; char c; } __Pyx_pad_double; -typedef struct { long double x; char c; } __Pyx_pad_longdouble; -typedef struct { void *x; char c; } __Pyx_pad_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); - case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); - case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { - switch (ch) { - case 'c': - return 'H'; - case 'b': case 'h': case 'i': - case 'l': case 'q': case 's': case 'p': - return 'I'; - case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': - return 'U'; - case 'f': case 'd': case 'g': - return (is_complex ? 'C' : 'R'); - case 'O': - return 'O'; - case 'P': - return 'P'; - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { - if (ctx->head == NULL || ctx->head->field == &ctx->root) { - const char* expected; - const char* quote; - if (ctx->head == NULL) { - expected = "end"; - quote = ""; - } else { - expected = ctx->head->field->type->name; - quote = "'"; - } - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected %s%s%s but got %s", - quote, expected, quote, - __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); - } else { - __Pyx_StructField* field = ctx->head->field; - __Pyx_StructField* parent = (ctx->head - 1)->field; - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", - field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), - parent->type->name, field->name); - } -} -static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { - char group; - size_t size, offset, arraysize = 1; - if (ctx->enc_type == 0) return 0; - if (ctx->head->field->type->arraysize[0]) { - int i, ndim = 0; - if (ctx->enc_type == 's' || ctx->enc_type == 'p') { - ctx->is_valid_array = ctx->head->field->type->ndim == 1; - ndim = 1; - if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { - PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %zu", - ctx->head->field->type->arraysize[0], ctx->enc_count); - return -1; - } - } - if (!ctx->is_valid_array) { - PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", - ctx->head->field->type->ndim, ndim); - return -1; - } - for (i = 0; i < ctx->head->field->type->ndim; i++) { - arraysize *= ctx->head->field->type->arraysize[i]; - } - ctx->is_valid_array = 0; - ctx->enc_count = 1; - } - group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); - do { - __Pyx_StructField* field = ctx->head->field; - __Pyx_TypeInfo* type = field->type; - if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { - size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); - } else { - size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); - } - if (ctx->enc_packmode == '@') { - size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); - size_t align_mod_offset; - if (align_at == 0) return -1; - align_mod_offset = ctx->fmt_offset % align_at; - if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; - if (ctx->struct_alignment == 0) - ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, - ctx->is_complex); - } - if (type->size != size || type->typegroup != group) { - if (type->typegroup == 'C' && type->fields != NULL) { - size_t parent_offset = ctx->head->parent_offset + field->offset; - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = parent_offset; - continue; - } - if ((type->typegroup == 'H' || group == 'H') && type->size == size) { - } else { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - } - offset = ctx->head->parent_offset + field->offset; - if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; - } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } - } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; -} -static PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number, ndim; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ndim = ctx->head->field->type->ndim; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; - } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; - } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; - } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; -} -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; - } - break; - case '}': - { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } - } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; - } - CYTHON_FALLTHROUGH; - case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && - (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - CYTHON_FALLTHROUGH; - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: - { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; - } - } - } -} - -/* BufferGetAndValidate */ - static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { - if (unlikely(info->buf == NULL)) return; - if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; - __Pyx_ReleaseBuffer(info); -} -static void __Pyx_ZeroBuffer(Py_buffer* buf) { - buf->buf = NULL; - buf->obj = NULL; - buf->strides = __Pyx_zeros; - buf->shape = __Pyx_zeros; - buf->suboffsets = __Pyx_minusones; -} -static int __Pyx__GetBufferAndValidate( - Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, - int nd, int cast, __Pyx_BufFmt_StackElem* stack) -{ - buf->buf = NULL; - if (unlikely(__Pyx_GetBuffer(obj, buf, flags) == -1)) { - __Pyx_ZeroBuffer(buf); - return -1; - } - if (unlikely(buf->ndim != nd)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - nd, buf->ndim); - goto fail; - } - if (!cast) { - __Pyx_BufFmt_Context ctx; - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; - } - if (unlikely((size_t)buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", - buf->itemsize, (buf->itemsize > 1) ? "s" : "", - dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; - return 0; -fail:; - __Pyx_SafeReleaseBuffer(buf); - return -1; -} - -/* PyErrFetchRestore */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -} -#endif - -/* GetTopmostException */ - #if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* PyErrExceptionMatches */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* GetException */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* PyObjectCall */ - #if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { - PyObject *result; - ternaryfunc call = Py_TYPE(func)->tp_call; - if (unlikely(!call)) - return PyObject_Call(func, arg, kw); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = (*call)(func, arg, kw); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* RaiseException */ - #if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* Import */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* PyDictVersioning */ - #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; -} -static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) { - PyObject **dictptr = NULL; - Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset; - if (offset) { -#if CYTHON_COMPILING_IN_CPYTHON - dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj); -#else - dictptr = _PyObject_GetDictPtr(obj); -#endif - } - return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; -} -static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) - return 0; - return obj_dict_version == __Pyx_get_object_dict_version(obj); -} -#endif - -/* CLineInTraceback */ - #ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ - #include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - if ((0)) {} - view->obj = NULL; - Py_DECREF(obj); -} -#endif - - - /* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); 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"C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include\\numpy\\ufuncobject.h", - "C:\\Users\\USER\\Desktop\\MDA_analysis\\mdanalysis\\package\\MDAnalysis\\analysis\\encore\\dimensionality_reduction\\include\\spe.h" - ], - "extra_compile_args": [ - "-std=c99", - "-ffast-math", - "-funroll-loops", - "-fsigned-zeros", - "-O3" - ], - "include_dirs": [ - "C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include", - "C:\\Users\\USER\\Desktop\\MDA_analysis\\mdanalysis\\package\\MDAnalysis/analysis/encore/dimensionality_reduction/include" - ], - "name": "MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed", - "sources": [ - "MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx", - "MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c" - ] - }, - "module_name": "MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed" -} -END: Cython Metadata */ - 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template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } -# else -# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) -# endif -#endif -#ifndef CYTHON_NCP_UNUSED -# if CYTHON_COMPILING_IN_CPYTHON -# define CYTHON_NCP_UNUSED -# else -# define CYTHON_NCP_UNUSED CYTHON_UNUSED -# endif -#endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) -#ifdef _MSC_VER - #ifndef _MSC_STDINT_H_ - #if _MSC_VER < 1300 - typedef unsigned char uint8_t; - typedef unsigned int uint32_t; - #else - typedef unsigned __int8 uint8_t; - typedef unsigned __int32 uint32_t; - #endif - #endif -#else - #include -#endif -#ifndef CYTHON_FALLTHROUGH - #if defined(__cplusplus) && __cplusplus >= 201103L - #if __has_cpp_attribute(fallthrough) - #define CYTHON_FALLTHROUGH [[fallthrough]] - #elif __has_cpp_attribute(clang::fallthrough) - #define CYTHON_FALLTHROUGH [[clang::fallthrough]] - #elif __has_cpp_attribute(gnu::fallthrough) - #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] - #endif - 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#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - 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- Py_INCREF(k[i+1]); - i += 2; - } - nk = i / 2; - } - else { - kwtuple = NULL; - k = NULL; - } - closure = PyFunction_GET_CLOSURE(func); -#if PY_MAJOR_VERSION >= 3 - kwdefs = PyFunction_GET_KW_DEFAULTS(func); -#endif - if (argdefs != NULL) { - d = &PyTuple_GET_ITEM(argdefs, 0); - nd = Py_SIZE(argdefs); - } - else { - d = NULL; - nd = 0; - } -#if PY_MAJOR_VERSION >= 3 - result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, kwdefs, closure); -#else - result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, closure); -#endif - Py_XDECREF(kwtuple); -done: - Py_LeaveRecursiveCall(); - return result; -} -#endif -#endif - -/* PyObjectCall */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { - PyObject *result; - ternaryfunc call = Py_TYPE(func)->tp_call; - if (unlikely(!call)) - return PyObject_Call(func, arg, kw); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = (*call)(func, arg, kw); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCall2Args */ -static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { - PyObject *args, *result = NULL; - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyFunction_FastCall(function, args, 2); - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyCFunction_FastCall(function, args, 2); - } - #endif - args = PyTuple_New(2); - if (unlikely(!args)) goto done; - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 0, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 1, arg2); - Py_INCREF(function); - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); -done: - return result; -} - -/* PyObjectCallMethO */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { - PyObject *self, *result; - PyCFunction cfunc; - cfunc = PyCFunction_GET_FUNCTION(func); - self = PyCFunction_GET_SELF(func); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = cfunc(self, arg); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallOneArg */ -#if CYTHON_COMPILING_IN_CPYTHON -static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_New(1); - if (unlikely(!args)) return NULL; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif - if (likely(PyCFunction_Check(func))) { - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (__Pyx_PyFastCFunction_Check(func)) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } - } - return __Pyx__PyObject_CallOneArg(func, arg); -} -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -#endif - -/* ExtTypeTest */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(__Pyx_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* IsLittleEndian */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) -{ - union { - uint32_t u32; - uint8_t u8[4]; - } S; - S.u32 = 0x01020304; - return S.u8[0] == 4; -} - -/* BufferFormatCheck */ -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type) { - stack[0].field = &ctx->root; - stack[0].parent_offset = 0; - ctx->root.type = type; - ctx->root.name = "buffer dtype"; - ctx->root.offset = 0; - ctx->head = stack; - ctx->head->field = &ctx->root; - ctx->fmt_offset = 0; - ctx->head->parent_offset = 0; - ctx->new_packmode = '@'; - ctx->enc_packmode = '@'; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->is_complex = 0; - ctx->is_valid_array = 0; - ctx->struct_alignment = 0; - while (type->typegroup == 'S') { - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = 0; - type = type->fields->type; - } -} -static int __Pyx_BufFmt_ParseNumber(const char** ts) { - int count; - const char* t = *ts; - if (*t < '0' || *t > '9') { - return -1; - } else { - count = *t++ - '0'; - while (*t >= '0' && *t <= '9') { - count *= 10; - count += *t++ - '0'; - } - } - *ts = t; - return count; -} -static int __Pyx_BufFmt_ExpectNumber(const char **ts) { - int number = __Pyx_BufFmt_ParseNumber(ts); - if (number == -1) - PyErr_Format(PyExc_ValueError,\ - "Does not understand character buffer dtype format string ('%c')", **ts); - return number; -} -static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { - PyErr_Format(PyExc_ValueError, - "Unexpected format string character: '%c'", ch); -} -static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { - switch (ch) { - case '?': return "'bool'"; - case 'c': return "'char'"; - case 'b': return "'signed char'"; - case 'B': return "'unsigned char'"; - case 'h': return "'short'"; - case 'H': return "'unsigned short'"; - case 'i': return "'int'"; - case 'I': return "'unsigned int'"; - case 'l': return "'long'"; - case 'L': return "'unsigned long'"; - case 'q': return "'long long'"; - case 'Q': return "'unsigned long long'"; - case 'f': return (is_complex ? "'complex float'" : "'float'"); - case 'd': return (is_complex ? "'complex double'" : "'double'"); - case 'g': return (is_complex ? "'complex long double'" : "'long double'"); - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - case 's': case 'p': return "a string"; - case 0: return "end"; - default: return "unparseable format string"; - } -} -static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return 2; - case 'i': case 'I': case 'l': case 'L': return 4; - case 'q': case 'Q': return 8; - case 'f': return (is_complex ? 8 : 4); - case 'd': return (is_complex ? 16 : 8); - case 'g': { - PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); - return 0; - } - case 'O': case 'P': return sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(short); - case 'i': case 'I': return sizeof(int); - case 'l': case 'L': return sizeof(long); - #ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(PY_LONG_LONG); - #endif - case 'f': return sizeof(float) * (is_complex ? 2 : 1); - case 'd': return sizeof(double) * (is_complex ? 2 : 1); - case 'g': return sizeof(long double) * (is_complex ? 2 : 1); - case 'O': case 'P': return sizeof(void*); - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -typedef struct { char c; short x; } __Pyx_st_short; -typedef struct { char c; int x; } __Pyx_st_int; -typedef struct { char c; long x; } __Pyx_st_long; -typedef struct { char c; float x; } __Pyx_st_float; -typedef struct { char c; double x; } __Pyx_st_double; -typedef struct { char c; long double x; } __Pyx_st_longdouble; -typedef struct { char c; void *x; } __Pyx_st_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_st_float) - sizeof(float); - case 'd': return sizeof(__Pyx_st_double) - sizeof(double); - case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -/* These are for computing the padding at the end of the struct to align - on the first member of the struct. This will probably the same as above, - but we don't have any guarantees. - */ -typedef struct { short x; char c; } __Pyx_pad_short; -typedef struct { int x; char c; } __Pyx_pad_int; -typedef struct { long x; char c; } __Pyx_pad_long; -typedef struct { float x; char c; } __Pyx_pad_float; -typedef struct { double x; char c; } __Pyx_pad_double; -typedef struct { long double x; char c; } __Pyx_pad_longdouble; -typedef struct { void *x; char c; } __Pyx_pad_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); - case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); - case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { - switch (ch) { - case 'c': - return 'H'; - case 'b': case 'h': case 'i': - case 'l': case 'q': case 's': case 'p': - return 'I'; - case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': - return 'U'; - case 'f': case 'd': case 'g': - return (is_complex ? 'C' : 'R'); - case 'O': - return 'O'; - case 'P': - return 'P'; - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { - if (ctx->head == NULL || ctx->head->field == &ctx->root) { - const char* expected; - const char* quote; - if (ctx->head == NULL) { - expected = "end"; - quote = ""; - } else { - expected = ctx->head->field->type->name; - quote = "'"; - } - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected %s%s%s but got %s", - quote, expected, quote, - __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); - } else { - __Pyx_StructField* field = ctx->head->field; - __Pyx_StructField* parent = (ctx->head - 1)->field; - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", - field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), - parent->type->name, field->name); - } -} -static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { - char group; - size_t size, offset, arraysize = 1; - if (ctx->enc_type == 0) return 0; - if (ctx->head->field->type->arraysize[0]) { - int i, ndim = 0; - if (ctx->enc_type == 's' || ctx->enc_type == 'p') { - ctx->is_valid_array = ctx->head->field->type->ndim == 1; - ndim = 1; - if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { - PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %zu", - ctx->head->field->type->arraysize[0], ctx->enc_count); - return -1; - } - } - if (!ctx->is_valid_array) { - PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", - ctx->head->field->type->ndim, ndim); - return -1; - } - for (i = 0; i < ctx->head->field->type->ndim; i++) { - arraysize *= ctx->head->field->type->arraysize[i]; - } - ctx->is_valid_array = 0; - ctx->enc_count = 1; - } - group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); - do { - __Pyx_StructField* field = ctx->head->field; - __Pyx_TypeInfo* type = field->type; - if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { - size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); - } else { - size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); - } - if (ctx->enc_packmode == '@') { - size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); - size_t align_mod_offset; - if (align_at == 0) return -1; - align_mod_offset = ctx->fmt_offset % align_at; - if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; - if (ctx->struct_alignment == 0) - ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, - ctx->is_complex); - } - if (type->size != size || type->typegroup != group) { - if (type->typegroup == 'C' && type->fields != NULL) { - size_t parent_offset = ctx->head->parent_offset + field->offset; - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = parent_offset; - continue; - } - if ((type->typegroup == 'H' || group == 'H') && type->size == size) { - } else { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - } - offset = ctx->head->parent_offset + field->offset; - if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; - } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } - } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; -} -static PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number, ndim; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ndim = ctx->head->field->type->ndim; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; - } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; - } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; - } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; -} -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; - } - break; - case '}': - { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } - } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; - } - CYTHON_FALLTHROUGH; - case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && - (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - CYTHON_FALLTHROUGH; - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: - { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; - } - } - } -} - -/* BufferGetAndValidate */ - static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { - if (unlikely(info->buf == NULL)) return; - if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; - __Pyx_ReleaseBuffer(info); -} -static void __Pyx_ZeroBuffer(Py_buffer* buf) { - buf->buf = NULL; - buf->obj = NULL; - buf->strides = __Pyx_zeros; - buf->shape = __Pyx_zeros; - buf->suboffsets = __Pyx_minusones; -} -static int __Pyx__GetBufferAndValidate( - Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, - int nd, int cast, __Pyx_BufFmt_StackElem* stack) -{ - buf->buf = NULL; - if (unlikely(__Pyx_GetBuffer(obj, buf, flags) == -1)) { - __Pyx_ZeroBuffer(buf); - return -1; - } - if (unlikely(buf->ndim != nd)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - nd, buf->ndim); - goto fail; - } - if (!cast) { - __Pyx_BufFmt_Context ctx; - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; - } - if (unlikely((size_t)buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", - buf->itemsize, (buf->itemsize > 1) ? "s" : "", - dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; - return 0; -fail:; - __Pyx_SafeReleaseBuffer(buf); - return -1; -} - -/* PyErrFetchRestore */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -} -#endif - -/* GetTopmostException */ - #if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* PyErrExceptionMatches */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* GetException */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* RaiseException */ - #if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* Import */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* CLineInTraceback */ - #ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ - #include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - if ((0)) {} - view->obj = NULL; - Py_DECREF(obj); -} -#endif - - - /* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* FastTypeChecks */ - #if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; - if (a == b) - return 1; - } - return b == &PyBaseObject_Type; -} -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { - PyObject *mro; - if (a == b) return 1; - mro = a->tp_mro; - if (likely(mro)) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(mro); - for (i = 0; i < n; i++) { - if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) - return 1; - } - return 0; - } - return __Pyx_InBases(a, b); -} -#if PY_MAJOR_VERSION == 2 -static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { - PyObject *exception, *value, *tb; - int res; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&exception, &value, &tb); - res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - if (!res) { - res = PyObject_IsSubclass(err, exc_type2); - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - } - __Pyx_ErrRestore(exception, value, tb); - return res; -} -#else -static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { - int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; - if (!res) { - res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); - } - return res; -} -#endif -static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - assert(PyExceptionClass_Check(exc_type)); - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; i '9'); - break; - } - if (rt_from_call[i] != ctversion[i]) { - same = 0; - break; - } - } - if (!same) { - char rtversion[5] = {'\0'}; 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#define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #elif !defined(CYTHON_FAST_THREAD_STATE) - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000) - #endif - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000) - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) - #endif - #ifndef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1) - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #elif !defined(CYTHON_USE_EXC_INFO_STACK) - #define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3) - #endif - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 - #endif -#endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #if PY_MAJOR_VERSION < 3 - #include "longintrepr.h" - #endif - #undef SHIFT - #undef BASE - #undef MASK - #ifdef SIZEOF_VOID_P - enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) }; - #endif -#endif -#ifndef __has_attribute - #define __has_attribute(x) 0 -#endif -#ifndef __has_cpp_attribute - #define __has_cpp_attribute(x) 0 -#endif -#ifndef CYTHON_RESTRICT - #if defined(__GNUC__) - #define CYTHON_RESTRICT __restrict__ - #elif defined(_MSC_VER) && _MSC_VER >= 1400 - #define CYTHON_RESTRICT __restrict - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_RESTRICT restrict - #else - #define CYTHON_RESTRICT - #endif -#endif -#ifndef CYTHON_UNUSED -# if defined(__GNUC__) -# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -#endif -#ifndef CYTHON_MAYBE_UNUSED_VAR -# if defined(__cplusplus) - template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } -# else -# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) -# endif -#endif -#ifndef CYTHON_NCP_UNUSED -# if CYTHON_COMPILING_IN_CPYTHON -# define CYTHON_NCP_UNUSED -# else -# define CYTHON_NCP_UNUSED CYTHON_UNUSED -# endif -#endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) -#ifdef _MSC_VER - #ifndef _MSC_STDINT_H_ - #if _MSC_VER < 1300 - typedef unsigned char uint8_t; - typedef unsigned int uint32_t; - #else - typedef unsigned __int8 uint8_t; - typedef unsigned __int32 uint32_t; - #endif - #endif -#else - #include -#endif -#ifndef CYTHON_FALLTHROUGH - #if defined(__cplusplus) && __cplusplus >= 201103L - #if __has_cpp_attribute(fallthrough) - #define CYTHON_FALLTHROUGH [[fallthrough]] - #elif __has_cpp_attribute(clang::fallthrough) - #define CYTHON_FALLTHROUGH [[clang::fallthrough]] - #elif __has_cpp_attribute(gnu::fallthrough) - #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] - #endif - #endif - #ifndef CYTHON_FALLTHROUGH - #if __has_attribute(fallthrough) - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - #else - #define CYTHON_FALLTHROUGH - #endif - #endif - #if defined(__clang__ ) && defined(__apple_build_version__) - #if __apple_build_version__ < 7000000 - #undef CYTHON_FALLTHROUGH - #define CYTHON_FALLTHROUGH - #endif - #endif -#endif - -#ifndef __cplusplus - #error "Cython files generated with the C++ option must be compiled with a C++ compiler." -#endif -#ifndef CYTHON_INLINE - #if defined(__clang__) - #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) - #else - #define CYTHON_INLINE inline - #endif -#endif -template -void __Pyx_call_destructor(T& x) { - x.~T(); -} -template -class __Pyx_FakeReference { - public: - __Pyx_FakeReference() : ptr(NULL) { } - __Pyx_FakeReference(const T& ref) : ptr(const_cast(&ref)) { } - T *operator->() { return ptr; } - T *operator&() { return ptr; } - operator T&() { return *ptr; } - template bool operator ==(U other) { return *ptr == other; } - template bool operator !=(U other) { return *ptr != other; } - private: - T *ptr; -}; - -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - if (type) { - PyErr_Restore(type, value, traceback); - } - return co; - } -#else - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_STACKLESS - #define METH_STACKLESS 0 -#endif -#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) - #ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - #endif - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); - typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast - #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1 - #define PyMem_RawMalloc(n) PyMem_Malloc(n) - #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) - #define PyMem_RawFree(p) PyMem_Free(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#elif PY_VERSION_HEX >= 0x03060000 - #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() -#elif PY_VERSION_HEX >= 0x03000000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#else - #define __Pyx_PyThreadState_Current _PyThreadState_Current -#endif -#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) -#include "pythread.h" -#define Py_tss_NEEDS_INIT 0 -typedef int Py_tss_t; -static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { - *key = PyThread_create_key(); - return 0; -} -static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { - Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); - *key = Py_tss_NEEDS_INIT; - return key; -} -static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { - PyObject_Free(key); -} -static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { - return *key != Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { - PyThread_delete_key(*key); - *key = Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { - return PyThread_set_key_value(*key, value); -} -static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { - return PyThread_get_key_value(*key); -} -#endif -#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) -#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) -#else -#define __Pyx_PyDict_NewPresized(n) PyDict_New() -#endif -#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION - #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) -#else - #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS -#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) -#else -#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_READY(op) (0) - #else - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #endif - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) - #else - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) - #endif - #endif -#else - #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 - #define __Pyx_PyUnicode_READY(op) (0) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) - #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) - #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) - #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) -#endif -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) -#else - #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ - PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? 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PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) -#if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) -#else - #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) -#endif -#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII) - #define PyObject_ASCII(o) PyObject_Repr(o) -#endif -#if PY_MAJOR_VERSION >= 3 - #define PyBaseString_Type PyUnicode_Type - #define PyStringObject PyUnicodeObject - #define PyString_Type PyUnicode_Type - #define PyString_Check PyUnicode_Check - #define PyString_CheckExact PyUnicode_CheckExact -#ifndef PyObject_Unicode - #define PyObject_Unicode PyObject_Str -#endif -#endif -#if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) - #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) -#else - #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) - #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) -#endif -#ifndef PySet_CheckExact - #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) -#endif -#if PY_VERSION_HEX >= 0x030900A4 - #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt) - #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size) -#else - #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt) - #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size) -#endif -#if CYTHON_ASSUME_SAFE_MACROS - #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) -#else - #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq) -#endif -#if PY_MAJOR_VERSION >= 3 - #define PyIntObject PyLongObject - #define PyInt_Type PyLong_Type - #define PyInt_Check(op) PyLong_Check(op) - #define PyInt_CheckExact(op) PyLong_CheckExact(op) - #define PyInt_FromString PyLong_FromString - #define PyInt_FromUnicode PyLong_FromUnicode - #define PyInt_FromLong PyLong_FromLong - #define PyInt_FromSize_t PyLong_FromSize_t - #define PyInt_FromSsize_t PyLong_FromSsize_t - #define PyInt_AsLong PyLong_AsLong - #define PyInt_AS_LONG PyLong_AS_LONG - #define PyInt_AsSsize_t PyLong_AsSsize_t - #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask - #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask - #define PyNumber_Int PyNumber_Long -#endif -#if PY_MAJOR_VERSION >= 3 - #define PyBoolObject PyLongObject -#endif -#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY - #ifndef PyUnicode_InternFromString - #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) - #endif -#endif -#if PY_VERSION_HEX < 0x030200A4 - typedef long Py_hash_t; - #define __Pyx_PyInt_FromHash_t PyInt_FromLong - #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsHash_t -#else - #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t - #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsSsize_t -#endif -#if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyMethod_New(func, self, klass) ((self) ? 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- default_encoding_c = PyBytes_AsString(default_encoding); - if (!default_encoding_c) goto bad; - if (strcmp(default_encoding_c, "ascii") == 0) { - __Pyx_sys_getdefaultencoding_not_ascii = 0; - } else { - char ascii_chars[128]; - int c; - for (c = 0; c < 128; c++) { - ascii_chars[c] = c; - } - __Pyx_sys_getdefaultencoding_not_ascii = 1; - ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); - if (!ascii_chars_u) goto bad; - ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); - if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { - PyErr_Format( - PyExc_ValueError, - "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", - default_encoding_c); - goto bad; - } - Py_DECREF(ascii_chars_u); - Py_DECREF(ascii_chars_b); - } - Py_DECREF(default_encoding); - return 0; -bad: - Py_XDECREF(default_encoding); - Py_XDECREF(ascii_chars_u); 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-#else -#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) -#endif - -/* RaiseException.proto */ -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); - -/* SliceObject.proto */ -#define __Pyx_PyObject_DelSlice(obj, cstart, cstop, py_start, py_stop, py_slice, has_cstart, has_cstop, wraparound)\ - __Pyx_PyObject_SetSlice(obj, (PyObject*)NULL, cstart, cstop, py_start, py_stop, py_slice, has_cstart, has_cstop, wraparound) -static CYTHON_INLINE int __Pyx_PyObject_SetSlice( - PyObject* obj, PyObject* value, Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** py_start, PyObject** py_stop, PyObject** py_slice, - int has_cstart, int has_cstop, int wraparound); - -/* GetItemInt.proto */ -#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ - __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, - int is_list, int wraparound, int boundscheck); - -/* ObjectGetItem.proto */ -#if CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key); -#else -#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key) -#endif - -/* PyIntCompare.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, long inplace); - -/* SliceObject.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice( - PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** py_start, PyObject** py_stop, PyObject** py_slice, - int has_cstart, int has_cstop, int wraparound); - -/* ArgTypeTest.proto */ -#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\ - ((likely((Py_TYPE(obj) == type) | (none_allowed && (obj == Py_None)))) ? 1 :\ - __Pyx__ArgTypeTest(obj, type, name, exact)) -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact); - -/* IterFinish.proto */ -static CYTHON_INLINE int __Pyx_IterFinish(void); - -/* PyObjectGetMethod.proto */ -static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method); - -/* PyObjectCallMethod0.proto */ -static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name); - -/* RaiseNeedMoreValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); - -/* RaiseTooManyValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); - -/* UnpackItemEndCheck.proto */ -static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); - -/* RaiseNoneIterError.proto */ -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); - -/* UnpackTupleError.proto */ -static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); - -/* UnpackTuple2.proto */ -#define __Pyx_unpack_tuple2(tuple, value1, value2, is_tuple, has_known_size, decref_tuple)\ - (likely(is_tuple || PyTuple_Check(tuple)) ?\ - (likely(has_known_size || PyTuple_GET_SIZE(tuple) == 2) ?\ - __Pyx_unpack_tuple2_exact(tuple, value1, value2, decref_tuple) :\ - (__Pyx_UnpackTupleError(tuple, 2), -1)) :\ - __Pyx_unpack_tuple2_generic(tuple, value1, value2, has_known_size, decref_tuple)) -static CYTHON_INLINE int __Pyx_unpack_tuple2_exact( - PyObject* tuple, PyObject** value1, PyObject** value2, int decref_tuple); -static int __Pyx_unpack_tuple2_generic( - PyObject* tuple, PyObject** value1, PyObject** value2, int has_known_size, int decref_tuple); - -/* dict_iter.proto */ -static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name, - Py_ssize_t* p_orig_length, int* p_is_dict); -static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos, - PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict); - -/* MergeKeywords.proto */ -static int __Pyx_MergeKeywords(PyObject *kwdict, PyObject *source_mapping); - -/* FastTypeChecks.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2); -#else -#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) -#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type) -#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2)) -#endif -#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) - -/* None.proto */ -static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname); - -/* ListCompAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len)) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) -#endif - -/* IncludeStringH.proto */ -#include - -/* BytesEquals.proto */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); - -/* UnicodeEquals.proto */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); - -/* GetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* PyObject_GenericGetAttrNoDict.proto */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); -#else -#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr -#endif - -/* PyObject_GenericGetAttr.proto */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name); -#else -#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr -#endif - -/* PyObjectGetAttrStrNoError.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name); - -/* SetupReduce.proto */ -static int __Pyx_setup_reduce(PyObject* type_obj); - -/* TypeImport.proto */ -#ifndef __PYX_HAVE_RT_ImportType_proto -#define __PYX_HAVE_RT_ImportType_proto -enum __Pyx_ImportType_CheckSize { - __Pyx_ImportType_CheckSize_Error = 0, - __Pyx_ImportType_CheckSize_Warn = 1, - __Pyx_ImportType_CheckSize_Ignore = 2 -}; -static PyTypeObject *__Pyx_ImportType(PyObject* module, const char *module_name, const char *class_name, size_t size, enum __Pyx_ImportType_CheckSize check_size); -#endif - -/* Import.proto */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); - -/* ImportFrom.proto */ -static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); - -/* ClassMethod.proto */ -#include "descrobject.h" -static CYTHON_UNUSED PyObject* __Pyx_Method_ClassMethod(PyObject *method); - -/* GetNameInClass.proto */ -#define __Pyx_GetNameInClass(var, nmspace, name) (var) = __Pyx__GetNameInClass(nmspace, name) -static PyObject *__Pyx__GetNameInClass(PyObject *nmspace, PyObject *name); - -/* CLineInTraceback.proto */ -#ifdef CYTHON_CLINE_IN_TRACEBACK -#define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) -#else -static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line); -#endif - -/* CodeObjectCache.proto */ -typedef struct { - PyCodeObject* code_object; - int code_line; -} __Pyx_CodeObjectCacheEntry; -struct __Pyx_CodeObjectCache { - int count; - int max_count; - __Pyx_CodeObjectCacheEntry* entries; -}; -static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); -static PyCodeObject *__pyx_find_code_object(int code_line); -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); - -/* AddTraceback.proto */ -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename); - -/* GCCDiagnostics.proto */ -#if defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6)) -#define __Pyx_HAS_GCC_DIAGNOSTIC -#endif - -/* RealImag.proto */ -#if CYTHON_CCOMPLEX - #ifdef __cplusplus - #define __Pyx_CREAL(z) ((z).real()) - #define __Pyx_CIMAG(z) ((z).imag()) - #else - #define __Pyx_CREAL(z) (__real__(z)) - #define __Pyx_CIMAG(z) (__imag__(z)) - #endif -#else - #define __Pyx_CREAL(z) ((z).real) - #define __Pyx_CIMAG(z) ((z).imag) -#endif -#if defined(__cplusplus) && CYTHON_CCOMPLEX\ - && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103) - #define __Pyx_SET_CREAL(z,x) ((z).real(x)) - #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) -#else - #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) - #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) -#endif - -/* Arithmetic.proto */ -#if CYTHON_CCOMPLEX - #define __Pyx_c_eq_float(a, b) ((a)==(b)) - #define __Pyx_c_sum_float(a, b) ((a)+(b)) - #define __Pyx_c_diff_float(a, b) ((a)-(b)) - #define __Pyx_c_prod_float(a, b) ((a)*(b)) - #define __Pyx_c_quot_float(a, b) ((a)/(b)) - #define __Pyx_c_neg_float(a) (-(a)) - #ifdef __cplusplus - #define __Pyx_c_is_zero_float(z) ((z)==(float)0) - #define __Pyx_c_conj_float(z) (::std::conj(z)) - #if 1 - #define __Pyx_c_abs_float(z) (::std::abs(z)) - #define __Pyx_c_pow_float(a, b) (::std::pow(a, b)) - #endif - #else - #define __Pyx_c_is_zero_float(z) ((z)==0) - #define __Pyx_c_conj_float(z) (conjf(z)) - #if 1 - #define __Pyx_c_abs_float(z) (cabsf(z)) - #define __Pyx_c_pow_float(a, b) (cpowf(a, b)) - #endif - #endif -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex); - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex); - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex); - #endif -#endif - -/* Arithmetic.proto */ -#if CYTHON_CCOMPLEX - #define __Pyx_c_eq_double(a, b) ((a)==(b)) - #define __Pyx_c_sum_double(a, b) ((a)+(b)) - #define __Pyx_c_diff_double(a, b) ((a)-(b)) - #define __Pyx_c_prod_double(a, b) ((a)*(b)) - #define __Pyx_c_quot_double(a, b) ((a)/(b)) - #define __Pyx_c_neg_double(a) (-(a)) - #ifdef __cplusplus - #define __Pyx_c_is_zero_double(z) ((z)==(double)0) - #define __Pyx_c_conj_double(z) (::std::conj(z)) - #if 1 - #define __Pyx_c_abs_double(z) (::std::abs(z)) - #define __Pyx_c_pow_double(a, b) (::std::pow(a, b)) - #endif - #else - #define __Pyx_c_is_zero_double(z) ((z)==0) - #define __Pyx_c_conj_double(z) (conj(z)) - #if 1 - #define __Pyx_c_abs_double(z) (cabs(z)) - #define __Pyx_c_pow_double(a, b) (cpow(a, b)) - #endif - #endif -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex); - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex); - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex); - #endif -#endif - -/* CIntFromPy.proto */ -static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value); - -/* CIntFromPy.proto */ -static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); - -/* CIntFromPy.proto */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); - -/* CIntFromPy.proto */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); - -/* FetchCommonType.proto */ -static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); - -/* SwapException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* PyObjectCallMethod1.proto */ -static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg); - -/* CoroutineBase.proto */ -typedef PyObject *(*__pyx_coroutine_body_t)(PyObject *, PyThreadState *, PyObject *); -#if CYTHON_USE_EXC_INFO_STACK -#define __Pyx_ExcInfoStruct _PyErr_StackItem -#else -typedef struct { - PyObject *exc_type; - PyObject *exc_value; - PyObject *exc_traceback; -} __Pyx_ExcInfoStruct; -#endif -typedef struct { - PyObject_HEAD - __pyx_coroutine_body_t body; - PyObject *closure; - __Pyx_ExcInfoStruct gi_exc_state; - PyObject *gi_weakreflist; - PyObject *classobj; - PyObject *yieldfrom; - PyObject *gi_name; - PyObject *gi_qualname; - PyObject *gi_modulename; - PyObject *gi_code; - PyObject *gi_frame; - int resume_label; - char is_running; -} __pyx_CoroutineObject; -static __pyx_CoroutineObject *__Pyx__Coroutine_New( - PyTypeObject *type, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure, - PyObject *name, PyObject *qualname, PyObject *module_name); -static __pyx_CoroutineObject *__Pyx__Coroutine_NewInit( - __pyx_CoroutineObject *gen, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure, - PyObject *name, PyObject *qualname, PyObject *module_name); -static CYTHON_INLINE void __Pyx_Coroutine_ExceptionClear(__Pyx_ExcInfoStruct *self); -static int __Pyx_Coroutine_clear(PyObject *self); -static PyObject *__Pyx_Coroutine_Send(PyObject *self, PyObject *value); -static PyObject *__Pyx_Coroutine_Close(PyObject *self); -static PyObject *__Pyx_Coroutine_Throw(PyObject *gen, PyObject *args); -#if CYTHON_USE_EXC_INFO_STACK -#define __Pyx_Coroutine_SwapException(self) -#define __Pyx_Coroutine_ResetAndClearException(self) __Pyx_Coroutine_ExceptionClear(&(self)->gi_exc_state) -#else -#define __Pyx_Coroutine_SwapException(self) {\ - __Pyx_ExceptionSwap(&(self)->gi_exc_state.exc_type, &(self)->gi_exc_state.exc_value, &(self)->gi_exc_state.exc_traceback);\ - __Pyx_Coroutine_ResetFrameBackpointer(&(self)->gi_exc_state);\ - } -#define __Pyx_Coroutine_ResetAndClearException(self) {\ - __Pyx_ExceptionReset((self)->gi_exc_state.exc_type, (self)->gi_exc_state.exc_value, (self)->gi_exc_state.exc_traceback);\ - (self)->gi_exc_state.exc_type = (self)->gi_exc_state.exc_value = (self)->gi_exc_state.exc_traceback = NULL;\ - } -#endif -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyGen_FetchStopIterationValue(pvalue)\ - __Pyx_PyGen__FetchStopIterationValue(__pyx_tstate, pvalue) -#else -#define __Pyx_PyGen_FetchStopIterationValue(pvalue)\ - __Pyx_PyGen__FetchStopIterationValue(__Pyx_PyThreadState_Current, pvalue) -#endif -static int __Pyx_PyGen__FetchStopIterationValue(PyThreadState *tstate, PyObject **pvalue); 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-static const char __pyx_k_send[] = "send"; -static const char __pyx_k_test[] = "__test__"; -static const char __pyx_k_time[] = "time"; -static const char __pyx_k_warn[] = "warn"; -static const char __pyx_k_class[] = "__class__"; -static const char __pyx_k_close[] = "close"; -static const char __pyx_k_dtype[] = "_dtype"; -static const char __pyx_k_frame[] = "frame"; -static const char __pyx_k_items[] = "items"; -static const char __pyx_k_numpy[] = "numpy"; -static const char __pyx_k_order[] = "order"; -static const char __pyx_k_other[] = "other"; -static const char __pyx_k_range[] = "range"; -static const char __pyx_k_throw[] = "throw"; -static const char __pyx_k_forces[] = "forces"; -static const char __pyx_k_format[] = "format"; -static const char __pyx_k_get_dt[] = "_get_dt"; -static const char __pyx_k_import[] = "__import__"; -static const char __pyx_k_reader[] = "reader"; -static const char __pyx_k_reduce[] = "__reduce__"; -static const char __pyx_k_float32[] = "float32"; -static const char __pyx_k_genexpr[] = "genexpr"; -static const char __pyx_k_n_atoms[] = "n_atoms"; -static const char __pyx_k_ndarray[] = "ndarray"; -static const char __pyx_k_numbers[] = "numbers"; -static const char __pyx_k_selfcls[] = "selfcls"; -static const char __pyx_k_weakref[] = "weakref"; -static const char __pyx_k_Integral[] = "Integral"; -static const char __pyx_k_KeyError[] = "KeyError"; -static const char __pyx_k_Timestep[] = "Timestep"; -static const char __pyx_k_deepcopy[] = "deepcopy"; -static const char __pyx_k_forces_2[] = "_forces"; -static const char __pyx_k_getstate[] = "__getstate__"; -static const char __pyx_k_lib_util[] = "lib.util"; -static const char __pyx_k_reader_2[] = "_reader"; -static const char __pyx_k_setstate[] = "__setstate__"; -static const char __pyx_k_unitcell[] = "_unitcell"; -static const char __pyx_k_warnings[] = "warnings"; -static const char __pyx_k_Namespace[] = "Namespace"; -static const char __pyx_k_TypeError[] = "TypeError"; -static const char __pyx_k_n_atoms_2[] = "_n_atoms"; -static const char __pyx_k_positions[] = "positions"; -static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; -static const char __pyx_k_Timestep_0[] = "< Timestep {0}"; -static const char __pyx_k_ValueError[] = "ValueError"; -static const char __pyx_k_box_volume[] = "box_volume"; -static const char __pyx_k_deepcopy_2[] = "__deepcopy__"; -static const char __pyx_k_dimensions[] = "dimensions"; -static const char __pyx_k_exceptions[] = "exceptions"; -static const char __pyx_k_has_forces[] = "has_forces"; -static const char __pyx_k_velocities[] = "velocities"; -static const char __pyx_k_ImportError[] = "ImportError"; -static const char __pyx_k_NoDataError[] = "NoDataError"; -static const char __pyx_k_time_offset[] = "time_offset"; -static const char __pyx_k_has_forces_2[] = "_has_forces"; -static const char __pyx_k_velocities_2[] = "_velocities"; -static const char __pyx_k_from_timestep[] = "from_timestep"; -static const char __pyx_k_has_positions[] = "has_positions"; -static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; -static const char __pyx_k_triclinic_box[] = "triclinic_box"; -static const char __pyx_k_AttributeError[] = "AttributeError"; -static const char __pyx_k_NotImplemented[] = "NotImplemented"; -static const char __pyx_k_has_velocities[] = "has_velocities"; -static const char __pyx_k_Timestep___iter[] = "Timestep.__iter__"; -static const char __pyx_k_has_positions_2[] = "_has_positions"; -static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; -static const char __pyx_k_from_coordinates[] = "from_coordinates"; -static const char __pyx_k_has_velocities_2[] = "_has_velocities"; -static const char __pyx_k_triclinic_vectors[] = "triclinic_vectors"; -static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; -static const char __pyx_k_This_Timestep_has_no[] = "This Timestep has no "; -static const char __pyx_k_with_unit_cell_dimensions_0[] = " with unit cell dimensions {0} >"; -static const char __pyx_k_Timestep_triclinic_dimensions[] = "Timestep.triclinic_dimensions.__get__ (line 482)"; -static const char __pyx_k_MDAnalysis_coordinates_timestep[] = "MDAnalysis.coordinates.timestep"; -static const char __pyx_k_This_Timestep_has_no_velocities[] = "This Timestep has no velocities information"; -static const char __pyx_k_Timestep_Class_mod_MDAnalysis_c[] = "\nTimestep Class --- :mod:`MDAnalysis.coordinates.timestep`\n============================================================\n\nDerive other Timestep, classes from the classes in this module.\nThe derived classes must follow the :ref:`Trajectory API`.\n\nTimestep\n--------\n\nA :class:`Timestep` holds information for the current time frame in\nthe trajectory. It is one of the central data structures in\nMDAnalysis.\n\n.. class:: Timestep\n\n .. automethod:: __init__\n .. automethod:: from_coordinates\n .. automethod:: from_timestep\n .. autoattribute:: n_atoms\n .. attribute:: frame\n\n frame number (0-based)\n\n .. versionchanged:: 0.11.0\n Frames now 0-based; was 1-based\n\n\n .. autoattribute:: time\n .. autoattribute:: dt\n .. autoattribute:: positions\n .. autoattribute:: velocities\n .. autoattribute:: forces\n .. autoattribute:: has_positions\n .. autoattribute:: has_velocities\n .. autoattribute:: has_forces\n .. attribute:: _pos\n\n :class:`numpy.ndarray` of dtype :class:`~numpy.float32` of shape\n (*n_atoms*, 3) and internal C order, holding the raw\n cartesian coordinates (in MDAnalysis units, i.e. \303\205).\n\n .. Note::\n\n Normally one does not directly access :attr:`_pos` but uses\n the :meth:`~MDAnalysis.core.groups.AtomGroup.coordinates`\n method of an :class:`~MDAnalysis.core.groups.AtomGroup` but\n sometimes it can be faster to directly use the raw\n coordinates. Any changes to this array are immediately\n reflected in atom positions. If the frame is written to a new\n trajectory then the coordinates are changed. If a new\n trajectory frame is loaded, then *all* contents of\n :attr:`_pos` are overwritten.\n\n .. attribute:: _velocities\n\n :class:`numpy.ndarray` of dtype :class:`~numpy.float32`. of shape\n (*n_atoms*, 3), holding the raw velocities (in MDAnalysis\n units, i.e. typically \303\205/p""s).\n\n .. Note::\n\n Normally velocities are accessed through the\n :attr:`velocities` or the\n :meth:`~MDAnalysis.core.groups.AtomGroup.velocities`\n method of an :class:`~MDAnalysis.core.groups.AtomGroup`\n\n :attr:`~Timestep._velocities` only exists if the :attr:`has_velocities`\n flag is True\n\n .. versionadded:: 0.7.5\n\n .. attribute:: _forces\n\n :class:`numpy.ndarray` of dtype :class:`~numpy.float32`. of shape\n (*n_atoms*, 3), holding the forces\n\n :attr:`~Timestep._forces` only exists if :attr:`has_forces`\n is True\n\n .. versionadded:: 0.11.0\n Added as optional to :class:`Timestep`\n\n .. autoattribute:: dtype\n .. autoattribute:: dimensions\n .. autoattribute:: triclinic_dimensions\n .. autoattribute:: volume\n .. attribute:: data\n\n :class:`dict` that holds arbitrary per Timestep data\n\n .. versionadded:: 0.11.0\n\n .. automethod:: __getitem__\n .. automethod:: __eq__\n .. automethod:: __iter__\n .. automethod:: copy\n .. automethod:: copy_slice\n\n"; -static const char __pyx_k_from_coordinates_locals_genexpr[] = "from_coordinates..genexpr"; -static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; -static const char __pyx_k_selfcls_object_has_no_attribute[] = "{selfcls} object has no attribute '{attr}'"; -static const char __pyx_k_Lengths_of_input_data_mismatched[] = "Lengths of input data mismatched"; -static const char __pyx_k_Must_specify_at_least_one_set_of[] = "Must specify at least one set of data"; -static const char __pyx_k_Reader_has_no_dt_information_set[] = "Reader has no dt information, set to 1.0 ps"; -static const char __pyx_k_Selection_type_must_be_compatibl[] = "Selection type must be compatible with slicing the coordinates"; -static const char __pyx_k_The_unitcell_dimensions_represen[] = "The unitcell dimensions represented as triclinic vectors\n\n Returns\n -------\n numpy.ndarray\n A (3, 3) numpy.ndarray of unit cell vectors\n\n Examples\n --------\n The unitcell for a given system can be queried as either three\n vectors lengths followed by their respective angle, or as three\n triclinic vectors.\n\n >>> ts.dimensions\n array([ 13., 14., 15., 90., 90., 90.], dtype=float32)\n >>> ts.triclinic_dimensions\n array([[ 13., 0., 0.],\n [ 0., 14., 0.],\n [ 0., 0., 15.]], dtype=float32)\n\n Setting the attribute also works::\n\n >>> ts.triclinic_dimensions = [[15, 0, 0], [5, 15, 0], [5, 5, 15]]\n >>> ts.dimensions\n array([ 15. , 15.81138802, 16.58312416, 67.58049774,\n 72.45159912, 71.56504822], dtype=float32)\n\n See Also\n --------\n :func:`MDAnalysis.lib.mdamath.triclinic_vectors`\n\n\n .. versionadded:: 0.11.0\n "; -static const char __pyx_k_This_Timestep_has_no_force_infor[] = "This Timestep has no force information"; -static const char __pyx_k_This_Timestep_has_no_position_in[] = "This Timestep has no position information"; -static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; -static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; -static PyObject *__pyx_n_s_AttributeError; -static PyObject *__pyx_n_u_C; -static PyObject *__pyx_n_s_ImportError; -static PyObject *__pyx_n_s_Integral; -static PyObject *__pyx_n_s_KeyError; -static PyObject *__pyx_kp_u_Lengths_of_input_data_mismatched; -static PyObject *__pyx_n_s_MDAnalysis_coordinates_timestep; -static PyObject *__pyx_kp_u_Must_specify_at_least_one_set_of; -static PyObject *__pyx_n_s_Namespace; -static PyObject *__pyx_n_s_NoDataError; -static PyObject *__pyx_n_s_NotImplemented; -static PyObject *__pyx_kp_u_Reader_has_no_dt_information_set; 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/* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_23copy(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_25__deepcopy__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_27__getstate__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_29__getnewargs_ex__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_31__setstate__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self, PyObject *__pyx_v_state); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_33copy_slice(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self, PyObject *__pyx_v_sel); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_2dt___get__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); /* proto */ -static int __pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_2dt_2__set__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self, PyObject *__pyx_v_new); /* proto */ -static int __pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_2dt_4__del__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_4time___get__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); /* proto */ -static int __pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_4time_2__set__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self, PyObject *__pyx_v_new); /* proto */ -static int __pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_4time_4__del__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_5frame___get__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); /* proto */ -static int __pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_5frame_2__set__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_9_unitcell___get__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); /* proto */ -static int __pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_9_unitcell_2__set__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ -static int __pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_9_unitcell_4__del__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_4_pos___get__(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self); 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/* proto */ -static PyObject *__pyx_pf_10MDAnalysis_11coordinates_8timestep_8Timestep_37__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static PyObject *__pyx_tp_new_10MDAnalysis_11coordinates_8timestep_Timestep(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct_2___iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static __Pyx_CachedCFunction __pyx_umethod_PyDict_Type_get = {0, &__pyx_n_s_get, 0, 0, 0}; -static PyObject *__pyx_float_1_0; -static PyObject *__pyx_int_0; 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Py_INCREF(Py_None); - p->_forces = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); - p->_dtype = Py_None; Py_INCREF(Py_None); - p->data = ((PyObject*)Py_None); Py_INCREF(Py_None); - p->_reader = Py_None; Py_INCREF(Py_None); - p->aux = Py_None; Py_INCREF(Py_None); - if (unlikely(__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_1__cinit__(o, a, k) < 0)) goto bad; - return o; - bad: - Py_DECREF(o); o = 0; - return NULL; -} - -static void __pyx_tp_dealloc_10MDAnalysis_11coordinates_8timestep_Timestep(PyObject *o) { - struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *p = (struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *)o; - #if CYTHON_USE_TP_FINALIZE - if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { - if (PyObject_CallFinalizerFromDealloc(o)) return; - } - #endif - PyObject_GC_UnTrack(o); - { - PyObject *etype, *eval, *etb; - PyErr_Fetch(&etype, &eval, &etb); - __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); - __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_5__dealloc__(o); - __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); - PyErr_Restore(etype, eval, etb); - } - Py_CLEAR(p->_unitcell); - Py_CLEAR(p->_pos); - Py_CLEAR(p->_velocities); - Py_CLEAR(p->_forces); - Py_CLEAR(p->_dtype); - Py_CLEAR(p->data); - Py_CLEAR(p->_reader); - Py_CLEAR(p->aux); - (*Py_TYPE(o)->tp_free)(o); -} - -static int __pyx_tp_traverse_10MDAnalysis_11coordinates_8timestep_Timestep(PyObject *o, visitproc v, void *a) { - int e; - struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *p = (struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep *)o; - if (p->_unitcell) { - e = (*v)(((PyObject *)p->_unitcell), a); if (e) return e; - } - if (p->_pos) { - e = (*v)(((PyObject *)p->_pos), a); if (e) return e; - } - if (p->_velocities) { - e = (*v)(((PyObject *)p->_velocities), a); if (e) return e; - } - if (p->_forces) { - e = (*v)(((PyObject *)p->_forces), a); if (e) return e; - } - if (p->_dtype) { - e = (*v)(p->_dtype, a); 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- Py_XDECREF(tmp); - tmp = ((PyObject*)p->data); - p->data = ((PyObject*)Py_None); Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->_reader); - p->_reader = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->aux); - p->aux = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - return 0; -} -static PyObject *__pyx_sq_item_10MDAnalysis_11coordinates_8timestep_Timestep(PyObject *o, Py_ssize_t i) { - PyObject *r; - PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; - r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); - Py_DECREF(x); - return r; -} - -static PyObject *__pyx_tp_getattro_10MDAnalysis_11coordinates_8timestep_Timestep(PyObject *o, PyObject *n) { - PyObject *v = __Pyx_PyObject_GenericGetAttr(o, n); - if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_Clear(); - v = __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_15__getattr__(o, n); - } - return v; -} - -static PyObject *__pyx_tp_richcompare_10MDAnalysis_11coordinates_8timestep_Timestep(PyObject *o1, PyObject *o2, int op) { - switch (op) { - case Py_EQ: { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_11__eq__(o1, o2); 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Py_False : Py_True; - Py_INCREF(ret); - } - return ret; - } - default: { - return __Pyx_NewRef(Py_NotImplemented); - } - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_n_atoms(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_7n_atoms_1__get__(o); -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_dtype(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_5dtype_1__get__(o); -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_has_positions(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_13has_positions_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_has_positions(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_13has_positions_3__set__(o, v); 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- } - else { - PyErr_SetString(PyExc_NotImplementedError, "__del__"); - return -1; - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_positions(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_9positions_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_positions(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_9positions_3__set__(o, v); - } - else { - PyErr_SetString(PyExc_NotImplementedError, "__del__"); - return -1; - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__x(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_2_x_1__get__(o); -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__y(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_2_y_1__get__(o); -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__z(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_2_z_1__get__(o); -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_dimensions(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_10dimensions_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_dimensions(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_10dimensions_3__set__(o, v); - } - else { - PyErr_SetString(PyExc_NotImplementedError, "__del__"); - return -1; - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_volume(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_6volume_1__get__(o); -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_triclinic_dimensions(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_20triclinic_dimensions_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_triclinic_dimensions(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_20triclinic_dimensions_3__set__(o, v); - } - else { - PyErr_SetString(PyExc_NotImplementedError, "__del__"); - return -1; - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_velocities(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_10velocities_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_velocities(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_10velocities_3__set__(o, v); - } - else { - PyErr_SetString(PyExc_NotImplementedError, "__del__"); - return -1; - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_forces(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_6forces_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_forces(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_6forces_3__set__(o, v); - } - else { - PyErr_SetString(PyExc_NotImplementedError, "__del__"); - return -1; - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_dt(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_2dt_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_dt(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_2dt_3__set__(o, v); - } - else { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_2dt_5__del__(o); - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_time(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_4time_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_time(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_4time_3__set__(o, v); - } - else { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_4time_5__del__(o); - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_frame(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_5frame_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_frame(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_5frame_3__set__(o, v); - } - else { - PyErr_SetString(PyExc_NotImplementedError, "__del__"); - return -1; - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__unitcell(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_9_unitcell_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep__unitcell(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_9_unitcell_3__set__(o, v); - } - else { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_9_unitcell_5__del__(o); - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__pos(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_4_pos_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep__pos(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_4_pos_3__set__(o, v); - } - else { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_4_pos_5__del__(o); - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__velocities(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_11_velocities_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep__velocities(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_11_velocities_3__set__(o, v); - } - else { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_11_velocities_5__del__(o); - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__forces(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_7_forces_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep__forces(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_7_forces_3__set__(o, v); - } - else { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_7_forces_5__del__(o); - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_data(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_4data_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_data(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_4data_3__set__(o, v); - } - else { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_4data_5__del__(o); - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__reader(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_7_reader_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep__reader(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_7_reader_3__set__(o, v); - } - else { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_7_reader_5__del__(o); - } -} - -static PyObject *__pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_aux(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_3aux_1__get__(o); -} - -static int __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_aux(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { - if (v) { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_3aux_3__set__(o, v); - } - else { - return __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_3aux_5__del__(o); - } -} - -static PyMethodDef __pyx_methods_10MDAnalysis_11coordinates_8timestep_Timestep[] = { - {"from_timestep", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_7from_timestep, METH_VARARGS|METH_KEYWORDS, __pyx_doc_10MDAnalysis_11coordinates_8timestep_8Timestep_6from_timestep}, - {"from_coordinates", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_9from_coordinates, METH_VARARGS|METH_KEYWORDS, __pyx_doc_10MDAnalysis_11coordinates_8timestep_8Timestep_8from_coordinates}, - {"__getattr__", (PyCFunction)__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_15__getattr__, METH_O|METH_COEXIST, 0}, - {"copy", (PyCFunction)__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_24copy, METH_NOARGS, __pyx_doc_10MDAnalysis_11coordinates_8timestep_8Timestep_23copy}, - {"__deepcopy__", (PyCFunction)__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_26__deepcopy__, METH_NOARGS, __pyx_doc_10MDAnalysis_11coordinates_8timestep_8Timestep_25__deepcopy__}, - {"__getstate__", (PyCFunction)__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_28__getstate__, METH_NOARGS, __pyx_doc_10MDAnalysis_11coordinates_8timestep_8Timestep_27__getstate__}, - {"__getnewargs_ex__", (PyCFunction)__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_30__getnewargs_ex__, METH_NOARGS, __pyx_doc_10MDAnalysis_11coordinates_8timestep_8Timestep_29__getnewargs_ex__}, - {"__setstate__", (PyCFunction)__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_32__setstate__, METH_O, __pyx_doc_10MDAnalysis_11coordinates_8timestep_8Timestep_31__setstate__}, - {"copy_slice", (PyCFunction)__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_34copy_slice, METH_O, __pyx_doc_10MDAnalysis_11coordinates_8timestep_8Timestep_33copy_slice}, - {"__reduce_cython__", (PyCFunction)__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_36__reduce_cython__, METH_NOARGS, __pyx_doc_10MDAnalysis_11coordinates_8timestep_8Timestep_35__reduce_cython__}, - {"__setstate_cython__", (PyCFunction)__pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_38__setstate_cython__, METH_O, __pyx_doc_10MDAnalysis_11coordinates_8timestep_8Timestep_37__setstate_cython__}, - {0, 0, 0, 0} -}; - -static struct PyGetSetDef __pyx_getsets_10MDAnalysis_11coordinates_8timestep_Timestep[] = { - {(char *)"n_atoms", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_n_atoms, 0, (char *)"A read only view of the number of atoms this Timestep has\n\n .. versionchanged:: 0.11.0\n Changed to read only property\n ", 0}, - {(char *)"dtype", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_dtype, 0, (char *)"The NumPy dtype of the timestep, all arrays in the timestep will\n have this dtype. Currently hardcoded to :class:`~numpy.float32`.\n\n .. versionadded:: 2.3.0\n Added dtype\n ", 0}, - {(char *)"has_positions", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_has_positions, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_has_positions, (char *)"A boolean of whether this Timestep has position data\n This can be changed to ``True`` or ``False`` to allocate space for\n or remove the data.\n\n .. versionadded:: 0.11.0\n ", 0}, - {(char *)"has_velocities", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_has_velocities, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_has_velocities, (char *)"A boolean of whether this Timestep has velocity data\n This can be changed to ``True`` or ``False`` to allocate space for\n or remove the data.\n\n .. versionadded:: 0.11.0\n ", 0}, - {(char *)"has_forces", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_has_forces, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_has_forces, (char *)"A boolean of whether this Timestep has force data\n This can be changed to ``True`` or ``False`` to allocate space for\n or remove the data.\n\n .. versionadded:: 0.11.0\n ", 0}, - {(char *)"positions", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_positions, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_positions, (char *)"A record of the positions of all atoms in this Timestep\n Setting this attribute will add positions to the Timestep if they\n weren't originally present.\n\n Returns\n -------\n positions : numpy.ndarray with dtype numpy.float32\n position data of shape ``(n_atoms, 3)`` for all atoms\n\n Raises\n ------\n :exc:`MDAnalysis.exceptions.NoDataError`\n if the Timestep has no position data\n\n\n .. versionchanged:: 0.11.0\n Now can raise :exc:`NoDataError` when no position data present\n ", 0}, - {(char *)"_x", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__x, 0, (char *)"A view onto the x dimension of position data\n\n .. versionchanged:: 0.11.0\n Now read only\n ", 0}, - {(char *)"_y", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__y, 0, (char *)"A view onto the y dimension of position data\n\n .. versionchanged:: 0.11.0\n Now read only\n ", 0}, - {(char *)"_z", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__z, 0, (char *)"A view onto the z dimension of position data\n\n .. versionchanged:: 0.11.0\n Now read only\n ", 0}, - {(char *)"dimensions", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_dimensions, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_dimensions, (char *)"View of unitcell dimensions (*A*, *B*, *C*, *alpha*, *beta*, *gamma*)\n\n lengths *a*, *b*, *c* are in the MDAnalysis length unit (\303\205), and\n angles are in degrees.\n ", 0}, - {(char *)"volume", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_volume, 0, (char *)"volume of the unitcell", 0}, - {(char *)"triclinic_dimensions", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_triclinic_dimensions, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_triclinic_dimensions, (char *)"The unitcell dimensions represented as triclinic vectors\n\n Returns\n -------\n numpy.ndarray\n A (3, 3) numpy.ndarray of unit cell vectors\n\n Examples\n --------\n The unitcell for a given system can be queried as either three\n vectors lengths followed by their respective angle, or as three\n triclinic vectors.\n\n >>> ts.dimensions\n array([ 13., 14., 15., 90., 90., 90.], dtype=float32)\n >>> ts.triclinic_dimensions\n array([[ 13., 0., 0.],\n [ 0., 14., 0.],\n [ 0., 0., 15.]], dtype=float32)\n\n Setting the attribute also works::\n\n >>> ts.triclinic_dimensions = [[15, 0, 0], [5, 15, 0], [5, 5, 15]]\n >>> ts.dimensions\n array([ 15. , 15.81138802, 16.58312416, 67.58049774,\n 72.45159912, 71.56504822], dtype=float32)\n\n See Also\n --------\n :func:`MDAnalysis.lib.mdamath.triclinic_vectors`\n\n\n .. versionadded:: 0.11.0\n ", 0}, - {(char *)"velocities", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_velocities, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_velocities, (char *)"A record of the velocities of all atoms in this Timestep\n Setting this attribute will add velocities to the Timestep if they\n weren't originally present.\n\n Returns\n -------\n velocities : numpy.ndarray with dtype numpy.float32\n velocity data of shape ``(n_atoms, 3)`` for all atoms\n\n Raises\n ------\n :exc:`MDAnalysis.exceptions.NoDataError`\n if the Timestep has no velocity data\n\n\n .. versionadded:: 0.11.0\n ", 0}, - {(char *)"forces", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_forces, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_forces, (char *)"A record of the forces of all atoms in this Timestep\n Setting this attribute will add forces to the Timestep if they\n weren't originally present.\n\n Returns\n -------\n\n forces : numpy.ndarray with dtype numpy.float32\n force data of shape ``(n_atoms, 3)`` for all atoms\n Raises\n ------\n\n :exc:`MDAnalysis.exceptions.NoDataError`\n if the Timestep has no force data\n .. versionadded:: 0.11.0\n ", 0}, - {(char *)"dt", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_dt, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_dt, (char *)"The time difference in ps between timesteps\n\n Note\n ----\n This defaults to 1.0 ps in the absence of time data\n\n\n .. versionadded:: 0.11.0\n ", 0}, - {(char *)"time", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_time, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_time, (char *)"The time in ps of this timestep\n\n This is calculated as::\n\n time = ts.data['time_offset'] + ts.time\n\n Or, if the trajectory doesn't provide time information::\n\n time = ts.data['time_offset'] + ts.frame * ts.dt\n\n .. versionadded:: 0.11.0\n ", 0}, - {(char *)"frame", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_frame, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_frame, (char *)"frame: 'int64_t'", 0}, - {(char *)"_unitcell", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__unitcell, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep__unitcell, (char *)"_unitcell: numpy.ndarray", 0}, - {(char *)"_pos", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__pos, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep__pos, (char *)"_pos: numpy.ndarray", 0}, - {(char *)"_velocities", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__velocities, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep__velocities, (char *)"_velocities: numpy.ndarray", 0}, - {(char *)"_forces", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__forces, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep__forces, (char *)"_forces: numpy.ndarray", 0}, - {(char *)"data", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_data, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_data, (char *)"data: dict", 0}, - {(char *)"_reader", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep__reader, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep__reader, (char *)"_reader: object", 0}, - {(char *)"aux", __pyx_getprop_10MDAnalysis_11coordinates_8timestep_8Timestep_aux, __pyx_setprop_10MDAnalysis_11coordinates_8timestep_8Timestep_aux, (char *)"aux: object", 0}, - {0, 0, 0, 0, 0} -}; - -static PySequenceMethods __pyx_tp_as_sequence_Timestep = { - __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_17__len__, /*sq_length*/ - 0, /*sq_concat*/ - 0, /*sq_repeat*/ - __pyx_sq_item_10MDAnalysis_11coordinates_8timestep_Timestep, /*sq_item*/ - 0, /*sq_slice*/ - 0, /*sq_ass_item*/ - 0, /*sq_ass_slice*/ - 0, /*sq_contains*/ - 0, /*sq_inplace_concat*/ - 0, /*sq_inplace_repeat*/ -}; - -static PyMappingMethods __pyx_tp_as_mapping_Timestep = { - __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_17__len__, /*mp_length*/ - __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_13__getitem__, /*mp_subscript*/ - 0, /*mp_ass_subscript*/ -}; - -static PyTypeObject __pyx_type_10MDAnalysis_11coordinates_8timestep_Timestep = { - PyVarObject_HEAD_INIT(0, 0) - "MDAnalysis.coordinates.timestep.Timestep", /*tp_name*/ - sizeof(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep_Timestep), /*tp_basicsize*/ - 0, /*tp_itemsize*/ - __pyx_tp_dealloc_10MDAnalysis_11coordinates_8timestep_Timestep, /*tp_dealloc*/ - #if PY_VERSION_HEX < 0x030800b4 - 0, /*tp_print*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 - 0, /*tp_vectorcall_offset*/ - #endif - 0, /*tp_getattr*/ - 0, /*tp_setattr*/ - #if PY_MAJOR_VERSION < 3 - 0, /*tp_compare*/ - #endif - #if PY_MAJOR_VERSION >= 3 - 0, /*tp_as_async*/ - #endif - __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_22__repr__, /*tp_repr*/ - 0, /*tp_as_number*/ - &__pyx_tp_as_sequence_Timestep, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_Timestep, /*tp_as_mapping*/ - 0, /*tp_hash*/ - 0, /*tp_call*/ - 0, /*tp_str*/ - __pyx_tp_getattro_10MDAnalysis_11coordinates_8timestep_Timestep, /*tp_getattro*/ - 0, /*tp_setattro*/ - 0, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - "Timestep(uint64_t n_atoms, **kwargs)\nTimestep data for one frame\n\n :Methods:\n\n ``ts = Timestep(n_atoms)``\n\n create a timestep object with space for n_atoms\n\n\n .. versionchanged:: 0.11.0\n Added :meth:`from_timestep` and :meth:`from_coordinates` constructor\n methods.\n :class:`Timestep` init now only accepts integer creation.\n :attr:`n_atoms` now a read only property.\n :attr:`frame` now 0-based instead of 1-based.\n Attributes `status` and `step` removed.\n .. versionchanged:: 2.0.0\n Timestep now can be (un)pickled. Weakref for Reader\n will be dropped.\n Timestep now stores in to numpy array memory in 'C' order rather than\n 'F' (Fortran).\n .. versionchanged:: 2.3.0\n Timestep is now a Cython extension type.\n All arrays are now forced to be C contiguous using the NumPy C API.\n ", /*tp_doc*/ - __pyx_tp_traverse_10MDAnalysis_11coordinates_8timestep_Timestep, /*tp_traverse*/ - __pyx_tp_clear_10MDAnalysis_11coordinates_8timestep_Timestep, /*tp_clear*/ - __pyx_tp_richcompare_10MDAnalysis_11coordinates_8timestep_Timestep, /*tp_richcompare*/ - 0, /*tp_weaklistoffset*/ - __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_19__iter__, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_10MDAnalysis_11coordinates_8timestep_Timestep, /*tp_methods*/ - 0, /*tp_members*/ - __pyx_getsets_10MDAnalysis_11coordinates_8timestep_Timestep, /*tp_getset*/ - 0, /*tp_base*/ - 0, /*tp_dict*/ - 0, /*tp_descr_get*/ - 0, /*tp_descr_set*/ - 0, /*tp_dictoffset*/ - __pyx_pw_10MDAnalysis_11coordinates_8timestep_8Timestep_3__init__, /*tp_init*/ - 0, /*tp_alloc*/ - __pyx_tp_new_10MDAnalysis_11coordinates_8timestep_Timestep, /*tp_new*/ - 0, /*tp_free*/ - 0, /*tp_is_gc*/ - 0, /*tp_bases*/ - 0, /*tp_mro*/ - 0, /*tp_cache*/ - 0, /*tp_subclasses*/ - 0, /*tp_weaklist*/ - 0, /*tp_del*/ - 0, /*tp_version_tag*/ - #if PY_VERSION_HEX >= 0x030400a1 - 0, /*tp_finalize*/ - #endif - #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) - 0, /*tp_vectorcall*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 - 0, /*tp_print*/ - #endif - #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 - 0, /*tp_pypy_flags*/ - #endif -}; - -static struct __pyx_obj_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates *__pyx_freelist_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates[8]; -static int __pyx_freecount_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates = 0; - -static PyObject *__pyx_tp_new_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { - PyObject *o; - if (CYTHON_COMPILING_IN_CPYTHON && likely((__pyx_freecount_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates > 0) & (t->tp_basicsize == sizeof(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates)))) { - o = (PyObject*)__pyx_freelist_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates[--__pyx_freecount_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates]; - memset(o, 0, sizeof(struct __pyx_obj_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates)); - (void) PyObject_INIT(o, t); - PyObject_GC_Track(o); - } else { - o = (*t->tp_alloc)(t, 0); - if (unlikely(!o)) return 0; - } - return o; -} - -static void __pyx_tp_dealloc_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates(PyObject *o) { - struct __pyx_obj_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates *p = (struct __pyx_obj_10MDAnalysis_11coordinates_8timestep___pyx_scope_struct__from_coordinates *)o; - 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- #else - "%s() got an unexpected keyword argument '%U'", - function_name, key); - #endif -bad: - return -1; -} - -/* RaiseArgTupleInvalid */ -static void __Pyx_RaiseArgtupleInvalid( - const char* func_name, - int exact, - Py_ssize_t num_min, - Py_ssize_t num_max, - Py_ssize_t num_found) -{ - Py_ssize_t num_expected; - const char *more_or_less; - if (num_found < num_min) { - num_expected = num_min; - more_or_less = "at least"; - } else { - num_expected = num_max; - more_or_less = "at most"; - } - if (exact) { - more_or_less = "exactly"; - } - PyErr_Format(PyExc_TypeError, - "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", - func_name, more_or_less, num_expected, - (num_expected == 1) ? "" : "s", num_found); -} - -/* ExtTypeTest */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(__Pyx_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* PyDictVersioning */ -#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; -} -static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) { - PyObject **dictptr = NULL; - Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset; - if (offset) { -#if CYTHON_COMPILING_IN_CPYTHON - dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj); -#else - dictptr = _PyObject_GetDictPtr(obj); -#endif - } - return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; -} -static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) - return 0; - return obj_dict_version == __Pyx_get_object_dict_version(obj); -} -#endif - -/* GetModuleGlobalName */ -#if CYTHON_USE_DICT_VERSIONS -static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value) -#else -static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name) -#endif -{ - PyObject *result; -#if !CYTHON_AVOID_BORROWED_REFS -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 - result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } else if (unlikely(PyErr_Occurred())) { - return NULL; - } -#else - result = PyDict_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } -#endif -#else - result = PyObject_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } - PyErr_Clear(); -#endif - return __Pyx_GetBuiltinName(name); -} - -/* DictGetItem */ -#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY -static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { - PyObject *value; - value = PyDict_GetItemWithError(d, key); - if (unlikely(!value)) { - if (!PyErr_Occurred()) { - if (unlikely(PyTuple_Check(key))) { - PyObject* args = PyTuple_Pack(1, key); - if (likely(args)) { - PyErr_SetObject(PyExc_KeyError, args); - Py_DECREF(args); - } - } else { - PyErr_SetObject(PyExc_KeyError, key); - } - } - return NULL; - } - Py_INCREF(value); - return value; -} -#endif - -/* GetTopmostException */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* PyErrExceptionMatches */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* PyErrFetchRestore */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -} -#endif - -/* PyCFunctionFastCall */ -#if CYTHON_FAST_PYCCALL -static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) { - PyCFunctionObject *func = (PyCFunctionObject*)func_obj; - PyCFunction meth = PyCFunction_GET_FUNCTION(func); - PyObject *self = PyCFunction_GET_SELF(func); - int flags = PyCFunction_GET_FLAGS(func); - assert(PyCFunction_Check(func)); - assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))); - assert(nargs >= 0); - assert(nargs == 0 || args != NULL); - /* _PyCFunction_FastCallDict() must not be called with an exception set, - because it may clear it (directly or indirectly) and so the - caller loses its exception */ - assert(!PyErr_Occurred()); - if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) { - return (*((__Pyx_PyCFunctionFastWithKeywords)(void*)meth)) (self, args, nargs, NULL); - } else { - return (*((__Pyx_PyCFunctionFast)(void*)meth)) (self, args, nargs); - } -} -#endif - -/* PyFunctionFastCall */ -#if CYTHON_FAST_PYCALL -static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, - PyObject *globals) { - PyFrameObject *f; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject **fastlocals; - Py_ssize_t i; - PyObject *result; - assert(globals != NULL); - /* XXX Perhaps we should create a specialized - PyFrame_New() that doesn't take locals, but does - take builtins without sanity checking them. - */ - assert(tstate != NULL); - f = PyFrame_New(tstate, co, globals, NULL); - if (f == NULL) { - return NULL; - } - fastlocals = __Pyx_PyFrame_GetLocalsplus(f); - for (i = 0; i < na; i++) { - Py_INCREF(*args); - fastlocals[i] = *args++; - } - result = PyEval_EvalFrameEx(f,0); - ++tstate->recursion_depth; - Py_DECREF(f); - --tstate->recursion_depth; - return result; -} -#if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { - PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); - PyObject *globals = PyFunction_GET_GLOBALS(func); - PyObject *argdefs = PyFunction_GET_DEFAULTS(func); - PyObject *closure; -#if PY_MAJOR_VERSION >= 3 - PyObject *kwdefs; -#endif - PyObject *kwtuple, **k; - PyObject **d; - Py_ssize_t nd; - Py_ssize_t nk; - PyObject *result; - assert(kwargs == NULL || PyDict_Check(kwargs)); - nk = kwargs ? PyDict_Size(kwargs) : 0; - if (Py_EnterRecursiveCall((char*)" while calling a Python object")) { - return NULL; - } - if ( -#if PY_MAJOR_VERSION >= 3 - co->co_kwonlyargcount == 0 && -#endif - likely(kwargs == NULL || nk == 0) && - co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { - if (argdefs == NULL && co->co_argcount == nargs) { - result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); - goto done; - } - else if (nargs == 0 && argdefs != NULL - && co->co_argcount == Py_SIZE(argdefs)) { - /* function called with no arguments, but all parameters have - a default value: use default values as arguments .*/ - args = &PyTuple_GET_ITEM(argdefs, 0); - result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); - goto done; - } - } - if (kwargs != NULL) { - Py_ssize_t pos, i; - kwtuple = PyTuple_New(2 * nk); - if (kwtuple == NULL) { - result = NULL; - goto done; - } - k = &PyTuple_GET_ITEM(kwtuple, 0); - pos = i = 0; - while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { - Py_INCREF(k[i]); - Py_INCREF(k[i+1]); - i += 2; - } - nk = i / 2; - } - else { - kwtuple = NULL; - k = NULL; - } - closure = PyFunction_GET_CLOSURE(func); -#if PY_MAJOR_VERSION >= 3 - kwdefs = PyFunction_GET_KW_DEFAULTS(func); -#endif - if (argdefs != NULL) { - d = &PyTuple_GET_ITEM(argdefs, 0); - nd = Py_SIZE(argdefs); - } - else { - d = NULL; - nd = 0; - } -#if PY_MAJOR_VERSION >= 3 - result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, kwdefs, closure); -#else - result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, closure); -#endif - Py_XDECREF(kwtuple); -done: - Py_LeaveRecursiveCall(); - return result; -} -#endif -#endif - -/* PyObjectCall */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { - PyObject *result; - ternaryfunc call = Py_TYPE(func)->tp_call; - if (unlikely(!call)) - return PyObject_Call(func, arg, kw); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = (*call)(func, arg, kw); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCall2Args */ -static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { - PyObject *args, *result = NULL; - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyFunction_FastCall(function, args, 2); - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyCFunction_FastCall(function, args, 2); - } - #endif - args = PyTuple_New(2); - if (unlikely(!args)) goto done; - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 0, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 1, arg2); - Py_INCREF(function); - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); -done: - return result; -} - -/* PyObjectCallMethO */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { - PyObject *self, *result; - PyCFunction cfunc; - cfunc = PyCFunction_GET_FUNCTION(func); - self = PyCFunction_GET_SELF(func); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = cfunc(self, arg); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallOneArg */ -#if CYTHON_COMPILING_IN_CPYTHON -static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_New(1); - if (unlikely(!args)) return NULL; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif - if (likely(PyCFunction_Check(func))) { - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (__Pyx_PyFastCFunction_Check(func)) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } - } - return __Pyx__PyObject_CallOneArg(func, arg); -} -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -#endif - -/* UnpackUnboundCMethod */ -static int __Pyx_TryUnpackUnboundCMethod(__Pyx_CachedCFunction* target) { - PyObject *method; - method = __Pyx_PyObject_GetAttrStr(target->type, *target->method_name); - if (unlikely(!method)) - return -1; - target->method = method; -#if CYTHON_COMPILING_IN_CPYTHON - #if PY_MAJOR_VERSION >= 3 - if (likely(__Pyx_TypeCheck(method, &PyMethodDescr_Type))) - #endif - { - PyMethodDescrObject *descr = (PyMethodDescrObject*) method; - target->func = descr->d_method->ml_meth; - target->flag = descr->d_method->ml_flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_STACKLESS); - } -#endif - return 0; -} - -/* CallUnboundCMethod1 */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_CallUnboundCMethod1(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg) { - if (likely(cfunc->func)) { - int flag = cfunc->flag; - if (flag == METH_O) { - return (*(cfunc->func))(self, arg); - } else if (PY_VERSION_HEX >= 0x030600B1 && flag == METH_FASTCALL) { - #if PY_VERSION_HEX >= 0x030700A0 - return (*(__Pyx_PyCFunctionFast)(void*)(PyCFunction)cfunc->func)(self, &arg, 1); - #else - return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, &arg, 1, NULL); - #endif - } else if (PY_VERSION_HEX >= 0x030700A0 && flag == (METH_FASTCALL | METH_KEYWORDS)) { - return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, &arg, 1, NULL); - } - } - return __Pyx__CallUnboundCMethod1(cfunc, self, arg); -} -#endif -static PyObject* __Pyx__CallUnboundCMethod1(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg){ - PyObject *args, *result = NULL; - if (unlikely(!cfunc->func && !cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL; -#if CYTHON_COMPILING_IN_CPYTHON - if (cfunc->func && (cfunc->flag & METH_VARARGS)) { - args = PyTuple_New(1); - if (unlikely(!args)) goto bad; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - if (cfunc->flag & METH_KEYWORDS) - result = (*(PyCFunctionWithKeywords)(void*)(PyCFunction)cfunc->func)(self, args, NULL); - else - result = (*cfunc->func)(self, args); - } else { - args = PyTuple_New(2); - if (unlikely(!args)) goto bad; - Py_INCREF(self); - PyTuple_SET_ITEM(args, 0, self); - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 1, arg); - result = __Pyx_PyObject_Call(cfunc->method, args, NULL); - } -#else - args = PyTuple_Pack(2, self, arg); - if (unlikely(!args)) goto bad; - result = __Pyx_PyObject_Call(cfunc->method, args, NULL); -#endif -bad: - Py_XDECREF(args); - return result; -} - -/* CallUnboundCMethod2 */ -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030600B1 -static CYTHON_INLINE PyObject *__Pyx_CallUnboundCMethod2(__Pyx_CachedCFunction *cfunc, PyObject *self, PyObject *arg1, PyObject *arg2) { - if (likely(cfunc->func)) { - PyObject *args[2] = {arg1, arg2}; - if (cfunc->flag == METH_FASTCALL) { - #if PY_VERSION_HEX >= 0x030700A0 - return (*(__Pyx_PyCFunctionFast)(void*)(PyCFunction)cfunc->func)(self, args, 2); - #else - return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, args, 2, NULL); - #endif - } - #if PY_VERSION_HEX >= 0x030700A0 - if (cfunc->flag == (METH_FASTCALL | METH_KEYWORDS)) - return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, args, 2, NULL); - #endif - } - return __Pyx__CallUnboundCMethod2(cfunc, self, arg1, arg2); -} -#endif -static PyObject* __Pyx__CallUnboundCMethod2(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg1, PyObject* arg2){ - PyObject *args, *result = NULL; - if (unlikely(!cfunc->func && !cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL; -#if CYTHON_COMPILING_IN_CPYTHON - if (cfunc->func && (cfunc->flag & METH_VARARGS)) { - args = PyTuple_New(2); - if (unlikely(!args)) goto bad; - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 0, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 1, arg2); - if (cfunc->flag & METH_KEYWORDS) - result = (*(PyCFunctionWithKeywords)(void*)(PyCFunction)cfunc->func)(self, args, NULL); - else - result = (*cfunc->func)(self, args); - } else { - args = PyTuple_New(3); - if (unlikely(!args)) goto bad; - Py_INCREF(self); - PyTuple_SET_ITEM(args, 0, self); - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 1, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 2, arg2); - result = __Pyx_PyObject_Call(cfunc->method, args, NULL); - } -#else - args = PyTuple_Pack(3, self, arg1, arg2); - if (unlikely(!args)) goto bad; - result = __Pyx_PyObject_Call(cfunc->method, args, NULL); -#endif -bad: - Py_XDECREF(args); - return result; -} - -/* dict_getitem_default */ -static PyObject* __Pyx_PyDict_GetItemDefault(PyObject* d, PyObject* key, PyObject* default_value) { - PyObject* value; -#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY - value = PyDict_GetItemWithError(d, key); - if (unlikely(!value)) { - if (unlikely(PyErr_Occurred())) - return NULL; - value = default_value; - } - Py_INCREF(value); - if ((1)); -#else - if (PyString_CheckExact(key) || PyUnicode_CheckExact(key) || PyInt_CheckExact(key)) { - value = PyDict_GetItem(d, key); - if (unlikely(!value)) { - value = default_value; - } - Py_INCREF(value); - } -#endif - else { - if (default_value == Py_None) - value = __Pyx_CallUnboundCMethod1(&__pyx_umethod_PyDict_Type_get, d, key); - else - value = __Pyx_CallUnboundCMethod2(&__pyx_umethod_PyDict_Type_get, d, key, default_value); - } - return value; -} - -/* PyObjectSetAttrStr */ -#if CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) { - PyTypeObject* tp = Py_TYPE(obj); - if (likely(tp->tp_setattro)) - return tp->tp_setattro(obj, attr_name, value); -#if PY_MAJOR_VERSION < 3 - if (likely(tp->tp_setattr)) - return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value); -#endif - return PyObject_SetAttr(obj, attr_name, value); -} -#endif - -/* PyObjectCallNoArg */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, NULL, 0); - } -#endif -#if defined(__Pyx_CyFunction_USED) && defined(NDEBUG) - if (likely(PyCFunction_Check(func) || __Pyx_CyFunction_Check(func))) -#else - if (likely(PyCFunction_Check(func))) -#endif - { - if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { - return __Pyx_PyObject_CallMethO(func, NULL); - } - } - return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL); -} -#endif - -/* RaiseException */ -#if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* SliceObject */ -static CYTHON_INLINE int __Pyx_PyObject_SetSlice(PyObject* obj, PyObject* value, - Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, - int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { -#if CYTHON_USE_TYPE_SLOTS - PyMappingMethods* mp; -#if PY_MAJOR_VERSION < 3 - PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; - if (likely(ms && ms->sq_ass_slice)) { - if (!has_cstart) { - if (_py_start && (*_py_start != Py_None)) { - cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); - if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstart = 0; - } - if (!has_cstop) { - if (_py_stop && (*_py_stop != Py_None)) { - cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); - if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstop = PY_SSIZE_T_MAX; - } - if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { - Py_ssize_t l = ms->sq_length(obj); - if (likely(l >= 0)) { - if (cstop < 0) { - cstop += l; - if (cstop < 0) cstop = 0; - } - if (cstart < 0) { - cstart += l; - if (cstart < 0) cstart = 0; - } - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - goto bad; - PyErr_Clear(); - } - } - return ms->sq_ass_slice(obj, cstart, cstop, value); - } -#endif - mp = Py_TYPE(obj)->tp_as_mapping; - if (likely(mp && mp->mp_ass_subscript)) -#endif - { - int result; - PyObject *py_slice, *py_start, *py_stop; - if (_py_slice) { - py_slice = *_py_slice; - } else { - PyObject* owned_start = NULL; - PyObject* owned_stop = NULL; - if (_py_start) { - py_start = *_py_start; - } else { - if (has_cstart) { - owned_start = py_start = PyInt_FromSsize_t(cstart); - if (unlikely(!py_start)) goto bad; - } else - py_start = Py_None; - } - if (_py_stop) { - py_stop = *_py_stop; - } else { - if (has_cstop) { - owned_stop = py_stop = PyInt_FromSsize_t(cstop); - if (unlikely(!py_stop)) { - Py_XDECREF(owned_start); - goto bad; - } - } else - py_stop = Py_None; - } - py_slice = PySlice_New(py_start, py_stop, Py_None); - Py_XDECREF(owned_start); - Py_XDECREF(owned_stop); - if (unlikely(!py_slice)) goto bad; - } -#if CYTHON_USE_TYPE_SLOTS - result = mp->mp_ass_subscript(obj, py_slice, value); -#else - result = value ? PyObject_SetItem(obj, py_slice, value) : PyObject_DelItem(obj, py_slice); -#endif - if (!_py_slice) { - Py_DECREF(py_slice); - } - return result; - } - PyErr_Format(PyExc_TypeError, - "'%.200s' object does not support slice %.10s", - Py_TYPE(obj)->tp_name, value ? "assignment" : "deletion"); -bad: - return -1; -} - -/* GetItemInt */ -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { - PyObject *r; - if (!j) return NULL; - r = PyObject_GetItem(o, j); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyList_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyTuple_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } - else if (PyTuple_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } else { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_item)) { - if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { - Py_ssize_t l = m->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return NULL; - PyErr_Clear(); - } - } - return m->sq_item(o, i); - } - } -#else - if (is_list || PySequence_Check(o)) { - return PySequence_GetItem(o, i); - } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -} - -/* ObjectGetItem */ -#if CYTHON_USE_TYPE_SLOTS -static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { - PyObject *runerr = NULL; - Py_ssize_t key_value; - PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; - if (unlikely(!(m && m->sq_item))) { - PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); - return NULL; - } - key_value = __Pyx_PyIndex_AsSsize_t(index); - if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { - return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); - } - if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { - PyErr_Clear(); - PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); - } - return NULL; -} -static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { - PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; - if (likely(m && m->mp_subscript)) { - return m->mp_subscript(obj, key); - } - return __Pyx_PyObject_GetIndex(obj, key); -} -#endif - -/* PyIntCompare */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED long inplace) { - if (op1 == op2) { - Py_RETURN_TRUE; - } - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - const long b = intval; - long a = PyInt_AS_LONG(op1); - if (a == b) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - int unequal; - unsigned long uintval; - Py_ssize_t size = Py_SIZE(op1); - const digit* digits = ((PyLongObject*)op1)->ob_digit; - if (intval == 0) { - if (size == 0) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } else if (intval < 0) { - if (size >= 0) - Py_RETURN_FALSE; - intval = -intval; - size = -size; - } else { - if (size <= 0) - Py_RETURN_FALSE; - } - uintval = (unsigned long) intval; -#if PyLong_SHIFT * 4 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 4)) { - unequal = (size != 5) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[4] != ((uintval >> (4 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif -#if PyLong_SHIFT * 3 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 3)) { - unequal = (size != 4) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif -#if PyLong_SHIFT * 2 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 2)) { - unequal = (size != 3) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif -#if PyLong_SHIFT * 1 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 1)) { - unequal = (size != 2) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif - unequal = (size != 1) || (((unsigned long) digits[0]) != (uintval & (unsigned long) PyLong_MASK)); - if (unequal == 0) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - if ((double)a == (double)b) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } - return ( - PyObject_RichCompare(op1, op2, Py_EQ)); -} - -/* SliceObject */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, - Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, - int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { -#if CYTHON_USE_TYPE_SLOTS - PyMappingMethods* mp; -#if PY_MAJOR_VERSION < 3 - PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; - if (likely(ms && ms->sq_slice)) { - if (!has_cstart) { - if (_py_start && (*_py_start != Py_None)) { - cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); - if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstart = 0; - } - if (!has_cstop) { - if (_py_stop && (*_py_stop != Py_None)) { - cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); - if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstop = PY_SSIZE_T_MAX; - } - if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { - Py_ssize_t l = ms->sq_length(obj); - if (likely(l >= 0)) { - if (cstop < 0) { - cstop += l; - if (cstop < 0) cstop = 0; - } - if (cstart < 0) { - cstart += l; - if (cstart < 0) cstart = 0; - } - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - goto bad; - PyErr_Clear(); - } - } - return ms->sq_slice(obj, cstart, cstop); - } -#endif - mp = Py_TYPE(obj)->tp_as_mapping; - if (likely(mp && mp->mp_subscript)) -#endif - { - PyObject* result; - PyObject *py_slice, *py_start, *py_stop; - if (_py_slice) { - py_slice = *_py_slice; - } else { - PyObject* owned_start = NULL; - PyObject* owned_stop = NULL; - if (_py_start) { - py_start = *_py_start; - } else { - if (has_cstart) { - owned_start = py_start = PyInt_FromSsize_t(cstart); - if (unlikely(!py_start)) goto bad; - } else - py_start = Py_None; - } - if (_py_stop) { - py_stop = *_py_stop; - } else { - if (has_cstop) { - owned_stop = py_stop = PyInt_FromSsize_t(cstop); - if (unlikely(!py_stop)) { - Py_XDECREF(owned_start); - goto bad; - } - } else - py_stop = Py_None; - } - py_slice = PySlice_New(py_start, py_stop, Py_None); - Py_XDECREF(owned_start); - Py_XDECREF(owned_stop); - if (unlikely(!py_slice)) goto bad; - } -#if CYTHON_USE_TYPE_SLOTS - result = mp->mp_subscript(obj, py_slice); -#else - result = PyObject_GetItem(obj, py_slice); -#endif - if (!_py_slice) { - Py_DECREF(py_slice); - } - return result; - } - PyErr_Format(PyExc_TypeError, - "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name); -bad: - return NULL; -} - -/* ArgTypeTest */ -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) -{ - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - else if (exact) { - #if PY_MAJOR_VERSION == 2 - if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; - #endif - } - else { - if (likely(__Pyx_TypeCheck(obj, type))) return 1; - } - PyErr_Format(PyExc_TypeError, - "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", - name, type->tp_name, Py_TYPE(obj)->tp_name); - return 0; -} - -/* IterFinish */ -static CYTHON_INLINE int __Pyx_IterFinish(void) { -#if CYTHON_FAST_THREAD_STATE - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* exc_type = tstate->curexc_type; - if (unlikely(exc_type)) { - if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) { - PyObject *exc_value, *exc_tb; - exc_value = tstate->curexc_value; - exc_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; - Py_DECREF(exc_type); - Py_XDECREF(exc_value); - Py_XDECREF(exc_tb); - return 0; - } else { - return -1; - } - } - return 0; -#else - if (unlikely(PyErr_Occurred())) { - if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { - PyErr_Clear(); - return 0; - } else { - return -1; - } - } - return 0; -#endif -} - -/* PyObjectGetMethod */ -static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method) { - PyObject *attr; -#if CYTHON_UNPACK_METHODS && CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_PYTYPE_LOOKUP - PyTypeObject *tp = Py_TYPE(obj); - PyObject *descr; - descrgetfunc f = NULL; - PyObject **dictptr, *dict; - int meth_found = 0; - assert (*method == NULL); - if (unlikely(tp->tp_getattro != PyObject_GenericGetAttr)) { - attr = __Pyx_PyObject_GetAttrStr(obj, name); - goto try_unpack; - } - if (unlikely(tp->tp_dict == NULL) && unlikely(PyType_Ready(tp) < 0)) { - return 0; - } - descr = _PyType_Lookup(tp, name); - if (likely(descr != NULL)) { - Py_INCREF(descr); -#if PY_MAJOR_VERSION >= 3 - #ifdef __Pyx_CyFunction_USED - if (likely(PyFunction_Check(descr) || (Py_TYPE(descr) == &PyMethodDescr_Type) || __Pyx_CyFunction_Check(descr))) - #else - if (likely(PyFunction_Check(descr) || (Py_TYPE(descr) == &PyMethodDescr_Type))) - #endif -#else - #ifdef __Pyx_CyFunction_USED - if (likely(PyFunction_Check(descr) || __Pyx_CyFunction_Check(descr))) - #else - if (likely(PyFunction_Check(descr))) - #endif -#endif - { - meth_found = 1; - } else { - f = Py_TYPE(descr)->tp_descr_get; - if (f != NULL && PyDescr_IsData(descr)) { - attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); - Py_DECREF(descr); - goto try_unpack; - } - } - } - dictptr = _PyObject_GetDictPtr(obj); - if (dictptr != NULL && (dict = *dictptr) != NULL) { - Py_INCREF(dict); - attr = __Pyx_PyDict_GetItemStr(dict, name); - if (attr != NULL) { - Py_INCREF(attr); - Py_DECREF(dict); - Py_XDECREF(descr); - goto try_unpack; - } - Py_DECREF(dict); - } - if (meth_found) { - *method = descr; - return 1; - } - if (f != NULL) { - attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); - Py_DECREF(descr); - goto try_unpack; - } - if (descr != NULL) { - *method = descr; - return 0; - } - PyErr_Format(PyExc_AttributeError, -#if PY_MAJOR_VERSION >= 3 - "'%.50s' object has no attribute '%U'", - tp->tp_name, name); -#else - "'%.50s' object has no attribute '%.400s'", - tp->tp_name, PyString_AS_STRING(name)); -#endif - return 0; -#else - attr = __Pyx_PyObject_GetAttrStr(obj, name); - goto try_unpack; -#endif -try_unpack: -#if CYTHON_UNPACK_METHODS - if (likely(attr) && PyMethod_Check(attr) && likely(PyMethod_GET_SELF(attr) == obj)) { - PyObject *function = PyMethod_GET_FUNCTION(attr); - Py_INCREF(function); - Py_DECREF(attr); - *method = function; - return 1; - } -#endif - *method = attr; - return 0; -} - -/* PyObjectCallMethod0 */ -static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) { - PyObject *method = NULL, *result = NULL; - int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method); - if (likely(is_method)) { - result = __Pyx_PyObject_CallOneArg(method, obj); - Py_DECREF(method); - return result; - } - if (unlikely(!method)) goto bad; - result = __Pyx_PyObject_CallNoArg(method); - Py_DECREF(method); -bad: - return result; -} - -/* RaiseNeedMoreValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -/* RaiseTooManyValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -/* UnpackItemEndCheck */ -static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { - if (unlikely(retval)) { - Py_DECREF(retval); - __Pyx_RaiseTooManyValuesError(expected); - return -1; - } - return __Pyx_IterFinish(); -} - -/* RaiseNoneIterError */ -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); -} - -/* UnpackTupleError */ -static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { - if (t == Py_None) { - __Pyx_RaiseNoneNotIterableError(); - } else if (PyTuple_GET_SIZE(t) < index) { - __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t)); - } else { - __Pyx_RaiseTooManyValuesError(index); - } -} - -/* UnpackTuple2 */ -static CYTHON_INLINE int __Pyx_unpack_tuple2_exact( - PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, int decref_tuple) { - PyObject *value1 = NULL, *value2 = NULL; -#if CYTHON_COMPILING_IN_PYPY - value1 = PySequence_ITEM(tuple, 0); if (unlikely(!value1)) goto bad; - value2 = PySequence_ITEM(tuple, 1); if (unlikely(!value2)) goto bad; -#else - value1 = PyTuple_GET_ITEM(tuple, 0); Py_INCREF(value1); - value2 = PyTuple_GET_ITEM(tuple, 1); Py_INCREF(value2); -#endif - if (decref_tuple) { - Py_DECREF(tuple); - } - *pvalue1 = value1; - *pvalue2 = value2; - return 0; -#if CYTHON_COMPILING_IN_PYPY -bad: - Py_XDECREF(value1); - Py_XDECREF(value2); - if (decref_tuple) { Py_XDECREF(tuple); } - return -1; -#endif -} -static int __Pyx_unpack_tuple2_generic(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, - int has_known_size, int decref_tuple) { - Py_ssize_t index; - PyObject *value1 = NULL, *value2 = NULL, *iter = NULL; - iternextfunc iternext; - iter = PyObject_GetIter(tuple); - if (unlikely(!iter)) goto bad; - if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; } - iternext = Py_TYPE(iter)->tp_iternext; - value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; } - value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; } - if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad; - Py_DECREF(iter); - *pvalue1 = value1; - *pvalue2 = value2; - return 0; -unpacking_failed: - if (!has_known_size && __Pyx_IterFinish() == 0) - __Pyx_RaiseNeedMoreValuesError(index); -bad: - Py_XDECREF(iter); - Py_XDECREF(value1); - Py_XDECREF(value2); - if (decref_tuple) { Py_XDECREF(tuple); } - return -1; -} - -/* dict_iter */ -static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name, - Py_ssize_t* p_orig_length, int* p_source_is_dict) { - is_dict = is_dict || likely(PyDict_CheckExact(iterable)); - *p_source_is_dict = is_dict; - if (is_dict) { -#if !CYTHON_COMPILING_IN_PYPY - *p_orig_length = PyDict_Size(iterable); - Py_INCREF(iterable); - return iterable; -#elif PY_MAJOR_VERSION >= 3 - static PyObject *py_items = NULL, *py_keys = NULL, *py_values = NULL; - PyObject **pp = NULL; - if (method_name) { - const char *name = PyUnicode_AsUTF8(method_name); - if (strcmp(name, "iteritems") == 0) pp = &py_items; - else if (strcmp(name, "iterkeys") == 0) pp = &py_keys; - else if (strcmp(name, "itervalues") == 0) pp = &py_values; - if (pp) { - if (!*pp) { - *pp = PyUnicode_FromString(name + 4); - if (!*pp) - return NULL; - } - method_name = *pp; - } - } -#endif - } - *p_orig_length = 0; - if (method_name) { - PyObject* iter; - iterable = __Pyx_PyObject_CallMethod0(iterable, method_name); - if (!iterable) - return NULL; -#if !CYTHON_COMPILING_IN_PYPY - if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable)) - return iterable; -#endif - iter = PyObject_GetIter(iterable); - Py_DECREF(iterable); - return iter; - } - return PyObject_GetIter(iterable); -} -static CYTHON_INLINE int __Pyx_dict_iter_next( - PyObject* iter_obj, CYTHON_NCP_UNUSED Py_ssize_t orig_length, CYTHON_NCP_UNUSED Py_ssize_t* ppos, - PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) { - PyObject* next_item; -#if !CYTHON_COMPILING_IN_PYPY - if (source_is_dict) { - PyObject *key, *value; - if (unlikely(orig_length != PyDict_Size(iter_obj))) { - PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration"); - return -1; - } - if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) { - return 0; - } - if (pitem) { - PyObject* tuple = PyTuple_New(2); - if (unlikely(!tuple)) { - return -1; - } - Py_INCREF(key); - Py_INCREF(value); - PyTuple_SET_ITEM(tuple, 0, key); - PyTuple_SET_ITEM(tuple, 1, value); - *pitem = tuple; - } else { - if (pkey) { - Py_INCREF(key); - *pkey = key; - } - if (pvalue) { - Py_INCREF(value); - *pvalue = value; - } - } - return 1; - } else if (PyTuple_CheckExact(iter_obj)) { - Py_ssize_t pos = *ppos; - if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0; - *ppos = pos + 1; - next_item = PyTuple_GET_ITEM(iter_obj, pos); - Py_INCREF(next_item); - } else if (PyList_CheckExact(iter_obj)) { - Py_ssize_t pos = *ppos; - if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0; - *ppos = pos + 1; - next_item = PyList_GET_ITEM(iter_obj, pos); - Py_INCREF(next_item); - } else -#endif - { - next_item = PyIter_Next(iter_obj); - if (unlikely(!next_item)) { - return __Pyx_IterFinish(); - } - } - if (pitem) { - *pitem = next_item; - } else if (pkey && pvalue) { - if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1)) - return -1; - } else if (pkey) { - *pkey = next_item; - } else { - *pvalue = next_item; - } - return 1; -} - -/* MergeKeywords */ -static int __Pyx_MergeKeywords(PyObject *kwdict, PyObject *source_mapping) { - PyObject *iter, *key = NULL, *value = NULL; - int source_is_dict, result; - Py_ssize_t orig_length, ppos = 0; - iter = __Pyx_dict_iterator(source_mapping, 0, __pyx_n_s_items, &orig_length, &source_is_dict); - if (unlikely(!iter)) { - PyObject *args; - if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad; - PyErr_Clear(); - args = PyTuple_Pack(1, source_mapping); - if (likely(args)) { - PyObject *fallback = PyObject_Call((PyObject*)&PyDict_Type, args, NULL); - Py_DECREF(args); - if (likely(fallback)) { - iter = __Pyx_dict_iterator(fallback, 1, __pyx_n_s_items, &orig_length, &source_is_dict); - Py_DECREF(fallback); - } - } - if (unlikely(!iter)) goto bad; - } - while (1) { - result = __Pyx_dict_iter_next(iter, orig_length, &ppos, &key, &value, NULL, source_is_dict); - if (unlikely(result < 0)) goto bad; - if (!result) break; - if (unlikely(PyDict_Contains(kwdict, key))) { - __Pyx_RaiseDoubleKeywordsError("function", key); - result = -1; - } else { - result = PyDict_SetItem(kwdict, key, value); - } - Py_DECREF(key); - Py_DECREF(value); - if (unlikely(result < 0)) goto bad; - } - Py_XDECREF(iter); - return 0; -bad: - Py_XDECREF(iter); - return -1; -} - -/* FastTypeChecks */ -#if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; - if (a == b) - return 1; - } - return b == &PyBaseObject_Type; -} -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { - PyObject *mro; - if (a == b) return 1; - mro = a->tp_mro; - if (likely(mro)) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(mro); - for (i = 0; i < n; i++) { - if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) - return 1; - } - return 0; - } - return __Pyx_InBases(a, b); -} -#if PY_MAJOR_VERSION == 2 -static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { - PyObject *exception, *value, *tb; - int res; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&exception, &value, &tb); - res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - if (!res) { - res = PyObject_IsSubclass(err, exc_type2); - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - } - __Pyx_ErrRestore(exception, value, tb); - return res; -} -#else -static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { - int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; - if (!res) { - res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); - } - return res; -} -#endif -static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - assert(PyExceptionClass_Check(exc_type)); - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; iob_shash; - hash2 = ((PyBytesObject*)s2)->ob_shash; - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - return (equals == Py_NE); - } -#endif - result = memcmp(ps1, ps2, (size_t)length); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -#endif -} - -/* UnicodeEquals */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else -#if PY_MAJOR_VERSION < 3 - PyObject* owned_ref = NULL; -#endif - int s1_is_unicode, s2_is_unicode; - if (s1 == s2) { - goto return_eq; - } - s1_is_unicode = PyUnicode_CheckExact(s1); - s2_is_unicode = PyUnicode_CheckExact(s2); -#if PY_MAJOR_VERSION < 3 - if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { - owned_ref = PyUnicode_FromObject(s2); - if (unlikely(!owned_ref)) - return -1; - s2 = owned_ref; - s2_is_unicode = 1; - } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { - owned_ref = PyUnicode_FromObject(s1); - if (unlikely(!owned_ref)) - return -1; - s1 = owned_ref; - s1_is_unicode = 1; - } else if (((!s2_is_unicode) & (!s1_is_unicode))) { - return __Pyx_PyBytes_Equals(s1, s2, equals); - } -#endif - if (s1_is_unicode & s2_is_unicode) { - Py_ssize_t length; - int kind; - void *data1, *data2; - if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) - return -1; - length = __Pyx_PyUnicode_GET_LENGTH(s1); - if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { - goto return_ne; - } -#if CYTHON_USE_UNICODE_INTERNALS - { - Py_hash_t hash1, hash2; - #if CYTHON_PEP393_ENABLED - hash1 = ((PyASCIIObject*)s1)->hash; - hash2 = ((PyASCIIObject*)s2)->hash; - #else - hash1 = ((PyUnicodeObject*)s1)->hash; - hash2 = ((PyUnicodeObject*)s2)->hash; - #endif - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - goto return_ne; - } - } -#endif - kind = __Pyx_PyUnicode_KIND(s1); - if (kind != __Pyx_PyUnicode_KIND(s2)) { - goto return_ne; - } - data1 = __Pyx_PyUnicode_DATA(s1); - data2 = __Pyx_PyUnicode_DATA(s2); - if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { - goto return_ne; - } else if (length == 1) { - goto return_eq; - } else { - int result = memcmp(data1, data2, (size_t)(length * kind)); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & s2_is_unicode) { - goto return_ne; - } else if ((s2 == Py_None) & s1_is_unicode) { - goto return_ne; - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -return_eq: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ); -return_ne: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_NE); -#endif -} - -/* GetException */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* PyObject_GenericGetAttrNoDict */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { - PyErr_Format(PyExc_AttributeError, -#if PY_MAJOR_VERSION >= 3 - "'%.50s' object has no attribute '%U'", - tp->tp_name, attr_name); -#else - "'%.50s' object has no attribute '%.400s'", - tp->tp_name, PyString_AS_STRING(attr_name)); -#endif - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { - PyObject *descr; - PyTypeObject *tp = Py_TYPE(obj); - if (unlikely(!PyString_Check(attr_name))) { - return PyObject_GenericGetAttr(obj, attr_name); - } - assert(!tp->tp_dictoffset); - descr = _PyType_Lookup(tp, attr_name); - if (unlikely(!descr)) { - return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); - } - Py_INCREF(descr); - #if PY_MAJOR_VERSION < 3 - if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) - #endif - { - descrgetfunc f = Py_TYPE(descr)->tp_descr_get; - if (unlikely(f)) { - PyObject *res = f(descr, obj, (PyObject *)tp); - Py_DECREF(descr); - return res; - } - } - return descr; -} -#endif - -/* PyObject_GenericGetAttr */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { - if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { - return PyObject_GenericGetAttr(obj, attr_name); - } - return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); -} -#endif - -/* PyObjectGetAttrStrNoError */ -static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - __Pyx_PyErr_Clear(); -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { - PyObject *result; -#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 - PyTypeObject* tp = Py_TYPE(obj); - if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { - return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); - } -#endif - result = __Pyx_PyObject_GetAttrStr(obj, attr_name); - if (unlikely(!result)) { - __Pyx_PyObject_GetAttrStr_ClearAttributeError(); - } - return result; -} - -/* SetupReduce */ -static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { - int ret; - PyObject *name_attr; - name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name); - if (likely(name_attr)) { - ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); - } else { - ret = -1; - } - if (unlikely(ret < 0)) { - PyErr_Clear(); - ret = 0; - } - Py_XDECREF(name_attr); - return ret; -} -static int __Pyx_setup_reduce(PyObject* type_obj) { - int ret = 0; - PyObject *object_reduce = NULL; - PyObject *object_getstate = NULL; - PyObject *object_reduce_ex = NULL; - PyObject *reduce = NULL; - PyObject *reduce_ex = NULL; - PyObject *reduce_cython = NULL; - PyObject *setstate = NULL; - PyObject *setstate_cython = NULL; - PyObject *getstate = NULL; -#if CYTHON_USE_PYTYPE_LOOKUP - getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate); -#else - getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate); - if (!getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (getstate) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate); -#else - object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate); - if (!object_getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (object_getstate != getstate) { - goto __PYX_GOOD; - } - } -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; - if (reduce_ex == object_reduce_ex) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; - if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); - if (likely(reduce_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (reduce == object_reduce || PyErr_Occurred()) { - goto __PYX_BAD; - } - setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); - if (!setstate) PyErr_Clear(); - if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); - if (likely(setstate_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (!setstate || PyErr_Occurred()) { - goto __PYX_BAD; - } - } - PyType_Modified((PyTypeObject*)type_obj); - } - } - goto __PYX_GOOD; -__PYX_BAD: - if (!PyErr_Occurred()) - PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); - ret = -1; -__PYX_GOOD: -#if !CYTHON_USE_PYTYPE_LOOKUP - Py_XDECREF(object_reduce); - Py_XDECREF(object_reduce_ex); - Py_XDECREF(object_getstate); - Py_XDECREF(getstate); -#endif - Py_XDECREF(reduce); - Py_XDECREF(reduce_ex); - Py_XDECREF(reduce_cython); - Py_XDECREF(setstate); - Py_XDECREF(setstate_cython); - return ret; -} - -/* TypeImport */ -#ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* Import */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* ImportFrom */ -static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { - PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); - if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_Format(PyExc_ImportError, - #if PY_MAJOR_VERSION < 3 - "cannot import name %.230s", PyString_AS_STRING(name)); - #else - "cannot import name %S", name); - #endif - } - return value; -} - -/* ClassMethod */ -static PyObject* __Pyx_Method_ClassMethod(PyObject *method) { -#if CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM <= 0x05080000 - if (PyObject_TypeCheck(method, &PyWrapperDescr_Type)) { - return PyClassMethod_New(method); - } -#else -#if CYTHON_COMPILING_IN_PYSTON || CYTHON_COMPILING_IN_PYPY - if (PyMethodDescr_Check(method)) -#else - #if PY_MAJOR_VERSION == 2 - static PyTypeObject *methoddescr_type = NULL; - if (methoddescr_type == NULL) { - PyObject *meth = PyObject_GetAttrString((PyObject*)&PyList_Type, "append"); - if (!meth) return NULL; - methoddescr_type = Py_TYPE(meth); - Py_DECREF(meth); - } - #else - PyTypeObject *methoddescr_type = &PyMethodDescr_Type; - #endif - if (__Pyx_TypeCheck(method, methoddescr_type)) -#endif - { - PyMethodDescrObject *descr = (PyMethodDescrObject *)method; - #if PY_VERSION_HEX < 0x03020000 - PyTypeObject *d_type = descr->d_type; - #else - PyTypeObject *d_type = descr->d_common.d_type; - #endif - return PyDescr_NewClassMethod(d_type, descr->d_method); - } -#endif - else if (PyMethod_Check(method)) { - return PyClassMethod_New(PyMethod_GET_FUNCTION(method)); - } - else { - return PyClassMethod_New(method); - } -} - -/* GetNameInClass */ -static PyObject *__Pyx_GetGlobalNameAfterAttributeLookup(PyObject *name) { - PyObject *result; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - return NULL; - __Pyx_PyErr_Clear(); - __Pyx_GetModuleGlobalNameUncached(result, name); - return result; -} -static PyObject *__Pyx__GetNameInClass(PyObject *nmspace, PyObject *name) { - PyObject *result; - result = __Pyx_PyObject_GetAttrStr(nmspace, name); - if (!result) { - result = __Pyx_GetGlobalNameAfterAttributeLookup(name); - } - return result; -} - -/* CLineInTraceback */ -#ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ -#include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -/* CIntFromPyVerify */ -#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* Declarations */ -#if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ -#if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ -#if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ -#if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* CIntFromPy */ -static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(uint64_t) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(uint64_t, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (uint64_t) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (uint64_t) 0; - case 1: __PYX_VERIFY_RETURN_INT(uint64_t, digit, digits[0]) - case 2: - if (8 * sizeof(uint64_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(uint64_t) >= 2 * PyLong_SHIFT) { - return (uint64_t) (((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(uint64_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(uint64_t) >= 3 * PyLong_SHIFT) { - return (uint64_t) (((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(uint64_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(uint64_t) >= 4 * PyLong_SHIFT) { - return (uint64_t) (((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (uint64_t) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(uint64_t) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (uint64_t) 0; - case -1: __PYX_VERIFY_RETURN_INT(uint64_t, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(uint64_t, digit, +digits[0]) - case -2: - if (8 * sizeof(uint64_t) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(uint64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT) { - return (uint64_t) (((uint64_t)-1)*(((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(uint64_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT) { - return (uint64_t) ((((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(uint64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT) { - return (uint64_t) (((uint64_t)-1)*(((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(uint64_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT) { - return (uint64_t) ((((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(uint64_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(uint64_t) - 1 > 4 * PyLong_SHIFT) { - return (uint64_t) (((uint64_t)-1)*(((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(uint64_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(uint64_t) - 1 > 4 * PyLong_SHIFT) { - return (uint64_t) ((((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); - } - } - break; - } -#endif - if (sizeof(uint64_t) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(uint64_t, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(uint64_t, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - uint64_t val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (uint64_t) -1; - } - } else { - uint64_t val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (uint64_t) -1; - val = __Pyx_PyInt_As_uint64_t(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to uint64_t"); - return (uint64_t) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to uint64_t"); - return (uint64_t) -1; -} - -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(uint64_t) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(uint64_t) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(uint64_t) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(uint64_t), - little, !is_unsigned); - } -} - -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int64_t) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int64_t) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int64_t) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int64_t), - little, !is_unsigned); - } -} - -/* CIntFromPy */ -static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int64_t) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int64_t, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int64_t) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int64_t) 0; - case 1: __PYX_VERIFY_RETURN_INT(int64_t, digit, digits[0]) - case 2: - if (8 * sizeof(int64_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) >= 2 * PyLong_SHIFT) { - return (int64_t) (((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int64_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) >= 3 * PyLong_SHIFT) { - return (int64_t) (((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int64_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) >= 4 * PyLong_SHIFT) { - return (int64_t) (((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int64_t) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int64_t) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int64_t) 0; - case -1: __PYX_VERIFY_RETURN_INT(int64_t, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int64_t, digit, +digits[0]) - case -2: - if (8 * sizeof(int64_t) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { - return (int64_t) (((int64_t)-1)*(((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int64_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { - return (int64_t) ((((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { - return (int64_t) (((int64_t)-1)*(((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int64_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { - return (int64_t) ((((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT) { - return (int64_t) (((int64_t)-1)*(((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int64_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT) { - return (int64_t) ((((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int64_t) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int64_t, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int64_t, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int64_t val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int64_t) -1; - } - } else { - int64_t val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int64_t) -1; - val = __Pyx_PyInt_As_int64_t(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int64_t"); - return (int64_t) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int64_t"); - return (int64_t) -1; -} - -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPy */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntFromPy */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* FetchCommonType */ -static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { - PyObject* fake_module; - PyTypeObject* cached_type = NULL; - fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI); - if (!fake_module) return NULL; - Py_INCREF(fake_module); - cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name); - if (cached_type) { - if (!PyType_Check((PyObject*)cached_type)) { - PyErr_Format(PyExc_TypeError, - "Shared Cython type %.200s is not a type object", - type->tp_name); - goto bad; - } - if (cached_type->tp_basicsize != type->tp_basicsize) { - PyErr_Format(PyExc_TypeError, - "Shared Cython type %.200s has the wrong size, try recompiling", - type->tp_name); - goto bad; - } - } else { - if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad; - PyErr_Clear(); - if (PyType_Ready(type) < 0) goto bad; - if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0) - goto bad; - Py_INCREF(type); - cached_type = type; - } -done: - Py_DECREF(fake_module); - return cached_type; -bad: - Py_XDECREF(cached_type); - cached_type = NULL; - goto done; -} - -/* SwapException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = *type; - exc_info->exc_value = *value; - exc_info->exc_traceback = *tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = *type; - tstate->exc_value = *value; - tstate->exc_traceback = *tb; - #endif - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); - PyErr_SetExcInfo(*type, *value, *tb); - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#endif - -/* PyObjectCallMethod1 */ -static PyObject* __Pyx__PyObject_CallMethod1(PyObject* method, PyObject* arg) { - PyObject *result = __Pyx_PyObject_CallOneArg(method, arg); - Py_DECREF(method); - return result; -} -static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) { - PyObject *method = NULL, *result; - int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method); - if (likely(is_method)) { - result = __Pyx_PyObject_Call2Args(method, obj, arg); - Py_DECREF(method); - return result; - } - if (unlikely(!method)) return NULL; - return __Pyx__PyObject_CallMethod1(method, arg); -} - -/* CoroutineBase */ -#include -#include -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -#define __Pyx_Coroutine_Undelegate(gen) Py_CLEAR((gen)->yieldfrom) -static int __Pyx_PyGen__FetchStopIterationValue(CYTHON_UNUSED PyThreadState *__pyx_tstate, PyObject **pvalue) { - PyObject *et, *ev, *tb; - PyObject *value = NULL; - __Pyx_ErrFetch(&et, &ev, &tb); - if (!et) { - Py_XDECREF(tb); - Py_XDECREF(ev); - Py_INCREF(Py_None); - *pvalue = Py_None; - return 0; - } - if (likely(et == PyExc_StopIteration)) { - if (!ev) { - Py_INCREF(Py_None); - value = Py_None; - } -#if PY_VERSION_HEX >= 0x030300A0 - else if (Py_TYPE(ev) == (PyTypeObject*)PyExc_StopIteration) { - value = ((PyStopIterationObject *)ev)->value; - Py_INCREF(value); - Py_DECREF(ev); - } -#endif - else if (unlikely(PyTuple_Check(ev))) { - if (PyTuple_GET_SIZE(ev) >= 1) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - value = PyTuple_GET_ITEM(ev, 0); - Py_INCREF(value); -#else - value = PySequence_ITEM(ev, 0); -#endif - } else { - Py_INCREF(Py_None); - value = Py_None; - } - Py_DECREF(ev); - } - else if (!__Pyx_TypeCheck(ev, (PyTypeObject*)PyExc_StopIteration)) { - value = ev; - } - if (likely(value)) { - Py_XDECREF(tb); - Py_DECREF(et); - *pvalue = value; - return 0; - } - } else if (!__Pyx_PyErr_GivenExceptionMatches(et, PyExc_StopIteration)) { - __Pyx_ErrRestore(et, ev, tb); - return -1; - } - PyErr_NormalizeException(&et, &ev, &tb); - if (unlikely(!PyObject_TypeCheck(ev, (PyTypeObject*)PyExc_StopIteration))) { - __Pyx_ErrRestore(et, ev, tb); - return -1; - } - Py_XDECREF(tb); - Py_DECREF(et); -#if PY_VERSION_HEX >= 0x030300A0 - value = ((PyStopIterationObject *)ev)->value; - Py_INCREF(value); - Py_DECREF(ev); -#else - { - PyObject* args = __Pyx_PyObject_GetAttrStr(ev, __pyx_n_s_args); - Py_DECREF(ev); - if (likely(args)) { - value = PySequence_GetItem(args, 0); - Py_DECREF(args); - } - if (unlikely(!value)) { - __Pyx_ErrRestore(NULL, NULL, NULL); - Py_INCREF(Py_None); - value = Py_None; - } - } -#endif - *pvalue = value; - return 0; -} -static CYTHON_INLINE -void __Pyx_Coroutine_ExceptionClear(__Pyx_ExcInfoStruct *exc_state) { - PyObject *t, *v, *tb; - t = exc_state->exc_type; - v = exc_state->exc_value; - tb = exc_state->exc_traceback; - exc_state->exc_type = NULL; - exc_state->exc_value = NULL; - exc_state->exc_traceback = NULL; - Py_XDECREF(t); - Py_XDECREF(v); - Py_XDECREF(tb); -} -#define __Pyx_Coroutine_AlreadyRunningError(gen) (__Pyx__Coroutine_AlreadyRunningError(gen), (PyObject*)NULL) -static void __Pyx__Coroutine_AlreadyRunningError(CYTHON_UNUSED __pyx_CoroutineObject *gen) { - const char *msg; - if ((0)) { - #ifdef __Pyx_Coroutine_USED - } else if (__Pyx_Coroutine_Check((PyObject*)gen)) { - msg = "coroutine already executing"; - #endif - #ifdef __Pyx_AsyncGen_USED - } else if (__Pyx_AsyncGen_CheckExact((PyObject*)gen)) { - msg = "async generator already executing"; - #endif - } else { - msg = "generator already executing"; - } - PyErr_SetString(PyExc_ValueError, msg); -} -#define __Pyx_Coroutine_NotStartedError(gen) (__Pyx__Coroutine_NotStartedError(gen), (PyObject*)NULL) -static void __Pyx__Coroutine_NotStartedError(CYTHON_UNUSED PyObject *gen) { - const char *msg; - if ((0)) { - #ifdef __Pyx_Coroutine_USED - } else if (__Pyx_Coroutine_Check(gen)) { - msg = "can't send non-None value to a just-started coroutine"; - #endif - #ifdef __Pyx_AsyncGen_USED - } else if (__Pyx_AsyncGen_CheckExact(gen)) { - msg = "can't send non-None value to a just-started async generator"; - #endif - } else { - msg = "can't send non-None value to a just-started generator"; - } - PyErr_SetString(PyExc_TypeError, msg); -} -#define __Pyx_Coroutine_AlreadyTerminatedError(gen, value, closing) (__Pyx__Coroutine_AlreadyTerminatedError(gen, value, closing), (PyObject*)NULL) -static void __Pyx__Coroutine_AlreadyTerminatedError(CYTHON_UNUSED PyObject *gen, PyObject *value, CYTHON_UNUSED int closing) { - #ifdef __Pyx_Coroutine_USED - if (!closing && __Pyx_Coroutine_Check(gen)) { - PyErr_SetString(PyExc_RuntimeError, "cannot reuse already awaited coroutine"); - } else - #endif - if (value) { - #ifdef __Pyx_AsyncGen_USED - if (__Pyx_AsyncGen_CheckExact(gen)) - PyErr_SetNone(__Pyx_PyExc_StopAsyncIteration); - else - #endif - PyErr_SetNone(PyExc_StopIteration); - } -} -static -PyObject *__Pyx_Coroutine_SendEx(__pyx_CoroutineObject *self, PyObject *value, int closing) { - __Pyx_PyThreadState_declare - PyThreadState *tstate; - __Pyx_ExcInfoStruct *exc_state; - PyObject *retval; - assert(!self->is_running); - if (unlikely(self->resume_label == 0)) { - if (unlikely(value && value != Py_None)) { - return __Pyx_Coroutine_NotStartedError((PyObject*)self); - } - } - if (unlikely(self->resume_label == -1)) { - return __Pyx_Coroutine_AlreadyTerminatedError((PyObject*)self, value, closing); - } -#if CYTHON_FAST_THREAD_STATE - __Pyx_PyThreadState_assign - tstate = __pyx_tstate; -#else - tstate = __Pyx_PyThreadState_Current; -#endif - exc_state = &self->gi_exc_state; - if (exc_state->exc_type) { - #if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_PYSTON - #else - if (exc_state->exc_traceback) { - PyTracebackObject *tb = (PyTracebackObject *) exc_state->exc_traceback; - PyFrameObject *f = tb->tb_frame; - assert(f->f_back == NULL); - #if PY_VERSION_HEX >= 0x030B00A1 - f->f_back = PyThreadState_GetFrame(tstate); - #else - Py_XINCREF(tstate->frame); - f->f_back = tstate->frame; - #endif - } - #endif - } -#if CYTHON_USE_EXC_INFO_STACK - exc_state->previous_item = tstate->exc_info; - tstate->exc_info = exc_state; -#else - if (exc_state->exc_type) { - __Pyx_ExceptionSwap(&exc_state->exc_type, &exc_state->exc_value, &exc_state->exc_traceback); - } else { - __Pyx_Coroutine_ExceptionClear(exc_state); - __Pyx_ExceptionSave(&exc_state->exc_type, &exc_state->exc_value, &exc_state->exc_traceback); - } -#endif - self->is_running = 1; - retval = self->body((PyObject *) self, tstate, value); - self->is_running = 0; -#if CYTHON_USE_EXC_INFO_STACK - exc_state = &self->gi_exc_state; - tstate->exc_info = exc_state->previous_item; - exc_state->previous_item = NULL; - __Pyx_Coroutine_ResetFrameBackpointer(exc_state); -#endif - return retval; -} -static CYTHON_INLINE void __Pyx_Coroutine_ResetFrameBackpointer(__Pyx_ExcInfoStruct *exc_state) { - PyObject *exc_tb = exc_state->exc_traceback; - if (likely(exc_tb)) { -#if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_PYSTON -#else - PyTracebackObject *tb = (PyTracebackObject *) exc_tb; - PyFrameObject *f = tb->tb_frame; - Py_CLEAR(f->f_back); -#endif - } -} -static CYTHON_INLINE -PyObject *__Pyx_Coroutine_MethodReturn(CYTHON_UNUSED PyObject* gen, PyObject *retval) { - if (unlikely(!retval)) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (!__Pyx_PyErr_Occurred()) { - PyObject *exc = PyExc_StopIteration; - #ifdef __Pyx_AsyncGen_USED - if (__Pyx_AsyncGen_CheckExact(gen)) - exc = __Pyx_PyExc_StopAsyncIteration; - #endif - __Pyx_PyErr_SetNone(exc); - } - } - return retval; -} -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3) -static CYTHON_INLINE -PyObject *__Pyx_PyGen_Send(PyGenObject *gen, PyObject *arg) { -#if PY_VERSION_HEX <= 0x030A00A1 - return _PyGen_Send(gen, arg); -#else - PyObject *result; - if (PyIter_Send((PyObject*)gen, arg ? arg : Py_None, &result) == PYGEN_RETURN) { - if (PyAsyncGen_CheckExact(gen)) { - assert(result == Py_None); - PyErr_SetNone(PyExc_StopAsyncIteration); - } - else if (result == Py_None) { - PyErr_SetNone(PyExc_StopIteration); - } - else { - _PyGen_SetStopIterationValue(result); - } - Py_CLEAR(result); - } - return result; -#endif -} -#endif -static CYTHON_INLINE -PyObject *__Pyx_Coroutine_FinishDelegation(__pyx_CoroutineObject *gen) { - PyObject *ret; - PyObject *val = NULL; - __Pyx_Coroutine_Undelegate(gen); - __Pyx_PyGen__FetchStopIterationValue(__Pyx_PyThreadState_Current, &val); - ret = __Pyx_Coroutine_SendEx(gen, val, 0); - Py_XDECREF(val); - return ret; -} -static PyObject *__Pyx_Coroutine_Send(PyObject *self, PyObject *value) { - PyObject *retval; - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject*) self; - PyObject *yf = gen->yieldfrom; - if (unlikely(gen->is_running)) - return __Pyx_Coroutine_AlreadyRunningError(gen); - if (yf) { - PyObject *ret; - gen->is_running = 1; - #ifdef __Pyx_Generator_USED - if (__Pyx_Generator_CheckExact(yf)) { - ret = __Pyx_Coroutine_Send(yf, value); - } else - #endif - #ifdef __Pyx_Coroutine_USED - if (__Pyx_Coroutine_Check(yf)) { - ret = __Pyx_Coroutine_Send(yf, value); - } else - #endif - #ifdef __Pyx_AsyncGen_USED - if (__pyx_PyAsyncGenASend_CheckExact(yf)) { - ret = __Pyx_async_gen_asend_send(yf, value); - } else - #endif - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3) - if (PyGen_CheckExact(yf)) { - ret = __Pyx_PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value); - } else - #endif - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03050000 && defined(PyCoro_CheckExact) && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3) - if (PyCoro_CheckExact(yf)) { - ret = __Pyx_PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value); - } else - #endif - { - if (value == Py_None) - ret = Py_TYPE(yf)->tp_iternext(yf); - else - ret = __Pyx_PyObject_CallMethod1(yf, __pyx_n_s_send, value); - } - gen->is_running = 0; - if (likely(ret)) { - return ret; - } - retval = __Pyx_Coroutine_FinishDelegation(gen); - } else { - retval = __Pyx_Coroutine_SendEx(gen, value, 0); - } - return __Pyx_Coroutine_MethodReturn(self, retval); -} -static int __Pyx_Coroutine_CloseIter(__pyx_CoroutineObject *gen, PyObject *yf) { - PyObject *retval = NULL; - int err = 0; - #ifdef __Pyx_Generator_USED - if (__Pyx_Generator_CheckExact(yf)) { - retval = __Pyx_Coroutine_Close(yf); - if (!retval) - return -1; - } else - #endif - #ifdef __Pyx_Coroutine_USED - if (__Pyx_Coroutine_Check(yf)) { - retval = __Pyx_Coroutine_Close(yf); - if (!retval) - return -1; - } else - if (__Pyx_CoroutineAwait_CheckExact(yf)) { - retval = __Pyx_CoroutineAwait_Close((__pyx_CoroutineAwaitObject*)yf, NULL); - if (!retval) - return -1; - } else - #endif - #ifdef __Pyx_AsyncGen_USED - if (__pyx_PyAsyncGenASend_CheckExact(yf)) { - retval = __Pyx_async_gen_asend_close(yf, NULL); - } else - if (__pyx_PyAsyncGenAThrow_CheckExact(yf)) { - retval = __Pyx_async_gen_athrow_close(yf, NULL); - } else - #endif - { - PyObject *meth; - gen->is_running = 1; - meth = __Pyx_PyObject_GetAttrStr(yf, __pyx_n_s_close); - if (unlikely(!meth)) { - if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_WriteUnraisable(yf); - } - PyErr_Clear(); - } else { - retval = PyObject_CallFunction(meth, NULL); - Py_DECREF(meth); - if (!retval) - err = -1; - } - gen->is_running = 0; - } - Py_XDECREF(retval); - return err; -} -static PyObject *__Pyx_Generator_Next(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject*) self; - PyObject *yf = gen->yieldfrom; - if (unlikely(gen->is_running)) - return __Pyx_Coroutine_AlreadyRunningError(gen); - if (yf) { - PyObject *ret; - gen->is_running = 1; - #ifdef __Pyx_Generator_USED - if (__Pyx_Generator_CheckExact(yf)) { - ret = __Pyx_Generator_Next(yf); - } else - #endif - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3) - if (PyGen_CheckExact(yf)) { - ret = __Pyx_PyGen_Send((PyGenObject*)yf, NULL); - } else - #endif - #ifdef __Pyx_Coroutine_USED - if (__Pyx_Coroutine_Check(yf)) { - ret = __Pyx_Coroutine_Send(yf, Py_None); - } else - #endif - ret = Py_TYPE(yf)->tp_iternext(yf); - gen->is_running = 0; - if (likely(ret)) { - return ret; - } - return __Pyx_Coroutine_FinishDelegation(gen); - } - return __Pyx_Coroutine_SendEx(gen, Py_None, 0); -} -static PyObject *__Pyx_Coroutine_Close_Method(PyObject *self, CYTHON_UNUSED PyObject *arg) { - return __Pyx_Coroutine_Close(self); -} -static PyObject *__Pyx_Coroutine_Close(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; - PyObject *retval, *raised_exception; - PyObject *yf = gen->yieldfrom; - int err = 0; - if (unlikely(gen->is_running)) - return __Pyx_Coroutine_AlreadyRunningError(gen); - if (yf) { - Py_INCREF(yf); - err = __Pyx_Coroutine_CloseIter(gen, yf); - __Pyx_Coroutine_Undelegate(gen); - Py_DECREF(yf); - } - if (err == 0) - PyErr_SetNone(PyExc_GeneratorExit); - retval = __Pyx_Coroutine_SendEx(gen, NULL, 1); - if (unlikely(retval)) { - const char *msg; - Py_DECREF(retval); - if ((0)) { - #ifdef __Pyx_Coroutine_USED - } else if (__Pyx_Coroutine_Check(self)) { - msg = "coroutine ignored GeneratorExit"; - #endif - #ifdef __Pyx_AsyncGen_USED - } else if (__Pyx_AsyncGen_CheckExact(self)) { -#if PY_VERSION_HEX < 0x03060000 - msg = "async generator ignored GeneratorExit - might require Python 3.6+ finalisation (PEP 525)"; -#else - msg = "async generator ignored GeneratorExit"; -#endif - #endif - } else { - msg = "generator ignored GeneratorExit"; - } - PyErr_SetString(PyExc_RuntimeError, msg); - return NULL; - } - raised_exception = PyErr_Occurred(); - if (likely(!raised_exception || __Pyx_PyErr_GivenExceptionMatches2(raised_exception, PyExc_GeneratorExit, PyExc_StopIteration))) { - if (raised_exception) PyErr_Clear(); - Py_INCREF(Py_None); - return Py_None; - } - return NULL; -} -static PyObject *__Pyx__Coroutine_Throw(PyObject *self, PyObject *typ, PyObject *val, PyObject *tb, - PyObject *args, int close_on_genexit) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; - PyObject *yf = gen->yieldfrom; - if (unlikely(gen->is_running)) - return __Pyx_Coroutine_AlreadyRunningError(gen); - if (yf) { - PyObject *ret; - Py_INCREF(yf); - if (__Pyx_PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit) && close_on_genexit) { - int err = __Pyx_Coroutine_CloseIter(gen, yf); - Py_DECREF(yf); - __Pyx_Coroutine_Undelegate(gen); - if (err < 0) - return __Pyx_Coroutine_MethodReturn(self, __Pyx_Coroutine_SendEx(gen, NULL, 0)); - goto throw_here; - } - gen->is_running = 1; - if (0 - #ifdef __Pyx_Generator_USED - || __Pyx_Generator_CheckExact(yf) - #endif - #ifdef __Pyx_Coroutine_USED - || __Pyx_Coroutine_Check(yf) - #endif - ) { - ret = __Pyx__Coroutine_Throw(yf, typ, val, tb, args, close_on_genexit); - #ifdef __Pyx_Coroutine_USED - } else if (__Pyx_CoroutineAwait_CheckExact(yf)) { - ret = __Pyx__Coroutine_Throw(((__pyx_CoroutineAwaitObject*)yf)->coroutine, typ, val, tb, args, close_on_genexit); - #endif - } else { - PyObject *meth = __Pyx_PyObject_GetAttrStr(yf, __pyx_n_s_throw); - if (unlikely(!meth)) { - Py_DECREF(yf); - if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { - gen->is_running = 0; - return NULL; - } - PyErr_Clear(); - __Pyx_Coroutine_Undelegate(gen); - gen->is_running = 0; - goto throw_here; - } - if (likely(args)) { - ret = PyObject_CallObject(meth, args); - } else { - ret = PyObject_CallFunctionObjArgs(meth, typ, val, tb, NULL); - } - Py_DECREF(meth); - } - gen->is_running = 0; - Py_DECREF(yf); - if (!ret) { - ret = __Pyx_Coroutine_FinishDelegation(gen); - } - return __Pyx_Coroutine_MethodReturn(self, ret); - } -throw_here: - __Pyx_Raise(typ, val, tb, NULL); - return __Pyx_Coroutine_MethodReturn(self, __Pyx_Coroutine_SendEx(gen, NULL, 0)); -} -static PyObject *__Pyx_Coroutine_Throw(PyObject *self, PyObject *args) { - PyObject *typ; - PyObject *val = NULL; - PyObject *tb = NULL; - if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb)) - return NULL; - return __Pyx__Coroutine_Throw(self, typ, val, tb, args, 1); -} -static CYTHON_INLINE int __Pyx_Coroutine_traverse_excstate(__Pyx_ExcInfoStruct *exc_state, visitproc visit, void *arg) { - Py_VISIT(exc_state->exc_type); - Py_VISIT(exc_state->exc_value); - Py_VISIT(exc_state->exc_traceback); - return 0; -} -static int __Pyx_Coroutine_traverse(__pyx_CoroutineObject *gen, visitproc visit, void *arg) { - Py_VISIT(gen->closure); - Py_VISIT(gen->classobj); - Py_VISIT(gen->yieldfrom); - return __Pyx_Coroutine_traverse_excstate(&gen->gi_exc_state, visit, arg); -} -static int __Pyx_Coroutine_clear(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; - Py_CLEAR(gen->closure); - Py_CLEAR(gen->classobj); - Py_CLEAR(gen->yieldfrom); - __Pyx_Coroutine_ExceptionClear(&gen->gi_exc_state); -#ifdef __Pyx_AsyncGen_USED - if (__Pyx_AsyncGen_CheckExact(self)) { - Py_CLEAR(((__pyx_PyAsyncGenObject*)gen)->ag_finalizer); - } -#endif - Py_CLEAR(gen->gi_code); - Py_CLEAR(gen->gi_frame); - Py_CLEAR(gen->gi_name); - Py_CLEAR(gen->gi_qualname); - Py_CLEAR(gen->gi_modulename); - return 0; -} -static void __Pyx_Coroutine_dealloc(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; - PyObject_GC_UnTrack(gen); - if (gen->gi_weakreflist != NULL) - PyObject_ClearWeakRefs(self); - if (gen->resume_label >= 0) { - PyObject_GC_Track(self); -#if PY_VERSION_HEX >= 0x030400a1 && CYTHON_USE_TP_FINALIZE - if (PyObject_CallFinalizerFromDealloc(self)) -#else - Py_TYPE(gen)->tp_del(self); - if (Py_REFCNT(self) > 0) -#endif - { - return; - } - PyObject_GC_UnTrack(self); - } -#ifdef __Pyx_AsyncGen_USED - if (__Pyx_AsyncGen_CheckExact(self)) { - /* We have to handle this case for asynchronous generators - right here, because this code has to be between UNTRACK - and GC_Del. */ - Py_CLEAR(((__pyx_PyAsyncGenObject*)self)->ag_finalizer); - } -#endif - __Pyx_Coroutine_clear(self); - PyObject_GC_Del(gen); -} -static void __Pyx_Coroutine_del(PyObject *self) { - PyObject *error_type, *error_value, *error_traceback; - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; - __Pyx_PyThreadState_declare - if (gen->resume_label < 0) { - return; - } -#if !CYTHON_USE_TP_FINALIZE - assert(self->ob_refcnt == 0); - __Pyx_SET_REFCNT(self, 1); -#endif - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&error_type, &error_value, &error_traceback); -#ifdef __Pyx_AsyncGen_USED - if (__Pyx_AsyncGen_CheckExact(self)) { - __pyx_PyAsyncGenObject *agen = (__pyx_PyAsyncGenObject*)self; - PyObject *finalizer = agen->ag_finalizer; - if (finalizer && !agen->ag_closed) { - PyObject *res = __Pyx_PyObject_CallOneArg(finalizer, self); - if (unlikely(!res)) { - PyErr_WriteUnraisable(self); - } else { - Py_DECREF(res); - } - __Pyx_ErrRestore(error_type, error_value, error_traceback); - return; - } - } -#endif - if (unlikely(gen->resume_label == 0 && !error_value)) { -#ifdef __Pyx_Coroutine_USED -#ifdef __Pyx_Generator_USED - if (!__Pyx_Generator_CheckExact(self)) -#endif - { - PyObject_GC_UnTrack(self); -#if PY_MAJOR_VERSION >= 3 || defined(PyErr_WarnFormat) - if (unlikely(PyErr_WarnFormat(PyExc_RuntimeWarning, 1, "coroutine '%.50S' was never awaited", gen->gi_qualname) < 0)) - PyErr_WriteUnraisable(self); -#else - {PyObject *msg; - char *cmsg; - #if CYTHON_COMPILING_IN_PYPY - msg = NULL; - cmsg = (char*) "coroutine was never awaited"; - #else - char *cname; - PyObject *qualname; - qualname = gen->gi_qualname; - cname = PyString_AS_STRING(qualname); - msg = PyString_FromFormat("coroutine '%.50s' was never awaited", cname); - if (unlikely(!msg)) { - PyErr_Clear(); - cmsg = (char*) "coroutine was never awaited"; - } else { - cmsg = PyString_AS_STRING(msg); - } - #endif - if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, cmsg, 1) < 0)) - PyErr_WriteUnraisable(self); - Py_XDECREF(msg);} -#endif - PyObject_GC_Track(self); - } -#endif - } else { - PyObject *res = __Pyx_Coroutine_Close(self); - if (unlikely(!res)) { - if (PyErr_Occurred()) - PyErr_WriteUnraisable(self); - } else { - Py_DECREF(res); - } - } - __Pyx_ErrRestore(error_type, error_value, error_traceback); -#if !CYTHON_USE_TP_FINALIZE - assert(Py_REFCNT(self) > 0); - if (--self->ob_refcnt == 0) { - return; - } - { - Py_ssize_t refcnt = Py_REFCNT(self); - _Py_NewReference(self); - __Pyx_SET_REFCNT(self, refcnt); - } -#if CYTHON_COMPILING_IN_CPYTHON - assert(PyType_IS_GC(Py_TYPE(self)) && - _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED); - _Py_DEC_REFTOTAL; -#endif -#ifdef COUNT_ALLOCS - --Py_TYPE(self)->tp_frees; - --Py_TYPE(self)->tp_allocs; -#endif -#endif -} -static PyObject * -__Pyx_Coroutine_get_name(__pyx_CoroutineObject *self, CYTHON_UNUSED void *context) -{ - PyObject *name = self->gi_name; - if (unlikely(!name)) name = Py_None; - Py_INCREF(name); - return name; -} -static int -__Pyx_Coroutine_set_name(__pyx_CoroutineObject *self, PyObject *value, CYTHON_UNUSED void *context) -{ - PyObject *tmp; -#if PY_MAJOR_VERSION >= 3 - if (unlikely(value == NULL || !PyUnicode_Check(value))) -#else - if (unlikely(value == NULL || !PyString_Check(value))) -#endif - { - PyErr_SetString(PyExc_TypeError, - "__name__ must be set to a string object"); - return -1; - } - tmp = self->gi_name; - Py_INCREF(value); - self->gi_name = value; - Py_XDECREF(tmp); - return 0; -} -static PyObject * -__Pyx_Coroutine_get_qualname(__pyx_CoroutineObject *self, CYTHON_UNUSED void *context) -{ - PyObject *name = self->gi_qualname; - if (unlikely(!name)) name = Py_None; - Py_INCREF(name); - return name; -} -static int -__Pyx_Coroutine_set_qualname(__pyx_CoroutineObject *self, PyObject *value, CYTHON_UNUSED void *context) -{ - PyObject *tmp; -#if PY_MAJOR_VERSION >= 3 - if (unlikely(value == NULL || !PyUnicode_Check(value))) -#else - if (unlikely(value == NULL || !PyString_Check(value))) -#endif - { - PyErr_SetString(PyExc_TypeError, - "__qualname__ must be set to a string object"); - return -1; - } - tmp = self->gi_qualname; - Py_INCREF(value); - self->gi_qualname = value; - Py_XDECREF(tmp); - return 0; -} -static PyObject * -__Pyx_Coroutine_get_frame(__pyx_CoroutineObject *self, CYTHON_UNUSED void *context) -{ - PyObject *frame = self->gi_frame; - if (!frame) { - if (unlikely(!self->gi_code)) { - Py_RETURN_NONE; - } - frame = (PyObject *) PyFrame_New( - PyThreadState_Get(), /*PyThreadState *tstate,*/ - (PyCodeObject*) self->gi_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (unlikely(!frame)) - return NULL; - self->gi_frame = frame; - } - Py_INCREF(frame); - return frame; -} -static __pyx_CoroutineObject *__Pyx__Coroutine_New( - PyTypeObject* type, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure, - PyObject *name, PyObject *qualname, PyObject *module_name) { - __pyx_CoroutineObject *gen = PyObject_GC_New(__pyx_CoroutineObject, type); - if (unlikely(!gen)) - return NULL; - return __Pyx__Coroutine_NewInit(gen, body, code, closure, name, qualname, module_name); -} -static __pyx_CoroutineObject *__Pyx__Coroutine_NewInit( - __pyx_CoroutineObject *gen, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure, - PyObject *name, PyObject *qualname, PyObject *module_name) { - gen->body = body; - gen->closure = closure; - Py_XINCREF(closure); - gen->is_running = 0; - gen->resume_label = 0; - gen->classobj = NULL; - gen->yieldfrom = NULL; - gen->gi_exc_state.exc_type = NULL; - gen->gi_exc_state.exc_value = NULL; - gen->gi_exc_state.exc_traceback = NULL; -#if CYTHON_USE_EXC_INFO_STACK - gen->gi_exc_state.previous_item = NULL; -#endif - gen->gi_weakreflist = NULL; - Py_XINCREF(qualname); - gen->gi_qualname = qualname; - Py_XINCREF(name); - gen->gi_name = name; - Py_XINCREF(module_name); - gen->gi_modulename = module_name; - Py_XINCREF(code); - gen->gi_code = code; - gen->gi_frame = NULL; - PyObject_GC_Track(gen); - return gen; -} - -/* PatchModuleWithCoroutine */ -static PyObject* __Pyx_Coroutine_patch_module(PyObject* module, const char* py_code) { -#if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) - int result; - PyObject *globals, *result_obj; - globals = PyDict_New(); if (unlikely(!globals)) goto ignore; - result = PyDict_SetItemString(globals, "_cython_coroutine_type", - #ifdef __Pyx_Coroutine_USED - (PyObject*)__pyx_CoroutineType); - #else - Py_None); - #endif - if (unlikely(result < 0)) goto ignore; - result = PyDict_SetItemString(globals, "_cython_generator_type", - #ifdef __Pyx_Generator_USED - (PyObject*)__pyx_GeneratorType); - #else - Py_None); - #endif - if (unlikely(result < 0)) goto ignore; - if (unlikely(PyDict_SetItemString(globals, "_module", module) < 0)) goto ignore; - if (unlikely(PyDict_SetItemString(globals, "__builtins__", __pyx_b) < 0)) goto ignore; - result_obj = PyRun_String(py_code, Py_file_input, globals, globals); - if (unlikely(!result_obj)) goto ignore; - Py_DECREF(result_obj); - Py_DECREF(globals); - return module; -ignore: - Py_XDECREF(globals); - PyErr_WriteUnraisable(module); - if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, "Cython module failed to patch module with custom type", 1) < 0)) { - Py_DECREF(module); - module = NULL; - } -#else - py_code++; -#endif - return module; -} - -/* PatchGeneratorABC */ -#ifndef CYTHON_REGISTER_ABCS -#define CYTHON_REGISTER_ABCS 1 -#endif -#if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) -static PyObject* __Pyx_patch_abc_module(PyObject *module); -static PyObject* __Pyx_patch_abc_module(PyObject *module) { - module = __Pyx_Coroutine_patch_module( - module, "" -"if _cython_generator_type is not None:\n" -" try: Generator = _module.Generator\n" -" except AttributeError: pass\n" -" else: Generator.register(_cython_generator_type)\n" -"if _cython_coroutine_type is not None:\n" -" try: Coroutine = _module.Coroutine\n" -" except AttributeError: pass\n" -" else: Coroutine.register(_cython_coroutine_type)\n" - ); - return module; -} -#endif -static int __Pyx_patch_abc(void) { -#if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) - static int abc_patched = 0; - if (CYTHON_REGISTER_ABCS && !abc_patched) { - PyObject *module; - module = PyImport_ImportModule((PY_MAJOR_VERSION >= 3) ? "collections.abc" : "collections"); - if (!module) { - PyErr_WriteUnraisable(NULL); - if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, - ((PY_MAJOR_VERSION >= 3) ? - "Cython module failed to register with collections.abc module" : - "Cython module failed to register with collections module"), 1) < 0)) { - return -1; - } - } else { - module = __Pyx_patch_abc_module(module); - abc_patched = 1; - if (unlikely(!module)) - return -1; - Py_DECREF(module); - } - module = PyImport_ImportModule("backports_abc"); - if (module) { - module = __Pyx_patch_abc_module(module); - Py_XDECREF(module); - } - if (!module) { - PyErr_Clear(); - } - } -#else - if ((0)) __Pyx_Coroutine_patch_module(NULL, NULL); -#endif - return 0; -} - -/* Generator */ -static PyMethodDef __pyx_Generator_methods[] = { - {"send", (PyCFunction) __Pyx_Coroutine_Send, METH_O, - (char*) PyDoc_STR("send(arg) -> send 'arg' into generator,\nreturn next yielded value or raise StopIteration.")}, - {"throw", (PyCFunction) __Pyx_Coroutine_Throw, METH_VARARGS, - (char*) PyDoc_STR("throw(typ[,val[,tb]]) -> raise exception in generator,\nreturn next yielded value or raise StopIteration.")}, - {"close", (PyCFunction) __Pyx_Coroutine_Close_Method, METH_NOARGS, - (char*) PyDoc_STR("close() -> raise GeneratorExit inside generator.")}, - {0, 0, 0, 0} -}; 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#define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #undef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 0 - #undef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 0 - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 - #endif -#elif defined(PY_NOGIL) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 1 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #ifndef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 1 - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 1 - #endif - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 -#else - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 1 - #define CYTHON_COMPILING_IN_NOGIL 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #elif !defined(CYTHON_USE_PYTYPE_LOOKUP) - #define CYTHON_USE_PYTYPE_LOOKUP 1 - #endif - #if PY_MAJOR_VERSION < 3 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #elif !defined(CYTHON_USE_PYLONG_INTERNALS) - #define CYTHON_USE_PYLONG_INTERNALS 1 - #endif - #ifndef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 1 - #endif - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #elif !defined(CYTHON_USE_UNICODE_WRITER) - #define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #elif !defined(CYTHON_FAST_THREAD_STATE) - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000) - #endif - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000) - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) - #endif - #ifndef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1) - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #elif !defined(CYTHON_USE_EXC_INFO_STACK) - #define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3) - #endif - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 - #endif -#endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #if PY_MAJOR_VERSION < 3 - #include "longintrepr.h" - #endif - #undef SHIFT - #undef BASE - #undef MASK - #ifdef SIZEOF_VOID_P - enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) }; - #endif -#endif -#ifndef __has_attribute - #define __has_attribute(x) 0 -#endif -#ifndef __has_cpp_attribute - #define __has_cpp_attribute(x) 0 -#endif -#ifndef CYTHON_RESTRICT - #if defined(__GNUC__) - #define CYTHON_RESTRICT __restrict__ - #elif defined(_MSC_VER) && _MSC_VER >= 1400 - #define CYTHON_RESTRICT __restrict - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_RESTRICT restrict - #else - #define CYTHON_RESTRICT - #endif -#endif -#ifndef CYTHON_UNUSED -# if defined(__GNUC__) -# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -#endif -#ifndef CYTHON_MAYBE_UNUSED_VAR -# if defined(__cplusplus) - template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } -# else -# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) -# endif -#endif -#ifndef CYTHON_NCP_UNUSED -# if CYTHON_COMPILING_IN_CPYTHON -# define CYTHON_NCP_UNUSED -# else -# define CYTHON_NCP_UNUSED CYTHON_UNUSED -# endif -#endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) -#ifdef _MSC_VER - #ifndef _MSC_STDINT_H_ - #if _MSC_VER < 1300 - typedef unsigned char uint8_t; - typedef unsigned int uint32_t; - #else - typedef unsigned __int8 uint8_t; - typedef unsigned __int32 uint32_t; - #endif - #endif -#else - #include -#endif -#ifndef CYTHON_FALLTHROUGH - #if defined(__cplusplus) && __cplusplus >= 201103L - #if __has_cpp_attribute(fallthrough) - #define CYTHON_FALLTHROUGH [[fallthrough]] - #elif __has_cpp_attribute(clang::fallthrough) - #define CYTHON_FALLTHROUGH [[clang::fallthrough]] - #elif __has_cpp_attribute(gnu::fallthrough) - #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] - #endif - #endif - #ifndef CYTHON_FALLTHROUGH - #if __has_attribute(fallthrough) - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - #else - #define CYTHON_FALLTHROUGH - #endif - #endif - #if defined(__clang__ ) && defined(__apple_build_version__) - #if __apple_build_version__ < 7000000 - #undef CYTHON_FALLTHROUGH - #define CYTHON_FALLTHROUGH - #endif - #endif -#endif - -#ifndef __cplusplus - #error "Cython files generated with the C++ option must be compiled with a C++ compiler." -#endif -#ifndef CYTHON_INLINE - #if defined(__clang__) - #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) - #else - #define CYTHON_INLINE inline - #endif -#endif -template -void __Pyx_call_destructor(T& x) { - x.~T(); -} -template -class __Pyx_FakeReference { - public: - __Pyx_FakeReference() : ptr(NULL) { } - __Pyx_FakeReference(const T& ref) : ptr(const_cast(&ref)) { } - T *operator->() { return ptr; } - T *operator&() { return ptr; } - operator T&() { return *ptr; } - template bool operator ==(U other) { return *ptr == other; } - template bool operator !=(U other) { return *ptr != other; } - private: - T *ptr; -}; - -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - if (type) { - PyErr_Restore(type, value, traceback); - } - return co; - } -#else - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_STACKLESS - #define METH_STACKLESS 0 -#endif -#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) - #ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - #endif - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); - typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast - #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1 - #define PyMem_RawMalloc(n) PyMem_Malloc(n) - #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) - #define PyMem_RawFree(p) PyMem_Free(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#elif PY_VERSION_HEX >= 0x03060000 - #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() -#elif PY_VERSION_HEX >= 0x03000000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#else - #define __Pyx_PyThreadState_Current _PyThreadState_Current -#endif -#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) -#include "pythread.h" -#define Py_tss_NEEDS_INIT 0 -typedef int Py_tss_t; -static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { - *key = PyThread_create_key(); - return 0; -} -static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { - Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); - *key = Py_tss_NEEDS_INIT; - return key; -} -static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { - PyObject_Free(key); -} -static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { - return *key != Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { - PyThread_delete_key(*key); - *key = Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { - return PyThread_set_key_value(*key, value); -} -static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { - return PyThread_get_key_value(*key); -} -#endif -#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) -#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) -#else -#define __Pyx_PyDict_NewPresized(n) PyDict_New() -#endif -#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION - #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) -#else - #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS -#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) -#else -#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_READY(op) (0) - #else - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #endif - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) - #else - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) - #endif - #endif -#else - #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 - #define __Pyx_PyUnicode_READY(op) (0) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) - #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) - #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) - #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) -#endif -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) -#else - #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ - PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) -#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? 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- default_encoding_c = PyBytes_AsString(default_encoding); - if (!default_encoding_c) goto bad; - if (strcmp(default_encoding_c, "ascii") == 0) { - __Pyx_sys_getdefaultencoding_not_ascii = 0; - } else { - char ascii_chars[128]; - int c; - for (c = 0; c < 128; c++) { - ascii_chars[c] = c; - } - __Pyx_sys_getdefaultencoding_not_ascii = 1; - ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); - if (!ascii_chars_u) goto bad; - ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); - if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { - PyErr_Format( - PyExc_ValueError, - "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", - default_encoding_c); - goto bad; - } - Py_DECREF(ascii_chars_u); - Py_DECREF(ascii_chars_b); - } - Py_DECREF(default_encoding); - return 0; -bad: - Py_XDECREF(default_encoding); - Py_XDECREF(ascii_chars_u); 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- #include "frameobject.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif - #define __Pxy_PyFrame_Initialize_Offsets()\ - ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\ - (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus))) - #define __Pyx_PyFrame_GetLocalsplus(frame)\ - (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset)) -#endif // CYTHON_FAST_PYCALL -#endif - -/* PyObjectCall.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); -#else -#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) -#endif - -/* PyObjectCall2Args.proto */ -static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2); - -/* PyObjectCallMethO.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); -#endif - -/* PyObjectCallOneArg.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); - -/* IncludeStringH.proto */ -#include - -/* MemviewSliceInit.proto */ -#define __Pyx_BUF_MAX_NDIMS %(BUF_MAX_NDIMS)d -#define __Pyx_MEMVIEW_DIRECT 1 -#define __Pyx_MEMVIEW_PTR 2 -#define __Pyx_MEMVIEW_FULL 4 -#define __Pyx_MEMVIEW_CONTIG 8 -#define __Pyx_MEMVIEW_STRIDED 16 -#define __Pyx_MEMVIEW_FOLLOW 32 -#define __Pyx_IS_C_CONTIG 1 -#define __Pyx_IS_F_CONTIG 2 -static int __Pyx_init_memviewslice( - struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference); -static CYTHON_INLINE int __pyx_add_acquisition_count_locked( - __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); -static CYTHON_INLINE int __pyx_sub_acquisition_count_locked( - __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); -#define __pyx_get_slice_count_pointer(memview) (memview->acquisition_count_aligned_p) -#define __pyx_get_slice_count(memview) (*__pyx_get_slice_count_pointer(memview)) -#define __PYX_INC_MEMVIEW(slice, have_gil) __Pyx_INC_MEMVIEW(slice, have_gil, __LINE__) -#define __PYX_XDEC_MEMVIEW(slice, have_gil) __Pyx_XDEC_MEMVIEW(slice, have_gil, __LINE__) -static CYTHON_INLINE void __Pyx_INC_MEMVIEW(__Pyx_memviewslice *, int, int); -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *, int, int); - -/* GetTopmostException.proto */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate); -#endif - -/* PyThreadStateGet.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate; -#define __Pyx_PyThreadState_assign __pyx_tstate = __Pyx_PyThreadState_Current; -#define __Pyx_PyErr_Occurred() __pyx_tstate->curexc_type -#else -#define __Pyx_PyThreadState_declare -#define __Pyx_PyThreadState_assign -#define __Pyx_PyErr_Occurred() PyErr_Occurred() -#endif - -/* SaveResetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -#else -#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) -#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) -#endif - -/* PyErrExceptionMatches.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) -static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); -#else -#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) -#endif - -/* GetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* PyErrFetchRestore.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL) -#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb) -#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb) -#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb) -#define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#if CYTHON_COMPILING_IN_CPYTHON -#define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL)) -#else -#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) -#endif -#else -#define __Pyx_PyErr_Clear() PyErr_Clear() -#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) -#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb) -#define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb) -#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb) -#endif - -/* RaiseException.proto */ -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); - -/* ListCompAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len)) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) -#endif - -/* ArgTypeTest.proto */ -#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\ - ((likely((Py_TYPE(obj) == type) | (none_allowed && (obj == Py_None)))) ? 1 :\ - __Pyx__ArgTypeTest(obj, type, name, exact)) -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact); - -/* BytesEquals.proto */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); - -/* UnicodeEquals.proto */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); - -/* StrEquals.proto */ -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals -#else -#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals -#endif - -/* DivInt[Py_ssize_t].proto */ -static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); - -/* UnaryNegOverflows.proto */ -#define UNARY_NEG_WOULD_OVERFLOW(x)\ - (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) - -static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *); /*proto*/ -/* GetAttr.proto */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); - -/* GetItemInt.proto */ -#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ - __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, - int is_list, int wraparound, int boundscheck); - -/* ObjectGetItem.proto */ -#if CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key); -#else -#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key) -#endif - -/* decode_c_string_utf16.proto */ -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = 0; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16LE(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = -1; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16BE(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = 1; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} - -/* decode_c_string.proto */ -static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); - -/* GetAttr3.proto */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); - -/* RaiseTooManyValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); - -/* RaiseNeedMoreValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); - -/* RaiseNoneIterError.proto */ -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); - -/* ExtTypeTest.proto */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); - -/* SwapException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* Import.proto */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); - -/* FastTypeChecks.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2); -#else -#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) -#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type) -#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2)) -#endif -#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) - -static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); -#else -#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace, zerodivision_check)\ - (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) -#endif - -/* ListExtend.proto */ -static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { -#if CYTHON_COMPILING_IN_CPYTHON - PyObject* none = _PyList_Extend((PyListObject*)L, v); - if (unlikely(!none)) - return -1; - Py_DECREF(none); - return 0; -#else - return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); -#endif -} - -/* ListAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) -#endif - -/* None.proto */ -static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); - -/* DivInt[long].proto */ -static CYTHON_INLINE long __Pyx_div_long(long, long); - -/* PySequenceContains.proto */ -static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) { - int result = PySequence_Contains(seq, item); - return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); -} - -/* ImportFrom.proto */ -static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); - -/* HasAttr.proto */ -static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); - -/* PyObject_GenericGetAttrNoDict.proto */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); -#else -#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr -#endif - -/* PyObject_GenericGetAttr.proto */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name); -#else -#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr -#endif - -/* SetVTable.proto */ -static int __Pyx_SetVtable(PyObject *dict, void *vtable); - -/* PyObjectGetAttrStrNoError.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name); - -/* SetupReduce.proto */ -static int __Pyx_setup_reduce(PyObject* type_obj); - -/* TypeImport.proto */ -#ifndef __PYX_HAVE_RT_ImportType_proto -#define __PYX_HAVE_RT_ImportType_proto -enum __Pyx_ImportType_CheckSize { - __Pyx_ImportType_CheckSize_Error = 0, - __Pyx_ImportType_CheckSize_Warn = 1, - __Pyx_ImportType_CheckSize_Ignore = 2 -}; -static PyTypeObject *__Pyx_ImportType(PyObject* module, const char *module_name, const char *class_name, size_t size, enum __Pyx_ImportType_CheckSize check_size); -#endif - -/* CLineInTraceback.proto */ -#ifdef CYTHON_CLINE_IN_TRACEBACK -#define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) -#else -static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line); -#endif - -/* CodeObjectCache.proto */ -typedef struct { - PyCodeObject* code_object; - int code_line; -} __Pyx_CodeObjectCacheEntry; -struct __Pyx_CodeObjectCache { - int count; - int max_count; - __Pyx_CodeObjectCacheEntry* entries; -}; -static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); -static PyCodeObject *__pyx_find_code_object(int code_line); -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); - -/* AddTraceback.proto */ -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename); - -#if PY_MAJOR_VERSION < 3 - static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); - static void __Pyx_ReleaseBuffer(Py_buffer *view); -#else - #define __Pyx_GetBuffer PyObject_GetBuffer - #define __Pyx_ReleaseBuffer PyBuffer_Release -#endif - - -/* BufferStructDeclare.proto */ -typedef struct { - Py_ssize_t shape, strides, suboffsets; -} __Pyx_Buf_DimInfo; -typedef struct { - size_t refcount; - Py_buffer pybuffer; -} __Pyx_Buffer; -typedef struct { - __Pyx_Buffer *rcbuffer; - char *data; - __Pyx_Buf_DimInfo diminfo[8]; -} __Pyx_LocalBuf_ND; - -/* MemviewSliceIsContig.proto */ -static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim); - -/* OverlappingSlices.proto */ -static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize); - -/* Capsule.proto */ -static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); - -/* IsLittleEndian.proto */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void); - -/* BufferFormatCheck.proto */ -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type); - -/* TypeInfoCompare.proto */ -static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); 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-static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj); - -/* CppExceptionConversion.proto */ -#ifndef __Pyx_CppExn2PyErr -#include -#include -#include -#include -static void __Pyx_CppExn2PyErr() { - try { - if (PyErr_Occurred()) - ; // let the latest Python exn pass through and ignore the current one - else - throw; - } catch (const std::bad_alloc& exn) { - PyErr_SetString(PyExc_MemoryError, exn.what()); - } catch (const std::bad_cast& exn) { - PyErr_SetString(PyExc_TypeError, exn.what()); - } catch (const std::bad_typeid& exn) { - PyErr_SetString(PyExc_TypeError, exn.what()); - } catch (const std::domain_error& exn) { - PyErr_SetString(PyExc_ValueError, exn.what()); - } catch (const std::invalid_argument& exn) { - PyErr_SetString(PyExc_ValueError, exn.what()); - } catch (const std::ios_base::failure& exn) { - PyErr_SetString(PyExc_IOError, exn.what()); - } catch (const std::out_of_range& exn) { - PyErr_SetString(PyExc_IndexError, exn.what()); - } catch (const std::overflow_error& exn) { - PyErr_SetString(PyExc_OverflowError, exn.what()); 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- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex); - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex); - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex); - #endif -#endif - -/* MemviewSliceCopyTemplate.proto */ -static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object); 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-static const char __pyx_k_id[] = "id"; -static const char __pyx_k_np[] = "np"; -static const char __pyx_k_all[] = "__all__"; -static const char __pyx_k_box[] = "box"; -static const char __pyx_k_end[] = "end"; -static const char __pyx_k_new[] = "__new__"; -static const char __pyx_k_obj[] = "obj"; -static const char __pyx_k_base[] = "base"; -static const char __pyx_k_dict[] = "__dict__"; -static const char __pyx_k_hi_x[] = "hi_x"; -static const char __pyx_k_hi_y[] = "hi_y"; -static const char __pyx_k_hi_z[] = "hi_z"; -static const char __pyx_k_intp[] = "intp"; -static const char __pyx_k_lo_x[] = "lo_x"; -static const char __pyx_k_lo_y[] = "lo_y"; -static const char __pyx_k_lo_z[] = "lo_z"; -static const char __pyx_k_main[] = "__main__"; -static const char __pyx_k_mode[] = "mode"; -static const char __pyx_k_name[] = "name"; -static const char __pyx_k_ndim[] = "ndim"; -static const char __pyx_k_norm[] = "norm"; -static const char __pyx_k_pack[] = "pack"; -static const char __pyx_k_size[] = "size"; -static const char __pyx_k_step[] = "step"; -static const char __pyx_k_stop[] = "stop"; -static const char __pyx_k_test[] = "__test__"; -static const char __pyx_k_ASCII[] = "ASCII"; -static const char __pyx_k_class[] = "__class__"; -static const char __pyx_k_coord[] = "coord"; -static const char __pyx_k_dtype[] = "dtype"; -static const char __pyx_k_error[] = "error"; -static const char __pyx_k_flags[] = "flags"; -static const char __pyx_k_nreal[] = "nreal"; -static const char __pyx_k_numpy[] = "numpy"; -static const char __pyx_k_other[] = "other"; -static const char __pyx_k_range[] = "range"; -static const char __pyx_k_shape[] = "shape"; -static const char __pyx_k_start[] = "start"; -static const char __pyx_k_encode[] = "encode"; -static const char __pyx_k_format[] = "format"; -static const char __pyx_k_import[] = "__import__"; -static const char __pyx_k_name_2[] = "__name__"; -static const char __pyx_k_output[] = "output"; -static const char __pyx_k_pickle[] = "pickle"; -static const char __pyx_k_reduce[] = "__reduce__"; -static const char __pyx_k_shiftX[] = "shiftX"; -static const char __pyx_k_shiftY[] = "shiftY"; -static const char __pyx_k_shiftZ[] = "shiftZ"; -static const char __pyx_k_struct[] = "struct"; -static const char __pyx_k_unpack[] = "unpack"; -static const char __pyx_k_update[] = "update"; -static const char __pyx_k_asarray[] = "asarray"; -static const char __pyx_k_float32[] = "float32"; -static const char __pyx_k_fortran[] = "fortran"; -static const char __pyx_k_indices[] = "indices"; -static const char __pyx_k_mdamath[] = "mdamath"; -static const char __pyx_k_memview[] = "memview"; -static const char __pyx_k_reshape[] = "reshape"; -static const char __pyx_k_results[] = "results"; -static const char __pyx_k_Ellipsis[] = "Ellipsis"; -static const char __pyx_k_getstate[] = "__getstate__"; -static const char __pyx_k_itemsize[] = "itemsize"; -static const char __pyx_k_pyx_type[] = "__pyx_type"; -static const char __pyx_k_setstate[] = "__setstate__"; -static const char __pyx_k_TypeError[] = "TypeError"; -static const char __pyx_k_enumerate[] = "enumerate"; -static const char __pyx_k_pyx_state[] = "__pyx_state"; -static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; -static const char __pyx_k_IndexError[] = "IndexError"; -static const char __pyx_k_ValueError[] = "ValueError"; -static const char __pyx_k_pyx_result[] = "__pyx_result"; -static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; -static const char __pyx_k_reciprocal[] = "reciprocal"; -static const char __pyx_k_ImportError[] = "ImportError"; -static const char __pyx_k_MemoryError[] = "MemoryError"; -static const char __pyx_k_PickleError[] = "PickleError"; -static const char __pyx_k_coordinates[] = "coordinates"; -static const char __pyx_k_translation[] = "translation"; -static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; -static const char __pyx_k_stringsource[] = "stringsource"; -static const char __pyx_k_undo_augment[] = "undo_augment"; -static const char __pyx_k_OverflowError[] = "OverflowError"; -static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; -static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; -static const char __pyx_k_View_MemoryView[] = "View.MemoryView"; -static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; -static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; -static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; -static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; -static const char __pyx_k_pyx_unpickle_Enum[] = "__pyx_unpickle_Enum"; -static const char __pyx_k_triclinic_vectors[] = "triclinic_vectors"; -static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; -static const char __pyx_k_strided_and_direct[] = ""; -static const char __pyx_k_augment_coordinates[] = "augment_coordinates"; -static const char __pyx_k_strided_and_indirect[] = ""; -static const char __pyx_k_contiguous_and_direct[] = ""; -static const char __pyx_k_MemoryView_of_r_object[] = ""; -static const char __pyx_k_MDAnalysis_lib__augment[] = "MDAnalysis.lib._augment"; -static const char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; -static const char __pyx_k_contiguous_and_indirect[] = ""; -static const char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; -static const char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; -static const char __pyx_k_MDAnalysis_lib__augment_pyx[] = "MDAnalysis\\lib\\_augment.pyx"; -static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; -static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; -static const char __pyx_k_strided_and_direct_or_indirect[] = ""; -static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; -static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; -static const char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; -static const char __pyx_k_Cannot_assign_to_read_only_memor[] = "Cannot assign to read-only memoryview"; -static const char __pyx_k_Cannot_create_writable_memory_vi[] = "Cannot create writable memory view from read-only memoryview"; -static const char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; -static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0xb068931, 0x82a3537, 0x6ae9995) = (name))"; -static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; -static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; -static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; -static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; -static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; -static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; -static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; -static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; -static PyObject *__pyx_n_s_ASCII; -static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; -static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; -static PyObject *__pyx_kp_s_Cannot_assign_to_read_only_memor; -static PyObject *__pyx_kp_s_Cannot_create_writable_memory_vi; -static PyObject *__pyx_kp_s_Cannot_index_with_type_s; -static PyObject *__pyx_n_s_Ellipsis; -static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; -static PyObject *__pyx_n_s_ImportError; -static PyObject *__pyx_kp_s_Incompatible_checksums_0x_x_vs_0; -static PyObject *__pyx_n_s_IndexError; -static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; -static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; -static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; -static PyObject *__pyx_n_s_MDAnalysis_lib__augment; -static PyObject *__pyx_kp_s_MDAnalysis_lib__augment_pyx; -static PyObject *__pyx_n_s_MemoryError; -static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; -static PyObject *__pyx_kp_s_MemoryView_of_r_object; -static PyObject *__pyx_n_s_N; -static PyObject *__pyx_n_b_O; -static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; -static PyObject *__pyx_n_s_OverflowError; -static PyObject *__pyx_n_s_PickleError; -static PyObject *__pyx_n_s_TypeError; -static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; -static PyObject *__pyx_n_s_ValueError; -static PyObject *__pyx_n_s_View_MemoryView; -static PyObject *__pyx_n_s_all; -static PyObject *__pyx_n_s_allocate_buffer; -static PyObject *__pyx_n_s_asarray; -static PyObject *__pyx_n_s_augment_coordinates; -static PyObject *__pyx_n_u_augment_coordinates; -static PyObject *__pyx_n_s_base; -static PyObject *__pyx_n_s_box; -static PyObject *__pyx_n_s_c; -static PyObject *__pyx_n_u_c; -static PyObject *__pyx_n_s_class; -static PyObject *__pyx_n_s_cline_in_traceback; -static PyObject *__pyx_kp_s_contiguous_and_direct; -static PyObject *__pyx_kp_s_contiguous_and_indirect; -static PyObject *__pyx_n_s_coord; -static PyObject *__pyx_n_s_coordinates; -static PyObject *__pyx_n_s_dict; -static PyObject *__pyx_n_s_dm; -static PyObject *__pyx_n_s_dtype; -static PyObject *__pyx_n_s_dtype_is_object; -static PyObject *__pyx_n_s_encode; -static PyObject *__pyx_n_s_end; -static PyObject *__pyx_n_s_enumerate; -static PyObject *__pyx_n_s_error; -static PyObject *__pyx_n_s_flags; -static PyObject *__pyx_n_s_float32; -static PyObject *__pyx_n_s_format; -static PyObject *__pyx_n_s_fortran; -static PyObject *__pyx_n_u_fortran; -static PyObject *__pyx_n_s_getstate; -static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; -static PyObject *__pyx_n_s_hi_x; -static PyObject *__pyx_n_s_hi_y; -static PyObject *__pyx_n_s_hi_z; -static PyObject *__pyx_n_s_i; -static PyObject *__pyx_n_s_id; -static PyObject *__pyx_n_s_import; -static PyObject *__pyx_n_s_indices; -static PyObject *__pyx_n_s_intp; -static PyObject *__pyx_n_s_itemsize; -static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; -static PyObject *__pyx_n_s_j; -static PyObject *__pyx_n_s_lo_x; -static PyObject *__pyx_n_s_lo_y; -static PyObject *__pyx_n_s_lo_z; -static PyObject *__pyx_n_s_main; -static PyObject *__pyx_n_s_mdamath; -static PyObject *__pyx_n_s_memview; -static PyObject *__pyx_n_s_mode; -static PyObject *__pyx_n_s_n; -static PyObject *__pyx_n_s_name; -static PyObject *__pyx_n_s_name_2; -static PyObject *__pyx_n_s_ndim; -static PyObject *__pyx_n_s_new; -static PyObject *__pyx_kp_s_no_default___reduce___due_to_non; -static PyObject *__pyx_n_s_norm; -static PyObject *__pyx_n_s_np; -static PyObject *__pyx_n_s_nreal; -static PyObject *__pyx_n_s_numpy; -static PyObject *__pyx_kp_u_numpy_core_multiarray_failed_to; -static PyObject *__pyx_kp_u_numpy_core_umath_failed_to_impor; -static PyObject *__pyx_n_s_obj; -static PyObject *__pyx_n_s_other; -static PyObject *__pyx_n_s_output; -static PyObject *__pyx_n_s_pack; -static PyObject *__pyx_n_s_pickle; -static PyObject *__pyx_n_s_pyx_PickleError; -static PyObject *__pyx_n_s_pyx_checksum; -static PyObject *__pyx_n_s_pyx_getbuffer; -static PyObject *__pyx_n_s_pyx_result; -static PyObject *__pyx_n_s_pyx_state; -static PyObject *__pyx_n_s_pyx_type; -static PyObject *__pyx_n_s_pyx_unpickle_Enum; -static PyObject *__pyx_n_s_pyx_vtable; -static PyObject *__pyx_n_s_r; -static PyObject *__pyx_n_s_range; -static PyObject *__pyx_n_s_reciprocal; -static PyObject *__pyx_n_s_reduce; -static PyObject *__pyx_n_s_reduce_cython; -static PyObject *__pyx_n_s_reduce_ex; -static PyObject *__pyx_n_s_reshape; -static PyObject *__pyx_n_s_results; -static PyObject *__pyx_n_s_setstate; -static PyObject *__pyx_n_s_setstate_cython; -static PyObject *__pyx_n_s_shape; -static PyObject *__pyx_n_s_shiftX; -static PyObject *__pyx_n_s_shiftY; -static PyObject *__pyx_n_s_shiftZ; -static PyObject *__pyx_n_s_size; -static PyObject *__pyx_n_s_start; -static PyObject *__pyx_n_s_step; -static PyObject *__pyx_n_s_stop; -static PyObject *__pyx_kp_s_strided_and_direct; -static PyObject *__pyx_kp_s_strided_and_direct_or_indirect; -static PyObject *__pyx_kp_s_strided_and_indirect; -static PyObject *__pyx_kp_s_stringsource; -static PyObject *__pyx_n_s_struct; -static PyObject *__pyx_n_s_test; -static PyObject *__pyx_n_s_translation; -static PyObject *__pyx_n_s_triclinic_vectors; -static PyObject *__pyx_kp_s_unable_to_allocate_array_data; -static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; -static PyObject *__pyx_n_s_undo_augment; -static PyObject *__pyx_n_u_undo_augment; -static PyObject *__pyx_n_s_unpack; -static PyObject *__pyx_n_s_update; -static PyObject *__pyx_pf_10MDAnalysis_3lib_8_augment_augment_coordinates(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_coordinates, __Pyx_memviewslice __pyx_v_box, float __pyx_v_r); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_8_augment_2undo_augment(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_results, __Pyx_memviewslice __pyx_v_translation, int __pyx_v_nreal); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__len__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_12__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ -static PyObject *__pyx_pf___pyx_array___reduce_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_array_2__setstate_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_MemviewEnum_2__setstate_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ -static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); 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/*proto*/ -static char __pyx_doc_10MDAnalysis_3lib_8_augment_augment_coordinates[] = "Calculates the periodic images of particles which are within a distance\n `r` from the box walls.\n\n The algorithm works by generating explicit periodic images of atoms residing\n close to any of the six box walls. The steps involved in generating images\n involves the evaluation of reciprocal box vectors followed by the\n calculation of distances of atoms from the walls by means of projection onto\n the reciprocal vectors. If the distance is less than a specified cutoff\n distance, relevant periodic images are generated using box translation\n vectors :math:`\\vec{t}` with\n\n .. math:: \\vec{t}=l\\cdot\\vec{a}+m\\cdot\\vec{b}+n\\cdot \\vec{c}\\,,\n\n where :math:`l,\\,m,\\,n \\in \\{-1,\\,0,\\,1\\}` are the neighboring cell indices\n in :math:`x`-, :math:`y`-, and :math:`z`-direction relative to the central\n cell with box vectors :math:`\\vec{a},\\,\\vec{b},\\,\\vec{c}`.\n\n For instance, an atom close to the :math:`xy`-plane containing the origin\n will generate a periodic image outside the central cell and close to the\n opposite :math:`xy`-plane of the box, i.e., shifted by\n :math:`\\vec{t} = 0\\cdot\\vec{a}+0\\cdot\\vec{b}+1\\cdot\\vec{c}=\\vec{c}`.\n\n Likewise, if the particle is close to more than one box walls, images along\n the diagonals are also generated::\n\n x x\n +------------+ +------------+\n | | augment | |\n | | -------> | |\n | o | x | o |\n +------------+ +------------+\n\n Parameters\n ----------\n coordinates : numpy.ndarray\n Input coordinate array of shape ``(n, 3)`` and dtype ``numpy.float32``\n used to generate duplicate images in the vicinity of the central cell. All\n coordinates must be within the primary unit cell.\n box : numpy.ndarray\n Box dimensio""ns of shape ``(6,)`` and dtype ``numpy.float32``. The\n dimensions must be provided in the same format as returned\n by :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`:\n ``[lx, ly, lz, alpha, beta, gamma]``\n r : float\n Thickness of cutoff region for duplicate image generation.\n\n Returns\n -------\n output : numpy.ndarray\n Coordinates of duplicate (augmented) particles (dtype ``numpy.float32``).\n indices : numpy.ndarray\n Original indices of the augmented coordinates (dtype ``numpy.int64``).\n Maps the indices of augmented particles to their original particle index\n such that ``indices[augmented_index] = original_index``.\n\n Note\n ----\n Output does not return coordinates from the initial array.\n To merge the particles with their respective images, the following operation\n is necessary when generating the images:\n\n .. code-block:: python\n\n images, mapping = augment_coordinates(coordinates, box, max_cutoff)\n all_coords = numpy.concatenate([coordinates, images])\n\n\n See Also\n --------\n :meth:`undo_augment`\n\n\n .. versionadded:: 0.19.0\n "; 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} - __pyx_t_1 = ((__pyx_v_step < 0) != 0); - __pyx_t_2 = __pyx_t_1; - __pyx_L6_bool_binop_done:; - __pyx_v_negative_step = __pyx_t_2; - - /* "View.MemoryView":839 - * negative_step = have_step != 0 and step < 0 - * - * if have_step and step == 0: # <<<<<<<<<<<<<< - * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) - * - */ - __pyx_t_1 = (__pyx_v_have_step != 0); - if (__pyx_t_1) { - } else { - __pyx_t_2 = __pyx_t_1; - goto __pyx_L9_bool_binop_done; - } - __pyx_t_1 = ((__pyx_v_step == 0) != 0); - __pyx_t_2 = __pyx_t_1; - __pyx_L9_bool_binop_done:; - if (__pyx_t_2) { - - /* "View.MemoryView":840 - * - * if have_step and step == 0: - * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Step may not be zero (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 840, __pyx_L1_error) - - /* "View.MemoryView":839 - * negative_step = have_step != 0 and step < 0 - * - * if have_step and step == 0: # <<<<<<<<<<<<<< - * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) - * - */ - } - - /* "View.MemoryView":843 - * - * - * if have_start: # <<<<<<<<<<<<<< - * if start < 0: - * start += shape - */ - __pyx_t_2 = (__pyx_v_have_start != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":844 - * - * if have_start: - * if start < 0: # <<<<<<<<<<<<<< - * start += shape - * if start < 0: - */ - __pyx_t_2 = ((__pyx_v_start < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":845 - * if have_start: - * if start < 0: - * start += shape # <<<<<<<<<<<<<< - * if start < 0: - * start = 0 - */ - __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - - /* "View.MemoryView":846 - * if start < 0: - * start += shape - * if start < 0: # <<<<<<<<<<<<<< - * start = 0 - * elif start >= shape: - */ - __pyx_t_2 = ((__pyx_v_start < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":847 - * start += shape - * if start < 0: - * start = 0 # <<<<<<<<<<<<<< - * elif start >= shape: - * if negative_step: - */ - __pyx_v_start = 0; - - /* "View.MemoryView":846 - * if start < 0: - * start += shape - * if start < 0: # <<<<<<<<<<<<<< - * start = 0 - * elif start >= shape: - */ - } - - /* "View.MemoryView":844 - * - * if have_start: - * if start < 0: # <<<<<<<<<<<<<< - * start += shape - * if start < 0: - */ - goto __pyx_L12; - } - - /* "View.MemoryView":848 - * if start < 0: - * start = 0 - * elif start >= shape: # <<<<<<<<<<<<<< - * if negative_step: - * start = shape - 1 - */ - __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":849 - * start = 0 - * elif start >= shape: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":850 - * elif start >= shape: - * if negative_step: - * start = shape - 1 # <<<<<<<<<<<<<< - * else: - * start = shape - */ - __pyx_v_start = (__pyx_v_shape - 1); - - /* "View.MemoryView":849 - * start = 0 - 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- /* "View.MemoryView":854 - * start = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - goto __pyx_L15; - } - - /* "View.MemoryView":857 - * start = shape - 1 - * else: - * start = 0 # <<<<<<<<<<<<<< - * - * if have_stop: - */ - /*else*/ { - __pyx_v_start = 0; - } - __pyx_L15:; - } - __pyx_L11:; - - /* "View.MemoryView":859 - * start = 0 - * - * if have_stop: # <<<<<<<<<<<<<< - * if stop < 0: - * stop += shape - */ - __pyx_t_2 = (__pyx_v_have_stop != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":860 - * - * if have_stop: - * if stop < 0: # <<<<<<<<<<<<<< - * stop += shape - * if stop < 0: - */ - __pyx_t_2 = ((__pyx_v_stop < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":861 - * if have_stop: - * if stop < 0: - * stop += shape # <<<<<<<<<<<<<< - * if stop < 0: - * stop = 0 - */ - __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); - - /* "View.MemoryView":862 - * if stop < 0: - * stop += shape - * if stop < 0: # <<<<<<<<<<<<<< - * stop = 0 - * elif stop > shape: - */ - __pyx_t_2 = ((__pyx_v_stop < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":863 - * stop += shape - * if stop < 0: - * stop = 0 # <<<<<<<<<<<<<< - * elif stop > shape: - * stop = shape - */ - __pyx_v_stop = 0; - - /* "View.MemoryView":862 - * if stop < 0: - * stop += shape - * if stop < 0: # <<<<<<<<<<<<<< - * stop = 0 - * elif stop > shape: - */ - } - - /* "View.MemoryView":860 - * - * if have_stop: - * if stop < 0: # <<<<<<<<<<<<<< - * stop += shape - * if stop < 0: - */ - goto __pyx_L17; - } - - /* "View.MemoryView":864 - * if stop < 0: - * stop = 0 - * elif stop > shape: # <<<<<<<<<<<<<< - * stop = shape - * else: - */ - __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":865 - * stop = 0 - * elif stop > shape: - * stop = shape # <<<<<<<<<<<<<< - * else: - * if negative_step: - */ - __pyx_v_stop = __pyx_v_shape; - - /* "View.MemoryView":864 - * if stop < 0: - * stop = 0 - * elif stop > shape: # <<<<<<<<<<<<<< - 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if (__pyx_t_2) { - - /* "View.MemoryView":873 - * - * if not have_step: - * step = 1 # <<<<<<<<<<<<<< - * - * - */ - __pyx_v_step = 1; - - /* "View.MemoryView":872 - * stop = shape - * - * if not have_step: # <<<<<<<<<<<<<< - * step = 1 - * - */ - } - - /* "View.MemoryView":877 - * - * with cython.cdivision(True): - * new_shape = (stop - start) // step # <<<<<<<<<<<<<< - * - * if (stop - start) - step * new_shape: - */ - __pyx_v_new_shape = ((__pyx_v_stop - __pyx_v_start) / __pyx_v_step); - - /* "View.MemoryView":879 - * new_shape = (stop - start) // step - * - * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< - * new_shape += 1 - * - */ - __pyx_t_2 = (((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":880 - * - * if (stop - start) - step * new_shape: - * new_shape += 1 # <<<<<<<<<<<<<< - * - * if new_shape < 0: - */ - __pyx_v_new_shape = (__pyx_v_new_shape + 1); - - /* "View.MemoryView":879 - * new_shape = (stop - 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- /* "View.MemoryView":888 - * dst.strides[new_ndim] = stride * step - * dst.shape[new_ndim] = new_shape - * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< - * - * - */ - (__pyx_v_dst->suboffsets[__pyx_v_new_ndim]) = __pyx_v_suboffset; - } - __pyx_L3:; - - /* "View.MemoryView":891 - * - * - * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< - * dst.data += start * stride - * else: - */ - __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":892 - * - * if suboffset_dim[0] < 0: - * dst.data += start * stride # <<<<<<<<<<<<<< - * else: - * dst.suboffsets[suboffset_dim[0]] += start * stride - */ - __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); - - /* "View.MemoryView":891 - * - * - * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< - * dst.data += start * stride - * else: - */ - goto __pyx_L23; - } - - /* "View.MemoryView":894 - * dst.data += start * stride - * else: - * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< - 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int __pyx_t_3; - int __pyx_t_4; - - /* "View.MemoryView":1123 - * """ - * cdef int i - * cdef Py_ssize_t c_stride = 0 # <<<<<<<<<<<<<< - * cdef Py_ssize_t f_stride = 0 - * - */ - __pyx_v_c_stride = 0; - - /* "View.MemoryView":1124 - * cdef int i - * cdef Py_ssize_t c_stride = 0 - * cdef Py_ssize_t f_stride = 0 # <<<<<<<<<<<<<< - * - * for i in range(ndim - 1, -1, -1): - */ - __pyx_v_f_stride = 0; - - /* "View.MemoryView":1126 - * cdef Py_ssize_t f_stride = 0 - * - * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< - * if mslice.shape[i] > 1: - * c_stride = mslice.strides[i] - */ - for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { - __pyx_v_i = __pyx_t_1; - - /* "View.MemoryView":1127 - * - * for i in range(ndim - 1, -1, -1): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * c_stride = mslice.strides[i] - * break - */ - __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1128 - * for i in range(ndim - 1, -1, -1): - * if mslice.shape[i] > 1: - * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< - * break - * - */ - __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - - /* "View.MemoryView":1129 - * if mslice.shape[i] > 1: - * c_stride = mslice.strides[i] - * break # <<<<<<<<<<<<<< - * - * for i in range(ndim): - */ - goto __pyx_L4_break; - - /* "View.MemoryView":1127 - * - * for i in range(ndim - 1, -1, -1): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * c_stride = mslice.strides[i] - * break - */ - } - } - __pyx_L4_break:; - - /* "View.MemoryView":1131 - * break - * - * for i in range(ndim): # <<<<<<<<<<<<<< - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] - */ - __pyx_t_1 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_1; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { - __pyx_v_i = __pyx_t_4; - - /* "View.MemoryView":1132 - * - * for i in range(ndim): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * f_stride = mslice.strides[i] - * break - */ - __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1133 - * for i in range(ndim): - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< - * break - * - */ - __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - - /* "View.MemoryView":1134 - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] - * break # <<<<<<<<<<<<<< - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): - */ - goto __pyx_L7_break; - - /* "View.MemoryView":1132 - * - * for i in range(ndim): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * f_stride = mslice.strides[i] - * break - */ - } - } - __pyx_L7_break:; - - /* "View.MemoryView":1136 - * break - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< - * return 'C' - * else: - */ - __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1137 - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): - * return 'C' # <<<<<<<<<<<<<< - * else: - * return 'F' - */ - __pyx_r = 'C'; - goto __pyx_L0; - - /* "View.MemoryView":1136 - * break - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< - * return 'C' - * else: - */ - } - - /* "View.MemoryView":1139 - * return 'C' - * else: - * return 'F' # <<<<<<<<<<<<<< - * - * @cython.cdivision(True) - */ - /*else*/ { - __pyx_r = 'F'; - goto __pyx_L0; - } - - /* "View.MemoryView":1118 - * - * @cname('__pyx_get_best_slice_order') - * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< - * """ - * Figure out the best memory access order for a given slice. - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1142 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - -static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v_src_strides, char *__pyx_v_dst_data, Py_ssize_t *__pyx_v_dst_strides, Py_ssize_t *__pyx_v_src_shape, Py_ssize_t *__pyx_v_dst_shape, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - CYTHON_UNUSED Py_ssize_t __pyx_v_i; - CYTHON_UNUSED Py_ssize_t __pyx_v_src_extent; - Py_ssize_t __pyx_v_dst_extent; - Py_ssize_t __pyx_v_src_stride; - Py_ssize_t __pyx_v_dst_stride; - int __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - Py_ssize_t __pyx_t_4; - Py_ssize_t __pyx_t_5; - Py_ssize_t __pyx_t_6; - - /* "View.MemoryView":1149 - * - * cdef Py_ssize_t i - * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] - */ - __pyx_v_src_extent = (__pyx_v_src_shape[0]); - - /* "View.MemoryView":1150 - * cdef Py_ssize_t i - * cdef Py_ssize_t src_extent = src_shape[0] - * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t src_stride = src_strides[0] - * cdef Py_ssize_t dst_stride = dst_strides[0] - */ - __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); - - /* "View.MemoryView":1151 - * cdef Py_ssize_t src_extent = src_shape[0] - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - */ - __pyx_v_src_stride = (__pyx_v_src_strides[0]); - - /* "View.MemoryView":1152 - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] - * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< - * - * if ndim == 1: - */ - __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); - - /* "View.MemoryView":1154 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); - if (__pyx_t_2) { - } else { - __pyx_t_1 = __pyx_t_2; - goto __pyx_L5_bool_binop_done; - } - __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); - if (__pyx_t_2) { - } else { - __pyx_t_1 = __pyx_t_2; - goto __pyx_L5_bool_binop_done; - } - - /* "View.MemoryView":1156 - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< - * memcpy(dst_data, src_data, itemsize * dst_extent) - * else: - */ - __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); - if (__pyx_t_2) { - __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); - } - __pyx_t_3 = (__pyx_t_2 != 0); - __pyx_t_1 = __pyx_t_3; - __pyx_L5_bool_binop_done:; - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - if (__pyx_t_1) { - - /* "View.MemoryView":1157 - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - 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*/ - (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); - - /* "View.MemoryView":1161 - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * else: - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1162 - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L4:; - - /* "View.MemoryView":1154 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1164 - * dst_data += dst_stride - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * _copy_strided_to_strided(src_data, src_strides + 1, - * dst_data, dst_strides + 1, - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - __pyx_t_5 = __pyx_t_4; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1165 - * else: - * for i in range(dst_extent): - * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< - * dst_data, dst_strides + 1, - * src_shape + 1, dst_shape + 1, - */ - _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - - /* "View.MemoryView":1169 - * src_shape + 1, dst_shape + 1, - * ndim - 1, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1170 - * ndim - 1, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L3:; - - /* "View.MemoryView":1142 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - - /* function exit code */ -} - -/* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - -static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - - /* "View.MemoryView":1175 - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< - * src.shape, dst.shape, ndim, itemsize) - * - */ - _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - - /* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - - /* function exit code */ -} - -/* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { - Py_ssize_t __pyx_v_shape; - Py_ssize_t __pyx_v_size; - Py_ssize_t __pyx_r; - Py_ssize_t __pyx_t_1; - Py_ssize_t *__pyx_t_2; - Py_ssize_t *__pyx_t_3; - Py_ssize_t *__pyx_t_4; - - /* "View.MemoryView":1181 - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: - * "Return the size of the memory occupied by the slice in number of bytes" - 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- Py_INCREF(function); - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); -done: - return result; -} - -/* PyObjectCallMethO */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { - PyObject *self, *result; - PyCFunction cfunc; - cfunc = PyCFunction_GET_FUNCTION(func); - self = PyCFunction_GET_SELF(func); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = cfunc(self, arg); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallOneArg */ -#if CYTHON_COMPILING_IN_CPYTHON -static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_New(1); - if (unlikely(!args)) return NULL; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif - if (likely(PyCFunction_Check(func))) { - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (__Pyx_PyFastCFunction_Check(func)) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } - } - return __Pyx__PyObject_CallOneArg(func, arg); -} -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -#endif - -/* MemviewSliceInit */ -static int -__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference) -{ - __Pyx_RefNannyDeclarations - int i, retval=-1; - Py_buffer *buf = &memview->view; - __Pyx_RefNannySetupContext("init_memviewslice", 0); - if (unlikely(memviewslice->memview || memviewslice->data)) { - PyErr_SetString(PyExc_ValueError, - "memviewslice is already initialized!"); - goto fail; - } - if (buf->strides) { - for (i = 0; i < ndim; i++) { - memviewslice->strides[i] = buf->strides[i]; - } - } else { - Py_ssize_t stride = buf->itemsize; - for (i = ndim - 1; i >= 0; i--) { - memviewslice->strides[i] = stride; - stride *= buf->shape[i]; - } - } - for (i = 0; i < ndim; i++) { - memviewslice->shape[i] = buf->shape[i]; - if (buf->suboffsets) { - memviewslice->suboffsets[i] = buf->suboffsets[i]; - } else { - memviewslice->suboffsets[i] = -1; - } - } - memviewslice->memview = memview; - memviewslice->data = (char *)buf->buf; - if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { - Py_INCREF(memview); - } - retval = 0; - goto no_fail; -fail: - memviewslice->memview = 0; - memviewslice->data = 0; - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} -#ifndef Py_NO_RETURN -#define Py_NO_RETURN -#endif -static void __pyx_fatalerror(const char *fmt, ...) Py_NO_RETURN { - va_list vargs; - char msg[200]; -#if PY_VERSION_HEX >= 0x030A0000 || defined(HAVE_STDARG_PROTOTYPES) - va_start(vargs, fmt); -#else - va_start(vargs); -#endif - vsnprintf(msg, 200, fmt, vargs); - va_end(vargs); - Py_FatalError(msg); -} -static CYTHON_INLINE int -__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)++; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE int -__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)--; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE void -__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) -{ - int first_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) - return; - if (unlikely(__pyx_get_slice_count(memview) < 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - first_time = __pyx_add_acquisition_count(memview) == 0; - if (unlikely(first_time)) { - if (have_gil) { - Py_INCREF((PyObject *) memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_INCREF((PyObject *) memview); - PyGILState_Release(_gilstate); - } - } -} -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, - int have_gil, int lineno) { - int last_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) { - memslice->memview = NULL; - return; - } - if (unlikely(__pyx_get_slice_count(memview) <= 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - last_time = __pyx_sub_acquisition_count(memview) == 1; - memslice->data = NULL; - if (unlikely(last_time)) { - if (have_gil) { - Py_CLEAR(memslice->memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_CLEAR(memslice->memview); - PyGILState_Release(_gilstate); - } - } else { - memslice->memview = NULL; - } -} - -/* GetTopmostException */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* PyErrExceptionMatches */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* GetException */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* PyErrFetchRestore */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -} -#endif - -/* RaiseException */ -#if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* ArgTypeTest */ -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) -{ - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - else if (exact) { - #if PY_MAJOR_VERSION == 2 - if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; - #endif - } - else { - if (likely(__Pyx_TypeCheck(obj, type))) return 1; - } - PyErr_Format(PyExc_TypeError, - "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", - name, type->tp_name, Py_TYPE(obj)->tp_name); - return 0; -} - -/* BytesEquals */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { - const char *ps1, *ps2; - Py_ssize_t length = PyBytes_GET_SIZE(s1); - if (length != PyBytes_GET_SIZE(s2)) - return (equals == Py_NE); - ps1 = PyBytes_AS_STRING(s1); - ps2 = PyBytes_AS_STRING(s2); - if (ps1[0] != ps2[0]) { - return (equals == Py_NE); - } else if (length == 1) { - return (equals == Py_EQ); - } else { - int result; -#if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000) - Py_hash_t hash1, hash2; - hash1 = ((PyBytesObject*)s1)->ob_shash; - hash2 = ((PyBytesObject*)s2)->ob_shash; - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - return (equals == Py_NE); - } -#endif - result = memcmp(ps1, ps2, (size_t)length); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -#endif -} - -/* UnicodeEquals */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else -#if PY_MAJOR_VERSION < 3 - PyObject* owned_ref = NULL; -#endif - int s1_is_unicode, s2_is_unicode; - if (s1 == s2) { - goto return_eq; - } - s1_is_unicode = PyUnicode_CheckExact(s1); - s2_is_unicode = PyUnicode_CheckExact(s2); -#if PY_MAJOR_VERSION < 3 - if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { - owned_ref = PyUnicode_FromObject(s2); - if (unlikely(!owned_ref)) - return -1; - s2 = owned_ref; - s2_is_unicode = 1; - } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { - owned_ref = PyUnicode_FromObject(s1); - if (unlikely(!owned_ref)) - return -1; - s1 = owned_ref; - s1_is_unicode = 1; - } else if (((!s2_is_unicode) & (!s1_is_unicode))) { - return __Pyx_PyBytes_Equals(s1, s2, equals); - } -#endif - if (s1_is_unicode & s2_is_unicode) { - Py_ssize_t length; - int kind; - void *data1, *data2; - if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) - return -1; - length = __Pyx_PyUnicode_GET_LENGTH(s1); - if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { - goto return_ne; - } -#if CYTHON_USE_UNICODE_INTERNALS - { - Py_hash_t hash1, hash2; - #if CYTHON_PEP393_ENABLED - hash1 = ((PyASCIIObject*)s1)->hash; - hash2 = ((PyASCIIObject*)s2)->hash; - #else - hash1 = ((PyUnicodeObject*)s1)->hash; - hash2 = ((PyUnicodeObject*)s2)->hash; - #endif - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - goto return_ne; - } - } -#endif - kind = __Pyx_PyUnicode_KIND(s1); - if (kind != __Pyx_PyUnicode_KIND(s2)) { - goto return_ne; - } - data1 = __Pyx_PyUnicode_DATA(s1); - data2 = __Pyx_PyUnicode_DATA(s2); - if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { - goto return_ne; - } else if (length == 1) { - goto return_eq; - } else { - int result = memcmp(data1, data2, (size_t)(length * kind)); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & s2_is_unicode) { - goto return_ne; - } else if ((s2 == Py_None) & s1_is_unicode) { - goto return_ne; - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -return_eq: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ); -return_ne: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_NE); -#endif -} - -/* DivInt[Py_ssize_t] */ -static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { - Py_ssize_t q = a / b; - Py_ssize_t r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* GetAttr */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { -#if CYTHON_USE_TYPE_SLOTS -#if PY_MAJOR_VERSION >= 3 - if (likely(PyUnicode_Check(n))) -#else - if (likely(PyString_Check(n))) -#endif - return __Pyx_PyObject_GetAttrStr(o, n); -#endif - return PyObject_GetAttr(o, n); -} - -/* GetItemInt */ -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { - PyObject *r; - if (!j) return NULL; - r = PyObject_GetItem(o, j); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyList_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyTuple_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } - else if (PyTuple_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } else { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_item)) { - if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { - Py_ssize_t l = m->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return NULL; - PyErr_Clear(); - } - } - return m->sq_item(o, i); - } - } -#else - if (is_list || PySequence_Check(o)) { - return PySequence_GetItem(o, i); - } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -} - -/* ObjectGetItem */ -#if CYTHON_USE_TYPE_SLOTS -static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { - PyObject *runerr = NULL; - Py_ssize_t key_value; - PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; - if (unlikely(!(m && m->sq_item))) { - PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); - return NULL; - } - key_value = __Pyx_PyIndex_AsSsize_t(index); - if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { - return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); - } - if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { - PyErr_Clear(); - PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); - } - return NULL; -} -static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { - PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; - if (likely(m && m->mp_subscript)) { - return m->mp_subscript(obj, key); - } - return __Pyx_PyObject_GetIndex(obj, key); -} -#endif - -/* decode_c_string */ -static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { - Py_ssize_t length; - if (unlikely((start < 0) | (stop < 0))) { - size_t slen = strlen(cstring); - if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { - PyErr_SetString(PyExc_OverflowError, - "c-string too long to convert to Python"); - return NULL; - } - length = (Py_ssize_t) slen; - if (start < 0) { - start += length; - if (start < 0) - start = 0; - } - if (stop < 0) - stop += length; - } - if (unlikely(stop <= start)) - return __Pyx_NewRef(__pyx_empty_unicode); - length = stop - start; - cstring += start; - if (decode_func) { - return decode_func(cstring, length, errors); - } else { - return PyUnicode_Decode(cstring, length, encoding, errors); - } -} - -/* GetAttr3 */ -static PyObject *__Pyx_GetAttr3Default(PyObject *d) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - return NULL; - __Pyx_PyErr_Clear(); - Py_INCREF(d); - return d; -} -static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { - PyObject *r = __Pyx_GetAttr(o, n); - return (likely(r)) ? r : __Pyx_GetAttr3Default(d); -} - -/* RaiseTooManyValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -/* RaiseNeedMoreValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -/* RaiseNoneIterError */ -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); -} - -/* ExtTypeTest */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(__Pyx_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* SwapException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = *type; - exc_info->exc_value = *value; - exc_info->exc_traceback = *tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = *type; - tstate->exc_value = *value; - tstate->exc_traceback = *tb; - #endif - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); - PyErr_SetExcInfo(*type, *value, *tb); - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#endif - -/* Import */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* FastTypeChecks */ -#if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; - if (a == b) - return 1; - } - return b == &PyBaseObject_Type; -} -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { - PyObject *mro; - if (a == b) return 1; - mro = a->tp_mro; - if (likely(mro)) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(mro); - for (i = 0; i < n; i++) { - if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) - return 1; - } - return 0; - } - return __Pyx_InBases(a, b); -} -#if PY_MAJOR_VERSION == 2 -static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { - PyObject *exception, *value, *tb; - int res; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&exception, &value, &tb); - res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - if (!res) { - res = PyObject_IsSubclass(err, exc_type2); - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - } - __Pyx_ErrRestore(exception, value, tb); - return res; -} -#else -static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { - int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; - if (!res) { - res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); - } - return res; -} -#endif -static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - assert(PyExceptionClass_Check(exc_type)); - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; i= 0 || (x^b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - default: return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - } - x = a + b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla + llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("add", return NULL) - result = ((double)a) + (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); -} -#endif - -/* None */ -static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { - PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); -} - -/* DivInt[long] */ -static CYTHON_INLINE long __Pyx_div_long(long a, long b) { - long q = a / b; - long r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* ImportFrom */ -static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { - PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); - if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_Format(PyExc_ImportError, - #if PY_MAJOR_VERSION < 3 - "cannot import name %.230s", PyString_AS_STRING(name)); - #else - "cannot import name %S", name); - #endif - } - return value; -} - -/* HasAttr */ -static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { - PyObject *r; - if (unlikely(!__Pyx_PyBaseString_Check(n))) { - PyErr_SetString(PyExc_TypeError, - "hasattr(): attribute name must be string"); - return -1; - } - r = __Pyx_GetAttr(o, n); - if (unlikely(!r)) { - PyErr_Clear(); - return 0; - } else { - Py_DECREF(r); - return 1; - } -} - -/* PyObject_GenericGetAttrNoDict */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { - PyErr_Format(PyExc_AttributeError, -#if PY_MAJOR_VERSION >= 3 - "'%.50s' object has no attribute '%U'", - tp->tp_name, attr_name); -#else - "'%.50s' object has no attribute '%.400s'", - tp->tp_name, PyString_AS_STRING(attr_name)); -#endif - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { - PyObject *descr; - PyTypeObject *tp = Py_TYPE(obj); - if (unlikely(!PyString_Check(attr_name))) { - return PyObject_GenericGetAttr(obj, attr_name); - } - assert(!tp->tp_dictoffset); - descr = _PyType_Lookup(tp, attr_name); - if (unlikely(!descr)) { - return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); - } - Py_INCREF(descr); - #if PY_MAJOR_VERSION < 3 - if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) - #endif - { - descrgetfunc f = Py_TYPE(descr)->tp_descr_get; - if (unlikely(f)) { - PyObject *res = f(descr, obj, (PyObject *)tp); - Py_DECREF(descr); - return res; - } - } - return descr; -} -#endif - -/* PyObject_GenericGetAttr */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { - if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { - return PyObject_GenericGetAttr(obj, attr_name); - } - return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); -} -#endif - -/* SetVTable */ -static int __Pyx_SetVtable(PyObject *dict, void *vtable) { -#if PY_VERSION_HEX >= 0x02070000 - PyObject *ob = PyCapsule_New(vtable, 0, 0); -#else - PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); -#endif - if (!ob) - goto bad; - if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) - goto bad; - Py_DECREF(ob); - return 0; -bad: - Py_XDECREF(ob); - return -1; -} - -/* PyObjectGetAttrStrNoError */ -static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - __Pyx_PyErr_Clear(); -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { - PyObject *result; -#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 - PyTypeObject* tp = Py_TYPE(obj); - if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { - return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); - } -#endif - result = __Pyx_PyObject_GetAttrStr(obj, attr_name); - if (unlikely(!result)) { - __Pyx_PyObject_GetAttrStr_ClearAttributeError(); - } - return result; -} - -/* SetupReduce */ -static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { - int ret; - PyObject *name_attr; - name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2); - if (likely(name_attr)) { - ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); - } else { - ret = -1; - } - if (unlikely(ret < 0)) { - PyErr_Clear(); - ret = 0; - } - Py_XDECREF(name_attr); - return ret; -} -static int __Pyx_setup_reduce(PyObject* type_obj) { - int ret = 0; - PyObject *object_reduce = NULL; - PyObject *object_getstate = NULL; - PyObject *object_reduce_ex = NULL; - PyObject *reduce = NULL; - PyObject *reduce_ex = NULL; - PyObject *reduce_cython = NULL; - PyObject *setstate = NULL; - PyObject *setstate_cython = NULL; - PyObject *getstate = NULL; -#if CYTHON_USE_PYTYPE_LOOKUP - getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate); -#else - getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate); - if (!getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (getstate) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate); -#else - object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate); - if (!object_getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (object_getstate != getstate) { - goto __PYX_GOOD; - } - } -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; - if (reduce_ex == object_reduce_ex) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; - if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); - if (likely(reduce_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (reduce == object_reduce || PyErr_Occurred()) { - goto __PYX_BAD; - } - setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); - if (!setstate) PyErr_Clear(); - if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); - if (likely(setstate_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (!setstate || PyErr_Occurred()) { - goto __PYX_BAD; - } - } - PyType_Modified((PyTypeObject*)type_obj); - } - } - goto __PYX_GOOD; -__PYX_BAD: - if (!PyErr_Occurred()) - PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); - ret = -1; -__PYX_GOOD: -#if !CYTHON_USE_PYTYPE_LOOKUP - Py_XDECREF(object_reduce); - Py_XDECREF(object_reduce_ex); - Py_XDECREF(object_getstate); - Py_XDECREF(getstate); -#endif - Py_XDECREF(reduce); - Py_XDECREF(reduce_ex); - Py_XDECREF(reduce_cython); - Py_XDECREF(setstate); - Py_XDECREF(setstate_cython); - return ret; -} - -/* TypeImport */ -#ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* CLineInTraceback */ -#ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ -#include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - if ((0)) {} - view->obj = NULL; - Py_DECREF(obj); -} -#endif - - -/* MemviewSliceIsContig */ -static int -__pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim) -{ - int i, index, step, start; - Py_ssize_t itemsize = mvs.memview->view.itemsize; - if (order == 'F') { - step = 1; - start = 0; - } else { - step = -1; - start = ndim - 1; - } - for (i = 0; i < ndim; i++) { - index = start + step * i; - if (mvs.suboffsets[index] >= 0 || mvs.strides[index] != itemsize) - return 0; - itemsize *= mvs.shape[index]; - } - return 1; -} - -/* OverlappingSlices */ -static void -__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, - void **out_start, void **out_end, - int ndim, size_t itemsize) -{ - char *start, *end; - int i; - start = end = slice->data; - for (i = 0; i < ndim; i++) { - Py_ssize_t stride = slice->strides[i]; - Py_ssize_t extent = slice->shape[i]; - if (extent == 0) { - *out_start = *out_end = start; - return; - } else { - if (stride > 0) - end += stride * (extent - 1); - else - start += stride * (extent - 1); - } - } - *out_start = start; - *out_end = end + itemsize; -} -static int -__pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize) -{ - void *start1, *end1, *start2, *end2; - __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); - __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); - return (start1 < end2) && (start2 < end1); -} - -/* Capsule */ -static CYTHON_INLINE PyObject * -__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) -{ - PyObject *cobj; -#if PY_VERSION_HEX >= 0x02070000 - cobj = PyCapsule_New(p, sig, NULL); -#else - cobj = PyCObject_FromVoidPtr(p, NULL); -#endif - return cobj; -} - -/* IsLittleEndian */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) -{ - union { - uint32_t u32; - uint8_t u8[4]; - } S; - S.u32 = 0x01020304; - return S.u8[0] == 4; -} - -/* BufferFormatCheck */ -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type) { - stack[0].field = &ctx->root; - stack[0].parent_offset = 0; - ctx->root.type = type; - ctx->root.name = "buffer dtype"; - ctx->root.offset = 0; - ctx->head = stack; - ctx->head->field = &ctx->root; - ctx->fmt_offset = 0; - ctx->head->parent_offset = 0; - ctx->new_packmode = '@'; - ctx->enc_packmode = '@'; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->is_complex = 0; - ctx->is_valid_array = 0; - ctx->struct_alignment = 0; - while (type->typegroup == 'S') { - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = 0; - type = type->fields->type; - } -} -static int __Pyx_BufFmt_ParseNumber(const char** ts) { - int count; - const char* t = *ts; - if (*t < '0' || *t > '9') { - return -1; - } else { - count = *t++ - '0'; - while (*t >= '0' && *t <= '9') { - count *= 10; - count += *t++ - '0'; - } - } - *ts = t; - return count; -} -static int __Pyx_BufFmt_ExpectNumber(const char **ts) { - int number = __Pyx_BufFmt_ParseNumber(ts); - if (number == -1) - PyErr_Format(PyExc_ValueError,\ - "Does not understand character buffer dtype format string ('%c')", **ts); - return number; -} -static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { - PyErr_Format(PyExc_ValueError, - "Unexpected format string character: '%c'", ch); -} -static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { - switch (ch) { - case '?': return "'bool'"; - case 'c': return "'char'"; - case 'b': return "'signed char'"; - case 'B': return "'unsigned char'"; - case 'h': return "'short'"; - case 'H': return "'unsigned short'"; - case 'i': return "'int'"; - case 'I': return "'unsigned int'"; - case 'l': return "'long'"; - case 'L': return "'unsigned long'"; - case 'q': return "'long long'"; - case 'Q': return "'unsigned long long'"; - case 'f': return (is_complex ? "'complex float'" : "'float'"); - case 'd': return (is_complex ? "'complex double'" : "'double'"); - case 'g': return (is_complex ? "'complex long double'" : "'long double'"); - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - case 's': case 'p': return "a string"; - case 0: return "end"; - default: return "unparseable format string"; - } -} -static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return 2; - case 'i': case 'I': case 'l': case 'L': return 4; - case 'q': case 'Q': return 8; - case 'f': return (is_complex ? 8 : 4); - case 'd': return (is_complex ? 16 : 8); - case 'g': { - PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); - return 0; - } - case 'O': case 'P': return sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(short); - case 'i': case 'I': return sizeof(int); - case 'l': case 'L': return sizeof(long); - #ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(PY_LONG_LONG); - #endif - case 'f': return sizeof(float) * (is_complex ? 2 : 1); - case 'd': return sizeof(double) * (is_complex ? 2 : 1); - case 'g': return sizeof(long double) * (is_complex ? 2 : 1); - case 'O': case 'P': return sizeof(void*); - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -typedef struct { char c; short x; } __Pyx_st_short; -typedef struct { char c; int x; } __Pyx_st_int; -typedef struct { char c; long x; } __Pyx_st_long; -typedef struct { char c; float x; } __Pyx_st_float; -typedef struct { char c; double x; } __Pyx_st_double; -typedef struct { char c; long double x; } __Pyx_st_longdouble; -typedef struct { char c; void *x; } __Pyx_st_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_st_float) - sizeof(float); - case 'd': return sizeof(__Pyx_st_double) - sizeof(double); - case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -/* These are for computing the padding at the end of the struct to align - on the first member of the struct. This will probably the same as above, - but we don't have any guarantees. - */ -typedef struct { short x; char c; } __Pyx_pad_short; -typedef struct { int x; char c; } __Pyx_pad_int; -typedef struct { long x; char c; } __Pyx_pad_long; -typedef struct { float x; char c; } __Pyx_pad_float; -typedef struct { double x; char c; } __Pyx_pad_double; -typedef struct { long double x; char c; } __Pyx_pad_longdouble; -typedef struct { void *x; char c; } __Pyx_pad_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); - case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); - case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { - switch (ch) { - case 'c': - return 'H'; - case 'b': case 'h': case 'i': - case 'l': case 'q': case 's': case 'p': - return 'I'; - case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': - return 'U'; - case 'f': case 'd': case 'g': - return (is_complex ? 'C' : 'R'); - case 'O': - return 'O'; - case 'P': - return 'P'; - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { - if (ctx->head == NULL || ctx->head->field == &ctx->root) { - const char* expected; - const char* quote; - if (ctx->head == NULL) { - expected = "end"; - quote = ""; - } else { - expected = ctx->head->field->type->name; - quote = "'"; - } - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected %s%s%s but got %s", - quote, expected, quote, - __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); - } else { - __Pyx_StructField* field = ctx->head->field; - __Pyx_StructField* parent = (ctx->head - 1)->field; - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", - field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), - parent->type->name, field->name); - } -} -static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { - char group; - size_t size, offset, arraysize = 1; - if (ctx->enc_type == 0) return 0; - if (ctx->head->field->type->arraysize[0]) { - int i, ndim = 0; - if (ctx->enc_type == 's' || ctx->enc_type == 'p') { - ctx->is_valid_array = ctx->head->field->type->ndim == 1; - ndim = 1; - if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { - PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %zu", - ctx->head->field->type->arraysize[0], ctx->enc_count); - return -1; - } - } - if (!ctx->is_valid_array) { - PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", - ctx->head->field->type->ndim, ndim); - return -1; - } - for (i = 0; i < ctx->head->field->type->ndim; i++) { - arraysize *= ctx->head->field->type->arraysize[i]; - } - ctx->is_valid_array = 0; - ctx->enc_count = 1; - } - group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); - do { - __Pyx_StructField* field = ctx->head->field; - __Pyx_TypeInfo* type = field->type; - if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { - size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); - } else { - size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); - } - if (ctx->enc_packmode == '@') { - size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); - size_t align_mod_offset; - if (align_at == 0) return -1; - align_mod_offset = ctx->fmt_offset % align_at; - if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; - if (ctx->struct_alignment == 0) - ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, - ctx->is_complex); - } - if (type->size != size || type->typegroup != group) { - if (type->typegroup == 'C' && type->fields != NULL) { - size_t parent_offset = ctx->head->parent_offset + field->offset; - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = parent_offset; - continue; - } - if ((type->typegroup == 'H' || group == 'H') && type->size == size) { - } else { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - } - offset = ctx->head->parent_offset + field->offset; - if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; - } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } - } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; -} -static PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number, ndim; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ndim = ctx->head->field->type->ndim; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; - } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; - } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; - } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; -} -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; - } - break; - case '}': - { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } - } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; - } - CYTHON_FALLTHROUGH; - case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && - (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - CYTHON_FALLTHROUGH; - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: - { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; - } - } - } -} - -/* TypeInfoCompare */ - static int -__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) -{ - int i; - if (!a || !b) - return 0; - if (a == b) - return 1; - if (a->size != b->size || a->typegroup != b->typegroup || - a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { - if (a->typegroup == 'H' || b->typegroup == 'H') { - return a->size == b->size; - } else { - return 0; - } - } - if (a->ndim) { - for (i = 0; i < a->ndim; i++) - if (a->arraysize[i] != b->arraysize[i]) - return 0; - } - if (a->typegroup == 'S') { - if (a->flags != b->flags) - return 0; - if (a->fields || b->fields) { - if (!(a->fields && b->fields)) - return 0; - for (i = 0; a->fields[i].type && b->fields[i].type; i++) { - __Pyx_StructField *field_a = a->fields + i; - __Pyx_StructField *field_b = b->fields + i; - if (field_a->offset != field_b->offset || - !__pyx_typeinfo_cmp(field_a->type, field_b->type)) - return 0; - } - return !a->fields[i].type && !b->fields[i].type; - } - } - return 1; -} - -/* MemviewSliceValidateAndInit */ - static int -__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) -{ - if (buf->shape[dim] <= 1) - return 1; - if (buf->strides) { - if (spec & __Pyx_MEMVIEW_CONTIG) { - if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { - if (unlikely(buf->strides[dim] != sizeof(void *))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly contiguous " - "in dimension %d.", dim); - goto fail; - } - } else if (unlikely(buf->strides[dim] != buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_FOLLOW) { - Py_ssize_t stride = buf->strides[dim]; - if (stride < 0) - stride = -stride; - if (unlikely(stride < buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - } else { - if (unlikely(spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1)) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not contiguous in " - "dimension %d", dim); - goto fail; - } else if (unlikely(spec & (__Pyx_MEMVIEW_PTR))) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not indirect in " - "dimension %d", dim); - goto fail; - } else if (unlikely(buf->suboffsets)) { - PyErr_SetString(PyExc_ValueError, - "Buffer exposes suboffsets but no strides"); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) -{ - if (spec & __Pyx_MEMVIEW_DIRECT) { - if (unlikely(buf->suboffsets && buf->suboffsets[dim] >= 0)) { - PyErr_Format(PyExc_ValueError, - "Buffer not compatible with direct access " - "in dimension %d.", dim); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_PTR) { - if (unlikely(!buf->suboffsets || (buf->suboffsets[dim] < 0))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly accessible " - "in dimension %d.", dim); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) -{ - int i; - if (c_or_f_flag & __Pyx_IS_F_CONTIG) { - Py_ssize_t stride = 1; - for (i = 0; i < ndim; i++) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not fortran contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { - Py_ssize_t stride = 1; - for (i = ndim - 1; i >- 1; i--) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not C contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } - return 1; -fail: - return 0; -} -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj) -{ - struct __pyx_memoryview_obj *memview, *new_memview; - __Pyx_RefNannyDeclarations - Py_buffer *buf; - int i, spec = 0, retval = -1; - __Pyx_BufFmt_Context ctx; - int from_memoryview = __pyx_memoryview_check(original_obj); - __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); - if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) - original_obj)->typeinfo)) { - memview = (struct __pyx_memoryview_obj *) original_obj; - new_memview = NULL; - } else { - memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - original_obj, buf_flags, 0, dtype); - new_memview = memview; - if (unlikely(!memview)) - goto fail; - } - buf = &memview->view; - if (unlikely(buf->ndim != ndim)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - ndim, buf->ndim); - goto fail; - } - if (new_memview) { - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (unlikely(!__Pyx_BufFmt_CheckString(&ctx, buf->format))) goto fail; - } - if (unlikely((unsigned) buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " - "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", - buf->itemsize, - (buf->itemsize > 1) ? "s" : "", - dtype->name, - dtype->size, - (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->len > 0) { - for (i = 0; i < ndim; i++) { - spec = axes_specs[i]; - if (unlikely(!__pyx_check_strides(buf, i, ndim, spec))) - goto fail; - if (unlikely(!__pyx_check_suboffsets(buf, i, ndim, spec))) - goto fail; - } - if (unlikely(buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))) - goto fail; - } - if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, - new_memview != NULL) == -1)) { - goto fail; - } - retval = 0; - goto no_fail; -fail: - Py_XDECREF(new_memview); - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_FOLLOW), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 2, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 1, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_intp_t(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 1, - &__Pyx_TypeInfo_nn___pyx_t_5numpy_intp_t, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* MemviewDtypeToObject */ - static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp) { - return (PyObject *) PyFloat_FromDouble(*(float *) itemp); -} -static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj) { - float value = __pyx_PyFloat_AsFloat(obj); - if ((value == (float)-1) && PyErr_Occurred()) - return 0; - *(float *) itemp = value; - return 1; -} - -/* MemviewDtypeToObject */ - static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_5numpy_intp_t(const char *itemp) { - return (PyObject *) __Pyx_PyInt_From_Py_intptr_t(*(__pyx_t_5numpy_intp_t *) itemp); -} -static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_intp_t(const char *itemp, PyObject *obj) { - __pyx_t_5numpy_intp_t value = __Pyx_PyInt_As_Py_intptr_t(obj); - if ((value == ((npy_intp)-1)) && PyErr_Occurred()) - return 0; - *(__pyx_t_5numpy_intp_t *) itemp = value; - return 1; -} - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* MemviewSliceCopyTemplate */ - static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object) -{ - __Pyx_RefNannyDeclarations - int i; - __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; - struct __pyx_memoryview_obj *from_memview = from_mvs->memview; - Py_buffer *buf = &from_memview->view; - PyObject *shape_tuple = NULL; - PyObject *temp_int = NULL; - struct __pyx_array_obj *array_obj = NULL; - struct __pyx_memoryview_obj *memview_obj = NULL; - __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); - for (i = 0; i < ndim; i++) { - if (unlikely(from_mvs->suboffsets[i] >= 0)) { - PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " - "indirect dimensions (axis %d)", i); - goto fail; - } - } - shape_tuple = PyTuple_New(ndim); - if (unlikely(!shape_tuple)) { - goto fail; - } - __Pyx_GOTREF(shape_tuple); - for(i = 0; i < ndim; i++) { - temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); - if(unlikely(!temp_int)) { - goto fail; - } else { - PyTuple_SET_ITEM(shape_tuple, i, temp_int); - temp_int = NULL; - } - } - array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); - if (unlikely(!array_obj)) { - goto fail; - } - __Pyx_GOTREF(array_obj); - memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - (PyObject *) array_obj, contig_flag, - dtype_is_object, - from_mvs->memview->typeinfo); - if (unlikely(!memview_obj)) - goto fail; - if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) - goto fail; - if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, - dtype_is_object) < 0)) - goto fail; - goto no_fail; -fail: - __Pyx_XDECREF(new_mvs.memview); - new_mvs.memview = NULL; - new_mvs.data = NULL; -no_fail: - __Pyx_XDECREF(shape_tuple); - __Pyx_XDECREF(temp_int); - __Pyx_XDECREF(array_obj); - __Pyx_RefNannyFinishContext(); - return new_mvs; -} - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = (Py_intptr_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(Py_intptr_t) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(Py_intptr_t) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(Py_intptr_t) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(Py_intptr_t) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(Py_intptr_t) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(Py_intptr_t), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_As_Py_intptr_t(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = (Py_intptr_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(Py_intptr_t) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (Py_intptr_t) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (Py_intptr_t) 0; - case 1: __PYX_VERIFY_RETURN_INT(Py_intptr_t, digit, digits[0]) - case 2: - if (8 * sizeof(Py_intptr_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) >= 2 * PyLong_SHIFT) { - return (Py_intptr_t) (((((Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(Py_intptr_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) >= 3 * PyLong_SHIFT) { - return (Py_intptr_t) (((((((Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(Py_intptr_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) >= 4 * PyLong_SHIFT) { - return (Py_intptr_t) (((((((((Py_intptr_t)digits[3]) << PyLong_SHIFT) | (Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (Py_intptr_t) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(Py_intptr_t) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(Py_intptr_t) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (Py_intptr_t) 0; - case -1: __PYX_VERIFY_RETURN_INT(Py_intptr_t, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(Py_intptr_t, digit, +digits[0]) - case -2: - if (8 * sizeof(Py_intptr_t) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 2 * PyLong_SHIFT) { - return (Py_intptr_t) (((Py_intptr_t)-1)*(((((Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(Py_intptr_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 2 * PyLong_SHIFT) { - return (Py_intptr_t) ((((((Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(Py_intptr_t) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 3 * PyLong_SHIFT) { - return (Py_intptr_t) (((Py_intptr_t)-1)*(((((((Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(Py_intptr_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 3 * PyLong_SHIFT) { - return (Py_intptr_t) ((((((((Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(Py_intptr_t) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 4 * PyLong_SHIFT) { - return (Py_intptr_t) (((Py_intptr_t)-1)*(((((((((Py_intptr_t)digits[3]) << PyLong_SHIFT) | (Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(Py_intptr_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 4 * PyLong_SHIFT) { - return (Py_intptr_t) ((((((((((Py_intptr_t)digits[3]) << PyLong_SHIFT) | (Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - } -#endif - if (sizeof(Py_intptr_t) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(Py_intptr_t) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - Py_intptr_t val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (Py_intptr_t) -1; - } - } else { - Py_intptr_t val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (Py_intptr_t) -1; - val = __Pyx_PyInt_As_Py_intptr_t(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to Py_intptr_t"); - return (Py_intptr_t) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to Py_intptr_t"); - return (Py_intptr_t) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const size_t neg_one = (size_t) -1, const_zero = (size_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(size_t) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(size_t, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (size_t) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (size_t) 0; - case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, digits[0]) - case 2: - if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) >= 2 * PyLong_SHIFT) { - return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) >= 3 * PyLong_SHIFT) { - return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) >= 4 * PyLong_SHIFT) { - return (size_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (size_t) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(size_t) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (size_t) 0; - case -1: __PYX_VERIFY_RETURN_INT(size_t, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, +digits[0]) - case -2: - if (8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { - return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { - return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { - return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { - return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { - return (size_t) (((size_t)-1)*(((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { - return (size_t) ((((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - } -#endif - if (sizeof(size_t) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(size_t) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - size_t val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (size_t) -1; - } - } else { - size_t val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (size_t) -1; - val = __Pyx_PyInt_As_size_t(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to size_t"); - return (size_t) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to size_t"); - return (size_t) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const char neg_one = (char) -1, const_zero = (char) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(char) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (char) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (char) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(char) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) - case -2: - if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - } -#endif - if (sizeof(char) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - char val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (char) -1; - } - } else { - char val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (char) -1; - val = __Pyx_PyInt_As_char(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to char"); - return (char) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to char"); - return (char) -1; -} - -/* CheckBinaryVersion */ - static int __Pyx_check_binary_version(void) { - char ctversion[5]; - int same=1, i, found_dot; - const char* rt_from_call = Py_GetVersion(); - PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); - found_dot = 0; - for (i = 0; i < 4; i++) { - if (!ctversion[i]) { - same = (rt_from_call[i] < '0' || rt_from_call[i] > '9'); - break; - } - if (rt_from_call[i] != ctversion[i]) { - same = 0; - break; - } - } - if (!same) { - char rtversion[5] = {'\0'}; - char message[200]; - for (i=0; i<4; ++i) { - if (rt_from_call[i] == '.') { - if (found_dot) break; - found_dot = 1; - } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') { - break; - } - rtversion[i] = rt_from_call[i]; - } - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* FunctionImport */ - #ifndef __PYX_HAVE_RT_ImportFunction -#define __PYX_HAVE_RT_ImportFunction -static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig) { - PyObject *d = 0; - PyObject *cobj = 0; - union { - void (*fp)(void); - void *p; - } tmp; - d = PyObject_GetAttrString(module, (char *)"__pyx_capi__"); - if (!d) - goto bad; - cobj = PyDict_GetItemString(d, funcname); - if (!cobj) { - PyErr_Format(PyExc_ImportError, - "%.200s does not export expected C function %.200s", - PyModule_GetName(module), funcname); - goto bad; - } -#if PY_VERSION_HEX >= 0x02070000 - if (!PyCapsule_IsValid(cobj, sig)) { - PyErr_Format(PyExc_TypeError, - "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)", - PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj)); - goto bad; - } - tmp.p = PyCapsule_GetPointer(cobj, sig); -#else - {const char *desc, *s1, *s2; - desc = (const char *)PyCObject_GetDesc(cobj); - if (!desc) - goto bad; - s1 = desc; s2 = sig; - while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; } - if (*s1 != *s2) { - PyErr_Format(PyExc_TypeError, - "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)", - PyModule_GetName(module), funcname, sig, desc); - goto bad; - } - tmp.p = PyCObject_AsVoidPtr(cobj);} -#endif - *f = tmp.fp; - if (!(*f)) - goto bad; - Py_DECREF(d); - return 0; -bad: - Py_XDECREF(d); - return -1; -} -#endif - -/* InitStrings */ - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - if (PyObject_Hash(*t->p) == -1) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT -#if !CYTHON_PEP393_ENABLED -static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); - return NULL; - } - } - } -#endif - *length = PyBytes_GET_SIZE(defenc); - return defenc_c; -} -#else -static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (likely(PyUnicode_IS_ASCII(o))) { - *length = PyUnicode_GET_LENGTH(o); - return PyUnicode_AsUTF8(o); - } else { - PyUnicode_AsASCIIString(o); - return NULL; - } -#else - return PyUnicode_AsUTF8AndSize(o, length); -#endif -} -#endif -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { - return __Pyx_PyUnicode_AsStringAndSize(o, length); - } else -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - if (PyByteArray_Check(o)) { - *length = PyByteArray_GET_SIZE(o); - return PyByteArray_AS_STRING(o); - } else -#endif - { - char* result; - int r = PyBytes_AsStringAndSize(o, &result, length); - if (unlikely(r < 0)) { - return NULL; - } else { - return result; - } - } -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - int is_true = x == Py_True; - if (is_true | (x == Py_False) | (x == Py_None)) return is_true; - else return PyObject_IsTrue(x); -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) { - int retval; - if (unlikely(!x)) return -1; - retval = __Pyx_PyObject_IsTrue(x); - Py_DECREF(x); - return retval; -} -static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { -#if PY_MAJOR_VERSION >= 3 - if (PyLong_Check(result)) { - if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, - "__int__ returned non-int (type %.200s). " - "The ability to return an instance of a strict subclass of int " - "is deprecated, and may be removed in a future version of Python.", - Py_TYPE(result)->tp_name)) { - Py_DECREF(result); - return NULL; - } - return result; - } -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - type_name, type_name, Py_TYPE(result)->tp_name); - Py_DECREF(result); - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS - PyNumberMethods *m; -#endif - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x) || PyLong_Check(x))) -#else - if (likely(PyLong_Check(x))) -#endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS - m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = m->nb_int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = m->nb_long(x); - } - #else - if (likely(m && m->nb_int)) { - name = "int"; - res = m->nb_int(x); - } - #endif -#else - if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) { - res = PyNumber_Int(x); - } -#endif - if (likely(res)) { -#if PY_MAJOR_VERSION < 3 - if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) { -#else - if (unlikely(!PyLong_CheckExact(res))) { -#endif - return __Pyx_PyNumber_IntOrLongWrongResultType(res, name); - } - } - else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_TypeError, - "an integer is required"); - } - return res; -} -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { - Py_ssize_t ival; - PyObject *x; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(b); - } -#endif - if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - if (size == -1) ival = -ival; - return ival; - } else { - switch (size) { - case 2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - } - } - #endif - return PyLong_AsSsize_t(b); - } - x = PyNumber_Index(b); - if (!x) return -1; - ival = PyInt_AsSsize_t(x); - Py_DECREF(x); - return ival; -} -static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) { - if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) { - return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o); -#if PY_MAJOR_VERSION < 3 - } else if (likely(PyInt_CheckExact(o))) { - return PyInt_AS_LONG(o); -#endif - } else { - Py_ssize_t ival; - PyObject *x; - x = PyNumber_Index(o); - if (!x) return -1; - ival = PyInt_AsLong(x); - Py_DECREF(x); - return ival; - } -} -static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) { - return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False); -} -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { - return PyInt_FromSize_t(ival); -} - - -#endif /* Py_PYTHON_H */ diff --git a/package/MDAnalysis/lib/_cutil.cpp b/package/MDAnalysis/lib/_cutil.cpp deleted file mode 100644 index 10364f910dd..00000000000 --- a/package/MDAnalysis/lib/_cutil.cpp +++ /dev/null @@ -1,28266 +0,0 @@ -/* Generated by Cython 0.29.33 */ - -/* BEGIN: Cython Metadata -{ - "distutils": { - "depends": [ - "C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include\\numpy\\arrayobject.h", - "C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include\\numpy\\arrayscalars.h", - "C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include\\numpy\\ndarrayobject.h", - "C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include\\numpy\\ndarraytypes.h", - "C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include\\numpy\\ufuncobject.h", - "C:\\Users\\USER\\Desktop\\MDA_analysis\\mdanalysis\\package\\MDAnalysis\\lib\\include\\calc_distances.h" - ], - "extra_compile_args": [ - "-ffast-math", - "-O3", - "-funroll-loops", - "-fsigned-zeros", - "-std=c++11" - ], - "include_dirs": [ - "C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include", - "C:\\Users\\USER\\Desktop\\MDA_analysis\\mdanalysis\\package\\MDAnalysis/lib/include" - ], - "language": "c++", - "name": "MDAnalysis.lib._cutil", - "sources": [ - "MDAnalysis/lib/_cutil.pyx" - ] - }, - "module_name": "MDAnalysis.lib._cutil" -} -END: Cython Metadata */ - -#ifndef PY_SSIZE_T_CLEAN -#define PY_SSIZE_T_CLEAN -#endif /* PY_SSIZE_T_CLEAN */ -#include "Python.h" -#ifndef Py_PYTHON_H - #error Python headers needed to compile C extensions, please install development version of Python. -#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) - #error Cython requires Python 2.6+ or Python 3.3+. -#else -#define CYTHON_ABI "0_29_33" -#define CYTHON_HEX_VERSION 0x001D21F0 -#define CYTHON_FUTURE_DIVISION 1 -#include -#ifndef offsetof - #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) -#endif -#if !defined(WIN32) && !defined(MS_WINDOWS) - #ifndef __stdcall - #define __stdcall - #endif - #ifndef __cdecl - #define __cdecl - #endif - #ifndef __fastcall - #define __fastcall - #endif -#endif -#ifndef DL_IMPORT - #define DL_IMPORT(t) t -#endif -#ifndef DL_EXPORT - #define DL_EXPORT(t) t -#endif -#define __PYX_COMMA , -#ifndef HAVE_LONG_LONG - #if PY_VERSION_HEX >= 0x02070000 - #define HAVE_LONG_LONG - #endif -#endif -#ifndef PY_LONG_LONG - #define PY_LONG_LONG LONG_LONG -#endif -#ifndef Py_HUGE_VAL - #define Py_HUGE_VAL HUGE_VAL -#endif -#ifdef PYPY_VERSION - #define CYTHON_COMPILING_IN_PYPY 1 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 0 - #undef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 0 - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #if PY_VERSION_HEX < 0x03050000 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #undef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 0 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #undef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 1 - #undef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 0 - #undef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 0 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #undef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 0 - #undef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 0 - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 - #endif -#elif defined(PYSTON_VERSION) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 1 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #undef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 0 - #undef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 0 - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 - #endif -#elif defined(PY_NOGIL) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 1 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #ifndef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 1 - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 1 - #endif - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 -#else - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 1 - #define CYTHON_COMPILING_IN_NOGIL 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #elif !defined(CYTHON_USE_PYTYPE_LOOKUP) - #define CYTHON_USE_PYTYPE_LOOKUP 1 - #endif - #if PY_MAJOR_VERSION < 3 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #elif !defined(CYTHON_USE_PYLONG_INTERNALS) - #define CYTHON_USE_PYLONG_INTERNALS 1 - #endif - #ifndef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 1 - #endif - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #elif !defined(CYTHON_USE_UNICODE_WRITER) - #define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #elif !defined(CYTHON_FAST_THREAD_STATE) - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000) - #endif - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000) - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) - #endif - #ifndef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1) - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #elif !defined(CYTHON_USE_EXC_INFO_STACK) - #define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3) - #endif - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 - #endif -#endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #if PY_MAJOR_VERSION < 3 - #include "longintrepr.h" - #endif - #undef SHIFT - #undef BASE - #undef MASK - #ifdef SIZEOF_VOID_P - enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) }; - #endif -#endif -#ifndef __has_attribute - #define __has_attribute(x) 0 -#endif -#ifndef __has_cpp_attribute - #define __has_cpp_attribute(x) 0 -#endif -#ifndef CYTHON_RESTRICT - #if defined(__GNUC__) - #define CYTHON_RESTRICT __restrict__ - #elif defined(_MSC_VER) && _MSC_VER >= 1400 - #define CYTHON_RESTRICT __restrict - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_RESTRICT restrict - #else - #define CYTHON_RESTRICT - #endif -#endif -#ifndef CYTHON_UNUSED -# if defined(__GNUC__) -# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -#endif -#ifndef CYTHON_MAYBE_UNUSED_VAR -# if defined(__cplusplus) - template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } -# else -# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) -# endif -#endif -#ifndef CYTHON_NCP_UNUSED -# if CYTHON_COMPILING_IN_CPYTHON -# define CYTHON_NCP_UNUSED -# else -# define CYTHON_NCP_UNUSED CYTHON_UNUSED -# endif -#endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) -#ifdef _MSC_VER - #ifndef _MSC_STDINT_H_ - #if _MSC_VER < 1300 - typedef unsigned char uint8_t; - typedef unsigned int uint32_t; - #else - typedef unsigned __int8 uint8_t; - typedef unsigned __int32 uint32_t; - #endif - #endif -#else - #include -#endif -#ifndef CYTHON_FALLTHROUGH - #if defined(__cplusplus) && __cplusplus >= 201103L - #if __has_cpp_attribute(fallthrough) - #define CYTHON_FALLTHROUGH [[fallthrough]] - #elif __has_cpp_attribute(clang::fallthrough) - #define CYTHON_FALLTHROUGH [[clang::fallthrough]] - #elif __has_cpp_attribute(gnu::fallthrough) - #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] - #endif - #endif - #ifndef CYTHON_FALLTHROUGH - #if __has_attribute(fallthrough) - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - #else - #define CYTHON_FALLTHROUGH - #endif - #endif - #if defined(__clang__ ) && defined(__apple_build_version__) - #if __apple_build_version__ < 7000000 - #undef CYTHON_FALLTHROUGH - #define CYTHON_FALLTHROUGH - #endif - #endif -#endif - -#ifndef __cplusplus - #error "Cython files generated with the C++ option must be compiled with a C++ compiler." -#endif -#ifndef CYTHON_INLINE - #if defined(__clang__) - #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) - #else - #define CYTHON_INLINE inline - #endif -#endif -template -void __Pyx_call_destructor(T& x) { - x.~T(); -} -template -class __Pyx_FakeReference { - public: - __Pyx_FakeReference() : ptr(NULL) { } - __Pyx_FakeReference(const T& ref) : ptr(const_cast(&ref)) { } - T *operator->() { return ptr; } - T *operator&() { return ptr; } - operator T&() { return *ptr; } - template bool operator ==(U other) { return *ptr == other; } - template bool operator !=(U other) { return *ptr != other; } - private: - T *ptr; -}; - -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - if (type) { - PyErr_Restore(type, value, traceback); - } - return co; - } -#else - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_STACKLESS - #define METH_STACKLESS 0 -#endif -#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) - #ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - #endif - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); - typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast - #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1 - #define PyMem_RawMalloc(n) PyMem_Malloc(n) - #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) - #define PyMem_RawFree(p) PyMem_Free(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#elif PY_VERSION_HEX >= 0x03060000 - #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() -#elif PY_VERSION_HEX >= 0x03000000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#else - #define __Pyx_PyThreadState_Current _PyThreadState_Current -#endif -#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) -#include "pythread.h" -#define Py_tss_NEEDS_INIT 0 -typedef int Py_tss_t; -static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { - *key = PyThread_create_key(); - return 0; -} -static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { - Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); - *key = Py_tss_NEEDS_INIT; - return key; -} -static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { - PyObject_Free(key); -} -static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { - return *key != Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { - PyThread_delete_key(*key); - *key = Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { - return PyThread_set_key_value(*key, value); -} -static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { - return PyThread_get_key_value(*key); -} -#endif -#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) -#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) -#else -#define __Pyx_PyDict_NewPresized(n) PyDict_New() -#endif -#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION - #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) -#else - #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS -#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) -#else -#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_READY(op) (0) - #else - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #endif - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) - #else - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? 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-value : value) -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); -#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) -#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) -#define __Pyx_PyBytes_FromString PyBytes_FromString -#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); -#if PY_MAJOR_VERSION < 3 - #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString - #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize -#else - #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString - #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize -#endif -#define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) -#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) -#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) -#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) -#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) -static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { - const Py_UNICODE *u_end = u; - while (*u_end++) ; - return (size_t)(u_end - u - 1); -} -#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) -#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode -#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode -#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) -#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*); -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); -#define __Pyx_PySequence_Tuple(obj)\ - (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj)) -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); -static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*); -#if CYTHON_ASSUME_SAFE_MACROS -#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) -#else -#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) -#endif -#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) -#else -#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) -#endif -#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII -static int __Pyx_sys_getdefaultencoding_not_ascii; -static int __Pyx_init_sys_getdefaultencoding_params(void) { - PyObject* sys; - PyObject* default_encoding = NULL; - PyObject* ascii_chars_u = NULL; - PyObject* ascii_chars_b = NULL; - const char* default_encoding_c; - sys = PyImport_ImportModule("sys"); - if (!sys) goto bad; - default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); - Py_DECREF(sys); - if (!default_encoding) goto bad; - default_encoding_c = PyBytes_AsString(default_encoding); - if (!default_encoding_c) goto bad; - if (strcmp(default_encoding_c, "ascii") == 0) { - __Pyx_sys_getdefaultencoding_not_ascii = 0; - } else { - char ascii_chars[128]; - int c; - for (c = 0; c < 128; c++) { - ascii_chars[c] = c; - } - __Pyx_sys_getdefaultencoding_not_ascii = 1; - ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); - if (!ascii_chars_u) goto bad; - ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); - if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { - PyErr_Format( - PyExc_ValueError, - "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", - default_encoding_c); - goto bad; - } - Py_DECREF(ascii_chars_u); - Py_DECREF(ascii_chars_b); - } - Py_DECREF(default_encoding); - return 0; -bad: - Py_XDECREF(default_encoding); - Py_XDECREF(ascii_chars_u); 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-#endif - -/* CodeObjectCache.proto */ -typedef struct { - PyCodeObject* code_object; - int code_line; -} __Pyx_CodeObjectCacheEntry; -struct __Pyx_CodeObjectCache { - int count; - int max_count; - __Pyx_CodeObjectCacheEntry* entries; -}; -static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); -static PyCodeObject *__pyx_find_code_object(int code_line); -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); - -/* AddTraceback.proto */ -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename); - -#if PY_MAJOR_VERSION < 3 - static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); - static void __Pyx_ReleaseBuffer(Py_buffer *view); -#else - #define __Pyx_GetBuffer PyObject_GetBuffer - #define __Pyx_ReleaseBuffer PyBuffer_Release -#endif - - -/* BufferStructDeclare.proto */ -typedef struct { - Py_ssize_t shape, strides, suboffsets; -} __Pyx_Buf_DimInfo; -typedef struct { - size_t refcount; - Py_buffer pybuffer; -} __Pyx_Buffer; -typedef struct { - __Pyx_Buffer *rcbuffer; - char *data; - __Pyx_Buf_DimInfo diminfo[8]; -} __Pyx_LocalBuf_ND; - -/* MemviewSliceIsContig.proto */ -static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim); - -/* OverlappingSlices.proto */ -static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize); - -/* Capsule.proto */ -static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); - -/* IsLittleEndian.proto */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void); - -/* BufferFormatCheck.proto */ -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type); - -/* TypeInfoCompare.proto */ -static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); - -/* MemviewSliceValidateAndInit.proto */ -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_intp_t(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_nn___pyx_t_5numpy_intp_t(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_nn___pyx_t_5numpy_float64_t(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_d_dc_nn___pyx_t_5numpy_float64_t(PyObject *, int writable_flag); - -/* GCCDiagnostics.proto */ -#if defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6)) -#define __Pyx_HAS_GCC_DIAGNOSTIC -#endif - -/* MemviewDtypeToObject.proto */ -static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_5numpy_intp_t(const char *itemp); -static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_intp_t(const char *itemp, PyObject *obj); - -/* CppExceptionConversion.proto */ -#ifndef __Pyx_CppExn2PyErr -#include -#include -#include -#include -static void __Pyx_CppExn2PyErr() { - try { - if (PyErr_Occurred()) - ; // let the latest Python exn pass through and ignore the current one - else - throw; - } catch (const std::bad_alloc& exn) { - PyErr_SetString(PyExc_MemoryError, exn.what()); - } catch (const std::bad_cast& exn) { - PyErr_SetString(PyExc_TypeError, exn.what()); - } catch (const std::bad_typeid& exn) { - PyErr_SetString(PyExc_TypeError, exn.what()); - } catch (const std::domain_error& exn) { - PyErr_SetString(PyExc_ValueError, exn.what()); - } catch (const std::invalid_argument& exn) { - PyErr_SetString(PyExc_ValueError, exn.what()); - } catch (const std::ios_base::failure& exn) { - PyErr_SetString(PyExc_IOError, exn.what()); - } catch (const std::out_of_range& exn) { - PyErr_SetString(PyExc_IndexError, exn.what()); - } catch (const std::overflow_error& exn) { - PyErr_SetString(PyExc_OverflowError, exn.what()); - } catch (const std::range_error& exn) { - PyErr_SetString(PyExc_ArithmeticError, exn.what()); - } catch (const std::underflow_error& exn) { - PyErr_SetString(PyExc_ArithmeticError, exn.what()); - } catch (const std::exception& exn) { - PyErr_SetString(PyExc_RuntimeError, exn.what()); - } - catch (...) - { - PyErr_SetString(PyExc_RuntimeError, "Unknown exception"); - } -} -#endif - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_unsigned_char(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_Py_ssize_t(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *, int writable_flag); - -/* MemviewDtypeToObject.proto */ -static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp); -static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_float(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_int(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_float64_t(PyObject *, int writable_flag); - -/* MemviewDtypeToObject.proto */ -static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_5numpy_float64_t(const char *itemp); -static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_float64_t(const char *itemp, PyObject *obj); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_int64_t(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_nn___pyx_t_5numpy_int32_t(PyObject *, int writable_flag); - -/* RealImag.proto */ -#if CYTHON_CCOMPLEX - #ifdef __cplusplus - #define __Pyx_CREAL(z) ((z).real()) - #define __Pyx_CIMAG(z) ((z).imag()) - #else - #define __Pyx_CREAL(z) (__real__(z)) - #define __Pyx_CIMAG(z) (__imag__(z)) - #endif -#else - #define __Pyx_CREAL(z) ((z).real) - #define __Pyx_CIMAG(z) ((z).imag) -#endif -#if defined(__cplusplus) && CYTHON_CCOMPLEX\ - && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103) - #define __Pyx_SET_CREAL(z,x) ((z).real(x)) - #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) -#else - #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) - #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) -#endif - -/* Arithmetic.proto */ -#if CYTHON_CCOMPLEX - #define __Pyx_c_eq_float(a, b) ((a)==(b)) - #define __Pyx_c_sum_float(a, b) ((a)+(b)) - #define __Pyx_c_diff_float(a, b) ((a)-(b)) - #define __Pyx_c_prod_float(a, b) ((a)*(b)) - #define __Pyx_c_quot_float(a, b) ((a)/(b)) - #define __Pyx_c_neg_float(a) (-(a)) - #ifdef __cplusplus - #define __Pyx_c_is_zero_float(z) ((z)==(float)0) - #define __Pyx_c_conj_float(z) (::std::conj(z)) - #if 1 - #define __Pyx_c_abs_float(z) (::std::abs(z)) - #define __Pyx_c_pow_float(a, b) (::std::pow(a, b)) - #endif - #else - #define __Pyx_c_is_zero_float(z) ((z)==0) - #define __Pyx_c_conj_float(z) (conjf(z)) - #if 1 - #define __Pyx_c_abs_float(z) (cabsf(z)) - #define __Pyx_c_pow_float(a, b) (cpowf(a, b)) - #endif - #endif -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex); - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex); - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex); - #endif -#endif - -/* Arithmetic.proto */ -#if CYTHON_CCOMPLEX - #define __Pyx_c_eq_double(a, b) ((a)==(b)) - #define __Pyx_c_sum_double(a, b) ((a)+(b)) - #define __Pyx_c_diff_double(a, b) ((a)-(b)) - #define __Pyx_c_prod_double(a, b) ((a)*(b)) - #define __Pyx_c_quot_double(a, b) ((a)/(b)) - #define __Pyx_c_neg_double(a) (-(a)) - #ifdef __cplusplus - #define __Pyx_c_is_zero_double(z) ((z)==(double)0) - #define __Pyx_c_conj_double(z) (::std::conj(z)) - #if 1 - #define __Pyx_c_abs_double(z) (::std::abs(z)) - #define __Pyx_c_pow_double(a, b) (::std::pow(a, b)) - #endif - #else - #define __Pyx_c_is_zero_double(z) ((z)==0) - #define __Pyx_c_conj_double(z) (conj(z)) - #if 1 - #define __Pyx_c_abs_double(z) (cabs(z)) - #define __Pyx_c_pow_double(a, b) (cpow(a, b)) - #endif - #endif -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex); - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex); - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex); - #endif -#endif - -/* MemviewSliceCopyTemplate.proto */ -static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value); - -/* CIntFromPy.proto */ -static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_As_Py_intptr_t(PyObject *); - -/* CIntFromPy.proto */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); - -/* CIntFromPy.proto */ -static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *); - -/* CIntFromPy.proto */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); - -/* CIntFromPy.proto */ -static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); - -/* CheckBinaryVersion.proto */ -static int __Pyx_check_binary_version(void); - -/* FunctionExport.proto */ -static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig); - -/* InitStrings.proto */ -static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); - -static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *__pyx_v_self); /* proto*/ -static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto*/ -static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj); /* proto*/ -static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_dst, PyObject *__pyx_v_src); /* proto*/ -static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memoryview_obj *__pyx_v_self, struct __pyx_memoryview_obj *__pyx_v_dst, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ -static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ -static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ - -/* Module declarations from 'cython.view' */ - -/* Module declarations from 'cython' */ - -/* Module declarations from 'cpython.buffer' */ - -/* Module declarations from 'libc.string' */ - -/* Module declarations from 'libc.stdio' */ - -/* Module declarations from '__builtin__' */ - -/* Module declarations from 'cpython.type' */ -static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; - -/* Module declarations from 'cpython' */ - -/* Module declarations from 'cpython.object' */ - -/* Module declarations from 'cpython.ref' */ - -/* Module declarations from 'cpython.mem' */ - -/* Module declarations from 'numpy' */ - -/* Module declarations from 'numpy' */ -static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; -static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; -static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; -static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; -static PyTypeObject *__pyx_ptype_5numpy_generic = 0; -static PyTypeObject *__pyx_ptype_5numpy_number = 0; -static PyTypeObject *__pyx_ptype_5numpy_integer = 0; -static PyTypeObject *__pyx_ptype_5numpy_signedinteger = 0; -static PyTypeObject *__pyx_ptype_5numpy_unsignedinteger = 0; -static PyTypeObject *__pyx_ptype_5numpy_inexact = 0; -static PyTypeObject *__pyx_ptype_5numpy_floating = 0; -static PyTypeObject *__pyx_ptype_5numpy_complexfloating = 0; -static PyTypeObject *__pyx_ptype_5numpy_flexible = 0; -static PyTypeObject *__pyx_ptype_5numpy_character = 0; -static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; -static CYTHON_INLINE int __pyx_f_5numpy_import_array(void); /*proto*/ - -/* Module declarations from 'libc.math' */ - -/* Module declarations from 'libcpp.utility' */ - -/* Module declarations from 'libcpp.set' */ - -/* Module declarations from 'libcpp.map' */ - -/* Module declarations from 'libcpp.vector' */ - -/* Module declarations from 'MDAnalysis.lib._cutil' */ -static PyTypeObject *__pyx_array_type = 0; -static PyTypeObject *__pyx_MemviewEnum_type = 0; -static PyTypeObject *__pyx_memoryview_type = 0; -static PyTypeObject *__pyx_memoryviewslice_type = 0; -static PyObject *generic = 0; -static PyObject *strided = 0; -static PyObject *indirect = 0; -static PyObject *contiguous = 0; -static PyObject *indirect_contiguous = 0; -static int __pyx_memoryview_thread_locks_used; -static PyThread_type_lock __pyx_memoryview_thread_locks[8]; -static __pyx_t_10MDAnalysis_3lib_6_cutil_intset __pyx_f_10MDAnalysis_3lib_6_cutil_difference(__pyx_t_10MDAnalysis_3lib_6_cutil_intset, __pyx_t_10MDAnalysis_3lib_6_cutil_intset); /*proto*/ -static __pyx_t_5numpy_float64_t __pyx_f_10MDAnalysis_3lib_6_cutil__sarrus_det_single(__Pyx_memviewslice, int __pyx_skip_dispatch); /*proto*/ -static PyArrayObject *__pyx_f_10MDAnalysis_3lib_6_cutil__sarrus_det_multiple(__Pyx_memviewslice, int __pyx_skip_dispatch); /*proto*/ -static PyObject *__pyx_convert_vector_to_py_int(const std::vector &); /*proto*/ -static struct __pyx_array_obj *__pyx_array_new(PyObject *, Py_ssize_t, char *, char *, char *); /*proto*/ -static void *__pyx_align_pointer(void *, size_t); /*proto*/ -static PyObject *__pyx_memoryview_new(PyObject *, int, int, __Pyx_TypeInfo *); /*proto*/ -static CYTHON_INLINE int __pyx_memoryview_check(PyObject *); /*proto*/ -static PyObject *_unellipsify(PyObject *, int); /*proto*/ -static PyObject *assert_direct_dimensions(Py_ssize_t *, int); /*proto*/ -static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_obj *, PyObject *); /*proto*/ -static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int, int); /*proto*/ -static char *__pyx_pybuffer_index(Py_buffer *, char *, Py_ssize_t, Py_ssize_t); /*proto*/ -static int __pyx_memslice_transpose(__Pyx_memviewslice *); /*proto*/ -static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice, int, PyObject *(*)(char *), int (*)(char *, PyObject *), int); /*proto*/ -static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/ -static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/ -static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/ -static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/ -static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/ -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/ -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/ -static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/ -static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/ -static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/ -static int __pyx_memoryview_err(PyObject *, char *); /*proto*/ -static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/ -static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/ -static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/ -static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ -static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ -static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ -static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ -static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *, PyObject *); /*proto*/ -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_intp_t = { "intp_t", NULL, sizeof(__pyx_t_5numpy_intp_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_intp_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_intp_t), 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t = { "float64_t", NULL, sizeof(__pyx_t_5numpy_float64_t), { 0 }, 0, 'R', 0, 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_unsigned_char = { "unsigned char", NULL, sizeof(unsigned char), { 0 }, 0, IS_UNSIGNED(unsigned char) ? 'U' : 'I', IS_UNSIGNED(unsigned char), 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_Py_ssize_t = { "Py_ssize_t", NULL, sizeof(Py_ssize_t), { 0 }, 0, IS_UNSIGNED(Py_ssize_t) ? 'U' : 'I', IS_UNSIGNED(Py_ssize_t), 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_float = { "float", NULL, sizeof(float), { 0 }, 0, 'R', 0, 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_int = { "int", NULL, sizeof(int), { 0 }, 0, IS_UNSIGNED(int) ? 'U' : 'I', IS_UNSIGNED(int), 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t = { "int64_t", NULL, sizeof(__pyx_t_5numpy_int64_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int64_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int64_t), 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int32_t = { "int32_t", NULL, sizeof(__pyx_t_5numpy_int32_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int32_t) ? 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-static const char __pyx_k_ix[] = "ix"; -static const char __pyx_k_np[] = "np"; -static const char __pyx_k_all[] = "__all__"; -static const char __pyx_k_box[] = "box"; -static const char __pyx_k_new[] = "__new__"; -static const char __pyx_k_obj[] = "obj"; -static const char __pyx_k_out[] = "out"; -static const char __pyx_k_ref[] = "ref"; -static const char __pyx_k_vec[] = "vec"; -static const char __pyx_k_arr1[] = "arr1"; -static const char __pyx_k_arr2[] = "arr2"; -static const char __pyx_k_atom[] = "atom"; -static const char __pyx_k_base[] = "base"; -static const char __pyx_k_dict[] = "__dict__"; -static const char __pyx_k_done[] = "done"; -static const char __pyx_k_hits[] = "hits"; -static const char __pyx_k_in2d[] = "_in2d"; -static const char __pyx_k_intp[] = "intp"; -static const char __pyx_k_main[] = "__main__"; -static const char __pyx_k_mode[] = "mode"; -static const char __pyx_k_name[] = "name"; -static const char __pyx_k_ndim[] = "ndim"; -static const char __pyx_k_pack[] = "pack"; -static const char __pyx_k_size[] = "size"; -static const char __pyx_k_sort[] = "sort"; -static const char __pyx_k_step[] = "step"; -static const char __pyx_k_stop[] = "stop"; -static const char __pyx_k_test[] = "__test__"; -static const char __pyx_k_todo[] = "todo"; -static const char __pyx_k_ASCII[] = "ASCII"; -static const char __pyx_k_array[] = "array"; -static const char __pyx_k_atoms[] = "atoms"; -static const char __pyx_k_bonds[] = "bonds"; -static const char __pyx_k_class[] = "__class__"; -static const char __pyx_k_dtype[] = "dtype"; -static const char __pyx_k_empty[] = "empty"; -static const char __pyx_k_error[] = "error"; -static const char __pyx_k_flags[] = "flags"; -static const char __pyx_k_frags[] = "frags"; -static const char __pyx_k_int32[] = "int32"; -static const char __pyx_k_int64[] = "int64"; -static const char __pyx_k_numpy[] = "numpy"; -static const char __pyx_k_ortho[] = "ortho"; -static const char __pyx_k_other[] = "other"; -static const char __pyx_k_range[] = "range"; -static const char __pyx_k_shape[] = "shape"; -static const char __pyx_k_start[] = "start"; -static const char __pyx_k_uint8[] = "uint8"; -static const char __pyx_k_zeros[] = "zeros"; -static const char __pyx_k_astype[] = "astype"; -static const char __pyx_k_encode[] = "encode"; -static const char __pyx_k_format[] = "format"; -static const char __pyx_k_import[] = "__import__"; -static const char __pyx_k_name_2[] = "__name__"; -static const char __pyx_k_natoms[] = "natoms"; -static const char __pyx_k_newpos[] = "newpos"; -static const char __pyx_k_nloops[] = "nloops"; -static const char __pyx_k_oldpos[] = "oldpos"; -static const char __pyx_k_pickle[] = "pickle"; -static const char __pyx_k_reduce[] = "__reduce__"; -static const char __pyx_k_result[] = "result"; -static const char __pyx_k_struct[] = "struct"; -static const char __pyx_k_unpack[] = "unpack"; -static const char __pyx_k_update[] = "update"; -static const char __pyx_k_values[] = "values"; -static const char __pyx_k_asarray[] = "asarray"; -static const char __pyx_k_bonding[] = "bonding"; -static const char __pyx_k_bondmap[] = "bondmap"; -static const char __pyx_k_float32[] = "float32"; -static const char __pyx_k_float64[] = "float64"; -static const char __pyx_k_fortran[] = "fortran"; -static const char __pyx_k_inplace[] = "inplace"; -static const char __pyx_k_ix_view[] = "ix_view"; -static const char __pyx_k_mdamath[] = "mdamath"; -static const char __pyx_k_memview[] = "memview"; -static const char __pyx_k_results[] = "results"; -static const char __pyx_k_tri_box[] = "tri_box"; -static const char __pyx_k_Ellipsis[] = "Ellipsis"; -static const char __pyx_k_bondlist[] = "bondlist"; -static const char __pyx_k_getstate[] = "__getstate__"; -static const char __pyx_k_half_box[] = "half_box"; -static const char __pyx_k_itemsize[] = "itemsize"; -static const char __pyx_k_n_values[] = "n_values"; -static const char __pyx_k_pyx_type[] = "__pyx_type"; -static const char __pyx_k_setstate[] = "__setstate__"; -static const char __pyx_k_TypeError[] = "TypeError"; -static const char __pyx_k_atomgroup[] = "atomgroup"; -static const char __pyx_k_enumerate[] = "enumerate"; -static const char __pyx_k_frag_done[] = "frag_done"; -static const char __pyx_k_frag_todo[] = "frag_todo"; -static const char __pyx_k_ix_to_rel[] = "ix_to_rel"; -static const char __pyx_k_positions[] = "positions"; -static const char __pyx_k_pyx_state[] = "__pyx_state"; -static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; -static const char __pyx_k_refpoints[] = "refpoints"; -static const char __pyx_k_this_frag[] = "this_frag"; -static const char __pyx_k_IndexError[] = "IndexError"; -static const char __pyx_k_MDAnalysis[] = "MDAnalysis"; -static const char __pyx_k_ValueError[] = "ValueError"; -static const char __pyx_k_atoms_view[] = "atoms_view"; -static const char __pyx_k_bonds_view[] = "bonds_view"; -static const char __pyx_k_dimensions[] = "dimensions"; -static const char __pyx_k_make_whole[] = "make_whole"; -static const char __pyx_k_pyx_result[] = "__pyx_result"; -static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; -static const char __pyx_k_to_indices[] = "to_indices"; -static const char __pyx_k_ImportError[] = "ImportError"; -static const char __pyx_k_MemoryError[] = "MemoryError"; -static const char __pyx_k_NoDataError[] = "NoDataError"; -static const char __pyx_k_PickleError[] = "PickleError"; -static const char __pyx_k_inverse_box[] = "inverse_box"; -static const char __pyx_k_is_monotonic[] = "is_monotonic"; -static const char __pyx_k_is_unwrapped[] = "is_unwrapped"; -static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; -static const char __pyx_k_stringsource[] = "stringsource"; -static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; -static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; -static const char __pyx_k_unique_int_1d[] = "unique_int_1d"; -static const char __pyx_k_AttributeError[] = "AttributeError"; -static const char __pyx_k_find_fragments[] = "find_fragments"; -static const char __pyx_k_reference_atom[] = "reference_atom"; -static const char __pyx_k_View_MemoryView[] = "View.MemoryView"; -static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; -static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; -static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; -static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; -static const char __pyx_k_pyx_unpickle_Enum[] = "__pyx_unpickle_Enum"; -static const char __pyx_k_sarrus_det_single[] = "_sarrus_det_single"; -static const char __pyx_k_triclinic_vectors[] = "triclinic_vectors"; -static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; -static const char __pyx_k_strided_and_direct[] = ""; -static const char __pyx_k_sarrus_det_multiple[] = "_sarrus_det_multiple"; -static const char __pyx_k_strided_and_indirect[] = ""; -static const char __pyx_k_MDAnalysis_lib__cutil[] = "MDAnalysis.lib._cutil"; -static const char __pyx_k_contiguous_and_direct[] = ""; -static const char __pyx_k_MemoryView_of_r_object[] = ""; -static const char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; -static const char __pyx_k_contiguous_and_indirect[] = ""; -static const char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; -static const char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; -static const char __pyx_k_MDAnalysis_lib__cutil_pyx[] = "MDAnalysis\\lib\\_cutil.pyx"; -static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; -static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; -static const char __pyx_k_Both_arrays_must_be_n_2_arrays[] = "Both arrays must be (n, 2) arrays"; -static const char __pyx_k_strided_and_direct_or_indirect[] = ""; -static const char __pyx_k_Reference_atom_not_in_atomgroup[] = "Reference atom not in atomgroup"; -static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; -static const char __pyx_k_AtomGroup_was_not_contiguous_fro[] = "AtomGroup was not contiguous from bonds, process failed"; -static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; -static const char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; -static const char __pyx_k_Cannot_assign_to_read_only_memor[] = "Cannot assign to read-only memoryview"; -static const char __pyx_k_Cannot_create_writable_memory_vi[] = "Cannot create writable memory view from read-only memoryview"; -static const char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; -static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0xb068931, 0x82a3537, 0x6ae9995) = (name))"; -static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; -static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; -static const char __pyx_k_No_box_information_available_You[] = "No box information available. You can set dimensions using 'atomgroup.dimensions='"; -static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; -static const char __pyx_k_The_atomgroup_is_required_to_hav[] = "The atomgroup is required to have bonds"; -static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; -static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; -static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; -static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; -static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; -static PyObject *__pyx_n_s_ASCII; -static PyObject *__pyx_kp_u_AtomGroup_was_not_contiguous_fro; -static PyObject *__pyx_n_s_AttributeError; -static PyObject *__pyx_kp_u_Both_arrays_must_be_n_2_arrays; 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*/ - (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); - - /* "View.MemoryView":1161 - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * else: - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1162 - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L4:; - - /* "View.MemoryView":1154 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1164 - * dst_data += dst_stride - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * _copy_strided_to_strided(src_data, src_strides + 1, - * dst_data, dst_strides + 1, - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - __pyx_t_5 = __pyx_t_4; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1165 - * else: - * for i in range(dst_extent): - * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< - * dst_data, dst_strides + 1, - * src_shape + 1, dst_shape + 1, - */ - _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - - /* "View.MemoryView":1169 - * src_shape + 1, dst_shape + 1, - * ndim - 1, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1170 - * ndim - 1, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L3:; - - /* "View.MemoryView":1142 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - - /* function exit code */ -} - -/* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - -static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - - /* "View.MemoryView":1175 - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< - * src.shape, dst.shape, ndim, itemsize) - * - */ - _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - - /* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - - /* function exit code */ -} - -/* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { - Py_ssize_t __pyx_v_shape; - Py_ssize_t __pyx_v_size; - Py_ssize_t __pyx_r; - Py_ssize_t __pyx_t_1; - Py_ssize_t *__pyx_t_2; - Py_ssize_t *__pyx_t_3; - Py_ssize_t *__pyx_t_4; - - /* "View.MemoryView":1181 - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize # <<<<<<<<<<<<<< - * - * for shape in src.shape[:ndim]: - */ - __pyx_t_1 = __pyx_v_src->memview->view.itemsize; - __pyx_v_size = __pyx_t_1; - - /* "View.MemoryView":1183 - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - * - * for shape in src.shape[:ndim]: # <<<<<<<<<<<<<< - * size *= shape - * - */ - __pyx_t_3 = (__pyx_v_src->shape + __pyx_v_ndim); - for (__pyx_t_4 = __pyx_v_src->shape; __pyx_t_4 < __pyx_t_3; __pyx_t_4++) { - __pyx_t_2 = __pyx_t_4; - __pyx_v_shape = (__pyx_t_2[0]); - - /* "View.MemoryView":1184 - * - * for shape in src.shape[:ndim]: - * size *= shape # <<<<<<<<<<<<<< - * - * return size - */ - __pyx_v_size = (__pyx_v_size * __pyx_v_shape); - } - - /* "View.MemoryView":1186 - * size *= shape - * - * return size # <<<<<<<<<<<<<< - * - * @cname('__pyx_fill_contig_strides_array') - */ - __pyx_r = __pyx_v_size; - goto __pyx_L0; - - /* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1189 - * - * @cname('__pyx_fill_contig_strides_array') - * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< - * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, - * int ndim, char order) nogil: - */ - -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { - int __pyx_v_idx; - Py_ssize_t __pyx_r; - int __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - int __pyx_t_4; - - /* "View.MemoryView":1198 - * cdef int idx - * - * if order == 'F': # <<<<<<<<<<<<<< - * for idx in range(ndim): - * strides[idx] = stride - */ - __pyx_t_1 = ((__pyx_v_order == 'F') != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1199 - * - * if order == 'F': - * for idx in range(ndim): # <<<<<<<<<<<<<< - * strides[idx] = stride - * stride *= shape[idx] - */ - __pyx_t_2 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_2; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { - __pyx_v_idx = __pyx_t_4; - - /* "View.MemoryView":1200 - * if order == 'F': - * for idx in range(ndim): - * strides[idx] = stride # <<<<<<<<<<<<<< - * stride *= shape[idx] - * else: - */ - (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - - /* "View.MemoryView":1201 - * for idx in range(ndim): - * strides[idx] = stride - * stride *= shape[idx] # <<<<<<<<<<<<<< - * else: - * for idx in range(ndim - 1, -1, -1): - */ - __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); - } - - /* "View.MemoryView":1198 - * cdef int idx - * - * if order == 'F': # <<<<<<<<<<<<<< - * for idx in range(ndim): - * strides[idx] = stride - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1203 - * stride *= shape[idx] - * else: - * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< - * strides[idx] = stride - * stride *= shape[idx] - */ - /*else*/ { - for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { - __pyx_v_idx = __pyx_t_2; - - /* "View.MemoryView":1204 - * else: - * for idx in range(ndim - 1, -1, -1): - * strides[idx] = stride # <<<<<<<<<<<<<< - * stride *= shape[idx] - * - */ - (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - - /* "View.MemoryView":1205 - * for idx in range(ndim - 1, -1, -1): - * strides[idx] = stride - * stride *= shape[idx] # <<<<<<<<<<<<<< - * - * return stride - */ - __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); - } - } - __pyx_L3:; - - /* "View.MemoryView":1207 - * stride *= shape[idx] - * - * return stride # <<<<<<<<<<<<<< - * - * @cname('__pyx_memoryview_copy_data_to_temp') - */ - __pyx_r = __pyx_v_stride; - goto __pyx_L0; - - /* "View.MemoryView":1189 - * - * @cname('__pyx_fill_contig_strides_array') - * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< - * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, - * int ndim, char order) nogil: - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1210 - * - * @cname('__pyx_memoryview_copy_data_to_temp') - * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *tmpslice, - * char order, - */ - -static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_tmpslice, char __pyx_v_order, int __pyx_v_ndim) { - int __pyx_v_i; - void *__pyx_v_result; - size_t __pyx_v_itemsize; - size_t __pyx_v_size; - void *__pyx_r; - Py_ssize_t __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - struct __pyx_memoryview_obj *__pyx_t_4; - int __pyx_t_5; - int __pyx_t_6; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - - /* "View.MemoryView":1221 - * cdef void *result - * - * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< - * cdef size_t size = slice_get_size(src, ndim) - * - */ - __pyx_t_1 = __pyx_v_src->memview->view.itemsize; - __pyx_v_itemsize = __pyx_t_1; - - /* "View.MemoryView":1222 - * - * cdef size_t itemsize = src.memview.view.itemsize - * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<< - * - * result = malloc(size) - */ - __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim); - - /* "View.MemoryView":1224 - * cdef size_t size = slice_get_size(src, ndim) - * - * result = malloc(size) # <<<<<<<<<<<<<< - * if not result: - * _err(MemoryError, NULL) - */ - __pyx_v_result = malloc(__pyx_v_size); - - /* "View.MemoryView":1225 - * - * result = malloc(size) - * if not result: # <<<<<<<<<<<<<< - * _err(MemoryError, NULL) - * - */ - __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1226 - * result = malloc(size) - * if not result: - * _err(MemoryError, NULL) # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 1226, __pyx_L1_error) - - /* "View.MemoryView":1225 - * - * result = malloc(size) - * if not result: # <<<<<<<<<<<<<< - * _err(MemoryError, NULL) - * - */ - } - - /* "View.MemoryView":1229 - * - * - * tmpslice.data = result # <<<<<<<<<<<<<< - * tmpslice.memview = src.memview - * for i in range(ndim): - */ - __pyx_v_tmpslice->data = ((char *)__pyx_v_result); - - /* "View.MemoryView":1230 - * - * tmpslice.data = result - * tmpslice.memview = src.memview # <<<<<<<<<<<<<< - * for i in range(ndim): - * tmpslice.shape[i] = src.shape[i] - */ - __pyx_t_4 = __pyx_v_src->memview; - __pyx_v_tmpslice->memview = __pyx_t_4; - - /* "View.MemoryView":1231 - * tmpslice.data = result - * tmpslice.memview = src.memview - * for i in range(ndim): # <<<<<<<<<<<<<< - * tmpslice.shape[i] = src.shape[i] - * tmpslice.suboffsets[i] = -1 - */ - __pyx_t_3 = __pyx_v_ndim; - __pyx_t_5 = __pyx_t_3; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1232 - * tmpslice.memview = src.memview - * for i in range(ndim): - * tmpslice.shape[i] = src.shape[i] # <<<<<<<<<<<<<< - * tmpslice.suboffsets[i] = -1 - * - */ - (__pyx_v_tmpslice->shape[__pyx_v_i]) = (__pyx_v_src->shape[__pyx_v_i]); - - /* "View.MemoryView":1233 - * for i in range(ndim): - * tmpslice.shape[i] = src.shape[i] - * tmpslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< - * - * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, - */ - (__pyx_v_tmpslice->suboffsets[__pyx_v_i]) = -1L; - } - - /* "View.MemoryView":1235 - * tmpslice.suboffsets[i] = -1 - * - * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, # <<<<<<<<<<<<<< - * ndim, order) - * - */ - (void)(__pyx_fill_contig_strides_array((&(__pyx_v_tmpslice->shape[0])), (&(__pyx_v_tmpslice->strides[0])), __pyx_v_itemsize, __pyx_v_ndim, __pyx_v_order)); - - /* "View.MemoryView":1239 - * - * - * for i in range(ndim): # <<<<<<<<<<<<<< - * if tmpslice.shape[i] == 1: - * tmpslice.strides[i] = 0 - */ - __pyx_t_3 = __pyx_v_ndim; - __pyx_t_5 = __pyx_t_3; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1240 - * - * for i in range(ndim): - * if tmpslice.shape[i] == 1: # <<<<<<<<<<<<<< - * tmpslice.strides[i] = 0 - * - */ - __pyx_t_2 = (((__pyx_v_tmpslice->shape[__pyx_v_i]) == 1) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1241 - * for i in range(ndim): - * if tmpslice.shape[i] == 1: - * tmpslice.strides[i] = 0 # <<<<<<<<<<<<<< - * - * if slice_is_contig(src[0], order, ndim): - */ - (__pyx_v_tmpslice->strides[__pyx_v_i]) = 0; - - /* "View.MemoryView":1240 - * - * for i in range(ndim): - * if tmpslice.shape[i] == 1: # <<<<<<<<<<<<<< - * tmpslice.strides[i] = 0 - * - */ - } - } - - /* "View.MemoryView":1243 - * tmpslice.strides[i] = 0 - * - * if slice_is_contig(src[0], order, ndim): # <<<<<<<<<<<<<< - * memcpy(result, src.data, size) - * else: - */ - __pyx_t_2 = (__pyx_memviewslice_is_contig((__pyx_v_src[0]), __pyx_v_order, __pyx_v_ndim) != 0); - if (__pyx_t_2) { - 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* if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< - * if src.shape[i] == 1: - * broadcasting = True - */ - } - - /* "View.MemoryView":1301 - * _err_extents(i, dst.shape[i], src.shape[i]) - * - * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - */ - __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1302 - * - * if src.suboffsets[i] >= 0: - * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<< - * - * if slices_overlap(&src, &dst, ndim, itemsize): - */ - __pyx_t_6 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1302, __pyx_L1_error) - - /* "View.MemoryView":1301 - * _err_extents(i, dst.shape[i], src.shape[i]) - * - * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - */ - } - } - - /* "View.MemoryView":1304 - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< - * - * if not slice_is_contig(src, order, ndim): - */ - __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1306 - * if slices_overlap(&src, &dst, ndim, itemsize): - * - * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< - * order = get_best_order(&dst, ndim) - * - */ - __pyx_t_2 = ((!(__pyx_memviewslice_is_contig(__pyx_v_src, __pyx_v_order, __pyx_v_ndim) != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1307 - * - * if not slice_is_contig(src, order, ndim): - * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<< - * - * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) - */ - __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim); - - /* "View.MemoryView":1306 - * if slices_overlap(&src, &dst, ndim, itemsize): - * - * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< - * order = get_best_order(&dst, ndim) - * - */ - } - - /* "View.MemoryView":1309 - * order = get_best_order(&dst, ndim) - * - * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<< - * src = tmp - * - */ - __pyx_t_7 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_7 == ((void *)NULL))) __PYX_ERR(2, 1309, __pyx_L1_error) - __pyx_v_tmpdata = __pyx_t_7; - - /* "View.MemoryView":1310 - * - * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) - * src = tmp # <<<<<<<<<<<<<< - * - * if not broadcasting: - */ - __pyx_v_src = __pyx_v_tmp; - - /* "View.MemoryView":1304 - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< - * - * if not slice_is_contig(src, order, ndim): - */ - } - - /* "View.MemoryView":1312 - * src = tmp - * - * if not broadcasting: # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1315 - * - * - * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - */ - __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'C', __pyx_v_ndim) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1316 - * - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) # <<<<<<<<<<<<<< - * elif slice_is_contig(src, 'F', ndim): - * direct_copy = slice_is_contig(dst, 'F', ndim) - */ - __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'C', __pyx_v_ndim); - - /* "View.MemoryView":1315 - * - * - * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - */ - goto __pyx_L12; - } - - /* "View.MemoryView":1317 - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - */ - __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'F', __pyx_v_ndim) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1318 - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - * direct_copy = slice_is_contig(dst, 'F', ndim) # <<<<<<<<<<<<<< - * - * if direct_copy: - */ - __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'F', __pyx_v_ndim); - - /* "View.MemoryView":1317 - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - */ - } - __pyx_L12:; - - /* "View.MemoryView":1320 - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - * if direct_copy: # <<<<<<<<<<<<<< - * - * refcount_copying(&dst, dtype_is_object, ndim, False) - */ - __pyx_t_2 = (__pyx_v_direct_copy != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1322 - * if direct_copy: - * - * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) - * refcount_copying(&dst, dtype_is_object, ndim, True) - */ - __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - - /* "View.MemoryView":1323 - * - * refcount_copying(&dst, dtype_is_object, ndim, False) - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< - * refcount_copying(&dst, dtype_is_object, ndim, True) - * free(tmpdata) - */ - (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim))); - - /* "View.MemoryView":1324 - * refcount_copying(&dst, dtype_is_object, ndim, False) - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) - * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< - * free(tmpdata) - * return 0 - */ - __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - 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} - #endif - PyObject_GC_UnTrack(o); - Py_CLEAR(p->name); - (*Py_TYPE(o)->tp_free)(o); -} - -static int __pyx_tp_traverse_Enum(PyObject *o, visitproc v, void *a) { - int e; - struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; - if (p->name) { - e = (*v)(p->name, a); if (e) return e; - } - return 0; -} - -static int __pyx_tp_clear_Enum(PyObject *o) { - PyObject* tmp; - struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; - tmp = ((PyObject*)p->name); - p->name = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - return 0; -} - -static PyMethodDef __pyx_methods_Enum[] = { - {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_MemviewEnum_1__reduce_cython__, METH_NOARGS, 0}, - {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_MemviewEnum_3__setstate_cython__, METH_O, 0}, - {0, 0, 0, 0} -}; - -static PyTypeObject __pyx_type___pyx_MemviewEnum = { - PyVarObject_HEAD_INIT(0, 0) - "MDAnalysis.lib._cutil.Enum", /*tp_name*/ - sizeof(struct __pyx_MemviewEnum_obj), /*tp_basicsize*/ - 0, /*tp_itemsize*/ - __pyx_tp_dealloc_Enum, /*tp_dealloc*/ - #if PY_VERSION_HEX < 0x030800b4 - 0, /*tp_print*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 - 0, /*tp_vectorcall_offset*/ - #endif - 0, /*tp_getattr*/ - 0, /*tp_setattr*/ - #if PY_MAJOR_VERSION < 3 - 0, /*tp_compare*/ - #endif - #if PY_MAJOR_VERSION >= 3 - 0, /*tp_as_async*/ - #endif - __pyx_MemviewEnum___repr__, /*tp_repr*/ - 0, /*tp_as_number*/ - 0, /*tp_as_sequence*/ - 0, /*tp_as_mapping*/ - 0, /*tp_hash*/ - 0, /*tp_call*/ - 0, /*tp_str*/ - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - 0, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - 0, /*tp_doc*/ - __pyx_tp_traverse_Enum, /*tp_traverse*/ - __pyx_tp_clear_Enum, /*tp_clear*/ - 0, /*tp_richcompare*/ - 0, /*tp_weaklistoffset*/ - 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_Enum, /*tp_methods*/ - 0, /*tp_members*/ - 0, /*tp_getset*/ - 0, /*tp_base*/ - 0, /*tp_dict*/ - 0, /*tp_descr_get*/ - 0, /*tp_descr_set*/ - 0, /*tp_dictoffset*/ - __pyx_MemviewEnum___init__, /*tp_init*/ - 0, /*tp_alloc*/ - __pyx_tp_new_Enum, /*tp_new*/ - 0, /*tp_free*/ - 0, /*tp_is_gc*/ - 0, /*tp_bases*/ - 0, /*tp_mro*/ - 0, /*tp_cache*/ - 0, /*tp_subclasses*/ - 0, /*tp_weaklist*/ - 0, /*tp_del*/ - 0, /*tp_version_tag*/ - #if PY_VERSION_HEX >= 0x030400a1 - 0, /*tp_finalize*/ - #endif - #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) - 0, /*tp_vectorcall*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 - 0, /*tp_print*/ - #endif - #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 - 0, /*tp_pypy_flags*/ - #endif -}; -static struct __pyx_vtabstruct_memoryview __pyx_vtable_memoryview; - -static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_memoryview_obj *p; - PyObject *o; - if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { - o = (*t->tp_alloc)(t, 0); - } else { - o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); - } - if (unlikely(!o)) return 0; - p = ((struct __pyx_memoryview_obj *)o); - p->__pyx_vtab = __pyx_vtabptr_memoryview; - p->obj = Py_None; Py_INCREF(Py_None); - p->_size = Py_None; Py_INCREF(Py_None); - p->_array_interface = Py_None; Py_INCREF(Py_None); - p->view.obj = NULL; - if (unlikely(__pyx_memoryview___cinit__(o, a, k) < 0)) goto bad; - return o; - bad: - Py_DECREF(o); o = 0; - return NULL; -} - -static void __pyx_tp_dealloc_memoryview(PyObject *o) { - struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; - #if CYTHON_USE_TP_FINALIZE - if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { - if (PyObject_CallFinalizerFromDealloc(o)) return; - } - #endif - PyObject_GC_UnTrack(o); - { - PyObject *etype, *eval, *etb; - PyErr_Fetch(&etype, &eval, &etb); - __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); - __pyx_memoryview___dealloc__(o); - __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); - PyErr_Restore(etype, eval, etb); - } - Py_CLEAR(p->obj); - Py_CLEAR(p->_size); - Py_CLEAR(p->_array_interface); - (*Py_TYPE(o)->tp_free)(o); -} - -static int __pyx_tp_traverse_memoryview(PyObject *o, visitproc v, void *a) { - int e; - struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; - if (p->obj) { - e = (*v)(p->obj, a); if (e) return e; - } - if (p->_size) { - e = (*v)(p->_size, a); if (e) return e; - } - if (p->_array_interface) { - e = (*v)(p->_array_interface, a); if (e) return e; - } - if (p->view.obj) { - e = (*v)(p->view.obj, a); if (e) return e; - } - return 0; -} - -static int __pyx_tp_clear_memoryview(PyObject *o) { - PyObject* tmp; - struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; - tmp = ((PyObject*)p->obj); - p->obj = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->_size); - p->_size = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->_array_interface); - p->_array_interface = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - Py_CLEAR(p->view.obj); - return 0; -} -static PyObject *__pyx_sq_item_memoryview(PyObject *o, Py_ssize_t i) { - PyObject *r; - PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; - r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); - Py_DECREF(x); - return r; -} - -static int __pyx_mp_ass_subscript_memoryview(PyObject *o, PyObject *i, PyObject *v) { - if (v) { - return __pyx_memoryview___setitem__(o, i, v); - } - else { - PyErr_Format(PyExc_NotImplementedError, - "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name); - return -1; - } -} - -static PyObject *__pyx_getprop___pyx_memoryview_T(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_1T_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_base(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_4base_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_shape(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_5shape_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_strides(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_7strides_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_suboffsets(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_10suboffsets_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_ndim(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_4ndim_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_itemsize(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_8itemsize_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_nbytes(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_6nbytes_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_size(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_4size_1__get__(o); -} - -static PyMethodDef __pyx_methods_memoryview[] = { - {"is_c_contig", (PyCFunction)__pyx_memoryview_is_c_contig, METH_NOARGS, 0}, - {"is_f_contig", (PyCFunction)__pyx_memoryview_is_f_contig, METH_NOARGS, 0}, - {"copy", (PyCFunction)__pyx_memoryview_copy, METH_NOARGS, 0}, - {"copy_fortran", (PyCFunction)__pyx_memoryview_copy_fortran, METH_NOARGS, 0}, - {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_1__reduce_cython__, METH_NOARGS, 0}, - {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_3__setstate_cython__, METH_O, 0}, - {0, 0, 0, 0} -}; - -static struct PyGetSetDef __pyx_getsets_memoryview[] = { - {(char *)"T", __pyx_getprop___pyx_memoryview_T, 0, (char *)0, 0}, - {(char *)"base", __pyx_getprop___pyx_memoryview_base, 0, (char *)0, 0}, - {(char *)"shape", __pyx_getprop___pyx_memoryview_shape, 0, (char *)0, 0}, - {(char *)"strides", __pyx_getprop___pyx_memoryview_strides, 0, (char *)0, 0}, - {(char *)"suboffsets", __pyx_getprop___pyx_memoryview_suboffsets, 0, (char *)0, 0}, - {(char *)"ndim", __pyx_getprop___pyx_memoryview_ndim, 0, (char *)0, 0}, - {(char *)"itemsize", __pyx_getprop___pyx_memoryview_itemsize, 0, (char *)0, 0}, - {(char *)"nbytes", __pyx_getprop___pyx_memoryview_nbytes, 0, (char *)0, 0}, - {(char *)"size", __pyx_getprop___pyx_memoryview_size, 0, (char *)0, 0}, - {0, 0, 0, 0, 0} -}; - -static PySequenceMethods __pyx_tp_as_sequence_memoryview = { - __pyx_memoryview___len__, /*sq_length*/ - 0, /*sq_concat*/ - 0, /*sq_repeat*/ - __pyx_sq_item_memoryview, /*sq_item*/ - 0, /*sq_slice*/ - 0, /*sq_ass_item*/ - 0, /*sq_ass_slice*/ - 0, /*sq_contains*/ - 0, /*sq_inplace_concat*/ - 0, /*sq_inplace_repeat*/ -}; - -static PyMappingMethods __pyx_tp_as_mapping_memoryview = { - __pyx_memoryview___len__, /*mp_length*/ - __pyx_memoryview___getitem__, /*mp_subscript*/ - __pyx_mp_ass_subscript_memoryview, /*mp_ass_subscript*/ -}; - -static PyBufferProcs __pyx_tp_as_buffer_memoryview = { - #if PY_MAJOR_VERSION < 3 - 0, /*bf_getreadbuffer*/ - #endif - #if PY_MAJOR_VERSION < 3 - 0, /*bf_getwritebuffer*/ - #endif - #if PY_MAJOR_VERSION < 3 - 0, /*bf_getsegcount*/ - #endif - #if PY_MAJOR_VERSION < 3 - 0, /*bf_getcharbuffer*/ - #endif - __pyx_memoryview_getbuffer, /*bf_getbuffer*/ - 0, /*bf_releasebuffer*/ -}; - -static PyTypeObject __pyx_type___pyx_memoryview = { - PyVarObject_HEAD_INIT(0, 0) - "MDAnalysis.lib._cutil.memoryview", /*tp_name*/ - sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/ - 0, /*tp_itemsize*/ - __pyx_tp_dealloc_memoryview, /*tp_dealloc*/ - #if PY_VERSION_HEX < 0x030800b4 - 0, /*tp_print*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 - 0, /*tp_vectorcall_offset*/ - #endif - 0, /*tp_getattr*/ - 0, /*tp_setattr*/ - #if PY_MAJOR_VERSION < 3 - 0, /*tp_compare*/ - #endif - #if PY_MAJOR_VERSION >= 3 - 0, /*tp_as_async*/ - #endif - __pyx_memoryview___repr__, /*tp_repr*/ - 0, /*tp_as_number*/ - &__pyx_tp_as_sequence_memoryview, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_memoryview, /*tp_as_mapping*/ - 0, /*tp_hash*/ - 0, /*tp_call*/ - __pyx_memoryview___str__, /*tp_str*/ - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_memoryview, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - 0, /*tp_doc*/ - __pyx_tp_traverse_memoryview, /*tp_traverse*/ - __pyx_tp_clear_memoryview, /*tp_clear*/ - 0, /*tp_richcompare*/ - 0, /*tp_weaklistoffset*/ - 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_memoryview, /*tp_methods*/ - 0, /*tp_members*/ - __pyx_getsets_memoryview, /*tp_getset*/ - 0, /*tp_base*/ - 0, /*tp_dict*/ - 0, /*tp_descr_get*/ - 0, /*tp_descr_set*/ - 0, /*tp_dictoffset*/ - 0, /*tp_init*/ - 0, /*tp_alloc*/ - __pyx_tp_new_memoryview, /*tp_new*/ - 0, /*tp_free*/ - 0, /*tp_is_gc*/ - 0, /*tp_bases*/ - 0, /*tp_mro*/ - 0, /*tp_cache*/ - 0, /*tp_subclasses*/ - 0, /*tp_weaklist*/ - 0, /*tp_del*/ - 0, /*tp_version_tag*/ - #if PY_VERSION_HEX >= 0x030400a1 - 0, /*tp_finalize*/ - #endif - #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) - 0, /*tp_vectorcall*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 - 0, /*tp_print*/ - #endif - #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 - 0, /*tp_pypy_flags*/ - #endif -}; -static struct __pyx_vtabstruct__memoryviewslice __pyx_vtable__memoryviewslice; - -static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_memoryviewslice_obj *p; - PyObject *o = __pyx_tp_new_memoryview(t, a, k); - if (unlikely(!o)) return 0; - p = ((struct __pyx_memoryviewslice_obj *)o); - p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_memoryview*)__pyx_vtabptr__memoryviewslice; - p->from_object = Py_None; Py_INCREF(Py_None); - p->from_slice.memview = NULL; - return o; -} - -static void __pyx_tp_dealloc__memoryviewslice(PyObject *o) { - struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; - #if CYTHON_USE_TP_FINALIZE - if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { - if (PyObject_CallFinalizerFromDealloc(o)) return; - } - #endif - PyObject_GC_UnTrack(o); - { - PyObject *etype, *eval, *etb; - PyErr_Fetch(&etype, &eval, &etb); - __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); - __pyx_memoryviewslice___dealloc__(o); - __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); - PyErr_Restore(etype, eval, etb); - } - Py_CLEAR(p->from_object); - PyObject_GC_Track(o); - __pyx_tp_dealloc_memoryview(o); -} - -static int __pyx_tp_traverse__memoryviewslice(PyObject *o, visitproc v, void *a) { - int e; - struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; - e = __pyx_tp_traverse_memoryview(o, v, a); if (e) return e; - if (p->from_object) { - e = (*v)(p->from_object, a); if (e) return e; - } - return 0; -} - -static int __pyx_tp_clear__memoryviewslice(PyObject *o) { - PyObject* tmp; - struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; - __pyx_tp_clear_memoryview(o); - tmp = ((PyObject*)p->from_object); - p->from_object = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - __PYX_XDEC_MEMVIEW(&p->from_slice, 1); - return 0; -} - -static PyObject *__pyx_getprop___pyx_memoryviewslice_base(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_16_memoryviewslice_4base_1__get__(o); -} - -static PyMethodDef __pyx_methods__memoryviewslice[] = { - {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_memoryviewslice_1__reduce_cython__, METH_NOARGS, 0}, - {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_memoryviewslice_3__setstate_cython__, METH_O, 0}, - {0, 0, 0, 0} -}; - -static struct PyGetSetDef __pyx_getsets__memoryviewslice[] = { - {(char *)"base", __pyx_getprop___pyx_memoryviewslice_base, 0, (char *)0, 0}, - {0, 0, 0, 0, 0} -}; - -static PyTypeObject __pyx_type___pyx_memoryviewslice = { - PyVarObject_HEAD_INIT(0, 0) - "MDAnalysis.lib._cutil._memoryviewslice", /*tp_name*/ - sizeof(struct __pyx_memoryviewslice_obj), /*tp_basicsize*/ - 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- return __Pyx_PyFunction_FastCall(function, args, 2); - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyCFunction_FastCall(function, args, 2); - } - #endif - args = PyTuple_New(2); - if (unlikely(!args)) goto done; - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 0, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 1, arg2); - Py_INCREF(function); - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); -done: - return result; -} - -/* PyObjectCallMethO */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { - PyObject *self, *result; - PyCFunction cfunc; - cfunc = PyCFunction_GET_FUNCTION(func); - self = PyCFunction_GET_SELF(func); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = cfunc(self, arg); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallOneArg */ -#if CYTHON_COMPILING_IN_CPYTHON -static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_New(1); - if (unlikely(!args)) return NULL; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif - if (likely(PyCFunction_Check(func))) { - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (__Pyx_PyFastCFunction_Check(func)) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } - } - return __Pyx__PyObject_CallOneArg(func, arg); -} -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -#endif - -/* MemviewSliceInit */ -static int -__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference) -{ - __Pyx_RefNannyDeclarations - int i, retval=-1; - Py_buffer *buf = &memview->view; - __Pyx_RefNannySetupContext("init_memviewslice", 0); - if (unlikely(memviewslice->memview || memviewslice->data)) { - PyErr_SetString(PyExc_ValueError, - "memviewslice is already initialized!"); - goto fail; - } - if (buf->strides) { - for (i = 0; i < ndim; i++) { - memviewslice->strides[i] = buf->strides[i]; - } - } else { - Py_ssize_t stride = buf->itemsize; - for (i = ndim - 1; i >= 0; i--) { - memviewslice->strides[i] = stride; - stride *= buf->shape[i]; - } - } - for (i = 0; i < ndim; i++) { - memviewslice->shape[i] = buf->shape[i]; - if (buf->suboffsets) { - memviewslice->suboffsets[i] = buf->suboffsets[i]; - } else { - memviewslice->suboffsets[i] = -1; - } - } - memviewslice->memview = memview; - memviewslice->data = (char *)buf->buf; - if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { - Py_INCREF(memview); - } - retval = 0; - goto no_fail; -fail: - memviewslice->memview = 0; - memviewslice->data = 0; - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} -#ifndef Py_NO_RETURN -#define Py_NO_RETURN -#endif -static void __pyx_fatalerror(const char *fmt, ...) Py_NO_RETURN { - va_list vargs; - char msg[200]; -#if PY_VERSION_HEX >= 0x030A0000 || defined(HAVE_STDARG_PROTOTYPES) - va_start(vargs, fmt); -#else - va_start(vargs); -#endif - vsnprintf(msg, 200, fmt, vargs); - va_end(vargs); - Py_FatalError(msg); -} -static CYTHON_INLINE int -__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)++; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE int -__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)--; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE void -__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) -{ - int first_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) - return; - if (unlikely(__pyx_get_slice_count(memview) < 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - first_time = __pyx_add_acquisition_count(memview) == 0; - if (unlikely(first_time)) { - if (have_gil) { - Py_INCREF((PyObject *) memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_INCREF((PyObject *) memview); - PyGILState_Release(_gilstate); - } - } -} -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, - int have_gil, int lineno) { - int last_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) { - memslice->memview = NULL; - return; - } - if (unlikely(__pyx_get_slice_count(memview) <= 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - last_time = __pyx_sub_acquisition_count(memview) == 1; - memslice->data = NULL; - if (unlikely(last_time)) { - if (have_gil) { - Py_CLEAR(memslice->memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_CLEAR(memslice->memview); - PyGILState_Release(_gilstate); - } - } else { - memslice->memview = NULL; - } -} - -/* RaiseArgTupleInvalid */ -static void __Pyx_RaiseArgtupleInvalid( - const char* func_name, - int exact, - Py_ssize_t num_min, - Py_ssize_t num_max, - Py_ssize_t num_found) -{ - Py_ssize_t num_expected; - const char *more_or_less; - if (num_found < num_min) { - num_expected = num_min; - more_or_less = "at least"; - } else { - num_expected = num_max; - more_or_less = "at most"; - } - if (exact) { - more_or_less = "exactly"; - } - PyErr_Format(PyExc_TypeError, - "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", - func_name, more_or_less, num_expected, - (num_expected == 1) ? "" : "s", num_found); -} - -/* RaiseDoubleKeywords */ -static void __Pyx_RaiseDoubleKeywordsError( - const char* func_name, - PyObject* kw_name) -{ - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION >= 3 - "%s() got multiple values for keyword argument '%U'", func_name, kw_name); - #else - "%s() got multiple values for keyword argument '%s'", func_name, - PyString_AsString(kw_name)); - #endif -} - -/* ParseKeywords */ -static int __Pyx_ParseOptionalKeywords( - PyObject *kwds, - PyObject **argnames[], - PyObject *kwds2, - PyObject *values[], - Py_ssize_t num_pos_args, - const char* function_name) -{ - PyObject *key = 0, *value = 0; - Py_ssize_t pos = 0; - PyObject*** name; - PyObject*** first_kw_arg = argnames + num_pos_args; - while (PyDict_Next(kwds, &pos, &key, &value)) { - name = first_kw_arg; - while (*name && (**name != key)) name++; - if (*name) { - values[name-argnames] = value; - continue; - } - name = first_kw_arg; - #if PY_MAJOR_VERSION < 3 - if (likely(PyString_Check(key))) { - while (*name) { - if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) - && _PyString_Eq(**name, key)) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - if ((**argname == key) || ( - (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) - && _PyString_Eq(**argname, key))) { - goto arg_passed_twice; - } - argname++; - } - } - } else - #endif - if (likely(PyUnicode_Check(key))) { - while (*name) { - int cmp = (**name == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**name, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - int cmp = (**argname == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**argname, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) goto arg_passed_twice; - argname++; - } - } - } else - goto invalid_keyword_type; - if (kwds2) { - if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; - } else { - goto invalid_keyword; - } - } - return 0; -arg_passed_twice: - __Pyx_RaiseDoubleKeywordsError(function_name, key); - goto bad; -invalid_keyword_type: - PyErr_Format(PyExc_TypeError, - "%.200s() keywords must be strings", function_name); - goto bad; -invalid_keyword: - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION < 3 - "%.200s() got an unexpected keyword argument '%.200s'", - function_name, PyString_AsString(key)); - #else - "%s() got an unexpected keyword argument '%U'", - function_name, key); - #endif -bad: - return -1; -} - -/* PyErrFetchRestore */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -} -#endif - -/* RaiseException */ -#if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* WriteUnraisableException */ -static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, - CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, - int full_traceback, CYTHON_UNUSED int nogil) { - PyObject *old_exc, *old_val, *old_tb; - PyObject *ctx; - __Pyx_PyThreadState_declare -#ifdef WITH_THREAD - PyGILState_STATE state; - if (nogil) - state = PyGILState_Ensure(); - else state = (PyGILState_STATE)0; -#endif - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); - if (full_traceback) { - Py_XINCREF(old_exc); - Py_XINCREF(old_val); - Py_XINCREF(old_tb); - __Pyx_ErrRestore(old_exc, old_val, old_tb); - PyErr_PrintEx(1); - } - #if PY_MAJOR_VERSION < 3 - ctx = PyString_FromString(name); - #else - ctx = PyUnicode_FromString(name); - #endif - __Pyx_ErrRestore(old_exc, old_val, old_tb); - if (!ctx) { - PyErr_WriteUnraisable(Py_None); - } else { - PyErr_WriteUnraisable(ctx); - Py_DECREF(ctx); - } -#ifdef WITH_THREAD - if (nogil) - PyGILState_Release(state); -#endif -} - -/* SliceObject */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, - Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, - int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { -#if CYTHON_USE_TYPE_SLOTS - PyMappingMethods* mp; -#if PY_MAJOR_VERSION < 3 - PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; - if (likely(ms && ms->sq_slice)) { - if (!has_cstart) { - if (_py_start && (*_py_start != Py_None)) { - cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); - if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstart = 0; - } - if (!has_cstop) { - if (_py_stop && (*_py_stop != Py_None)) { - cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); - if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstop = PY_SSIZE_T_MAX; - } - if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { - Py_ssize_t l = ms->sq_length(obj); - if (likely(l >= 0)) { - if (cstop < 0) { - cstop += l; - if (cstop < 0) cstop = 0; - } - if (cstart < 0) { - cstart += l; - if (cstart < 0) cstart = 0; - } - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - goto bad; - PyErr_Clear(); - } - } - return ms->sq_slice(obj, cstart, cstop); - } -#endif - mp = Py_TYPE(obj)->tp_as_mapping; - if (likely(mp && mp->mp_subscript)) -#endif - { - PyObject* result; - PyObject *py_slice, *py_start, *py_stop; - if (_py_slice) { - py_slice = *_py_slice; - } else { - PyObject* owned_start = NULL; - PyObject* owned_stop = NULL; - if (_py_start) { - py_start = *_py_start; - } else { - if (has_cstart) { - owned_start = py_start = PyInt_FromSsize_t(cstart); - if (unlikely(!py_start)) goto bad; - } else - py_start = Py_None; - } - if (_py_stop) { - py_stop = *_py_stop; - } else { - if (has_cstop) { - owned_stop = py_stop = PyInt_FromSsize_t(cstop); - if (unlikely(!py_stop)) { - Py_XDECREF(owned_start); - goto bad; - } - } else - py_stop = Py_None; - } - py_slice = PySlice_New(py_start, py_stop, Py_None); - Py_XDECREF(owned_start); - Py_XDECREF(owned_stop); - if (unlikely(!py_slice)) goto bad; - } -#if CYTHON_USE_TYPE_SLOTS - result = mp->mp_subscript(obj, py_slice); -#else - result = PyObject_GetItem(obj, py_slice); -#endif - if (!_py_slice) { - Py_DECREF(py_slice); - } - return result; - } - PyErr_Format(PyExc_TypeError, - "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name); -bad: - return NULL; -} - -/* GetItemInt */ -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { - PyObject *r; - if (!j) return NULL; - r = PyObject_GetItem(o, j); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyList_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyTuple_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } - else if (PyTuple_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } else { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_item)) { - if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { - Py_ssize_t l = m->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return NULL; - PyErr_Clear(); - } - } - return m->sq_item(o, i); - } - } -#else - if (is_list || PySequence_Check(o)) { - return PySequence_GetItem(o, i); - } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -} - -/* Import */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* ImportFrom */ -static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { - PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); - if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_Format(PyExc_ImportError, - #if PY_MAJOR_VERSION < 3 - "cannot import name %.230s", PyString_AS_STRING(name)); - #else - "cannot import name %S", name); - #endif - } - return value; -} - -/* PyObjectCallNoArg */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, NULL, 0); - } -#endif -#if defined(__Pyx_CyFunction_USED) && defined(NDEBUG) - if (likely(PyCFunction_Check(func) || __Pyx_CyFunction_Check(func))) -#else - if (likely(PyCFunction_Check(func))) -#endif - { - if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { - return __Pyx_PyObject_CallMethO(func, NULL); - } - } - return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL); -} -#endif - -/* GetTopmostException */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* FastTypeChecks */ -#if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; - if (a == b) - return 1; - } - return b == &PyBaseObject_Type; -} -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { - PyObject *mro; - if (a == b) return 1; - mro = a->tp_mro; - if (likely(mro)) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(mro); - for (i = 0; i < n; i++) { - if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) - return 1; - } - return 0; - } - return __Pyx_InBases(a, b); -} -#if PY_MAJOR_VERSION == 2 -static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { - PyObject *exception, *value, *tb; - int res; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&exception, &value, &tb); - res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - if (!res) { - res = PyObject_IsSubclass(err, exc_type2); - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - } - __Pyx_ErrRestore(exception, value, tb); - return res; -} -#else -static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { - int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; - if (!res) { - res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); - } - return res; -} -#endif -static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - assert(PyExceptionClass_Check(exc_type)); - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* None */ -static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { - PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); -} - -/* PyObjectSetAttrStr */ -#if CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) { - PyTypeObject* tp = Py_TYPE(obj); - if (likely(tp->tp_setattro)) - return tp->tp_setattro(obj, attr_name, value); -#if PY_MAJOR_VERSION < 3 - if (likely(tp->tp_setattr)) - return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value); -#endif - return PyObject_SetAttr(obj, attr_name, value); -} -#endif - -/* ExtTypeTest */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(__Pyx_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* PyErrExceptionMatches */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* ArgTypeTest */ -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) -{ - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - else if (exact) { - #if PY_MAJOR_VERSION == 2 - if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; - #endif - } - else { - if (likely(__Pyx_TypeCheck(obj, type))) return 1; - } - PyErr_Format(PyExc_TypeError, - "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", - name, type->tp_name, Py_TYPE(obj)->tp_name); - return 0; -} - -/* BytesEquals */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { - const char *ps1, *ps2; - Py_ssize_t length = PyBytes_GET_SIZE(s1); - if (length != PyBytes_GET_SIZE(s2)) - return (equals == Py_NE); - ps1 = PyBytes_AS_STRING(s1); - ps2 = PyBytes_AS_STRING(s2); - if (ps1[0] != ps2[0]) { - return (equals == Py_NE); - } else if (length == 1) { - return (equals == Py_EQ); - } else { - int result; -#if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000) - Py_hash_t hash1, hash2; - hash1 = ((PyBytesObject*)s1)->ob_shash; - hash2 = ((PyBytesObject*)s2)->ob_shash; - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - return (equals == Py_NE); - } -#endif - result = memcmp(ps1, ps2, (size_t)length); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -#endif -} - -/* UnicodeEquals */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else -#if PY_MAJOR_VERSION < 3 - PyObject* owned_ref = NULL; -#endif - int s1_is_unicode, s2_is_unicode; - if (s1 == s2) { - goto return_eq; - } - s1_is_unicode = PyUnicode_CheckExact(s1); - s2_is_unicode = PyUnicode_CheckExact(s2); -#if PY_MAJOR_VERSION < 3 - if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { - owned_ref = PyUnicode_FromObject(s2); - if (unlikely(!owned_ref)) - return -1; - s2 = owned_ref; - s2_is_unicode = 1; - } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { - owned_ref = PyUnicode_FromObject(s1); - if (unlikely(!owned_ref)) - return -1; - s1 = owned_ref; - s1_is_unicode = 1; - } else if (((!s2_is_unicode) & (!s1_is_unicode))) { - return __Pyx_PyBytes_Equals(s1, s2, equals); - } -#endif - if (s1_is_unicode & s2_is_unicode) { - Py_ssize_t length; - int kind; - void *data1, *data2; - if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) - return -1; - length = __Pyx_PyUnicode_GET_LENGTH(s1); - if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { - goto return_ne; - } -#if CYTHON_USE_UNICODE_INTERNALS - { - Py_hash_t hash1, hash2; - #if CYTHON_PEP393_ENABLED - hash1 = ((PyASCIIObject*)s1)->hash; - hash2 = ((PyASCIIObject*)s2)->hash; - #else - hash1 = ((PyUnicodeObject*)s1)->hash; - hash2 = ((PyUnicodeObject*)s2)->hash; - #endif - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - goto return_ne; - } - } -#endif - kind = __Pyx_PyUnicode_KIND(s1); - if (kind != __Pyx_PyUnicode_KIND(s2)) { - goto return_ne; - } - data1 = __Pyx_PyUnicode_DATA(s1); - data2 = __Pyx_PyUnicode_DATA(s2); - if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { - goto return_ne; - } else if (length == 1) { - goto return_eq; - } else { - int result = memcmp(data1, data2, (size_t)(length * kind)); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & s2_is_unicode) { - goto return_ne; - } else if ((s2 == Py_None) & s1_is_unicode) { - goto return_ne; - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -return_eq: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ); -return_ne: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_NE); -#endif -} - -/* DivInt[Py_ssize_t] */ -static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { - Py_ssize_t q = a / b; - Py_ssize_t r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* GetAttr */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { -#if CYTHON_USE_TYPE_SLOTS -#if PY_MAJOR_VERSION >= 3 - if (likely(PyUnicode_Check(n))) -#else - if (likely(PyString_Check(n))) -#endif - return __Pyx_PyObject_GetAttrStr(o, n); -#endif - return PyObject_GetAttr(o, n); -} - -/* ObjectGetItem */ -#if CYTHON_USE_TYPE_SLOTS -static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { - PyObject *runerr = NULL; - Py_ssize_t key_value; - PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; - if (unlikely(!(m && m->sq_item))) { - PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); - return NULL; - } - key_value = __Pyx_PyIndex_AsSsize_t(index); - if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { - return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); - } - if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { - PyErr_Clear(); - PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); - } - return NULL; -} -static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { - PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; - if (likely(m && m->mp_subscript)) { - return m->mp_subscript(obj, key); - } - return __Pyx_PyObject_GetIndex(obj, key); -} -#endif - -/* decode_c_string */ -static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { - Py_ssize_t length; - if (unlikely((start < 0) | (stop < 0))) { - size_t slen = strlen(cstring); - if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { - PyErr_SetString(PyExc_OverflowError, - "c-string too long to convert to Python"); - return NULL; - } - length = (Py_ssize_t) slen; - if (start < 0) { - start += length; - if (start < 0) - start = 0; - } - if (stop < 0) - stop += length; - } - if (unlikely(stop <= start)) - return __Pyx_NewRef(__pyx_empty_unicode); - length = stop - start; - cstring += start; - if (decode_func) { - return decode_func(cstring, length, errors); - } else { - return PyUnicode_Decode(cstring, length, encoding, errors); - } -} - -/* GetAttr3 */ -static PyObject *__Pyx_GetAttr3Default(PyObject *d) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - return NULL; - __Pyx_PyErr_Clear(); - Py_INCREF(d); - return d; -} -static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { - PyObject *r = __Pyx_GetAttr(o, n); - return (likely(r)) ? r : __Pyx_GetAttr3Default(d); -} - -/* RaiseTooManyValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -/* RaiseNeedMoreValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -/* RaiseNoneIterError */ -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); -} - -/* SwapException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = *type; - exc_info->exc_value = *value; - exc_info->exc_traceback = *tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = *type; - tstate->exc_value = *value; - tstate->exc_traceback = *tb; - #endif - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); - PyErr_SetExcInfo(*type, *value, *tb); - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#endif - -/* PyIntBinop */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, int inplace, int zerodivision_check) { - (void)inplace; - (void)zerodivision_check; - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - const long b = intval; - long x; - long a = PyInt_AS_LONG(op1); - x = (long)((unsigned long)a + b); - if (likely((x^a) >= 0 || (x^b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - default: return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - } - x = a + b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla + llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("add", return NULL) - result = ((double)a) + (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); -} -#endif - -/* DivInt[long] */ -static CYTHON_INLINE long __Pyx_div_long(long a, long b) { - long q = a / b; - long r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* HasAttr */ -static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { - PyObject *r; - if (unlikely(!__Pyx_PyBaseString_Check(n))) { - PyErr_SetString(PyExc_TypeError, - "hasattr(): attribute name must be string"); - return -1; - } - r = __Pyx_GetAttr(o, n); - if (unlikely(!r)) { - PyErr_Clear(); - return 0; - } else { - Py_DECREF(r); - return 1; - } -} - -/* PyObject_GenericGetAttrNoDict */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { - PyErr_Format(PyExc_AttributeError, -#if PY_MAJOR_VERSION >= 3 - "'%.50s' object has no attribute '%U'", - tp->tp_name, attr_name); -#else - "'%.50s' object has no attribute '%.400s'", - tp->tp_name, PyString_AS_STRING(attr_name)); -#endif - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { - PyObject *descr; - PyTypeObject *tp = Py_TYPE(obj); - if (unlikely(!PyString_Check(attr_name))) { - return PyObject_GenericGetAttr(obj, attr_name); - } - assert(!tp->tp_dictoffset); - descr = _PyType_Lookup(tp, attr_name); - if (unlikely(!descr)) { - return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); - } - Py_INCREF(descr); - #if PY_MAJOR_VERSION < 3 - if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) - #endif - { - descrgetfunc f = Py_TYPE(descr)->tp_descr_get; - if (unlikely(f)) { - PyObject *res = f(descr, obj, (PyObject *)tp); - Py_DECREF(descr); - return res; - } - } - return descr; -} -#endif - -/* PyObject_GenericGetAttr */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { - if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { - return PyObject_GenericGetAttr(obj, attr_name); - } - return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); -} -#endif - -/* SetVTable */ -static int __Pyx_SetVtable(PyObject *dict, void *vtable) { -#if PY_VERSION_HEX >= 0x02070000 - PyObject *ob = PyCapsule_New(vtable, 0, 0); -#else - PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); -#endif - if (!ob) - goto bad; - if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) - goto bad; - Py_DECREF(ob); - return 0; -bad: - Py_XDECREF(ob); - return -1; -} - -/* PyObjectGetAttrStrNoError */ -static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - __Pyx_PyErr_Clear(); -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { - PyObject *result; -#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 - PyTypeObject* tp = Py_TYPE(obj); - if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { - return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); - } -#endif - result = __Pyx_PyObject_GetAttrStr(obj, attr_name); - if (unlikely(!result)) { - __Pyx_PyObject_GetAttrStr_ClearAttributeError(); - } - return result; -} - -/* SetupReduce */ -static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { - int ret; - PyObject *name_attr; - name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2); - if (likely(name_attr)) { - ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); - } else { - ret = -1; - } - if (unlikely(ret < 0)) { - PyErr_Clear(); - ret = 0; - } - Py_XDECREF(name_attr); - return ret; -} -static int __Pyx_setup_reduce(PyObject* type_obj) { - int ret = 0; - PyObject *object_reduce = NULL; - PyObject *object_getstate = NULL; - PyObject *object_reduce_ex = NULL; - PyObject *reduce = NULL; - PyObject *reduce_ex = NULL; - PyObject *reduce_cython = NULL; - PyObject *setstate = NULL; - PyObject *setstate_cython = NULL; - PyObject *getstate = NULL; -#if CYTHON_USE_PYTYPE_LOOKUP - getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate); -#else - getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate); - if (!getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (getstate) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate); -#else - object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate); - if (!object_getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (object_getstate != getstate) { - goto __PYX_GOOD; - } - } -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; - if (reduce_ex == object_reduce_ex) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; - if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); - if (likely(reduce_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (reduce == object_reduce || PyErr_Occurred()) { - goto __PYX_BAD; - } - setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); - if (!setstate) PyErr_Clear(); - if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); - if (likely(setstate_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (!setstate || PyErr_Occurred()) { - goto __PYX_BAD; - } - } - PyType_Modified((PyTypeObject*)type_obj); - } - } - goto __PYX_GOOD; -__PYX_BAD: - if (!PyErr_Occurred()) - PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); - ret = -1; -__PYX_GOOD: -#if !CYTHON_USE_PYTYPE_LOOKUP - Py_XDECREF(object_reduce); - Py_XDECREF(object_reduce_ex); - Py_XDECREF(object_getstate); - Py_XDECREF(getstate); -#endif - Py_XDECREF(reduce); - Py_XDECREF(reduce_ex); - Py_XDECREF(reduce_cython); - Py_XDECREF(setstate); - Py_XDECREF(setstate_cython); - return ret; -} - -/* TypeImport */ -#ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* CLineInTraceback */ -#ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ -#include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - if ((0)) {} - view->obj = NULL; - Py_DECREF(obj); -} -#endif - - -/* MemviewSliceIsContig */ -static int -__pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim) -{ - int i, index, step, start; - Py_ssize_t itemsize = mvs.memview->view.itemsize; - if (order == 'F') { - step = 1; - start = 0; - } else { - step = -1; - start = ndim - 1; - } - for (i = 0; i < ndim; i++) { - index = start + step * i; - if (mvs.suboffsets[index] >= 0 || mvs.strides[index] != itemsize) - return 0; - itemsize *= mvs.shape[index]; - } - return 1; -} - -/* OverlappingSlices */ -static void -__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, - void **out_start, void **out_end, - int ndim, size_t itemsize) -{ - char *start, *end; - int i; - start = end = slice->data; - for (i = 0; i < ndim; i++) { - Py_ssize_t stride = slice->strides[i]; - Py_ssize_t extent = slice->shape[i]; - if (extent == 0) { - *out_start = *out_end = start; - return; - } else { - if (stride > 0) - end += stride * (extent - 1); - else - start += stride * (extent - 1); - } - } - *out_start = start; - *out_end = end + itemsize; -} -static int -__pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize) -{ - void *start1, *end1, *start2, *end2; - __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); - __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); - return (start1 < end2) && (start2 < end1); -} - -/* Capsule */ -static CYTHON_INLINE PyObject * -__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) -{ - PyObject *cobj; -#if PY_VERSION_HEX >= 0x02070000 - cobj = PyCapsule_New(p, sig, NULL); -#else - cobj = PyCObject_FromVoidPtr(p, NULL); -#endif - return cobj; -} - -/* IsLittleEndian */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) -{ - union { - uint32_t u32; - uint8_t u8[4]; - } S; - S.u32 = 0x01020304; - return S.u8[0] == 4; -} - -/* BufferFormatCheck */ -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type) { - stack[0].field = &ctx->root; - stack[0].parent_offset = 0; - ctx->root.type = type; - ctx->root.name = "buffer dtype"; - ctx->root.offset = 0; - ctx->head = stack; - ctx->head->field = &ctx->root; - ctx->fmt_offset = 0; - ctx->head->parent_offset = 0; - ctx->new_packmode = '@'; - ctx->enc_packmode = '@'; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->is_complex = 0; - ctx->is_valid_array = 0; - ctx->struct_alignment = 0; - while (type->typegroup == 'S') { - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = 0; - type = type->fields->type; - } -} -static int __Pyx_BufFmt_ParseNumber(const char** ts) { - int count; - const char* t = *ts; - if (*t < '0' || *t > '9') { - return -1; - } else { - count = *t++ - '0'; - while (*t >= '0' && *t <= '9') { - count *= 10; - count += *t++ - '0'; - } - } - *ts = t; - return count; -} -static int __Pyx_BufFmt_ExpectNumber(const char **ts) { - int number = __Pyx_BufFmt_ParseNumber(ts); - if (number == -1) - PyErr_Format(PyExc_ValueError,\ - "Does not understand character buffer dtype format string ('%c')", **ts); - return number; -} -static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { - PyErr_Format(PyExc_ValueError, - "Unexpected format string character: '%c'", ch); -} -static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { - switch (ch) { - case '?': return "'bool'"; - case 'c': return "'char'"; - case 'b': return "'signed char'"; - case 'B': return "'unsigned char'"; - case 'h': return "'short'"; - case 'H': return "'unsigned short'"; - case 'i': return "'int'"; - case 'I': return "'unsigned int'"; - case 'l': return "'long'"; - case 'L': return "'unsigned long'"; - case 'q': return "'long long'"; - case 'Q': return "'unsigned long long'"; - case 'f': return (is_complex ? "'complex float'" : "'float'"); - case 'd': return (is_complex ? "'complex double'" : "'double'"); - case 'g': return (is_complex ? "'complex long double'" : "'long double'"); - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - case 's': case 'p': return "a string"; - case 0: return "end"; - default: return "unparseable format string"; - } -} -static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return 2; - case 'i': case 'I': case 'l': case 'L': return 4; - case 'q': case 'Q': return 8; - case 'f': return (is_complex ? 8 : 4); - case 'd': return (is_complex ? 16 : 8); - case 'g': { - PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); - return 0; - } - case 'O': case 'P': return sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(short); - case 'i': case 'I': return sizeof(int); - case 'l': case 'L': return sizeof(long); - #ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(PY_LONG_LONG); - #endif - case 'f': return sizeof(float) * (is_complex ? 2 : 1); - case 'd': return sizeof(double) * (is_complex ? 2 : 1); - case 'g': return sizeof(long double) * (is_complex ? 2 : 1); - case 'O': case 'P': return sizeof(void*); - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -typedef struct { char c; short x; } __Pyx_st_short; -typedef struct { char c; int x; } __Pyx_st_int; -typedef struct { char c; long x; } __Pyx_st_long; -typedef struct { char c; float x; } __Pyx_st_float; -typedef struct { char c; double x; } __Pyx_st_double; -typedef struct { char c; long double x; } __Pyx_st_longdouble; -typedef struct { char c; void *x; } __Pyx_st_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_st_float) - sizeof(float); - case 'd': return sizeof(__Pyx_st_double) - sizeof(double); - case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -/* These are for computing the padding at the end of the struct to align - on the first member of the struct. This will probably the same as above, - but we don't have any guarantees. - */ -typedef struct { short x; char c; } __Pyx_pad_short; -typedef struct { int x; char c; } __Pyx_pad_int; -typedef struct { long x; char c; } __Pyx_pad_long; -typedef struct { float x; char c; } __Pyx_pad_float; -typedef struct { double x; char c; } __Pyx_pad_double; -typedef struct { long double x; char c; } __Pyx_pad_longdouble; -typedef struct { void *x; char c; } __Pyx_pad_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); - case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); - case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { - switch (ch) { - case 'c': - return 'H'; - case 'b': case 'h': case 'i': - case 'l': case 'q': case 's': case 'p': - return 'I'; - case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': - return 'U'; - case 'f': case 'd': case 'g': - return (is_complex ? 'C' : 'R'); - case 'O': - return 'O'; - case 'P': - return 'P'; - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { - if (ctx->head == NULL || ctx->head->field == &ctx->root) { - const char* expected; - const char* quote; - if (ctx->head == NULL) { - expected = "end"; - quote = ""; - } else { - expected = ctx->head->field->type->name; - quote = "'"; - } - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected %s%s%s but got %s", - quote, expected, quote, - __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); - } else { - __Pyx_StructField* field = ctx->head->field; - __Pyx_StructField* parent = (ctx->head - 1)->field; - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", - field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), - parent->type->name, field->name); - } -} -static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { - char group; - size_t size, offset, arraysize = 1; - if (ctx->enc_type == 0) return 0; - if (ctx->head->field->type->arraysize[0]) { - int i, ndim = 0; - if (ctx->enc_type == 's' || ctx->enc_type == 'p') { - ctx->is_valid_array = ctx->head->field->type->ndim == 1; - ndim = 1; - if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { - PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %zu", - ctx->head->field->type->arraysize[0], ctx->enc_count); - return -1; - } - } - if (!ctx->is_valid_array) { - PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", - ctx->head->field->type->ndim, ndim); - return -1; - } - for (i = 0; i < ctx->head->field->type->ndim; i++) { - arraysize *= ctx->head->field->type->arraysize[i]; - } - ctx->is_valid_array = 0; - ctx->enc_count = 1; - } - group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); - do { - __Pyx_StructField* field = ctx->head->field; - __Pyx_TypeInfo* type = field->type; - if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { - size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); - } else { - size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); - } - if (ctx->enc_packmode == '@') { - size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); - size_t align_mod_offset; - if (align_at == 0) return -1; - align_mod_offset = ctx->fmt_offset % align_at; - if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; - if (ctx->struct_alignment == 0) - ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, - ctx->is_complex); - } - if (type->size != size || type->typegroup != group) { - if (type->typegroup == 'C' && type->fields != NULL) { - size_t parent_offset = ctx->head->parent_offset + field->offset; - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = parent_offset; - continue; - } - if ((type->typegroup == 'H' || group == 'H') && type->size == size) { - } else { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - } - offset = ctx->head->parent_offset + field->offset; - if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; - } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } - } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; -} -static PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number, ndim; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ndim = ctx->head->field->type->ndim; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; - } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; - } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; - } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; -} -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; - } - break; - case '}': - { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } - } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; - } - CYTHON_FALLTHROUGH; - case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && - (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - CYTHON_FALLTHROUGH; - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: - { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; - } - } - } -} - -/* TypeInfoCompare */ - static int -__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) -{ - int i; - if (!a || !b) - return 0; - if (a == b) - return 1; - if (a->size != b->size || a->typegroup != b->typegroup || - a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { - if (a->typegroup == 'H' || b->typegroup == 'H') { - return a->size == b->size; - } else { - return 0; - } - } - if (a->ndim) { - for (i = 0; i < a->ndim; i++) - if (a->arraysize[i] != b->arraysize[i]) - return 0; - } - if (a->typegroup == 'S') { - if (a->flags != b->flags) - return 0; - if (a->fields || b->fields) { - if (!(a->fields && b->fields)) - return 0; - for (i = 0; a->fields[i].type && b->fields[i].type; i++) { - __Pyx_StructField *field_a = a->fields + i; - __Pyx_StructField *field_b = b->fields + i; - if (field_a->offset != field_b->offset || - !__pyx_typeinfo_cmp(field_a->type, field_b->type)) - return 0; - } - return !a->fields[i].type && !b->fields[i].type; - } - } - return 1; -} - -/* MemviewSliceValidateAndInit */ - static int -__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) -{ - if (buf->shape[dim] <= 1) - return 1; - if (buf->strides) { - if (spec & __Pyx_MEMVIEW_CONTIG) { - if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { - if (unlikely(buf->strides[dim] != sizeof(void *))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly contiguous " - "in dimension %d.", dim); - goto fail; - } - } else if (unlikely(buf->strides[dim] != buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_FOLLOW) { - Py_ssize_t stride = buf->strides[dim]; - if (stride < 0) - stride = -stride; - if (unlikely(stride < buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - } else { - if (unlikely(spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1)) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not contiguous in " - "dimension %d", dim); - goto fail; - } else if (unlikely(spec & (__Pyx_MEMVIEW_PTR))) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not indirect in " - "dimension %d", dim); - goto fail; - } else if (unlikely(buf->suboffsets)) { - PyErr_SetString(PyExc_ValueError, - "Buffer exposes suboffsets but no strides"); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) -{ - if (spec & __Pyx_MEMVIEW_DIRECT) { - if (unlikely(buf->suboffsets && buf->suboffsets[dim] >= 0)) { - PyErr_Format(PyExc_ValueError, - "Buffer not compatible with direct access " - "in dimension %d.", dim); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_PTR) { - if (unlikely(!buf->suboffsets || (buf->suboffsets[dim] < 0))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly accessible " - "in dimension %d.", dim); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) -{ - int i; - if (c_or_f_flag & __Pyx_IS_F_CONTIG) { - Py_ssize_t stride = 1; - for (i = 0; i < ndim; i++) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not fortran contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { - Py_ssize_t stride = 1; - for (i = ndim - 1; i >- 1; i--) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not C contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } - return 1; -fail: - return 0; -} -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj) -{ - struct __pyx_memoryview_obj *memview, *new_memview; - __Pyx_RefNannyDeclarations - Py_buffer *buf; - int i, spec = 0, retval = -1; - __Pyx_BufFmt_Context ctx; - int from_memoryview = __pyx_memoryview_check(original_obj); - __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); - if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) - original_obj)->typeinfo)) { - memview = (struct __pyx_memoryview_obj *) original_obj; - new_memview = NULL; - } else { - memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - original_obj, buf_flags, 0, dtype); - new_memview = memview; - if (unlikely(!memview)) - goto fail; - } - buf = &memview->view; - if (unlikely(buf->ndim != ndim)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - ndim, buf->ndim); - goto fail; - } - if (new_memview) { - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (unlikely(!__Pyx_BufFmt_CheckString(&ctx, buf->format))) goto fail; - } - if (unlikely((unsigned) buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " - "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", - buf->itemsize, - (buf->itemsize > 1) ? "s" : "", - dtype->name, - dtype->size, - (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->len > 0) { - for (i = 0; i < ndim; i++) { - spec = axes_specs[i]; - if (unlikely(!__pyx_check_strides(buf, i, ndim, spec))) - goto fail; - if (unlikely(!__pyx_check_suboffsets(buf, i, ndim, spec))) - goto fail; - } - if (unlikely(buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))) - goto fail; - } - if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, - new_memview != NULL) == -1)) { - goto fail; - } - retval = 0; - goto no_fail; -fail: - Py_XDECREF(new_memview); - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_intp_t(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 1, - &__Pyx_TypeInfo_nn___pyx_t_5numpy_intp_t, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_nn___pyx_t_5numpy_intp_t(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 2, - &__Pyx_TypeInfo_nn___pyx_t_5numpy_intp_t, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_nn___pyx_t_5numpy_float64_t(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_FOLLOW), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 2, - &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_d_dc_nn___pyx_t_5numpy_float64_t(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_FOLLOW), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_FOLLOW), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 3, - &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* MemviewDtypeToObject */ - static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_5numpy_intp_t(const char *itemp) { - return (PyObject *) __Pyx_PyInt_From_Py_intptr_t(*(__pyx_t_5numpy_intp_t *) itemp); -} -static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_intp_t(const char *itemp, PyObject *obj) { - __pyx_t_5numpy_intp_t value = __Pyx_PyInt_As_Py_intptr_t(obj); - if ((value == ((npy_intp)-1)) && PyErr_Occurred()) - return 0; - *(__pyx_t_5numpy_intp_t *) itemp = value; - return 1; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_unsigned_char(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 1, - &__Pyx_TypeInfo_unsigned_char, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_Py_ssize_t(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 1, - &__Pyx_TypeInfo_Py_ssize_t, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 2, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* MemviewDtypeToObject */ - static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp) { - return (PyObject *) PyFloat_FromDouble(*(float *) itemp); -} -static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj) { - float value = __pyx_PyFloat_AsFloat(obj); - if ((value == (float)-1) && PyErr_Occurred()) - return 0; - *(float *) itemp = value; - return 1; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 1, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_int(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 2, - &__Pyx_TypeInfo_int, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_float64_t(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 1, - &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* MemviewDtypeToObject */ - static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_5numpy_float64_t(const char *itemp) { - return (PyObject *) PyFloat_FromDouble(*(__pyx_t_5numpy_float64_t *) itemp); -} -static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_float64_t(const char *itemp, PyObject *obj) { - __pyx_t_5numpy_float64_t value = __pyx_PyFloat_AsDouble(obj); - if ((value == ((npy_float64)-1)) && PyErr_Occurred()) - return 0; - *(__pyx_t_5numpy_float64_t *) itemp = value; - return 1; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_int64_t(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 1, - &__Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_nn___pyx_t_5numpy_int32_t(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 2, - &__Pyx_TypeInfo_nn___pyx_t_5numpy_int32_t, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* MemviewSliceCopyTemplate */ - static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object) -{ - __Pyx_RefNannyDeclarations - int i; - __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; - struct __pyx_memoryview_obj *from_memview = from_mvs->memview; - Py_buffer *buf = &from_memview->view; - PyObject *shape_tuple = NULL; - PyObject *temp_int = NULL; - struct __pyx_array_obj *array_obj = NULL; - struct __pyx_memoryview_obj *memview_obj = NULL; - __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); - for (i = 0; i < ndim; i++) { - if (unlikely(from_mvs->suboffsets[i] >= 0)) { - PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " - "indirect dimensions (axis %d)", i); - goto fail; - } - } - shape_tuple = PyTuple_New(ndim); - if (unlikely(!shape_tuple)) { - goto fail; - } - __Pyx_GOTREF(shape_tuple); - for(i = 0; i < ndim; i++) { - temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); - if(unlikely(!temp_int)) { - goto fail; - } else { - PyTuple_SET_ITEM(shape_tuple, i, temp_int); - temp_int = NULL; - } - } - array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); - if (unlikely(!array_obj)) { - goto fail; - } - __Pyx_GOTREF(array_obj); - memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - (PyObject *) array_obj, contig_flag, - dtype_is_object, - from_mvs->memview->typeinfo); - if (unlikely(!memview_obj)) - goto fail; - if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) - goto fail; - if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, - dtype_is_object) < 0)) - goto fail; - goto no_fail; -fail: - __Pyx_XDECREF(new_mvs.memview); - new_mvs.memview = NULL; - new_mvs.data = NULL; -no_fail: - __Pyx_XDECREF(shape_tuple); - __Pyx_XDECREF(temp_int); - __Pyx_XDECREF(array_obj); - __Pyx_RefNannyFinishContext(); - return new_mvs; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = (Py_intptr_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(Py_intptr_t) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(Py_intptr_t) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(Py_intptr_t) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(Py_intptr_t) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(Py_intptr_t) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(Py_intptr_t), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_As_Py_intptr_t(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = (Py_intptr_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(Py_intptr_t) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (Py_intptr_t) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (Py_intptr_t) 0; - case 1: __PYX_VERIFY_RETURN_INT(Py_intptr_t, digit, digits[0]) - case 2: - if (8 * sizeof(Py_intptr_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) >= 2 * PyLong_SHIFT) { - return (Py_intptr_t) (((((Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(Py_intptr_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) >= 3 * PyLong_SHIFT) { - return (Py_intptr_t) (((((((Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(Py_intptr_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) >= 4 * PyLong_SHIFT) { - return (Py_intptr_t) (((((((((Py_intptr_t)digits[3]) << PyLong_SHIFT) | (Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (Py_intptr_t) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(Py_intptr_t) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(Py_intptr_t) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (Py_intptr_t) 0; - case -1: __PYX_VERIFY_RETURN_INT(Py_intptr_t, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(Py_intptr_t, digit, +digits[0]) - case -2: - if (8 * sizeof(Py_intptr_t) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 2 * PyLong_SHIFT) { - return (Py_intptr_t) (((Py_intptr_t)-1)*(((((Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(Py_intptr_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 2 * PyLong_SHIFT) { - return (Py_intptr_t) ((((((Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(Py_intptr_t) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 3 * PyLong_SHIFT) { - return (Py_intptr_t) (((Py_intptr_t)-1)*(((((((Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(Py_intptr_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 3 * PyLong_SHIFT) { - return (Py_intptr_t) ((((((((Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(Py_intptr_t) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 4 * PyLong_SHIFT) { - return (Py_intptr_t) (((Py_intptr_t)-1)*(((((((((Py_intptr_t)digits[3]) << PyLong_SHIFT) | (Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(Py_intptr_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(Py_intptr_t) - 1 > 4 * PyLong_SHIFT) { - return (Py_intptr_t) ((((((((((Py_intptr_t)digits[3]) << PyLong_SHIFT) | (Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]))); - } - } - break; - } -#endif - if (sizeof(Py_intptr_t) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(Py_intptr_t) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - Py_intptr_t val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (Py_intptr_t) -1; - } - } else { - Py_intptr_t val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (Py_intptr_t) -1; - val = __Pyx_PyInt_As_Py_intptr_t(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to Py_intptr_t"); - return (Py_intptr_t) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to Py_intptr_t"); - return (Py_intptr_t) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const size_t neg_one = (size_t) -1, const_zero = (size_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(size_t) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(size_t, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (size_t) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (size_t) 0; - case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, digits[0]) - case 2: - if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) >= 2 * PyLong_SHIFT) { - return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) >= 3 * PyLong_SHIFT) { - return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) >= 4 * PyLong_SHIFT) { - return (size_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (size_t) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(size_t) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (size_t) 0; - case -1: __PYX_VERIFY_RETURN_INT(size_t, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, +digits[0]) - case -2: - if (8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { - return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { - return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { - return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { - return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { - return (size_t) (((size_t)-1)*(((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { - return (size_t) ((((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - } -#endif - if (sizeof(size_t) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(size_t) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - size_t val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (size_t) -1; - } - } else { - size_t val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (size_t) -1; - val = __Pyx_PyInt_As_size_t(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to size_t"); - return (size_t) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to size_t"); - return (size_t) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const char neg_one = (char) -1, const_zero = (char) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(char) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (char) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (char) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(char) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) - case -2: - if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - } -#endif - if (sizeof(char) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - char val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (char) -1; - } - } else { - char val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (char) -1; - val = __Pyx_PyInt_As_char(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to char"); - return (char) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to char"); - return (char) -1; -} - -/* CheckBinaryVersion */ - static int __Pyx_check_binary_version(void) { - char ctversion[5]; - int same=1, i, found_dot; - const char* rt_from_call = Py_GetVersion(); - PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); - found_dot = 0; - for (i = 0; i < 4; i++) { - if (!ctversion[i]) { - same = (rt_from_call[i] < '0' || rt_from_call[i] > '9'); - break; - } - if (rt_from_call[i] != ctversion[i]) { - same = 0; - break; - } - } - if (!same) { - char rtversion[5] = {'\0'}; - char message[200]; - for (i=0; i<4; ++i) { - if (rt_from_call[i] == '.') { - if (found_dot) break; - found_dot = 1; - } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') { - break; - } - rtversion[i] = rt_from_call[i]; - } - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* FunctionExport */ - static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig) { - PyObject *d = 0; - PyObject *cobj = 0; - union { - void (*fp)(void); - void *p; - } tmp; - d = PyObject_GetAttrString(__pyx_m, (char *)"__pyx_capi__"); - if (!d) { - PyErr_Clear(); - d = PyDict_New(); - if (!d) - goto bad; - Py_INCREF(d); - if (PyModule_AddObject(__pyx_m, (char *)"__pyx_capi__", d) < 0) - goto bad; - } - tmp.fp = f; -#if PY_VERSION_HEX >= 0x02070000 - cobj = PyCapsule_New(tmp.p, sig, 0); -#else - cobj = PyCObject_FromVoidPtrAndDesc(tmp.p, (void *)sig, 0); -#endif - if (!cobj) - goto bad; - if (PyDict_SetItemString(d, name, cobj) < 0) - goto bad; - Py_DECREF(cobj); - Py_DECREF(d); - return 0; -bad: - Py_XDECREF(cobj); - Py_XDECREF(d); - return -1; -} - -/* InitStrings */ - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - if (PyObject_Hash(*t->p) == -1) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT -#if !CYTHON_PEP393_ENABLED -static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); - return NULL; - } - } - } -#endif - *length = PyBytes_GET_SIZE(defenc); - return defenc_c; -} -#else -static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (likely(PyUnicode_IS_ASCII(o))) { - *length = PyUnicode_GET_LENGTH(o); - return PyUnicode_AsUTF8(o); - } else { - PyUnicode_AsASCIIString(o); - return NULL; - } -#else - return PyUnicode_AsUTF8AndSize(o, length); -#endif -} -#endif -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { - return __Pyx_PyUnicode_AsStringAndSize(o, length); - } else -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - if (PyByteArray_Check(o)) { - *length = PyByteArray_GET_SIZE(o); - return PyByteArray_AS_STRING(o); - } else -#endif - { - char* result; - int r = PyBytes_AsStringAndSize(o, &result, length); - if (unlikely(r < 0)) { - return NULL; - } else { - return result; - } - } -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - int is_true = x == Py_True; - if (is_true | (x == Py_False) | (x == Py_None)) return is_true; - else return PyObject_IsTrue(x); -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) { - int retval; - if (unlikely(!x)) return -1; - retval = __Pyx_PyObject_IsTrue(x); - Py_DECREF(x); - return retval; -} -static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { -#if PY_MAJOR_VERSION >= 3 - if (PyLong_Check(result)) { - if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, - "__int__ returned non-int (type %.200s). " - "The ability to return an instance of a strict subclass of int " - "is deprecated, and may be removed in a future version of Python.", - Py_TYPE(result)->tp_name)) { - Py_DECREF(result); - return NULL; - } - return result; - } -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - type_name, type_name, Py_TYPE(result)->tp_name); - Py_DECREF(result); - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS - PyNumberMethods *m; -#endif - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x) || PyLong_Check(x))) -#else - if (likely(PyLong_Check(x))) -#endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS - m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = m->nb_int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = m->nb_long(x); - } - #else - if (likely(m && m->nb_int)) { - name = "int"; - res = m->nb_int(x); - } - #endif -#else - if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) { - res = PyNumber_Int(x); - } -#endif - if (likely(res)) { -#if PY_MAJOR_VERSION < 3 - if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) { -#else - if (unlikely(!PyLong_CheckExact(res))) { -#endif - return __Pyx_PyNumber_IntOrLongWrongResultType(res, name); - } - } - else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_TypeError, - "an integer is required"); - } - return res; -} -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { - Py_ssize_t ival; - PyObject *x; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(b); - } -#endif - if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - if (size == -1) ival = -ival; - return ival; - } else { - switch (size) { - case 2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - 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PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - 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PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) - #endif - #endif -#else - #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 - #define __Pyx_PyUnicode_READY(op) (0) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) - #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) - #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) - #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) -#endif -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) -#else - #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ - PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? 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((void)(klass), PyMethod_New(func, self)) : __Pyx_NewRef(func)) -#else - #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) -#endif -#if CYTHON_USE_ASYNC_SLOTS - #if PY_VERSION_HEX >= 0x030500B1 - #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods - #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) - #else - #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) - #endif -#else - #define __Pyx_PyType_AsAsync(obj) NULL -#endif -#ifndef __Pyx_PyAsyncMethodsStruct - typedef struct { - unaryfunc am_await; - unaryfunc am_aiter; - unaryfunc am_anext; - } __Pyx_PyAsyncMethodsStruct; -#endif - -#if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS) - #if !defined(_USE_MATH_DEFINES) - #define _USE_MATH_DEFINES - #endif -#endif -#include -#ifdef NAN -#define __PYX_NAN() ((float) NAN) -#else -static CYTHON_INLINE float __PYX_NAN() { - float value; - memset(&value, 0xFF, sizeof(value)); - return value; -} -#endif -#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL) -#define __Pyx_truncl trunc -#else -#define __Pyx_truncl truncl -#endif - -#define __PYX_MARK_ERR_POS(f_index, lineno) \ - { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; } -#define __PYX_ERR(f_index, lineno, Ln_error) \ - { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; } - -#ifndef __PYX_EXTERN_C - #ifdef __cplusplus - #define __PYX_EXTERN_C extern "C" - #else - #define __PYX_EXTERN_C extern - #endif -#endif - -#define __PYX_HAVE__MDAnalysis__lib__c_distances -#define __PYX_HAVE_API__MDAnalysis__lib__c_distances -/* Early includes */ -#include -#include -#include -#include "numpy/arrayobject.h" -#include "numpy/ndarrayobject.h" -#include "numpy/ndarraytypes.h" -#include "numpy/arrayscalars.h" -#include "numpy/ufuncobject.h" - - /* NumPy API declarations from "numpy/__init__.pxd" */ - -#include -#include -#include "string.h" -#include "calc_distances.h" -#include "pythread.h" -#include -#include "pystate.h" -#ifdef _OPENMP -#include -#endif /* _OPENMP */ - -#if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS) -#define CYTHON_WITHOUT_ASSERTIONS -#endif - -typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding; - const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; - -#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 -#define __PYX_DEFAULT_STRING_ENCODING_IS_UTF8 0 -#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT (PY_MAJOR_VERSION >= 3 && __PYX_DEFAULT_STRING_ENCODING_IS_UTF8) -#define __PYX_DEFAULT_STRING_ENCODING "" -#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString -#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize -#define __Pyx_uchar_cast(c) ((unsigned char)c) -#define __Pyx_long_cast(x) ((long)x) -#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ - (sizeof(type) < sizeof(Py_ssize_t)) ||\ - (sizeof(type) > sizeof(Py_ssize_t) &&\ - likely(v < (type)PY_SSIZE_T_MAX ||\ - v == (type)PY_SSIZE_T_MAX) &&\ - (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ - v == (type)PY_SSIZE_T_MIN))) ||\ - (sizeof(type) == sizeof(Py_ssize_t) &&\ - (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ - v == (type)PY_SSIZE_T_MAX))) ) -static CYTHON_INLINE int __Pyx_is_valid_index(Py_ssize_t i, Py_ssize_t limit) { - return (size_t) i < (size_t) limit; -} -#if defined (__cplusplus) && __cplusplus >= 201103L - #include - #define __Pyx_sst_abs(value) std::abs(value) -#elif SIZEOF_INT >= SIZEOF_SIZE_T - #define __Pyx_sst_abs(value) abs(value) -#elif SIZEOF_LONG >= SIZEOF_SIZE_T - #define __Pyx_sst_abs(value) labs(value) -#elif defined (_MSC_VER) - #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value)) -#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define __Pyx_sst_abs(value) llabs(value) -#elif defined (__GNUC__) - #define __Pyx_sst_abs(value) __builtin_llabs(value) -#else - #define __Pyx_sst_abs(value) ((value<0) ? -value : value) -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); -#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) -#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) -#define __Pyx_PyBytes_FromString PyBytes_FromString -#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); -#if PY_MAJOR_VERSION < 3 - #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString - #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize -#else - #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString - #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize -#endif -#define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) -#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) -#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) -#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) -#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) -static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { - const Py_UNICODE *u_end = u; - while (*u_end++) ; - return (size_t)(u_end - u - 1); -} -#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) -#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode -#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode -#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) -#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*); -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); -#define __Pyx_PySequence_Tuple(obj)\ - (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj)) -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); -static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*); -#if CYTHON_ASSUME_SAFE_MACROS -#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) -#else -#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) -#endif -#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) -#else -#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) -#endif -#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII -static int __Pyx_sys_getdefaultencoding_not_ascii; -static int __Pyx_init_sys_getdefaultencoding_params(void) { - PyObject* sys; - PyObject* default_encoding = NULL; - PyObject* ascii_chars_u = NULL; - PyObject* ascii_chars_b = NULL; - const char* default_encoding_c; - sys = PyImport_ImportModule("sys"); - if (!sys) goto bad; - default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); - Py_DECREF(sys); - if (!default_encoding) goto bad; 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- -/* UnicodeAsUCS4.proto */ -static CYTHON_INLINE Py_UCS4 __Pyx_PyUnicode_AsPy_UCS4(PyObject*); - -/* object_ord.proto */ -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyObject_Ord(c)\ - (likely(PyUnicode_Check(c)) ? 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- PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) -#endif - -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); -#else -#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace, zerodivision_check)\ - (inplace ? 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-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m, - PyObject *dict); -static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m, - PyObject *dict); -static int __pyx_CyFunction_init(void); - -/* FusedFunction.proto */ -typedef struct { - __pyx_CyFunctionObject func; - PyObject *__signatures__; - PyObject *type; - PyObject *self; -} __pyx_FusedFunctionObject; -static PyObject *__pyx_FusedFunction_New(PyMethodDef *ml, int flags, - PyObject *qualname, PyObject *closure, - PyObject *module, PyObject *globals, - PyObject *code); -static int __pyx_FusedFunction_clear(__pyx_FusedFunctionObject *self); -static PyTypeObject *__pyx_FusedFunctionType = NULL; -static int __pyx_FusedFunction_init(void); -#define __Pyx_FusedFunction_USED - -/* CLineInTraceback.proto */ -#ifdef CYTHON_CLINE_IN_TRACEBACK -#define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) -#else -static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line); -#endif - -/* CodeObjectCache.proto */ -typedef struct { - PyCodeObject* code_object; - int code_line; -} __Pyx_CodeObjectCacheEntry; -struct __Pyx_CodeObjectCache { - int count; - int max_count; - __Pyx_CodeObjectCacheEntry* entries; -}; -static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); -static PyCodeObject *__pyx_find_code_object(int code_line); -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); - -/* AddTraceback.proto */ -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename); - -#if PY_MAJOR_VERSION < 3 - static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); - static void __Pyx_ReleaseBuffer(Py_buffer *view); -#else - #define __Pyx_GetBuffer PyObject_GetBuffer - #define __Pyx_ReleaseBuffer PyBuffer_Release -#endif - - -/* BufferStructDeclare.proto */ -typedef struct { - Py_ssize_t shape, strides, suboffsets; -} __Pyx_Buf_DimInfo; -typedef struct { - size_t refcount; - Py_buffer pybuffer; -} __Pyx_Buffer; -typedef struct { - __Pyx_Buffer *rcbuffer; - char *data; - __Pyx_Buf_DimInfo diminfo[8]; -} __Pyx_LocalBuf_ND; - -/* MemviewSliceIsContig.proto */ -static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim); - -/* OverlappingSlices.proto */ -static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize); - -/* Capsule.proto */ -static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); - -/* IsLittleEndian.proto */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void); - -/* BufferFormatCheck.proto */ -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type); - -/* TypeInfoCompare.proto */ -static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); - -/* MemviewSliceValidateAndInit.proto */ -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_double(PyObject *, int writable_flag); - -/* GCCDiagnostics.proto */ -#if defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6)) -#define __Pyx_HAS_GCC_DIAGNOSTIC -#endif - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_float(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_double(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_float(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_float(PyObject *, int writable_flag); - -/* MemviewDtypeToObject.proto */ -static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp); -static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj); - -/* MemviewDtypeToObject.proto */ -static CYTHON_INLINE PyObject *__pyx_memview_get_double(const char *itemp); -static CYTHON_INLINE int __pyx_memview_set_double(const char *itemp, PyObject *obj); - -/* RealImag.proto */ -#if CYTHON_CCOMPLEX - #ifdef __cplusplus - #define __Pyx_CREAL(z) ((z).real()) - #define __Pyx_CIMAG(z) ((z).imag()) - #else - #define __Pyx_CREAL(z) (__real__(z)) - #define __Pyx_CIMAG(z) (__imag__(z)) - #endif -#else - #define __Pyx_CREAL(z) ((z).real) - #define __Pyx_CIMAG(z) ((z).imag) -#endif -#if defined(__cplusplus) && CYTHON_CCOMPLEX\ - && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103) - #define __Pyx_SET_CREAL(z,x) ((z).real(x)) - #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) -#else - #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) - #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) -#endif - -/* Arithmetic.proto */ -#if CYTHON_CCOMPLEX - #define __Pyx_c_eq_float(a, b) ((a)==(b)) - #define __Pyx_c_sum_float(a, b) ((a)+(b)) - #define __Pyx_c_diff_float(a, b) ((a)-(b)) - #define __Pyx_c_prod_float(a, b) ((a)*(b)) - #define __Pyx_c_quot_float(a, b) ((a)/(b)) - #define __Pyx_c_neg_float(a) (-(a)) - #ifdef __cplusplus - #define __Pyx_c_is_zero_float(z) ((z)==(float)0) - #define __Pyx_c_conj_float(z) (::std::conj(z)) - #if 1 - #define __Pyx_c_abs_float(z) (::std::abs(z)) - #define __Pyx_c_pow_float(a, b) (::std::pow(a, b)) - #endif - #else - #define __Pyx_c_is_zero_float(z) ((z)==0) - #define __Pyx_c_conj_float(z) (conjf(z)) - #if 1 - #define __Pyx_c_abs_float(z) (cabsf(z)) - #define __Pyx_c_pow_float(a, b) (cpowf(a, b)) - #endif - #endif -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex); - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex); - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex); - #endif -#endif - -/* Arithmetic.proto */ -#if CYTHON_CCOMPLEX - #define __Pyx_c_eq_double(a, b) ((a)==(b)) - #define __Pyx_c_sum_double(a, b) ((a)+(b)) - #define __Pyx_c_diff_double(a, b) ((a)-(b)) - #define __Pyx_c_prod_double(a, b) ((a)*(b)) - #define __Pyx_c_quot_double(a, b) ((a)/(b)) - #define __Pyx_c_neg_double(a) (-(a)) - #ifdef __cplusplus - #define __Pyx_c_is_zero_double(z) ((z)==(double)0) - #define __Pyx_c_conj_double(z) (::std::conj(z)) - #if 1 - #define __Pyx_c_abs_double(z) (::std::abs(z)) - #define __Pyx_c_pow_double(a, b) (::std::pow(a, b)) - #endif - #else - #define __Pyx_c_is_zero_double(z) ((z)==0) - #define __Pyx_c_conj_double(z) (conj(z)) - #if 1 - #define __Pyx_c_abs_double(z) (cabs(z)) - #define __Pyx_c_pow_double(a, b) (cpow(a, b)) - #endif - #endif -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex); - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex); - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex); - #endif -#endif - -/* MemviewSliceCopyTemplate.proto */ -static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value); - -/* TypeInfoToFormat.proto */ -struct __pyx_typeinfo_string { - char string[3]; -}; -static struct __pyx_typeinfo_string __Pyx_TypeInfoToFormat(__Pyx_TypeInfo *type); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); - -/* CIntFromPy.proto */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); - -/* BytesContains.proto */ -static CYTHON_INLINE int __Pyx_BytesContains(PyObject* bytes, char character); - -/* ImportNumPyArray.proto */ -static PyObject *__pyx_numpy_ndarray = NULL; -static PyObject* __Pyx_ImportNumPyArrayTypeIfAvailable(void); - -/* CIntFromPy.proto */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); - -/* CIntFromPy.proto */ -static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); - -/* CheckBinaryVersion.proto */ -static int __Pyx_check_binary_version(void); 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/*proto*/ -static CYTHON_INLINE void __pyx_fuse_0__pyx_f_10MDAnalysis_3lib_11c_distances__minimum_image_triclinic(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice); /*proto*/ -static CYTHON_INLINE void __pyx_fuse_1__pyx_f_10MDAnalysis_3lib_11c_distances__minimum_image_triclinic(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice); /*proto*/ -static struct __pyx_array_obj *__pyx_array_new(PyObject *, Py_ssize_t, char *, char *, char *); /*proto*/ -static void *__pyx_align_pointer(void *, size_t); /*proto*/ -static PyObject *__pyx_memoryview_new(PyObject *, int, int, __Pyx_TypeInfo *); /*proto*/ -static CYTHON_INLINE int __pyx_memoryview_check(PyObject *); /*proto*/ -static PyObject *_unellipsify(PyObject *, int); /*proto*/ -static PyObject *assert_direct_dimensions(Py_ssize_t *, int); /*proto*/ -static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_obj *, PyObject *); /*proto*/ -static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int, int); /*proto*/ -static char *__pyx_pybuffer_index(Py_buffer *, char *, Py_ssize_t, Py_ssize_t); /*proto*/ -static int __pyx_memslice_transpose(__Pyx_memviewslice *); /*proto*/ -static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice, int, PyObject *(*)(char *), int (*)(char *, PyObject *), int); /*proto*/ -static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/ -static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/ -static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/ -static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/ -static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/ -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/ -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/ -static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/ -static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/ -static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/ -static int __pyx_memoryview_err(PyObject *, char *); /*proto*/ -static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/ -static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/ -static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/ -static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ -static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ -static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ -static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ -static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *, PyObject *); /*proto*/ -static PyObject *__pyx_format_from_typeinfo(__Pyx_TypeInfo *); /*proto*/ -static __Pyx_TypeInfo __Pyx_TypeInfo_float = { "float", NULL, sizeof(float), { 0 }, 0, 'R', 0, 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_double = { "double", NULL, sizeof(double), { 0 }, 0, 'R', 0, 0 }; -#define __Pyx_MODULE_NAME "MDAnalysis.lib.c_distances" -extern int __pyx_module_is_main_MDAnalysis__lib__c_distances; -int __pyx_module_is_main_MDAnalysis__lib__c_distances = 0; - -/* Implementation of 'MDAnalysis.lib.c_distances' */ -static PyObject *__pyx_builtin_range; -static PyObject *__pyx_builtin_TypeError; -static PyObject *__pyx_builtin_ImportError; -static PyObject *__pyx_builtin_ValueError; -static PyObject *__pyx_builtin_MemoryError; -static PyObject *__pyx_builtin_enumerate; -static PyObject *__pyx_builtin_Ellipsis; -static PyObject *__pyx_builtin_id; -static PyObject *__pyx_builtin_IndexError; -static const char __pyx_k_[] = "()"; -static const char __pyx_k_O[] = "O"; -static const char __pyx_k_T[] = "T{"; - static const char __pyx_k_c[] = "c"; - static const char __pyx_k_i[] = "i"; - static const char __pyx_k_j[] = "j"; - static const char __pyx_k_n[] = "n"; - static const char __pyx_k_s[] = "s"; - static const char __pyx_k__2[] = "|"; - static const char __pyx_k_id[] = "id"; - static const char __pyx_k_rr[] = "rr"; - static const char __pyx_k__26[] = "^"; - static const char __pyx_k__27[] = ""; - static const char __pyx_k__28[] = ":"; -static const char __pyx_k__29[] = "}"; -static const char __pyx_k__30[] = ","; -static const char __pyx_k_box[] = "box"; -static const char __pyx_k_new[] = "__new__"; -static const char __pyx_k_obj[] = "obj"; -static const char __pyx_k_ref[] = "ref"; -static const char __pyx_k_s_2[] = "(%s)"; -static const char __pyx_k_args[] = "args"; -static const char __pyx_k_base[] = "base"; -static const char __pyx_k_conf[] = "conf"; -static const char __pyx_k_dict[] = "__dict__"; -static const char __pyx_k_dist[] = "dist"; -static const char __pyx_k_join[] = "join"; -static const char __pyx_k_kind[] = "kind"; -static const char __pyx_k_main[] = "__main__"; -static const char __pyx_k_mode[] = "mode"; -static const char __pyx_k_name[] = "name"; -static const char __pyx_k_ndim[] = "ndim"; -static const char __pyx_k_pack[] = "pack"; -static const char __pyx_k_rows[] = "rows"; -static const char __pyx_k_size[] = "size"; -static const char __pyx_k_step[] = "step"; -static const char __pyx_k_stop[] = "stop"; -static const char __pyx_k_test[] = "__test__"; -static const char __pyx_k_ASCII[] = "ASCII"; -static const char __pyx_k_class[] = "__class__"; -static const char __pyx_k_coord[] = "coord"; -static const char __pyx_k_dtype[] = "dtype"; -static const char __pyx_k_error[] = "error"; -static const char __pyx_k_flags[] = "flags"; -static const char __pyx_k_float[] = "float"; -static const char __pyx_k_numpy[] = "numpy"; -static const char __pyx_k_range[] = "range"; -static const char __pyx_k_shape[] = "shape"; -static const char __pyx_k_split[] = "split"; -static const char __pyx_k_start[] = "start"; -static const char __pyx_k_strip[] = "strip"; -static const char __pyx_k_coords[] = "coords"; -static const char __pyx_k_cutoff[] = "cutoff"; -static const char __pyx_k_double[] = "double"; -static const char __pyx_k_encode[] = "encode"; -static const char __pyx_k_format[] = "format"; -static const char __pyx_k_import[] = "__import__"; -static const char __pyx_k_kwargs[] = "kwargs"; -static const char __pyx_k_name_2[] = "__name__"; -static const char __pyx_k_output[] = "output"; -static const char __pyx_k_pickle[] = "pickle"; -static const char __pyx_k_reduce[] = "__reduce__"; -static const char __pyx_k_refnum[] = "refnum"; -static const char __pyx_k_result[] = "result"; -static const char __pyx_k_struct[] = "struct"; -static const char __pyx_k_unpack[] = "unpack"; -static const char __pyx_k_update[] = "update"; -static const char __pyx_k_box_inv[] = "box_inv"; -static const char __pyx_k_confnum[] = "confnum"; -static const char __pyx_k_coords1[] = "coords1"; -static const char __pyx_k_coords2[] = "coords2"; -static const char __pyx_k_coords3[] = "coords3"; -static const char __pyx_k_coords4[] = "coords4"; -static const char __pyx_k_cutoff2[] = "cutoff2"; -static const char __pyx_k_fortran[] = "fortran"; -static const char __pyx_k_memview[] = "memview"; -static const char __pyx_k_results[] = "results"; -static const char __pyx_k_vectors[] = "vectors"; -static const char __pyx_k_Ellipsis[] = "Ellipsis"; -static const char __pyx_k_box_view[] = "box_view"; -static const char __pyx_k_defaults[] = "defaults"; -static const char __pyx_k_getstate[] = "__getstate__"; -static const char __pyx_k_itemsize[] = "itemsize"; -static const char __pyx_k_pyx_type[] = "__pyx_type"; -static const char __pyx_k_setstate[] = "__setstate__"; -static const char __pyx_k_TypeError[] = "TypeError"; -static const char __pyx_k_enumerate[] = "enumerate"; -static const char __pyx_k_numcoords[] = "numcoords"; -static const char __pyx_k_ortho_pbc[] = "ortho_pbc"; -static const char __pyx_k_pyx_state[] = "__pyx_state"; -static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; -static const char __pyx_k_IndexError[] = "IndexError"; -static const char __pyx_k_UINT64_MAX[] = "_UINT64_MAX"; -static const char __pyx_k_ValueError[] = "ValueError"; -static const char __pyx_k_calc_angle[] = "calc_angle"; -static const char __pyx_k_coord_view[] = "coord_view"; -static const char __pyx_k_pyx_result[] = "__pyx_result"; -static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; -static const char __pyx_k_signatures[] = "signatures"; -static const char __pyx_k_ImportError[] = "ImportError"; -static const char __pyx_k_MemoryError[] = "MemoryError"; -static const char __pyx_k_PickleError[] = "PickleError"; -static const char __pyx_k_box_inverse[] = "box_inverse"; -static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; -static const char __pyx_k_stringsource[] = "stringsource"; -static const char __pyx_k_calc_dihedral[] = "calc_dihedral"; -static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; -static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; -static const char __pyx_k_triclinic_pbc[] = "triclinic_pbc"; -static const char __pyx_k_OPENMP_ENABLED[] = "OPENMP_ENABLED"; -static const char __pyx_k_View_MemoryView[] = "View.MemoryView"; -static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; -static const char __pyx_k_coord_transform[] = "coord_transform"; -static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; -static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; -static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; -static const char __pyx_k_sparse_contacts[] = "sparse_contacts"; -static const char __pyx_k_box_inverse_view[] = "box_inverse_view"; -static const char __pyx_k_calc_angle_ortho[] = "calc_angle_ortho"; -static const char __pyx_k_pyx_unpickle_Enum[] = "__pyx_unpickle_Enum"; -static const char __pyx_k_calc_bond_distance[] = "calc_bond_distance"; -static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; -static const char __pyx_k_contact_matrix_pbc[] = "contact_matrix_pbc"; -static const char __pyx_k_strided_and_direct[] = ""; -static const char __pyx_k_calc_dihedral_ortho[] = "calc_dihedral_ortho"; -static const char __pyx_k_calc_distance_array[] = "calc_distance_array"; -static const char __pyx_k_calc_angle_triclinic[] = "calc_angle_triclinic"; -static const char __pyx_k_strided_and_indirect[] = ""; -static const char __pyx_k_contact_matrix_no_pbc[] = "contact_matrix_no_pbc"; -static const char __pyx_k_contiguous_and_direct[] = ""; -static const char __pyx_k_MemoryView_of_r_object[] = ""; 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-static const char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; -static const char __pyx_k_Cannot_assign_to_read_only_memor[] = "Cannot assign to read-only memoryview"; -static const char __pyx_k_Cannot_create_writable_memory_vi[] = "Cannot create writable memory view from read-only memoryview"; -static const char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; -static const char __pyx_k_Expected_at_least_d_argument_s_g[] = "Expected at least %d argument%s, got %d"; -static const char __pyx_k_Function_call_with_ambiguous_arg[] = "Function call with ambiguous argument types"; -static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0xb068931, 0x82a3537, 0x6ae9995) = (name))"; -static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; -static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; -static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; -static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; -static const char __pyx_k_calc_self_distance_array_triclin[] = "calc_self_distance_array_triclinic"; -static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; -static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; -static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; -static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; -static PyObject *__pyx_kp_s_; -static PyObject *__pyx_n_s_ASCII; -static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; -static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; -static PyObject *__pyx_kp_s_Cannot_assign_to_read_only_memor; -static PyObject *__pyx_kp_s_Cannot_create_writable_memory_vi; -static PyObject *__pyx_kp_s_Cannot_index_with_type_s; -static PyObject *__pyx_n_s_Ellipsis; -static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; -static PyObject *__pyx_kp_s_Expected_at_least_d_argument_s_g; -static PyObject *__pyx_kp_s_Function_call_with_ambiguous_arg; -static PyObject *__pyx_n_s_ImportError; -static PyObject *__pyx_kp_s_Incompatible_checksums_0x_x_vs_0; -static PyObject *__pyx_n_s_IndexError; -static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; -static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; -static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; -static PyObject *__pyx_n_s_MDAnalysis_lib_c_distances; -static PyObject *__pyx_kp_s_MDAnalysis_lib_c_distances_pyx; -static PyObject *__pyx_n_s_MemoryError; -static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; -static PyObject *__pyx_kp_s_MemoryView_of_r_object; -static PyObject *__pyx_kp_s_No_matching_signature_found; -static PyObject *__pyx_n_b_O; -static PyObject *__pyx_n_s_OPENMP_ENABLED; -static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; -static PyObject *__pyx_n_s_PickleError; -static PyObject *__pyx_kp_b_T; -static PyObject *__pyx_n_s_TypeError; -static PyObject *__pyx_n_s_UINT64_MAX; -static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; -static PyObject *__pyx_n_s_ValueError; -static PyObject *__pyx_n_s_View_MemoryView; -static PyObject *__pyx_kp_s__2; -static PyObject *__pyx_kp_b__26; -static PyObject *__pyx_kp_b__27; -static PyObject *__pyx_kp_b__28; -static PyObject *__pyx_kp_b__29; -static PyObject *__pyx_kp_u__30; -static PyObject *__pyx_n_s_allocate_buffer; -static PyObject *__pyx_n_s_args; -static PyObject *__pyx_n_s_base; -static PyObject *__pyx_n_s_box; -static PyObject *__pyx_n_s_box_inv; -static PyObject *__pyx_n_s_box_inverse; -static PyObject *__pyx_n_s_box_inverse_view; -static PyObject *__pyx_n_s_box_view; -static PyObject *__pyx_n_s_c; -static PyObject *__pyx_n_u_c; -static PyObject *__pyx_n_s_calc_angle; -static PyObject *__pyx_n_s_calc_angle_ortho; -static PyObject *__pyx_n_s_calc_angle_triclinic; -static PyObject *__pyx_n_s_calc_bond_distance; -static PyObject *__pyx_n_s_calc_bond_distance_ortho; -static PyObject *__pyx_n_s_calc_bond_distance_triclinic; -static PyObject *__pyx_n_s_calc_dihedral; -static PyObject *__pyx_n_s_calc_dihedral_ortho; -static PyObject *__pyx_n_s_calc_dihedral_triclinic; -static PyObject *__pyx_n_s_calc_distance_array; -static PyObject *__pyx_n_s_calc_distance_array_ortho; -static PyObject *__pyx_n_s_calc_distance_array_triclinic; -static PyObject *__pyx_n_s_calc_self_distance_array; -static PyObject *__pyx_n_s_calc_self_distance_array_ortho; -static PyObject *__pyx_n_s_calc_self_distance_array_triclin; -static PyObject *__pyx_n_s_class; -static PyObject *__pyx_n_s_cline_in_traceback; -static PyObject *__pyx_n_s_conf; -static PyObject *__pyx_n_s_confnum; -static PyObject *__pyx_n_s_contact_matrix_no_pbc; -static PyObject *__pyx_n_s_contact_matrix_pbc; -static PyObject *__pyx_kp_s_contiguous_and_direct; -static PyObject *__pyx_kp_s_contiguous_and_indirect; -static PyObject *__pyx_n_s_coord; -static PyObject *__pyx_n_s_coord_transform; -static PyObject *__pyx_n_s_coord_view; -static PyObject *__pyx_n_s_coords; -static PyObject *__pyx_n_s_coords1; -static PyObject *__pyx_n_s_coords2; -static PyObject *__pyx_n_s_coords3; -static PyObject *__pyx_n_s_coords4; -static PyObject *__pyx_n_s_cutoff; -static PyObject *__pyx_n_s_cutoff2; -static PyObject *__pyx_n_s_defaults; -static PyObject *__pyx_n_s_dict; -static PyObject *__pyx_n_s_dist; -static PyObject *__pyx_n_s_double; -static PyObject *__pyx_n_s_dtype; -static PyObject *__pyx_n_s_dtype_is_object; -static PyObject *__pyx_n_s_encode; -static PyObject *__pyx_n_s_enumerate; -static PyObject *__pyx_n_s_error; -static PyObject *__pyx_n_s_flags; -static PyObject *__pyx_n_s_float; -static PyObject *__pyx_n_s_format; -static PyObject *__pyx_n_s_fortran; -static PyObject *__pyx_n_u_fortran; -static PyObject *__pyx_n_s_getstate; -static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; -static PyObject *__pyx_n_s_i; -static PyObject *__pyx_n_s_id; -static PyObject *__pyx_n_s_import; -static PyObject *__pyx_n_s_itemsize; -static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; -static PyObject *__pyx_n_s_j; -static PyObject *__pyx_n_s_join; -static PyObject *__pyx_n_s_kind; -static PyObject *__pyx_n_s_kwargs; -static PyObject *__pyx_n_s_main; -static PyObject *__pyx_n_s_memview; -static PyObject *__pyx_n_s_minimize_vectors_ortho; -static PyObject *__pyx_n_s_minimize_vectors_triclinic; -static PyObject *__pyx_n_s_mode; -static PyObject *__pyx_n_s_n; -static PyObject *__pyx_n_s_name; -static PyObject *__pyx_n_s_name_2; -static PyObject *__pyx_n_s_ndim; -static PyObject *__pyx_n_s_new; -static PyObject *__pyx_kp_s_no_default___reduce___due_to_non; -static PyObject *__pyx_n_s_numcoords; -static PyObject *__pyx_n_s_numpy; -static PyObject *__pyx_kp_u_numpy_core_multiarray_failed_to; -static PyObject *__pyx_kp_u_numpy_core_umath_failed_to_impor; -static PyObject *__pyx_n_s_obj; -static PyObject *__pyx_n_s_ortho_pbc; -static PyObject *__pyx_n_s_output; -static PyObject *__pyx_n_s_pack; -static PyObject *__pyx_n_s_pickle; -static PyObject *__pyx_n_s_pyx_PickleError; -static PyObject *__pyx_n_s_pyx_checksum; -static PyObject *__pyx_n_s_pyx_getbuffer; -static PyObject *__pyx_n_s_pyx_result; -static PyObject *__pyx_n_s_pyx_state; -static PyObject *__pyx_n_s_pyx_type; -static PyObject *__pyx_n_s_pyx_unpickle_Enum; -static PyObject *__pyx_n_s_pyx_vtable; -static PyObject *__pyx_n_s_range; -static PyObject *__pyx_n_s_reduce; -static PyObject *__pyx_n_s_reduce_cython; -static PyObject *__pyx_n_s_reduce_ex; -static PyObject *__pyx_n_s_ref; -static PyObject *__pyx_n_s_refnum; -static PyObject *__pyx_n_s_result; -static PyObject *__pyx_n_s_results; -static PyObject *__pyx_n_s_rows; -static PyObject *__pyx_n_s_rr; -static PyObject *__pyx_n_s_s; -static PyObject *__pyx_kp_u_s_2; -static PyObject *__pyx_n_s_setstate; -static PyObject *__pyx_n_s_setstate_cython; -static PyObject *__pyx_n_s_shape; -static PyObject *__pyx_n_s_signatures; -static PyObject *__pyx_n_s_size; -static PyObject *__pyx_n_s_sparse_contacts; -static PyObject *__pyx_n_s_split; -static PyObject *__pyx_n_s_start; -static PyObject *__pyx_n_s_step; -static PyObject *__pyx_n_s_stop; -static PyObject *__pyx_kp_s_strided_and_direct; -static PyObject *__pyx_kp_s_strided_and_direct_or_indirect; -static PyObject *__pyx_kp_s_strided_and_indirect; -static PyObject *__pyx_kp_s_stringsource; -static PyObject *__pyx_n_s_strip; -static PyObject *__pyx_n_s_struct; -static PyObject *__pyx_n_s_test; -static PyObject *__pyx_n_s_triclinic_pbc; -static PyObject *__pyx_kp_s_unable_to_allocate_array_data; -static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; -static PyObject *__pyx_n_s_unpack; -static PyObject *__pyx_n_s_update; -static PyObject *__pyx_n_s_vectors; -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_calc_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_2calc_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_4calc_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_6calc_self_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_8calc_self_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_10calc_self_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_12coord_transform(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_14calc_bond_distance(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_16calc_bond_distance_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_18calc_bond_distance_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_20calc_angle(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_22calc_angle_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_24calc_angle_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_26calc_dihedral(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_28calc_dihedral_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_30calc_dihedral_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_32ortho_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_34triclinic_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_36contact_matrix_no_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_coord, PyObject *__pyx_v_sparse_contacts, PyObject *__pyx_v_cutoff); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_38contact_matrix_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_coord, PyObject *__pyx_v_sparse_contacts, PyObject *__pyx_v_box, PyObject *__pyx_v_cutoff); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_40_minimize_vectors_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_signatures, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs, CYTHON_UNUSED PyObject *__pyx_v_defaults); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_44_minimize_vectors_ortho(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_vectors, __Pyx_memviewslice __pyx_v_box, __Pyx_memviewslice __pyx_v_output); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_46_minimize_vectors_ortho(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_vectors, __Pyx_memviewslice __pyx_v_box, __Pyx_memviewslice __pyx_v_output); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_42_minimize_vectors_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_signatures, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs, CYTHON_UNUSED PyObject *__pyx_v_defaults); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_50_minimize_vectors_triclinic(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_vectors, __Pyx_memviewslice __pyx_v_box, __Pyx_memviewslice __pyx_v_output); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_11c_distances_52_minimize_vectors_triclinic(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_vectors, __Pyx_memviewslice __pyx_v_box, __Pyx_memviewslice __pyx_v_output); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__len__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_12__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ -static PyObject *__pyx_pf___pyx_array___reduce_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_array_2__setstate_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); 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- - /* "MDAnalysis/lib/c_distances.pyx":323 - * if box[i] > 0: - * s = inverse_box[i] * dx[i] - * dx[i] = box[i] * (s - cround(s)) # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_4 = __pyx_v_i; - __pyx_t_2 = __pyx_v_i; - *((float *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_2 * __pyx_v_dx.strides[0]) )) = ((*((float *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_4 * __pyx_v_box.strides[0]) ))) * (__pyx_v_s - round(__pyx_v_s))); - - /* "MDAnalysis/lib/c_distances.pyx":321 - * - * for i in range(3): - * if box[i] > 0: # <<<<<<<<<<<<<< - * s = inverse_box[i] * dx[i] - * dx[i] = box[i] * (s - cround(s)) - */ - } - } - - /* "MDAnalysis/lib/c_distances.pyx":301 - * @cython.boundscheck(False) - * @cython.wraparound(False) - * cdef inline void _minimum_image_orthogonal(cython.floating[:] dx, # <<<<<<<<<<<<<< - * cython.floating[:] box, - * cython.floating[:] inverse_box) nogil: - */ - - /* function exit code */ -} - -static CYTHON_INLINE void __pyx_fuse_1__pyx_f_10MDAnalysis_3lib_11c_distances__minimum_image_orthogonal(__Pyx_memviewslice __pyx_v_dx, __Pyx_memviewslice __pyx_v_box, __Pyx_memviewslice __pyx_v_inverse_box) { - int __pyx_v_i; 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- - /* "MDAnalysis/lib/c_distances.pyx":323 - * if box[i] > 0: - * s = inverse_box[i] * dx[i] - * dx[i] = box[i] * (s - cround(s)) # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_4 = __pyx_v_i; - __pyx_t_2 = __pyx_v_i; - *((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_2 * __pyx_v_dx.strides[0]) )) = ((*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_4 * __pyx_v_box.strides[0]) ))) * (__pyx_v_s - round(__pyx_v_s))); - - /* "MDAnalysis/lib/c_distances.pyx":321 - * - * for i in range(3): - * if box[i] > 0: # <<<<<<<<<<<<<< - * s = inverse_box[i] * dx[i] - * dx[i] = box[i] * (s - cround(s)) - */ - } - } - - /* "MDAnalysis/lib/c_distances.pyx":301 - * @cython.boundscheck(False) - * @cython.wraparound(False) - * cdef inline void _minimum_image_orthogonal(cython.floating[:] dx, # <<<<<<<<<<<<<< - * cython.floating[:] box, - * cython.floating[:] inverse_box) nogil: - */ - - /* function exit code */ -} - -/* "MDAnalysis/lib/c_distances.pyx":328 - * @cython.boundscheck(False) - * @cython.wraparound(False) - * cdef inline void _minimum_image_triclinic(cython.floating[:] dx, # <<<<<<<<<<<<<< - * cython.floating[:] box, - * cython.floating[:] inverse_box) nogil: - */ - -static CYTHON_INLINE void __pyx_fuse_0__pyx_f_10MDAnalysis_3lib_11c_distances__minimum_image_triclinic(__Pyx_memviewslice __pyx_v_dx, __Pyx_memviewslice __pyx_v_box, __Pyx_memviewslice __pyx_v_inverse_box) { - float __pyx_v_dx_min[3]; 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- - /* "MDAnalysis/lib/c_distances.pyx":359 - * dx[1] -= s * box[7] - * dx[2] -= s * box[8] - * s = cround(inverse_box[1] * dx[1]) # <<<<<<<<<<<<<< - * dx[0] -= s * box[3] - * dx[1] -= s * box[4] - */ - __pyx_t_2 = 1; - __pyx_t_1 = 1; - __pyx_v_s = round(((*((float *) ( /* dim=0 */ (__pyx_v_inverse_box.data + __pyx_t_2 * __pyx_v_inverse_box.strides[0]) ))) * (*((float *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_1 * __pyx_v_dx.strides[0]) ))))); - - /* "MDAnalysis/lib/c_distances.pyx":360 - * dx[2] -= s * box[8] - * s = cround(inverse_box[1] * dx[1]) - * dx[0] -= s * box[3] # <<<<<<<<<<<<<< - * dx[1] -= s * box[4] - * s = cround(inverse_box[0] * dx[0]) - */ - __pyx_t_1 = 3; - __pyx_t_2 = 0; - *((float *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_2 * __pyx_v_dx.strides[0]) )) -= (__pyx_v_s * (*((float *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_1 * __pyx_v_box.strides[0]) )))); - - /* "MDAnalysis/lib/c_distances.pyx":361 - * s = cround(inverse_box[1] * dx[1]) - * dx[0] -= s * box[3] - * dx[1] -= s * box[4] # <<<<<<<<<<<<<< - * s = cround(inverse_box[0] * dx[0]) - * dx[0] -= s * box[0] - */ - __pyx_t_1 = 4; 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__pyx_t_3 < 2; __pyx_t_3+=1) { - __pyx_v_ix = __pyx_t_3; - - /* "MDAnalysis/lib/c_distances.pyx":375 - * # then check all images to see which combination of 1 cell shifts gives the best shift - * for ix in range(-1, 2): - * rx = dx[0] + box[0] * ix # <<<<<<<<<<<<<< - * for iy in range(-1, 2): - * ry[0] = rx + box[3] * iy - */ - __pyx_t_2 = 0; - __pyx_t_1 = 0; - __pyx_v_rx = ((*((float *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_2 * __pyx_v_dx.strides[0]) ))) + ((*((float *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_1 * __pyx_v_box.strides[0]) ))) * __pyx_v_ix)); - - /* "MDAnalysis/lib/c_distances.pyx":376 - * for ix in range(-1, 2): - * rx = dx[0] + box[0] * ix - * for iy in range(-1, 2): # <<<<<<<<<<<<<< - * ry[0] = rx + box[3] * iy - * ry[1] = dx[1] + box[4] * iy - */ - for (__pyx_t_4 = -1; __pyx_t_4 < 2; __pyx_t_4+=1) { - __pyx_v_iy = __pyx_t_4; - - /* "MDAnalysis/lib/c_distances.pyx":377 - * rx = dx[0] + box[0] * ix - * for iy in range(-1, 2): - * ry[0] = rx + box[3] * iy # <<<<<<<<<<<<<< - * ry[1] = dx[1] + box[4] * iy - * for iz in range(-1, 2): - */ - __pyx_t_1 = 3; 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- (__pyx_v_rz[0]) = ((__pyx_v_ry[0]) + ((*((float *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_2 * __pyx_v_box.strides[0]) ))) * __pyx_v_iz)); - - /* "MDAnalysis/lib/c_distances.pyx":381 - * for iz in range(-1, 2): - * rz[0] = ry[0] + box[6] * iz - * rz[1] = ry[1] + box[7] * iz # <<<<<<<<<<<<<< - * rz[2] = dx[2] + box[8] * iz - * dsq = rz[0] * rz[0] + rz[1] * rz[1] + rz[2] * rz[2] - */ - __pyx_t_2 = 7; - (__pyx_v_rz[1]) = ((__pyx_v_ry[1]) + ((*((float *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_2 * __pyx_v_box.strides[0]) ))) * __pyx_v_iz)); - - /* "MDAnalysis/lib/c_distances.pyx":382 - * rz[0] = ry[0] + box[6] * iz - * rz[1] = ry[1] + box[7] * iz - * rz[2] = dx[2] + box[8] * iz # <<<<<<<<<<<<<< - * dsq = rz[0] * rz[0] + rz[1] * rz[1] + rz[2] * rz[2] - * if (dsq < dsq_min): - */ - __pyx_t_2 = 2; - __pyx_t_1 = 8; - (__pyx_v_rz[2]) = ((*((float *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_2 * __pyx_v_dx.strides[0]) ))) + ((*((float *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_1 * __pyx_v_box.strides[0]) ))) * __pyx_v_iz)); - - /* "MDAnalysis/lib/c_distances.pyx":383 - * rz[1] = ry[1] + box[7] * iz - * rz[2] = dx[2] + box[8] * iz - * dsq = rz[0] * rz[0] + rz[1] * rz[1] + rz[2] * rz[2] # <<<<<<<<<<<<<< - * if (dsq < dsq_min): - * dsq_min = dsq - */ - __pyx_v_dsq = ((((__pyx_v_rz[0]) * (__pyx_v_rz[0])) + ((__pyx_v_rz[1]) * (__pyx_v_rz[1]))) + ((__pyx_v_rz[2]) * (__pyx_v_rz[2]))); - - /* "MDAnalysis/lib/c_distances.pyx":384 - * rz[2] = dx[2] + box[8] * iz - * dsq = rz[0] * rz[0] + rz[1] * rz[1] + rz[2] * rz[2] - * if (dsq < dsq_min): # <<<<<<<<<<<<<< - * dsq_min = dsq - * dx_min[0] = rz[0] - */ - __pyx_t_6 = ((__pyx_v_dsq < __pyx_v_dsq_min) != 0); - if (__pyx_t_6) { - - /* "MDAnalysis/lib/c_distances.pyx":385 - * dsq = rz[0] * rz[0] + rz[1] * rz[1] + rz[2] * rz[2] - * if (dsq < dsq_min): - * dsq_min = dsq # <<<<<<<<<<<<<< - * dx_min[0] = rz[0] - * dx_min[1] = rz[1] - */ - __pyx_v_dsq_min = __pyx_v_dsq; - - /* "MDAnalysis/lib/c_distances.pyx":386 - * if (dsq < dsq_min): - * dsq_min = dsq - * dx_min[0] = rz[0] # <<<<<<<<<<<<<< - * dx_min[1] = rz[1] - * dx_min[2] = rz[2] - */ - (__pyx_v_dx_min[0]) = (__pyx_v_rz[0]); - - /* "MDAnalysis/lib/c_distances.pyx":387 - * dsq_min = dsq - * dx_min[0] = rz[0] - * dx_min[1] = rz[1] # <<<<<<<<<<<<<< - * dx_min[2] = rz[2] - * - */ - (__pyx_v_dx_min[1]) = (__pyx_v_rz[1]); - - /* "MDAnalysis/lib/c_distances.pyx":388 - * dx_min[0] = rz[0] - * dx_min[1] = rz[1] - * dx_min[2] = rz[2] # <<<<<<<<<<<<<< - * - * dx[0] = dx_min[0] - */ - (__pyx_v_dx_min[2]) = (__pyx_v_rz[2]); - - /* "MDAnalysis/lib/c_distances.pyx":384 - * rz[2] = dx[2] + box[8] * iz - * dsq = rz[0] * rz[0] + rz[1] * rz[1] + rz[2] * rz[2] - * if (dsq < dsq_min): # <<<<<<<<<<<<<< - * dsq_min = dsq - * dx_min[0] = rz[0] - */ - } - } - } - } - - /* "MDAnalysis/lib/c_distances.pyx":390 - * dx_min[2] = rz[2] - * - * dx[0] = dx_min[0] # <<<<<<<<<<<<<< - * dx[1] = dx_min[1] - * dx[2] = dx_min[2] - */ - __pyx_t_1 = 0; - *((float *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_1 * __pyx_v_dx.strides[0]) )) = (__pyx_v_dx_min[0]); - - /* "MDAnalysis/lib/c_distances.pyx":391 - * - * dx[0] = dx_min[0] - * dx[1] = dx_min[1] # <<<<<<<<<<<<<< - * dx[2] = dx_min[2] - * - */ - __pyx_t_1 = 1; - *((float *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_1 * __pyx_v_dx.strides[0]) )) = (__pyx_v_dx_min[1]); - - /* "MDAnalysis/lib/c_distances.pyx":392 - * dx[0] = dx_min[0] - * dx[1] = dx_min[1] - * dx[2] = dx_min[2] # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_1 = 2; - *((float *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_1 * __pyx_v_dx.strides[0]) )) = (__pyx_v_dx_min[2]); - - /* "MDAnalysis/lib/c_distances.pyx":328 - * @cython.boundscheck(False) - * @cython.wraparound(False) - * cdef inline void _minimum_image_triclinic(cython.floating[:] dx, # <<<<<<<<<<<<<< - * cython.floating[:] box, - * cython.floating[:] inverse_box) nogil: - */ - - /* function exit code */ -} - -static CYTHON_INLINE void __pyx_fuse_1__pyx_f_10MDAnalysis_3lib_11c_distances__minimum_image_triclinic(__Pyx_memviewslice __pyx_v_dx, __Pyx_memviewslice __pyx_v_box, __Pyx_memviewslice __pyx_v_inverse_box) { - double __pyx_v_dx_min[3]; - double __pyx_v_s; - double __pyx_v_dsq; - double __pyx_v_dsq_min; - double __pyx_v_rx; - double __pyx_v_ry[2]; - double __pyx_v_rz[3]; - int __pyx_v_ix; - int __pyx_v_iy; - int __pyx_v_iz; - Py_ssize_t __pyx_t_1; - Py_ssize_t __pyx_t_2; - int __pyx_t_3; - int __pyx_t_4; - int __pyx_t_5; - int __pyx_t_6; - - /* "MDAnalysis/lib/c_distances.pyx":355 - * - * # first make shift only 1 cell in any direction - * s = cround(inverse_box[2] * dx[2]) # <<<<<<<<<<<<<< - * dx[0] -= s * box[6] - * dx[1] -= s * box[7] - */ - __pyx_t_1 = 2; - __pyx_t_2 = 2; - __pyx_v_s = round(((*((double *) ( /* dim=0 */ (__pyx_v_inverse_box.data + __pyx_t_1 * __pyx_v_inverse_box.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_2 * __pyx_v_dx.strides[0]) ))))); - - /* "MDAnalysis/lib/c_distances.pyx":356 - * # first make shift only 1 cell in any direction - * s = cround(inverse_box[2] * dx[2]) - * dx[0] -= s * box[6] # <<<<<<<<<<<<<< - * dx[1] -= s * box[7] - * dx[2] -= s * box[8] - */ - __pyx_t_2 = 6; - __pyx_t_1 = 0; - *((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_1 * __pyx_v_dx.strides[0]) )) -= (__pyx_v_s * (*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_2 * __pyx_v_box.strides[0]) )))); - - /* "MDAnalysis/lib/c_distances.pyx":357 - * s = cround(inverse_box[2] * dx[2]) - * dx[0] -= s * box[6] - * dx[1] -= s * box[7] # <<<<<<<<<<<<<< - * dx[2] -= s * box[8] - * s = cround(inverse_box[1] * dx[1]) - */ - __pyx_t_2 = 7; - __pyx_t_1 = 1; - *((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_1 * __pyx_v_dx.strides[0]) )) -= (__pyx_v_s * (*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_2 * __pyx_v_box.strides[0]) )))); - - /* "MDAnalysis/lib/c_distances.pyx":358 - * dx[0] -= s * box[6] - * dx[1] -= s * box[7] - * dx[2] -= s * box[8] # <<<<<<<<<<<<<< - * s = cround(inverse_box[1] * dx[1]) - * dx[0] -= s * box[3] - */ - __pyx_t_2 = 8; - __pyx_t_1 = 2; - *((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_1 * __pyx_v_dx.strides[0]) )) -= (__pyx_v_s * (*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_2 * __pyx_v_box.strides[0]) )))); - - /* "MDAnalysis/lib/c_distances.pyx":359 - * dx[1] -= s * box[7] - * dx[2] -= s * box[8] - * s = cround(inverse_box[1] * dx[1]) # <<<<<<<<<<<<<< - * dx[0] -= s * box[3] - * dx[1] -= s * box[4] - */ - __pyx_t_2 = 1; - __pyx_t_1 = 1; - __pyx_v_s = round(((*((double *) ( /* dim=0 */ (__pyx_v_inverse_box.data + __pyx_t_2 * __pyx_v_inverse_box.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_1 * __pyx_v_dx.strides[0]) ))))); - - /* "MDAnalysis/lib/c_distances.pyx":360 - * dx[2] -= s * box[8] - * s = cround(inverse_box[1] * dx[1]) - * dx[0] -= s * box[3] # <<<<<<<<<<<<<< - * dx[1] -= s * box[4] - * s = cround(inverse_box[0] * dx[0]) - */ - __pyx_t_1 = 3; - __pyx_t_2 = 0; - *((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_2 * __pyx_v_dx.strides[0]) )) -= (__pyx_v_s * (*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_1 * __pyx_v_box.strides[0]) )))); - - /* "MDAnalysis/lib/c_distances.pyx":361 - * s = cround(inverse_box[1] * dx[1]) - * dx[0] -= s * box[3] - * dx[1] -= s * box[4] # <<<<<<<<<<<<<< - * s = cround(inverse_box[0] * dx[0]) - * dx[0] -= s * box[0] - */ - __pyx_t_1 = 4; - __pyx_t_2 = 1; - *((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_2 * __pyx_v_dx.strides[0]) )) -= (__pyx_v_s * (*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_1 * __pyx_v_box.strides[0]) )))); - - /* "MDAnalysis/lib/c_distances.pyx":362 - * dx[0] -= s * box[3] - * dx[1] -= s * box[4] - * s = cround(inverse_box[0] * dx[0]) # <<<<<<<<<<<<<< - * dx[0] -= s * box[0] - * - */ - __pyx_t_1 = 0; - __pyx_t_2 = 0; - __pyx_v_s = round(((*((double *) ( /* dim=0 */ (__pyx_v_inverse_box.data + __pyx_t_1 * __pyx_v_inverse_box.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_2 * __pyx_v_dx.strides[0]) ))))); - - /* "MDAnalysis/lib/c_distances.pyx":363 - * dx[1] -= s * box[4] - * s = cround(inverse_box[0] * dx[0]) - * dx[0] -= s * box[0] # <<<<<<<<<<<<<< - * - * if cython.floating is float: - */ - __pyx_t_2 = 0; - __pyx_t_1 = 0; - *((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_1 * __pyx_v_dx.strides[0]) )) -= (__pyx_v_s * (*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_2 * __pyx_v_box.strides[0]) )))); - - /* "MDAnalysis/lib/c_distances.pyx":368 - * dsq_min = FLT_MAX - * else: - * dsq_min = DBL_MAX # <<<<<<<<<<<<<< - * dx_min[0] = 0.0 - * dx_min[1] = 0.0 - */ - __pyx_v_dsq_min = DBL_MAX; - - /* "MDAnalysis/lib/c_distances.pyx":369 - * else: - * dsq_min = DBL_MAX - * dx_min[0] = 0.0 # <<<<<<<<<<<<<< - * dx_min[1] = 0.0 - * dx_min[2] = 0.0 - */ - (__pyx_v_dx_min[0]) = 0.0; - - /* "MDAnalysis/lib/c_distances.pyx":370 - * dsq_min = DBL_MAX - * dx_min[0] = 0.0 - * dx_min[1] = 0.0 # <<<<<<<<<<<<<< - * dx_min[2] = 0.0 - * - */ - (__pyx_v_dx_min[1]) = 0.0; - - /* "MDAnalysis/lib/c_distances.pyx":371 - * dx_min[0] = 0.0 - * dx_min[1] = 0.0 - * dx_min[2] = 0.0 # <<<<<<<<<<<<<< - * - * # then check all images to see which combination of 1 cell shifts gives the best shift - */ - (__pyx_v_dx_min[2]) = 0.0; - - /* "MDAnalysis/lib/c_distances.pyx":374 - * - * # then check all images to see which combination of 1 cell shifts gives the best shift - * for ix in range(-1, 2): # <<<<<<<<<<<<<< - * rx = dx[0] + box[0] * ix - * for iy in range(-1, 2): - */ - for (__pyx_t_3 = -1; __pyx_t_3 < 2; __pyx_t_3+=1) { - __pyx_v_ix = __pyx_t_3; - - /* "MDAnalysis/lib/c_distances.pyx":375 - * # then check all images to see which combination of 1 cell shifts gives the best shift - * for ix in range(-1, 2): - * rx = dx[0] + box[0] * ix # <<<<<<<<<<<<<< - * for iy in range(-1, 2): - * ry[0] = rx + box[3] * iy - */ - __pyx_t_2 = 0; - __pyx_t_1 = 0; - __pyx_v_rx = ((*((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_2 * __pyx_v_dx.strides[0]) ))) + ((*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_1 * __pyx_v_box.strides[0]) ))) * __pyx_v_ix)); - - /* "MDAnalysis/lib/c_distances.pyx":376 - * for ix in range(-1, 2): - * rx = dx[0] + box[0] * ix - * for iy in range(-1, 2): # <<<<<<<<<<<<<< - * ry[0] = rx + box[3] * iy - * ry[1] = dx[1] + box[4] * iy - */ - for (__pyx_t_4 = -1; __pyx_t_4 < 2; __pyx_t_4+=1) { - __pyx_v_iy = __pyx_t_4; - - /* "MDAnalysis/lib/c_distances.pyx":377 - * rx = dx[0] + box[0] * ix - * for iy in range(-1, 2): - * ry[0] = rx + box[3] * iy # <<<<<<<<<<<<<< - * ry[1] = dx[1] + box[4] * iy - * for iz in range(-1, 2): - */ - __pyx_t_1 = 3; - (__pyx_v_ry[0]) = (__pyx_v_rx + ((*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_1 * __pyx_v_box.strides[0]) ))) * __pyx_v_iy)); - - /* "MDAnalysis/lib/c_distances.pyx":378 - * for iy in range(-1, 2): - * ry[0] = rx + box[3] * iy - * ry[1] = dx[1] + box[4] * iy # <<<<<<<<<<<<<< - * for iz in range(-1, 2): - * rz[0] = ry[0] + box[6] * iz - */ - __pyx_t_1 = 1; - __pyx_t_2 = 4; - (__pyx_v_ry[1]) = ((*((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_1 * __pyx_v_dx.strides[0]) ))) + ((*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_2 * __pyx_v_box.strides[0]) ))) * __pyx_v_iy)); - - /* "MDAnalysis/lib/c_distances.pyx":379 - * ry[0] = rx + box[3] * iy - * ry[1] = dx[1] + box[4] * iy - * for iz in range(-1, 2): # <<<<<<<<<<<<<< - * rz[0] = ry[0] + box[6] * iz - * rz[1] = ry[1] + box[7] * iz - */ - for (__pyx_t_5 = -1; __pyx_t_5 < 2; __pyx_t_5+=1) { - __pyx_v_iz = __pyx_t_5; - - /* "MDAnalysis/lib/c_distances.pyx":380 - * ry[1] = dx[1] + box[4] * iy - * for iz in range(-1, 2): - * rz[0] = ry[0] + box[6] * iz # <<<<<<<<<<<<<< - * rz[1] = ry[1] + box[7] * iz - * rz[2] = dx[2] + box[8] * iz - */ - __pyx_t_2 = 6; - (__pyx_v_rz[0]) = ((__pyx_v_ry[0]) + ((*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_2 * __pyx_v_box.strides[0]) ))) * __pyx_v_iz)); - - /* "MDAnalysis/lib/c_distances.pyx":381 - * for iz in range(-1, 2): - * rz[0] = ry[0] + box[6] * iz - * rz[1] = ry[1] + box[7] * iz # <<<<<<<<<<<<<< - * rz[2] = dx[2] + box[8] * iz - * dsq = rz[0] * rz[0] + rz[1] * rz[1] + rz[2] * rz[2] - */ - __pyx_t_2 = 7; - (__pyx_v_rz[1]) = ((__pyx_v_ry[1]) + ((*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_2 * __pyx_v_box.strides[0]) ))) * __pyx_v_iz)); - - /* "MDAnalysis/lib/c_distances.pyx":382 - * rz[0] = ry[0] + box[6] * iz - * rz[1] = ry[1] + box[7] * iz - * rz[2] = dx[2] + box[8] * iz # <<<<<<<<<<<<<< - * dsq = rz[0] * rz[0] + rz[1] * rz[1] + rz[2] * rz[2] - * if (dsq < dsq_min): - */ - __pyx_t_2 = 2; - __pyx_t_1 = 8; - (__pyx_v_rz[2]) = ((*((double *) ( /* dim=0 */ (__pyx_v_dx.data + __pyx_t_2 * __pyx_v_dx.strides[0]) ))) + ((*((double *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_1 * __pyx_v_box.strides[0]) ))) * __pyx_v_iz)); - - /* "MDAnalysis/lib/c_distances.pyx":383 - * rz[1] = ry[1] + box[7] * iz - * rz[2] = dx[2] + box[8] * iz - * dsq = rz[0] * rz[0] + rz[1] * rz[1] + rz[2] * rz[2] # <<<<<<<<<<<<<< - * if (dsq < dsq_min): - * dsq_min = dsq - */ - __pyx_v_dsq = ((((__pyx_v_rz[0]) * (__pyx_v_rz[0])) + ((__pyx_v_rz[1]) * (__pyx_v_rz[1]))) + ((__pyx_v_rz[2]) * (__pyx_v_rz[2]))); - - /* "MDAnalysis/lib/c_distances.pyx":384 - * rz[2] = dx[2] + box[8] * iz - * dsq = rz[0] * rz[0] + rz[1] * rz[1] + rz[2] * rz[2] - * if (dsq < dsq_min): # <<<<<<<<<<<<<< - * dsq_min = dsq - * dx_min[0] = rz[0] - */ - __pyx_t_6 = ((__pyx_v_dsq < __pyx_v_dsq_min) != 0); 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*/ - (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); - - /* "View.MemoryView":1161 - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * else: - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1162 - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L4:; - - /* "View.MemoryView":1154 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1164 - * dst_data += dst_stride - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * _copy_strided_to_strided(src_data, src_strides + 1, - * dst_data, dst_strides + 1, - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - __pyx_t_5 = __pyx_t_4; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1165 - * else: - * for i in range(dst_extent): - * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< - * dst_data, dst_strides + 1, - * src_shape + 1, dst_shape + 1, - */ - _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - - /* "View.MemoryView":1169 - * src_shape + 1, dst_shape + 1, - * ndim - 1, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1170 - * ndim - 1, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L3:; - - /* "View.MemoryView":1142 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - - /* function exit code */ -} - -/* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - -static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - - /* "View.MemoryView":1175 - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< - * src.shape, dst.shape, ndim, itemsize) - * - */ - _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - - /* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - - /* function exit code */ -} - -/* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { - Py_ssize_t __pyx_v_shape; - Py_ssize_t __pyx_v_size; - Py_ssize_t __pyx_r; - Py_ssize_t __pyx_t_1; - Py_ssize_t *__pyx_t_2; - Py_ssize_t *__pyx_t_3; - Py_ssize_t *__pyx_t_4; - - /* "View.MemoryView":1181 - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize # <<<<<<<<<<<<<< - * - * for shape in src.shape[:ndim]: - */ - __pyx_t_1 = __pyx_v_src->memview->view.itemsize; - __pyx_v_size = __pyx_t_1; - - /* "View.MemoryView":1183 - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - * - * for shape in src.shape[:ndim]: # <<<<<<<<<<<<<< - * size *= shape - * - */ - __pyx_t_3 = (__pyx_v_src->shape + __pyx_v_ndim); - for (__pyx_t_4 = __pyx_v_src->shape; __pyx_t_4 < __pyx_t_3; __pyx_t_4++) { - __pyx_t_2 = __pyx_t_4; - __pyx_v_shape = (__pyx_t_2[0]); - - /* "View.MemoryView":1184 - * - * for shape in src.shape[:ndim]: - * size *= shape # <<<<<<<<<<<<<< - * - * return size - */ - __pyx_v_size = (__pyx_v_size * __pyx_v_shape); - } - - /* "View.MemoryView":1186 - * size *= shape - * - * return size # <<<<<<<<<<<<<< - * - * @cname('__pyx_fill_contig_strides_array') - */ - __pyx_r = __pyx_v_size; - goto __pyx_L0; - - /* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1189 - * - * @cname('__pyx_fill_contig_strides_array') - * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< - * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, - * int ndim, char order) nogil: - */ - -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { - int __pyx_v_idx; - Py_ssize_t __pyx_r; - int __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - int __pyx_t_4; - - /* "View.MemoryView":1198 - * cdef int idx - * - * if order == 'F': # <<<<<<<<<<<<<< - * for idx in range(ndim): - * strides[idx] = stride - */ - __pyx_t_1 = ((__pyx_v_order == 'F') != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1199 - * - * if order == 'F': - * for idx in range(ndim): # <<<<<<<<<<<<<< - * strides[idx] = stride - * stride *= shape[idx] - */ - __pyx_t_2 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_2; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { - __pyx_v_idx = __pyx_t_4; - - /* "View.MemoryView":1200 - * if order == 'F': - * for idx in range(ndim): - * strides[idx] = stride # <<<<<<<<<<<<<< - * stride *= shape[idx] - * else: - */ - (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - - /* "View.MemoryView":1201 - * for idx in range(ndim): - * strides[idx] = stride - * stride *= shape[idx] # <<<<<<<<<<<<<< - * else: - * for idx in range(ndim - 1, -1, -1): - */ - __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); - } - - /* "View.MemoryView":1198 - * cdef int idx - * - * if order == 'F': # <<<<<<<<<<<<<< - * for idx in range(ndim): - * strides[idx] = stride - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1203 - * stride *= shape[idx] - * else: - * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< - * strides[idx] = stride - * stride *= shape[idx] - */ - /*else*/ { - for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { - __pyx_v_idx = __pyx_t_2; - - /* "View.MemoryView":1204 - * else: - * for idx in range(ndim - 1, -1, -1): - * strides[idx] = stride # <<<<<<<<<<<<<< - * stride *= shape[idx] - * - */ - (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - - /* "View.MemoryView":1205 - * for idx in range(ndim - 1, -1, -1): - * strides[idx] = stride - * stride *= shape[idx] # <<<<<<<<<<<<<< - * - * return stride - */ - __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); - } - } - __pyx_L3:; - - /* "View.MemoryView":1207 - * stride *= shape[idx] - * - * return stride # <<<<<<<<<<<<<< - * - * @cname('__pyx_memoryview_copy_data_to_temp') - */ - __pyx_r = __pyx_v_stride; - goto __pyx_L0; - - /* "View.MemoryView":1189 - * - * @cname('__pyx_fill_contig_strides_array') - * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< - * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, - * int ndim, char order) nogil: - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1210 - * - * @cname('__pyx_memoryview_copy_data_to_temp') - * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *tmpslice, - * char order, - */ - -static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_tmpslice, char __pyx_v_order, int __pyx_v_ndim) { - int __pyx_v_i; - void *__pyx_v_result; - size_t __pyx_v_itemsize; - size_t __pyx_v_size; - void *__pyx_r; - Py_ssize_t __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - struct __pyx_memoryview_obj *__pyx_t_4; - int __pyx_t_5; - int __pyx_t_6; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - - /* "View.MemoryView":1221 - * cdef void *result - * - * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< - * cdef size_t size = slice_get_size(src, ndim) - * - */ - __pyx_t_1 = __pyx_v_src->memview->view.itemsize; - __pyx_v_itemsize = __pyx_t_1; - - /* "View.MemoryView":1222 - * - * cdef size_t itemsize = src.memview.view.itemsize - * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<< - * - * result = malloc(size) - */ - __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim); - - /* "View.MemoryView":1224 - * cdef size_t size = slice_get_size(src, ndim) - * - * result = malloc(size) # <<<<<<<<<<<<<< - * if not result: - * _err(MemoryError, NULL) - */ - __pyx_v_result = malloc(__pyx_v_size); - - /* "View.MemoryView":1225 - * - * result = malloc(size) - * if not result: # <<<<<<<<<<<<<< - * _err(MemoryError, NULL) - * - */ - __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1226 - * result = malloc(size) - * if not result: - * _err(MemoryError, NULL) # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(2, 1226, __pyx_L1_error) - - /* "View.MemoryView":1225 - * - * result = malloc(size) - * if not result: # <<<<<<<<<<<<<< - * _err(MemoryError, NULL) - * - */ - } - - /* "View.MemoryView":1229 - * - * - * tmpslice.data = result # <<<<<<<<<<<<<< - * tmpslice.memview = src.memview - * for i in range(ndim): - */ - __pyx_v_tmpslice->data = ((char *)__pyx_v_result); - - /* "View.MemoryView":1230 - * - * tmpslice.data = result - * tmpslice.memview = src.memview # <<<<<<<<<<<<<< - * for i in range(ndim): - * tmpslice.shape[i] = src.shape[i] - */ - __pyx_t_4 = __pyx_v_src->memview; - __pyx_v_tmpslice->memview = __pyx_t_4; - - /* "View.MemoryView":1231 - * tmpslice.data = result - * tmpslice.memview = src.memview - * for i in range(ndim): # <<<<<<<<<<<<<< - * tmpslice.shape[i] = src.shape[i] - * tmpslice.suboffsets[i] = -1 - */ - __pyx_t_3 = __pyx_v_ndim; - __pyx_t_5 = __pyx_t_3; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1232 - * tmpslice.memview = src.memview - * for i in range(ndim): - * tmpslice.shape[i] = src.shape[i] # <<<<<<<<<<<<<< - * tmpslice.suboffsets[i] = -1 - * - */ - (__pyx_v_tmpslice->shape[__pyx_v_i]) = (__pyx_v_src->shape[__pyx_v_i]); - - /* "View.MemoryView":1233 - * for i in range(ndim): - * tmpslice.shape[i] = src.shape[i] - * tmpslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< - * - * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, - */ - (__pyx_v_tmpslice->suboffsets[__pyx_v_i]) = -1L; - } - - /* "View.MemoryView":1235 - * tmpslice.suboffsets[i] = -1 - * - * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, # <<<<<<<<<<<<<< - * ndim, order) - * - */ - (void)(__pyx_fill_contig_strides_array((&(__pyx_v_tmpslice->shape[0])), (&(__pyx_v_tmpslice->strides[0])), __pyx_v_itemsize, __pyx_v_ndim, __pyx_v_order)); - - /* "View.MemoryView":1239 - * - * - * for i in range(ndim): # <<<<<<<<<<<<<< - * if tmpslice.shape[i] == 1: - * tmpslice.strides[i] = 0 - */ - __pyx_t_3 = __pyx_v_ndim; - __pyx_t_5 = __pyx_t_3; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1240 - * - * for i in range(ndim): - * if tmpslice.shape[i] == 1: # <<<<<<<<<<<<<< - * tmpslice.strides[i] = 0 - * - */ - __pyx_t_2 = (((__pyx_v_tmpslice->shape[__pyx_v_i]) == 1) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1241 - * for i in range(ndim): - * if tmpslice.shape[i] == 1: - * tmpslice.strides[i] = 0 # <<<<<<<<<<<<<< - * - * if slice_is_contig(src[0], order, ndim): - */ - (__pyx_v_tmpslice->strides[__pyx_v_i]) = 0; - - /* "View.MemoryView":1240 - * - * for i in range(ndim): - * if tmpslice.shape[i] == 1: # <<<<<<<<<<<<<< - * tmpslice.strides[i] = 0 - * - */ - } - } - - /* "View.MemoryView":1243 - * tmpslice.strides[i] = 0 - * - * if slice_is_contig(src[0], order, ndim): # <<<<<<<<<<<<<< - * memcpy(result, src.data, size) - * else: - */ - __pyx_t_2 = (__pyx_memviewslice_is_contig((__pyx_v_src[0]), __pyx_v_order, __pyx_v_ndim) != 0); - if (__pyx_t_2) { - 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* if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< - * if src.shape[i] == 1: - * broadcasting = True - */ - } - - /* "View.MemoryView":1301 - * _err_extents(i, dst.shape[i], src.shape[i]) - * - * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - */ - __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1302 - * - * if src.suboffsets[i] >= 0: - * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<< - * - * if slices_overlap(&src, &dst, ndim, itemsize): - */ - __pyx_t_6 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(2, 1302, __pyx_L1_error) - - /* "View.MemoryView":1301 - * _err_extents(i, dst.shape[i], src.shape[i]) - * - * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - */ - } - } - - /* "View.MemoryView":1304 - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< - * - * if not slice_is_contig(src, order, ndim): - */ - __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1306 - * if slices_overlap(&src, &dst, ndim, itemsize): - * - * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< - * order = get_best_order(&dst, ndim) - * - */ - __pyx_t_2 = ((!(__pyx_memviewslice_is_contig(__pyx_v_src, __pyx_v_order, __pyx_v_ndim) != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1307 - * - * if not slice_is_contig(src, order, ndim): - * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<< - * - * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) - */ - __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim); - - /* "View.MemoryView":1306 - * if slices_overlap(&src, &dst, ndim, itemsize): - * - * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< - * order = get_best_order(&dst, ndim) - * - */ - } - - /* "View.MemoryView":1309 - * order = get_best_order(&dst, ndim) - * - * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<< - * src = tmp - * - */ - __pyx_t_7 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_7 == ((void *)NULL))) __PYX_ERR(2, 1309, __pyx_L1_error) - __pyx_v_tmpdata = __pyx_t_7; - - /* "View.MemoryView":1310 - * - * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) - * src = tmp # <<<<<<<<<<<<<< - * - * if not broadcasting: - */ - __pyx_v_src = __pyx_v_tmp; - - /* "View.MemoryView":1304 - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< - * - * if not slice_is_contig(src, order, ndim): - */ - } - - /* "View.MemoryView":1312 - * src = tmp - * - * if not broadcasting: # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1315 - * - * - * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - */ - __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'C', __pyx_v_ndim) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1316 - * - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) # <<<<<<<<<<<<<< - * elif slice_is_contig(src, 'F', ndim): - * direct_copy = slice_is_contig(dst, 'F', ndim) - */ - __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'C', __pyx_v_ndim); - - /* "View.MemoryView":1315 - * - * - * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - */ - goto __pyx_L12; - } - - /* "View.MemoryView":1317 - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - */ - __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'F', __pyx_v_ndim) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1318 - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - * direct_copy = slice_is_contig(dst, 'F', ndim) # <<<<<<<<<<<<<< - * - * if direct_copy: - */ - __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'F', __pyx_v_ndim); - - /* "View.MemoryView":1317 - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - */ - } - __pyx_L12:; - - /* "View.MemoryView":1320 - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - * if direct_copy: # <<<<<<<<<<<<<< - * - * refcount_copying(&dst, dtype_is_object, ndim, False) - */ - __pyx_t_2 = (__pyx_v_direct_copy != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1322 - * if direct_copy: - * - * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) - * refcount_copying(&dst, dtype_is_object, ndim, True) - */ - __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - - /* "View.MemoryView":1323 - * - * refcount_copying(&dst, dtype_is_object, ndim, False) - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< - * refcount_copying(&dst, dtype_is_object, ndim, True) - * free(tmpdata) - */ - (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim))); - - /* "View.MemoryView":1324 - * refcount_copying(&dst, dtype_is_object, ndim, False) - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) - * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< - * free(tmpdata) - * return 0 - */ - __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - 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"" : "s", num_found); -} - -/* RaiseDoubleKeywords */ -static void __Pyx_RaiseDoubleKeywordsError( - const char* func_name, - PyObject* kw_name) -{ - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION >= 3 - "%s() got multiple values for keyword argument '%U'", func_name, kw_name); - #else - "%s() got multiple values for keyword argument '%s'", func_name, - PyString_AsString(kw_name)); - #endif -} - -/* ParseKeywords */ -static int __Pyx_ParseOptionalKeywords( - PyObject *kwds, - PyObject **argnames[], - PyObject *kwds2, - PyObject *values[], - Py_ssize_t num_pos_args, - const char* function_name) -{ - PyObject *key = 0, *value = 0; - Py_ssize_t pos = 0; - PyObject*** name; - PyObject*** first_kw_arg = argnames + num_pos_args; - while (PyDict_Next(kwds, &pos, &key, &value)) { - name = first_kw_arg; - while (*name && (**name != key)) name++; - if (*name) { - values[name-argnames] = value; - continue; - } - name = first_kw_arg; - #if PY_MAJOR_VERSION < 3 - if (likely(PyString_Check(key))) { - while (*name) { - if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) - && _PyString_Eq(**name, key)) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - if ((**argname == key) || ( - (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) - && _PyString_Eq(**argname, key))) { - goto arg_passed_twice; - } - argname++; - } - } - } else - #endif - if (likely(PyUnicode_Check(key))) { - while (*name) { - int cmp = (**name == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**name, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - int cmp = (**argname == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**argname, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) goto arg_passed_twice; - argname++; - } - } - } else - goto invalid_keyword_type; - if (kwds2) { - if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; - } else { - goto invalid_keyword; - } - } - return 0; -arg_passed_twice: - __Pyx_RaiseDoubleKeywordsError(function_name, key); - goto bad; -invalid_keyword_type: - PyErr_Format(PyExc_TypeError, - "%.200s() keywords must be strings", function_name); - goto bad; -invalid_keyword: - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION < 3 - "%.200s() got an unexpected keyword argument '%.200s'", - function_name, PyString_AsString(key)); - #else - "%s() got an unexpected keyword argument '%U'", - function_name, key); - #endif -bad: - return -1; -} - -/* ArgTypeTest */ -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) -{ - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - else if (exact) { - #if PY_MAJOR_VERSION == 2 - if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; - #endif - } - else { - if (likely(__Pyx_TypeCheck(obj, type))) return 1; - } - PyErr_Format(PyExc_TypeError, - "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", - name, type->tp_name, Py_TYPE(obj)->tp_name); - return 0; -} - -/* MemviewSliceInit */ -static int -__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference) -{ - __Pyx_RefNannyDeclarations - int i, retval=-1; - Py_buffer *buf = &memview->view; - __Pyx_RefNannySetupContext("init_memviewslice", 0); - if (unlikely(memviewslice->memview || memviewslice->data)) { - PyErr_SetString(PyExc_ValueError, - "memviewslice is already initialized!"); - goto fail; - } - if (buf->strides) { - for (i = 0; i < ndim; i++) { - memviewslice->strides[i] = buf->strides[i]; - } - } else { - Py_ssize_t stride = buf->itemsize; - for (i = ndim - 1; i >= 0; i--) { - memviewslice->strides[i] = stride; - stride *= buf->shape[i]; - } - } - for (i = 0; i < ndim; i++) { - memviewslice->shape[i] = buf->shape[i]; - if (buf->suboffsets) { - memviewslice->suboffsets[i] = buf->suboffsets[i]; - } else { - memviewslice->suboffsets[i] = -1; - } - } - memviewslice->memview = memview; - memviewslice->data = (char *)buf->buf; - if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { - Py_INCREF(memview); - } - retval = 0; - goto no_fail; -fail: - memviewslice->memview = 0; - memviewslice->data = 0; - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} -#ifndef Py_NO_RETURN -#define Py_NO_RETURN -#endif -static void __pyx_fatalerror(const char *fmt, ...) Py_NO_RETURN { - va_list vargs; - char msg[200]; -#if PY_VERSION_HEX >= 0x030A0000 || defined(HAVE_STDARG_PROTOTYPES) - va_start(vargs, fmt); -#else - va_start(vargs); -#endif - vsnprintf(msg, 200, fmt, vargs); - va_end(vargs); - Py_FatalError(msg); -} -static CYTHON_INLINE int -__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)++; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE int -__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)--; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE void -__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) -{ - int first_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) - return; - if (unlikely(__pyx_get_slice_count(memview) < 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - first_time = __pyx_add_acquisition_count(memview) == 0; - if (unlikely(first_time)) { - if (have_gil) { - Py_INCREF((PyObject *) memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_INCREF((PyObject *) memview); - PyGILState_Release(_gilstate); - } - } -} -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, - int have_gil, int lineno) { - int last_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) { - memslice->memview = NULL; - return; - } - if (unlikely(__pyx_get_slice_count(memview) <= 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - last_time = __pyx_sub_acquisition_count(memview) == 1; - memslice->data = NULL; - if (unlikely(last_time)) { - if (have_gil) { - Py_CLEAR(memslice->memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_CLEAR(memslice->memview); - PyGILState_Release(_gilstate); - } - } else { - memslice->memview = NULL; - } -} - -/* PyFloatBinop */ -#if !CYTHON_COMPILING_IN_PYPY -#define __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(operand) if (unlikely(zerodivision_check && ((operand) == 0))) {\ - PyErr_SetString(PyExc_ZeroDivisionError, "float division by zero");\ - return NULL;\ -} -static PyObject* __Pyx_PyFloat_TrueDivideCObj(PyObject *op1, PyObject *op2, double floatval, int inplace, int zerodivision_check) { - const double a = floatval; - double b, result; - (void)inplace; - (void)zerodivision_check; - if (likely(PyFloat_CheckExact(op2))) { - b = PyFloat_AS_DOUBLE(op2); - __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(b) - } else - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op2))) { - b = (double) PyInt_AS_LONG(op2); - __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(b) - } else - #endif - if (likely(PyLong_CheckExact(op2))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)op2)->ob_digit; - const Py_ssize_t size = Py_SIZE(op2); - switch (size) { - case 0: __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(0) break; - case -1: b = -(double) digits[0]; break; - case 1: b = (double) digits[0]; break; - case -2: - case 2: - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (1 * PyLong_SHIFT < 53))) { - b = (double) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - if ((8 * sizeof(unsigned long) < 53) || (2 * PyLong_SHIFT < 53) || (b < (double) ((PY_LONG_LONG)1 << 53))) { - if (size == -2) - b = -b; - break; - } - } - CYTHON_FALLTHROUGH; - case -3: - case 3: - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (2 * PyLong_SHIFT < 53))) { - b = (double) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - if ((8 * sizeof(unsigned long) < 53) || (3 * PyLong_SHIFT < 53) || (b < (double) ((PY_LONG_LONG)1 << 53))) { - if (size == -3) - b = -b; - break; - } - } - CYTHON_FALLTHROUGH; - case -4: - case 4: - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (3 * PyLong_SHIFT < 53))) { - b = (double) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - if ((8 * sizeof(unsigned long) < 53) || (4 * PyLong_SHIFT < 53) || (b < (double) ((PY_LONG_LONG)1 << 53))) { - if (size == -4) - b = -b; - break; - } - } - CYTHON_FALLTHROUGH; - default: - #else - { - #endif - b = PyLong_AsDouble(op2); - if (unlikely(b == -1.0 && PyErr_Occurred())) return NULL; - __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(b) - } - } else { - return (inplace ? PyNumber_InPlaceTrueDivide : PyNumber_TrueDivide)(op1, op2); - } - __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(b) - PyFPE_START_PROTECT("divide", return NULL) - result = a / b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); -} -#endif - -/* DictGetItem */ - #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY -static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { - PyObject *value; - value = PyDict_GetItemWithError(d, key); - if (unlikely(!value)) { - if (!PyErr_Occurred()) { - if (unlikely(PyTuple_Check(key))) { - PyObject* args = PyTuple_Pack(1, key); - if (likely(args)) { - PyErr_SetObject(PyExc_KeyError, args); - Py_DECREF(args); - } - } else { - PyErr_SetObject(PyExc_KeyError, key); - } - } - return NULL; - } - Py_INCREF(value); - return value; -} -#endif - -/* PyCFunctionFastCall */ - #if CYTHON_FAST_PYCCALL -static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) { - PyCFunctionObject *func = (PyCFunctionObject*)func_obj; - PyCFunction meth = PyCFunction_GET_FUNCTION(func); - PyObject *self = PyCFunction_GET_SELF(func); - int flags = PyCFunction_GET_FLAGS(func); - assert(PyCFunction_Check(func)); - assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))); - assert(nargs >= 0); - assert(nargs == 0 || args != NULL); - /* _PyCFunction_FastCallDict() must not be called with an exception set, - because it may clear it (directly or indirectly) and so the - caller loses its exception */ - assert(!PyErr_Occurred()); - if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) { - return (*((__Pyx_PyCFunctionFastWithKeywords)(void*)meth)) (self, args, nargs, NULL); - } else { - return (*((__Pyx_PyCFunctionFast)(void*)meth)) (self, args, nargs); - } -} -#endif - -/* PyFunctionFastCall */ - #if CYTHON_FAST_PYCALL -static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, - PyObject *globals) { - PyFrameObject *f; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject **fastlocals; - Py_ssize_t i; - PyObject *result; - assert(globals != NULL); - /* XXX Perhaps we should create a specialized - PyFrame_New() that doesn't take locals, but does - take builtins without sanity checking them. - */ - assert(tstate != NULL); - f = PyFrame_New(tstate, co, globals, NULL); - if (f == NULL) { - return NULL; - } - fastlocals = __Pyx_PyFrame_GetLocalsplus(f); - for (i = 0; i < na; i++) { - Py_INCREF(*args); - fastlocals[i] = *args++; - } - result = PyEval_EvalFrameEx(f,0); - ++tstate->recursion_depth; - Py_DECREF(f); - --tstate->recursion_depth; - return result; -} -#if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { - PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); - PyObject *globals = PyFunction_GET_GLOBALS(func); - PyObject *argdefs = PyFunction_GET_DEFAULTS(func); - PyObject *closure; -#if PY_MAJOR_VERSION >= 3 - PyObject *kwdefs; -#endif - PyObject *kwtuple, **k; - PyObject **d; - Py_ssize_t nd; - Py_ssize_t nk; - PyObject *result; - assert(kwargs == NULL || PyDict_Check(kwargs)); - nk = kwargs ? PyDict_Size(kwargs) : 0; - if (Py_EnterRecursiveCall((char*)" while calling a Python object")) { - return NULL; - } - if ( -#if PY_MAJOR_VERSION >= 3 - co->co_kwonlyargcount == 0 && -#endif - likely(kwargs == NULL || nk == 0) && - co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { - if (argdefs == NULL && co->co_argcount == nargs) { - result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); - goto done; - } - else if (nargs == 0 && argdefs != NULL - && co->co_argcount == Py_SIZE(argdefs)) { - /* function called with no arguments, but all parameters have - a default value: use default values as arguments .*/ - args = &PyTuple_GET_ITEM(argdefs, 0); - result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); - goto done; - } - } - if (kwargs != NULL) { - Py_ssize_t pos, i; - kwtuple = PyTuple_New(2 * nk); - if (kwtuple == NULL) { - result = NULL; - goto done; - } - k = &PyTuple_GET_ITEM(kwtuple, 0); - pos = i = 0; - while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { - Py_INCREF(k[i]); - Py_INCREF(k[i+1]); - i += 2; - } - nk = i / 2; - } - else { - kwtuple = NULL; - k = NULL; - } - closure = PyFunction_GET_CLOSURE(func); -#if PY_MAJOR_VERSION >= 3 - kwdefs = PyFunction_GET_KW_DEFAULTS(func); -#endif - if (argdefs != NULL) { - d = &PyTuple_GET_ITEM(argdefs, 0); - nd = Py_SIZE(argdefs); - } - else { - d = NULL; - nd = 0; - } -#if PY_MAJOR_VERSION >= 3 - result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, kwdefs, closure); -#else - result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, closure); -#endif - Py_XDECREF(kwtuple); -done: - Py_LeaveRecursiveCall(); - return result; -} -#endif -#endif - -/* PyObjectCall */ - #if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { - PyObject *result; - ternaryfunc call = Py_TYPE(func)->tp_call; - if (unlikely(!call)) - return PyObject_Call(func, arg, kw); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = (*call)(func, arg, kw); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallMethO */ - #if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { - PyObject *self, *result; - PyCFunction cfunc; - cfunc = PyCFunction_GET_FUNCTION(func); - self = PyCFunction_GET_SELF(func); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = cfunc(self, arg); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallOneArg */ - #if CYTHON_COMPILING_IN_CPYTHON -static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_New(1); - if (unlikely(!args)) return NULL; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif - if (likely(PyCFunction_Check(func))) { - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (__Pyx_PyFastCFunction_Check(func)) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } - } - return __Pyx__PyObject_CallOneArg(func, arg); -} -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -#endif - -/* PyErrFetchRestore */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -} -#endif - -/* RaiseException */ - #if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* UnicodeAsUCS4 */ - static CYTHON_INLINE Py_UCS4 __Pyx_PyUnicode_AsPy_UCS4(PyObject* x) { - Py_ssize_t length; - #if CYTHON_PEP393_ENABLED - length = PyUnicode_GET_LENGTH(x); - if (likely(length == 1)) { - return PyUnicode_READ_CHAR(x, 0); - } - #else - length = PyUnicode_GET_SIZE(x); - if (likely(length == 1)) { - return PyUnicode_AS_UNICODE(x)[0]; - } - #if Py_UNICODE_SIZE == 2 - else if (PyUnicode_GET_SIZE(x) == 2) { - Py_UCS4 high_val = PyUnicode_AS_UNICODE(x)[0]; - if (high_val >= 0xD800 && high_val <= 0xDBFF) { - Py_UCS4 low_val = PyUnicode_AS_UNICODE(x)[1]; - if (low_val >= 0xDC00 && low_val <= 0xDFFF) { - return 0x10000 + (((high_val & ((1<<10)-1)) << 10) | (low_val & ((1<<10)-1))); - } - } - } - #endif - #endif - PyErr_Format(PyExc_ValueError, - "only single character unicode strings can be converted to Py_UCS4, " - "got length %" CYTHON_FORMAT_SSIZE_T "d", length); - return (Py_UCS4)-1; -} - -/* object_ord */ - static long __Pyx__PyObject_Ord(PyObject* c) { - Py_ssize_t size; - if (PyBytes_Check(c)) { - size = PyBytes_GET_SIZE(c); - if (likely(size == 1)) { - return (unsigned char) PyBytes_AS_STRING(c)[0]; - } -#if PY_MAJOR_VERSION < 3 - } else if (PyUnicode_Check(c)) { - return (long)__Pyx_PyUnicode_AsPy_UCS4(c); -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - } else if (PyByteArray_Check(c)) { - size = PyByteArray_GET_SIZE(c); - if (likely(size == 1)) { - return (unsigned char) PyByteArray_AS_STRING(c)[0]; - } -#endif - } else { - PyErr_Format(PyExc_TypeError, - "ord() expected string of length 1, but %.200s found", Py_TYPE(c)->tp_name); - return (long)(Py_UCS4)-1; - } - PyErr_Format(PyExc_TypeError, - "ord() expected a character, but string of length %zd found", size); - return (long)(Py_UCS4)-1; -} - -/* SetItemInt */ - static int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) { - int r; - if (!j) return -1; - r = PyObject_SetItem(o, j, v); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, int is_list, - CYTHON_NCP_UNUSED int wraparound, CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = (!wraparound) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o)); - if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o)))) { - PyObject* old = PyList_GET_ITEM(o, n); - Py_INCREF(v); - PyList_SET_ITEM(o, n, v); - Py_DECREF(old); - return 1; - } - } else { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_ass_item)) { - if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { - Py_ssize_t l = m->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return -1; - PyErr_Clear(); - } - } - return m->sq_ass_item(o, i, v); - } - } -#else -#if CYTHON_COMPILING_IN_PYPY - if (is_list || (PySequence_Check(o) && !PyDict_Check(o))) -#else - if (is_list || PySequence_Check(o)) -#endif - { - return PySequence_SetItem(o, i, v); - } -#endif - return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v); -} - -/* IterFinish */ - static CYTHON_INLINE int __Pyx_IterFinish(void) { -#if CYTHON_FAST_THREAD_STATE - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* exc_type = tstate->curexc_type; - if (unlikely(exc_type)) { - if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) { - PyObject *exc_value, *exc_tb; - exc_value = tstate->curexc_value; - exc_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; - Py_DECREF(exc_type); - Py_XDECREF(exc_value); - Py_XDECREF(exc_tb); - return 0; - } else { - return -1; - } - } - return 0; -#else - if (unlikely(PyErr_Occurred())) { - if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { - PyErr_Clear(); - return 0; - } else { - return -1; - } - } - return 0; -#endif -} - -/* PyObjectCallNoArg */ - #if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, NULL, 0); - } -#endif -#if defined(__Pyx_CyFunction_USED) && defined(NDEBUG) - if (likely(PyCFunction_Check(func) || __Pyx_CyFunction_Check(func))) -#else - if (likely(PyCFunction_Check(func))) -#endif - { - if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { - return __Pyx_PyObject_CallMethO(func, NULL); - } - } - return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL); -} -#endif - -/* PyObjectGetMethod */ - static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method) { - PyObject *attr; -#if CYTHON_UNPACK_METHODS && CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_PYTYPE_LOOKUP - PyTypeObject *tp = Py_TYPE(obj); - PyObject *descr; - descrgetfunc f = NULL; - PyObject **dictptr, *dict; - int meth_found = 0; - assert (*method == NULL); - if (unlikely(tp->tp_getattro != PyObject_GenericGetAttr)) { - attr = __Pyx_PyObject_GetAttrStr(obj, name); - goto try_unpack; - } - if (unlikely(tp->tp_dict == NULL) && unlikely(PyType_Ready(tp) < 0)) { - return 0; - } - descr = _PyType_Lookup(tp, name); - if (likely(descr != NULL)) { - Py_INCREF(descr); -#if PY_MAJOR_VERSION >= 3 - #ifdef __Pyx_CyFunction_USED - if (likely(PyFunction_Check(descr) || (Py_TYPE(descr) == &PyMethodDescr_Type) || __Pyx_CyFunction_Check(descr))) - #else - if (likely(PyFunction_Check(descr) || (Py_TYPE(descr) == &PyMethodDescr_Type))) - #endif -#else - #ifdef __Pyx_CyFunction_USED - if (likely(PyFunction_Check(descr) || __Pyx_CyFunction_Check(descr))) - #else - if (likely(PyFunction_Check(descr))) - #endif -#endif - { - meth_found = 1; - } else { - f = Py_TYPE(descr)->tp_descr_get; - if (f != NULL && PyDescr_IsData(descr)) { - attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); - Py_DECREF(descr); - goto try_unpack; - } - } - } - dictptr = _PyObject_GetDictPtr(obj); - if (dictptr != NULL && (dict = *dictptr) != NULL) { - Py_INCREF(dict); - attr = __Pyx_PyDict_GetItemStr(dict, name); - if (attr != NULL) { - Py_INCREF(attr); - Py_DECREF(dict); - Py_XDECREF(descr); - goto try_unpack; - } - Py_DECREF(dict); - } - if (meth_found) { - *method = descr; - return 1; - } - if (f != NULL) { - attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); - Py_DECREF(descr); - goto try_unpack; - } - if (descr != NULL) { - *method = descr; - return 0; - } - PyErr_Format(PyExc_AttributeError, -#if PY_MAJOR_VERSION >= 3 - "'%.50s' object has no attribute '%U'", - tp->tp_name, name); -#else - "'%.50s' object has no attribute '%.400s'", - tp->tp_name, PyString_AS_STRING(name)); -#endif - return 0; -#else - attr = __Pyx_PyObject_GetAttrStr(obj, name); - goto try_unpack; -#endif -try_unpack: -#if CYTHON_UNPACK_METHODS - if (likely(attr) && PyMethod_Check(attr) && likely(PyMethod_GET_SELF(attr) == obj)) { - PyObject *function = PyMethod_GET_FUNCTION(attr); - Py_INCREF(function); - Py_DECREF(attr); - *method = function; - return 1; - } -#endif - *method = attr; - return 0; -} - -/* PyObjectCallMethod0 */ - static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) { - PyObject *method = NULL, *result = NULL; - int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method); - if (likely(is_method)) { - result = __Pyx_PyObject_CallOneArg(method, obj); - Py_DECREF(method); - return result; - } - if (unlikely(!method)) goto bad; - result = __Pyx_PyObject_CallNoArg(method); - Py_DECREF(method); -bad: - return result; -} - -/* RaiseNeedMoreValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -/* RaiseTooManyValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -/* UnpackItemEndCheck */ - static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { - if (unlikely(retval)) { - Py_DECREF(retval); - __Pyx_RaiseTooManyValuesError(expected); - return -1; - } - return __Pyx_IterFinish(); -} - -/* RaiseNoneIterError */ - static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); -} - -/* UnpackTupleError */ - static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { - if (t == Py_None) { - __Pyx_RaiseNoneNotIterableError(); - } else if (PyTuple_GET_SIZE(t) < index) { - __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t)); - } else { - __Pyx_RaiseTooManyValuesError(index); - } -} - -/* UnpackTuple2 */ - static CYTHON_INLINE int __Pyx_unpack_tuple2_exact( - PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, int decref_tuple) { - PyObject *value1 = NULL, *value2 = NULL; -#if CYTHON_COMPILING_IN_PYPY - value1 = PySequence_ITEM(tuple, 0); if (unlikely(!value1)) goto bad; - value2 = PySequence_ITEM(tuple, 1); if (unlikely(!value2)) goto bad; -#else - value1 = PyTuple_GET_ITEM(tuple, 0); Py_INCREF(value1); - value2 = PyTuple_GET_ITEM(tuple, 1); Py_INCREF(value2); -#endif - if (decref_tuple) { - Py_DECREF(tuple); - } - *pvalue1 = value1; - *pvalue2 = value2; - return 0; -#if CYTHON_COMPILING_IN_PYPY -bad: - Py_XDECREF(value1); - Py_XDECREF(value2); - if (decref_tuple) { Py_XDECREF(tuple); } - return -1; -#endif -} -static int __Pyx_unpack_tuple2_generic(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, - int has_known_size, int decref_tuple) { - Py_ssize_t index; - PyObject *value1 = NULL, *value2 = NULL, *iter = NULL; - iternextfunc iternext; - iter = PyObject_GetIter(tuple); - if (unlikely(!iter)) goto bad; - if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; } - iternext = Py_TYPE(iter)->tp_iternext; - value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; } - value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; } - if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad; - Py_DECREF(iter); - *pvalue1 = value1; - *pvalue2 = value2; - return 0; -unpacking_failed: - if (!has_known_size && __Pyx_IterFinish() == 0) - __Pyx_RaiseNeedMoreValuesError(index); -bad: - Py_XDECREF(iter); - Py_XDECREF(value1); - Py_XDECREF(value2); - if (decref_tuple) { Py_XDECREF(tuple); } - return -1; -} - -/* dict_iter */ - static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name, - Py_ssize_t* p_orig_length, int* p_source_is_dict) { - is_dict = is_dict || likely(PyDict_CheckExact(iterable)); - *p_source_is_dict = is_dict; - if (is_dict) { -#if !CYTHON_COMPILING_IN_PYPY - *p_orig_length = PyDict_Size(iterable); - Py_INCREF(iterable); - return iterable; -#elif PY_MAJOR_VERSION >= 3 - static PyObject *py_items = NULL, *py_keys = NULL, *py_values = NULL; - PyObject **pp = NULL; - if (method_name) { - const char *name = PyUnicode_AsUTF8(method_name); - if (strcmp(name, "iteritems") == 0) pp = &py_items; - else if (strcmp(name, "iterkeys") == 0) pp = &py_keys; - else if (strcmp(name, "itervalues") == 0) pp = &py_values; - if (pp) { - if (!*pp) { - *pp = PyUnicode_FromString(name + 4); - if (!*pp) - return NULL; - } - method_name = *pp; - } - } -#endif - } - *p_orig_length = 0; - if (method_name) { - PyObject* iter; - iterable = __Pyx_PyObject_CallMethod0(iterable, method_name); - if (!iterable) - return NULL; -#if !CYTHON_COMPILING_IN_PYPY - if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable)) - return iterable; -#endif - iter = PyObject_GetIter(iterable); - Py_DECREF(iterable); - return iter; - } - return PyObject_GetIter(iterable); -} -static CYTHON_INLINE int __Pyx_dict_iter_next( - PyObject* iter_obj, CYTHON_NCP_UNUSED Py_ssize_t orig_length, CYTHON_NCP_UNUSED Py_ssize_t* ppos, - PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) { - PyObject* next_item; -#if !CYTHON_COMPILING_IN_PYPY - if (source_is_dict) { - PyObject *key, *value; - if (unlikely(orig_length != PyDict_Size(iter_obj))) { - PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration"); - return -1; - } - if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) { - return 0; - } - if (pitem) { - PyObject* tuple = PyTuple_New(2); - if (unlikely(!tuple)) { - return -1; - } - Py_INCREF(key); - Py_INCREF(value); - PyTuple_SET_ITEM(tuple, 0, key); - PyTuple_SET_ITEM(tuple, 1, value); - *pitem = tuple; - } else { - if (pkey) { - Py_INCREF(key); - *pkey = key; - } - if (pvalue) { - Py_INCREF(value); - *pvalue = value; - } - } - return 1; - } else if (PyTuple_CheckExact(iter_obj)) { - Py_ssize_t pos = *ppos; - if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0; - *ppos = pos + 1; - next_item = PyTuple_GET_ITEM(iter_obj, pos); - Py_INCREF(next_item); - } else if (PyList_CheckExact(iter_obj)) { - Py_ssize_t pos = *ppos; - if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0; - *ppos = pos + 1; - next_item = PyList_GET_ITEM(iter_obj, pos); - Py_INCREF(next_item); - } else -#endif - { - next_item = PyIter_Next(iter_obj); - if (unlikely(!next_item)) { - return __Pyx_IterFinish(); - } - } - if (pitem) { - *pitem = next_item; - } else if (pkey && pvalue) { - if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1)) - return -1; - } else if (pkey) { - *pkey = next_item; - } else { - *pvalue = next_item; - } - return 1; -} - -/* PyObjectCall2Args */ - static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { - PyObject *args, *result = NULL; - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyFunction_FastCall(function, args, 2); - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyCFunction_FastCall(function, args, 2); - } - #endif - args = PyTuple_New(2); - if (unlikely(!args)) goto done; - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 0, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 1, arg2); - Py_INCREF(function); - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); -done: - return result; -} - -/* GetItemInt */ - static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { - PyObject *r; - if (!j) return NULL; - r = PyObject_GetItem(o, j); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyList_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyTuple_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } - else if (PyTuple_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } else { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_item)) { - if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { - Py_ssize_t l = m->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return NULL; - PyErr_Clear(); - } - } - return m->sq_item(o, i); - } - } -#else - if (is_list || PySequence_Check(o)) { - return PySequence_GetItem(o, i); - } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -} - -/* GetTopmostException */ - #if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* PyErrExceptionMatches */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* GetException */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* BytesEquals */ - static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { - const char *ps1, *ps2; - Py_ssize_t length = PyBytes_GET_SIZE(s1); - if (length != PyBytes_GET_SIZE(s2)) - return (equals == Py_NE); - ps1 = PyBytes_AS_STRING(s1); - ps2 = PyBytes_AS_STRING(s2); - if (ps1[0] != ps2[0]) { - return (equals == Py_NE); - } else if (length == 1) { - return (equals == Py_EQ); - } else { - int result; -#if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000) - Py_hash_t hash1, hash2; - hash1 = ((PyBytesObject*)s1)->ob_shash; - hash2 = ((PyBytesObject*)s2)->ob_shash; - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - return (equals == Py_NE); - } -#endif - result = memcmp(ps1, ps2, (size_t)length); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -#endif -} - -/* UnicodeEquals */ - static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else -#if PY_MAJOR_VERSION < 3 - PyObject* owned_ref = NULL; -#endif - int s1_is_unicode, s2_is_unicode; - if (s1 == s2) { - goto return_eq; - } - s1_is_unicode = PyUnicode_CheckExact(s1); - s2_is_unicode = PyUnicode_CheckExact(s2); -#if PY_MAJOR_VERSION < 3 - if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { - owned_ref = PyUnicode_FromObject(s2); - if (unlikely(!owned_ref)) - return -1; - s2 = owned_ref; - s2_is_unicode = 1; - } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { - owned_ref = PyUnicode_FromObject(s1); - if (unlikely(!owned_ref)) - return -1; - s1 = owned_ref; - s1_is_unicode = 1; - } else if (((!s2_is_unicode) & (!s1_is_unicode))) { - return __Pyx_PyBytes_Equals(s1, s2, equals); - } -#endif - if (s1_is_unicode & s2_is_unicode) { - Py_ssize_t length; - int kind; - void *data1, *data2; - if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) - return -1; - length = __Pyx_PyUnicode_GET_LENGTH(s1); - if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { - goto return_ne; - } -#if CYTHON_USE_UNICODE_INTERNALS - { - Py_hash_t hash1, hash2; - #if CYTHON_PEP393_ENABLED - hash1 = ((PyASCIIObject*)s1)->hash; - hash2 = ((PyASCIIObject*)s2)->hash; - #else - hash1 = ((PyUnicodeObject*)s1)->hash; - hash2 = ((PyUnicodeObject*)s2)->hash; - #endif - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - goto return_ne; - } - } -#endif - kind = __Pyx_PyUnicode_KIND(s1); - if (kind != __Pyx_PyUnicode_KIND(s2)) { - goto return_ne; - } - data1 = __Pyx_PyUnicode_DATA(s1); - data2 = __Pyx_PyUnicode_DATA(s2); - if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { - goto return_ne; - } else if (length == 1) { - goto return_eq; - } else { - int result = memcmp(data1, data2, (size_t)(length * kind)); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & s2_is_unicode) { - goto return_ne; - } else if ((s2 == Py_None) & s1_is_unicode) { - goto return_ne; - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -return_eq: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ); -return_ne: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_NE); -#endif -} - -/* DivInt[Py_ssize_t] */ - static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { - Py_ssize_t q = a / b; - Py_ssize_t r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* GetAttr */ - static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { -#if CYTHON_USE_TYPE_SLOTS -#if PY_MAJOR_VERSION >= 3 - if (likely(PyUnicode_Check(n))) -#else - if (likely(PyString_Check(n))) -#endif - return __Pyx_PyObject_GetAttrStr(o, n); -#endif - return PyObject_GetAttr(o, n); -} - -/* ObjectGetItem */ - #if CYTHON_USE_TYPE_SLOTS -static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { - PyObject *runerr = NULL; - Py_ssize_t key_value; - PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; - if (unlikely(!(m && m->sq_item))) { - PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); - return NULL; - } - key_value = __Pyx_PyIndex_AsSsize_t(index); - if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { - return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); - } - if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { - PyErr_Clear(); - PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); - } - return NULL; -} -static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { - PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; - if (likely(m && m->mp_subscript)) { - return m->mp_subscript(obj, key); - } - return __Pyx_PyObject_GetIndex(obj, key); -} -#endif - -/* decode_c_string */ - static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { - Py_ssize_t length; - if (unlikely((start < 0) | (stop < 0))) { - size_t slen = strlen(cstring); - if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { - PyErr_SetString(PyExc_OverflowError, - "c-string too long to convert to Python"); - return NULL; - } - length = (Py_ssize_t) slen; - if (start < 0) { - start += length; - if (start < 0) - start = 0; - } - if (stop < 0) - stop += length; - } - if (unlikely(stop <= start)) - return __Pyx_NewRef(__pyx_empty_unicode); - length = stop - start; - cstring += start; - if (decode_func) { - return decode_func(cstring, length, errors); - } else { - return PyUnicode_Decode(cstring, length, encoding, errors); - } -} - -/* GetAttr3 */ - static PyObject *__Pyx_GetAttr3Default(PyObject *d) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - return NULL; - __Pyx_PyErr_Clear(); - Py_INCREF(d); - return d; -} -static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { - PyObject *r = __Pyx_GetAttr(o, n); - return (likely(r)) ? r : __Pyx_GetAttr3Default(d); -} - -/* PyDictVersioning */ - #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; -} -static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) { - PyObject **dictptr = NULL; - Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset; - if (offset) { -#if CYTHON_COMPILING_IN_CPYTHON - dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj); -#else - dictptr = _PyObject_GetDictPtr(obj); -#endif - } - return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; -} -static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) - return 0; - return obj_dict_version == __Pyx_get_object_dict_version(obj); -} -#endif - -/* GetModuleGlobalName */ - #if CYTHON_USE_DICT_VERSIONS -static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value) -#else -static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name) -#endif -{ - PyObject *result; -#if !CYTHON_AVOID_BORROWED_REFS -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 - result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } else if (unlikely(PyErr_Occurred())) { - return NULL; - } -#else - result = PyDict_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } -#endif -#else - result = PyObject_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } - PyErr_Clear(); -#endif - return __Pyx_GetBuiltinName(name); -} - -/* ExtTypeTest */ - static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(__Pyx_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* SwapException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = *type; - exc_info->exc_value = *value; - exc_info->exc_traceback = *tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = *type; - tstate->exc_value = *value; - tstate->exc_traceback = *tb; - #endif - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); - PyErr_SetExcInfo(*type, *value, *tb); - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#endif - -/* Import */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* FastTypeChecks */ - #if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; - if (a == b) - return 1; - } - return b == &PyBaseObject_Type; -} -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { - PyObject *mro; - if (a == b) return 1; - mro = a->tp_mro; - if (likely(mro)) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(mro); - for (i = 0; i < n; i++) { - if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) - return 1; - } - return 0; - } - return __Pyx_InBases(a, b); -} -#if PY_MAJOR_VERSION == 2 -static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { - PyObject *exception, *value, *tb; - int res; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&exception, &value, &tb); - res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - if (!res) { - res = PyObject_IsSubclass(err, exc_type2); - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - } - __Pyx_ErrRestore(exception, value, tb); - return res; -} -#else -static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { - int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; - if (!res) { - res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); - } - return res; -} -#endif -static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - assert(PyExceptionClass_Check(exc_type)); - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; i= 0 || (x^b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - default: return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - } - x = a + b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla + llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("add", return NULL) - result = ((double)a) + (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); -} -#endif - -/* None */ - static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { - PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); -} - -/* DivInt[long] */ - static CYTHON_INLINE long __Pyx_div_long(long a, long b) { - long q = a / b; - long r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* ImportFrom */ - static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { - PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); - if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_Format(PyExc_ImportError, - #if PY_MAJOR_VERSION < 3 - "cannot import name %.230s", PyString_AS_STRING(name)); - #else - "cannot import name %S", name); - #endif - } - return value; -} - -/* HasAttr */ - static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { - PyObject *r; - if (unlikely(!__Pyx_PyBaseString_Check(n))) { - PyErr_SetString(PyExc_TypeError, - "hasattr(): attribute name must be string"); - return -1; - } - r = __Pyx_GetAttr(o, n); - if (unlikely(!r)) { - PyErr_Clear(); - return 0; - } else { - Py_DECREF(r); - return 1; - } -} - -/* StringJoin */ - #if !CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) { - return PyObject_CallMethodObjArgs(sep, __pyx_n_s_join, values, NULL); -} -#endif - -/* PyObject_GenericGetAttrNoDict */ - #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { - PyErr_Format(PyExc_AttributeError, -#if PY_MAJOR_VERSION >= 3 - "'%.50s' object has no attribute '%U'", - tp->tp_name, attr_name); -#else - "'%.50s' object has no attribute '%.400s'", - tp->tp_name, PyString_AS_STRING(attr_name)); -#endif - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { - PyObject *descr; - PyTypeObject *tp = Py_TYPE(obj); - if (unlikely(!PyString_Check(attr_name))) { - return PyObject_GenericGetAttr(obj, attr_name); - } - assert(!tp->tp_dictoffset); - descr = _PyType_Lookup(tp, attr_name); - if (unlikely(!descr)) { - return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); - } - Py_INCREF(descr); - #if PY_MAJOR_VERSION < 3 - if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) - #endif - { - descrgetfunc f = Py_TYPE(descr)->tp_descr_get; - if (unlikely(f)) { - PyObject *res = f(descr, obj, (PyObject *)tp); - Py_DECREF(descr); - return res; - } - } - return descr; -} -#endif - -/* PyObject_GenericGetAttr */ - #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { - if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { - return PyObject_GenericGetAttr(obj, attr_name); - } - return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); -} -#endif - -/* SetVTable */ - static int __Pyx_SetVtable(PyObject *dict, void *vtable) { -#if PY_VERSION_HEX >= 0x02070000 - PyObject *ob = PyCapsule_New(vtable, 0, 0); -#else - PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); -#endif - if (!ob) - goto bad; - if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) - goto bad; - Py_DECREF(ob); - return 0; -bad: - Py_XDECREF(ob); - return -1; -} - -/* PyObjectGetAttrStrNoError */ - static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - __Pyx_PyErr_Clear(); -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { - PyObject *result; -#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 - PyTypeObject* tp = Py_TYPE(obj); - if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { - return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); - } -#endif - result = __Pyx_PyObject_GetAttrStr(obj, attr_name); - if (unlikely(!result)) { - __Pyx_PyObject_GetAttrStr_ClearAttributeError(); - } - return result; -} - -/* SetupReduce */ - static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { - int ret; - PyObject *name_attr; - name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2); - if (likely(name_attr)) { - ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); - } else { - ret = -1; - } - if (unlikely(ret < 0)) { - PyErr_Clear(); - ret = 0; - } - Py_XDECREF(name_attr); - return ret; -} -static int __Pyx_setup_reduce(PyObject* type_obj) { - int ret = 0; - PyObject *object_reduce = NULL; - PyObject *object_getstate = NULL; - PyObject *object_reduce_ex = NULL; - PyObject *reduce = NULL; - PyObject *reduce_ex = NULL; - PyObject *reduce_cython = NULL; - PyObject *setstate = NULL; - PyObject *setstate_cython = NULL; - PyObject *getstate = NULL; -#if CYTHON_USE_PYTYPE_LOOKUP - getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate); -#else - getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate); - if (!getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (getstate) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate); -#else - object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate); - if (!object_getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (object_getstate != getstate) { - goto __PYX_GOOD; - } - } -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; - if (reduce_ex == object_reduce_ex) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; - if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); - if (likely(reduce_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (reduce == object_reduce || PyErr_Occurred()) { - goto __PYX_BAD; - } - setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); - if (!setstate) PyErr_Clear(); - if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); - if (likely(setstate_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (!setstate || PyErr_Occurred()) { - goto __PYX_BAD; - } - } - PyType_Modified((PyTypeObject*)type_obj); - } - } - goto __PYX_GOOD; -__PYX_BAD: - if (!PyErr_Occurred()) - PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); - ret = -1; -__PYX_GOOD: -#if !CYTHON_USE_PYTYPE_LOOKUP - Py_XDECREF(object_reduce); - Py_XDECREF(object_reduce_ex); - Py_XDECREF(object_getstate); - Py_XDECREF(getstate); -#endif - Py_XDECREF(reduce); - Py_XDECREF(reduce_ex); - Py_XDECREF(reduce_cython); - Py_XDECREF(setstate); - Py_XDECREF(setstate_cython); - return ret; -} - -/* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* FetchCommonType */ - static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { - PyObject* fake_module; - PyTypeObject* cached_type = NULL; - fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI); - if (!fake_module) return NULL; - Py_INCREF(fake_module); - cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name); - if (cached_type) { - if (!PyType_Check((PyObject*)cached_type)) { - PyErr_Format(PyExc_TypeError, - "Shared Cython type %.200s is not a type object", - type->tp_name); - goto bad; - } - if (cached_type->tp_basicsize != type->tp_basicsize) { - PyErr_Format(PyExc_TypeError, - "Shared Cython type %.200s has the wrong size, try recompiling", - type->tp_name); - goto bad; - } - } else { - if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad; - PyErr_Clear(); - if (PyType_Ready(type) < 0) goto bad; - if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0) - goto bad; - Py_INCREF(type); - cached_type = type; - } -done: - Py_DECREF(fake_module); - return cached_type; -bad: - Py_XDECREF(cached_type); - cached_type = NULL; - goto done; -} - -/* CythonFunctionShared */ - #include -static PyObject * -__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) -{ - if (unlikely(op->func_doc == NULL)) { - if (op->func.m_ml->ml_doc) { -#if PY_MAJOR_VERSION >= 3 - op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc); -#else - op->func_doc = PyString_FromString(op->func.m_ml->ml_doc); -#endif - if (unlikely(op->func_doc == NULL)) - return NULL; - } else { - Py_INCREF(Py_None); - return Py_None; - } - } - Py_INCREF(op->func_doc); - return op->func_doc; -} -static int -__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value, CYTHON_UNUSED void *context) -{ - PyObject *tmp = op->func_doc; - if (value == NULL) { - value = Py_None; - } - Py_INCREF(value); - op->func_doc = value; - Py_XDECREF(tmp); - return 0; -} -static PyObject * -__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *context) -{ - if (unlikely(op->func_name == NULL)) { -#if PY_MAJOR_VERSION >= 3 - op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name); -#else - op->func_name = PyString_InternFromString(op->func.m_ml->ml_name); -#endif - if (unlikely(op->func_name == NULL)) - return NULL; - } - Py_INCREF(op->func_name); - return op->func_name; -} -static int -__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value, CYTHON_UNUSED void *context) -{ - PyObject *tmp; -#if PY_MAJOR_VERSION >= 3 - if (unlikely(value == NULL || !PyUnicode_Check(value))) -#else - if (unlikely(value == NULL || !PyString_Check(value))) -#endif - { - PyErr_SetString(PyExc_TypeError, - "__name__ must be set to a string object"); - return -1; - } - tmp = op->func_name; - Py_INCREF(value); - op->func_name = value; - Py_XDECREF(tmp); - return 0; -} -static PyObject * -__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *context) -{ - Py_INCREF(op->func_qualname); - return op->func_qualname; -} -static int -__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value, CYTHON_UNUSED void *context) -{ - PyObject *tmp; -#if PY_MAJOR_VERSION >= 3 - if (unlikely(value == NULL || !PyUnicode_Check(value))) -#else - if (unlikely(value == NULL || !PyString_Check(value))) -#endif - { - PyErr_SetString(PyExc_TypeError, - "__qualname__ must be set to a string object"); - return -1; - } - tmp = op->func_qualname; - Py_INCREF(value); - op->func_qualname = value; - Py_XDECREF(tmp); - return 0; -} -static PyObject * -__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure) -{ - PyObject *self; - self = m->func_closure; - if (self == NULL) - self = Py_None; - Py_INCREF(self); - return self; -} -static PyObject * -__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *context) -{ - if (unlikely(op->func_dict == NULL)) { - op->func_dict = PyDict_New(); 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-} -static int -__pyx_FusedFunction_traverse(__pyx_FusedFunctionObject *self, - visitproc visit, - void *arg) -{ - Py_VISIT(self->self); - Py_VISIT(self->type); - Py_VISIT(self->__signatures__); - return __Pyx_CyFunction_traverse((__pyx_CyFunctionObject *) self, visit, arg); -} -static int -__pyx_FusedFunction_clear(__pyx_FusedFunctionObject *self) -{ - Py_CLEAR(self->self); - Py_CLEAR(self->type); - Py_CLEAR(self->__signatures__); - return __Pyx_CyFunction_clear((__pyx_CyFunctionObject *) self); -} -static PyObject * -__pyx_FusedFunction_descr_get(PyObject *self, PyObject *obj, PyObject *type) -{ - __pyx_FusedFunctionObject *func, *meth; - func = (__pyx_FusedFunctionObject *) self; - if (func->self || func->func.flags & __Pyx_CYFUNCTION_STATICMETHOD) { - Py_INCREF(self); - return self; - } - if (obj == Py_None) - obj = NULL; - meth = (__pyx_FusedFunctionObject *) __pyx_FusedFunction_New( - ((PyCFunctionObject *) func)->m_ml, - ((__pyx_CyFunctionObject *) func)->flags, - ((__pyx_CyFunctionObject *) func)->func_qualname, - ((__pyx_CyFunctionObject *) func)->func_closure, - ((PyCFunctionObject *) func)->m_module, - ((__pyx_CyFunctionObject *) func)->func_globals, - ((__pyx_CyFunctionObject *) func)->func_code); - if (!meth) - return NULL; - if (func->func.defaults) { - PyObject **pydefaults; - int i; - if (!__Pyx_CyFunction_InitDefaults((PyObject*)meth, - func->func.defaults_size, - func->func.defaults_pyobjects)) { - Py_XDECREF((PyObject*)meth); - return NULL; - } - memcpy(meth->func.defaults, func->func.defaults, func->func.defaults_size); - pydefaults = __Pyx_CyFunction_Defaults(PyObject *, meth); - for (i = 0; i < meth->func.defaults_pyobjects; i++) - Py_XINCREF(pydefaults[i]); - } - Py_XINCREF(func->func.func_classobj); - meth->func.func_classobj = func->func.func_classobj; - Py_XINCREF(func->__signatures__); - meth->__signatures__ = func->__signatures__; - Py_XINCREF(type); - meth->type = type; - Py_XINCREF(func->func.defaults_tuple); - meth->func.defaults_tuple = func->func.defaults_tuple; - if (func->func.flags & __Pyx_CYFUNCTION_CLASSMETHOD) - obj = type; - Py_XINCREF(obj); - meth->self = obj; - return (PyObject *) meth; -} -static PyObject * -_obj_to_str(PyObject *obj) -{ - if (PyType_Check(obj)) - return PyObject_GetAttr(obj, __pyx_n_s_name_2); - else - return PyObject_Str(obj); -} -static PyObject * -__pyx_FusedFunction_getitem(__pyx_FusedFunctionObject *self, PyObject *idx) -{ - PyObject *signature = NULL; - PyObject *unbound_result_func; - PyObject *result_func = NULL; - if (self->__signatures__ == NULL) { - PyErr_SetString(PyExc_TypeError, "Function is not fused"); - return NULL; - } - if (PyTuple_Check(idx)) { - PyObject *list = PyList_New(0); - Py_ssize_t n = PyTuple_GET_SIZE(idx); - PyObject *sep = NULL; - int i; - if (unlikely(!list)) - return NULL; - for (i = 0; i < n; i++) { - int ret; - PyObject *string; -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - PyObject *item = PyTuple_GET_ITEM(idx, i); -#else - PyObject *item = PySequence_ITEM(idx, i); if (unlikely(!item)) goto __pyx_err; -#endif - string = _obj_to_str(item); -#if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS) - Py_DECREF(item); -#endif - if (unlikely(!string)) goto __pyx_err; - ret = PyList_Append(list, string); - Py_DECREF(string); - if (unlikely(ret < 0)) goto __pyx_err; - } - sep = PyUnicode_FromString("|"); - if (likely(sep)) - signature = PyUnicode_Join(sep, list); -__pyx_err: -; - Py_DECREF(list); - Py_XDECREF(sep); - } else { - signature = _obj_to_str(idx); - } - if (!signature) - return NULL; - unbound_result_func = PyObject_GetItem(self->__signatures__, signature); - if (unbound_result_func) { - if (self->self || self->type) { - __pyx_FusedFunctionObject *unbound = (__pyx_FusedFunctionObject *) unbound_result_func; - Py_CLEAR(unbound->func.func_classobj); - Py_XINCREF(self->func.func_classobj); - unbound->func.func_classobj = self->func.func_classobj; - result_func = __pyx_FusedFunction_descr_get(unbound_result_func, - self->self, self->type); - } else { - result_func = unbound_result_func; - Py_INCREF(result_func); - } - } - Py_DECREF(signature); - Py_XDECREF(unbound_result_func); - return result_func; -} -static PyObject * -__pyx_FusedFunction_callfunction(PyObject *func, PyObject *args, PyObject *kw) -{ - __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *) func; - int static_specialized = (cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD && - !((__pyx_FusedFunctionObject *) func)->__signatures__); - if (cyfunc->flags & __Pyx_CYFUNCTION_CCLASS && !static_specialized) { - return __Pyx_CyFunction_CallAsMethod(func, args, kw); - } else { - return __Pyx_CyFunction_Call(func, args, kw); - } -} -static PyObject * -__pyx_FusedFunction_call(PyObject *func, PyObject *args, PyObject *kw) -{ - __pyx_FusedFunctionObject *binding_func = (__pyx_FusedFunctionObject *) func; - Py_ssize_t argc = PyTuple_GET_SIZE(args); - PyObject *new_args = NULL; - __pyx_FusedFunctionObject *new_func = NULL; - PyObject *result = NULL; - PyObject *self = NULL; - int is_staticmethod = binding_func->func.flags & __Pyx_CYFUNCTION_STATICMETHOD; - int is_classmethod = binding_func->func.flags & __Pyx_CYFUNCTION_CLASSMETHOD; - if (binding_func->self) { - Py_ssize_t i; - new_args = PyTuple_New(argc + 1); - if (!new_args) - return NULL; - self = binding_func->self; -#if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS) - Py_INCREF(self); -#endif - Py_INCREF(self); - PyTuple_SET_ITEM(new_args, 0, self); - for (i = 0; i < argc; i++) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - PyObject *item = PyTuple_GET_ITEM(args, i); - Py_INCREF(item); -#else - PyObject *item = PySequence_ITEM(args, i); if (unlikely(!item)) goto bad; -#endif - PyTuple_SET_ITEM(new_args, i + 1, item); - } - args = new_args; - } else if (binding_func->type) { - if (argc < 1) { - PyErr_SetString(PyExc_TypeError, "Need at least one argument, 0 given."); - return NULL; - } -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - self = PyTuple_GET_ITEM(args, 0); -#else - self = PySequence_ITEM(args, 0); if (unlikely(!self)) return NULL; -#endif - } - if (self && !is_classmethod && !is_staticmethod) { - int is_instance = PyObject_IsInstance(self, binding_func->type); - if (unlikely(!is_instance)) { - PyErr_Format(PyExc_TypeError, - "First argument should be of type %.200s, got %.200s.", - ((PyTypeObject *) binding_func->type)->tp_name, - Py_TYPE(self)->tp_name); - goto bad; - } else if (unlikely(is_instance == -1)) { - goto bad; - } - } -#if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS) - Py_XDECREF(self); - self = NULL; -#endif - if (binding_func->__signatures__) { - PyObject *tup; - if (is_staticmethod && binding_func->func.flags & __Pyx_CYFUNCTION_CCLASS) { - tup = PyTuple_Pack(3, args, - kw == NULL ? 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Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ - #include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); 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i++) { - Py_ssize_t stride = slice->strides[i]; - Py_ssize_t extent = slice->shape[i]; - if (extent == 0) { - *out_start = *out_end = start; - return; - } else { - if (stride > 0) - end += stride * (extent - 1); - else - start += stride * (extent - 1); - } - } - *out_start = start; - *out_end = end + itemsize; -} -static int -__pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize) -{ - void *start1, *end1, *start2, *end2; - __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); - __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); - return (start1 < end2) && (start2 < end1); -} - -/* Capsule */ - static CYTHON_INLINE PyObject * -__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) -{ - PyObject *cobj; -#if PY_VERSION_HEX >= 0x02070000 - cobj = PyCapsule_New(p, sig, NULL); -#else - cobj = PyCObject_FromVoidPtr(p, NULL); -#endif - return cobj; -} - -/* IsLittleEndian */ - static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) -{ - union { - uint32_t u32; - uint8_t u8[4]; - } S; - S.u32 = 0x01020304; - return S.u8[0] == 4; -} - -/* BufferFormatCheck */ - static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type) { - stack[0].field = &ctx->root; - stack[0].parent_offset = 0; - ctx->root.type = type; - ctx->root.name = "buffer dtype"; - ctx->root.offset = 0; - ctx->head = stack; - ctx->head->field = &ctx->root; - ctx->fmt_offset = 0; - ctx->head->parent_offset = 0; - ctx->new_packmode = '@'; - ctx->enc_packmode = '@'; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->is_complex = 0; - ctx->is_valid_array = 0; - ctx->struct_alignment = 0; - while (type->typegroup == 'S') { - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = 0; - type = type->fields->type; - } -} -static int __Pyx_BufFmt_ParseNumber(const char** ts) { - int count; - const char* t = *ts; - if (*t < '0' || *t > '9') { - return -1; - } else { - count = *t++ - '0'; - while (*t >= '0' && *t <= '9') { - count *= 10; - count += *t++ - '0'; - } - } - *ts = t; - return count; -} -static int __Pyx_BufFmt_ExpectNumber(const char **ts) { - int number = __Pyx_BufFmt_ParseNumber(ts); - if (number == -1) - PyErr_Format(PyExc_ValueError,\ - "Does not understand character buffer dtype format string ('%c')", **ts); - return number; -} -static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { - PyErr_Format(PyExc_ValueError, - "Unexpected format string character: '%c'", ch); -} -static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { - switch (ch) { - case '?': return "'bool'"; - case 'c': return "'char'"; - case 'b': return "'signed char'"; - case 'B': return "'unsigned char'"; - case 'h': return "'short'"; - case 'H': return "'unsigned short'"; - case 'i': return "'int'"; - case 'I': return "'unsigned int'"; - case 'l': return "'long'"; - case 'L': return "'unsigned long'"; - case 'q': return "'long long'"; - case 'Q': return "'unsigned long long'"; - case 'f': return (is_complex ? "'complex float'" : "'float'"); - case 'd': return (is_complex ? "'complex double'" : "'double'"); - case 'g': return (is_complex ? "'complex long double'" : "'long double'"); - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - case 's': case 'p': return "a string"; - case 0: return "end"; - default: return "unparseable format string"; - } -} -static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return 2; - case 'i': case 'I': case 'l': case 'L': return 4; - case 'q': case 'Q': return 8; - case 'f': return (is_complex ? 8 : 4); - case 'd': return (is_complex ? 16 : 8); - case 'g': { - PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); - return 0; - } - case 'O': case 'P': return sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(short); - case 'i': case 'I': return sizeof(int); - case 'l': case 'L': return sizeof(long); - #ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(PY_LONG_LONG); - #endif - case 'f': return sizeof(float) * (is_complex ? 2 : 1); - case 'd': return sizeof(double) * (is_complex ? 2 : 1); - case 'g': return sizeof(long double) * (is_complex ? 2 : 1); - case 'O': case 'P': return sizeof(void*); - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -typedef struct { char c; short x; } __Pyx_st_short; -typedef struct { char c; int x; } __Pyx_st_int; -typedef struct { char c; long x; } __Pyx_st_long; -typedef struct { char c; float x; } __Pyx_st_float; -typedef struct { char c; double x; } __Pyx_st_double; -typedef struct { char c; long double x; } __Pyx_st_longdouble; -typedef struct { char c; void *x; } __Pyx_st_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_st_float) - sizeof(float); - case 'd': return sizeof(__Pyx_st_double) - sizeof(double); - case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -/* These are for computing the padding at the end of the struct to align - on the first member of the struct. This will probably the same as above, - but we don't have any guarantees. - */ -typedef struct { short x; char c; } __Pyx_pad_short; -typedef struct { int x; char c; } __Pyx_pad_int; -typedef struct { long x; char c; } __Pyx_pad_long; -typedef struct { float x; char c; } __Pyx_pad_float; -typedef struct { double x; char c; } __Pyx_pad_double; -typedef struct { long double x; char c; } __Pyx_pad_longdouble; -typedef struct { void *x; char c; } __Pyx_pad_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); - case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); - case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { - switch (ch) { - case 'c': - return 'H'; - case 'b': case 'h': case 'i': - case 'l': case 'q': case 's': case 'p': - return 'I'; - case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': - return 'U'; - case 'f': case 'd': case 'g': - return (is_complex ? 'C' : 'R'); - case 'O': - return 'O'; - case 'P': - return 'P'; - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { - if (ctx->head == NULL || ctx->head->field == &ctx->root) { - const char* expected; - const char* quote; - if (ctx->head == NULL) { - expected = "end"; - quote = ""; - } else { - expected = ctx->head->field->type->name; - quote = "'"; - } - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected %s%s%s but got %s", - quote, expected, quote, - __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); - } else { - __Pyx_StructField* field = ctx->head->field; - __Pyx_StructField* parent = (ctx->head - 1)->field; - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", - field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), - parent->type->name, field->name); - } -} -static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { - char group; - size_t size, offset, arraysize = 1; - if (ctx->enc_type == 0) return 0; - if (ctx->head->field->type->arraysize[0]) { - int i, ndim = 0; - if (ctx->enc_type == 's' || ctx->enc_type == 'p') { - ctx->is_valid_array = ctx->head->field->type->ndim == 1; - ndim = 1; - if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { - PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %zu", - ctx->head->field->type->arraysize[0], ctx->enc_count); - return -1; - } - } - if (!ctx->is_valid_array) { - PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", - ctx->head->field->type->ndim, ndim); - return -1; - } - for (i = 0; i < ctx->head->field->type->ndim; i++) { - arraysize *= ctx->head->field->type->arraysize[i]; - } - ctx->is_valid_array = 0; - ctx->enc_count = 1; - } - group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); - do { - __Pyx_StructField* field = ctx->head->field; - __Pyx_TypeInfo* type = field->type; - if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { - size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); - } else { - size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); - } - if (ctx->enc_packmode == '@') { - size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); - size_t align_mod_offset; - if (align_at == 0) return -1; - align_mod_offset = ctx->fmt_offset % align_at; - if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; - if (ctx->struct_alignment == 0) - ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, - ctx->is_complex); - } - if (type->size != size || type->typegroup != group) { - if (type->typegroup == 'C' && type->fields != NULL) { - size_t parent_offset = ctx->head->parent_offset + field->offset; - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = parent_offset; - continue; - } - if ((type->typegroup == 'H' || group == 'H') && type->size == size) { - } else { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - } - offset = ctx->head->parent_offset + field->offset; - if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; - } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } - } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; -} -static PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number, ndim; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ndim = ctx->head->field->type->ndim; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; - } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; - } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; - } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; -} -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; - } - break; - case '}': - { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } - } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; - } - CYTHON_FALLTHROUGH; - case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && - (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - CYTHON_FALLTHROUGH; - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: - { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; - } - } - } -} - -/* TypeInfoCompare */ - static int -__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) -{ - int i; - if (!a || !b) - return 0; - if (a == b) - return 1; - if (a->size != b->size || a->typegroup != b->typegroup || - a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { - if (a->typegroup == 'H' || b->typegroup == 'H') { - return a->size == b->size; - } else { - return 0; - } - } - if (a->ndim) { - for (i = 0; i < a->ndim; i++) - if (a->arraysize[i] != b->arraysize[i]) - return 0; - } - if (a->typegroup == 'S') { - if (a->flags != b->flags) - return 0; - if (a->fields || b->fields) { - if (!(a->fields && b->fields)) - return 0; - for (i = 0; a->fields[i].type && b->fields[i].type; i++) { - __Pyx_StructField *field_a = a->fields + i; - __Pyx_StructField *field_b = b->fields + i; - if (field_a->offset != field_b->offset || - !__pyx_typeinfo_cmp(field_a->type, field_b->type)) - return 0; - } - return !a->fields[i].type && !b->fields[i].type; - } - } - return 1; -} - -/* MemviewSliceValidateAndInit */ - static int -__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) -{ - if (buf->shape[dim] <= 1) - return 1; - if (buf->strides) { - if (spec & __Pyx_MEMVIEW_CONTIG) { - if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { - if (unlikely(buf->strides[dim] != sizeof(void *))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly contiguous " - "in dimension %d.", dim); - goto fail; - } - } else if (unlikely(buf->strides[dim] != buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_FOLLOW) { - Py_ssize_t stride = buf->strides[dim]; - if (stride < 0) - stride = -stride; - if (unlikely(stride < buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - } else { - if (unlikely(spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1)) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not contiguous in " - "dimension %d", dim); - goto fail; - } else if (unlikely(spec & (__Pyx_MEMVIEW_PTR))) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not indirect in " - "dimension %d", dim); - goto fail; - } else if (unlikely(buf->suboffsets)) { - PyErr_SetString(PyExc_ValueError, - "Buffer exposes suboffsets but no strides"); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) -{ - if (spec & __Pyx_MEMVIEW_DIRECT) { - if (unlikely(buf->suboffsets && buf->suboffsets[dim] >= 0)) { - PyErr_Format(PyExc_ValueError, - "Buffer not compatible with direct access " - "in dimension %d.", dim); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_PTR) { - if (unlikely(!buf->suboffsets || (buf->suboffsets[dim] < 0))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly accessible " - "in dimension %d.", dim); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) -{ - int i; - if (c_or_f_flag & __Pyx_IS_F_CONTIG) { - Py_ssize_t stride = 1; - for (i = 0; i < ndim; i++) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not fortran contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { - Py_ssize_t stride = 1; - for (i = ndim - 1; i >- 1; i--) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not C contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } - return 1; -fail: - return 0; -} -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj) -{ - struct __pyx_memoryview_obj *memview, *new_memview; - __Pyx_RefNannyDeclarations - Py_buffer *buf; - int i, spec = 0, retval = -1; - __Pyx_BufFmt_Context ctx; - int from_memoryview = __pyx_memoryview_check(original_obj); - __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); - if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) - original_obj)->typeinfo)) { - memview = (struct __pyx_memoryview_obj *) original_obj; - new_memview = NULL; - } else { - memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - original_obj, buf_flags, 0, dtype); - new_memview = memview; - if (unlikely(!memview)) - goto fail; - } - buf = &memview->view; - if (unlikely(buf->ndim != ndim)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - ndim, buf->ndim); - goto fail; - } - if (new_memview) { - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (unlikely(!__Pyx_BufFmt_CheckString(&ctx, buf->format))) goto fail; - } - if (unlikely((unsigned) buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " - "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", - buf->itemsize, - (buf->itemsize > 1) ? "s" : "", - dtype->name, - dtype->size, - (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->len > 0) { - for (i = 0; i < ndim; i++) { - spec = axes_specs[i]; - if (unlikely(!__pyx_check_strides(buf, i, ndim, spec))) - goto fail; - if (unlikely(!__pyx_check_suboffsets(buf, i, ndim, spec))) - goto fail; - } - if (unlikely(buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))) - goto fail; - } - if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, - new_memview != NULL) == -1)) { - goto fail; - } - retval = 0; - goto no_fail; -fail: - Py_XDECREF(new_memview); - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 2, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_double(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 2, - &__Pyx_TypeInfo_double, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 1, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_double(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 1, - &__Pyx_TypeInfo_double, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_FOLLOW), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 2, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 1, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* MemviewDtypeToObject */ - static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp) { - return (PyObject *) PyFloat_FromDouble(*(float *) itemp); -} -static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj) { - float value = __pyx_PyFloat_AsFloat(obj); - if ((value == (float)-1) && PyErr_Occurred()) - return 0; - *(float *) itemp = value; - return 1; -} - -/* MemviewDtypeToObject */ - static CYTHON_INLINE PyObject *__pyx_memview_get_double(const char *itemp) { - return (PyObject *) PyFloat_FromDouble(*(double *) itemp); -} -static CYTHON_INLINE int __pyx_memview_set_double(const char *itemp, PyObject *obj) { - double value = __pyx_PyFloat_AsDouble(obj); - if ((value == (double)-1) && PyErr_Occurred()) - return 0; - *(double *) itemp = value; - return 1; -} - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* MemviewSliceCopyTemplate */ - static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object) -{ - __Pyx_RefNannyDeclarations - int i; - __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; - struct __pyx_memoryview_obj *from_memview = from_mvs->memview; - Py_buffer *buf = &from_memview->view; - PyObject *shape_tuple = NULL; - PyObject *temp_int = NULL; - struct __pyx_array_obj *array_obj = NULL; - struct __pyx_memoryview_obj *memview_obj = NULL; - __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); - for (i = 0; i < ndim; i++) { - if (unlikely(from_mvs->suboffsets[i] >= 0)) { - PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " - "indirect dimensions (axis %d)", i); - goto fail; - } - } - shape_tuple = PyTuple_New(ndim); - if (unlikely(!shape_tuple)) { - goto fail; - } - __Pyx_GOTREF(shape_tuple); - for(i = 0; i < ndim; i++) { - temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); - if(unlikely(!temp_int)) { - goto fail; - } else { - PyTuple_SET_ITEM(shape_tuple, i, temp_int); - temp_int = NULL; - } - } - array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); - if (unlikely(!array_obj)) { - goto fail; - } - __Pyx_GOTREF(array_obj); - memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - (PyObject *) array_obj, contig_flag, - dtype_is_object, - from_mvs->memview->typeinfo); - if (unlikely(!memview_obj)) - goto fail; - if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) - goto fail; - if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, - dtype_is_object) < 0)) - goto fail; - goto no_fail; -fail: - __Pyx_XDECREF(new_mvs.memview); - new_mvs.memview = NULL; - new_mvs.data = NULL; -no_fail: - __Pyx_XDECREF(shape_tuple); - __Pyx_XDECREF(temp_int); - __Pyx_XDECREF(array_obj); - __Pyx_RefNannyFinishContext(); - return new_mvs; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(uint64_t) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(uint64_t) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(uint64_t) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(uint64_t), - little, !is_unsigned); - } -} - -/* TypeInfoToFormat */ - static struct __pyx_typeinfo_string __Pyx_TypeInfoToFormat(__Pyx_TypeInfo *type) { - struct __pyx_typeinfo_string result = { {0} }; - char *buf = (char *) result.string; - size_t size = type->size; - switch (type->typegroup) { - case 'H': - *buf = 'c'; - break; - case 'I': - case 'U': - if (size == 1) - *buf = (type->is_unsigned) ? 'B' : 'b'; - else if (size == 2) - *buf = (type->is_unsigned) ? 'H' : 'h'; - else if (size == 4) - *buf = (type->is_unsigned) ? 'I' : 'i'; - else if (size == 8) - *buf = (type->is_unsigned) ? 'Q' : 'q'; - break; - case 'P': - *buf = 'P'; - break; - case 'C': - { - __Pyx_TypeInfo complex_type = *type; - complex_type.typegroup = 'R'; - complex_type.size /= 2; - *buf++ = 'Z'; - *buf = __Pyx_TypeInfoToFormat(&complex_type).string[0]; - break; - } - case 'R': - if (size == 4) - *buf = 'f'; - else if (size == 8) - *buf = 'd'; - else - *buf = 'g'; - break; - } - return result; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* BytesContains */ - static CYTHON_INLINE int __Pyx_BytesContains(PyObject* bytes, char character) { - const Py_ssize_t length = PyBytes_GET_SIZE(bytes); - char* char_start = PyBytes_AS_STRING(bytes); - return memchr(char_start, (unsigned char)character, (size_t)length) != NULL; -} - -/* ImportNumPyArray */ - static PyObject* __Pyx__ImportNumPyArray(void) { - PyObject *numpy_module, *ndarray_object = NULL; - numpy_module = __Pyx_Import(__pyx_n_s_numpy, NULL, 0); - if (likely(numpy_module)) { - ndarray_object = PyObject_GetAttrString(numpy_module, "ndarray"); - Py_DECREF(numpy_module); - } - if (unlikely(!ndarray_object)) { - PyErr_Clear(); - } - if (unlikely(!ndarray_object || !PyObject_TypeCheck(ndarray_object, &PyType_Type))) { - Py_XDECREF(ndarray_object); - Py_INCREF(Py_None); - ndarray_object = Py_None; - } - return ndarray_object; -} -static CYTHON_INLINE PyObject* __Pyx_ImportNumPyArrayTypeIfAvailable(void) { - if (unlikely(!__pyx_numpy_ndarray)) { - __pyx_numpy_ndarray = __Pyx__ImportNumPyArray(); - } - Py_INCREF(__pyx_numpy_ndarray); - return __pyx_numpy_ndarray; -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const char neg_one = (char) -1, const_zero = (char) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(char) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (char) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (char) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(char) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) - case -2: - if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - } -#endif - if (sizeof(char) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - char val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (char) -1; - } - } else { - char val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (char) -1; - val = __Pyx_PyInt_As_char(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to char"); - return (char) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to char"); - return (char) -1; -} - -/* CheckBinaryVersion */ - static int __Pyx_check_binary_version(void) { - char ctversion[5]; - int same=1, i, found_dot; - const char* rt_from_call = Py_GetVersion(); - PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); - found_dot = 0; - for (i = 0; i < 4; i++) { - if (!ctversion[i]) { - same = (rt_from_call[i] < '0' || rt_from_call[i] > '9'); - break; - } - if (rt_from_call[i] != ctversion[i]) { - same = 0; - break; - } - } - if (!same) { - char rtversion[5] = {'\0'}; - char message[200]; - for (i=0; i<4; ++i) { - if (rt_from_call[i] == '.') { - if (found_dot) break; - found_dot = 1; - } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') { - break; - } - rtversion[i] = rt_from_call[i]; - } - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* InitStrings */ - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - if (PyObject_Hash(*t->p) == -1) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT -#if !CYTHON_PEP393_ENABLED -static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); - return NULL; - } - } - } -#endif - *length = PyBytes_GET_SIZE(defenc); - return defenc_c; -} -#else -static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (likely(PyUnicode_IS_ASCII(o))) { - *length = PyUnicode_GET_LENGTH(o); - return PyUnicode_AsUTF8(o); - } else { - PyUnicode_AsASCIIString(o); - return NULL; - } -#else - return PyUnicode_AsUTF8AndSize(o, length); -#endif -} -#endif -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { - return __Pyx_PyUnicode_AsStringAndSize(o, length); - } else -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - if (PyByteArray_Check(o)) { - *length = PyByteArray_GET_SIZE(o); - return PyByteArray_AS_STRING(o); - } else -#endif - { - char* result; - int r = PyBytes_AsStringAndSize(o, &result, length); - if (unlikely(r < 0)) { - return NULL; - } else { - return result; - } - } -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - int is_true = x == Py_True; - if (is_true | (x == Py_False) | (x == Py_None)) return is_true; - else return PyObject_IsTrue(x); -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) { - int retval; - if (unlikely(!x)) return -1; - retval = __Pyx_PyObject_IsTrue(x); - Py_DECREF(x); - return retval; -} -static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { -#if PY_MAJOR_VERSION >= 3 - if (PyLong_Check(result)) { - if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, - "__int__ returned non-int (type %.200s). " - "The ability to return an instance of a strict subclass of int " - "is deprecated, and may be removed in a future version of Python.", - Py_TYPE(result)->tp_name)) { - Py_DECREF(result); - return NULL; - } - return result; - } -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - type_name, type_name, Py_TYPE(result)->tp_name); - Py_DECREF(result); - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS - PyNumberMethods *m; -#endif - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x) || PyLong_Check(x))) -#else - if (likely(PyLong_Check(x))) -#endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS - m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = m->nb_int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = m->nb_long(x); - } - #else - if (likely(m && m->nb_int)) { - name = "int"; - res = m->nb_int(x); - } - #endif -#else - if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) { - res = PyNumber_Int(x); - } -#endif - if (likely(res)) { -#if PY_MAJOR_VERSION < 3 - if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) { -#else - if (unlikely(!PyLong_CheckExact(res))) { -#endif - return __Pyx_PyNumber_IntOrLongWrongResultType(res, name); - } - } - else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_TypeError, - "an integer is required"); - } - return res; -} -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { - Py_ssize_t ival; - PyObject *x; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(b); - } -#endif - if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - if (size == -1) ival = -ival; - return ival; - } else { - switch (size) { - case 2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - } - } - #endif - return PyLong_AsSsize_t(b); - } - x = PyNumber_Index(b); - if (!x) return -1; - ival = PyInt_AsSsize_t(x); - Py_DECREF(x); - return ival; -} -static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) { - if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) { - return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o); -#if PY_MAJOR_VERSION < 3 - } else if (likely(PyInt_CheckExact(o))) { - return PyInt_AS_LONG(o); -#endif - } else { - Py_ssize_t ival; - PyObject *x; - x = PyNumber_Index(o); - if (!x) return -1; - ival = PyInt_AsLong(x); - Py_DECREF(x); - return ival; - } -} -static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) { - return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False); -} -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { - 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#define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) -#endif -#if !defined(WIN32) && !defined(MS_WINDOWS) - #ifndef __stdcall - #define __stdcall - #endif - #ifndef __cdecl - #define __cdecl - #endif - #ifndef __fastcall - #define __fastcall - #endif -#endif -#ifndef DL_IMPORT - #define DL_IMPORT(t) t -#endif -#ifndef DL_EXPORT - #define DL_EXPORT(t) t -#endif -#define __PYX_COMMA , -#ifndef HAVE_LONG_LONG - #if PY_VERSION_HEX >= 0x02070000 - #define HAVE_LONG_LONG - #endif -#endif -#ifndef PY_LONG_LONG - #define PY_LONG_LONG LONG_LONG -#endif -#ifndef Py_HUGE_VAL - #define Py_HUGE_VAL HUGE_VAL -#endif -#ifdef PYPY_VERSION - #define CYTHON_COMPILING_IN_PYPY 1 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 0 - #undef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 0 - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #if PY_VERSION_HEX < 0x03050000 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #undef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 0 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #undef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 1 - #undef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 0 - #undef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 0 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #undef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 0 - #undef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 0 - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 - #endif -#elif defined(PYSTON_VERSION) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 1 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #undef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 0 - #undef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 0 - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 - #endif -#elif defined(PY_NOGIL) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 1 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #ifndef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 1 - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 1 - #endif - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 -#else - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 1 - #define CYTHON_COMPILING_IN_NOGIL 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #elif !defined(CYTHON_USE_PYTYPE_LOOKUP) - #define CYTHON_USE_PYTYPE_LOOKUP 1 - #endif - #if PY_MAJOR_VERSION < 3 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #elif !defined(CYTHON_USE_PYLONG_INTERNALS) - #define CYTHON_USE_PYLONG_INTERNALS 1 - #endif - #ifndef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 1 - #endif - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #elif !defined(CYTHON_USE_UNICODE_WRITER) - #define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #elif !defined(CYTHON_FAST_THREAD_STATE) - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000) - #endif - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000) - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) - #endif - #ifndef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1) - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #elif !defined(CYTHON_USE_EXC_INFO_STACK) - #define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3) - #endif - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 - #endif -#endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #if PY_MAJOR_VERSION < 3 - #include "longintrepr.h" - #endif - #undef SHIFT - #undef BASE - #undef MASK - #ifdef SIZEOF_VOID_P - enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) }; - #endif -#endif -#ifndef __has_attribute - #define __has_attribute(x) 0 -#endif -#ifndef __has_cpp_attribute - #define __has_cpp_attribute(x) 0 -#endif -#ifndef CYTHON_RESTRICT - #if defined(__GNUC__) - #define CYTHON_RESTRICT __restrict__ - #elif defined(_MSC_VER) && _MSC_VER >= 1400 - #define CYTHON_RESTRICT __restrict - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_RESTRICT restrict - #else - #define CYTHON_RESTRICT - #endif -#endif -#ifndef CYTHON_UNUSED -# if defined(__GNUC__) -# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -#endif -#ifndef CYTHON_MAYBE_UNUSED_VAR -# if defined(__cplusplus) - template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } -# else -# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) -# endif -#endif -#ifndef CYTHON_NCP_UNUSED -# if CYTHON_COMPILING_IN_CPYTHON -# define CYTHON_NCP_UNUSED -# else -# define CYTHON_NCP_UNUSED CYTHON_UNUSED -# endif -#endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) -#ifdef _MSC_VER - #ifndef _MSC_STDINT_H_ - #if _MSC_VER < 1300 - typedef unsigned char uint8_t; - typedef unsigned int uint32_t; - #else - typedef unsigned __int8 uint8_t; - typedef unsigned __int32 uint32_t; - #endif - #endif -#else - #include -#endif -#ifndef CYTHON_FALLTHROUGH - #if defined(__cplusplus) && __cplusplus >= 201103L - #if __has_cpp_attribute(fallthrough) - #define CYTHON_FALLTHROUGH [[fallthrough]] - #elif __has_cpp_attribute(clang::fallthrough) - #define CYTHON_FALLTHROUGH [[clang::fallthrough]] - #elif __has_cpp_attribute(gnu::fallthrough) - #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] - #endif - #endif - #ifndef CYTHON_FALLTHROUGH - #if __has_attribute(fallthrough) - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - #else - #define CYTHON_FALLTHROUGH - #endif - #endif - #if defined(__clang__ ) && defined(__apple_build_version__) - #if __apple_build_version__ < 7000000 - #undef CYTHON_FALLTHROUGH - #define CYTHON_FALLTHROUGH - #endif - #endif -#endif - -#ifndef CYTHON_INLINE - #if defined(__clang__) - #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) - #elif defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline - #else - #define CYTHON_INLINE - #endif -#endif - -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - if (type) { - PyErr_Restore(type, value, traceback); - } - return co; - } -#else - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_STACKLESS - #define METH_STACKLESS 0 -#endif -#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) - #ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - #endif - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); - typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast - #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1 - #define PyMem_RawMalloc(n) PyMem_Malloc(n) - #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) - #define PyMem_RawFree(p) PyMem_Free(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#elif PY_VERSION_HEX >= 0x03060000 - #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() -#elif PY_VERSION_HEX >= 0x03000000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#else - #define __Pyx_PyThreadState_Current _PyThreadState_Current -#endif -#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) -#include "pythread.h" -#define Py_tss_NEEDS_INIT 0 -typedef int Py_tss_t; -static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { - *key = PyThread_create_key(); - return 0; -} -static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { - Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); - *key = Py_tss_NEEDS_INIT; - return key; -} -static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { - PyObject_Free(key); -} -static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { - return *key != Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { - PyThread_delete_key(*key); - *key = Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { - return PyThread_set_key_value(*key, value); -} -static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { - return PyThread_get_key_value(*key); -} -#endif -#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) -#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? 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PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? 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-static PyTypeObject *__pyx_ptype_5numpy_integer = 0; -static PyTypeObject *__pyx_ptype_5numpy_signedinteger = 0; -static PyTypeObject *__pyx_ptype_5numpy_unsignedinteger = 0; -static PyTypeObject *__pyx_ptype_5numpy_inexact = 0; -static PyTypeObject *__pyx_ptype_5numpy_floating = 0; -static PyTypeObject *__pyx_ptype_5numpy_complexfloating = 0; -static PyTypeObject *__pyx_ptype_5numpy_flexible = 0; -static PyTypeObject *__pyx_ptype_5numpy_character = 0; -static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; -static CYTHON_INLINE int __pyx_f_5numpy_import_array(void); /*proto*/ - -/* Module declarations from 'MDAnalysis.lib.c_distances_openmp' */ -#define __Pyx_MODULE_NAME "MDAnalysis.lib.c_distances_openmp" -extern int __pyx_module_is_main_MDAnalysis__lib__c_distances_openmp; -int __pyx_module_is_main_MDAnalysis__lib__c_distances_openmp = 0; - -/* Implementation of 'MDAnalysis.lib.c_distances_openmp' */ -static PyObject *__pyx_builtin_ImportError; -static const char __pyx_k_box[] = "box"; -static const char __pyx_k_ref[] = "ref"; -static const char __pyx_k_conf[] = "conf"; -static const char __pyx_k_main[] = "__main__"; -static const char __pyx_k_name[] = "__name__"; -static const char __pyx_k_test[] = "__test__"; -static const char __pyx_k_numpy[] = "numpy"; -static const char __pyx_k_coords[] = "coords"; -static const char __pyx_k_import[] = "__import__"; -static const char __pyx_k_refnum[] = "refnum"; -static const char __pyx_k_result[] = "result"; -static const char __pyx_k_confnum[] = "confnum"; -static const char __pyx_k_coords1[] = "coords1"; -static const char __pyx_k_coords2[] = "coords2"; -static const char __pyx_k_coords3[] = "coords3"; -static const char __pyx_k_coords4[] = "coords4"; -static const char __pyx_k_results[] = "results"; -static const char __pyx_k_numcoords[] = "numcoords"; -static const char __pyx_k_ortho_pbc[] = "ortho_pbc"; -static const char __pyx_k_calc_angle[] = "calc_angle"; -static const char __pyx_k_ImportError[] = "ImportError"; -static const char __pyx_k_calc_dihedral[] = "calc_dihedral"; -static const char __pyx_k_triclinic_pbc[] = "triclinic_pbc"; -static const char __pyx_k_OPENMP_ENABLED[] = "OPENMP_ENABLED"; -static const char __pyx_k_coord_transform[] = "coord_transform"; -static const char __pyx_k_calc_angle_ortho[] = "calc_angle_ortho"; -static const char __pyx_k_calc_bond_distance[] = "calc_bond_distance"; -static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; -static const char __pyx_k_calc_dihedral_ortho[] = "calc_dihedral_ortho"; -static const char __pyx_k_calc_distance_array[] = "calc_distance_array"; -static const char __pyx_k_calc_angle_triclinic[] = "calc_angle_triclinic"; -static const char __pyx_k_calc_dihedral_triclinic[] = "calc_dihedral_triclinic"; -static const char __pyx_k_calc_bond_distance_ortho[] = "calc_bond_distance_ortho"; -static const char __pyx_k_calc_self_distance_array[] = "calc_self_distance_array"; -static const char __pyx_k_calc_distance_array_ortho[] = "calc_distance_array_ortho"; -static const char __pyx_k_calc_bond_distance_triclinic[] = "calc_bond_distance_triclinic"; -static const char __pyx_k_calc_distance_array_triclinic[] = "calc_distance_array_triclinic"; -static const char __pyx_k_calc_self_distance_array_ortho[] = "calc_self_distance_array_ortho"; -static const char __pyx_k_Parallel_distance_calculation_l[] = "\nParallel distance calculation library --- :mod:`MDAnalysis.lib.c_distances_openmp`\n==================================================================================\n\n\nContains OpenMP versions of the contents of \"calc_distances.h\"\n"; -static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; -static const char __pyx_k_MDAnalysis_lib_c_distances_openm[] = "MDAnalysis\\lib\\c_distances_openmp.pyx"; -static const char __pyx_k_calc_self_distance_array_triclin[] = "calc_self_distance_array_triclinic"; -static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; -static const char __pyx_k_MDAnalysis_lib_c_distances_openm_2[] = "MDAnalysis.lib.c_distances_openmp"; -static PyObject *__pyx_n_s_ImportError; -static PyObject *__pyx_kp_s_MDAnalysis_lib_c_distances_openm; -static PyObject *__pyx_n_s_MDAnalysis_lib_c_distances_openm_2; -static PyObject *__pyx_n_s_OPENMP_ENABLED; -static PyObject *__pyx_n_s_box; -static PyObject *__pyx_n_s_calc_angle; -static PyObject *__pyx_n_s_calc_angle_ortho; -static PyObject *__pyx_n_s_calc_angle_triclinic; -static PyObject *__pyx_n_s_calc_bond_distance; -static PyObject *__pyx_n_s_calc_bond_distance_ortho; -static PyObject *__pyx_n_s_calc_bond_distance_triclinic; -static PyObject *__pyx_n_s_calc_dihedral; -static PyObject *__pyx_n_s_calc_dihedral_ortho; -static PyObject *__pyx_n_s_calc_dihedral_triclinic; -static PyObject *__pyx_n_s_calc_distance_array; -static PyObject *__pyx_n_s_calc_distance_array_ortho; -static PyObject *__pyx_n_s_calc_distance_array_triclinic; -static PyObject *__pyx_n_s_calc_self_distance_array; -static PyObject *__pyx_n_s_calc_self_distance_array_ortho; -static PyObject *__pyx_n_s_calc_self_distance_array_triclin; -static PyObject *__pyx_n_s_cline_in_traceback; -static PyObject *__pyx_n_s_conf; -static PyObject *__pyx_n_s_confnum; -static PyObject *__pyx_n_s_coord_transform; -static PyObject *__pyx_n_s_coords; -static PyObject *__pyx_n_s_coords1; -static PyObject *__pyx_n_s_coords2; -static PyObject *__pyx_n_s_coords3; -static PyObject *__pyx_n_s_coords4; -static PyObject *__pyx_n_s_import; -static PyObject *__pyx_n_s_main; -static PyObject *__pyx_n_s_name; -static PyObject *__pyx_n_s_numcoords; -static PyObject *__pyx_n_s_numpy; -static PyObject *__pyx_kp_u_numpy_core_multiarray_failed_to; -static PyObject *__pyx_kp_u_numpy_core_umath_failed_to_impor; -static PyObject *__pyx_n_s_ortho_pbc; -static PyObject *__pyx_n_s_ref; -static PyObject *__pyx_n_s_refnum; -static PyObject *__pyx_n_s_result; -static PyObject *__pyx_n_s_results; -static PyObject *__pyx_n_s_test; -static PyObject *__pyx_n_s_triclinic_pbc; -static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_calc_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_2calc_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_4calc_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_6calc_self_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_8calc_self_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_10calc_self_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_12coord_transform(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_14calc_bond_distance(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_16calc_bond_distance_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_18calc_bond_distance_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_18c_distances_openmp_20calc_angle(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_results); 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- goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* TypeImport */ -#ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* Import */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* PyDictVersioning */ -#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; -} -static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) { - PyObject **dictptr = NULL; - Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset; - if (offset) { -#if CYTHON_COMPILING_IN_CPYTHON - dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj); -#else - dictptr = _PyObject_GetDictPtr(obj); -#endif - } - return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; -} -static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) - return 0; - return obj_dict_version == __Pyx_get_object_dict_version(obj); -} -#endif - -/* CLineInTraceback */ -#ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ -#include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -/* Declarations */ -#if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ -#if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ -#if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ -#if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPyVerify */ -#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* CIntFromPy */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntFromPy */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* FastTypeChecks */ -#if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; 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#define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #undef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 0 - #undef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 0 - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 - #endif -#elif defined(PY_NOGIL) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 1 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #ifndef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 1 - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 1 - #endif - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 -#else - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 1 - #define CYTHON_COMPILING_IN_NOGIL 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #elif !defined(CYTHON_USE_PYTYPE_LOOKUP) - #define CYTHON_USE_PYTYPE_LOOKUP 1 - #endif - #if PY_MAJOR_VERSION < 3 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #elif !defined(CYTHON_USE_PYLONG_INTERNALS) - #define CYTHON_USE_PYLONG_INTERNALS 1 - #endif - #ifndef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 1 - #endif - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #elif !defined(CYTHON_USE_UNICODE_WRITER) - #define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #elif !defined(CYTHON_FAST_THREAD_STATE) - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000) - #endif - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000) - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) - #endif - #ifndef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1) - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #elif !defined(CYTHON_USE_EXC_INFO_STACK) - #define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3) - #endif - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 - #endif -#endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #if PY_MAJOR_VERSION < 3 - #include "longintrepr.h" - #endif - #undef SHIFT - #undef BASE - #undef MASK - #ifdef SIZEOF_VOID_P - enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) }; - #endif -#endif -#ifndef __has_attribute - #define __has_attribute(x) 0 -#endif -#ifndef __has_cpp_attribute - #define __has_cpp_attribute(x) 0 -#endif -#ifndef CYTHON_RESTRICT - #if defined(__GNUC__) - #define CYTHON_RESTRICT __restrict__ - #elif defined(_MSC_VER) && _MSC_VER >= 1400 - #define CYTHON_RESTRICT __restrict - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_RESTRICT restrict - #else - #define CYTHON_RESTRICT - #endif -#endif -#ifndef CYTHON_UNUSED -# if defined(__GNUC__) -# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -#endif -#ifndef CYTHON_MAYBE_UNUSED_VAR -# if defined(__cplusplus) - template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } -# else -# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) -# endif -#endif -#ifndef CYTHON_NCP_UNUSED -# if CYTHON_COMPILING_IN_CPYTHON -# define CYTHON_NCP_UNUSED -# else -# define CYTHON_NCP_UNUSED CYTHON_UNUSED -# endif -#endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) -#ifdef _MSC_VER - #ifndef _MSC_STDINT_H_ - #if _MSC_VER < 1300 - typedef unsigned char uint8_t; - typedef unsigned int uint32_t; - #else - typedef unsigned __int8 uint8_t; - typedef unsigned __int32 uint32_t; - #endif - #endif -#else - #include -#endif -#ifndef CYTHON_FALLTHROUGH - #if defined(__cplusplus) && __cplusplus >= 201103L - #if __has_cpp_attribute(fallthrough) - #define CYTHON_FALLTHROUGH [[fallthrough]] - #elif __has_cpp_attribute(clang::fallthrough) - #define CYTHON_FALLTHROUGH [[clang::fallthrough]] - #elif __has_cpp_attribute(gnu::fallthrough) - #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] - #endif - #endif - #ifndef CYTHON_FALLTHROUGH - #if __has_attribute(fallthrough) - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - #else - #define CYTHON_FALLTHROUGH - #endif - #endif - #if defined(__clang__ ) && defined(__apple_build_version__) - #if __apple_build_version__ < 7000000 - #undef CYTHON_FALLTHROUGH - #define CYTHON_FALLTHROUGH - #endif - #endif -#endif - -#ifndef CYTHON_INLINE - #if defined(__clang__) - #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) - #elif defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline - #else - #define CYTHON_INLINE - #endif -#endif - -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - if (type) { - PyErr_Restore(type, value, traceback); - } - return co; - } -#else - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_STACKLESS - #define METH_STACKLESS 0 -#endif -#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) - #ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - #endif - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); - typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast - #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1 - #define PyMem_RawMalloc(n) PyMem_Malloc(n) - #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) - #define PyMem_RawFree(p) PyMem_Free(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#elif PY_VERSION_HEX >= 0x03060000 - #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() -#elif PY_VERSION_HEX >= 0x03000000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#else - #define __Pyx_PyThreadState_Current _PyThreadState_Current -#endif -#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) -#include "pythread.h" -#define Py_tss_NEEDS_INIT 0 -typedef int Py_tss_t; -static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { - *key = PyThread_create_key(); - return 0; -} -static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { - Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); - *key = Py_tss_NEEDS_INIT; - return key; -} -static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { - PyObject_Free(key); -} -static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { - return *key != Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { - PyThread_delete_key(*key); - *key = Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { - return PyThread_set_key_value(*key, value); -} -static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { - return PyThread_get_key_value(*key); -} -#endif -#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) -#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) -#else -#define __Pyx_PyDict_NewPresized(n) PyDict_New() -#endif -#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION - #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) -#else - #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS -#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) -#else -#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_READY(op) (0) - #else - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #endif - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) - #else - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) - #endif - #endif -#else - #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 - #define __Pyx_PyUnicode_READY(op) (0) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) - #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) - #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) - #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) -#endif -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) -#else - #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ - PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) -#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? 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-value : value) -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); -#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) -#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) -#define __Pyx_PyBytes_FromString PyBytes_FromString -#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); -#if PY_MAJOR_VERSION < 3 - #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString - #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize -#else - #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString - #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize -#endif -#define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) -#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) -#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) -#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) -#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) -static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { - const Py_UNICODE *u_end = u; - while (*u_end++) ; - return (size_t)(u_end - u - 1); -} -#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) -#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode -#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode -#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) -#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*); -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); -#define __Pyx_PySequence_Tuple(obj)\ - (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj)) -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); -static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*); -#if CYTHON_ASSUME_SAFE_MACROS -#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) -#else -#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) -#endif -#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) -#else -#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) -#endif -#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII -static int __Pyx_sys_getdefaultencoding_not_ascii; -static int __Pyx_init_sys_getdefaultencoding_params(void) { - PyObject* sys; - PyObject* default_encoding = NULL; - PyObject* ascii_chars_u = NULL; - PyObject* ascii_chars_b = NULL; - const char* default_encoding_c; - sys = PyImport_ImportModule("sys"); - if (!sys) goto bad; - default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); - Py_DECREF(sys); - if (!default_encoding) goto bad; - default_encoding_c = PyBytes_AsString(default_encoding); - if (!default_encoding_c) goto bad; - if (strcmp(default_encoding_c, "ascii") == 0) { - __Pyx_sys_getdefaultencoding_not_ascii = 0; - } else { - char ascii_chars[128]; - int c; - for (c = 0; c < 128; c++) { - ascii_chars[c] = c; - } - __Pyx_sys_getdefaultencoding_not_ascii = 1; - ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); - if (!ascii_chars_u) goto bad; - ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); - if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { - PyErr_Format( - PyExc_ValueError, - "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", - default_encoding_c); - goto bad; - } - Py_DECREF(ascii_chars_u); - Py_DECREF(ascii_chars_b); - } - Py_DECREF(default_encoding); - return 0; -bad: - Py_XDECREF(default_encoding); - Py_XDECREF(ascii_chars_u); 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- -/* PyFunctionFastCall.proto */ -#if CYTHON_FAST_PYCALL -#define __Pyx_PyFunction_FastCall(func, args, nargs)\ - __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) -#if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs); -#else -#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs) -#endif -#define __Pyx_BUILD_ASSERT_EXPR(cond)\ - (sizeof(char [1 - 2*!(cond)]) - 1) -#ifndef Py_MEMBER_SIZE -#define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member) -#endif -#if CYTHON_FAST_PYCALL - static size_t __pyx_pyframe_localsplus_offset = 0; - #include "frameobject.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif - #define __Pxy_PyFrame_Initialize_Offsets()\ - ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\ - (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus))) - #define __Pyx_PyFrame_GetLocalsplus(frame)\ - (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset)) -#endif // CYTHON_FAST_PYCALL -#endif - -/* PyObjectCallMethO.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); -#endif - -/* PyObjectCallNoArg.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); -#else -#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) -#endif - -/* BufferIndexError.proto */ -static void __Pyx_RaiseBufferIndexError(int axis); - -/* PyDictVersioning.proto */ -#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS -#define __PYX_DICT_VERSION_INIT ((PY_UINT64_T) -1) -#define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) -#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)\ - (version_var) = __PYX_GET_DICT_VERSION(dict);\ - (cache_var) = (value); -#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) {\ - static PY_UINT64_T __pyx_dict_version = 0;\ - static PyObject *__pyx_dict_cached_value = NULL;\ - if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\ - (VAR) = __pyx_dict_cached_value;\ - } else {\ - (VAR) = __pyx_dict_cached_value = (LOOKUP);\ - __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\ - }\ -} -static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj); -static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj); -static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version); -#else -#define __PYX_GET_DICT_VERSION(dict) (0) -#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var) -#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) (VAR) = (LOOKUP); -#endif - -/* GetModuleGlobalName.proto */ -#if CYTHON_USE_DICT_VERSIONS -#define __Pyx_GetModuleGlobalName(var, name) do {\ - static PY_UINT64_T __pyx_dict_version = 0;\ - static PyObject *__pyx_dict_cached_value = NULL;\ - (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ - (likely(__pyx_dict_cached_value) ? __Pyx_NewRef(__pyx_dict_cached_value) : __Pyx_GetBuiltinName(name)) :\ - __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\ -} while(0) -#define __Pyx_GetModuleGlobalNameUncached(var, name) do {\ - PY_UINT64_T __pyx_dict_version;\ - PyObject *__pyx_dict_cached_value;\ - (var) = __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\ -} while(0) -static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value); -#else -#define __Pyx_GetModuleGlobalName(var, name) (var) = __Pyx__GetModuleGlobalName(name) -#define __Pyx_GetModuleGlobalNameUncached(var, name) (var) = __Pyx__GetModuleGlobalName(name) -static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name); -#endif - -/* ExtTypeTest.proto */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); - -/* GetTopmostException.proto */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate); -#endif - -/* SaveResetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -#else -#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) -#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) -#endif - -/* PyErrExceptionMatches.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) -static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); -#else -#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) -#endif - -/* GetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* RaiseArgTupleInvalid.proto */ -static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, - Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); - -/* RaiseDoubleKeywords.proto */ -static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); - -/* ParseKeywords.proto */ -static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ - PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ - const char* function_name); - -/* ArgTypeTest.proto */ -#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\ - ((likely((Py_TYPE(obj) == type) | (none_allowed && (obj == Py_None)))) ? 1 :\ - __Pyx__ArgTypeTest(obj, type, name, exact)) -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact); - -/* PyCFunctionFastCall.proto */ -#if CYTHON_FAST_PYCCALL -static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs); -#else -#define __Pyx_PyCFunction_FastCall(func, args, nargs) (assert(0), NULL) -#endif - -/* PyObjectCall2Args.proto */ -static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2); - -/* PyObjectCallOneArg.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); - -/* IncludeStringH.proto */ -#include - -/* BytesEquals.proto */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); - -/* UnicodeEquals.proto */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); - -/* StrEquals.proto */ -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals -#else -#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals -#endif - -/* DivInt[Py_ssize_t].proto */ -static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); - -/* UnaryNegOverflows.proto */ -#define UNARY_NEG_WOULD_OVERFLOW(x)\ - (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) - -static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *); /*proto*/ -/* GetAttr.proto */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); - -/* GetItemInt.proto */ -#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ - __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, - int is_list, int wraparound, int boundscheck); - -/* ObjectGetItem.proto */ -#if CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key); -#else -#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key) -#endif - -/* decode_c_string_utf16.proto */ -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = 0; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16LE(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = -1; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16BE(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = 1; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} - -/* decode_c_string.proto */ -static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); - -/* GetAttr3.proto */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); - -/* RaiseTooManyValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); - -/* RaiseNeedMoreValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); - -/* RaiseNoneIterError.proto */ -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); - -/* SwapException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* Import.proto */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); - -/* FastTypeChecks.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2); -#else -#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) -#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type) -#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2)) -#endif -#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) - -static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -/* ListCompAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len)) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) -#endif - -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); -#else -#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace, zerodivision_check)\ - (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) -#endif - -/* ListExtend.proto */ -static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { -#if CYTHON_COMPILING_IN_CPYTHON - PyObject* none = _PyList_Extend((PyListObject*)L, v); - if (unlikely(!none)) - return -1; - Py_DECREF(none); - return 0; -#else - return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); -#endif -} - -/* ListAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) -#endif - -/* None.proto */ -static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); - -/* DivInt[long].proto */ -static CYTHON_INLINE long __Pyx_div_long(long, long); - -/* PySequenceContains.proto */ -static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) { - int result = PySequence_Contains(seq, item); - return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); -} - -/* ImportFrom.proto */ -static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); - -/* HasAttr.proto */ -static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); - -/* PyObject_GenericGetAttrNoDict.proto */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); -#else -#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr -#endif - -/* PyObject_GenericGetAttr.proto */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name); -#else -#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr -#endif - -/* SetVTable.proto */ -static int __Pyx_SetVtable(PyObject *dict, void *vtable); - -/* PyObjectGetAttrStrNoError.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name); - -/* SetupReduce.proto */ -static int __Pyx_setup_reduce(PyObject* type_obj); - -/* TypeImport.proto */ -#ifndef __PYX_HAVE_RT_ImportType_proto -#define __PYX_HAVE_RT_ImportType_proto -enum __Pyx_ImportType_CheckSize { - __Pyx_ImportType_CheckSize_Error = 0, - __Pyx_ImportType_CheckSize_Warn = 1, - __Pyx_ImportType_CheckSize_Ignore = 2 -}; -static PyTypeObject *__Pyx_ImportType(PyObject* module, const char *module_name, const char *class_name, size_t size, enum __Pyx_ImportType_CheckSize check_size); -#endif - -/* CLineInTraceback.proto */ -#ifdef CYTHON_CLINE_IN_TRACEBACK -#define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) -#else -static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line); -#endif - -/* CodeObjectCache.proto */ -typedef struct { - PyCodeObject* code_object; - int code_line; -} __Pyx_CodeObjectCacheEntry; -struct __Pyx_CodeObjectCache { - int count; - int max_count; - __Pyx_CodeObjectCacheEntry* entries; -}; -static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); -static PyCodeObject *__pyx_find_code_object(int code_line); -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); - -/* AddTraceback.proto */ -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename); - -#if PY_MAJOR_VERSION < 3 - static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); - static void __Pyx_ReleaseBuffer(Py_buffer *view); -#else - #define __Pyx_GetBuffer PyObject_GetBuffer - #define __Pyx_ReleaseBuffer PyBuffer_Release -#endif - - -/* BufferStructDeclare.proto */ -typedef struct { - Py_ssize_t shape, strides, suboffsets; 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-static PyObject *__pyx_builtin_enumerate; -static PyObject *__pyx_builtin_range; -static PyObject *__pyx_builtin_Ellipsis; -static PyObject *__pyx_builtin_id; -static PyObject *__pyx_builtin_IndexError; -static const char __pyx_k_O[] = "O"; -static const char __pyx_k_c[] = "c"; -static const char __pyx_k_id[] = "id"; -static const char __pyx_k_np[] = "np"; -static const char __pyx_k_new[] = "__new__"; -static const char __pyx_k_obj[] = "obj"; -static const char __pyx_k_base[] = "base"; -static const char __pyx_k_copy[] = "copy"; -static const char __pyx_k_dict[] = "__dict__"; -static const char __pyx_k_main[] = "__main__"; -static const char __pyx_k_mode[] = "mode"; -static const char __pyx_k_name[] = "name"; -static const char __pyx_k_ndim[] = "ndim"; -static const char __pyx_k_pack[] = "pack"; -static const char __pyx_k_size[] = "size"; -static const char __pyx_k_step[] = "step"; -static const char __pyx_k_stop[] = "stop"; -static const char __pyx_k_test[] = "__test__"; -static const char __pyx_k_ASCII[] = "ASCII"; -static const char __pyx_k_array[] = "array"; -static const char __pyx_k_class[] = "__class__"; -static const char __pyx_k_error[] = "error"; -static const char __pyx_k_flags[] = "flags"; -static const char __pyx_k_numpy[] = "numpy"; -static const char __pyx_k_range[] = "range"; -static const char __pyx_k_shape[] = "shape"; -static const char __pyx_k_start[] = "start"; -static const char __pyx_k_encode[] = "encode"; -static const char __pyx_k_format[] = "format"; -static const char __pyx_k_import[] = "__import__"; -static const char __pyx_k_name_2[] = "__name__"; -static const char __pyx_k_pickle[] = "pickle"; -static const char __pyx_k_reduce[] = "__reduce__"; -static const char __pyx_k_struct[] = "struct"; -static const char __pyx_k_unpack[] = "unpack"; -static const char __pyx_k_update[] = "update"; -static const char __pyx_k_fortran[] = "fortran"; -static const char __pyx_k_memview[] = "memview"; -static const char __pyx_k_Ellipsis[] = "Ellipsis"; -static const char __pyx_k_getstate[] = "__getstate__"; -static const char __pyx_k_itemsize[] = "itemsize"; -static const char __pyx_k_pyx_type[] = "__pyx_type"; -static const char __pyx_k_setstate[] = "__setstate__"; -static const char __pyx_k_TypeError[] = "TypeError"; -static const char __pyx_k_enumerate[] = "enumerate"; -static const char __pyx_k_pyx_state[] = "__pyx_state"; -static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; -static const char __pyx_k_IndexError[] = "IndexError"; -static const char __pyx_k_ValueError[] = "ValueError"; -static const char __pyx_k_pyx_result[] = "__pyx_result"; -static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; -static const char __pyx_k_ImportError[] = "ImportError"; -static const char __pyx_k_MemoryError[] = "MemoryError"; -static const char __pyx_k_PickleError[] = "PickleError"; -static const char __pyx_k_ArrayWrapper[] = "ArrayWrapper"; -static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; -static const char __pyx_k_stringsource[] = "stringsource"; -static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; -static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; -static const char __pyx_k_View_MemoryView[] = "View.MemoryView"; -static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; -static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; -static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; -static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; -static const char __pyx_k_pyx_unpickle_Enum[] = "__pyx_unpickle_Enum"; -static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; -static const char __pyx_k_strided_and_direct[] = ""; -static const char __pyx_k_strided_and_indirect[] = ""; -static const char __pyx_k_contiguous_and_direct[] = ""; -static const char __pyx_k_MemoryView_of_r_object[] = ""; -static const char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; -static const char __pyx_k_contiguous_and_indirect[] = ""; -static const char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; -static const char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; -static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; -static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; -static const char __pyx_k_strided_and_direct_or_indirect[] = ""; -static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; -static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; -static const char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; -static const char __pyx_k_Cannot_assign_to_read_only_memor[] = "Cannot assign to read-only memoryview"; -static const char __pyx_k_Cannot_create_writable_memory_vi[] = "Cannot create writable memory view from read-only memoryview"; -static const char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; -static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0xb068931, 0x82a3537, 0x6ae9995) = (name))"; -static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; -static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; -static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; -static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; -static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; -static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; -static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; -static const char __pyx_k_self_data_ptr_self_dim_cannot_be[] = "self.data_ptr,self.dim cannot be converted to a Python object for pickling"; -static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; -static PyObject *__pyx_n_s_ASCII; -static PyObject *__pyx_n_s_ArrayWrapper; -static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; -static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; -static PyObject *__pyx_kp_s_Cannot_assign_to_read_only_memor; -static PyObject *__pyx_kp_s_Cannot_create_writable_memory_vi; -static PyObject *__pyx_kp_s_Cannot_index_with_type_s; -static PyObject *__pyx_n_s_Ellipsis; -static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; -static PyObject *__pyx_n_s_ImportError; -static PyObject *__pyx_kp_s_Incompatible_checksums_0x_x_vs_0; -static PyObject *__pyx_n_s_IndexError; -static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; -static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; -static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; -static PyObject *__pyx_n_s_MemoryError; -static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; -static PyObject *__pyx_kp_s_MemoryView_of_r_object; -static PyObject *__pyx_n_b_O; -static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; -static PyObject *__pyx_n_s_PickleError; -static PyObject *__pyx_n_s_TypeError; -static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; -static PyObject *__pyx_n_s_ValueError; -static PyObject *__pyx_n_s_View_MemoryView; -static PyObject *__pyx_n_s_allocate_buffer; -static PyObject *__pyx_n_s_array; -static PyObject *__pyx_n_s_base; -static PyObject *__pyx_n_s_c; -static PyObject *__pyx_n_u_c; -static PyObject *__pyx_n_s_class; -static PyObject *__pyx_n_s_cline_in_traceback; -static PyObject *__pyx_kp_s_contiguous_and_direct; -static PyObject *__pyx_kp_s_contiguous_and_indirect; -static PyObject *__pyx_n_s_copy; -static PyObject *__pyx_n_s_dict; -static PyObject *__pyx_n_s_dtype_is_object; -static PyObject *__pyx_n_s_encode; -static PyObject *__pyx_n_s_enumerate; -static PyObject *__pyx_n_s_error; -static PyObject *__pyx_n_s_flags; -static PyObject *__pyx_n_s_format; -static PyObject *__pyx_n_s_fortran; -static PyObject *__pyx_n_u_fortran; -static PyObject *__pyx_n_s_getstate; -static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; -static PyObject *__pyx_n_s_id; -static PyObject *__pyx_n_s_import; -static PyObject *__pyx_n_s_itemsize; -static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; -static PyObject *__pyx_n_s_main; -static PyObject *__pyx_n_s_memview; -static PyObject *__pyx_n_s_mode; -static PyObject *__pyx_n_s_name; -static PyObject *__pyx_n_s_name_2; -static PyObject *__pyx_n_s_ndim; -static PyObject *__pyx_n_s_new; -static PyObject *__pyx_kp_s_no_default___reduce___due_to_non; -static PyObject *__pyx_n_s_np; -static PyObject *__pyx_n_s_numpy; -static PyObject *__pyx_kp_u_numpy_core_multiarray_failed_to; -static PyObject *__pyx_kp_u_numpy_core_umath_failed_to_impor; -static PyObject *__pyx_n_s_obj; -static PyObject *__pyx_n_s_pack; -static PyObject *__pyx_n_s_pickle; -static PyObject *__pyx_n_s_pyx_PickleError; -static PyObject *__pyx_n_s_pyx_checksum; -static PyObject *__pyx_n_s_pyx_getbuffer; -static PyObject *__pyx_n_s_pyx_result; -static PyObject *__pyx_n_s_pyx_state; -static PyObject *__pyx_n_s_pyx_type; -static PyObject *__pyx_n_s_pyx_unpickle_Enum; -static PyObject *__pyx_n_s_pyx_vtable; -static PyObject *__pyx_n_s_range; -static PyObject *__pyx_n_s_reduce; -static PyObject *__pyx_n_s_reduce_cython; -static PyObject *__pyx_n_s_reduce_ex; -static PyObject *__pyx_kp_s_self_data_ptr_self_dim_cannot_be; -static PyObject *__pyx_n_s_setstate; -static PyObject *__pyx_n_s_setstate_cython; -static PyObject *__pyx_n_s_shape; -static PyObject *__pyx_n_s_size; -static PyObject *__pyx_n_s_start; -static PyObject *__pyx_n_s_step; -static PyObject *__pyx_n_s_stop; -static PyObject *__pyx_kp_s_strided_and_direct; -static PyObject *__pyx_kp_s_strided_and_direct_or_indirect; -static PyObject *__pyx_kp_s_strided_and_indirect; -static PyObject *__pyx_kp_s_stringsource; -static PyObject *__pyx_n_s_struct; -static PyObject *__pyx_n_s_test; -static PyObject *__pyx_kp_s_unable_to_allocate_array_data; -static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; -static PyObject *__pyx_n_s_unpack; -static PyObject *__pyx_n_s_update; -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_11cython_util_12ArrayWrapper___array__(struct __pyx_obj_10MDAnalysis_3lib_7formats_11cython_util_ArrayWrapper *__pyx_v_self); /* proto */ -static void __pyx_pf_10MDAnalysis_3lib_7formats_11cython_util_12ArrayWrapper_2__dealloc__(struct __pyx_obj_10MDAnalysis_3lib_7formats_11cython_util_ArrayWrapper *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_11cython_util_12ArrayWrapper_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_10MDAnalysis_3lib_7formats_11cython_util_ArrayWrapper *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_11cython_util_12ArrayWrapper_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_10MDAnalysis_3lib_7formats_11cython_util_ArrayWrapper *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__len__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_12__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ -static PyObject *__pyx_pf___pyx_array___reduce_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_array_2__setstate_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_MemviewEnum_2__setstate_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ -static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_memoryview___reduce_cython__(CYTHON_UNUSED struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_memoryview_2__setstate_cython__(CYTHON_UNUSED struct __pyx_memoryview_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static void __pyx_memoryviewslice___pyx_pf_15View_dot_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_memoryviewslice___reduce_cython__(CYTHON_UNUSED struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_memoryviewslice_2__setstate_cython__(CYTHON_UNUSED struct __pyx_memoryviewslice_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView___pyx_unpickle_Enum(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ -static PyObject *__pyx_tp_new_10MDAnalysis_3lib_7formats_11cython_util_ArrayWrapper(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k); 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- if (__pyx_t_2) { - - /* "View.MemoryView":845 - * if have_start: - * if start < 0: - * start += shape # <<<<<<<<<<<<<< - * if start < 0: - * start = 0 - */ - __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - - /* "View.MemoryView":846 - * if start < 0: - * start += shape - * if start < 0: # <<<<<<<<<<<<<< - * start = 0 - * elif start >= shape: - */ - __pyx_t_2 = ((__pyx_v_start < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":847 - * start += shape - * if start < 0: - * start = 0 # <<<<<<<<<<<<<< - * elif start >= shape: - * if negative_step: - */ - __pyx_v_start = 0; - - /* "View.MemoryView":846 - * if start < 0: - * start += shape - * if start < 0: # <<<<<<<<<<<<<< - * start = 0 - * elif start >= shape: - */ - } - - /* "View.MemoryView":844 - * - * if have_start: - * if start < 0: # <<<<<<<<<<<<<< - * start += shape - * if start < 0: - */ - goto __pyx_L12; - } - - /* "View.MemoryView":848 - * if start < 0: - * start = 0 - * elif start >= shape: # <<<<<<<<<<<<<< - * if negative_step: - * start = shape - 1 - */ - __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":849 - * start = 0 - * elif start >= shape: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":850 - * elif start >= shape: - * if negative_step: - * start = shape - 1 # <<<<<<<<<<<<<< - * else: - * start = shape - */ - __pyx_v_start = (__pyx_v_shape - 1); - - /* "View.MemoryView":849 - * start = 0 - * elif start >= shape: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - goto __pyx_L14; - } - - /* "View.MemoryView":852 - * start = shape - 1 - * else: - * start = shape # <<<<<<<<<<<<<< - * else: - * if negative_step: - */ - /*else*/ { - __pyx_v_start = __pyx_v_shape; - } - __pyx_L14:; - - /* "View.MemoryView":848 - * if start < 0: - * start = 0 - * elif start >= shape: # <<<<<<<<<<<<<< - * if negative_step: - * start = shape - 1 - */ - } - __pyx_L12:; - - /* "View.MemoryView":843 - * - * - * if have_start: # <<<<<<<<<<<<<< - * if start < 0: - * start += shape - */ - goto __pyx_L11; - } - - /* "View.MemoryView":854 - * start = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - /*else*/ { - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":855 - * else: - * if negative_step: - * start = shape - 1 # <<<<<<<<<<<<<< - * else: - * start = 0 - */ - __pyx_v_start = (__pyx_v_shape - 1); - - /* "View.MemoryView":854 - * start = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - goto __pyx_L15; - } - - /* "View.MemoryView":857 - * start = shape - 1 - * else: - * start = 0 # <<<<<<<<<<<<<< - * - * if have_stop: - */ - /*else*/ { - __pyx_v_start = 0; - } - __pyx_L15:; - } - __pyx_L11:; - - /* "View.MemoryView":859 - * start = 0 - * - * if have_stop: # <<<<<<<<<<<<<< - * if stop < 0: - * stop += shape - */ - __pyx_t_2 = (__pyx_v_have_stop != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":860 - * - * if have_stop: - * if stop < 0: # <<<<<<<<<<<<<< - * stop += shape - * if stop < 0: - */ - __pyx_t_2 = ((__pyx_v_stop < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":861 - * if have_stop: - * if stop < 0: - * stop += shape # <<<<<<<<<<<<<< - * if stop < 0: - * stop = 0 - */ - __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); - - /* "View.MemoryView":862 - * if stop < 0: - * stop += shape - * if stop < 0: # <<<<<<<<<<<<<< - * stop = 0 - * elif stop > shape: - */ - __pyx_t_2 = ((__pyx_v_stop < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":863 - * stop += shape - * if stop < 0: - * stop = 0 # <<<<<<<<<<<<<< - * elif stop > shape: - * stop = shape - */ - __pyx_v_stop = 0; - - /* "View.MemoryView":862 - * if stop < 0: - * stop += shape - * if stop < 0: # <<<<<<<<<<<<<< - * stop = 0 - * elif stop > shape: - */ - } - - /* "View.MemoryView":860 - * - * if have_stop: - * if stop < 0: # <<<<<<<<<<<<<< - * stop += shape - * if stop < 0: - */ - goto __pyx_L17; - } - - /* "View.MemoryView":864 - * if stop < 0: - * stop = 0 - * elif stop > shape: # <<<<<<<<<<<<<< - * stop = shape - * else: - */ - __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":865 - * stop = 0 - * elif stop > shape: - * stop = shape # <<<<<<<<<<<<<< - * else: - * if negative_step: - */ - __pyx_v_stop = __pyx_v_shape; - - /* "View.MemoryView":864 - * if stop < 0: - * stop = 0 - * elif stop > shape: # <<<<<<<<<<<<<< - * stop = shape - * else: - */ - } - __pyx_L17:; - - /* "View.MemoryView":859 - * start = 0 - * - * if have_stop: # <<<<<<<<<<<<<< - * if stop < 0: - * stop += shape - */ - goto __pyx_L16; - } - - /* "View.MemoryView":867 - * stop = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * stop = -1 - * else: - */ - /*else*/ { - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":868 - * else: - * if negative_step: - * stop = -1 # <<<<<<<<<<<<<< - * else: - * stop = shape - */ - __pyx_v_stop = -1L; - - /* "View.MemoryView":867 - * stop = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * stop = -1 - * else: - */ - goto __pyx_L19; - } - - /* "View.MemoryView":870 - * stop = -1 - * else: - * stop = shape # <<<<<<<<<<<<<< - * - * if not have_step: - */ - /*else*/ { - __pyx_v_stop = __pyx_v_shape; - } - __pyx_L19:; - } - __pyx_L16:; - - /* "View.MemoryView":872 - * stop = shape - * - * if not have_step: # <<<<<<<<<<<<<< - * step = 1 - * - */ - __pyx_t_2 = ((!(__pyx_v_have_step != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":873 - * - * if not have_step: - * step = 1 # <<<<<<<<<<<<<< - * - * - */ - __pyx_v_step = 1; - - /* "View.MemoryView":872 - * stop = shape - * - * if not have_step: # <<<<<<<<<<<<<< - * step = 1 - * - */ - } - - /* "View.MemoryView":877 - * - * with cython.cdivision(True): - * new_shape = (stop - start) // step # <<<<<<<<<<<<<< - * - * if (stop - start) - step * new_shape: - */ - __pyx_v_new_shape = ((__pyx_v_stop - __pyx_v_start) / __pyx_v_step); - - /* "View.MemoryView":879 - * new_shape = (stop - start) // step - * - * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< - * new_shape += 1 - * - */ - __pyx_t_2 = (((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":880 - * - * if (stop - start) - step * new_shape: - * new_shape += 1 # <<<<<<<<<<<<<< - * - * if new_shape < 0: - */ - __pyx_v_new_shape = (__pyx_v_new_shape + 1); - - /* "View.MemoryView":879 - * new_shape = (stop - start) // step - * - * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< - * new_shape += 1 - * - */ - } - - /* "View.MemoryView":882 - * new_shape += 1 - * - * if new_shape < 0: # <<<<<<<<<<<<<< - * new_shape = 0 - * - */ - __pyx_t_2 = ((__pyx_v_new_shape < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":883 - * - * if new_shape < 0: - * new_shape = 0 # <<<<<<<<<<<<<< - * - * - */ - __pyx_v_new_shape = 0; - - /* "View.MemoryView":882 - * new_shape += 1 - * - * if new_shape < 0: # <<<<<<<<<<<<<< - * new_shape = 0 - * - */ - } - - /* "View.MemoryView":886 - * - * - * dst.strides[new_ndim] = stride * step # <<<<<<<<<<<<<< - * dst.shape[new_ndim] = new_shape - * dst.suboffsets[new_ndim] = suboffset - */ - (__pyx_v_dst->strides[__pyx_v_new_ndim]) = (__pyx_v_stride * __pyx_v_step); - - /* "View.MemoryView":887 - * - * dst.strides[new_ndim] = stride * step - * dst.shape[new_ndim] = new_shape # <<<<<<<<<<<<<< - * dst.suboffsets[new_ndim] = suboffset - * - */ - (__pyx_v_dst->shape[__pyx_v_new_ndim]) = __pyx_v_new_shape; - - /* "View.MemoryView":888 - * dst.strides[new_ndim] = stride * step - * dst.shape[new_ndim] = new_shape - * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< - * - * - */ - (__pyx_v_dst->suboffsets[__pyx_v_new_ndim]) = __pyx_v_suboffset; - } - __pyx_L3:; - - /* "View.MemoryView":891 - * - * - * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< - * dst.data += start * stride - * else: - */ - __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":892 - * - * if suboffset_dim[0] < 0: - * dst.data += start * stride # <<<<<<<<<<<<<< - * else: - * dst.suboffsets[suboffset_dim[0]] += start * stride - */ - __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); - - /* "View.MemoryView":891 - * - * - * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< - * dst.data += start * stride - * else: - */ - goto __pyx_L23; - } - - /* "View.MemoryView":894 - * dst.data += start * stride - * else: - * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< - * - * if suboffset >= 0: - */ - /*else*/ { - __pyx_t_3 = (__pyx_v_suboffset_dim[0]); 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- if (__pyx_t_2) { - - /* "View.MemoryView":1128 - * for i in range(ndim - 1, -1, -1): - * if mslice.shape[i] > 1: - * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< - * break - * - */ - __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - - /* "View.MemoryView":1129 - * if mslice.shape[i] > 1: - * c_stride = mslice.strides[i] - * break # <<<<<<<<<<<<<< - * - * for i in range(ndim): - */ - goto __pyx_L4_break; - - /* "View.MemoryView":1127 - * - * for i in range(ndim - 1, -1, -1): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * c_stride = mslice.strides[i] - * break - */ - } - } - __pyx_L4_break:; - - /* "View.MemoryView":1131 - * break - * - * for i in range(ndim): # <<<<<<<<<<<<<< - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] - */ - __pyx_t_1 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_1; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { - __pyx_v_i = __pyx_t_4; - - /* "View.MemoryView":1132 - * - * for i in range(ndim): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * f_stride = mslice.strides[i] - * break - */ - __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1133 - * for i in range(ndim): - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< - * break - * - */ - __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - - /* "View.MemoryView":1134 - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] - * break # <<<<<<<<<<<<<< - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): - */ - goto __pyx_L7_break; - - /* "View.MemoryView":1132 - * - * for i in range(ndim): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * f_stride = mslice.strides[i] - * break - */ - } - } - __pyx_L7_break:; - - /* "View.MemoryView":1136 - * break - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< - * return 'C' - * else: - */ - __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1137 - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): - * return 'C' # <<<<<<<<<<<<<< - * else: - * return 'F' - */ - __pyx_r = 'C'; - goto __pyx_L0; - - /* "View.MemoryView":1136 - * break - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< - * return 'C' - * else: - */ - } - - /* "View.MemoryView":1139 - * return 'C' - * else: - * return 'F' # <<<<<<<<<<<<<< - * - * @cython.cdivision(True) - */ - /*else*/ { - __pyx_r = 'F'; - goto __pyx_L0; - } - - /* "View.MemoryView":1118 - * - * @cname('__pyx_get_best_slice_order') - * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< - * """ - * Figure out the best memory access order for a given slice. - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1142 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - -static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v_src_strides, char *__pyx_v_dst_data, Py_ssize_t *__pyx_v_dst_strides, Py_ssize_t *__pyx_v_src_shape, Py_ssize_t *__pyx_v_dst_shape, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - CYTHON_UNUSED Py_ssize_t __pyx_v_i; - CYTHON_UNUSED Py_ssize_t __pyx_v_src_extent; - Py_ssize_t __pyx_v_dst_extent; - Py_ssize_t __pyx_v_src_stride; - Py_ssize_t __pyx_v_dst_stride; - int __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - Py_ssize_t __pyx_t_4; - Py_ssize_t __pyx_t_5; - Py_ssize_t __pyx_t_6; - - /* "View.MemoryView":1149 - * - * cdef Py_ssize_t i - * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] - */ - __pyx_v_src_extent = (__pyx_v_src_shape[0]); - - /* "View.MemoryView":1150 - * cdef Py_ssize_t i - * cdef Py_ssize_t src_extent = src_shape[0] - * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t src_stride = src_strides[0] - * cdef Py_ssize_t dst_stride = dst_strides[0] - */ - __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); - - /* "View.MemoryView":1151 - * cdef Py_ssize_t src_extent = src_shape[0] - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - */ - __pyx_v_src_stride = (__pyx_v_src_strides[0]); - - /* "View.MemoryView":1152 - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] - * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< - * - * if ndim == 1: - */ - __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); - - /* "View.MemoryView":1154 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); - if (__pyx_t_2) { - } else { - __pyx_t_1 = __pyx_t_2; - goto __pyx_L5_bool_binop_done; - } - __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); - if (__pyx_t_2) { - } else { - __pyx_t_1 = __pyx_t_2; - goto __pyx_L5_bool_binop_done; - } - - /* "View.MemoryView":1156 - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< - * memcpy(dst_data, src_data, itemsize * dst_extent) - * else: - */ - __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); - if (__pyx_t_2) { - __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); - } - __pyx_t_3 = (__pyx_t_2 != 0); - __pyx_t_1 = __pyx_t_3; - __pyx_L5_bool_binop_done:; - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - if (__pyx_t_1) { - - /* "View.MemoryView":1157 - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent))); - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - goto __pyx_L4; - } - - /* "View.MemoryView":1159 - * memcpy(dst_data, src_data, itemsize * dst_extent) - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - __pyx_t_5 = __pyx_t_4; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1160 - * else: - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< - * src_data += src_stride - * dst_data += dst_stride - */ - (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); - - /* "View.MemoryView":1161 - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * else: - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1162 - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L4:; - - /* "View.MemoryView":1154 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1164 - * dst_data += dst_stride - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * _copy_strided_to_strided(src_data, src_strides + 1, - * dst_data, dst_strides + 1, - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - __pyx_t_5 = __pyx_t_4; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1165 - * else: - * for i in range(dst_extent): - * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< - * dst_data, dst_strides + 1, - * src_shape + 1, dst_shape + 1, - */ - _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - - /* "View.MemoryView":1169 - * src_shape + 1, dst_shape + 1, - * ndim - 1, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1170 - * ndim - 1, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L3:; - - /* "View.MemoryView":1142 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - - /* function exit code */ -} - -/* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - -static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - - /* "View.MemoryView":1175 - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< - * src.shape, dst.shape, ndim, itemsize) - * - */ - _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - - /* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - - /* function exit code */ -} - -/* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { - Py_ssize_t __pyx_v_shape; - Py_ssize_t __pyx_v_size; - Py_ssize_t __pyx_r; - Py_ssize_t __pyx_t_1; - Py_ssize_t *__pyx_t_2; - Py_ssize_t *__pyx_t_3; - Py_ssize_t *__pyx_t_4; - - /* "View.MemoryView":1181 - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize # <<<<<<<<<<<<<< - * - * for shape in src.shape[:ndim]: - */ - __pyx_t_1 = __pyx_v_src->memview->view.itemsize; - __pyx_v_size = __pyx_t_1; - - /* "View.MemoryView":1183 - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - * - * for shape in src.shape[:ndim]: # <<<<<<<<<<<<<< - * size *= shape - * - */ - __pyx_t_3 = (__pyx_v_src->shape + __pyx_v_ndim); - for (__pyx_t_4 = __pyx_v_src->shape; __pyx_t_4 < __pyx_t_3; __pyx_t_4++) { - __pyx_t_2 = __pyx_t_4; - __pyx_v_shape = (__pyx_t_2[0]); - - /* "View.MemoryView":1184 - * - * for shape in src.shape[:ndim]: - * size *= shape # <<<<<<<<<<<<<< - * - * return size - */ - __pyx_v_size = (__pyx_v_size * __pyx_v_shape); - } - - /* "View.MemoryView":1186 - * size *= shape - * - * return size # <<<<<<<<<<<<<< - * - * @cname('__pyx_fill_contig_strides_array') - */ - __pyx_r = __pyx_v_size; - goto __pyx_L0; - - /* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1189 - * - * @cname('__pyx_fill_contig_strides_array') - * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< - * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, - * int ndim, char order) nogil: - */ - -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { - int __pyx_v_idx; - Py_ssize_t __pyx_r; - int __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - int __pyx_t_4; - - /* "View.MemoryView":1198 - * cdef int idx - * - * if order == 'F': # <<<<<<<<<<<<<< - * for idx in range(ndim): - * strides[idx] = stride - */ - __pyx_t_1 = ((__pyx_v_order == 'F') != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1199 - * - * if order == 'F': - * for idx in range(ndim): # <<<<<<<<<<<<<< - * strides[idx] = stride - * stride *= shape[idx] - */ - __pyx_t_2 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_2; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; 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- __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } else if (unlikely(PyErr_Occurred())) { - return NULL; - } -#else - result = PyDict_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } -#endif -#else - result = PyObject_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } - PyErr_Clear(); -#endif - return __Pyx_GetBuiltinName(name); -} - -/* ExtTypeTest */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(__Pyx_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* GetTopmostException */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* PyErrExceptionMatches */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* GetException */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* RaiseArgTupleInvalid */ -static void __Pyx_RaiseArgtupleInvalid( - const char* func_name, - int exact, - Py_ssize_t num_min, - Py_ssize_t num_max, - Py_ssize_t num_found) -{ - Py_ssize_t num_expected; - const char *more_or_less; - if (num_found < num_min) { - num_expected = num_min; - more_or_less = "at least"; - } else { - num_expected = num_max; - more_or_less = "at most"; - } - if (exact) { - more_or_less = "exactly"; - } - PyErr_Format(PyExc_TypeError, - "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", - func_name, more_or_less, num_expected, - (num_expected == 1) ? "" : "s", num_found); -} - -/* RaiseDoubleKeywords */ -static void __Pyx_RaiseDoubleKeywordsError( - const char* func_name, - PyObject* kw_name) -{ - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION >= 3 - "%s() got multiple values for keyword argument '%U'", func_name, kw_name); - #else - "%s() got multiple values for keyword argument '%s'", func_name, - PyString_AsString(kw_name)); - #endif -} - -/* ParseKeywords */ -static int __Pyx_ParseOptionalKeywords( - PyObject *kwds, - PyObject **argnames[], - PyObject *kwds2, - PyObject *values[], - Py_ssize_t num_pos_args, - const char* function_name) -{ - PyObject *key = 0, *value = 0; - Py_ssize_t pos = 0; - PyObject*** name; - PyObject*** first_kw_arg = argnames + num_pos_args; - while (PyDict_Next(kwds, &pos, &key, &value)) { - name = first_kw_arg; - while (*name && (**name != key)) name++; - if (*name) { - values[name-argnames] = value; - continue; - } - name = first_kw_arg; - #if PY_MAJOR_VERSION < 3 - if (likely(PyString_Check(key))) { - while (*name) { - if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) - && _PyString_Eq(**name, key)) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - if ((**argname == key) || ( - (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) - && _PyString_Eq(**argname, key))) { - goto arg_passed_twice; - } - argname++; - } - } - } else - #endif - if (likely(PyUnicode_Check(key))) { - while (*name) { - int cmp = (**name == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**name, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - int cmp = (**argname == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**argname, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) goto arg_passed_twice; - argname++; - } - } - } else - goto invalid_keyword_type; - if (kwds2) { - if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; - } else { - goto invalid_keyword; - } - } - return 0; -arg_passed_twice: - __Pyx_RaiseDoubleKeywordsError(function_name, key); - goto bad; -invalid_keyword_type: - PyErr_Format(PyExc_TypeError, - "%.200s() keywords must be strings", function_name); - goto bad; -invalid_keyword: - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION < 3 - "%.200s() got an unexpected keyword argument '%.200s'", - function_name, PyString_AsString(key)); - #else - "%s() got an unexpected keyword argument '%U'", - function_name, key); - #endif -bad: - return -1; -} - -/* ArgTypeTest */ -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) -{ - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - else if (exact) { - #if PY_MAJOR_VERSION == 2 - if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; - #endif - } - else { - if (likely(__Pyx_TypeCheck(obj, type))) return 1; - } - PyErr_Format(PyExc_TypeError, - "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", - name, type->tp_name, Py_TYPE(obj)->tp_name); - return 0; -} - -/* PyCFunctionFastCall */ -#if CYTHON_FAST_PYCCALL -static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) { - PyCFunctionObject *func = (PyCFunctionObject*)func_obj; - PyCFunction meth = PyCFunction_GET_FUNCTION(func); - PyObject *self = PyCFunction_GET_SELF(func); - int flags = PyCFunction_GET_FLAGS(func); - assert(PyCFunction_Check(func)); - assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))); - assert(nargs >= 0); - assert(nargs == 0 || args != NULL); - /* _PyCFunction_FastCallDict() must not be called with an exception set, - because it may clear it (directly or indirectly) and so the - caller loses its exception */ - assert(!PyErr_Occurred()); - if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) { - return (*((__Pyx_PyCFunctionFastWithKeywords)(void*)meth)) (self, args, nargs, NULL); - } else { - return (*((__Pyx_PyCFunctionFast)(void*)meth)) (self, args, nargs); - } -} -#endif - -/* PyObjectCall2Args */ -static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { - PyObject *args, *result = NULL; - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyFunction_FastCall(function, args, 2); - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyCFunction_FastCall(function, args, 2); - } - #endif - args = PyTuple_New(2); - if (unlikely(!args)) goto done; - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 0, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 1, arg2); - Py_INCREF(function); - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); -done: - return result; -} - -/* PyObjectCallOneArg */ -#if CYTHON_COMPILING_IN_CPYTHON -static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_New(1); - if (unlikely(!args)) return NULL; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif - if (likely(PyCFunction_Check(func))) { - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (__Pyx_PyFastCFunction_Check(func)) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } - } - return __Pyx__PyObject_CallOneArg(func, arg); -} -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -#endif - -/* BytesEquals */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { - const char *ps1, *ps2; - Py_ssize_t length = PyBytes_GET_SIZE(s1); - if (length != PyBytes_GET_SIZE(s2)) - return (equals == Py_NE); - ps1 = PyBytes_AS_STRING(s1); - ps2 = PyBytes_AS_STRING(s2); - if (ps1[0] != ps2[0]) { - return (equals == Py_NE); - } else if (length == 1) { - return (equals == Py_EQ); - } else { - int result; -#if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000) - Py_hash_t hash1, hash2; - hash1 = ((PyBytesObject*)s1)->ob_shash; - hash2 = ((PyBytesObject*)s2)->ob_shash; - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - return (equals == Py_NE); - } -#endif - result = memcmp(ps1, ps2, (size_t)length); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -#endif -} - -/* UnicodeEquals */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else -#if PY_MAJOR_VERSION < 3 - PyObject* owned_ref = NULL; -#endif - int s1_is_unicode, s2_is_unicode; - if (s1 == s2) { - goto return_eq; - } - s1_is_unicode = PyUnicode_CheckExact(s1); - s2_is_unicode = PyUnicode_CheckExact(s2); -#if PY_MAJOR_VERSION < 3 - if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { - owned_ref = PyUnicode_FromObject(s2); - if (unlikely(!owned_ref)) - return -1; - s2 = owned_ref; - s2_is_unicode = 1; - } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { - owned_ref = PyUnicode_FromObject(s1); - if (unlikely(!owned_ref)) - return -1; - s1 = owned_ref; - s1_is_unicode = 1; - } else if (((!s2_is_unicode) & (!s1_is_unicode))) { - return __Pyx_PyBytes_Equals(s1, s2, equals); - } -#endif - if (s1_is_unicode & s2_is_unicode) { - Py_ssize_t length; - int kind; - void *data1, *data2; - if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) - return -1; - length = __Pyx_PyUnicode_GET_LENGTH(s1); - if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { - goto return_ne; - } -#if CYTHON_USE_UNICODE_INTERNALS - { - Py_hash_t hash1, hash2; - #if CYTHON_PEP393_ENABLED - hash1 = ((PyASCIIObject*)s1)->hash; - hash2 = ((PyASCIIObject*)s2)->hash; - #else - hash1 = ((PyUnicodeObject*)s1)->hash; - hash2 = ((PyUnicodeObject*)s2)->hash; - #endif - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - goto return_ne; - } - } -#endif - kind = __Pyx_PyUnicode_KIND(s1); - if (kind != __Pyx_PyUnicode_KIND(s2)) { - goto return_ne; - } - data1 = __Pyx_PyUnicode_DATA(s1); - data2 = __Pyx_PyUnicode_DATA(s2); - if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { - goto return_ne; - } else if (length == 1) { - goto return_eq; - } else { - int result = memcmp(data1, data2, (size_t)(length * kind)); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & s2_is_unicode) { - goto return_ne; - } else if ((s2 == Py_None) & s1_is_unicode) { - goto return_ne; - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -return_eq: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ); -return_ne: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_NE); -#endif -} - -/* DivInt[Py_ssize_t] */ -static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { - Py_ssize_t q = a / b; - Py_ssize_t r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* GetAttr */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { -#if CYTHON_USE_TYPE_SLOTS -#if PY_MAJOR_VERSION >= 3 - if (likely(PyUnicode_Check(n))) -#else - if (likely(PyString_Check(n))) -#endif - return __Pyx_PyObject_GetAttrStr(o, n); -#endif - return PyObject_GetAttr(o, n); -} - -/* GetItemInt */ -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { - PyObject *r; - if (!j) return NULL; - r = PyObject_GetItem(o, j); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyList_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyTuple_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } - else if (PyTuple_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } else { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_item)) { - if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { - Py_ssize_t l = m->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return NULL; - PyErr_Clear(); - } - } - return m->sq_item(o, i); - } - } -#else - if (is_list || PySequence_Check(o)) { - return PySequence_GetItem(o, i); - } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -} - -/* ObjectGetItem */ -#if CYTHON_USE_TYPE_SLOTS -static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { - PyObject *runerr = NULL; - Py_ssize_t key_value; - PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; - if (unlikely(!(m && m->sq_item))) { - PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); - return NULL; - } - key_value = __Pyx_PyIndex_AsSsize_t(index); - if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { - return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); - } - if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { - PyErr_Clear(); - PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); - } - return NULL; -} -static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { - PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; - if (likely(m && m->mp_subscript)) { - return m->mp_subscript(obj, key); - } - return __Pyx_PyObject_GetIndex(obj, key); -} -#endif - -/* decode_c_string */ -static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { - Py_ssize_t length; - if (unlikely((start < 0) | (stop < 0))) { - size_t slen = strlen(cstring); - if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { - PyErr_SetString(PyExc_OverflowError, - "c-string too long to convert to Python"); - return NULL; - } - length = (Py_ssize_t) slen; - if (start < 0) { - start += length; - if (start < 0) - start = 0; - } - if (stop < 0) - stop += length; - } - if (unlikely(stop <= start)) - return __Pyx_NewRef(__pyx_empty_unicode); - length = stop - start; - cstring += start; - if (decode_func) { - return decode_func(cstring, length, errors); - } else { - return PyUnicode_Decode(cstring, length, encoding, errors); - } -} - -/* GetAttr3 */ -static PyObject *__Pyx_GetAttr3Default(PyObject *d) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - return NULL; - __Pyx_PyErr_Clear(); - Py_INCREF(d); - return d; -} -static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { - PyObject *r = __Pyx_GetAttr(o, n); - return (likely(r)) ? r : __Pyx_GetAttr3Default(d); -} - -/* RaiseTooManyValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -/* RaiseNeedMoreValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -/* RaiseNoneIterError */ -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); -} - -/* SwapException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = *type; - exc_info->exc_value = *value; - exc_info->exc_traceback = *tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = *type; - tstate->exc_value = *value; - tstate->exc_traceback = *tb; - #endif - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); - PyErr_SetExcInfo(*type, *value, *tb); - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#endif - -/* Import */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* FastTypeChecks */ -#if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; - if (a == b) - return 1; - } - return b == &PyBaseObject_Type; -} -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { - PyObject *mro; - if (a == b) return 1; - mro = a->tp_mro; - if (likely(mro)) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(mro); - for (i = 0; i < n; i++) { - if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) - return 1; - } - return 0; - } - return __Pyx_InBases(a, b); -} -#if PY_MAJOR_VERSION == 2 -static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { - PyObject *exception, *value, *tb; - int res; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&exception, &value, &tb); - res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - if (!res) { - res = PyObject_IsSubclass(err, exc_type2); - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - } - __Pyx_ErrRestore(exception, value, tb); - return res; -} -#else -static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { - int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; - if (!res) { - res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); - } - return res; -} -#endif -static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - assert(PyExceptionClass_Check(exc_type)); - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; i= 0 || (x^b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - default: return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - } - x = a + b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla + llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("add", return NULL) - result = ((double)a) + (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); -} -#endif - -/* None */ -static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { - PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); -} - -/* DivInt[long] */ -static CYTHON_INLINE long __Pyx_div_long(long a, long b) { - long q = a / b; - long r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* ImportFrom */ -static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { - PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); - if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_Format(PyExc_ImportError, - #if PY_MAJOR_VERSION < 3 - "cannot import name %.230s", PyString_AS_STRING(name)); - #else - "cannot import name %S", name); - #endif - } - return value; -} - -/* HasAttr */ -static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { - PyObject *r; - if (unlikely(!__Pyx_PyBaseString_Check(n))) { - PyErr_SetString(PyExc_TypeError, - "hasattr(): attribute name must be string"); - return -1; - } - r = __Pyx_GetAttr(o, n); - if (unlikely(!r)) { - PyErr_Clear(); - return 0; - } else { - Py_DECREF(r); - return 1; - } -} - -/* PyObject_GenericGetAttrNoDict */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { - PyErr_Format(PyExc_AttributeError, -#if PY_MAJOR_VERSION >= 3 - "'%.50s' object has no attribute '%U'", - tp->tp_name, attr_name); -#else - "'%.50s' object has no attribute '%.400s'", - tp->tp_name, PyString_AS_STRING(attr_name)); -#endif - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { - PyObject *descr; - PyTypeObject *tp = Py_TYPE(obj); - if (unlikely(!PyString_Check(attr_name))) { - return PyObject_GenericGetAttr(obj, attr_name); - } - assert(!tp->tp_dictoffset); - descr = _PyType_Lookup(tp, attr_name); - if (unlikely(!descr)) { - return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); - } - Py_INCREF(descr); - #if PY_MAJOR_VERSION < 3 - if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) - #endif - { - descrgetfunc f = Py_TYPE(descr)->tp_descr_get; - if (unlikely(f)) { - PyObject *res = f(descr, obj, (PyObject *)tp); - Py_DECREF(descr); - return res; - } - } - return descr; -} -#endif - -/* PyObject_GenericGetAttr */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { - if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { - return PyObject_GenericGetAttr(obj, attr_name); - } - return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); -} -#endif - -/* SetVTable */ -static int __Pyx_SetVtable(PyObject *dict, void *vtable) { -#if PY_VERSION_HEX >= 0x02070000 - PyObject *ob = PyCapsule_New(vtable, 0, 0); -#else - PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); -#endif - if (!ob) - goto bad; - if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) - goto bad; - Py_DECREF(ob); - return 0; -bad: - Py_XDECREF(ob); - return -1; -} - -/* PyObjectGetAttrStrNoError */ -static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - __Pyx_PyErr_Clear(); -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { - PyObject *result; -#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 - PyTypeObject* tp = Py_TYPE(obj); - if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { - return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); - } -#endif - result = __Pyx_PyObject_GetAttrStr(obj, attr_name); - if (unlikely(!result)) { - __Pyx_PyObject_GetAttrStr_ClearAttributeError(); - } - return result; -} - -/* SetupReduce */ -static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { - int ret; - PyObject *name_attr; - name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2); - if (likely(name_attr)) { - ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); - } else { - ret = -1; - } - if (unlikely(ret < 0)) { - PyErr_Clear(); - ret = 0; - } - Py_XDECREF(name_attr); - return ret; -} -static int __Pyx_setup_reduce(PyObject* type_obj) { - int ret = 0; - PyObject *object_reduce = NULL; - PyObject *object_getstate = NULL; - PyObject *object_reduce_ex = NULL; - PyObject *reduce = NULL; - PyObject *reduce_ex = NULL; - PyObject *reduce_cython = NULL; - PyObject *setstate = NULL; - PyObject *setstate_cython = NULL; - PyObject *getstate = NULL; -#if CYTHON_USE_PYTYPE_LOOKUP - getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate); -#else - getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate); - if (!getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (getstate) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate); -#else - object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate); - if (!object_getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (object_getstate != getstate) { - goto __PYX_GOOD; - } - } -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; - if (reduce_ex == object_reduce_ex) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; - if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); - if (likely(reduce_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (reduce == object_reduce || PyErr_Occurred()) { - goto __PYX_BAD; - } - setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); - if (!setstate) PyErr_Clear(); - if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); - if (likely(setstate_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (!setstate || PyErr_Occurred()) { - goto __PYX_BAD; - } - } - PyType_Modified((PyTypeObject*)type_obj); - } - } - goto __PYX_GOOD; -__PYX_BAD: - if (!PyErr_Occurred()) - PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); - ret = -1; -__PYX_GOOD: -#if !CYTHON_USE_PYTYPE_LOOKUP - Py_XDECREF(object_reduce); - Py_XDECREF(object_reduce_ex); - Py_XDECREF(object_getstate); - Py_XDECREF(getstate); -#endif - Py_XDECREF(reduce); - Py_XDECREF(reduce_ex); - Py_XDECREF(reduce_cython); - Py_XDECREF(setstate); - Py_XDECREF(setstate_cython); - return ret; -} - -/* TypeImport */ -#ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* CLineInTraceback */ -#ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ -#include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - if ((0)) {} - view->obj = NULL; - Py_DECREF(obj); -} -#endif - - -/* MemviewSliceIsContig */ -static int -__pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim) -{ - int i, index, step, start; - Py_ssize_t itemsize = mvs.memview->view.itemsize; - if (order == 'F') { - step = 1; - start = 0; - } else { - step = -1; - start = ndim - 1; - } - for (i = 0; i < ndim; i++) { - index = start + step * i; - if (mvs.suboffsets[index] >= 0 || mvs.strides[index] != itemsize) - return 0; - itemsize *= mvs.shape[index]; - } - return 1; -} - -/* OverlappingSlices */ -static void -__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, - void **out_start, void **out_end, - int ndim, size_t itemsize) -{ - char *start, *end; - int i; - start = end = slice->data; - for (i = 0; i < ndim; i++) { - Py_ssize_t stride = slice->strides[i]; - Py_ssize_t extent = slice->shape[i]; - if (extent == 0) { - *out_start = *out_end = start; - return; - } else { - if (stride > 0) - end += stride * (extent - 1); - else - start += stride * (extent - 1); - } - } - *out_start = start; - *out_end = end + itemsize; -} -static int -__pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize) -{ - void *start1, *end1, *start2, *end2; - __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); - __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); - return (start1 < end2) && (start2 < end1); -} - -/* Capsule */ -static CYTHON_INLINE PyObject * -__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) -{ - PyObject *cobj; -#if PY_VERSION_HEX >= 0x02070000 - cobj = PyCapsule_New(p, sig, NULL); -#else - cobj = PyCObject_FromVoidPtr(p, NULL); -#endif - return cobj; -} - -/* CIntFromPyVerify */ -#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* MemviewDtypeToObject */ -static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_5numpy_int64_t(const char *itemp) { - return (PyObject *) __Pyx_PyInt_From_npy_int64(*(__pyx_t_5numpy_int64_t *) itemp); -} -static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_int64_t(const char *itemp, PyObject *obj) { - __pyx_t_5numpy_int64_t value = __Pyx_PyInt_As_npy_int64(obj); - if ((value == ((npy_int64)-1)) && PyErr_Occurred()) - return 0; - *(__pyx_t_5numpy_int64_t *) itemp = value; - return 1; -} - -/* Declarations */ -#if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ -#if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ -#if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ -#if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* MemviewSliceCopyTemplate */ -static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object) -{ - __Pyx_RefNannyDeclarations - int i; - __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; - struct __pyx_memoryview_obj *from_memview = from_mvs->memview; - Py_buffer *buf = &from_memview->view; - PyObject *shape_tuple = NULL; - PyObject *temp_int = NULL; - struct __pyx_array_obj *array_obj = NULL; - struct __pyx_memoryview_obj *memview_obj = NULL; - __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); - for (i = 0; i < ndim; i++) { - if (unlikely(from_mvs->suboffsets[i] >= 0)) { - PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " - "indirect dimensions (axis %d)", i); - goto fail; - } - } - shape_tuple = PyTuple_New(ndim); - if (unlikely(!shape_tuple)) { - goto fail; - } - __Pyx_GOTREF(shape_tuple); - for(i = 0; i < ndim; i++) { - temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); - if(unlikely(!temp_int)) { - goto fail; - } else { - PyTuple_SET_ITEM(shape_tuple, i, temp_int); - temp_int = NULL; - } - } - array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); - if (unlikely(!array_obj)) { - goto fail; - } - __Pyx_GOTREF(array_obj); - memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - (PyObject *) array_obj, contig_flag, - dtype_is_object, - from_mvs->memview->typeinfo); - if (unlikely(!memview_obj)) - goto fail; - if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) - goto fail; - if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, - dtype_is_object) < 0)) - goto fail; - goto no_fail; -fail: - __Pyx_XDECREF(new_mvs.memview); - new_mvs.memview = NULL; - new_mvs.data = NULL; -no_fail: - __Pyx_XDECREF(shape_tuple); - __Pyx_XDECREF(temp_int); - __Pyx_XDECREF(array_obj); - __Pyx_RefNannyFinishContext(); - return new_mvs; -} - -/* MemviewSliceInit */ -static int -__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference) -{ - __Pyx_RefNannyDeclarations - int i, retval=-1; - Py_buffer *buf = &memview->view; - __Pyx_RefNannySetupContext("init_memviewslice", 0); - if (unlikely(memviewslice->memview || memviewslice->data)) { - PyErr_SetString(PyExc_ValueError, - "memviewslice is already initialized!"); - goto fail; - } - if (buf->strides) { - for (i = 0; i < ndim; i++) { - memviewslice->strides[i] = buf->strides[i]; - } - } else { - Py_ssize_t stride = buf->itemsize; - for (i = ndim - 1; i >= 0; i--) { - memviewslice->strides[i] = stride; - stride *= buf->shape[i]; - } - } - for (i = 0; i < ndim; i++) { - memviewslice->shape[i] = buf->shape[i]; - if (buf->suboffsets) { - memviewslice->suboffsets[i] = buf->suboffsets[i]; - } else { - memviewslice->suboffsets[i] = -1; - } - } - memviewslice->memview = memview; - memviewslice->data = (char *)buf->buf; - if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { - Py_INCREF(memview); - } - retval = 0; - goto no_fail; -fail: - memviewslice->memview = 0; - memviewslice->data = 0; - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} -#ifndef Py_NO_RETURN -#define Py_NO_RETURN -#endif -static void __pyx_fatalerror(const char *fmt, ...) Py_NO_RETURN { - va_list vargs; - char msg[200]; -#if PY_VERSION_HEX >= 0x030A0000 || defined(HAVE_STDARG_PROTOTYPES) - va_start(vargs, fmt); -#else - va_start(vargs); -#endif - vsnprintf(msg, 200, fmt, vargs); - va_end(vargs); - Py_FatalError(msg); -} -static CYTHON_INLINE int -__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)++; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE int -__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)--; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE void -__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) -{ - int first_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) - return; - if (unlikely(__pyx_get_slice_count(memview) < 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - first_time = __pyx_add_acquisition_count(memview) == 0; - if (unlikely(first_time)) { - if (have_gil) { - Py_INCREF((PyObject *) memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_INCREF((PyObject *) memview); - PyGILState_Release(_gilstate); - } - } -} -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, - int have_gil, int lineno) { - int last_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) { - memslice->memview = NULL; - return; - } - if (unlikely(__pyx_get_slice_count(memview) <= 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - last_time = __pyx_sub_acquisition_count(memview) == 1; - memslice->data = NULL; - if (unlikely(last_time)) { - if (have_gil) { - Py_CLEAR(memslice->memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_CLEAR(memslice->memview); - PyGILState_Release(_gilstate); - } - } else { - memslice->memview = NULL; - } -} - -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_int64(npy_int64 value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const npy_int64 neg_one = (npy_int64) -1, const_zero = (npy_int64) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(npy_int64) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(npy_int64) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(npy_int64) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(npy_int64) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(npy_int64) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(npy_int64), - little, !is_unsigned); - } -} - -/* CIntFromPy */ -static CYTHON_INLINE npy_int64 __Pyx_PyInt_As_npy_int64(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const npy_int64 neg_one = (npy_int64) -1, const_zero = (npy_int64) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(npy_int64) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(npy_int64, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (npy_int64) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (npy_int64) 0; - case 1: __PYX_VERIFY_RETURN_INT(npy_int64, digit, digits[0]) - case 2: - if (8 * sizeof(npy_int64) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(npy_int64) >= 2 * PyLong_SHIFT) { - return (npy_int64) (((((npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(npy_int64) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(npy_int64) >= 3 * PyLong_SHIFT) { - return (npy_int64) (((((((npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(npy_int64) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(npy_int64) >= 4 * PyLong_SHIFT) { - return (npy_int64) (((((((((npy_int64)digits[3]) << PyLong_SHIFT) | (npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (npy_int64) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(npy_int64) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(npy_int64, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(npy_int64) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(npy_int64, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (npy_int64) 0; - case -1: __PYX_VERIFY_RETURN_INT(npy_int64, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(npy_int64, digit, +digits[0]) - case -2: - if (8 * sizeof(npy_int64) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { - return (npy_int64) (((npy_int64)-1)*(((((npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(npy_int64) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { - return (npy_int64) ((((((npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { - return (npy_int64) (((npy_int64)-1)*(((((((npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(npy_int64) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { - return (npy_int64) ((((((((npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(npy_int64) - 1 > 4 * PyLong_SHIFT) { - return (npy_int64) (((npy_int64)-1)*(((((((((npy_int64)digits[3]) << PyLong_SHIFT) | (npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(npy_int64) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(npy_int64) - 1 > 4 * PyLong_SHIFT) { - return (npy_int64) ((((((((((npy_int64)digits[3]) << PyLong_SHIFT) | (npy_int64)digits[2]) << PyLong_SHIFT) | (npy_int64)digits[1]) << PyLong_SHIFT) | (npy_int64)digits[0]))); - } - } - break; - } -#endif - if (sizeof(npy_int64) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(npy_int64, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(npy_int64) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(npy_int64, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - npy_int64 val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (npy_int64) -1; - } - } else { - npy_int64 val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (npy_int64) -1; - val = __Pyx_PyInt_As_npy_int64(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to npy_int64"); - return (npy_int64) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to npy_int64"); - return (npy_int64) -1; -} - -/* CIntFromPy */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntFromPy */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPy */ -static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const char neg_one = (char) -1, const_zero = (char) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(char) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (char) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (char) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(char) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) - case -2: - if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - } -#endif - if (sizeof(char) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - char val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (char) -1; - } - } else { - char val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (char) -1; - val = __Pyx_PyInt_As_char(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to char"); - return (char) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to char"); - return (char) -1; -} - -/* CheckBinaryVersion */ -static int __Pyx_check_binary_version(void) { - char ctversion[5]; - int same=1, i, found_dot; - const char* rt_from_call = Py_GetVersion(); - PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); - found_dot = 0; - for (i = 0; i < 4; i++) { - if (!ctversion[i]) { - same = (rt_from_call[i] < '0' || rt_from_call[i] > '9'); - break; - } - if (rt_from_call[i] != ctversion[i]) { - same = 0; - break; - } - } - if (!same) { - char rtversion[5] = {'\0'}; - char message[200]; - for (i=0; i<4; ++i) { - if (rt_from_call[i] == '.') { - if (found_dot) break; - found_dot = 1; - } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') { - break; - } - rtversion[i] = rt_from_call[i]; - } - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* FunctionExport */ -static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig) { - PyObject *d = 0; - PyObject *cobj = 0; - union { - void (*fp)(void); - void *p; - } tmp; - d = PyObject_GetAttrString(__pyx_m, (char *)"__pyx_capi__"); - if (!d) { - PyErr_Clear(); - d = PyDict_New(); - if (!d) - goto bad; - Py_INCREF(d); - if (PyModule_AddObject(__pyx_m, (char *)"__pyx_capi__", d) < 0) - goto bad; - } - tmp.fp = f; -#if PY_VERSION_HEX >= 0x02070000 - cobj = PyCapsule_New(tmp.p, sig, 0); -#else - cobj = PyCObject_FromVoidPtrAndDesc(tmp.p, (void *)sig, 0); -#endif - if (!cobj) - goto bad; - if (PyDict_SetItemString(d, name, cobj) < 0) - goto bad; - Py_DECREF(cobj); - Py_DECREF(d); - return 0; -bad: - Py_XDECREF(cobj); - Py_XDECREF(d); - return -1; -} - -/* InitStrings */ -static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - if (PyObject_Hash(*t->p) == -1) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT -#if !CYTHON_PEP393_ENABLED -static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); - return NULL; - } - } - } -#endif - *length = PyBytes_GET_SIZE(defenc); - return defenc_c; -} -#else -static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (likely(PyUnicode_IS_ASCII(o))) { - *length = PyUnicode_GET_LENGTH(o); - return PyUnicode_AsUTF8(o); - } else { - PyUnicode_AsASCIIString(o); - return NULL; - } -#else - return PyUnicode_AsUTF8AndSize(o, length); -#endif -} -#endif -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { - return __Pyx_PyUnicode_AsStringAndSize(o, length); - } else -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - if (PyByteArray_Check(o)) { - *length = PyByteArray_GET_SIZE(o); - return PyByteArray_AS_STRING(o); - } else -#endif - { - char* result; - int r = PyBytes_AsStringAndSize(o, &result, length); - if (unlikely(r < 0)) { - return NULL; - } else { - return result; - } - } -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - int is_true = x == Py_True; - if (is_true | (x == Py_False) | (x == Py_None)) return is_true; - else return PyObject_IsTrue(x); -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) { - int retval; - if (unlikely(!x)) return -1; - retval = __Pyx_PyObject_IsTrue(x); - Py_DECREF(x); - return retval; -} -static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { -#if PY_MAJOR_VERSION >= 3 - if (PyLong_Check(result)) { - if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, - "__int__ returned non-int (type %.200s). " - "The ability to return an instance of a strict subclass of int " - "is deprecated, and may be removed in a future version of Python.", - Py_TYPE(result)->tp_name)) { - Py_DECREF(result); - return NULL; - } - return result; - } -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - type_name, type_name, Py_TYPE(result)->tp_name); - Py_DECREF(result); - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS - PyNumberMethods *m; -#endif - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x) || PyLong_Check(x))) -#else - if (likely(PyLong_Check(x))) -#endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS - m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = m->nb_int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = m->nb_long(x); - } - #else - if (likely(m && m->nb_int)) { - 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#if defined(__clang__) - #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) - #elif defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline - #else - #define CYTHON_INLINE - #endif -#endif - -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - if (type) { - PyErr_Restore(type, value, traceback); - } - return co; - } -#else - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_STACKLESS - #define METH_STACKLESS 0 -#endif -#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) - #ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - #endif - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); - typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast - #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1 - #define PyMem_RawMalloc(n) PyMem_Malloc(n) - #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) - #define PyMem_RawFree(p) PyMem_Free(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#elif PY_VERSION_HEX >= 0x03060000 - #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() -#elif PY_VERSION_HEX >= 0x03000000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#else - #define __Pyx_PyThreadState_Current _PyThreadState_Current -#endif -#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) -#include "pythread.h" -#define Py_tss_NEEDS_INIT 0 -typedef int Py_tss_t; -static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { - *key = PyThread_create_key(); - return 0; -} -static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { - Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); - *key = Py_tss_NEEDS_INIT; - return key; -} -static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { - PyObject_Free(key); -} -static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { - return *key != Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { - PyThread_delete_key(*key); - *key = Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { - return PyThread_set_key_value(*key, value); -} -static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { - return PyThread_get_key_value(*key); -} -#endif -#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) -#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) -#else -#define __Pyx_PyDict_NewPresized(n) PyDict_New() -#endif -#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION - #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) -#else - #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS -#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) -#else -#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_READY(op) (0) - #else - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #endif - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) - #else - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) - #endif - #endif -#else - #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 - #define __Pyx_PyUnicode_READY(op) (0) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) - #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) - #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) - #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) -#endif -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) -#else - #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ - PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) -#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? 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-#else -#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) -#endif - -/* PyObjectCall2Args.proto */ -static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2); - -/* PyObjectCallMethO.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); -#endif - -/* PyObjectCallOneArg.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); - -/* PyObjectCallNoArg.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); -#else -#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) -#endif - -/* PyThreadStateGet.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate; -#define __Pyx_PyThreadState_assign __pyx_tstate = __Pyx_PyThreadState_Current; -#define __Pyx_PyErr_Occurred() __pyx_tstate->curexc_type -#else -#define __Pyx_PyThreadState_declare -#define __Pyx_PyThreadState_assign -#define __Pyx_PyErr_Occurred() PyErr_Occurred() -#endif - -/* PyErrFetchRestore.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL) -#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb) -#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb) -#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb) -#define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#if CYTHON_COMPILING_IN_CPYTHON -#define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL)) -#else -#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) -#endif -#else -#define __Pyx_PyErr_Clear() PyErr_Clear() -#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) -#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb) -#define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb) -#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb) -#endif - -/* WriteUnraisableException.proto */ -static void __Pyx_WriteUnraisable(const char *name, int clineno, - int lineno, const char *filename, - int full_traceback, int nogil); - -/* RaiseException.proto */ -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); - -/* GetItemInt.proto */ -#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ - __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, - int is_list, int wraparound, int boundscheck); - -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); -#else -#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace, zerodivision_check)\ - (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2)) -#endif - -/* IncludeStringH.proto */ -#include - -/* BytesEquals.proto */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); - -/* UnicodeEquals.proto */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); - -/* PyDictVersioning.proto */ -#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS -#define __PYX_DICT_VERSION_INIT ((PY_UINT64_T) -1) -#define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) -#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)\ - (version_var) = __PYX_GET_DICT_VERSION(dict);\ - (cache_var) = (value); -#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) {\ - static PY_UINT64_T __pyx_dict_version = 0;\ - static PyObject *__pyx_dict_cached_value = NULL;\ - if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\ - (VAR) = __pyx_dict_cached_value;\ - } else {\ - (VAR) = __pyx_dict_cached_value = (LOOKUP);\ - __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\ - }\ -} -static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj); -static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj); -static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version); -#else -#define __PYX_GET_DICT_VERSION(dict) (0) -#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var) -#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) (VAR) = (LOOKUP); -#endif - -/* GetModuleGlobalName.proto */ -#if CYTHON_USE_DICT_VERSIONS -#define __Pyx_GetModuleGlobalName(var, name) do {\ - static PY_UINT64_T __pyx_dict_version = 0;\ - static PyObject *__pyx_dict_cached_value = NULL;\ - (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ - (likely(__pyx_dict_cached_value) ? __Pyx_NewRef(__pyx_dict_cached_value) : __Pyx_GetBuiltinName(name)) :\ - __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\ -} while(0) -#define __Pyx_GetModuleGlobalNameUncached(var, name) do {\ - PY_UINT64_T __pyx_dict_version;\ - PyObject *__pyx_dict_cached_value;\ - (var) = __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\ -} while(0) -static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value); -#else -#define __Pyx_GetModuleGlobalName(var, name) (var) = __Pyx__GetModuleGlobalName(name) -#define __Pyx_GetModuleGlobalNameUncached(var, name) (var) = __Pyx__GetModuleGlobalName(name) -static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name); -#endif - -/* None.proto */ -static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname); - -/* PySequenceContains.proto */ -static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) { - int result = PySequence_Contains(seq, item); - return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); -} - -/* ListCompAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len)) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) -#endif - -/* GetTopmostException.proto */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate); -#endif - -/* SaveResetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -#else -#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) -#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) -#endif - -/* PyErrExceptionMatches.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) -static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); -#else -#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) -#endif - -/* GetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* ExtTypeTest.proto */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); - -/* ObjectGetItem.proto */ -#if CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key); -#else -#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key) -#endif - -/* MemviewSliceInit.proto */ -#define __Pyx_BUF_MAX_NDIMS %(BUF_MAX_NDIMS)d -#define __Pyx_MEMVIEW_DIRECT 1 -#define __Pyx_MEMVIEW_PTR 2 -#define __Pyx_MEMVIEW_FULL 4 -#define __Pyx_MEMVIEW_CONTIG 8 -#define __Pyx_MEMVIEW_STRIDED 16 -#define __Pyx_MEMVIEW_FOLLOW 32 -#define __Pyx_IS_C_CONTIG 1 -#define __Pyx_IS_F_CONTIG 2 -static int __Pyx_init_memviewslice( - struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference); -static CYTHON_INLINE int __pyx_add_acquisition_count_locked( - __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); -static CYTHON_INLINE int __pyx_sub_acquisition_count_locked( - __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); -#define __pyx_get_slice_count_pointer(memview) (memview->acquisition_count_aligned_p) -#define __pyx_get_slice_count(memview) (*__pyx_get_slice_count_pointer(memview)) -#define __PYX_INC_MEMVIEW(slice, have_gil) __Pyx_INC_MEMVIEW(slice, have_gil, __LINE__) -#define __PYX_XDEC_MEMVIEW(slice, have_gil) __Pyx_XDEC_MEMVIEW(slice, have_gil, __LINE__) -static CYTHON_INLINE void __Pyx_INC_MEMVIEW(__Pyx_memviewslice *, int, int); -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *, int, int); - -/* SliceObject.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice( - PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** py_start, PyObject** py_stop, PyObject** py_slice, - int has_cstart, int has_cstop, int wraparound); - -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); -#else -#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace, zerodivision_check)\ - (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) -#endif - -/* DictGetItem.proto */ -#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY -static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key); -#define __Pyx_PyObject_Dict_GetItem(obj, name)\ - (likely(PyDict_CheckExact(obj)) ?\ - __Pyx_PyDict_GetItem(obj, name) : PyObject_GetItem(obj, name)) -#else -#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) -#define __Pyx_PyObject_Dict_GetItem(obj, name) PyObject_GetItem(obj, name) -#endif - -/* IsLittleEndian.proto */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void); - -/* BufferFormatCheck.proto */ -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type); - -/* BufferGetAndValidate.proto */ -#define __Pyx_GetBufferAndValidate(buf, obj, dtype, flags, nd, cast, stack)\ - ((obj == Py_None || obj == NULL) ?\ - (__Pyx_ZeroBuffer(buf), 0) :\ - __Pyx__GetBufferAndValidate(buf, obj, dtype, flags, nd, cast, stack)) -static int __Pyx__GetBufferAndValidate(Py_buffer* buf, PyObject* obj, - __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); -static void __Pyx_ZeroBuffer(Py_buffer* buf); -static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); -static Py_ssize_t __Pyx_minusones[] = { -1, -1, -1, -1, -1, -1, -1, -1 }; -static Py_ssize_t __Pyx_zeros[] = { 0, 0, 0, 0, 0, 0, 0, 0 }; - -/* BufferFallbackError.proto */ -static void __Pyx_RaiseBufferFallbackError(void); - -/* ArgTypeTest.proto */ -#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\ - ((likely((Py_TYPE(obj) == type) | (none_allowed && (obj == Py_None)))) ? 1 :\ - __Pyx__ArgTypeTest(obj, type, name, exact)) -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact); - -/* StrEquals.proto */ -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals -#else -#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals -#endif - -/* DivInt[Py_ssize_t].proto */ -static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); - -/* UnaryNegOverflows.proto */ -#define UNARY_NEG_WOULD_OVERFLOW(x)\ - (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) - -static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *); /*proto*/ -/* GetAttr.proto */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); - -/* decode_c_string_utf16.proto */ -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = 0; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16LE(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = -1; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16BE(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = 1; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} - -/* decode_c_string.proto */ -static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); - -/* GetAttr3.proto */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); - -/* RaiseTooManyValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); - -/* RaiseNeedMoreValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); - -/* RaiseNoneIterError.proto */ -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); - -/* SwapException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* Import.proto */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); - -/* FastTypeChecks.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2); -#else -#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) -#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type) -#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2)) -#endif -#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) - -static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -/* ListExtend.proto */ -static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { -#if CYTHON_COMPILING_IN_CPYTHON - PyObject* none = _PyList_Extend((PyListObject*)L, v); - if (unlikely(!none)) - return -1; - Py_DECREF(none); - return 0; -#else - return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); -#endif -} - -/* ListAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) -#endif - -/* None.proto */ -static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); - -/* DivInt[long].proto */ -static CYTHON_INLINE long __Pyx_div_long(long, long); - -/* ImportFrom.proto */ -static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); - -/* HasAttr.proto */ -static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); - -/* PyObject_GenericGetAttrNoDict.proto */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); 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- -/* MemviewSliceValidateAndInit.proto */ -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_float(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_double(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsdsds_float(PyObject *, int writable_flag); - -/* RealImag.proto */ -#if CYTHON_CCOMPLEX - #ifdef __cplusplus - #define __Pyx_CREAL(z) ((z).real()) - #define __Pyx_CIMAG(z) ((z).imag()) - #else - #define __Pyx_CREAL(z) (__real__(z)) - #define __Pyx_CIMAG(z) (__imag__(z)) - #endif -#else - #define __Pyx_CREAL(z) ((z).real) - #define __Pyx_CIMAG(z) ((z).imag) -#endif -#if defined(__cplusplus) && CYTHON_CCOMPLEX\ - && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103) - #define __Pyx_SET_CREAL(z,x) ((z).real(x)) - #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) -#else - #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) - #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) -#endif - -/* Arithmetic.proto */ -#if CYTHON_CCOMPLEX - #define __Pyx_c_eq_float(a, b) ((a)==(b)) - #define __Pyx_c_sum_float(a, b) ((a)+(b)) - #define __Pyx_c_diff_float(a, b) ((a)-(b)) - #define __Pyx_c_prod_float(a, b) ((a)*(b)) - #define __Pyx_c_quot_float(a, b) ((a)/(b)) - #define __Pyx_c_neg_float(a) (-(a)) - #ifdef __cplusplus - #define __Pyx_c_is_zero_float(z) ((z)==(float)0) - #define __Pyx_c_conj_float(z) (::std::conj(z)) - #if 1 - #define __Pyx_c_abs_float(z) (::std::abs(z)) - #define __Pyx_c_pow_float(a, b) (::std::pow(a, b)) - #endif - #else - #define __Pyx_c_is_zero_float(z) ((z)==0) - #define __Pyx_c_conj_float(z) (conjf(z)) - #if 1 - #define __Pyx_c_abs_float(z) (cabsf(z)) - #define __Pyx_c_pow_float(a, b) (cpowf(a, b)) - #endif - #endif -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex); 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- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex); - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex); - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex); - #endif -#endif - -/* MemviewSliceCopyTemplate.proto */ -static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); - -/* CIntFromPy.proto */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); - -/* CIntFromPy.proto */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); - -/* CIntFromPy.proto */ -static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); - -/* FetchCommonType.proto */ -static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); - -/* PyObjectGetMethod.proto */ -static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method); - -/* PyObjectCallMethod1.proto */ -static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg); - -/* CoroutineBase.proto */ -typedef PyObject *(*__pyx_coroutine_body_t)(PyObject *, PyThreadState *, PyObject *); -#if CYTHON_USE_EXC_INFO_STACK -#define __Pyx_ExcInfoStruct _PyErr_StackItem -#else -typedef struct { - PyObject *exc_type; 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-static CYTHON_INLINE void __Pyx_Coroutine_ResetFrameBackpointer(__Pyx_ExcInfoStruct *exc_state); - -/* PatchModuleWithCoroutine.proto */ -static PyObject* __Pyx_Coroutine_patch_module(PyObject* module, const char* py_code); - -/* PatchGeneratorABC.proto */ -static int __Pyx_patch_abc(void); - -/* Generator.proto */ -#define __Pyx_Generator_USED -static PyTypeObject *__pyx_GeneratorType = 0; -#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType) -#define __Pyx_Generator_New(body, code, closure, name, qualname, module_name)\ - __Pyx__Coroutine_New(__pyx_GeneratorType, body, code, closure, name, qualname, module_name) -static PyObject *__Pyx_Generator_Next(PyObject *self); -static int __pyx_Generator_init(void); - -/* CheckBinaryVersion.proto */ -static int __Pyx_check_binary_version(void); - -/* FunctionExport.proto */ -static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig); - -/* InitStrings.proto */ -static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); - -static void __pyx_f_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile__read_header(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto*/ -static void __pyx_f_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile__setup_buffers(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto*/ -static int __pyx_f_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile__estimate_n_frames(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto*/ -static int __pyx_f_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_c_readframes_helper(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self, __Pyx_memviewslice __pyx_v_x, __Pyx_memviewslice __pyx_v_y, __Pyx_memviewslice __pyx_v_z, __Pyx_memviewslice __pyx_v_unitcell, int __pyx_v_first_frame); /* proto*/ -static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *__pyx_v_self); /* proto*/ -static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto*/ -static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj); /* proto*/ -static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_dst, PyObject *__pyx_v_src); /* proto*/ -static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memoryview_obj *__pyx_v_self, struct __pyx_memoryview_obj *__pyx_v_dst, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ -static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); 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/*proto*/ -static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/ -static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/ -static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/ -static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/ -static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/ -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/ -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/ -static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/ -static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/ -static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/ -static int __pyx_memoryview_err(PyObject *, char *); /*proto*/ -static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/ -static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/ -static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/ -static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ -static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ -static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ -static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ -static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *, PyObject *); /*proto*/ -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t = { "int64_t", NULL, sizeof(__pyx_t_5numpy_int64_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int64_t) ? 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-static PyObject *__pyx_builtin_id; -static PyObject *__pyx_builtin_IndexError; -static const char __pyx_k_C[] = "C"; -static const char __pyx_k_F[] = "F"; -static const char __pyx_k_O[] = "O"; -static const char __pyx_k_c[] = "c"; -static const char __pyx_k_r[] = "r"; -static const char __pyx_k_w[] = "w"; -static const char __pyx_k__4[] = ""; -static const char __pyx_k_id[] = "id"; -static const char __pyx_k_np[] = "np"; -static const char __pyx_k_os[] = "os"; -static const char __pyx_k_acf[] = "acf"; -static const char __pyx_k_afc[] = "afc"; -static const char __pyx_k_box[] = "box"; -static const char __pyx_k_caf[] = "caf"; -static const char __pyx_k_cfa[] = "cfa"; -static const char __pyx_k_fac[] = "fac"; -static const char __pyx_k_fca[] = "fca"; -static const char __pyx_k_new[] = "__new__"; -static const char __pyx_k_obj[] = "obj"; -static const char __pyx_k_sys[] = "sys"; -static const char __pyx_k_xyz[] = "xyz"; -static const char __pyx_k_args[] = "args"; -static const char __pyx_k_base[] = "base"; -static const char __pyx_k_dict[] = "__dict__"; -static const char __pyx_k_main[] = "__main__"; -static const char __pyx_k_mode[] = "mode"; -static const char __pyx_k_name[] = "name"; -static const char __pyx_k_ndim[] = "ndim"; -static const char __pyx_k_open[] = "open"; -static const char __pyx_k_pack[] = "pack"; -static const char __pyx_k_path[] = "path"; -static const char __pyx_k_read[] = "read"; -static const char __pyx_k_seek[] = "seek"; -static const char __pyx_k_send[] = "send"; -static const char __pyx_k_size[] = "size"; -static const char __pyx_k_step[] = "step"; -static const char __pyx_k_stop[] = "stop"; -static const char __pyx_k_test[] = "__test__"; -static const char __pyx_k_ASCII[] = "ASCII"; -static const char __pyx_k_FLOAT[] = "FLOAT"; -static const char __pyx_k_ascii[] = "ascii"; -static const char __pyx_k_class[] = "__class__"; -static const char __pyx_k_close[] = "close"; -static const char __pyx_k_delta[] = "delta"; -static const char __pyx_k_dtype[] = "dtype"; -static const char __pyx_k_error[] = "error"; -static const char __pyx_k_flags[] = "flags"; -static const char __pyx_k_fname[] = "fname"; -static const char __pyx_k_int64[] = "int64"; -static const char __pyx_k_nsavc[] = "nsavc"; -static const char __pyx_k_numpy[] = "numpy"; -static const char __pyx_k_order[] = "order"; -static const char __pyx_k_range[] = "range"; -static const char __pyx_k_shape[] = "shape"; -static const char __pyx_k_start[] = "start"; -static const char __pyx_k_throw[] = "throw"; -static const char __pyx_k_utf_8[] = "utf-8"; -static const char __pyx_k_zeros[] = "zeros"; -static const char __pyx_k_DOUBLE[] = "DOUBLE"; -static const char __pyx_k_decode[] = "decode"; -static const char __pyx_k_encode[] = "encode"; -static const char __pyx_k_exc_tb[] = "exc_tb"; -static const char __pyx_k_format[] = "format"; -static const char __pyx_k_ignore[] = "ignore"; -static const char __pyx_k_import[] = "__import__"; -static const char __pyx_k_isfile[] = "isfile"; -static const char __pyx_k_istart[] = "istart"; -static const char __pyx_k_name_2[] = "__name__"; -static const char __pyx_k_natoms[] = "natoms"; -static const char __pyx_k_pickle[] = "pickle"; -static const char __pyx_k_reduce[] = "__reduce__"; -static const char __pyx_k_string[] = "string"; -static const char __pyx_k_struct[] = "struct"; -static const char __pyx_k_unpack[] = "unpack"; -static const char __pyx_k_update[] = "update"; -static const char __pyx_k_DCDFile[] = "DCDFile"; -static const char __pyx_k_IOError[] = "IOError"; -static const char __pyx_k_Success[] = "Success"; -static const char __pyx_k_asarray[] = "asarray"; -static const char __pyx_k_exc_val[] = "exc_val"; -static const char __pyx_k_float32[] = "float32"; -static const char __pyx_k_float64[] = "float64"; -static const char __pyx_k_fortran[] = "fortran"; -static const char __pyx_k_genexpr[] = "genexpr"; -static const char __pyx_k_getsize[] = "getsize"; -static const char __pyx_k_indices[] = "indices"; -static const char __pyx_k_memview[] = "memview"; -static const char __pyx_k_remarks[] = "remarks"; -static const char __pyx_k_DCDFrame[] = "DCDFrame"; -static const char __pyx_k_EOFError[] = "EOFError"; -static const char __pyx_k_Ellipsis[] = "Ellipsis"; -static const char __pyx_k_exc_type[] = "exc_type"; -static const char __pyx_k_getstate[] = "__getstate__"; -static const char __pyx_k_itemsize[] = "itemsize"; -static const char __pyx_k_pyx_type[] = "__pyx_type"; -static const char __pyx_k_setstate[] = "__setstate__"; -static const char __pyx_k_TypeError[] = "TypeError"; -static const char __pyx_k_enumerate[] = "enumerate"; -static const char __pyx_k_printable[] = "printable"; -static const char __pyx_k_pyx_state[] = "__pyx_state"; -static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; -static const char __pyx_k_self_mode[] = "self.mode"; -static const char __pyx_k_DCD_ERRORS[] = "DCD_ERRORS"; -static const char __pyx_k_IndexError[] = "IndexError"; -static const char __pyx_k_Normal_EOF[] = "Normal EOF"; -static const char __pyx_k_ValueError[] = "ValueError"; -static const char __pyx_k_namedtuple[] = "namedtuple"; -static const char __pyx_k_pyx_result[] = "__pyx_result"; -static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; -static const char __pyx_k_ImportError[] = "ImportError"; -static const char __pyx_k_MemoryError[] = "MemoryError"; -static const char __pyx_k_PickleError[] = "PickleError"; -static const char __pyx_k_collections[] = "collections"; -static const char __pyx_k_is_periodic[] = "is_periodic"; -static const char __pyx_k_whence_vals[] = "_whence_vals"; -static const char __pyx_k_FIO_SEEK_CUR[] = "FIO_SEEK_CUR"; -static const char __pyx_k_FIO_SEEK_END[] = "FIO_SEEK_END"; -static const char __pyx_k_FIO_SEEK_SET[] = "FIO_SEEK_SET"; -static const char __pyx_k_No_file_open[] = "No file open"; -static const char __pyx_k_RuntimeError[] = "RuntimeError"; -static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; -static const char __pyx_k_stringsource[] = "stringsource"; -static const char __pyx_k_unkown_order[] = "unkown order '{}'"; -static const char __pyx_k_xyz_unitcell[] = "xyz unitcell"; -static const char __pyx_k_DCD_HAS_4DIMS[] = "DCD_HAS_4DIMS"; -static const char __pyx_k_DCD_IS_CHARMM[] = "DCD_IS_CHARMM"; -static const char __pyx_k_StopIteration[] = "StopIteration"; -static const char __pyx_k_malloc_failed[] = "malloc failed"; -static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; -static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; -static const char __pyx_k_View_MemoryView[] = "View.MemoryView"; -static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; -static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; -static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; -static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; -static const char __pyx_k_DCD_is_corrupted[] = "DCD is corrupted"; -static const char __pyx_k_pyx_unpickle_Enum[] = "__pyx_unpickle_Enum"; -static const char __pyx_k_UnicodeDecodeError[] = "UnicodeDecodeError"; -static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; -static const char __pyx_k_strided_and_direct[] = ""; -static const char __pyx_k_DCD_HAS_EXTRA_BLOCK[] = "DCD_HAS_EXTRA_BLOCK"; -static const char __pyx_k_strided_and_indirect[] = ""; -static const char __pyx_k_contiguous_and_direct[] = ""; -static const char __pyx_k_Header_already_written[] = "Header already written"; -static const char __pyx_k_MemoryView_of_r_object[] = ""; -static const char __pyx_k_DCD_file_does_not_exist[] = "DCD file does not exist"; -static const char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; -static const char __pyx_k_Open_of_DCD_file_failed[] = "Open of DCD file failed"; -static const char __pyx_k_contiguous_and_indirect[] = ""; -static const char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; -static const char __pyx_k_No_file_currently_opened[] = "No file currently opened"; -static const char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; -static const char __pyx_k_Reading_DCD_frames_failed[] = "Reading DCD frames failed: {}"; -static const char __pyx_k_Reading_DCD_header_failed[] = "Reading DCD header failed: {}"; -static const char __pyx_k_Writing_DCD_header_failed[] = "Writing DCD header failed: {}"; -static const char __pyx_k_output_file_already_exists[] = "output file already exists"; -static const char __pyx_k_format_of_DCD_file_is_wrong[] = "format of DCD file is wrong"; -static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; -static const char __pyx_k_couldn_t_open_file_ErrorCode[] = "couldn't open file: {}\nErrorCode: {}"; -static const char __pyx_k_read_call_on_DCD_file_failed[] = "read call on DCD file failed"; -static const char __pyx_k_MDAnalysis_lib_formats_libdcd[] = "MDAnalysis.lib.formats.libdcd"; -static const char __pyx_k_couldn_t_close_file_ErrorCode[] = "couldn't close file: {}\nErrorCode: {}"; -static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; -static const char __pyx_k_unkown_mode_use_either_r_or_w[] = "unkown mode '{}', use either r or w"; -static const char __pyx_k_DCD_seek_failed_with_DCD_error[] = "DCD seek failed with DCD error={}"; -static const char __pyx_k_strided_and_direct_or_indirect[] = ""; -static const char __pyx_k_Couldn_t_write_DCD_frame_reason[] = "Couldn't write DCD frame: reason {}"; -static const char __pyx_k_Incorrect_file_mode_for_writing[] = "Incorrect file mode for writing."; -static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; -static const char __pyx_k_opened_empty_file_No_frames_are[] = "opened empty file. No frames are saved"; -static const char __pyx_k_premature_EOF_found_in_DCD_file[] = "premature EOF found in DCD file"; -static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; -static const char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; -static const char __pyx_k_Cannot_assign_to_read_only_memor[] = "Cannot assign to read-only memoryview"; -static const char __pyx_k_Cannot_create_writable_memory_vi[] = "Cannot create writable memory view from read-only memoryview"; -static const char __pyx_k_DCDFile__read_header_locals_gene[] = "DCDFile._read_header..genexpr"; -static const char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; -static const char __pyx_k_File_opened_in_mode_Reading_only[] = "File opened in mode: {}. Reading only allow in mode \"r\""; -static const char __pyx_k_File_opened_in_mode_Writing_only[] = "File opened in mode: {}. Writing only allowed in mode \"w\""; -static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0xb068931, 0x82a3537, 0x6ae9995) = (name))"; -static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; -static const char __pyx_k_Invalid_frame_number_this_should[] = "Invalid frame number {} > {} -- this shouldnot happen."; -static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; -static const char __pyx_k_Low_level_DCD_trajectory_reading[] = "Low level DCD trajectory reading - :mod:`MDAnalysis.lib.formats.libdcd`\n------------------------------------------------------------------------\n\n:mod:`libdcd` contains the class :class:`DCDFile` to read and write frames of a\nDCD file. The class tries to behave similar to a normal file object.\n\n:mod:`libdcd` contains the classes :class:`DCDFile`, which can be used to read\nand write frames from and to DCD files. These classes are used internally by\nMDAnalysis in :mod:`MDAnalysis.coordinates.DCD`. They behave similar to normal\nfile objects.\n\nFor example, one can use a :class:`DCDFile` to directly calculate mean\ncoordinates (where the coordinates are stored in `x` attribute of the\n:class:`namedtuple` `frame`):\n\n.. code-block:: python\n :emphasize-lines: 1,2,5\n\n with DCDFile(\"trajectory.dcd\") as dcd:\n header = dcd.header\n mean = np.zeros((header['natoms'], 3))\n # iterate over trajectory\n for frame in dcd:\n mean += frame.x\n mean /= header['natoms']\n\n\nBesides iteration one can also seek to arbitrary frames using the\n:meth:`~DCDFile.seek` method. Note that instead of seeking to a byte-offset as\nfor normal Python streams, the seek and tell method of DCDFile operate on\ncomplete trajectory frames.\n\n.. rubric:: Acknowledgements\n\n:mod:`libdcd` contains and is originally based on DCD reading and writing code\nfrom VMD's `molfile`_ plugin and `catdcd`_.\n\n.. _molfile: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/\n.. _catdcd: http://www.ks.uiuc.edu/Development/MDTools/catdcd/\n\n"; -static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; -static const char __pyx_k_Reached_last_frame_in_DCD_seek_t[] = "Reached last frame in DCD, seek to 0"; -static const char __pyx_k_Trying_to_seek_over_max_number_o[] = "Trying to seek over max number of frames"; -static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; -static const char __pyx_k_box_size_is_wrong_should_be_6_go[] = "box size is wrong should be 6, got: {}"; -static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; -static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; -static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; -static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; -static const char __pyx_k_write_header_first_before_frames[] = "write header first before frames can be written"; -static const char __pyx_k_xyz_shape_is_wrong_should_be_nat[] = "xyz shape is wrong should be (natoms, 3), got:"; -static PyObject *__pyx_n_s_ASCII; -static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; -static PyObject *__pyx_n_u_C; -static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; -static PyObject *__pyx_kp_s_Cannot_assign_to_read_only_memor; -static PyObject *__pyx_kp_s_Cannot_create_writable_memory_vi; -static PyObject *__pyx_kp_s_Cannot_index_with_type_s; -static PyObject *__pyx_kp_u_Couldn_t_write_DCD_frame_reason; -static PyObject *__pyx_n_s_DCDFile; -static PyObject *__pyx_n_s_DCDFile__read_header_locals_gene; -static PyObject *__pyx_n_s_DCDFrame; -static PyObject *__pyx_n_u_DCDFrame; -static PyObject *__pyx_n_s_DCD_ERRORS; -static PyObject *__pyx_n_s_DCD_HAS_4DIMS; -static PyObject *__pyx_n_s_DCD_HAS_EXTRA_BLOCK; -static PyObject *__pyx_n_s_DCD_IS_CHARMM; -static PyObject *__pyx_kp_u_DCD_file_does_not_exist; -static PyObject *__pyx_kp_u_DCD_is_corrupted; -static PyObject *__pyx_kp_u_DCD_seek_failed_with_DCD_error; -static PyObject *__pyx_n_s_DOUBLE; -static PyObject *__pyx_n_s_EOFError; -static PyObject *__pyx_n_s_Ellipsis; -static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; -static PyObject *__pyx_n_u_F; -static PyObject *__pyx_n_u_FIO_SEEK_CUR; -static PyObject *__pyx_n_u_FIO_SEEK_END; -static PyObject *__pyx_n_u_FIO_SEEK_SET; -static PyObject *__pyx_n_s_FLOAT; -static PyObject *__pyx_kp_u_File_opened_in_mode_Reading_only; -static PyObject *__pyx_kp_u_File_opened_in_mode_Writing_only; -static PyObject *__pyx_kp_u_Header_already_written; -static PyObject *__pyx_n_s_IOError; -static PyObject *__pyx_n_s_ImportError; -static PyObject *__pyx_kp_s_Incompatible_checksums_0x_x_vs_0; -static PyObject *__pyx_kp_u_Incorrect_file_mode_for_writing; -static PyObject *__pyx_n_s_IndexError; -static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; -static PyObject *__pyx_kp_u_Invalid_frame_number_this_should; -static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; -static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; -static PyObject *__pyx_n_s_MDAnalysis_lib_formats_libdcd; -static PyObject *__pyx_n_s_MemoryError; -static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; -static PyObject *__pyx_kp_s_MemoryView_of_r_object; -static PyObject *__pyx_kp_u_No_file_currently_opened; -static PyObject *__pyx_kp_u_No_file_open; -static PyObject *__pyx_kp_u_Normal_EOF; -static PyObject *__pyx_n_b_O; -static PyObject *__pyx_kp_u_Open_of_DCD_file_failed; -static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; -static PyObject *__pyx_n_s_PickleError; -static PyObject *__pyx_kp_u_Reached_last_frame_in_DCD_seek_t; -static PyObject *__pyx_kp_u_Reading_DCD_frames_failed; -static PyObject *__pyx_kp_u_Reading_DCD_header_failed; -static PyObject *__pyx_n_s_RuntimeError; -static PyObject *__pyx_n_s_StopIteration; -static PyObject *__pyx_n_u_Success; -static PyObject *__pyx_kp_u_Trying_to_seek_over_max_number_o; -static PyObject *__pyx_n_s_TypeError; -static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; -static PyObject *__pyx_n_s_UnicodeDecodeError; -static PyObject *__pyx_n_s_ValueError; -static PyObject *__pyx_n_s_View_MemoryView; -static PyObject *__pyx_kp_u_Writing_DCD_header_failed; -static PyObject *__pyx_kp_u__4; -static PyObject *__pyx_n_u_acf; -static PyObject *__pyx_n_u_afc; -static PyObject *__pyx_n_s_allocate_buffer; -static PyObject *__pyx_n_s_args; -static PyObject *__pyx_n_s_asarray; -static PyObject *__pyx_n_u_ascii; -static PyObject *__pyx_n_s_base; -static PyObject *__pyx_n_s_box; -static PyObject *__pyx_kp_u_box_size_is_wrong_should_be_6_go; -static PyObject *__pyx_n_s_c; -static PyObject *__pyx_n_u_c; -static PyObject *__pyx_n_u_caf; -static PyObject *__pyx_n_u_cfa; -static PyObject *__pyx_n_s_class; -static PyObject *__pyx_n_s_cline_in_traceback; -static PyObject *__pyx_n_s_close; -static PyObject *__pyx_n_s_collections; -static PyObject *__pyx_kp_s_contiguous_and_direct; -static PyObject *__pyx_kp_s_contiguous_and_indirect; -static PyObject *__pyx_kp_u_couldn_t_close_file_ErrorCode; -static PyObject *__pyx_kp_u_couldn_t_open_file_ErrorCode; -static PyObject *__pyx_n_s_decode; -static PyObject *__pyx_n_s_delta; -static PyObject *__pyx_n_u_delta; -static PyObject *__pyx_n_s_dict; -static PyObject *__pyx_n_s_dtype; -static PyObject *__pyx_n_s_dtype_is_object; -static PyObject *__pyx_n_s_encode; -static PyObject *__pyx_n_s_enumerate; -static PyObject *__pyx_n_s_error; -static PyObject *__pyx_n_s_exc_tb; -static PyObject *__pyx_n_s_exc_type; -static PyObject *__pyx_n_s_exc_val; -static PyObject *__pyx_n_u_fac; -static PyObject *__pyx_n_u_fca; -static PyObject *__pyx_n_s_flags; -static PyObject *__pyx_n_s_float32; -static PyObject *__pyx_n_s_float64; -static PyObject *__pyx_n_s_fname; -static PyObject *__pyx_n_s_format; -static PyObject *__pyx_kp_u_format_of_DCD_file_is_wrong; -static PyObject *__pyx_n_s_fortran; -static PyObject *__pyx_n_u_fortran; -static PyObject *__pyx_n_s_genexpr; -static PyObject *__pyx_n_s_getsize; -static PyObject *__pyx_n_s_getstate; -static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; -static PyObject *__pyx_n_s_id; -static PyObject *__pyx_n_u_ignore; -static PyObject *__pyx_n_s_import; -static PyObject *__pyx_n_s_indices; -static PyObject *__pyx_n_s_int64; -static PyObject *__pyx_n_s_is_periodic; -static PyObject *__pyx_n_u_is_periodic; -static PyObject *__pyx_n_s_isfile; -static PyObject *__pyx_n_s_istart; -static PyObject *__pyx_n_u_istart; -static PyObject *__pyx_n_s_itemsize; -static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; -static PyObject *__pyx_n_s_main; -static PyObject *__pyx_kp_u_malloc_failed; -static PyObject *__pyx_n_s_memview; -static PyObject *__pyx_n_s_mode; -static PyObject *__pyx_n_s_name; -static PyObject *__pyx_n_s_name_2; -static PyObject *__pyx_n_s_namedtuple; -static PyObject *__pyx_n_s_natoms; -static PyObject *__pyx_n_u_natoms; -static PyObject *__pyx_n_s_ndim; -static PyObject *__pyx_n_s_new; -static PyObject *__pyx_kp_s_no_default___reduce___due_to_non; -static PyObject *__pyx_n_s_np; -static PyObject *__pyx_n_s_nsavc; -static PyObject *__pyx_n_u_nsavc; -static PyObject *__pyx_n_s_numpy; -static PyObject *__pyx_kp_u_numpy_core_multiarray_failed_to; -static PyObject *__pyx_kp_u_numpy_core_umath_failed_to_impor; -static PyObject *__pyx_n_s_obj; -static PyObject *__pyx_n_s_open; -static PyObject *__pyx_kp_u_opened_empty_file_No_frames_are; -static PyObject *__pyx_n_s_order; -static PyObject *__pyx_n_s_os; -static PyObject *__pyx_kp_u_output_file_already_exists; -static PyObject *__pyx_n_s_pack; -static PyObject *__pyx_n_s_path; -static PyObject *__pyx_n_s_pickle; -static PyObject *__pyx_kp_u_premature_EOF_found_in_DCD_file; -static PyObject *__pyx_n_s_printable; -static PyObject *__pyx_n_s_pyx_PickleError; -static PyObject *__pyx_n_s_pyx_checksum; -static PyObject *__pyx_n_s_pyx_getbuffer; -static PyObject *__pyx_n_s_pyx_result; -static PyObject *__pyx_n_s_pyx_state; -static PyObject *__pyx_n_s_pyx_type; -static PyObject *__pyx_n_s_pyx_unpickle_Enum; -static PyObject *__pyx_n_s_pyx_vtable; -static PyObject *__pyx_n_u_r; -static PyObject *__pyx_n_s_range; -static PyObject *__pyx_n_s_read; -static PyObject *__pyx_kp_u_read_call_on_DCD_file_failed; -static PyObject *__pyx_n_s_reduce; -static PyObject *__pyx_n_s_reduce_cython; -static PyObject *__pyx_n_s_reduce_ex; -static PyObject *__pyx_n_s_remarks; -static PyObject *__pyx_n_u_remarks; -static PyObject *__pyx_n_s_seek; -static PyObject *__pyx_kp_u_self_mode; -static PyObject *__pyx_n_s_send; -static PyObject *__pyx_n_s_setstate; -static PyObject *__pyx_n_s_setstate_cython; -static PyObject *__pyx_n_s_shape; -static PyObject *__pyx_n_s_size; -static PyObject *__pyx_n_s_start; -static PyObject *__pyx_n_s_step; -static PyObject *__pyx_n_s_stop; -static PyObject *__pyx_kp_s_strided_and_direct; -static PyObject *__pyx_kp_s_strided_and_direct_or_indirect; -static PyObject *__pyx_kp_s_strided_and_indirect; -static PyObject *__pyx_n_s_string; -static PyObject *__pyx_kp_s_stringsource; -static PyObject *__pyx_n_s_struct; -static PyObject *__pyx_n_s_sys; -static PyObject *__pyx_n_s_test; -static PyObject *__pyx_n_s_throw; -static PyObject *__pyx_kp_s_unable_to_allocate_array_data; -static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; -static PyObject *__pyx_kp_u_unkown_mode_use_either_r_or_w; -static PyObject *__pyx_kp_u_unkown_order; -static PyObject *__pyx_n_s_unpack; -static PyObject *__pyx_n_s_update; -static PyObject *__pyx_kp_u_utf_8; -static PyObject *__pyx_n_u_w; -static PyObject *__pyx_n_s_whence_vals; -static PyObject *__pyx_kp_u_write_header_first_before_frames; -static PyObject *__pyx_n_s_xyz; -static PyObject *__pyx_kp_u_xyz_shape_is_wrong_should_be_nat; -static PyObject *__pyx_kp_u_xyz_unitcell; -static PyObject *__pyx_n_s_zeros; -static int __pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile___cinit__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self, PyObject *__pyx_v_fname, PyObject *__pyx_v_mode); /* proto */ -static void __pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_2__dealloc__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_4__enter__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_6__exit__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_val, CYTHON_UNUSED PyObject *__pyx_v_exc_tb); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_8__iter__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_10__next__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_12__len__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_14__reduce__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_16__getstate__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_18__setstate__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self, PyObject *__pyx_v_state); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_20tell(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_22open(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self, PyObject *__pyx_v_mode); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_24close(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_12_read_header_genexpr(PyObject *__pyx_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_26seek(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self, int __pyx_v_frame); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_6header___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_15charmm_bitfield___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_28write_header(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self, PyObject *__pyx_v_remarks, int __pyx_v_natoms, int __pyx_v_istart, int __pyx_v_nsavc, float __pyx_v_delta, int __pyx_v_is_periodic); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_30write(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self, PyObject *__pyx_v_xyz, PyObject *__pyx_v_box); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_32read(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_34readframes(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self, PyObject *__pyx_v_start, PyObject *__pyx_v_stop, PyObject *__pyx_v_step, PyObject *__pyx_v_order, PyObject *__pyx_v_indices); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_5fname___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_11is_periodic___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_5ndims___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_8n_frames___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_15_firstframesize___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_10_framesize___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_12_header_size___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile *__pyx_v_self); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__len__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_12__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ -static PyObject *__pyx_pf___pyx_array___reduce_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_array_2__setstate_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_MemviewEnum_2__setstate_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v___pyx_state); 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- if (__pyx_t_2) { - - /* "View.MemoryView":845 - * if have_start: - * if start < 0: - * start += shape # <<<<<<<<<<<<<< - * if start < 0: - * start = 0 - */ - __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - - /* "View.MemoryView":846 - * if start < 0: - * start += shape - * if start < 0: # <<<<<<<<<<<<<< - * start = 0 - * elif start >= shape: - */ - __pyx_t_2 = ((__pyx_v_start < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":847 - * start += shape - * if start < 0: - * start = 0 # <<<<<<<<<<<<<< - * elif start >= shape: - * if negative_step: - */ - __pyx_v_start = 0; - - /* "View.MemoryView":846 - * if start < 0: - * start += shape - * if start < 0: # <<<<<<<<<<<<<< - * start = 0 - * elif start >= shape: - */ - } - - /* "View.MemoryView":844 - * - * if have_start: - * if start < 0: # <<<<<<<<<<<<<< - * start += shape - * if start < 0: - */ - goto __pyx_L12; - } - - /* "View.MemoryView":848 - * if start < 0: - * start = 0 - * elif start >= shape: # <<<<<<<<<<<<<< - * if negative_step: - * start = shape - 1 - */ - __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":849 - * start = 0 - * elif start >= shape: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":850 - * elif start >= shape: - * if negative_step: - * start = shape - 1 # <<<<<<<<<<<<<< - * else: - * start = shape - */ - __pyx_v_start = (__pyx_v_shape - 1); - - /* "View.MemoryView":849 - * start = 0 - * elif start >= shape: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - goto __pyx_L14; - } - - /* "View.MemoryView":852 - * start = shape - 1 - * else: - * start = shape # <<<<<<<<<<<<<< - * else: - * if negative_step: - */ - /*else*/ { - __pyx_v_start = __pyx_v_shape; - } - __pyx_L14:; - - /* "View.MemoryView":848 - * if start < 0: - * start = 0 - * elif start >= shape: # <<<<<<<<<<<<<< - * if negative_step: - * start = shape - 1 - */ - } - __pyx_L12:; - - /* "View.MemoryView":843 - * - * - * if have_start: # <<<<<<<<<<<<<< - * if start < 0: - * start += shape - */ - goto __pyx_L11; - } - - /* "View.MemoryView":854 - * start = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - /*else*/ { - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":855 - * else: - * if negative_step: - * start = shape - 1 # <<<<<<<<<<<<<< - * else: - * start = 0 - */ - __pyx_v_start = (__pyx_v_shape - 1); - - /* "View.MemoryView":854 - * start = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - goto __pyx_L15; - } - - /* "View.MemoryView":857 - * start = shape - 1 - * else: - * start = 0 # <<<<<<<<<<<<<< - * - * if have_stop: - */ - /*else*/ { - __pyx_v_start = 0; - } - __pyx_L15:; - } - __pyx_L11:; - - /* "View.MemoryView":859 - * start = 0 - * - * if have_stop: # <<<<<<<<<<<<<< - * if stop < 0: - * stop += shape - */ - __pyx_t_2 = (__pyx_v_have_stop != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":860 - * - * if have_stop: - * if stop < 0: # <<<<<<<<<<<<<< - * stop += shape - * if stop < 0: - */ - __pyx_t_2 = ((__pyx_v_stop < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":861 - * if have_stop: - * if stop < 0: - * stop += shape # <<<<<<<<<<<<<< - * if stop < 0: - * stop = 0 - */ - __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); - - /* "View.MemoryView":862 - * if stop < 0: - * stop += shape - * if stop < 0: # <<<<<<<<<<<<<< - * stop = 0 - * elif stop > shape: - */ - __pyx_t_2 = ((__pyx_v_stop < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":863 - * stop += shape - * if stop < 0: - * stop = 0 # <<<<<<<<<<<<<< - * elif stop > shape: - * stop = shape - */ - __pyx_v_stop = 0; - - /* "View.MemoryView":862 - * if stop < 0: - * stop += shape - * if stop < 0: # <<<<<<<<<<<<<< - * stop = 0 - * elif stop > shape: - */ - } - - /* "View.MemoryView":860 - * - * if have_stop: - * if stop < 0: # <<<<<<<<<<<<<< - * stop += shape - * if stop < 0: - */ - goto __pyx_L17; - } - - /* "View.MemoryView":864 - * if stop < 0: - * stop = 0 - * elif stop > shape: # <<<<<<<<<<<<<< - * stop = shape - * else: - */ - __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":865 - * stop = 0 - * elif stop > shape: - * stop = shape # <<<<<<<<<<<<<< - * else: - * if negative_step: - */ - __pyx_v_stop = __pyx_v_shape; - - /* "View.MemoryView":864 - * if stop < 0: - * stop = 0 - * elif stop > shape: # <<<<<<<<<<<<<< - * stop = shape - * else: - */ - } - __pyx_L17:; - - /* "View.MemoryView":859 - * start = 0 - * - * if have_stop: # <<<<<<<<<<<<<< - * if stop < 0: - * stop += shape - */ - goto __pyx_L16; - } - - /* "View.MemoryView":867 - * stop = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * stop = -1 - * else: - */ - /*else*/ { - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":868 - * else: - * if negative_step: - * stop = -1 # <<<<<<<<<<<<<< - * else: - * stop = shape - */ - __pyx_v_stop = -1L; - - /* "View.MemoryView":867 - * stop = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * stop = -1 - * else: - */ - goto __pyx_L19; - } - - /* "View.MemoryView":870 - * stop = -1 - * else: - * stop = shape # <<<<<<<<<<<<<< - * - * if not have_step: - */ - /*else*/ { - __pyx_v_stop = __pyx_v_shape; 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- - /* "View.MemoryView":888 - * dst.strides[new_ndim] = stride * step - * dst.shape[new_ndim] = new_shape - * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< - * - * - */ - (__pyx_v_dst->suboffsets[__pyx_v_new_ndim]) = __pyx_v_suboffset; - } - __pyx_L3:; - - /* "View.MemoryView":891 - * - * - * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< - * dst.data += start * stride - * else: - */ - __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":892 - * - * if suboffset_dim[0] < 0: - * dst.data += start * stride # <<<<<<<<<<<<<< - * else: - * dst.suboffsets[suboffset_dim[0]] += start * stride - */ - __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); - - /* "View.MemoryView":891 - * - * - * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< - * dst.data += start * stride - * else: - */ - goto __pyx_L23; - } - - /* "View.MemoryView":894 - * dst.data += start * stride - * else: - * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< - * - * if suboffset >= 0: - */ - /*else*/ { - __pyx_t_3 = (__pyx_v_suboffset_dim[0]); 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- if (__pyx_t_2) { - - /* "View.MemoryView":1128 - * for i in range(ndim - 1, -1, -1): - * if mslice.shape[i] > 1: - * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< - * break - * - */ - __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - - /* "View.MemoryView":1129 - * if mslice.shape[i] > 1: - * c_stride = mslice.strides[i] - * break # <<<<<<<<<<<<<< - * - * for i in range(ndim): - */ - goto __pyx_L4_break; - - /* "View.MemoryView":1127 - * - * for i in range(ndim - 1, -1, -1): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * c_stride = mslice.strides[i] - * break - */ - } - } - __pyx_L4_break:; - - /* "View.MemoryView":1131 - * break - * - * for i in range(ndim): # <<<<<<<<<<<<<< - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] - */ - __pyx_t_1 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_1; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { - __pyx_v_i = __pyx_t_4; - - /* "View.MemoryView":1132 - * - * for i in range(ndim): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * f_stride = mslice.strides[i] - * break - */ - __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1133 - * for i in range(ndim): - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< - * break - * - */ - __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - - /* "View.MemoryView":1134 - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] - * break # <<<<<<<<<<<<<< - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): - */ - goto __pyx_L7_break; - - /* "View.MemoryView":1132 - * - * for i in range(ndim): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * f_stride = mslice.strides[i] - * break - */ - } - } - __pyx_L7_break:; - - /* "View.MemoryView":1136 - * break - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< - * return 'C' - * else: - */ - __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1137 - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): - * return 'C' # <<<<<<<<<<<<<< - * else: - * return 'F' - */ - __pyx_r = 'C'; - goto __pyx_L0; - - /* "View.MemoryView":1136 - * break - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< - * return 'C' - * else: - */ - } - - /* "View.MemoryView":1139 - * return 'C' - * else: - * return 'F' # <<<<<<<<<<<<<< - * - * @cython.cdivision(True) - */ - /*else*/ { - __pyx_r = 'F'; - goto __pyx_L0; - } - - /* "View.MemoryView":1118 - * - * @cname('__pyx_get_best_slice_order') - * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< - * """ - * Figure out the best memory access order for a given slice. - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1142 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - -static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v_src_strides, char *__pyx_v_dst_data, Py_ssize_t *__pyx_v_dst_strides, Py_ssize_t *__pyx_v_src_shape, Py_ssize_t *__pyx_v_dst_shape, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - CYTHON_UNUSED Py_ssize_t __pyx_v_i; - CYTHON_UNUSED Py_ssize_t __pyx_v_src_extent; - Py_ssize_t __pyx_v_dst_extent; - Py_ssize_t __pyx_v_src_stride; - Py_ssize_t __pyx_v_dst_stride; - int __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - Py_ssize_t __pyx_t_4; - Py_ssize_t __pyx_t_5; - Py_ssize_t __pyx_t_6; - - /* "View.MemoryView":1149 - * - * cdef Py_ssize_t i - * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] - */ - __pyx_v_src_extent = (__pyx_v_src_shape[0]); - - /* "View.MemoryView":1150 - * cdef Py_ssize_t i - * cdef Py_ssize_t src_extent = src_shape[0] - * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t src_stride = src_strides[0] - * cdef Py_ssize_t dst_stride = dst_strides[0] - */ - __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); - - /* "View.MemoryView":1151 - * cdef Py_ssize_t src_extent = src_shape[0] - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - */ - __pyx_v_src_stride = (__pyx_v_src_strides[0]); - - /* "View.MemoryView":1152 - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] - * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< - * - * if ndim == 1: - */ - __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); - - /* "View.MemoryView":1154 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); - if (__pyx_t_2) { - } else { - __pyx_t_1 = __pyx_t_2; - goto __pyx_L5_bool_binop_done; - } - __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); - if (__pyx_t_2) { - } else { - __pyx_t_1 = __pyx_t_2; - goto __pyx_L5_bool_binop_done; - } - - /* "View.MemoryView":1156 - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< - * memcpy(dst_data, src_data, itemsize * dst_extent) - * else: - */ - __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); - if (__pyx_t_2) { - __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); - } - __pyx_t_3 = (__pyx_t_2 != 0); - __pyx_t_1 = __pyx_t_3; - __pyx_L5_bool_binop_done:; - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - if (__pyx_t_1) { - - /* "View.MemoryView":1157 - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent))); - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - goto __pyx_L4; - } - - /* "View.MemoryView":1159 - * memcpy(dst_data, src_data, itemsize * dst_extent) - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - __pyx_t_5 = __pyx_t_4; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1160 - * else: - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< - * src_data += src_stride - * dst_data += dst_stride - */ - (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); - - /* "View.MemoryView":1161 - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * else: - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1162 - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L4:; - - /* "View.MemoryView":1154 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1164 - * dst_data += dst_stride - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * _copy_strided_to_strided(src_data, src_strides + 1, - * dst_data, dst_strides + 1, - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - __pyx_t_5 = __pyx_t_4; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1165 - * else: - * for i in range(dst_extent): - * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< - * dst_data, dst_strides + 1, - * src_shape + 1, dst_shape + 1, - */ - _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - - /* "View.MemoryView":1169 - * src_shape + 1, dst_shape + 1, - * ndim - 1, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1170 - * ndim - 1, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L3:; - - /* "View.MemoryView":1142 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - - /* function exit code */ -} - -/* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - -static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - - /* "View.MemoryView":1175 - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< - * src.shape, dst.shape, ndim, itemsize) - * - */ - _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - - /* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - - /* function exit code */ -} - -/* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { - Py_ssize_t __pyx_v_shape; - Py_ssize_t __pyx_v_size; - Py_ssize_t __pyx_r; - Py_ssize_t __pyx_t_1; - Py_ssize_t *__pyx_t_2; - Py_ssize_t *__pyx_t_3; - Py_ssize_t *__pyx_t_4; - - /* "View.MemoryView":1181 - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize # <<<<<<<<<<<<<< - * - * for shape in src.shape[:ndim]: - */ - __pyx_t_1 = __pyx_v_src->memview->view.itemsize; - __pyx_v_size = __pyx_t_1; - - /* "View.MemoryView":1183 - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - * - * for shape in src.shape[:ndim]: # <<<<<<<<<<<<<< - * size *= shape - * - */ - __pyx_t_3 = (__pyx_v_src->shape + __pyx_v_ndim); - for (__pyx_t_4 = __pyx_v_src->shape; __pyx_t_4 < __pyx_t_3; __pyx_t_4++) { - __pyx_t_2 = __pyx_t_4; - __pyx_v_shape = (__pyx_t_2[0]); - - /* "View.MemoryView":1184 - * - * for shape in src.shape[:ndim]: - * size *= shape # <<<<<<<<<<<<<< - * - * return size - */ - __pyx_v_size = (__pyx_v_size * __pyx_v_shape); - } - - /* "View.MemoryView":1186 - * size *= shape - * - * return size # <<<<<<<<<<<<<< - * - * @cname('__pyx_fill_contig_strides_array') - */ - __pyx_r = __pyx_v_size; - goto __pyx_L0; - - /* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1189 - * - * @cname('__pyx_fill_contig_strides_array') - * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< - * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, - * int ndim, char order) nogil: - */ - -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { - int __pyx_v_idx; - Py_ssize_t __pyx_r; - int __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - int __pyx_t_4; - - /* "View.MemoryView":1198 - * cdef int idx - * - * if order == 'F': # <<<<<<<<<<<<<< - * for idx in range(ndim): - * strides[idx] = stride - */ - __pyx_t_1 = ((__pyx_v_order == 'F') != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1199 - * - * if order == 'F': - * for idx in range(ndim): # <<<<<<<<<<<<<< - * strides[idx] = stride - * stride *= shape[idx] - */ - __pyx_t_2 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_2; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; 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- -static struct PyGetSetDef __pyx_getsets_10MDAnalysis_3lib_7formats_6libdcd_DCDFile[] = { - {(char *)"header", __pyx_getprop_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_header, 0, (char *)"\n Returns\n -------\n dict of header values needed to write new dcd.\n natoms: number of atoms\n istart: starting frame number\n nsavc: number of frames between saves\n delta: integrator time step.\n charm: bitfield integer if file contains special CHARMM information\n remarks: remark string, max 240 bytes.\n\n\n ", 0}, - {(char *)"charmm_bitfield", __pyx_getprop_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_charmm_bitfield, 0, (char *)"This DCDFile reader can process files written by different MD simulation\n programs. For files produced by CHARMM or other programs that follow\n the same convention we are reading a special CHARMM bitfield that\n stores different flags about additional information that is stored in\n the dcd. The bit flags are:\n\n .. code::\n\n DCD_IS_CHARMM = 0x01\n DCD_HAS_4DIMS = 0x02\n DCD_HAS_EXTRA_BLOCK = 0x04\n\n Here `DCD_HAS_EXTRA_BLOCK` means that unitcell information is stored.\n\n ", 0}, - {(char *)"fname", __pyx_getprop_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_fname, 0, (char *)0, 0}, - {(char *)"is_periodic", __pyx_getprop_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_is_periodic, 0, (char *)0, 0}, - {(char *)"ndims", __pyx_getprop_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_ndims, 0, (char *)0, 0}, - {(char *)"n_frames", __pyx_getprop_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_n_frames, 0, (char *)0, 0}, - {(char *)"_firstframesize", __pyx_getprop_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile__firstframesize, 0, (char *)0, 0}, - {(char *)"_framesize", __pyx_getprop_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile__framesize, 0, (char *)0, 0}, - {(char *)"_header_size", __pyx_getprop_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile__header_size, 0, (char *)0, 0}, - {0, 0, 0, 0, 0} -}; - -static PySequenceMethods __pyx_tp_as_sequence_DCDFile = { - __pyx_pw_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_13__len__, /*sq_length*/ - 0, /*sq_concat*/ - 0, /*sq_repeat*/ - 0, /*sq_item*/ - 0, /*sq_slice*/ - 0, /*sq_ass_item*/ - 0, /*sq_ass_slice*/ - 0, /*sq_contains*/ - 0, /*sq_inplace_concat*/ - 0, /*sq_inplace_repeat*/ -}; - -static PyMappingMethods __pyx_tp_as_mapping_DCDFile = { - __pyx_pw_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_13__len__, /*mp_length*/ - 0, /*mp_subscript*/ - 0, /*mp_ass_subscript*/ -}; - -static PyTypeObject __pyx_type_10MDAnalysis_3lib_7formats_6libdcd_DCDFile = { - PyVarObject_HEAD_INIT(0, 0) - "MDAnalysis.lib.formats.libdcd.DCDFile", /*tp_name*/ - sizeof(struct __pyx_obj_10MDAnalysis_3lib_7formats_6libdcd_DCDFile), /*tp_basicsize*/ - 0, /*tp_itemsize*/ - __pyx_tp_dealloc_10MDAnalysis_3lib_7formats_6libdcd_DCDFile, /*tp_dealloc*/ - #if PY_VERSION_HEX < 0x030800b4 - 0, /*tp_print*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 - 0, /*tp_vectorcall_offset*/ - #endif - 0, /*tp_getattr*/ - 0, /*tp_setattr*/ - #if PY_MAJOR_VERSION < 3 - 0, /*tp_compare*/ - #endif - #if PY_MAJOR_VERSION >= 3 - 0, /*tp_as_async*/ - #endif - 0, /*tp_repr*/ - 0, /*tp_as_number*/ - &__pyx_tp_as_sequence_DCDFile, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_DCDFile, /*tp_as_mapping*/ - 0, /*tp_hash*/ - 0, /*tp_call*/ - 0, /*tp_str*/ - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - 0, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - "DCDFile(fname, mode='r')\n\n File like wrapper for DCD files\n\n This class can be similar to the normal file objects in python. The read()\n function will return a frame and all information in it instead of a single\n line. Additionally the context-manager protocol is supported as well.\n\n DCDFile can read typical DCD files created by e.g., CHARMM, NAMD, or LAMMPS. It\n reads raw data from the trajectory and hence interpretation of, for instance,\n different unitcell conventions or time and length units, has to be handled in\n higher level code. Reading and writing does not support fixed atoms or 4D\n coordinates.\n\n Parameters\n ----------\n fname : str\n The filename to open.\n mode : ('r', 'w')\n The mode in which to open the file, either 'r' read or 'w' write\n\n Examples\n --------\n >>> from MDAnalysis.lib.formats.libdcd import DCDFile\n >>> with DCDFile('foo.dcd') as f:\n >>> for frame in f:\n >>> print(frame.x)\n\n\n Notes\n -----\n DCD is not a well defined format. 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sizeof(struct __pyx_MemviewEnum_obj), /*tp_basicsize*/ - 0, /*tp_itemsize*/ - __pyx_tp_dealloc_Enum, /*tp_dealloc*/ - #if PY_VERSION_HEX < 0x030800b4 - 0, /*tp_print*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 - 0, /*tp_vectorcall_offset*/ - #endif - 0, /*tp_getattr*/ - 0, /*tp_setattr*/ - #if PY_MAJOR_VERSION < 3 - 0, /*tp_compare*/ - #endif - #if PY_MAJOR_VERSION >= 3 - 0, /*tp_as_async*/ - #endif - __pyx_MemviewEnum___repr__, /*tp_repr*/ - 0, /*tp_as_number*/ - 0, /*tp_as_sequence*/ - 0, /*tp_as_mapping*/ - 0, /*tp_hash*/ - 0, /*tp_call*/ - 0, /*tp_str*/ - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - 0, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - 0, /*tp_doc*/ - __pyx_tp_traverse_Enum, /*tp_traverse*/ - __pyx_tp_clear_Enum, /*tp_clear*/ - 0, /*tp_richcompare*/ - 0, /*tp_weaklistoffset*/ - 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_Enum, /*tp_methods*/ - 0, /*tp_members*/ - 0, /*tp_getset*/ - 0, /*tp_base*/ - 0, /*tp_dict*/ - 0, /*tp_descr_get*/ - 0, /*tp_descr_set*/ - 0, /*tp_dictoffset*/ - __pyx_MemviewEnum___init__, /*tp_init*/ - 0, /*tp_alloc*/ - __pyx_tp_new_Enum, /*tp_new*/ - 0, /*tp_free*/ - 0, /*tp_is_gc*/ - 0, /*tp_bases*/ - 0, /*tp_mro*/ - 0, /*tp_cache*/ - 0, /*tp_subclasses*/ - 0, /*tp_weaklist*/ - 0, /*tp_del*/ - 0, /*tp_version_tag*/ - #if PY_VERSION_HEX >= 0x030400a1 - 0, /*tp_finalize*/ - #endif - #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) - 0, /*tp_vectorcall*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 - 0, /*tp_print*/ - #endif - #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 - 0, /*tp_pypy_flags*/ - #endif -}; -static struct __pyx_vtabstruct_memoryview __pyx_vtable_memoryview; - -static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_memoryview_obj *p; - PyObject *o; - if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { - o = (*t->tp_alloc)(t, 0); - } else { - o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); - } - if (unlikely(!o)) return 0; - p = ((struct __pyx_memoryview_obj *)o); - p->__pyx_vtab = __pyx_vtabptr_memoryview; - p->obj = Py_None; Py_INCREF(Py_None); - p->_size = Py_None; Py_INCREF(Py_None); - p->_array_interface = Py_None; Py_INCREF(Py_None); - p->view.obj = NULL; - if (unlikely(__pyx_memoryview___cinit__(o, a, k) < 0)) goto bad; - return o; - bad: - Py_DECREF(o); o = 0; - return NULL; -} - -static void __pyx_tp_dealloc_memoryview(PyObject *o) { - struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; - #if CYTHON_USE_TP_FINALIZE - if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { - if (PyObject_CallFinalizerFromDealloc(o)) return; - } - #endif - PyObject_GC_UnTrack(o); - { - PyObject *etype, *eval, *etb; - PyErr_Fetch(&etype, &eval, &etb); - __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); - __pyx_memoryview___dealloc__(o); - __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); - PyErr_Restore(etype, eval, etb); - } - Py_CLEAR(p->obj); - Py_CLEAR(p->_size); - Py_CLEAR(p->_array_interface); - (*Py_TYPE(o)->tp_free)(o); -} - -static int __pyx_tp_traverse_memoryview(PyObject *o, visitproc v, void *a) { - int e; - struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; - if (p->obj) { - e = (*v)(p->obj, a); if (e) return e; - } - if (p->_size) { - e = (*v)(p->_size, a); if (e) return e; - } - if (p->_array_interface) { - e = (*v)(p->_array_interface, a); if (e) return e; - } - if (p->view.obj) { - e = (*v)(p->view.obj, a); if (e) return e; - } - return 0; -} - -static int __pyx_tp_clear_memoryview(PyObject *o) { - PyObject* tmp; - struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; - tmp = ((PyObject*)p->obj); - p->obj = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->_size); - p->_size = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->_array_interface); - p->_array_interface = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - Py_CLEAR(p->view.obj); - return 0; -} -static PyObject *__pyx_sq_item_memoryview(PyObject *o, Py_ssize_t i) { - PyObject *r; - PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; - r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); - Py_DECREF(x); - return r; -} - -static int __pyx_mp_ass_subscript_memoryview(PyObject *o, PyObject *i, PyObject *v) { - if (v) { - return __pyx_memoryview___setitem__(o, i, v); - } - else { - PyErr_Format(PyExc_NotImplementedError, - "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name); - return -1; - } -} - -static PyObject *__pyx_getprop___pyx_memoryview_T(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_1T_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_base(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_4base_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_shape(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_5shape_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_strides(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_7strides_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_suboffsets(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_10suboffsets_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_ndim(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_4ndim_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_itemsize(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_8itemsize_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_nbytes(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_6nbytes_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_size(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_4size_1__get__(o); -} - -static PyMethodDef __pyx_methods_memoryview[] = { - {"is_c_contig", (PyCFunction)__pyx_memoryview_is_c_contig, METH_NOARGS, 0}, - {"is_f_contig", (PyCFunction)__pyx_memoryview_is_f_contig, METH_NOARGS, 0}, - {"copy", (PyCFunction)__pyx_memoryview_copy, METH_NOARGS, 0}, - {"copy_fortran", (PyCFunction)__pyx_memoryview_copy_fortran, METH_NOARGS, 0}, - {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_1__reduce_cython__, METH_NOARGS, 0}, - {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_3__setstate_cython__, METH_O, 0}, - {0, 0, 0, 0} -}; - -static struct PyGetSetDef __pyx_getsets_memoryview[] = { - {(char *)"T", __pyx_getprop___pyx_memoryview_T, 0, (char *)0, 0}, - {(char *)"base", __pyx_getprop___pyx_memoryview_base, 0, (char *)0, 0}, - {(char *)"shape", __pyx_getprop___pyx_memoryview_shape, 0, (char *)0, 0}, - {(char *)"strides", __pyx_getprop___pyx_memoryview_strides, 0, (char *)0, 0}, - {(char *)"suboffsets", __pyx_getprop___pyx_memoryview_suboffsets, 0, (char *)0, 0}, - {(char *)"ndim", __pyx_getprop___pyx_memoryview_ndim, 0, (char *)0, 0}, - {(char *)"itemsize", __pyx_getprop___pyx_memoryview_itemsize, 0, (char *)0, 0}, - {(char *)"nbytes", __pyx_getprop___pyx_memoryview_nbytes, 0, (char *)0, 0}, - {(char *)"size", __pyx_getprop___pyx_memoryview_size, 0, (char *)0, 0}, - {0, 0, 0, 0, 0} -}; - -static PySequenceMethods __pyx_tp_as_sequence_memoryview = { - __pyx_memoryview___len__, /*sq_length*/ - 0, /*sq_concat*/ - 0, /*sq_repeat*/ - __pyx_sq_item_memoryview, /*sq_item*/ - 0, /*sq_slice*/ - 0, /*sq_ass_item*/ - 0, /*sq_ass_slice*/ - 0, /*sq_contains*/ - 0, /*sq_inplace_concat*/ - 0, /*sq_inplace_repeat*/ -}; - -static PyMappingMethods __pyx_tp_as_mapping_memoryview = { - __pyx_memoryview___len__, /*mp_length*/ - __pyx_memoryview___getitem__, /*mp_subscript*/ - __pyx_mp_ass_subscript_memoryview, /*mp_ass_subscript*/ -}; - -static PyBufferProcs __pyx_tp_as_buffer_memoryview = { - #if PY_MAJOR_VERSION < 3 - 0, /*bf_getreadbuffer*/ - #endif - #if PY_MAJOR_VERSION < 3 - 0, /*bf_getwritebuffer*/ - #endif - #if PY_MAJOR_VERSION < 3 - 0, /*bf_getsegcount*/ - #endif - #if PY_MAJOR_VERSION < 3 - 0, /*bf_getcharbuffer*/ - #endif - __pyx_memoryview_getbuffer, /*bf_getbuffer*/ - 0, /*bf_releasebuffer*/ -}; - -static PyTypeObject __pyx_type___pyx_memoryview = { - PyVarObject_HEAD_INIT(0, 0) - "MDAnalysis.lib.formats.libdcd.memoryview", /*tp_name*/ - sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/ - 0, /*tp_itemsize*/ - __pyx_tp_dealloc_memoryview, /*tp_dealloc*/ - #if PY_VERSION_HEX < 0x030800b4 - 0, /*tp_print*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 - 0, /*tp_vectorcall_offset*/ - #endif - 0, /*tp_getattr*/ - 0, /*tp_setattr*/ - #if PY_MAJOR_VERSION < 3 - 0, /*tp_compare*/ - #endif - #if PY_MAJOR_VERSION >= 3 - 0, /*tp_as_async*/ - #endif - __pyx_memoryview___repr__, /*tp_repr*/ - 0, /*tp_as_number*/ - &__pyx_tp_as_sequence_memoryview, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_memoryview, /*tp_as_mapping*/ - 0, /*tp_hash*/ - 0, /*tp_call*/ - __pyx_memoryview___str__, /*tp_str*/ - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_memoryview, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - 0, /*tp_doc*/ - __pyx_tp_traverse_memoryview, /*tp_traverse*/ - __pyx_tp_clear_memoryview, /*tp_clear*/ - 0, /*tp_richcompare*/ - 0, /*tp_weaklistoffset*/ - 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_memoryview, /*tp_methods*/ - 0, /*tp_members*/ - __pyx_getsets_memoryview, /*tp_getset*/ - 0, /*tp_base*/ - 0, /*tp_dict*/ - 0, /*tp_descr_get*/ - 0, /*tp_descr_set*/ - 0, /*tp_dictoffset*/ - 0, /*tp_init*/ - 0, /*tp_alloc*/ - __pyx_tp_new_memoryview, /*tp_new*/ - 0, /*tp_free*/ - 0, /*tp_is_gc*/ - 0, /*tp_bases*/ - 0, /*tp_mro*/ - 0, /*tp_cache*/ - 0, /*tp_subclasses*/ - 0, /*tp_weaklist*/ - 0, /*tp_del*/ - 0, /*tp_version_tag*/ - #if PY_VERSION_HEX >= 0x030400a1 - 0, /*tp_finalize*/ - 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#if CYTHON_USE_TP_FINALIZE - if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { - if (PyObject_CallFinalizerFromDealloc(o)) return; - } - #endif - PyObject_GC_UnTrack(o); - { - PyObject *etype, *eval, *etb; - PyErr_Fetch(&etype, &eval, &etb); - __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); - __pyx_memoryviewslice___dealloc__(o); - __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); - PyErr_Restore(etype, eval, etb); - } - Py_CLEAR(p->from_object); - PyObject_GC_Track(o); - __pyx_tp_dealloc_memoryview(o); -} - -static int __pyx_tp_traverse__memoryviewslice(PyObject *o, visitproc v, void *a) { - int e; - struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; - e = __pyx_tp_traverse_memoryview(o, v, a); if (e) return e; - if (p->from_object) { - e = (*v)(p->from_object, a); if (e) return e; - } - return 0; -} - -static int __pyx_tp_clear__memoryviewslice(PyObject *o) { - PyObject* tmp; - struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; - __pyx_tp_clear_memoryview(o); - tmp = ((PyObject*)p->from_object); - p->from_object = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - __PYX_XDEC_MEMVIEW(&p->from_slice, 1); - return 0; -} - -static PyObject *__pyx_getprop___pyx_memoryviewslice_base(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_16_memoryviewslice_4base_1__get__(o); -} - -static PyMethodDef __pyx_methods__memoryviewslice[] = { - {"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_memoryviewslice_1__reduce_cython__, METH_NOARGS, 0}, - {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_memoryviewslice_3__setstate_cython__, METH_O, 0}, - {0, 0, 0, 0} -}; - -static struct PyGetSetDef __pyx_getsets__memoryviewslice[] = { - {(char *)"base", __pyx_getprop___pyx_memoryviewslice_base, 0, (char *)0, 0}, - {0, 0, 0, 0, 0} -}; - -static PyTypeObject __pyx_type___pyx_memoryviewslice = { - PyVarObject_HEAD_INIT(0, 0) - "MDAnalysis.lib.formats.libdcd._memoryviewslice", /*tp_name*/ - sizeof(struct __pyx_memoryviewslice_obj), /*tp_basicsize*/ - 0, /*tp_itemsize*/ - __pyx_tp_dealloc__memoryviewslice, /*tp_dealloc*/ - #if PY_VERSION_HEX < 0x030800b4 - 0, /*tp_print*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 - 0, /*tp_vectorcall_offset*/ - #endif - 0, /*tp_getattr*/ - 0, /*tp_setattr*/ - #if PY_MAJOR_VERSION < 3 - 0, /*tp_compare*/ - #endif - #if PY_MAJOR_VERSION >= 3 - 0, /*tp_as_async*/ - #endif - #if CYTHON_COMPILING_IN_PYPY - __pyx_memoryview___repr__, /*tp_repr*/ - #else - 0, /*tp_repr*/ - #endif - 0, /*tp_as_number*/ - 0, /*tp_as_sequence*/ - 0, /*tp_as_mapping*/ - 0, /*tp_hash*/ - 0, /*tp_call*/ - #if CYTHON_COMPILING_IN_PYPY - __pyx_memoryview___str__, /*tp_str*/ - #else - 0, /*tp_str*/ - #endif - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - 0, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - "Internal class for passing memoryview slices to Python", /*tp_doc*/ - __pyx_tp_traverse__memoryviewslice, /*tp_traverse*/ - 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- Py_INCREF(k[i+1]); - i += 2; - } - nk = i / 2; - } - else { - kwtuple = NULL; - k = NULL; - } - closure = PyFunction_GET_CLOSURE(func); -#if PY_MAJOR_VERSION >= 3 - kwdefs = PyFunction_GET_KW_DEFAULTS(func); -#endif - if (argdefs != NULL) { - d = &PyTuple_GET_ITEM(argdefs, 0); - nd = Py_SIZE(argdefs); - } - else { - d = NULL; - nd = 0; - } -#if PY_MAJOR_VERSION >= 3 - result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, kwdefs, closure); -#else - result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, closure); -#endif - Py_XDECREF(kwtuple); -done: - Py_LeaveRecursiveCall(); - return result; -} -#endif -#endif - -/* PyObjectCall */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { - PyObject *result; - ternaryfunc call = Py_TYPE(func)->tp_call; - if (unlikely(!call)) - return PyObject_Call(func, arg, kw); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = (*call)(func, arg, kw); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCall2Args */ -static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { - PyObject *args, *result = NULL; - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyFunction_FastCall(function, args, 2); - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyCFunction_FastCall(function, args, 2); - } - #endif - args = PyTuple_New(2); - if (unlikely(!args)) goto done; - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 0, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 1, arg2); - Py_INCREF(function); - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); -done: - return result; -} - -/* PyObjectCallMethO */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { - PyObject *self, *result; - PyCFunction cfunc; - cfunc = PyCFunction_GET_FUNCTION(func); - self = PyCFunction_GET_SELF(func); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = cfunc(self, arg); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallOneArg */ -#if CYTHON_COMPILING_IN_CPYTHON -static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_New(1); - if (unlikely(!args)) return NULL; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif - if (likely(PyCFunction_Check(func))) { - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (__Pyx_PyFastCFunction_Check(func)) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } - } - return __Pyx__PyObject_CallOneArg(func, arg); -} -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -#endif - -/* PyObjectCallNoArg */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, NULL, 0); - } -#endif -#if defined(__Pyx_CyFunction_USED) && defined(NDEBUG) - if (likely(PyCFunction_Check(func) || __Pyx_CyFunction_Check(func))) -#else - if (likely(PyCFunction_Check(func))) -#endif - { - if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { - return __Pyx_PyObject_CallMethO(func, NULL); - } - } - return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL); -} -#endif - -/* PyErrFetchRestore */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -} -#endif - -/* WriteUnraisableException */ -static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, - CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, - int full_traceback, CYTHON_UNUSED int nogil) { - PyObject *old_exc, *old_val, *old_tb; - PyObject *ctx; - __Pyx_PyThreadState_declare -#ifdef WITH_THREAD - PyGILState_STATE state; - if (nogil) - state = PyGILState_Ensure(); - else state = (PyGILState_STATE)0; -#endif - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); - if (full_traceback) { - Py_XINCREF(old_exc); - Py_XINCREF(old_val); - Py_XINCREF(old_tb); - __Pyx_ErrRestore(old_exc, old_val, old_tb); - PyErr_PrintEx(1); - } - #if PY_MAJOR_VERSION < 3 - ctx = PyString_FromString(name); - #else - ctx = PyUnicode_FromString(name); - #endif - __Pyx_ErrRestore(old_exc, old_val, old_tb); - if (!ctx) { - PyErr_WriteUnraisable(Py_None); - } else { - PyErr_WriteUnraisable(ctx); - Py_DECREF(ctx); - } -#ifdef WITH_THREAD - if (nogil) - PyGILState_Release(state); -#endif -} - -/* RaiseException */ -#if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* GetItemInt */ -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { - PyObject *r; - if (!j) return NULL; - r = PyObject_GetItem(o, j); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyList_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyTuple_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } - else if (PyTuple_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } else { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_item)) { - if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { - Py_ssize_t l = m->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return NULL; - PyErr_Clear(); - } - } - return m->sq_item(o, i); - } - } -#else - if (is_list || PySequence_Check(o)) { - return PySequence_GetItem(o, i); - } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -} - -/* PyIntBinop */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, int inplace, int zerodivision_check) { - (void)inplace; - (void)zerodivision_check; - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - const long b = intval; - long x; - long a = PyInt_AS_LONG(op1); - x = (long)((unsigned long)a - b); - if (likely((x^a) >= 0 || (x^~b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_subtract(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - default: return PyLong_Type.tp_as_number->nb_subtract(op1, op2); - } - } - x = a - b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla - llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("subtract", return NULL) - result = ((double)a) - (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceSubtract : PyNumber_Subtract)(op1, op2); -} -#endif - -/* BytesEquals */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { - const char *ps1, *ps2; - Py_ssize_t length = PyBytes_GET_SIZE(s1); - if (length != PyBytes_GET_SIZE(s2)) - return (equals == Py_NE); - ps1 = PyBytes_AS_STRING(s1); - ps2 = PyBytes_AS_STRING(s2); - if (ps1[0] != ps2[0]) { - return (equals == Py_NE); - } else if (length == 1) { - return (equals == Py_EQ); - } else { - int result; -#if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000) - Py_hash_t hash1, hash2; - hash1 = ((PyBytesObject*)s1)->ob_shash; - hash2 = ((PyBytesObject*)s2)->ob_shash; - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - return (equals == Py_NE); - } -#endif - result = memcmp(ps1, ps2, (size_t)length); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -#endif -} - -/* UnicodeEquals */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else -#if PY_MAJOR_VERSION < 3 - PyObject* owned_ref = NULL; -#endif - int s1_is_unicode, s2_is_unicode; - if (s1 == s2) { - goto return_eq; - } - s1_is_unicode = PyUnicode_CheckExact(s1); - s2_is_unicode = PyUnicode_CheckExact(s2); -#if PY_MAJOR_VERSION < 3 - if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { - owned_ref = PyUnicode_FromObject(s2); - if (unlikely(!owned_ref)) - return -1; - s2 = owned_ref; - s2_is_unicode = 1; - } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { - owned_ref = PyUnicode_FromObject(s1); - if (unlikely(!owned_ref)) - return -1; - s1 = owned_ref; - s1_is_unicode = 1; - } else if (((!s2_is_unicode) & (!s1_is_unicode))) { - return __Pyx_PyBytes_Equals(s1, s2, equals); - } -#endif - if (s1_is_unicode & s2_is_unicode) { - Py_ssize_t length; - int kind; - void *data1, *data2; - if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) - return -1; - length = __Pyx_PyUnicode_GET_LENGTH(s1); - if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { - goto return_ne; - } -#if CYTHON_USE_UNICODE_INTERNALS - { - Py_hash_t hash1, hash2; - #if CYTHON_PEP393_ENABLED - hash1 = ((PyASCIIObject*)s1)->hash; - hash2 = ((PyASCIIObject*)s2)->hash; - #else - hash1 = ((PyUnicodeObject*)s1)->hash; - hash2 = ((PyUnicodeObject*)s2)->hash; - #endif - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - goto return_ne; - } - } -#endif - kind = __Pyx_PyUnicode_KIND(s1); - if (kind != __Pyx_PyUnicode_KIND(s2)) { - goto return_ne; - } - data1 = __Pyx_PyUnicode_DATA(s1); - data2 = __Pyx_PyUnicode_DATA(s2); - if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { - goto return_ne; - } else if (length == 1) { - goto return_eq; - } else { - int result = memcmp(data1, data2, (size_t)(length * kind)); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & s2_is_unicode) { - goto return_ne; - } else if ((s2 == Py_None) & s1_is_unicode) { - goto return_ne; - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -return_eq: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ); -return_ne: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_NE); -#endif -} - -/* PyDictVersioning */ -#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; -} -static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) { - PyObject **dictptr = NULL; - Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset; - if (offset) { -#if CYTHON_COMPILING_IN_CPYTHON - dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj); -#else - dictptr = _PyObject_GetDictPtr(obj); -#endif - } - return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; -} -static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) - return 0; - return obj_dict_version == __Pyx_get_object_dict_version(obj); -} -#endif - -/* GetModuleGlobalName */ -#if CYTHON_USE_DICT_VERSIONS -static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value) -#else -static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name) -#endif -{ - PyObject *result; -#if !CYTHON_AVOID_BORROWED_REFS -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 - result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } else if (unlikely(PyErr_Occurred())) { - return NULL; - } -#else - result = PyDict_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } -#endif -#else - result = PyObject_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } - PyErr_Clear(); -#endif - return __Pyx_GetBuiltinName(name); -} - -/* None */ -static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) { - PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname); -} - -/* GetTopmostException */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* PyErrExceptionMatches */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* GetException */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* ExtTypeTest */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(__Pyx_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* ObjectGetItem */ -#if CYTHON_USE_TYPE_SLOTS -static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { - PyObject *runerr = NULL; - Py_ssize_t key_value; - PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; - if (unlikely(!(m && m->sq_item))) { - PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); - return NULL; - } - key_value = __Pyx_PyIndex_AsSsize_t(index); - if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { - return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); - } - if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { - PyErr_Clear(); - PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); - } - return NULL; -} -static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { - PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; - if (likely(m && m->mp_subscript)) { - return m->mp_subscript(obj, key); - } - return __Pyx_PyObject_GetIndex(obj, key); -} -#endif - -/* MemviewSliceInit */ -static int -__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference) -{ - __Pyx_RefNannyDeclarations - int i, retval=-1; - Py_buffer *buf = &memview->view; - __Pyx_RefNannySetupContext("init_memviewslice", 0); - if (unlikely(memviewslice->memview || memviewslice->data)) { - PyErr_SetString(PyExc_ValueError, - "memviewslice is already initialized!"); - goto fail; - } - if (buf->strides) { - for (i = 0; i < ndim; i++) { - memviewslice->strides[i] = buf->strides[i]; - } - } else { - Py_ssize_t stride = buf->itemsize; - for (i = ndim - 1; i >= 0; i--) { - memviewslice->strides[i] = stride; - stride *= buf->shape[i]; - } - } - for (i = 0; i < ndim; i++) { - memviewslice->shape[i] = buf->shape[i]; - if (buf->suboffsets) { - memviewslice->suboffsets[i] = buf->suboffsets[i]; - } else { - memviewslice->suboffsets[i] = -1; - } - } - memviewslice->memview = memview; - memviewslice->data = (char *)buf->buf; - if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { - Py_INCREF(memview); - } - retval = 0; - goto no_fail; -fail: - memviewslice->memview = 0; - memviewslice->data = 0; - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} -#ifndef Py_NO_RETURN -#define Py_NO_RETURN -#endif -static void __pyx_fatalerror(const char *fmt, ...) Py_NO_RETURN { - va_list vargs; - char msg[200]; -#if PY_VERSION_HEX >= 0x030A0000 || defined(HAVE_STDARG_PROTOTYPES) - va_start(vargs, fmt); -#else - va_start(vargs); -#endif - vsnprintf(msg, 200, fmt, vargs); - va_end(vargs); - Py_FatalError(msg); -} -static CYTHON_INLINE int -__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)++; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE int -__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)--; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE void -__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) -{ - int first_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) - return; - if (unlikely(__pyx_get_slice_count(memview) < 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - first_time = __pyx_add_acquisition_count(memview) == 0; - if (unlikely(first_time)) { - if (have_gil) { - Py_INCREF((PyObject *) memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_INCREF((PyObject *) memview); - PyGILState_Release(_gilstate); - } - } -} -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, - int have_gil, int lineno) { - int last_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) { - memslice->memview = NULL; - return; - } - if (unlikely(__pyx_get_slice_count(memview) <= 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - last_time = __pyx_sub_acquisition_count(memview) == 1; - memslice->data = NULL; - if (unlikely(last_time)) { - if (have_gil) { - Py_CLEAR(memslice->memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_CLEAR(memslice->memview); - PyGILState_Release(_gilstate); - } - } else { - memslice->memview = NULL; - } -} - -/* SliceObject */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, - Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, - int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { -#if CYTHON_USE_TYPE_SLOTS - PyMappingMethods* mp; -#if PY_MAJOR_VERSION < 3 - PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; - if (likely(ms && ms->sq_slice)) { - if (!has_cstart) { - if (_py_start && (*_py_start != Py_None)) { - cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); - if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstart = 0; - } - if (!has_cstop) { - if (_py_stop && (*_py_stop != Py_None)) { - cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); - if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstop = PY_SSIZE_T_MAX; - } - if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { - Py_ssize_t l = ms->sq_length(obj); - if (likely(l >= 0)) { - if (cstop < 0) { - cstop += l; - if (cstop < 0) cstop = 0; - } - if (cstart < 0) { - cstart += l; - if (cstart < 0) cstart = 0; - } - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - goto bad; - PyErr_Clear(); - } - } - return ms->sq_slice(obj, cstart, cstop); - } -#endif - mp = Py_TYPE(obj)->tp_as_mapping; - if (likely(mp && mp->mp_subscript)) -#endif - { - PyObject* result; - PyObject *py_slice, *py_start, *py_stop; - if (_py_slice) { - py_slice = *_py_slice; - } else { - PyObject* owned_start = NULL; - PyObject* owned_stop = NULL; - if (_py_start) { - py_start = *_py_start; - } else { - if (has_cstart) { - owned_start = py_start = PyInt_FromSsize_t(cstart); - if (unlikely(!py_start)) goto bad; - } else - py_start = Py_None; - } - if (_py_stop) { - py_stop = *_py_stop; - } else { - if (has_cstop) { - owned_stop = py_stop = PyInt_FromSsize_t(cstop); - if (unlikely(!py_stop)) { - Py_XDECREF(owned_start); - goto bad; - } - } else - py_stop = Py_None; - } - py_slice = PySlice_New(py_start, py_stop, Py_None); - Py_XDECREF(owned_start); - Py_XDECREF(owned_stop); - if (unlikely(!py_slice)) goto bad; - } -#if CYTHON_USE_TYPE_SLOTS - result = mp->mp_subscript(obj, py_slice); -#else - result = PyObject_GetItem(obj, py_slice); -#endif - if (!_py_slice) { - Py_DECREF(py_slice); - } - return result; - } - PyErr_Format(PyExc_TypeError, - "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name); -bad: - return NULL; -} - -/* PyIntBinop */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, int inplace, int zerodivision_check) { - (void)inplace; - (void)zerodivision_check; - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - const long b = intval; - long x; - long a = PyInt_AS_LONG(op1); - x = (long)((unsigned long)a + b); - if (likely((x^a) >= 0 || (x^b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - default: return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - } - x = a + b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla + llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("add", return NULL) - result = ((double)a) + (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); -} -#endif - -/* DictGetItem */ -#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY -static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { - PyObject *value; - value = PyDict_GetItemWithError(d, key); - if (unlikely(!value)) { - if (!PyErr_Occurred()) { - if (unlikely(PyTuple_Check(key))) { - PyObject* args = PyTuple_Pack(1, key); - if (likely(args)) { - PyErr_SetObject(PyExc_KeyError, args); - Py_DECREF(args); - } - } else { - PyErr_SetObject(PyExc_KeyError, key); - } - } - return NULL; - } - Py_INCREF(value); - return value; -} -#endif - -/* IsLittleEndian */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) -{ - union { - uint32_t u32; - uint8_t u8[4]; - } S; - S.u32 = 0x01020304; - return S.u8[0] == 4; -} - -/* BufferFormatCheck */ -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type) { - stack[0].field = &ctx->root; - stack[0].parent_offset = 0; - ctx->root.type = type; - ctx->root.name = "buffer dtype"; - ctx->root.offset = 0; - ctx->head = stack; - ctx->head->field = &ctx->root; - ctx->fmt_offset = 0; - ctx->head->parent_offset = 0; - ctx->new_packmode = '@'; - ctx->enc_packmode = '@'; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->is_complex = 0; - ctx->is_valid_array = 0; - ctx->struct_alignment = 0; - while (type->typegroup == 'S') { - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = 0; - type = type->fields->type; - } -} -static int __Pyx_BufFmt_ParseNumber(const char** ts) { - int count; - const char* t = *ts; - if (*t < '0' || *t > '9') { - return -1; - } else { - count = *t++ - '0'; - while (*t >= '0' && *t <= '9') { - count *= 10; - count += *t++ - '0'; - } - } - *ts = t; - return count; -} -static int __Pyx_BufFmt_ExpectNumber(const char **ts) { - int number = __Pyx_BufFmt_ParseNumber(ts); - if (number == -1) - PyErr_Format(PyExc_ValueError,\ - "Does not understand character buffer dtype format string ('%c')", **ts); - return number; -} -static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { - PyErr_Format(PyExc_ValueError, - "Unexpected format string character: '%c'", ch); -} -static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { - switch (ch) { - case '?': return "'bool'"; - case 'c': return "'char'"; - case 'b': return "'signed char'"; - case 'B': return "'unsigned char'"; - case 'h': return "'short'"; - case 'H': return "'unsigned short'"; - case 'i': return "'int'"; - case 'I': return "'unsigned int'"; - case 'l': return "'long'"; - case 'L': return "'unsigned long'"; - case 'q': return "'long long'"; - case 'Q': return "'unsigned long long'"; - case 'f': return (is_complex ? "'complex float'" : "'float'"); - case 'd': return (is_complex ? "'complex double'" : "'double'"); - case 'g': return (is_complex ? "'complex long double'" : "'long double'"); - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - case 's': case 'p': return "a string"; - case 0: return "end"; - default: return "unparseable format string"; - } -} -static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return 2; - case 'i': case 'I': case 'l': case 'L': return 4; - case 'q': case 'Q': return 8; - case 'f': return (is_complex ? 8 : 4); - case 'd': return (is_complex ? 16 : 8); - case 'g': { - PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); - return 0; - } - case 'O': case 'P': return sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(short); - case 'i': case 'I': return sizeof(int); - case 'l': case 'L': return sizeof(long); - #ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(PY_LONG_LONG); - #endif - case 'f': return sizeof(float) * (is_complex ? 2 : 1); - case 'd': return sizeof(double) * (is_complex ? 2 : 1); - case 'g': return sizeof(long double) * (is_complex ? 2 : 1); - case 'O': case 'P': return sizeof(void*); - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -typedef struct { char c; short x; } __Pyx_st_short; -typedef struct { char c; int x; } __Pyx_st_int; -typedef struct { char c; long x; } __Pyx_st_long; -typedef struct { char c; float x; } __Pyx_st_float; -typedef struct { char c; double x; } __Pyx_st_double; -typedef struct { char c; long double x; } __Pyx_st_longdouble; -typedef struct { char c; void *x; } __Pyx_st_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_st_float) - sizeof(float); - case 'd': return sizeof(__Pyx_st_double) - sizeof(double); - case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -/* These are for computing the padding at the end of the struct to align - on the first member of the struct. This will probably the same as above, - but we don't have any guarantees. - */ -typedef struct { short x; char c; } __Pyx_pad_short; -typedef struct { int x; char c; } __Pyx_pad_int; -typedef struct { long x; char c; } __Pyx_pad_long; -typedef struct { float x; char c; } __Pyx_pad_float; -typedef struct { double x; char c; } __Pyx_pad_double; -typedef struct { long double x; char c; } __Pyx_pad_longdouble; -typedef struct { void *x; char c; } __Pyx_pad_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); - case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); - case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { - switch (ch) { - case 'c': - return 'H'; - case 'b': case 'h': case 'i': - case 'l': case 'q': case 's': case 'p': - return 'I'; - case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': - return 'U'; - case 'f': case 'd': case 'g': - return (is_complex ? 'C' : 'R'); - case 'O': - return 'O'; - case 'P': - return 'P'; - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { - if (ctx->head == NULL || ctx->head->field == &ctx->root) { - const char* expected; - const char* quote; - if (ctx->head == NULL) { - expected = "end"; - quote = ""; - } else { - expected = ctx->head->field->type->name; - quote = "'"; - } - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected %s%s%s but got %s", - quote, expected, quote, - __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); - } else { - __Pyx_StructField* field = ctx->head->field; - __Pyx_StructField* parent = (ctx->head - 1)->field; - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", - field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), - parent->type->name, field->name); - } -} -static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { - char group; - size_t size, offset, arraysize = 1; - if (ctx->enc_type == 0) return 0; - if (ctx->head->field->type->arraysize[0]) { - int i, ndim = 0; - if (ctx->enc_type == 's' || ctx->enc_type == 'p') { - ctx->is_valid_array = ctx->head->field->type->ndim == 1; - ndim = 1; - if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { - PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %zu", - ctx->head->field->type->arraysize[0], ctx->enc_count); - return -1; - } - } - if (!ctx->is_valid_array) { - PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", - ctx->head->field->type->ndim, ndim); - return -1; - } - for (i = 0; i < ctx->head->field->type->ndim; i++) { - arraysize *= ctx->head->field->type->arraysize[i]; - } - ctx->is_valid_array = 0; - ctx->enc_count = 1; - } - group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); - do { - __Pyx_StructField* field = ctx->head->field; - __Pyx_TypeInfo* type = field->type; - if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { - size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); - } else { - size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); - } - if (ctx->enc_packmode == '@') { - size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); - size_t align_mod_offset; - if (align_at == 0) return -1; - align_mod_offset = ctx->fmt_offset % align_at; - if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; - if (ctx->struct_alignment == 0) - ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, - ctx->is_complex); - } - if (type->size != size || type->typegroup != group) { - if (type->typegroup == 'C' && type->fields != NULL) { - size_t parent_offset = ctx->head->parent_offset + field->offset; - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = parent_offset; - continue; - } - if ((type->typegroup == 'H' || group == 'H') && type->size == size) { - } else { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - } - offset = ctx->head->parent_offset + field->offset; - if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; - } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } - } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; -} -static PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number, ndim; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ndim = ctx->head->field->type->ndim; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; - } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; - } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; - } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; -} -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; - } - break; - case '}': - { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } - } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; - } - CYTHON_FALLTHROUGH; - case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && - (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - CYTHON_FALLTHROUGH; - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: - { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; - } - } - } -} - -/* BufferGetAndValidate */ - static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { - if (unlikely(info->buf == NULL)) return; - if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; - __Pyx_ReleaseBuffer(info); -} -static void __Pyx_ZeroBuffer(Py_buffer* buf) { - buf->buf = NULL; - buf->obj = NULL; - buf->strides = __Pyx_zeros; - buf->shape = __Pyx_zeros; - buf->suboffsets = __Pyx_minusones; -} -static int __Pyx__GetBufferAndValidate( - Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, - int nd, int cast, __Pyx_BufFmt_StackElem* stack) -{ - buf->buf = NULL; - if (unlikely(__Pyx_GetBuffer(obj, buf, flags) == -1)) { - __Pyx_ZeroBuffer(buf); - return -1; - } - if (unlikely(buf->ndim != nd)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - nd, buf->ndim); - goto fail; - } - if (!cast) { - __Pyx_BufFmt_Context ctx; - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; - } - if (unlikely((size_t)buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", - buf->itemsize, (buf->itemsize > 1) ? "s" : "", - dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; - return 0; -fail:; - __Pyx_SafeReleaseBuffer(buf); - return -1; -} - -/* BufferFallbackError */ - static void __Pyx_RaiseBufferFallbackError(void) { - PyErr_SetString(PyExc_ValueError, - "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); -} - -/* ArgTypeTest */ - static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) -{ - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - else if (exact) { - #if PY_MAJOR_VERSION == 2 - if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; - #endif - } - else { - if (likely(__Pyx_TypeCheck(obj, type))) return 1; - } - PyErr_Format(PyExc_TypeError, - "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", - name, type->tp_name, Py_TYPE(obj)->tp_name); - return 0; -} - -/* DivInt[Py_ssize_t] */ - static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { - Py_ssize_t q = a / b; - Py_ssize_t r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* GetAttr */ - static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { -#if CYTHON_USE_TYPE_SLOTS -#if PY_MAJOR_VERSION >= 3 - if (likely(PyUnicode_Check(n))) -#else - if (likely(PyString_Check(n))) -#endif - return __Pyx_PyObject_GetAttrStr(o, n); -#endif - return PyObject_GetAttr(o, n); -} - -/* decode_c_string */ - static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { - Py_ssize_t length; - if (unlikely((start < 0) | (stop < 0))) { - size_t slen = strlen(cstring); - if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { - PyErr_SetString(PyExc_OverflowError, - "c-string too long to convert to Python"); - return NULL; - } - length = (Py_ssize_t) slen; - if (start < 0) { - start += length; - if (start < 0) - start = 0; - } - if (stop < 0) - stop += length; - } - if (unlikely(stop <= start)) - return __Pyx_NewRef(__pyx_empty_unicode); - length = stop - start; - cstring += start; - if (decode_func) { - return decode_func(cstring, length, errors); - } else { - return PyUnicode_Decode(cstring, length, encoding, errors); - } -} - -/* GetAttr3 */ - static PyObject *__Pyx_GetAttr3Default(PyObject *d) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - return NULL; - __Pyx_PyErr_Clear(); - Py_INCREF(d); - return d; -} -static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { - PyObject *r = __Pyx_GetAttr(o, n); - return (likely(r)) ? r : __Pyx_GetAttr3Default(d); -} - -/* RaiseTooManyValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -/* RaiseNeedMoreValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -/* RaiseNoneIterError */ - static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); -} - -/* SwapException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = *type; - exc_info->exc_value = *value; - exc_info->exc_traceback = *tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = *type; - tstate->exc_value = *value; - tstate->exc_traceback = *tb; - #endif - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); - PyErr_SetExcInfo(*type, *value, *tb); - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#endif - -/* Import */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* FastTypeChecks */ - #if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; - if (a == b) - return 1; - } - return b == &PyBaseObject_Type; -} -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { - PyObject *mro; - if (a == b) return 1; - mro = a->tp_mro; - if (likely(mro)) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(mro); - for (i = 0; i < n; i++) { - if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) - return 1; - } - return 0; - } - return __Pyx_InBases(a, b); -} -#if PY_MAJOR_VERSION == 2 -static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { - PyObject *exception, *value, *tb; - int res; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&exception, &value, &tb); - res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - if (!res) { - res = PyObject_IsSubclass(err, exc_type2); - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - } - __Pyx_ErrRestore(exception, value, tb); - return res; -} -#else -static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { - int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; - if (!res) { - res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); - } - return res; -} -#endif -static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - assert(PyExceptionClass_Check(exc_type)); - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; i= 3 - "'%.50s' object has no attribute '%U'", - tp->tp_name, attr_name); -#else - "'%.50s' object has no attribute '%.400s'", - tp->tp_name, PyString_AS_STRING(attr_name)); -#endif - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { - PyObject *descr; - PyTypeObject *tp = Py_TYPE(obj); - if (unlikely(!PyString_Check(attr_name))) { - return PyObject_GenericGetAttr(obj, attr_name); - } - assert(!tp->tp_dictoffset); - descr = _PyType_Lookup(tp, attr_name); - if (unlikely(!descr)) { - return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); - } - Py_INCREF(descr); - #if PY_MAJOR_VERSION < 3 - if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) - #endif - { - descrgetfunc f = Py_TYPE(descr)->tp_descr_get; - if (unlikely(f)) { - PyObject *res = f(descr, obj, (PyObject *)tp); - Py_DECREF(descr); - return res; - } - } - return descr; -} -#endif - -/* PyObject_GenericGetAttr */ - #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { - if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { - return PyObject_GenericGetAttr(obj, attr_name); - } - return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); -} -#endif - -/* SetVTable */ - static int __Pyx_SetVtable(PyObject *dict, void *vtable) { -#if PY_VERSION_HEX >= 0x02070000 - PyObject *ob = PyCapsule_New(vtable, 0, 0); -#else - PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); -#endif - if (!ob) - goto bad; - if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) - goto bad; - Py_DECREF(ob); - return 0; -bad: - Py_XDECREF(ob); - return -1; -} - -/* PyObjectGetAttrStrNoError */ - static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - __Pyx_PyErr_Clear(); -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { - PyObject *result; -#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 - PyTypeObject* tp = Py_TYPE(obj); - if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { - return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); - } -#endif - result = __Pyx_PyObject_GetAttrStr(obj, attr_name); - if (unlikely(!result)) { - __Pyx_PyObject_GetAttrStr_ClearAttributeError(); - } - return result; -} - -/* SetupReduce */ - static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { - int ret; - PyObject *name_attr; - name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2); - if (likely(name_attr)) { - ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); - } else { - ret = -1; - } - if (unlikely(ret < 0)) { - PyErr_Clear(); - ret = 0; - } - Py_XDECREF(name_attr); - return ret; -} -static int __Pyx_setup_reduce(PyObject* type_obj) { - int ret = 0; - PyObject *object_reduce = NULL; - PyObject *object_getstate = NULL; - PyObject *object_reduce_ex = NULL; - PyObject *reduce = NULL; - PyObject *reduce_ex = NULL; - PyObject *reduce_cython = NULL; - PyObject *setstate = NULL; - PyObject *setstate_cython = NULL; - PyObject *getstate = NULL; -#if CYTHON_USE_PYTYPE_LOOKUP - getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate); -#else - getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate); - if (!getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (getstate) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate); -#else - object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate); - if (!object_getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (object_getstate != getstate) { - goto __PYX_GOOD; - } - } -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; - if (reduce_ex == object_reduce_ex) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; - if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); - if (likely(reduce_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (reduce == object_reduce || PyErr_Occurred()) { - goto __PYX_BAD; - } - setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); - if (!setstate) PyErr_Clear(); - if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); - if (likely(setstate_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (!setstate || PyErr_Occurred()) { - goto __PYX_BAD; - } - } - PyType_Modified((PyTypeObject*)type_obj); - } - } - goto __PYX_GOOD; -__PYX_BAD: - if (!PyErr_Occurred()) - PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); - ret = -1; -__PYX_GOOD: -#if !CYTHON_USE_PYTYPE_LOOKUP - Py_XDECREF(object_reduce); - Py_XDECREF(object_reduce_ex); - Py_XDECREF(object_getstate); - Py_XDECREF(getstate); -#endif - Py_XDECREF(reduce); - Py_XDECREF(reduce_ex); - Py_XDECREF(reduce_cython); - Py_XDECREF(setstate); - Py_XDECREF(setstate_cython); - return ret; -} - -/* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* CLineInTraceback */ - #ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ - #include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - if ((0)) {} - view->obj = NULL; - Py_DECREF(obj); -} -#endif - - - /* MemviewSliceIsContig */ - static int -__pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim) -{ - int i, index, step, start; - Py_ssize_t itemsize = mvs.memview->view.itemsize; - if (order == 'F') { - step = 1; - start = 0; - } else { - step = -1; - start = ndim - 1; - } - for (i = 0; i < ndim; i++) { - index = start + step * i; - if (mvs.suboffsets[index] >= 0 || mvs.strides[index] != itemsize) - return 0; - itemsize *= mvs.shape[index]; - } - return 1; -} - -/* OverlappingSlices */ - static void -__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, - void **out_start, void **out_end, - int ndim, size_t itemsize) -{ - char *start, *end; - int i; - start = end = slice->data; - for (i = 0; i < ndim; i++) { - Py_ssize_t stride = slice->strides[i]; - Py_ssize_t extent = slice->shape[i]; - if (extent == 0) { - *out_start = *out_end = start; - return; - } else { - if (stride > 0) - end += stride * (extent - 1); - else - start += stride * (extent - 1); - } - } - *out_start = start; - *out_end = end + itemsize; -} -static int -__pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize) -{ - void *start1, *end1, *start2, *end2; - __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); - __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); - return (start1 < end2) && (start2 < end1); -} - -/* Capsule */ - static CYTHON_INLINE PyObject * -__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) -{ - PyObject *cobj; -#if PY_VERSION_HEX >= 0x02070000 - cobj = PyCapsule_New(p, sig, NULL); -#else - cobj = PyCObject_FromVoidPtr(p, NULL); -#endif - return cobj; -} - -/* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* TypeInfoCompare */ - static int -__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) -{ - int i; - if (!a || !b) - return 0; - if (a == b) - return 1; - if (a->size != b->size || a->typegroup != b->typegroup || - a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { - if (a->typegroup == 'H' || b->typegroup == 'H') { - return a->size == b->size; - } else { - return 0; - } - } - if (a->ndim) { - for (i = 0; i < a->ndim; i++) - if (a->arraysize[i] != b->arraysize[i]) - return 0; - } - if (a->typegroup == 'S') { - if (a->flags != b->flags) - return 0; - if (a->fields || b->fields) { - if (!(a->fields && b->fields)) - return 0; - for (i = 0; a->fields[i].type && b->fields[i].type; i++) { - __Pyx_StructField *field_a = a->fields + i; - __Pyx_StructField *field_b = b->fields + i; - if (field_a->offset != field_b->offset || - !__pyx_typeinfo_cmp(field_a->type, field_b->type)) - return 0; - } - return !a->fields[i].type && !b->fields[i].type; - } - } - return 1; -} - -/* MemviewSliceValidateAndInit */ - static int -__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) -{ - if (buf->shape[dim] <= 1) - return 1; - if (buf->strides) { - if (spec & __Pyx_MEMVIEW_CONTIG) { - if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { - if (unlikely(buf->strides[dim] != sizeof(void *))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly contiguous " - "in dimension %d.", dim); - goto fail; - } - } else if (unlikely(buf->strides[dim] != buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_FOLLOW) { - Py_ssize_t stride = buf->strides[dim]; - if (stride < 0) - stride = -stride; - if (unlikely(stride < buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - } else { - if (unlikely(spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1)) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not contiguous in " - "dimension %d", dim); - goto fail; - } else if (unlikely(spec & (__Pyx_MEMVIEW_PTR))) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not indirect in " - "dimension %d", dim); - goto fail; - } else if (unlikely(buf->suboffsets)) { - PyErr_SetString(PyExc_ValueError, - "Buffer exposes suboffsets but no strides"); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) -{ - if (spec & __Pyx_MEMVIEW_DIRECT) { - if (unlikely(buf->suboffsets && buf->suboffsets[dim] >= 0)) { - PyErr_Format(PyExc_ValueError, - "Buffer not compatible with direct access " - "in dimension %d.", dim); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_PTR) { - if (unlikely(!buf->suboffsets || (buf->suboffsets[dim] < 0))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly accessible " - "in dimension %d.", dim); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) -{ - int i; - if (c_or_f_flag & __Pyx_IS_F_CONTIG) { - Py_ssize_t stride = 1; - for (i = 0; i < ndim; i++) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not fortran contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { - Py_ssize_t stride = 1; - for (i = ndim - 1; i >- 1; i--) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not C contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } - return 1; -fail: - return 0; -} -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj) -{ - struct __pyx_memoryview_obj *memview, *new_memview; - __Pyx_RefNannyDeclarations - Py_buffer *buf; - int i, spec = 0, retval = -1; - __Pyx_BufFmt_Context ctx; - int from_memoryview = __pyx_memoryview_check(original_obj); - __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); - if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) - original_obj)->typeinfo)) { - memview = (struct __pyx_memoryview_obj *) original_obj; - new_memview = NULL; - } else { - memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - original_obj, buf_flags, 0, dtype); - new_memview = memview; - if (unlikely(!memview)) - goto fail; - } - buf = &memview->view; - if (unlikely(buf->ndim != ndim)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - ndim, buf->ndim); - goto fail; - } - if (new_memview) { - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (unlikely(!__Pyx_BufFmt_CheckString(&ctx, buf->format))) goto fail; - } - if (unlikely((unsigned) buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " - "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", - buf->itemsize, - (buf->itemsize > 1) ? "s" : "", - dtype->name, - dtype->size, - (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->len > 0) { - for (i = 0; i < ndim; i++) { - spec = axes_specs[i]; - if (unlikely(!__pyx_check_strides(buf, i, ndim, spec))) - goto fail; - if (unlikely(!__pyx_check_suboffsets(buf, i, ndim, spec))) - goto fail; - } - if (unlikely(buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))) - goto fail; - } - if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, - new_memview != NULL) == -1)) { - goto fail; - } - retval = 0; - goto no_fail; -fail: - Py_XDECREF(new_memview); - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 1, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_double(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 1, - &__Pyx_TypeInfo_double, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 2, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsdsds_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 3, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* MemviewSliceCopyTemplate */ - static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object) -{ - __Pyx_RefNannyDeclarations - int i; - __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; - struct __pyx_memoryview_obj *from_memview = from_mvs->memview; - Py_buffer *buf = &from_memview->view; - PyObject *shape_tuple = NULL; - PyObject *temp_int = NULL; - struct __pyx_array_obj *array_obj = NULL; - struct __pyx_memoryview_obj *memview_obj = NULL; - __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); - for (i = 0; i < ndim; i++) { - if (unlikely(from_mvs->suboffsets[i] >= 0)) { - PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " - "indirect dimensions (axis %d)", i); - goto fail; - } - } - shape_tuple = PyTuple_New(ndim); - if (unlikely(!shape_tuple)) { - goto fail; - } - __Pyx_GOTREF(shape_tuple); - for(i = 0; i < ndim; i++) { - temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); - if(unlikely(!temp_int)) { - goto fail; - } else { - PyTuple_SET_ITEM(shape_tuple, i, temp_int); - temp_int = NULL; - } - } - array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); - if (unlikely(!array_obj)) { - goto fail; - } - __Pyx_GOTREF(array_obj); - memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - (PyObject *) array_obj, contig_flag, - dtype_is_object, - from_mvs->memview->typeinfo); - if (unlikely(!memview_obj)) - goto fail; - if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) - goto fail; - if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, - dtype_is_object) < 0)) - goto fail; - goto no_fail; -fail: - __Pyx_XDECREF(new_mvs.memview); - new_mvs.memview = NULL; - new_mvs.data = NULL; -no_fail: - __Pyx_XDECREF(shape_tuple); - __Pyx_XDECREF(temp_int); - __Pyx_XDECREF(array_obj); - __Pyx_RefNannyFinishContext(); - return new_mvs; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const char neg_one = (char) -1, const_zero = (char) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(char) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (char) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (char) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(char) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) - case -2: - if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - } -#endif - if (sizeof(char) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - char val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (char) -1; - } - } else { - char val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (char) -1; - val = __Pyx_PyInt_As_char(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to char"); - return (char) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to char"); - return (char) -1; -} - -/* FetchCommonType */ - static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { - PyObject* fake_module; - PyTypeObject* cached_type = NULL; - fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI); - if (!fake_module) return NULL; - Py_INCREF(fake_module); - cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name); - if (cached_type) { - if (!PyType_Check((PyObject*)cached_type)) { - PyErr_Format(PyExc_TypeError, - "Shared Cython type %.200s is not a type object", - type->tp_name); - goto bad; - } - if (cached_type->tp_basicsize != type->tp_basicsize) { - PyErr_Format(PyExc_TypeError, - "Shared Cython type %.200s has the wrong size, try recompiling", - type->tp_name); - goto bad; - } - } else { - if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad; - PyErr_Clear(); - if (PyType_Ready(type) < 0) goto bad; - if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0) - goto bad; - Py_INCREF(type); - cached_type = type; - } -done: - Py_DECREF(fake_module); - return cached_type; -bad: - Py_XDECREF(cached_type); - cached_type = NULL; - goto done; -} - -/* PyObjectGetMethod */ - static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method) { - PyObject *attr; -#if CYTHON_UNPACK_METHODS && CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_PYTYPE_LOOKUP - PyTypeObject *tp = Py_TYPE(obj); - PyObject *descr; - descrgetfunc f = NULL; - PyObject **dictptr, *dict; - int meth_found = 0; - assert (*method == NULL); - if (unlikely(tp->tp_getattro != PyObject_GenericGetAttr)) { - attr = __Pyx_PyObject_GetAttrStr(obj, name); - goto try_unpack; - } - if (unlikely(tp->tp_dict == NULL) && unlikely(PyType_Ready(tp) < 0)) { - return 0; - } - descr = _PyType_Lookup(tp, name); - if (likely(descr != NULL)) { - Py_INCREF(descr); -#if PY_MAJOR_VERSION >= 3 - #ifdef __Pyx_CyFunction_USED - if (likely(PyFunction_Check(descr) || (Py_TYPE(descr) == &PyMethodDescr_Type) || __Pyx_CyFunction_Check(descr))) - #else - if (likely(PyFunction_Check(descr) || (Py_TYPE(descr) == &PyMethodDescr_Type))) - #endif -#else - #ifdef __Pyx_CyFunction_USED - if (likely(PyFunction_Check(descr) || __Pyx_CyFunction_Check(descr))) - #else - if (likely(PyFunction_Check(descr))) - #endif -#endif - { - meth_found = 1; - } else { - f = Py_TYPE(descr)->tp_descr_get; - if (f != NULL && PyDescr_IsData(descr)) { - attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); - Py_DECREF(descr); - goto try_unpack; - } - } - } - dictptr = _PyObject_GetDictPtr(obj); - if (dictptr != NULL && (dict = *dictptr) != NULL) { - Py_INCREF(dict); - attr = __Pyx_PyDict_GetItemStr(dict, name); - if (attr != NULL) { - Py_INCREF(attr); - Py_DECREF(dict); - Py_XDECREF(descr); - goto try_unpack; - } - Py_DECREF(dict); - } - if (meth_found) { - *method = descr; - return 1; - } - if (f != NULL) { - attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); - Py_DECREF(descr); - goto try_unpack; - } - if (descr != NULL) { - *method = descr; - return 0; - } - PyErr_Format(PyExc_AttributeError, -#if PY_MAJOR_VERSION >= 3 - "'%.50s' object has no attribute '%U'", - tp->tp_name, name); -#else - "'%.50s' object has no attribute '%.400s'", - tp->tp_name, PyString_AS_STRING(name)); -#endif - return 0; -#else - attr = __Pyx_PyObject_GetAttrStr(obj, name); - goto try_unpack; -#endif -try_unpack: -#if CYTHON_UNPACK_METHODS - if (likely(attr) && PyMethod_Check(attr) && likely(PyMethod_GET_SELF(attr) == obj)) { - PyObject *function = PyMethod_GET_FUNCTION(attr); - Py_INCREF(function); - Py_DECREF(attr); - *method = function; - return 1; - } -#endif - *method = attr; - return 0; -} - -/* PyObjectCallMethod1 */ - static PyObject* __Pyx__PyObject_CallMethod1(PyObject* method, PyObject* arg) { - PyObject *result = __Pyx_PyObject_CallOneArg(method, arg); - Py_DECREF(method); - return result; -} -static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) { - PyObject *method = NULL, *result; - int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method); - if (likely(is_method)) { - result = __Pyx_PyObject_Call2Args(method, obj, arg); - Py_DECREF(method); - return result; - } - if (unlikely(!method)) return NULL; - return __Pyx__PyObject_CallMethod1(method, arg); -} - -/* CoroutineBase */ - #include -#include -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -#define __Pyx_Coroutine_Undelegate(gen) Py_CLEAR((gen)->yieldfrom) -static int __Pyx_PyGen__FetchStopIterationValue(CYTHON_UNUSED PyThreadState *__pyx_tstate, PyObject **pvalue) { - PyObject *et, *ev, *tb; - PyObject *value = NULL; - __Pyx_ErrFetch(&et, &ev, &tb); - if (!et) { - Py_XDECREF(tb); - Py_XDECREF(ev); - Py_INCREF(Py_None); - *pvalue = Py_None; - return 0; - } - if (likely(et == PyExc_StopIteration)) { - if (!ev) { - Py_INCREF(Py_None); - value = Py_None; - } -#if PY_VERSION_HEX >= 0x030300A0 - else if (Py_TYPE(ev) == (PyTypeObject*)PyExc_StopIteration) { - value = ((PyStopIterationObject *)ev)->value; - Py_INCREF(value); - Py_DECREF(ev); - } -#endif - else if (unlikely(PyTuple_Check(ev))) { - if (PyTuple_GET_SIZE(ev) >= 1) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - value = PyTuple_GET_ITEM(ev, 0); - Py_INCREF(value); -#else - value = PySequence_ITEM(ev, 0); -#endif - } else { - Py_INCREF(Py_None); - value = Py_None; - } - Py_DECREF(ev); - } - else if (!__Pyx_TypeCheck(ev, (PyTypeObject*)PyExc_StopIteration)) { - value = ev; - } - if (likely(value)) { - Py_XDECREF(tb); - Py_DECREF(et); - *pvalue = value; - return 0; - } - } else if (!__Pyx_PyErr_GivenExceptionMatches(et, PyExc_StopIteration)) { - __Pyx_ErrRestore(et, ev, tb); - return -1; - } - PyErr_NormalizeException(&et, &ev, &tb); - if (unlikely(!PyObject_TypeCheck(ev, (PyTypeObject*)PyExc_StopIteration))) { - __Pyx_ErrRestore(et, ev, tb); - return -1; - } - Py_XDECREF(tb); - Py_DECREF(et); -#if PY_VERSION_HEX >= 0x030300A0 - value = ((PyStopIterationObject *)ev)->value; - Py_INCREF(value); - Py_DECREF(ev); -#else - { - PyObject* args = __Pyx_PyObject_GetAttrStr(ev, __pyx_n_s_args); - Py_DECREF(ev); - if (likely(args)) { - value = PySequence_GetItem(args, 0); - Py_DECREF(args); - } - if (unlikely(!value)) { - __Pyx_ErrRestore(NULL, NULL, NULL); - Py_INCREF(Py_None); - value = Py_None; - } - } -#endif - *pvalue = value; - return 0; -} -static CYTHON_INLINE -void __Pyx_Coroutine_ExceptionClear(__Pyx_ExcInfoStruct *exc_state) { - PyObject *t, *v, *tb; - t = exc_state->exc_type; - v = exc_state->exc_value; - tb = exc_state->exc_traceback; - exc_state->exc_type = NULL; - exc_state->exc_value = NULL; - exc_state->exc_traceback = NULL; - Py_XDECREF(t); - Py_XDECREF(v); - Py_XDECREF(tb); -} -#define __Pyx_Coroutine_AlreadyRunningError(gen) (__Pyx__Coroutine_AlreadyRunningError(gen), (PyObject*)NULL) -static void __Pyx__Coroutine_AlreadyRunningError(CYTHON_UNUSED __pyx_CoroutineObject *gen) { - const char *msg; - if ((0)) { - #ifdef __Pyx_Coroutine_USED - } else if (__Pyx_Coroutine_Check((PyObject*)gen)) { - msg = "coroutine already executing"; - #endif - #ifdef __Pyx_AsyncGen_USED - } else if (__Pyx_AsyncGen_CheckExact((PyObject*)gen)) { - msg = "async generator already executing"; - #endif - } else { - msg = "generator already executing"; - } - PyErr_SetString(PyExc_ValueError, msg); -} -#define __Pyx_Coroutine_NotStartedError(gen) (__Pyx__Coroutine_NotStartedError(gen), (PyObject*)NULL) -static void __Pyx__Coroutine_NotStartedError(CYTHON_UNUSED PyObject *gen) { - const char *msg; - if ((0)) { - #ifdef __Pyx_Coroutine_USED - } else if (__Pyx_Coroutine_Check(gen)) { - msg = "can't send non-None value to a just-started coroutine"; - #endif - #ifdef __Pyx_AsyncGen_USED - } else if (__Pyx_AsyncGen_CheckExact(gen)) { - msg = "can't send non-None value to a just-started async generator"; - #endif - } else { - msg = "can't send non-None value to a just-started generator"; - } - PyErr_SetString(PyExc_TypeError, msg); -} -#define __Pyx_Coroutine_AlreadyTerminatedError(gen, value, closing) (__Pyx__Coroutine_AlreadyTerminatedError(gen, value, closing), (PyObject*)NULL) -static void __Pyx__Coroutine_AlreadyTerminatedError(CYTHON_UNUSED PyObject *gen, PyObject *value, CYTHON_UNUSED int closing) { - #ifdef __Pyx_Coroutine_USED - if (!closing && __Pyx_Coroutine_Check(gen)) { - PyErr_SetString(PyExc_RuntimeError, "cannot reuse already awaited coroutine"); - } else - #endif - if (value) { - #ifdef __Pyx_AsyncGen_USED - if (__Pyx_AsyncGen_CheckExact(gen)) - PyErr_SetNone(__Pyx_PyExc_StopAsyncIteration); - else - #endif - PyErr_SetNone(PyExc_StopIteration); - } -} -static -PyObject *__Pyx_Coroutine_SendEx(__pyx_CoroutineObject *self, PyObject *value, int closing) { - __Pyx_PyThreadState_declare - PyThreadState *tstate; - __Pyx_ExcInfoStruct *exc_state; - PyObject *retval; - assert(!self->is_running); - if (unlikely(self->resume_label == 0)) { - if (unlikely(value && value != Py_None)) { - return __Pyx_Coroutine_NotStartedError((PyObject*)self); - } - } - if (unlikely(self->resume_label == -1)) { - return __Pyx_Coroutine_AlreadyTerminatedError((PyObject*)self, value, closing); - } -#if CYTHON_FAST_THREAD_STATE - __Pyx_PyThreadState_assign - tstate = __pyx_tstate; -#else - tstate = __Pyx_PyThreadState_Current; -#endif - exc_state = &self->gi_exc_state; - if (exc_state->exc_type) { - #if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_PYSTON - #else - if (exc_state->exc_traceback) { - PyTracebackObject *tb = (PyTracebackObject *) exc_state->exc_traceback; - PyFrameObject *f = tb->tb_frame; - assert(f->f_back == NULL); - #if PY_VERSION_HEX >= 0x030B00A1 - f->f_back = PyThreadState_GetFrame(tstate); - #else - Py_XINCREF(tstate->frame); - f->f_back = tstate->frame; - #endif - } - #endif - } -#if CYTHON_USE_EXC_INFO_STACK - exc_state->previous_item = tstate->exc_info; - tstate->exc_info = exc_state; -#else - if (exc_state->exc_type) { - __Pyx_ExceptionSwap(&exc_state->exc_type, &exc_state->exc_value, &exc_state->exc_traceback); - } else { - __Pyx_Coroutine_ExceptionClear(exc_state); - __Pyx_ExceptionSave(&exc_state->exc_type, &exc_state->exc_value, &exc_state->exc_traceback); - } -#endif - self->is_running = 1; - retval = self->body((PyObject *) self, tstate, value); - self->is_running = 0; -#if CYTHON_USE_EXC_INFO_STACK - exc_state = &self->gi_exc_state; - tstate->exc_info = exc_state->previous_item; - exc_state->previous_item = NULL; - __Pyx_Coroutine_ResetFrameBackpointer(exc_state); -#endif - return retval; -} -static CYTHON_INLINE void __Pyx_Coroutine_ResetFrameBackpointer(__Pyx_ExcInfoStruct *exc_state) { - PyObject *exc_tb = exc_state->exc_traceback; - if (likely(exc_tb)) { -#if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_PYSTON -#else - PyTracebackObject *tb = (PyTracebackObject *) exc_tb; - PyFrameObject *f = tb->tb_frame; - Py_CLEAR(f->f_back); -#endif - } -} -static CYTHON_INLINE -PyObject *__Pyx_Coroutine_MethodReturn(CYTHON_UNUSED PyObject* gen, PyObject *retval) { - if (unlikely(!retval)) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (!__Pyx_PyErr_Occurred()) { - PyObject *exc = PyExc_StopIteration; - #ifdef __Pyx_AsyncGen_USED - if (__Pyx_AsyncGen_CheckExact(gen)) - exc = __Pyx_PyExc_StopAsyncIteration; - #endif - __Pyx_PyErr_SetNone(exc); - } - } - return retval; -} -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3) -static CYTHON_INLINE -PyObject *__Pyx_PyGen_Send(PyGenObject *gen, PyObject *arg) { -#if PY_VERSION_HEX <= 0x030A00A1 - return _PyGen_Send(gen, arg); -#else - PyObject *result; - if (PyIter_Send((PyObject*)gen, arg ? arg : Py_None, &result) == PYGEN_RETURN) { - if (PyAsyncGen_CheckExact(gen)) { - assert(result == Py_None); - PyErr_SetNone(PyExc_StopAsyncIteration); - } - else if (result == Py_None) { - PyErr_SetNone(PyExc_StopIteration); - } - else { - _PyGen_SetStopIterationValue(result); - } - Py_CLEAR(result); - } - return result; -#endif -} -#endif -static CYTHON_INLINE -PyObject *__Pyx_Coroutine_FinishDelegation(__pyx_CoroutineObject *gen) { - PyObject *ret; - PyObject *val = NULL; - __Pyx_Coroutine_Undelegate(gen); - __Pyx_PyGen__FetchStopIterationValue(__Pyx_PyThreadState_Current, &val); - ret = __Pyx_Coroutine_SendEx(gen, val, 0); - Py_XDECREF(val); - return ret; -} -static PyObject *__Pyx_Coroutine_Send(PyObject *self, PyObject *value) { - PyObject *retval; - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject*) self; - PyObject *yf = gen->yieldfrom; - if (unlikely(gen->is_running)) - return __Pyx_Coroutine_AlreadyRunningError(gen); - if (yf) { - PyObject *ret; - gen->is_running = 1; - #ifdef __Pyx_Generator_USED - if (__Pyx_Generator_CheckExact(yf)) { - ret = __Pyx_Coroutine_Send(yf, value); - } else - #endif - #ifdef __Pyx_Coroutine_USED - if (__Pyx_Coroutine_Check(yf)) { - ret = __Pyx_Coroutine_Send(yf, value); - } else - #endif - #ifdef __Pyx_AsyncGen_USED - if (__pyx_PyAsyncGenASend_CheckExact(yf)) { - ret = __Pyx_async_gen_asend_send(yf, value); - } else - #endif - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3) - if (PyGen_CheckExact(yf)) { - ret = __Pyx_PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value); - } else - #endif - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03050000 && defined(PyCoro_CheckExact) && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3) - if (PyCoro_CheckExact(yf)) { - ret = __Pyx_PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value); - } else - #endif - { - if (value == Py_None) - ret = Py_TYPE(yf)->tp_iternext(yf); - else - ret = __Pyx_PyObject_CallMethod1(yf, __pyx_n_s_send, value); - } - gen->is_running = 0; - if (likely(ret)) { - return ret; - } - retval = __Pyx_Coroutine_FinishDelegation(gen); - } else { - retval = __Pyx_Coroutine_SendEx(gen, value, 0); - } - return __Pyx_Coroutine_MethodReturn(self, retval); -} -static int __Pyx_Coroutine_CloseIter(__pyx_CoroutineObject *gen, PyObject *yf) { - PyObject *retval = NULL; - int err = 0; - #ifdef __Pyx_Generator_USED - if (__Pyx_Generator_CheckExact(yf)) { - retval = __Pyx_Coroutine_Close(yf); - if (!retval) - return -1; - } else - #endif - #ifdef __Pyx_Coroutine_USED - if (__Pyx_Coroutine_Check(yf)) { - retval = __Pyx_Coroutine_Close(yf); - if (!retval) - return -1; - } else - if (__Pyx_CoroutineAwait_CheckExact(yf)) { - retval = __Pyx_CoroutineAwait_Close((__pyx_CoroutineAwaitObject*)yf, NULL); - if (!retval) - return -1; - } else - #endif - #ifdef __Pyx_AsyncGen_USED - if (__pyx_PyAsyncGenASend_CheckExact(yf)) { - retval = __Pyx_async_gen_asend_close(yf, NULL); - } else - if (__pyx_PyAsyncGenAThrow_CheckExact(yf)) { - retval = __Pyx_async_gen_athrow_close(yf, NULL); - } else - #endif - { - PyObject *meth; - gen->is_running = 1; - meth = __Pyx_PyObject_GetAttrStr(yf, __pyx_n_s_close); - if (unlikely(!meth)) { - if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_WriteUnraisable(yf); - } - PyErr_Clear(); - } else { - retval = PyObject_CallFunction(meth, NULL); - Py_DECREF(meth); - if (!retval) - err = -1; - } - gen->is_running = 0; - } - Py_XDECREF(retval); - return err; -} -static PyObject *__Pyx_Generator_Next(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject*) self; - PyObject *yf = gen->yieldfrom; - if (unlikely(gen->is_running)) - return __Pyx_Coroutine_AlreadyRunningError(gen); - if (yf) { - PyObject *ret; - gen->is_running = 1; - #ifdef __Pyx_Generator_USED - if (__Pyx_Generator_CheckExact(yf)) { - ret = __Pyx_Generator_Next(yf); - } else - #endif - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3) - if (PyGen_CheckExact(yf)) { - ret = __Pyx_PyGen_Send((PyGenObject*)yf, NULL); - } else - #endif - #ifdef __Pyx_Coroutine_USED - if (__Pyx_Coroutine_Check(yf)) { - ret = __Pyx_Coroutine_Send(yf, Py_None); - } else - #endif - ret = Py_TYPE(yf)->tp_iternext(yf); - gen->is_running = 0; - if (likely(ret)) { - return ret; - } - return __Pyx_Coroutine_FinishDelegation(gen); - } - return __Pyx_Coroutine_SendEx(gen, Py_None, 0); -} -static PyObject *__Pyx_Coroutine_Close_Method(PyObject *self, CYTHON_UNUSED PyObject *arg) { - return __Pyx_Coroutine_Close(self); -} -static PyObject *__Pyx_Coroutine_Close(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; - PyObject *retval, *raised_exception; - PyObject *yf = gen->yieldfrom; - int err = 0; - if (unlikely(gen->is_running)) - return __Pyx_Coroutine_AlreadyRunningError(gen); - if (yf) { - Py_INCREF(yf); - err = __Pyx_Coroutine_CloseIter(gen, yf); - __Pyx_Coroutine_Undelegate(gen); - Py_DECREF(yf); - } - if (err == 0) - PyErr_SetNone(PyExc_GeneratorExit); - retval = __Pyx_Coroutine_SendEx(gen, NULL, 1); - if (unlikely(retval)) { - const char *msg; - Py_DECREF(retval); - if ((0)) { - #ifdef __Pyx_Coroutine_USED - } else if (__Pyx_Coroutine_Check(self)) { - msg = "coroutine ignored GeneratorExit"; - #endif - #ifdef __Pyx_AsyncGen_USED - } else if (__Pyx_AsyncGen_CheckExact(self)) { -#if PY_VERSION_HEX < 0x03060000 - msg = "async generator ignored GeneratorExit - might require Python 3.6+ finalisation (PEP 525)"; -#else - msg = "async generator ignored GeneratorExit"; -#endif - #endif - } else { - msg = "generator ignored GeneratorExit"; - } - PyErr_SetString(PyExc_RuntimeError, msg); - return NULL; - } - raised_exception = PyErr_Occurred(); - if (likely(!raised_exception || __Pyx_PyErr_GivenExceptionMatches2(raised_exception, PyExc_GeneratorExit, PyExc_StopIteration))) { - if (raised_exception) PyErr_Clear(); - Py_INCREF(Py_None); - return Py_None; - } - return NULL; -} -static PyObject *__Pyx__Coroutine_Throw(PyObject *self, PyObject *typ, PyObject *val, PyObject *tb, - PyObject *args, int close_on_genexit) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; - PyObject *yf = gen->yieldfrom; - if (unlikely(gen->is_running)) - return __Pyx_Coroutine_AlreadyRunningError(gen); - if (yf) { - PyObject *ret; - Py_INCREF(yf); - if (__Pyx_PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit) && close_on_genexit) { - int err = __Pyx_Coroutine_CloseIter(gen, yf); - Py_DECREF(yf); - __Pyx_Coroutine_Undelegate(gen); - if (err < 0) - return __Pyx_Coroutine_MethodReturn(self, __Pyx_Coroutine_SendEx(gen, NULL, 0)); - goto throw_here; - } - gen->is_running = 1; - if (0 - #ifdef __Pyx_Generator_USED - || __Pyx_Generator_CheckExact(yf) - #endif - #ifdef __Pyx_Coroutine_USED - || __Pyx_Coroutine_Check(yf) - #endif - ) { - ret = __Pyx__Coroutine_Throw(yf, typ, val, tb, args, close_on_genexit); - #ifdef __Pyx_Coroutine_USED - } else if (__Pyx_CoroutineAwait_CheckExact(yf)) { - ret = __Pyx__Coroutine_Throw(((__pyx_CoroutineAwaitObject*)yf)->coroutine, typ, val, tb, args, close_on_genexit); - #endif - } else { - PyObject *meth = __Pyx_PyObject_GetAttrStr(yf, __pyx_n_s_throw); - if (unlikely(!meth)) { - Py_DECREF(yf); - if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { - gen->is_running = 0; - return NULL; - } - PyErr_Clear(); - __Pyx_Coroutine_Undelegate(gen); - gen->is_running = 0; - goto throw_here; - } - if (likely(args)) { - ret = PyObject_CallObject(meth, args); - } else { - ret = PyObject_CallFunctionObjArgs(meth, typ, val, tb, NULL); - } - Py_DECREF(meth); - } - gen->is_running = 0; - Py_DECREF(yf); - if (!ret) { - ret = __Pyx_Coroutine_FinishDelegation(gen); - } - return __Pyx_Coroutine_MethodReturn(self, ret); - } -throw_here: - __Pyx_Raise(typ, val, tb, NULL); - return __Pyx_Coroutine_MethodReturn(self, __Pyx_Coroutine_SendEx(gen, NULL, 0)); -} -static PyObject *__Pyx_Coroutine_Throw(PyObject *self, PyObject *args) { - PyObject *typ; - PyObject *val = NULL; - PyObject *tb = NULL; - if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb)) - return NULL; - return __Pyx__Coroutine_Throw(self, typ, val, tb, args, 1); -} -static CYTHON_INLINE int __Pyx_Coroutine_traverse_excstate(__Pyx_ExcInfoStruct *exc_state, visitproc visit, void *arg) { - Py_VISIT(exc_state->exc_type); - Py_VISIT(exc_state->exc_value); - Py_VISIT(exc_state->exc_traceback); - return 0; -} -static int __Pyx_Coroutine_traverse(__pyx_CoroutineObject *gen, visitproc visit, void *arg) { - Py_VISIT(gen->closure); - Py_VISIT(gen->classobj); - Py_VISIT(gen->yieldfrom); - return __Pyx_Coroutine_traverse_excstate(&gen->gi_exc_state, visit, arg); -} -static int __Pyx_Coroutine_clear(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; - Py_CLEAR(gen->closure); - Py_CLEAR(gen->classobj); - Py_CLEAR(gen->yieldfrom); - __Pyx_Coroutine_ExceptionClear(&gen->gi_exc_state); -#ifdef __Pyx_AsyncGen_USED - if (__Pyx_AsyncGen_CheckExact(self)) { - Py_CLEAR(((__pyx_PyAsyncGenObject*)gen)->ag_finalizer); - } -#endif - Py_CLEAR(gen->gi_code); - Py_CLEAR(gen->gi_frame); - Py_CLEAR(gen->gi_name); - Py_CLEAR(gen->gi_qualname); - Py_CLEAR(gen->gi_modulename); - return 0; -} -static void __Pyx_Coroutine_dealloc(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; - PyObject_GC_UnTrack(gen); - if (gen->gi_weakreflist != NULL) - PyObject_ClearWeakRefs(self); - if (gen->resume_label >= 0) { - PyObject_GC_Track(self); -#if PY_VERSION_HEX >= 0x030400a1 && CYTHON_USE_TP_FINALIZE - if (PyObject_CallFinalizerFromDealloc(self)) -#else - Py_TYPE(gen)->tp_del(self); - if (Py_REFCNT(self) > 0) -#endif - { - return; - } - PyObject_GC_UnTrack(self); - } -#ifdef __Pyx_AsyncGen_USED - if (__Pyx_AsyncGen_CheckExact(self)) { - /* We have to handle this case for asynchronous generators - right here, because this code has to be between UNTRACK - and GC_Del. */ - Py_CLEAR(((__pyx_PyAsyncGenObject*)self)->ag_finalizer); - } -#endif - __Pyx_Coroutine_clear(self); - PyObject_GC_Del(gen); -} -static void __Pyx_Coroutine_del(PyObject *self) { - PyObject *error_type, *error_value, *error_traceback; - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; - __Pyx_PyThreadState_declare - if (gen->resume_label < 0) { - return; - } -#if !CYTHON_USE_TP_FINALIZE - assert(self->ob_refcnt == 0); - __Pyx_SET_REFCNT(self, 1); -#endif - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&error_type, &error_value, &error_traceback); -#ifdef __Pyx_AsyncGen_USED - if (__Pyx_AsyncGen_CheckExact(self)) { - __pyx_PyAsyncGenObject *agen = (__pyx_PyAsyncGenObject*)self; - PyObject *finalizer = agen->ag_finalizer; - if (finalizer && !agen->ag_closed) { - PyObject *res = __Pyx_PyObject_CallOneArg(finalizer, self); - if (unlikely(!res)) { - PyErr_WriteUnraisable(self); - } else { - Py_DECREF(res); - } - __Pyx_ErrRestore(error_type, error_value, error_traceback); - return; - } - } -#endif - if (unlikely(gen->resume_label == 0 && !error_value)) { -#ifdef __Pyx_Coroutine_USED -#ifdef __Pyx_Generator_USED - if (!__Pyx_Generator_CheckExact(self)) -#endif - { - PyObject_GC_UnTrack(self); -#if PY_MAJOR_VERSION >= 3 || defined(PyErr_WarnFormat) - if (unlikely(PyErr_WarnFormat(PyExc_RuntimeWarning, 1, "coroutine '%.50S' was never awaited", gen->gi_qualname) < 0)) - PyErr_WriteUnraisable(self); -#else - {PyObject *msg; - char *cmsg; - #if CYTHON_COMPILING_IN_PYPY - msg = NULL; - cmsg = (char*) "coroutine was never awaited"; - #else - char *cname; - PyObject *qualname; - qualname = gen->gi_qualname; - cname = PyString_AS_STRING(qualname); - msg = PyString_FromFormat("coroutine '%.50s' was never awaited", cname); - if (unlikely(!msg)) { - PyErr_Clear(); - cmsg = (char*) "coroutine was never awaited"; - } else { - cmsg = PyString_AS_STRING(msg); - } - #endif - if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, cmsg, 1) < 0)) - PyErr_WriteUnraisable(self); - Py_XDECREF(msg);} -#endif - PyObject_GC_Track(self); - } -#endif - } else { - PyObject *res = __Pyx_Coroutine_Close(self); - if (unlikely(!res)) { - if (PyErr_Occurred()) - PyErr_WriteUnraisable(self); - } else { - Py_DECREF(res); - } - } - __Pyx_ErrRestore(error_type, error_value, error_traceback); -#if !CYTHON_USE_TP_FINALIZE - assert(Py_REFCNT(self) > 0); - if (--self->ob_refcnt == 0) { - return; - } - { - Py_ssize_t refcnt = Py_REFCNT(self); - _Py_NewReference(self); - __Pyx_SET_REFCNT(self, refcnt); - } -#if CYTHON_COMPILING_IN_CPYTHON - assert(PyType_IS_GC(Py_TYPE(self)) && - _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED); - _Py_DEC_REFTOTAL; -#endif -#ifdef COUNT_ALLOCS - --Py_TYPE(self)->tp_frees; - --Py_TYPE(self)->tp_allocs; -#endif -#endif -} -static PyObject * -__Pyx_Coroutine_get_name(__pyx_CoroutineObject *self, CYTHON_UNUSED void *context) -{ - PyObject *name = self->gi_name; - if (unlikely(!name)) name = Py_None; - Py_INCREF(name); - return name; -} -static int -__Pyx_Coroutine_set_name(__pyx_CoroutineObject *self, PyObject *value, CYTHON_UNUSED void *context) -{ - PyObject *tmp; -#if PY_MAJOR_VERSION >= 3 - if (unlikely(value == NULL || !PyUnicode_Check(value))) -#else - if (unlikely(value == NULL || !PyString_Check(value))) -#endif - { - PyErr_SetString(PyExc_TypeError, - "__name__ must be set to a string object"); - return -1; - } - tmp = self->gi_name; - Py_INCREF(value); - self->gi_name = value; - Py_XDECREF(tmp); - return 0; -} -static PyObject * -__Pyx_Coroutine_get_qualname(__pyx_CoroutineObject *self, CYTHON_UNUSED void *context) -{ - PyObject *name = self->gi_qualname; - if (unlikely(!name)) name = Py_None; - Py_INCREF(name); - return name; -} -static int -__Pyx_Coroutine_set_qualname(__pyx_CoroutineObject *self, PyObject *value, CYTHON_UNUSED void *context) -{ - PyObject *tmp; -#if PY_MAJOR_VERSION >= 3 - if (unlikely(value == NULL || !PyUnicode_Check(value))) -#else - if (unlikely(value == NULL || !PyString_Check(value))) -#endif - { - PyErr_SetString(PyExc_TypeError, - "__qualname__ must be set to a string object"); - return -1; - } - tmp = self->gi_qualname; - Py_INCREF(value); - self->gi_qualname = value; - Py_XDECREF(tmp); - return 0; -} -static PyObject * -__Pyx_Coroutine_get_frame(__pyx_CoroutineObject *self, CYTHON_UNUSED void *context) -{ - PyObject *frame = self->gi_frame; - if (!frame) { - if (unlikely(!self->gi_code)) { - Py_RETURN_NONE; - } - frame = (PyObject *) PyFrame_New( - PyThreadState_Get(), /*PyThreadState *tstate,*/ - (PyCodeObject*) self->gi_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (unlikely(!frame)) - return NULL; - self->gi_frame = frame; - } - Py_INCREF(frame); - return frame; -} -static __pyx_CoroutineObject *__Pyx__Coroutine_New( - PyTypeObject* type, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure, - PyObject *name, PyObject *qualname, PyObject *module_name) { - __pyx_CoroutineObject *gen = PyObject_GC_New(__pyx_CoroutineObject, type); - if (unlikely(!gen)) - return NULL; - return __Pyx__Coroutine_NewInit(gen, body, code, closure, name, qualname, module_name); -} -static __pyx_CoroutineObject *__Pyx__Coroutine_NewInit( - __pyx_CoroutineObject *gen, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure, - PyObject *name, PyObject *qualname, PyObject *module_name) { - gen->body = body; - gen->closure = closure; - Py_XINCREF(closure); - gen->is_running = 0; - gen->resume_label = 0; - gen->classobj = NULL; - gen->yieldfrom = NULL; - gen->gi_exc_state.exc_type = NULL; - gen->gi_exc_state.exc_value = NULL; - gen->gi_exc_state.exc_traceback = NULL; -#if CYTHON_USE_EXC_INFO_STACK - gen->gi_exc_state.previous_item = NULL; -#endif - gen->gi_weakreflist = NULL; - Py_XINCREF(qualname); - gen->gi_qualname = qualname; - Py_XINCREF(name); - gen->gi_name = name; - Py_XINCREF(module_name); - gen->gi_modulename = module_name; - Py_XINCREF(code); - gen->gi_code = code; - gen->gi_frame = NULL; - PyObject_GC_Track(gen); - return gen; -} - -/* PatchModuleWithCoroutine */ - static PyObject* __Pyx_Coroutine_patch_module(PyObject* module, const char* py_code) { -#if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) - int result; - PyObject *globals, *result_obj; - globals = PyDict_New(); if (unlikely(!globals)) goto ignore; - result = PyDict_SetItemString(globals, "_cython_coroutine_type", - #ifdef __Pyx_Coroutine_USED - (PyObject*)__pyx_CoroutineType); - #else - Py_None); - #endif - if (unlikely(result < 0)) goto ignore; - result = PyDict_SetItemString(globals, "_cython_generator_type", - #ifdef __Pyx_Generator_USED - (PyObject*)__pyx_GeneratorType); - #else - Py_None); - #endif - if (unlikely(result < 0)) goto ignore; - if (unlikely(PyDict_SetItemString(globals, "_module", module) < 0)) goto ignore; - if (unlikely(PyDict_SetItemString(globals, "__builtins__", __pyx_b) < 0)) goto ignore; - result_obj = PyRun_String(py_code, Py_file_input, globals, globals); - if (unlikely(!result_obj)) goto ignore; - Py_DECREF(result_obj); - Py_DECREF(globals); - return module; -ignore: - Py_XDECREF(globals); - PyErr_WriteUnraisable(module); - if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, "Cython module failed to patch module with custom type", 1) < 0)) { - Py_DECREF(module); - module = NULL; - } -#else - py_code++; -#endif - return module; -} - -/* PatchGeneratorABC */ - #ifndef CYTHON_REGISTER_ABCS -#define CYTHON_REGISTER_ABCS 1 -#endif -#if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) -static PyObject* __Pyx_patch_abc_module(PyObject *module); -static PyObject* __Pyx_patch_abc_module(PyObject *module) { - module = __Pyx_Coroutine_patch_module( - module, "" -"if _cython_generator_type is not None:\n" -" try: Generator = _module.Generator\n" -" except AttributeError: pass\n" -" else: Generator.register(_cython_generator_type)\n" -"if _cython_coroutine_type is not None:\n" -" try: Coroutine = _module.Coroutine\n" -" except AttributeError: pass\n" -" else: Coroutine.register(_cython_coroutine_type)\n" - ); - return module; -} -#endif -static int __Pyx_patch_abc(void) { -#if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) - static int abc_patched = 0; - if (CYTHON_REGISTER_ABCS && !abc_patched) { - PyObject *module; - module = PyImport_ImportModule((PY_MAJOR_VERSION >= 3) ? "collections.abc" : "collections"); - if (!module) { - PyErr_WriteUnraisable(NULL); - if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, - ((PY_MAJOR_VERSION >= 3) ? - "Cython module failed to register with collections.abc module" : - "Cython module failed to register with collections module"), 1) < 0)) { - return -1; - } - } else { - module = __Pyx_patch_abc_module(module); - abc_patched = 1; - if (unlikely(!module)) - return -1; - Py_DECREF(module); - } - module = PyImport_ImportModule("backports_abc"); - if (module) { - module = __Pyx_patch_abc_module(module); - Py_XDECREF(module); - } - if (!module) { - PyErr_Clear(); - } - } -#else - if ((0)) __Pyx_Coroutine_patch_module(NULL, NULL); -#endif - return 0; -} - -/* Generator */ - static PyMethodDef __pyx_Generator_methods[] = { - {"send", (PyCFunction) __Pyx_Coroutine_Send, METH_O, - (char*) PyDoc_STR("send(arg) -> send 'arg' into generator,\nreturn next yielded value or raise StopIteration.")}, - {"throw", (PyCFunction) __Pyx_Coroutine_Throw, METH_VARARGS, - (char*) PyDoc_STR("throw(typ[,val[,tb]]) -> raise exception in generator,\nreturn next yielded value or raise StopIteration.")}, - {"close", (PyCFunction) __Pyx_Coroutine_Close_Method, METH_NOARGS, - (char*) PyDoc_STR("close() -> raise GeneratorExit inside generator.")}, - {0, 0, 0, 0} -}; -static PyMemberDef __pyx_Generator_memberlist[] = { - {(char *) "gi_running", T_BOOL, offsetof(__pyx_CoroutineObject, is_running), READONLY, NULL}, - {(char*) "gi_yieldfrom", T_OBJECT, offsetof(__pyx_CoroutineObject, yieldfrom), READONLY, - (char*) PyDoc_STR("object being iterated by 'yield from', or None")}, - {(char*) "gi_code", T_OBJECT, offsetof(__pyx_CoroutineObject, gi_code), READONLY, NULL}, - {0, 0, 0, 0, 0} -}; -static PyGetSetDef __pyx_Generator_getsets[] = { - {(char *) "__name__", (getter)__Pyx_Coroutine_get_name, (setter)__Pyx_Coroutine_set_name, - (char*) PyDoc_STR("name of the generator"), 0}, - {(char *) "__qualname__", (getter)__Pyx_Coroutine_get_qualname, (setter)__Pyx_Coroutine_set_qualname, - (char*) PyDoc_STR("qualified name of the generator"), 0}, - {(char *) "gi_frame", (getter)__Pyx_Coroutine_get_frame, NULL, - (char*) PyDoc_STR("Frame of the generator"), 0}, - {0, 0, 0, 0, 0} -}; -static PyTypeObject __pyx_GeneratorType_type = { - PyVarObject_HEAD_INIT(0, 0) - "generator", - sizeof(__pyx_CoroutineObject), - 0, - (destructor) __Pyx_Coroutine_dealloc, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_HAVE_FINALIZE, - 0, - (traverseproc) __Pyx_Coroutine_traverse, - 0, - 0, - offsetof(__pyx_CoroutineObject, gi_weakreflist), - 0, - (iternextfunc) __Pyx_Generator_Next, - __pyx_Generator_methods, - __pyx_Generator_memberlist, - __pyx_Generator_getsets, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, -#if CYTHON_USE_TP_FINALIZE - 0, -#else - __Pyx_Coroutine_del, -#endif - 0, -#if CYTHON_USE_TP_FINALIZE - __Pyx_Coroutine_del, -#elif PY_VERSION_HEX >= 0x030400a1 - 0, -#endif -#if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) - 0, -#endif -#if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 - 0, -#endif -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 - 0, -#endif -}; -static int __pyx_Generator_init(void) { - __pyx_GeneratorType_type.tp_getattro = __Pyx_PyObject_GenericGetAttrNoDict; - __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter; - __pyx_GeneratorType = __Pyx_FetchCommonType(&__pyx_GeneratorType_type); - if (unlikely(!__pyx_GeneratorType)) { - return -1; - } - return 0; -} - -/* CheckBinaryVersion */ - static int __Pyx_check_binary_version(void) { - char ctversion[5]; - int same=1, i, found_dot; - const char* rt_from_call = Py_GetVersion(); - PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); - found_dot = 0; - for (i = 0; i < 4; i++) { - if (!ctversion[i]) { - same = (rt_from_call[i] < '0' || rt_from_call[i] > '9'); - break; - } - if (rt_from_call[i] != ctversion[i]) { - same = 0; - break; - } - } - if (!same) { - char rtversion[5] = {'\0'}; - char message[200]; - for (i=0; i<4; ++i) { - if (rt_from_call[i] == '.') { - if (found_dot) break; - found_dot = 1; - } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') { - break; - } - rtversion[i] = rt_from_call[i]; - } - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* FunctionExport */ - static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig) { - PyObject *d = 0; - PyObject *cobj = 0; - union { - void (*fp)(void); - void *p; - } tmp; - d = PyObject_GetAttrString(__pyx_m, (char *)"__pyx_capi__"); - if (!d) { - PyErr_Clear(); - d = PyDict_New(); - if (!d) - goto bad; - Py_INCREF(d); - if (PyModule_AddObject(__pyx_m, (char *)"__pyx_capi__", d) < 0) - goto bad; - } - tmp.fp = f; -#if PY_VERSION_HEX >= 0x02070000 - cobj = PyCapsule_New(tmp.p, sig, 0); -#else - cobj = PyCObject_FromVoidPtrAndDesc(tmp.p, (void *)sig, 0); -#endif - if (!cobj) - goto bad; - if (PyDict_SetItemString(d, name, cobj) < 0) - goto bad; - Py_DECREF(cobj); - Py_DECREF(d); - return 0; -bad: - Py_XDECREF(cobj); - Py_XDECREF(d); - return -1; -} - -/* InitStrings */ - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - if (PyObject_Hash(*t->p) == -1) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT -#if !CYTHON_PEP393_ENABLED -static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); - return NULL; - } - } - } -#endif - *length = PyBytes_GET_SIZE(defenc); - return defenc_c; -} -#else -static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (likely(PyUnicode_IS_ASCII(o))) { - *length = PyUnicode_GET_LENGTH(o); - return PyUnicode_AsUTF8(o); - } else { - PyUnicode_AsASCIIString(o); - return NULL; - } -#else - return PyUnicode_AsUTF8AndSize(o, length); -#endif -} -#endif -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { - return __Pyx_PyUnicode_AsStringAndSize(o, length); - } else -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - if (PyByteArray_Check(o)) { - *length = PyByteArray_GET_SIZE(o); - return PyByteArray_AS_STRING(o); - } else -#endif - { - char* result; - int r = PyBytes_AsStringAndSize(o, &result, length); - if (unlikely(r < 0)) { - return NULL; - } else { - return result; - } - } -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - int is_true = x == Py_True; - if (is_true | (x == Py_False) | (x == Py_None)) return is_true; - else return PyObject_IsTrue(x); -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) { - int retval; - if (unlikely(!x)) return -1; - retval = __Pyx_PyObject_IsTrue(x); - Py_DECREF(x); - return retval; -} -static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { -#if PY_MAJOR_VERSION >= 3 - if (PyLong_Check(result)) { - if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, - "__int__ returned non-int (type %.200s). " - "The ability to return an instance of a strict subclass of int " - "is deprecated, and may be removed in a future version of Python.", - Py_TYPE(result)->tp_name)) { - Py_DECREF(result); - return NULL; - } - return result; - } -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - type_name, type_name, Py_TYPE(result)->tp_name); - Py_DECREF(result); - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS - PyNumberMethods *m; -#endif - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x) || PyLong_Check(x))) -#else - if (likely(PyLong_Check(x))) -#endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS - m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = m->nb_int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = m->nb_long(x); - } - #else - if (likely(m && m->nb_int)) { - name = "int"; - res = m->nb_int(x); - } - #endif -#else - if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) { - res = PyNumber_Int(x); - } -#endif - if (likely(res)) { -#if PY_MAJOR_VERSION < 3 - if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) { -#else - if (unlikely(!PyLong_CheckExact(res))) { -#endif - return __Pyx_PyNumber_IntOrLongWrongResultType(res, name); - } - } - else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_TypeError, - "an integer is required"); - } - return res; -} -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { - Py_ssize_t ival; - PyObject *x; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(b); - } -#endif - if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - 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#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - if (type) { - PyErr_Restore(type, value, traceback); - } - return co; - } -#else - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_STACKLESS - #define METH_STACKLESS 0 -#endif -#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) - #ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - #endif - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); - typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast - #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1 - #define PyMem_RawMalloc(n) PyMem_Malloc(n) - #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) - #define PyMem_RawFree(p) PyMem_Free(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#elif PY_VERSION_HEX >= 0x03060000 - #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() -#elif PY_VERSION_HEX >= 0x03000000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#else - #define __Pyx_PyThreadState_Current _PyThreadState_Current -#endif -#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) -#include "pythread.h" -#define Py_tss_NEEDS_INIT 0 -typedef int Py_tss_t; -static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { - *key = PyThread_create_key(); - return 0; -} -static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { - Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); - *key = Py_tss_NEEDS_INIT; - return key; -} -static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { - PyObject_Free(key); -} -static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { - return *key != Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { - PyThread_delete_key(*key); - *key = Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { - return PyThread_set_key_value(*key, value); -} -static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { - return PyThread_get_key_value(*key); -} -#endif -#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) -#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) -#else -#define __Pyx_PyDict_NewPresized(n) PyDict_New() -#endif -#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION - #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) -#else - #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS -#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) -#else -#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_READY(op) (0) - #else - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #endif - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) - #else - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) - #endif - #endif -#else - #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 - #define __Pyx_PyUnicode_READY(op) (0) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) - #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) - #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) - #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) -#endif -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) -#else - #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ - PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) -#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? 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-#else -#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) -#endif - -/* PyObjectCall2Args.proto */ -static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2); - -/* PyObjectCallMethO.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); -#endif - -/* PyObjectCallOneArg.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); - -/* PyObjectCallNoArg.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); -#else -#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) -#endif - -/* PyThreadStateGet.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate; -#define __Pyx_PyThreadState_assign __pyx_tstate = __Pyx_PyThreadState_Current; -#define __Pyx_PyErr_Occurred() __pyx_tstate->curexc_type -#else -#define __Pyx_PyThreadState_declare -#define __Pyx_PyThreadState_assign -#define __Pyx_PyErr_Occurred() PyErr_Occurred() -#endif - -/* PyErrFetchRestore.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL) -#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb) -#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb) -#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb) -#define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#if CYTHON_COMPILING_IN_CPYTHON -#define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL)) -#else -#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) -#endif -#else -#define __Pyx_PyErr_Clear() PyErr_Clear() -#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) -#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb) -#define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb) -#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb) -#endif - -/* WriteUnraisableException.proto */ -static void __Pyx_WriteUnraisable(const char *name, int clineno, - int lineno, const char *filename, - int full_traceback, int nogil); - -/* PyDictVersioning.proto */ -#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS -#define __PYX_DICT_VERSION_INIT ((PY_UINT64_T) -1) -#define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) -#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)\ - (version_var) = __PYX_GET_DICT_VERSION(dict);\ - (cache_var) = (value); -#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) {\ - static PY_UINT64_T __pyx_dict_version = 0;\ - static PyObject *__pyx_dict_cached_value = NULL;\ - if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\ - (VAR) = __pyx_dict_cached_value;\ - } else {\ - (VAR) = __pyx_dict_cached_value = (LOOKUP);\ - __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\ - }\ -} -static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj); -static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj); -static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version); -#else -#define __PYX_GET_DICT_VERSION(dict) (0) -#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var) -#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) (VAR) = (LOOKUP); -#endif - -/* GetModuleGlobalName.proto */ -#if CYTHON_USE_DICT_VERSIONS -#define __Pyx_GetModuleGlobalName(var, name) do {\ - static PY_UINT64_T __pyx_dict_version = 0;\ - static PyObject *__pyx_dict_cached_value = NULL;\ - (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ - (likely(__pyx_dict_cached_value) ? __Pyx_NewRef(__pyx_dict_cached_value) : __Pyx_GetBuiltinName(name)) :\ - __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\ -} while(0) -#define __Pyx_GetModuleGlobalNameUncached(var, name) do {\ - PY_UINT64_T __pyx_dict_version;\ - PyObject *__pyx_dict_cached_value;\ - (var) = __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\ -} while(0) -static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value); -#else -#define __Pyx_GetModuleGlobalName(var, name) (var) = __Pyx__GetModuleGlobalName(name) -#define __Pyx_GetModuleGlobalNameUncached(var, name) (var) = __Pyx__GetModuleGlobalName(name) -static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name); -#endif - -/* GetItemInt.proto */ -#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ - __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, - int is_list, int wraparound, int boundscheck); - -/* RaiseException.proto */ -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); - -/* IncludeStringH.proto */ -#include - -/* BytesEquals.proto */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); - -/* UnicodeEquals.proto */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); - -/* RaiseTooManyValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); - -/* RaiseNeedMoreValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); - -/* IterFinish.proto */ -static CYTHON_INLINE int __Pyx_IterFinish(void); - -/* UnpackItemEndCheck.proto */ -static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); - -/* ExtTypeTest.proto */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); - -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); -#else -#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace, zerodivision_check)\ - (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2)) -#endif - -/* ObjectGetItem.proto */ -#if CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key); -#else -#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key) -#endif - -/* GetTopmostException.proto */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate); -#endif - -/* SaveResetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -#else -#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) -#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) -#endif - -/* PyErrExceptionMatches.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) -static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); -#else -#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) -#endif - -/* GetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* ArgTypeTest.proto */ -#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\ - ((likely((Py_TYPE(obj) == type) | (none_allowed && (obj == Py_None)))) ? 1 :\ - __Pyx__ArgTypeTest(obj, type, name, exact)) -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact); - -/* IsLittleEndian.proto */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void); - -/* BufferFormatCheck.proto */ -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type); - -/* BufferGetAndValidate.proto */ -#define __Pyx_GetBufferAndValidate(buf, obj, dtype, flags, nd, cast, stack)\ - ((obj == Py_None || obj == NULL) ?\ - (__Pyx_ZeroBuffer(buf), 0) :\ - __Pyx__GetBufferAndValidate(buf, obj, dtype, flags, nd, cast, stack)) -static int __Pyx__GetBufferAndValidate(Py_buffer* buf, PyObject* obj, - __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); -static void __Pyx_ZeroBuffer(Py_buffer* buf); -static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); -static Py_ssize_t __Pyx_minusones[] = { -1, -1, -1, -1, -1, -1, -1, -1 }; -static Py_ssize_t __Pyx_zeros[] = { 0, 0, 0, 0, 0, 0, 0, 0 }; - -#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0) -/* MemviewSliceInit.proto */ -#define __Pyx_BUF_MAX_NDIMS %(BUF_MAX_NDIMS)d -#define __Pyx_MEMVIEW_DIRECT 1 -#define __Pyx_MEMVIEW_PTR 2 -#define __Pyx_MEMVIEW_FULL 4 -#define __Pyx_MEMVIEW_CONTIG 8 -#define __Pyx_MEMVIEW_STRIDED 16 -#define __Pyx_MEMVIEW_FOLLOW 32 -#define __Pyx_IS_C_CONTIG 1 -#define __Pyx_IS_F_CONTIG 2 -static int __Pyx_init_memviewslice( - struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference); -static CYTHON_INLINE int __pyx_add_acquisition_count_locked( - __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); -static CYTHON_INLINE int __pyx_sub_acquisition_count_locked( - __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); -#define __pyx_get_slice_count_pointer(memview) (memview->acquisition_count_aligned_p) -#define __pyx_get_slice_count(memview) (*__pyx_get_slice_count_pointer(memview)) -#define __PYX_INC_MEMVIEW(slice, have_gil) __Pyx_INC_MEMVIEW(slice, have_gil, __LINE__) -#define __PYX_XDEC_MEMVIEW(slice, have_gil) __Pyx_XDEC_MEMVIEW(slice, have_gil, __LINE__) -static CYTHON_INLINE void __Pyx_INC_MEMVIEW(__Pyx_memviewslice *, int, int); -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *, int, int); - -/* SliceObject.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice( - PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** py_start, PyObject** py_stop, PyObject** py_slice, - int has_cstart, int has_cstop, int wraparound); - -/* StrEquals.proto */ -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals -#else -#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals -#endif - -/* DivInt[Py_ssize_t].proto */ -static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); - -/* UnaryNegOverflows.proto */ -#define UNARY_NEG_WOULD_OVERFLOW(x)\ - (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) - -static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *); /*proto*/ -/* GetAttr.proto */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); - -/* decode_c_string_utf16.proto */ -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = 0; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16LE(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = -1; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16BE(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = 1; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} - -/* decode_c_string.proto */ -static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); - -/* GetAttr3.proto */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); - -/* RaiseNoneIterError.proto */ -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); - -/* SwapException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* Import.proto */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); - -/* FastTypeChecks.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2); -#else -#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) -#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type) -#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2)) -#endif -#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) - -static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -/* ListCompAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len)) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) -#endif - -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); -#else -#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace, zerodivision_check)\ - (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) -#endif - -/* ListExtend.proto */ -static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { -#if CYTHON_COMPILING_IN_CPYTHON - PyObject* none = _PyList_Extend((PyListObject*)L, v); - if (unlikely(!none)) - return -1; - Py_DECREF(none); - return 0; -#else - return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); -#endif -} - -/* ListAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) -#endif - -/* None.proto */ -static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); - -/* DivInt[long].proto */ -static CYTHON_INLINE long __Pyx_div_long(long, long); - -/* PySequenceContains.proto */ -static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) { - int result = PySequence_Contains(seq, item); - return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); -} - -/* ImportFrom.proto */ -static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); - -/* HasAttr.proto */ -static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); - -/* PyObject_GenericGetAttrNoDict.proto */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); -#else -#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr -#endif - -/* PyObject_GenericGetAttr.proto */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name); 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/*proto*/ -static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *, PyObject *); /*proto*/ -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t = { "int64_t", NULL, sizeof(__pyx_t_5numpy_int64_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int64_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int64_t), 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t = { "float32_t", NULL, sizeof(__pyx_t_5numpy_float32_t), { 0 }, 0, 'R', 0, 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_10MDAnalysis_3lib_7formats_9libmdaxdr_DTYPE_T = { "DTYPE_T", NULL, sizeof(__pyx_t_10MDAnalysis_3lib_7formats_9libmdaxdr_DTYPE_T), { 0 }, 0, 'R', 0, 0 }; -#define __Pyx_MODULE_NAME "MDAnalysis.lib.formats.libmdaxdr" -extern int __pyx_module_is_main_MDAnalysis__lib__formats__libmdaxdr; -int __pyx_module_is_main_MDAnalysis__lib__formats__libmdaxdr = 0; - -/* Implementation of 'MDAnalysis.lib.formats.libmdaxdr' */ -static PyObject *__pyx_builtin_IOError; -static PyObject *__pyx_builtin_StopIteration; -static PyObject *__pyx_builtin_RuntimeError; -static PyObject *__pyx_builtin_EOFError; -static PyObject *__pyx_builtin_KeyError; -static PyObject *__pyx_builtin_ImportError; -static PyObject *__pyx_builtin_ValueError; -static PyObject *__pyx_builtin_MemoryError; -static PyObject *__pyx_builtin_enumerate; -static PyObject *__pyx_builtin_range; -static PyObject *__pyx_builtin_TypeError; -static PyObject *__pyx_builtin_Ellipsis; -static PyObject *__pyx_builtin_id; -static PyObject *__pyx_builtin_IndexError; -static const char __pyx_k_O[] = "O"; -static const char __pyx_k_c[] = "c"; -static const char __pyx_k_r[] = "r"; -static const char __pyx_k_w[] = "w"; -static const char __pyx_k_OK[] = "OK"; -static const char __pyx_k_id[] = "id"; -static const char __pyx_k_np[] = "np"; -static const char __pyx_k_box[] = "box"; -static const char __pyx_k_new[] = "__new__"; -static const char __pyx_k_obj[] = "obj"; -static const char __pyx_k_xyz[] = "xyz"; -static const char __pyx_k_base[] = "base"; -static const char __pyx_k_dict[] = "__dict__"; -static const char __pyx_k_keys[] = "keys"; -static const char __pyx_k_main[] = "__main__"; -static const char __pyx_k_mode[] = "mode"; -static const char __pyx_k_name[] = "name"; -static const char __pyx_k_ndim[] = "ndim"; -static const char __pyx_k_open[] = "open"; -static const char __pyx_k_pack[] = "pack"; -static const char __pyx_k_read[] = "read"; -static const char __pyx_k_seek[] = "seek"; -static const char __pyx_k_size[] = "size"; -static const char __pyx_k_step[] = "step"; -static const char __pyx_k_stop[] = "stop"; -static const char __pyx_k_test[] = "__test__"; -static const char __pyx_k_time[] = "time"; -static const char __pyx_k_ASCII[] = "ASCII"; -static const char __pyx_k_DTYPE[] = "DTYPE"; -static const char __pyx_k_array[] = "array"; -static const char __pyx_k_class[] = "__class__"; -static const char __pyx_k_close[] = "close"; -static const char __pyx_k_dtype[] = "dtype"; -static const char __pyx_k_error[] = "error"; -static const char __pyx_k_flags[] = "flags"; -static const char __pyx_k_float[] = "float"; -static const char __pyx_k_fname[] = "fname"; -static const char __pyx_k_magic[] = "magic"; -static const char __pyx_k_numpy[] = "numpy"; -static const char __pyx_k_range[] = "range"; -static const char __pyx_k_shape[] = "shape"; -static const char __pyx_k_start[] = "start"; -static const char __pyx_k_utf_8[] = "utf-8"; -static const char __pyx_k_decode[] = "decode"; -static const char __pyx_k_double[] = "double"; -static const char __pyx_k_encode[] = "encode"; -static const char __pyx_k_exc_tb[] = "exc_tb"; -static const char __pyx_k_exists[] = "exists"; -static const char __pyx_k_forces[] = "forces"; -static const char __pyx_k_format[] = "format"; -static const char __pyx_k_header[] = "header"; -static const char __pyx_k_import[] = "__import__"; -static const char __pyx_k_lambda[] = "_lambda"; -static const char __pyx_k_memory[] = "memory"; -static const char __pyx_k_name_2[] = "__name__"; -static const char __pyx_k_natoms[] = "natoms"; -static const char __pyx_k_offset[] = "offset"; -static const char __pyx_k_pickle[] = "pickle"; -static const char __pyx_k_reduce[] = "__reduce__"; -static const char __pyx_k_string[] = "string"; -static const char __pyx_k_struct[] = "struct"; -static const char __pyx_k_unpack[] = "unpack"; -static const char __pyx_k_update[] = "update"; -static const char __pyx_k_whence[] = "whence"; -static const char __pyx_k_IOError[] = "IOError"; -static const char __pyx_k_TRRFile[] = "TRRFile"; -static const char __pyx_k_XDRFile[] = "_XDRFile"; -static const char __pyx_k_XTCFile[] = "XTCFile"; -static const char __pyx_k_asarray[] = "asarray"; -static const char __pyx_k_exc_val[] = "exc_val"; -static const char __pyx_k_float32[] = "float32"; -static const char __pyx_k_fortran[] = "fortran"; -static const char __pyx_k_integer[] = "integer"; -static const char __pyx_k_memview[] = "memview"; -static const char __pyx_k_offsets[] = "offsets"; -static const char __pyx_k_os_path[] = "os.path"; -static const char __pyx_k_EOFError[] = "EOFError"; -static const char __pyx_k_Ellipsis[] = "Ellipsis"; -static const char __pyx_k_KeyError[] = "KeyError"; -static const char __pyx_k_SEEK_CUR[] = "SEEK_CUR"; -static const char __pyx_k_SEEK_END[] = "SEEK_END"; -static const char __pyx_k_SEEK_SET[] = "SEEK_SET"; -static const char __pyx_k_TRRFrame[] = "TRRFrame"; -static const char __pyx_k_XTCFrame[] = "XTCFrame"; -static const char __pyx_k_exc_type[] = "exc_type"; -static const char __pyx_k_getstate[] = "__getstate__"; -static const char __pyx_k_itemsize[] = "itemsize"; -static const char __pyx_k_notfound[] = "notfound"; -static const char __pyx_k_pyx_type[] = "__pyx_type"; -static const char __pyx_k_setstate[] = "__setstate__"; -static const char __pyx_k_velocity[] = "velocity"; -static const char __pyx_k_TypeError[] = "TypeError"; -static const char __pyx_k_endoffile[] = "endoffile"; -static const char __pyx_k_enumerate[] = "enumerate"; -static const char __pyx_k_positions[] = "positions"; -static const char __pyx_k_precision[] = "precision"; -static const char __pyx_k_pyx_state[] = "__pyx_state"; -static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; -static const char __pyx_k_self_mode[] = "self.mode"; -static const char __pyx_k_IndexError[] = "IndexError"; -static const char __pyx_k_ValueError[] = "ValueError"; -static const char __pyx_k_namedtuple[] = "namedtuple"; -static const char __pyx_k_pyx_result[] = "__pyx_result"; -static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; -static const char __pyx_k_velocities[] = "velocities"; -static const char __pyx_k_ImportError[] = "ImportError"; -static const char __pyx_k_MemoryError[] = "MemoryError"; -static const char __pyx_k_PickleError[] = "PickleError"; -static const char __pyx_k_calc_natoms[] = "_calc_natoms"; -static const char __pyx_k_collections[] = "collections"; -static const char __pyx_k_compression[] = "compression"; -static const char __pyx_k_whence_vals[] = "_whence_vals"; -static const char __pyx_k_RuntimeError[] = "RuntimeError"; -static const char __pyx_k_calc_offsets[] = "calc_offsets"; -static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; -static const char __pyx_k_stringsource[] = "stringsource"; -static const char __pyx_k_StopIteration[] = "StopIteration"; -static const char __pyx_k_error_message[] = "error_message"; -static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; -static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; -static const char __pyx_k_No_file_opened[] = "No file opened"; -static const char __pyx_k_TRR_read_error[] = "TRR read error = {}"; -static const char __pyx_k_XDR_read_error[] = "XDR read error = {}"; -static const char __pyx_k_XTC_read_error[] = "XTC read error = {}"; -static const char __pyx_k_TRR_write_error[] = "TRR write error = {}"; -static const char __pyx_k_View_MemoryView[] = "View.MemoryView"; -static const char __pyx_k_XTC_write_error[] = "XTC write error = {}"; -static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; -static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; -static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; -static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; -static const char __pyx_k_unsigned_integer[] = "unsigned integer"; -static const char __pyx_k_ascontiguousarray[] = "ascontiguousarray"; -static const char __pyx_k_pyx_unpickle_Enum[] = "__pyx_unpickle_Enum"; -static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; -static const char __pyx_k_strided_and_direct[] = ""; -static const char __pyx_k_File_does_not_exist[] = "File does not exist: {}"; -static const char __pyx_k_strided_and_indirect[] = ""; -static const char __pyx_k_x_box_step_time_prec[] = "x box step time prec"; -static const char __pyx_k_contiguous_and_direct[] = ""; -static const char __pyx_k_MemoryView_of_r_object[] = ""; -static const char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; -static const char __pyx_k_contiguous_and_indirect[] = ""; -static const char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; -static const char __pyx_k_No_file_currently_opened[] = "No file currently opened"; -static const char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; -static const char __pyx_k_Error_opening_XTC_TRR_file[] = "Error opening XTC/TRR file: {}"; -static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; -static const char __pyx_k_Can_t_seek_to_negative_frame[] = "Can't seek to negative frame"; -static const char __pyx_k_Couldn_t_close_file_XDR_error[] = "Couldn't close file: {} XDR error = {}"; -static const char __pyx_k_Couldn_t_read_number_of_atoms[] = "Couldn't read number of atoms: {}"; -static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; -static const char __pyx_k_strided_and_direct_or_indirect[] = ""; -static const char __pyx_k_Parameter_whence_must_be_one_of[] = "Parameter 'whence' must be one of {}"; -static const char __pyx_k_Previous_frames_contained_atoms[] = "Previous frames contained {} atoms. You are trying to write {} atoms."; -static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; -static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; -static const char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; -static const char __pyx_k_Cannot_assign_to_read_only_memor[] = "Cannot assign to read-only memoryview"; -static const char __pyx_k_Cannot_create_writable_memory_vi[] = "Cannot create writable memory view from read-only memoryview"; -static const char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; -static const char __pyx_k_File_opened_in_mode_Reading_only[] = "File opened in mode: {}. Reading only allow in mode \"r\""; -static const char __pyx_k_File_opened_in_mode_Writing_only[] = "File opened in mode: {}. Writing only allow in mode \"w\""; -static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0xb068931, 0x82a3537, 0x6ae9995) = (name))"; -static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; -static const char __pyx_k_Invalid_frame_number_this_should[] = "Invalid frame number {} > {} -- this shouldnot happen."; -static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; -static const char __pyx_k_Low_level_Gromacs_XDR_trajectory[] = "Low-level Gromacs XDR trajectory reading \342\200\224 :mod:`MDAnalysis.lib.formats.libmdaxdr`\n----------------------------------------------------------------------------------\n\n:mod:`libmdaxdr` contains the classes :class:`XTCFile` and\n:class:`TRRFile`. Both can be used to read and write frames from and to\nGromacs_ XTC and TRR files. These classes are used internally by MDAnalysis in\n:mod:`MDAnalysis.coordinates.XTC` and :mod:`MDAnalysis.coordinates.TRR`. They\nbehave similar to normal file objects.\n\nFor example, one can use a :class:`XTCFile` to directly calculate mean\ncoordinates (where the coordinates are stored in `x` attribute of the\n:class:`namedtuple` `frame`):\n\n.. code-block:: python\n :emphasize-lines: 1,2,5\n\n with XTCFile(\"trajectory.xtc\") as xtc:\n n_atoms = xtc.n_atoms\n mean = np.zeros((n_atoms, 3))\n # iterate over trajectory\n for frame in xtc:\n mean += frame.x\n\nThe :class:`XTCFile` class can be useful as a compressed storage format.\n\nBesides iteration, :class:`XTCFile` and :class:`TRRFile` one can also seek to\narbitrary frames using the :meth:`~XTCFile.seek` method. This is provided by\nlazily generating a offset list for stored frames. The offset list is generated\nthe first time :func:`len` or :`~XTCFile.seek` is called.\n\n(For more details on how to use :class:`XTCFile` and :class:`TRRFile` on their\nown please see the source code in `lib/formats/libmdaxdr.pyx`_ for the time being.)\n\n\n.. _Gromacs: http://www.gromacs.org\n.. _`lib/formats/libmdaxdr.pyx`:\n https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/lib/formats/libmdaxdr.pyx\n"; -static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; -static const char __pyx_k_Previous_frames_forces_contained[] = "Previous frames forces contained {} atoms. You are trying to write {} atoms."; -static const char __pyx_k_Previous_frames_used_precision_o[] = "Previous frames used precision of {}. You are trying to use {}"; -static const char __pyx_k_Previous_frames_velocity_contain[] = "Previous frames velocity contained {} atoms. You are trying to write {} atoms."; -static const char __pyx_k_Previous_frames_xyz_contained_at[] = "Previous frames xyz contained {} atoms. You are trying to write {} atoms."; -static const char __pyx_k_Reached_last_frame_in_TRR_seek_t[] = "Reached last frame in TRR, seek to 0"; -static const char __pyx_k_Reached_last_frame_in_XTC_seek_t[] = "Reached last frame in XTC, seek to 0"; -static const char __pyx_k_TRR_couldn_t_calculate_offsets_X[] = "TRR couldn't calculate offsets. XDR error = {}"; -static const char __pyx_k_Trying_to_seek_over_max_number_o[] = "Trying to seek over max number of frames"; -static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; -static const char __pyx_k_XDR_seek_failed_with_system_errn[] = "XDR seek failed with system errno={}"; -static const char __pyx_k_XTC_couldn_t_calculate_offsets_X[] = "XTC couldn't calculate offsets. XDR error = {}"; -static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; -static const char __pyx_k_mode_must_be_one_of_r_or_w_you_s[] = "mode must be one of \"r\" or \"w\", you supplied {}"; -static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; -static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; -static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; -static const char __pyx_k_x_v_f_box_step_time_lmbda_hasx_h[] = "x v f box step time lmbda hasx hasv hasf"; -static PyObject *__pyx_n_s_ASCII; -static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; -static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; -static PyObject *__pyx_kp_u_Can_t_seek_to_negative_frame; -static PyObject *__pyx_kp_s_Cannot_assign_to_read_only_memor; -static PyObject *__pyx_kp_s_Cannot_create_writable_memory_vi; -static PyObject *__pyx_kp_s_Cannot_index_with_type_s; -static PyObject *__pyx_kp_u_Couldn_t_close_file_XDR_error; -static PyObject *__pyx_kp_u_Couldn_t_read_number_of_atoms; -static PyObject *__pyx_n_s_DTYPE; -static PyObject *__pyx_n_s_EOFError; -static PyObject *__pyx_n_s_Ellipsis; -static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; -static PyObject *__pyx_kp_u_Error_opening_XTC_TRR_file; -static PyObject *__pyx_kp_u_File_does_not_exist; -static PyObject *__pyx_kp_u_File_opened_in_mode_Reading_only; -static PyObject *__pyx_kp_u_File_opened_in_mode_Writing_only; -static PyObject *__pyx_n_s_IOError; -static PyObject *__pyx_n_s_ImportError; -static PyObject *__pyx_kp_s_Incompatible_checksums_0x_x_vs_0; -static PyObject *__pyx_n_s_IndexError; -static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; -static PyObject *__pyx_kp_u_Invalid_frame_number_this_should; -static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; -static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; -static PyObject *__pyx_n_s_KeyError; -static PyObject *__pyx_n_s_MemoryError; -static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; -static PyObject *__pyx_kp_s_MemoryView_of_r_object; -static PyObject *__pyx_kp_u_No_file_currently_opened; -static PyObject *__pyx_kp_u_No_file_opened; -static PyObject *__pyx_n_b_O; -static PyObject *__pyx_n_u_OK; -static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; -static PyObject *__pyx_kp_u_Parameter_whence_must_be_one_of; -static PyObject *__pyx_n_s_PickleError; -static PyObject *__pyx_kp_u_Previous_frames_contained_atoms; -static PyObject *__pyx_kp_u_Previous_frames_forces_contained; -static PyObject *__pyx_kp_u_Previous_frames_used_precision_o; -static PyObject *__pyx_kp_u_Previous_frames_velocity_contain; -static PyObject *__pyx_kp_u_Previous_frames_xyz_contained_at; -static PyObject *__pyx_kp_u_Reached_last_frame_in_TRR_seek_t; -static PyObject *__pyx_kp_u_Reached_last_frame_in_XTC_seek_t; -static PyObject *__pyx_n_s_RuntimeError; -static PyObject *__pyx_n_u_SEEK_CUR; -static PyObject *__pyx_n_u_SEEK_END; -static PyObject *__pyx_n_u_SEEK_SET; -static PyObject *__pyx_n_s_StopIteration; -static PyObject *__pyx_n_s_TRRFile; -static PyObject *__pyx_n_s_TRRFrame; -static PyObject *__pyx_n_u_TRRFrame; -static PyObject *__pyx_kp_u_TRR_couldn_t_calculate_offsets_X; -static PyObject *__pyx_kp_u_TRR_read_error; -static PyObject *__pyx_kp_u_TRR_write_error; -static PyObject *__pyx_kp_u_Trying_to_seek_over_max_number_o; -static PyObject *__pyx_n_s_TypeError; -static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; -static PyObject *__pyx_n_s_ValueError; -static PyObject *__pyx_n_s_View_MemoryView; -static PyObject *__pyx_n_s_XDRFile; -static PyObject *__pyx_kp_u_XDR_read_error; -static PyObject *__pyx_kp_u_XDR_seek_failed_with_system_errn; -static PyObject *__pyx_n_s_XTCFile; -static PyObject *__pyx_n_s_XTCFrame; -static PyObject *__pyx_n_u_XTCFrame; -static PyObject *__pyx_kp_u_XTC_couldn_t_calculate_offsets_X; -static PyObject *__pyx_kp_u_XTC_read_error; -static PyObject *__pyx_kp_u_XTC_write_error; -static PyObject *__pyx_n_s_allocate_buffer; -static PyObject *__pyx_n_s_array; -static PyObject *__pyx_n_s_asarray; -static PyObject *__pyx_n_s_ascontiguousarray; -static PyObject *__pyx_n_s_base; -static PyObject *__pyx_n_s_box; -static PyObject *__pyx_n_s_c; -static PyObject *__pyx_n_u_c; -static PyObject *__pyx_n_s_calc_natoms; -static PyObject *__pyx_n_s_calc_offsets; -static PyObject *__pyx_n_s_class; -static PyObject *__pyx_n_s_cline_in_traceback; -static PyObject *__pyx_n_s_close; -static PyObject *__pyx_n_u_close; -static PyObject *__pyx_n_s_collections; -static PyObject *__pyx_n_u_compression; -static PyObject *__pyx_kp_s_contiguous_and_direct; -static PyObject *__pyx_kp_s_contiguous_and_indirect; -static PyObject *__pyx_n_s_decode; -static PyObject *__pyx_n_s_dict; -static PyObject *__pyx_n_u_double; -static PyObject *__pyx_n_s_dtype; -static PyObject *__pyx_n_s_dtype_is_object; -static PyObject *__pyx_n_s_encode; -static PyObject *__pyx_n_u_endoffile; -static PyObject *__pyx_n_s_enumerate; -static PyObject *__pyx_n_s_error; -static PyObject *__pyx_n_s_error_message; -static PyObject *__pyx_n_s_exc_tb; -static PyObject *__pyx_n_s_exc_type; -static PyObject *__pyx_n_s_exc_val; -static PyObject *__pyx_n_s_exists; -static PyObject *__pyx_n_s_flags; -static PyObject *__pyx_n_u_float; -static PyObject *__pyx_n_s_float32; -static PyObject *__pyx_n_s_fname; -static PyObject *__pyx_n_s_forces; -static PyObject *__pyx_n_s_format; -static PyObject *__pyx_n_s_fortran; -static PyObject *__pyx_n_u_fortran; -static PyObject *__pyx_n_s_getstate; -static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; -static PyObject *__pyx_n_u_header; -static PyObject *__pyx_n_s_id; -static PyObject *__pyx_n_s_import; -static PyObject *__pyx_n_u_integer; -static PyObject *__pyx_n_s_itemsize; -static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; -static PyObject *__pyx_n_s_keys; -static PyObject *__pyx_n_s_lambda; -static PyObject *__pyx_n_u_magic; -static PyObject *__pyx_n_s_main; -static PyObject *__pyx_n_u_memory; -static PyObject *__pyx_n_s_memview; -static PyObject *__pyx_n_s_mode; -static PyObject *__pyx_kp_u_mode_must_be_one_of_r_or_w_you_s; -static PyObject *__pyx_n_s_name; -static PyObject *__pyx_n_s_name_2; -static PyObject *__pyx_n_s_namedtuple; -static PyObject *__pyx_n_s_natoms; -static PyObject *__pyx_n_s_ndim; -static PyObject *__pyx_n_s_new; -static PyObject *__pyx_kp_s_no_default___reduce___due_to_non; -static PyObject *__pyx_n_u_notfound; -static PyObject *__pyx_n_s_np; -static PyObject *__pyx_n_s_numpy; -static PyObject *__pyx_kp_u_numpy_core_multiarray_failed_to; -static PyObject *__pyx_kp_u_numpy_core_umath_failed_to_impor; -static PyObject *__pyx_n_s_obj; -static PyObject *__pyx_n_s_offset; -static PyObject *__pyx_n_s_offsets; -static PyObject *__pyx_n_s_open; -static PyObject *__pyx_n_s_os_path; -static PyObject *__pyx_n_s_pack; -static PyObject *__pyx_n_s_pickle; -static PyObject *__pyx_n_s_positions; -static PyObject *__pyx_n_s_precision; -static PyObject *__pyx_n_s_pyx_PickleError; -static PyObject *__pyx_n_s_pyx_checksum; -static PyObject *__pyx_n_s_pyx_getbuffer; -static PyObject *__pyx_n_s_pyx_result; -static PyObject *__pyx_n_s_pyx_state; -static PyObject *__pyx_n_s_pyx_type; -static PyObject *__pyx_n_s_pyx_unpickle_Enum; -static PyObject *__pyx_n_s_pyx_vtable; -static PyObject *__pyx_n_b_r; -static PyObject *__pyx_n_u_r; -static PyObject *__pyx_n_s_range; -static PyObject *__pyx_n_s_read; -static PyObject *__pyx_n_s_reduce; -static PyObject *__pyx_n_s_reduce_cython; -static PyObject *__pyx_n_s_reduce_ex; -static PyObject *__pyx_n_s_seek; -static PyObject *__pyx_kp_u_self_mode; -static PyObject *__pyx_n_s_setstate; -static PyObject *__pyx_n_s_setstate_cython; -static PyObject *__pyx_n_s_shape; -static PyObject *__pyx_n_s_size; -static PyObject *__pyx_n_s_start; -static PyObject *__pyx_n_s_step; -static PyObject *__pyx_n_s_stop; -static PyObject *__pyx_kp_s_strided_and_direct; -static PyObject *__pyx_kp_s_strided_and_direct_or_indirect; -static PyObject *__pyx_kp_s_strided_and_indirect; -static PyObject *__pyx_n_u_string; -static PyObject *__pyx_kp_s_stringsource; -static PyObject *__pyx_n_s_struct; -static PyObject *__pyx_n_s_test; -static PyObject *__pyx_n_s_time; -static PyObject *__pyx_kp_s_unable_to_allocate_array_data; -static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; -static PyObject *__pyx_n_s_unpack; -static PyObject *__pyx_kp_u_unsigned_integer; -static PyObject *__pyx_n_s_update; -static PyObject *__pyx_kp_u_utf_8; -static PyObject *__pyx_n_s_velocities; -static PyObject *__pyx_n_s_velocity; -static PyObject *__pyx_n_b_w; -static PyObject *__pyx_n_u_w; -static PyObject *__pyx_n_s_whence; -static PyObject *__pyx_n_s_whence_vals; -static PyObject *__pyx_kp_u_x_box_step_time_prec; -static PyObject *__pyx_kp_u_x_v_f_box_step_time_lmbda_hasx_h; -static PyObject *__pyx_n_s_xyz; -static int __pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile___cinit__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self, PyObject *__pyx_v_fname, PyObject *__pyx_v_mode); /* proto */ -static void __pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_2__dealloc__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_4close(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_6open(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self, PyObject *__pyx_v_fname, PyObject *__pyx_v_mode); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_8__enter__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_10__exit__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_val, CYTHON_UNUSED PyObject *__pyx_v_exc_tb); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_12__iter__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_14__next__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_16__len__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_18__reduce__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_20__getstate__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_22__setstate__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self, PyObject *__pyx_v_state); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_24seek(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self, int __pyx_v_frame); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_26_bytes_seek(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self, int64_t __pyx_v_offset, PyObject *__pyx_v_whence); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_7offsets___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_28set_offsets(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self, PyArrayObject *__pyx_v_offsets); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_30tell(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_32_bytes_tell(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_7n_atoms___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_5fname___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_8_XDRFile_12_has_offsets___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7TRRFile__calc_natoms(CYTHON_UNUSED struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr_TRRFile *__pyx_v_self, PyObject *__pyx_v_fname); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7TRRFile_2calc_offsets(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr_TRRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7TRRFile_4read(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr_TRRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7TRRFile_6read_direct_xvf(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr_TRRFile *__pyx_v_self, __Pyx_memviewslice __pyx_v_positions, __Pyx_memviewslice __pyx_v_velocities, __Pyx_memviewslice __pyx_v_forces); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7TRRFile_8write(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr_TRRFile *__pyx_v_self, PyObject *__pyx_v_xyz, PyObject *__pyx_v_velocity, PyObject *__pyx_v_forces, PyObject *__pyx_v_box, int __pyx_v_step, float __pyx_v_time, float __pyx_v__lambda, int __pyx_v_natoms); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7XTCFile__calc_natoms(CYTHON_UNUSED struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr_XTCFile *__pyx_v_self, PyObject *__pyx_v_fname); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7XTCFile_2calc_offsets(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr_XTCFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7XTCFile_4read(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr_XTCFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7XTCFile_6read_direct_x(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr_XTCFile *__pyx_v_self, __Pyx_memviewslice __pyx_v_positions); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7XTCFile_8write(struct __pyx_obj_10MDAnalysis_3lib_7formats_9libmdaxdr_XTCFile *__pyx_v_self, PyObject *__pyx_v_xyz, PyObject *__pyx_v_box, int __pyx_v_step, float __pyx_v_time, float __pyx_v_precision); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__len__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_12__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ -static PyObject *__pyx_pf___pyx_array___reduce_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_array_2__setstate_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_MemviewEnum_2__setstate_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ -static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_memoryview___reduce_cython__(CYTHON_UNUSED struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_memoryview_2__setstate_cython__(CYTHON_UNUSED struct __pyx_memoryview_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static void __pyx_memoryviewslice___pyx_pf_15View_dot_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); 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- if (__pyx_t_2) { - - /* "View.MemoryView":845 - * if have_start: - * if start < 0: - * start += shape # <<<<<<<<<<<<<< - * if start < 0: - * start = 0 - */ - __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - - /* "View.MemoryView":846 - * if start < 0: - * start += shape - * if start < 0: # <<<<<<<<<<<<<< - * start = 0 - * elif start >= shape: - */ - __pyx_t_2 = ((__pyx_v_start < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":847 - * start += shape - * if start < 0: - * start = 0 # <<<<<<<<<<<<<< - * elif start >= shape: - * if negative_step: - */ - __pyx_v_start = 0; - - /* "View.MemoryView":846 - * if start < 0: - * start += shape - * if start < 0: # <<<<<<<<<<<<<< - * start = 0 - * elif start >= shape: - */ - } - - /* "View.MemoryView":844 - * - * if have_start: - * if start < 0: # <<<<<<<<<<<<<< - * start += shape - * if start < 0: - */ - goto __pyx_L12; - } - - /* "View.MemoryView":848 - * if start < 0: - * start = 0 - * elif start >= shape: # <<<<<<<<<<<<<< - * if negative_step: - * start = shape - 1 - */ - __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":849 - * start = 0 - * elif start >= shape: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":850 - * elif start >= shape: - * if negative_step: - * start = shape - 1 # <<<<<<<<<<<<<< - * else: - * start = shape - */ - __pyx_v_start = (__pyx_v_shape - 1); - - /* "View.MemoryView":849 - * start = 0 - * elif start >= shape: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - goto __pyx_L14; - } - - /* "View.MemoryView":852 - * start = shape - 1 - * else: - * start = shape # <<<<<<<<<<<<<< - * else: - * if negative_step: - */ - /*else*/ { - __pyx_v_start = __pyx_v_shape; - } - __pyx_L14:; - - /* "View.MemoryView":848 - * if start < 0: - * start = 0 - * elif start >= shape: # <<<<<<<<<<<<<< - * if negative_step: - * start = shape - 1 - */ - } - __pyx_L12:; - - /* "View.MemoryView":843 - * - * - * if have_start: # <<<<<<<<<<<<<< - * if start < 0: - * start += shape - */ - goto __pyx_L11; - } - - /* "View.MemoryView":854 - * start = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - /*else*/ { - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":855 - * else: - * if negative_step: - * start = shape - 1 # <<<<<<<<<<<<<< - * else: - * start = 0 - */ - __pyx_v_start = (__pyx_v_shape - 1); - - /* "View.MemoryView":854 - * start = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - goto __pyx_L15; - } - - /* "View.MemoryView":857 - * start = shape - 1 - * else: - * start = 0 # <<<<<<<<<<<<<< - * - * if have_stop: - */ - /*else*/ { - __pyx_v_start = 0; - } - __pyx_L15:; - } - __pyx_L11:; - - /* "View.MemoryView":859 - * start = 0 - * - * if have_stop: # <<<<<<<<<<<<<< - * if stop < 0: - * stop += shape - */ - __pyx_t_2 = (__pyx_v_have_stop != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":860 - * - * if have_stop: - * if stop < 0: # <<<<<<<<<<<<<< - * stop += shape - * if stop < 0: - */ - __pyx_t_2 = ((__pyx_v_stop < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":861 - * if have_stop: - * if stop < 0: - * stop += shape # <<<<<<<<<<<<<< - * if stop < 0: - * stop = 0 - */ - __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); - - /* "View.MemoryView":862 - * if stop < 0: - * stop += shape - * if stop < 0: # <<<<<<<<<<<<<< - * stop = 0 - * elif stop > shape: - */ - __pyx_t_2 = ((__pyx_v_stop < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":863 - * stop += shape - * if stop < 0: - * stop = 0 # <<<<<<<<<<<<<< - * elif stop > shape: - * stop = shape - */ - __pyx_v_stop = 0; - - /* "View.MemoryView":862 - * if stop < 0: - * stop += shape - * if stop < 0: # <<<<<<<<<<<<<< - * stop = 0 - * elif stop > shape: - */ - } - - /* "View.MemoryView":860 - * - * if have_stop: - * if stop < 0: # <<<<<<<<<<<<<< - * stop += shape - * if stop < 0: - */ - goto __pyx_L17; - } - - /* "View.MemoryView":864 - * if stop < 0: - * stop = 0 - * elif stop > shape: # <<<<<<<<<<<<<< - * stop = shape - * else: - */ - __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":865 - * stop = 0 - * elif stop > shape: - * stop = shape # <<<<<<<<<<<<<< - * else: - * if negative_step: - */ - __pyx_v_stop = __pyx_v_shape; - - /* "View.MemoryView":864 - * if stop < 0: - * stop = 0 - * elif stop > shape: # <<<<<<<<<<<<<< - * stop = shape - * else: - */ - } - __pyx_L17:; - - /* "View.MemoryView":859 - * start = 0 - * - * if have_stop: # <<<<<<<<<<<<<< - * if stop < 0: - * stop += shape - */ - goto __pyx_L16; - } - - /* "View.MemoryView":867 - * stop = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * stop = -1 - * else: - */ - /*else*/ { - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":868 - * else: - * if negative_step: - * stop = -1 # <<<<<<<<<<<<<< - * else: - * stop = shape - */ - __pyx_v_stop = -1L; - - /* "View.MemoryView":867 - * stop = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * stop = -1 - * else: - */ - goto __pyx_L19; - } - - /* "View.MemoryView":870 - * stop = -1 - * else: - * stop = shape # <<<<<<<<<<<<<< - * - * if not have_step: - */ - /*else*/ { - __pyx_v_stop = __pyx_v_shape; 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- - /* "View.MemoryView":888 - * dst.strides[new_ndim] = stride * step - * dst.shape[new_ndim] = new_shape - * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< - * - * - */ - (__pyx_v_dst->suboffsets[__pyx_v_new_ndim]) = __pyx_v_suboffset; - } - __pyx_L3:; - - /* "View.MemoryView":891 - * - * - * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< - * dst.data += start * stride - * else: - */ - __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":892 - * - * if suboffset_dim[0] < 0: - * dst.data += start * stride # <<<<<<<<<<<<<< - * else: - * dst.suboffsets[suboffset_dim[0]] += start * stride - */ - __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); - - /* "View.MemoryView":891 - * - * - * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< - * dst.data += start * stride - * else: - */ - goto __pyx_L23; - } - - /* "View.MemoryView":894 - * dst.data += start * stride - * else: - * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< - * - * if suboffset >= 0: - */ - /*else*/ { - __pyx_t_3 = (__pyx_v_suboffset_dim[0]); 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- if (__pyx_t_2) { - - /* "View.MemoryView":1128 - * for i in range(ndim - 1, -1, -1): - * if mslice.shape[i] > 1: - * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< - * break - * - */ - __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - - /* "View.MemoryView":1129 - * if mslice.shape[i] > 1: - * c_stride = mslice.strides[i] - * break # <<<<<<<<<<<<<< - * - * for i in range(ndim): - */ - goto __pyx_L4_break; - - /* "View.MemoryView":1127 - * - * for i in range(ndim - 1, -1, -1): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * c_stride = mslice.strides[i] - * break - */ - } - } - __pyx_L4_break:; - - /* "View.MemoryView":1131 - * break - * - * for i in range(ndim): # <<<<<<<<<<<<<< - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] - */ - __pyx_t_1 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_1; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { - __pyx_v_i = __pyx_t_4; - - /* "View.MemoryView":1132 - * - * for i in range(ndim): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * f_stride = mslice.strides[i] - * break - */ - __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1133 - * for i in range(ndim): - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< - * break - * - */ - __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - - /* "View.MemoryView":1134 - * if mslice.shape[i] > 1: - * f_stride = mslice.strides[i] - * break # <<<<<<<<<<<<<< - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): - */ - goto __pyx_L7_break; - - /* "View.MemoryView":1132 - * - * for i in range(ndim): - * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< - * f_stride = mslice.strides[i] - * break - */ - } - } - __pyx_L7_break:; - - /* "View.MemoryView":1136 - * break - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< - * return 'C' - * else: - */ - __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1137 - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): - * return 'C' # <<<<<<<<<<<<<< - * else: - * return 'F' - */ - __pyx_r = 'C'; - goto __pyx_L0; - - /* "View.MemoryView":1136 - * break - * - * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< - * return 'C' - * else: - */ - } - - /* "View.MemoryView":1139 - * return 'C' - * else: - * return 'F' # <<<<<<<<<<<<<< - * - * @cython.cdivision(True) - */ - /*else*/ { - __pyx_r = 'F'; - goto __pyx_L0; - } - - /* "View.MemoryView":1118 - * - * @cname('__pyx_get_best_slice_order') - * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< - * """ - * Figure out the best memory access order for a given slice. - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1142 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - -static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v_src_strides, char *__pyx_v_dst_data, Py_ssize_t *__pyx_v_dst_strides, Py_ssize_t *__pyx_v_src_shape, Py_ssize_t *__pyx_v_dst_shape, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - CYTHON_UNUSED Py_ssize_t __pyx_v_i; - CYTHON_UNUSED Py_ssize_t __pyx_v_src_extent; - Py_ssize_t __pyx_v_dst_extent; - Py_ssize_t __pyx_v_src_stride; - Py_ssize_t __pyx_v_dst_stride; - int __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - Py_ssize_t __pyx_t_4; - Py_ssize_t __pyx_t_5; - Py_ssize_t __pyx_t_6; - - /* "View.MemoryView":1149 - * - * cdef Py_ssize_t i - * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] - */ - __pyx_v_src_extent = (__pyx_v_src_shape[0]); - - /* "View.MemoryView":1150 - * cdef Py_ssize_t i - * cdef Py_ssize_t src_extent = src_shape[0] - * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t src_stride = src_strides[0] - * cdef Py_ssize_t dst_stride = dst_strides[0] - */ - __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); - - /* "View.MemoryView":1151 - * cdef Py_ssize_t src_extent = src_shape[0] - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - */ - __pyx_v_src_stride = (__pyx_v_src_strides[0]); - - /* "View.MemoryView":1152 - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] - * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< - * - * if ndim == 1: - */ - __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); - - /* "View.MemoryView":1154 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); - if (__pyx_t_2) { - } else { - __pyx_t_1 = __pyx_t_2; - goto __pyx_L5_bool_binop_done; - } - __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); - if (__pyx_t_2) { - } else { - __pyx_t_1 = __pyx_t_2; - goto __pyx_L5_bool_binop_done; - } - - /* "View.MemoryView":1156 - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< - * memcpy(dst_data, src_data, itemsize * dst_extent) - * else: - */ - __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); - if (__pyx_t_2) { - __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); - } - __pyx_t_3 = (__pyx_t_2 != 0); - __pyx_t_1 = __pyx_t_3; - __pyx_L5_bool_binop_done:; - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - if (__pyx_t_1) { - - /* "View.MemoryView":1157 - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent))); - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - goto __pyx_L4; - } - - /* "View.MemoryView":1159 - * memcpy(dst_data, src_data, itemsize * dst_extent) - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - __pyx_t_5 = __pyx_t_4; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1160 - * else: - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< - * src_data += src_stride - * dst_data += dst_stride - */ - (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); - - /* "View.MemoryView":1161 - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * else: - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1162 - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L4:; - - /* "View.MemoryView":1154 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1164 - * dst_data += dst_stride - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * _copy_strided_to_strided(src_data, src_strides + 1, - * dst_data, dst_strides + 1, - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - __pyx_t_5 = __pyx_t_4; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1165 - * else: - * for i in range(dst_extent): - * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< - * dst_data, dst_strides + 1, - * src_shape + 1, dst_shape + 1, - */ - _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - - /* "View.MemoryView":1169 - * src_shape + 1, dst_shape + 1, - * ndim - 1, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1170 - * ndim - 1, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L3:; - - /* "View.MemoryView":1142 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - - /* function exit code */ -} - -/* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - -static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - - /* "View.MemoryView":1175 - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< - * src.shape, dst.shape, ndim, itemsize) - * - */ - _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - - /* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - - /* function exit code */ -} - -/* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { - Py_ssize_t __pyx_v_shape; - Py_ssize_t __pyx_v_size; - Py_ssize_t __pyx_r; - Py_ssize_t __pyx_t_1; - Py_ssize_t *__pyx_t_2; - Py_ssize_t *__pyx_t_3; - Py_ssize_t *__pyx_t_4; - - /* "View.MemoryView":1181 - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize # <<<<<<<<<<<<<< - * - * for shape in src.shape[:ndim]: - */ - __pyx_t_1 = __pyx_v_src->memview->view.itemsize; - __pyx_v_size = __pyx_t_1; - - /* "View.MemoryView":1183 - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - * - * for shape in src.shape[:ndim]: # <<<<<<<<<<<<<< - * size *= shape - * - */ - __pyx_t_3 = (__pyx_v_src->shape + __pyx_v_ndim); - for (__pyx_t_4 = __pyx_v_src->shape; __pyx_t_4 < __pyx_t_3; __pyx_t_4++) { - __pyx_t_2 = __pyx_t_4; - __pyx_v_shape = (__pyx_t_2[0]); - - /* "View.MemoryView":1184 - * - * for shape in src.shape[:ndim]: - * size *= shape # <<<<<<<<<<<<<< - * - * return size - */ - __pyx_v_size = (__pyx_v_size * __pyx_v_shape); - } - - /* "View.MemoryView":1186 - * size *= shape - * - * return size # <<<<<<<<<<<<<< - * - * @cname('__pyx_fill_contig_strides_array') - */ - __pyx_r = __pyx_v_size; - goto __pyx_L0; - - /* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1189 - * - * @cname('__pyx_fill_contig_strides_array') - * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< - * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, - * int ndim, char order) nogil: - */ - -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { - int __pyx_v_idx; - Py_ssize_t __pyx_r; - int __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - int __pyx_t_4; - - /* "View.MemoryView":1198 - * cdef int idx - * - * if order == 'F': # <<<<<<<<<<<<<< - * for idx in range(ndim): - * strides[idx] = stride - */ - __pyx_t_1 = ((__pyx_v_order == 'F') != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1199 - * - * if order == 'F': - * for idx in range(ndim): # <<<<<<<<<<<<<< - * strides[idx] = stride - * stride *= shape[idx] - */ - __pyx_t_2 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_2; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; 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The read()\n function will return a frame and all information in it instead of a single\n line. 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0, /*tp_as_async*/ - #endif - __pyx_MemviewEnum___repr__, /*tp_repr*/ - 0, /*tp_as_number*/ - 0, /*tp_as_sequence*/ - 0, /*tp_as_mapping*/ - 0, /*tp_hash*/ - 0, /*tp_call*/ - 0, /*tp_str*/ - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - 0, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - 0, /*tp_doc*/ - __pyx_tp_traverse_Enum, /*tp_traverse*/ - __pyx_tp_clear_Enum, /*tp_clear*/ - 0, /*tp_richcompare*/ - 0, /*tp_weaklistoffset*/ - 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_Enum, /*tp_methods*/ - 0, /*tp_members*/ - 0, /*tp_getset*/ - 0, /*tp_base*/ - 0, /*tp_dict*/ - 0, /*tp_descr_get*/ - 0, /*tp_descr_set*/ - 0, /*tp_dictoffset*/ - __pyx_MemviewEnum___init__, /*tp_init*/ - 0, /*tp_alloc*/ - __pyx_tp_new_Enum, /*tp_new*/ - 0, /*tp_free*/ - 0, /*tp_is_gc*/ - 0, /*tp_bases*/ - 0, /*tp_mro*/ - 0, /*tp_cache*/ - 0, /*tp_subclasses*/ - 0, /*tp_weaklist*/ - 0, /*tp_del*/ - 0, /*tp_version_tag*/ - #if PY_VERSION_HEX >= 0x030400a1 - 0, /*tp_finalize*/ - #endif - #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) - 0, /*tp_vectorcall*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 - 0, /*tp_print*/ - #endif - #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 - 0, /*tp_pypy_flags*/ - #endif -}; -static struct __pyx_vtabstruct_memoryview __pyx_vtable_memoryview; - -static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_memoryview_obj *p; - PyObject *o; - if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { - o = (*t->tp_alloc)(t, 0); - } else { - o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); - } - if (unlikely(!o)) return 0; - p = ((struct __pyx_memoryview_obj *)o); - p->__pyx_vtab = __pyx_vtabptr_memoryview; - p->obj = Py_None; Py_INCREF(Py_None); - p->_size = Py_None; Py_INCREF(Py_None); - p->_array_interface = Py_None; Py_INCREF(Py_None); - 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if (p->obj) { - e = (*v)(p->obj, a); if (e) return e; - } - if (p->_size) { - e = (*v)(p->_size, a); if (e) return e; - } - if (p->_array_interface) { - e = (*v)(p->_array_interface, a); if (e) return e; - } - if (p->view.obj) { - e = (*v)(p->view.obj, a); if (e) return e; - } - return 0; -} - -static int __pyx_tp_clear_memoryview(PyObject *o) { - PyObject* tmp; - struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; - tmp = ((PyObject*)p->obj); - p->obj = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->_size); - p->_size = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->_array_interface); - p->_array_interface = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - Py_CLEAR(p->view.obj); - return 0; -} -static PyObject *__pyx_sq_item_memoryview(PyObject *o, Py_ssize_t i) { - PyObject *r; - PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; - r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); - Py_DECREF(x); - return r; -} - -static int __pyx_mp_ass_subscript_memoryview(PyObject *o, PyObject *i, PyObject *v) { - if (v) { - return __pyx_memoryview___setitem__(o, i, v); - } - else { - PyErr_Format(PyExc_NotImplementedError, - "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name); - return -1; - } -} - -static PyObject *__pyx_getprop___pyx_memoryview_T(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_1T_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_base(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_4base_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_shape(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_5shape_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_strides(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_7strides_1__get__(o); -} - -static PyObject *__pyx_getprop___pyx_memoryview_suboffsets(PyObject *o, CYTHON_UNUSED void *x) { - return __pyx_pw_15View_dot_MemoryView_10memoryview_10suboffsets_1__get__(o); -} - 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{"__reduce_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_1__reduce_cython__, METH_NOARGS, 0}, - {"__setstate_cython__", (PyCFunction)__pyx_pw___pyx_memoryview_3__setstate_cython__, METH_O, 0}, - {0, 0, 0, 0} -}; - -static struct PyGetSetDef __pyx_getsets_memoryview[] = { - {(char *)"T", __pyx_getprop___pyx_memoryview_T, 0, (char *)0, 0}, - {(char *)"base", __pyx_getprop___pyx_memoryview_base, 0, (char *)0, 0}, - {(char *)"shape", __pyx_getprop___pyx_memoryview_shape, 0, (char *)0, 0}, - {(char *)"strides", __pyx_getprop___pyx_memoryview_strides, 0, (char *)0, 0}, - {(char *)"suboffsets", __pyx_getprop___pyx_memoryview_suboffsets, 0, (char *)0, 0}, - {(char *)"ndim", __pyx_getprop___pyx_memoryview_ndim, 0, (char *)0, 0}, - {(char *)"itemsize", __pyx_getprop___pyx_memoryview_itemsize, 0, (char *)0, 0}, - {(char *)"nbytes", __pyx_getprop___pyx_memoryview_nbytes, 0, (char *)0, 0}, - {(char *)"size", __pyx_getprop___pyx_memoryview_size, 0, (char *)0, 0}, - {0, 0, 0, 0, 0} -}; - -static PySequenceMethods __pyx_tp_as_sequence_memoryview = { - 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sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/ - 0, /*tp_itemsize*/ - __pyx_tp_dealloc_memoryview, /*tp_dealloc*/ - #if PY_VERSION_HEX < 0x030800b4 - 0, /*tp_print*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 - 0, /*tp_vectorcall_offset*/ - #endif - 0, /*tp_getattr*/ - 0, /*tp_setattr*/ - #if PY_MAJOR_VERSION < 3 - 0, /*tp_compare*/ - #endif - #if PY_MAJOR_VERSION >= 3 - 0, /*tp_as_async*/ - #endif - __pyx_memoryview___repr__, /*tp_repr*/ - 0, /*tp_as_number*/ - &__pyx_tp_as_sequence_memoryview, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_memoryview, /*tp_as_mapping*/ - 0, /*tp_hash*/ - 0, /*tp_call*/ - __pyx_memoryview___str__, /*tp_str*/ - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_memoryview, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - 0, /*tp_doc*/ - __pyx_tp_traverse_memoryview, /*tp_traverse*/ - __pyx_tp_clear_memoryview, /*tp_clear*/ - 0, /*tp_richcompare*/ - 0, /*tp_weaklistoffset*/ - 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_memoryview, /*tp_methods*/ - 0, /*tp_members*/ - __pyx_getsets_memoryview, /*tp_getset*/ - 0, /*tp_base*/ - 0, /*tp_dict*/ - 0, /*tp_descr_get*/ - 0, /*tp_descr_set*/ - 0, /*tp_dictoffset*/ - 0, /*tp_init*/ - 0, /*tp_alloc*/ - __pyx_tp_new_memoryview, /*tp_new*/ - 0, /*tp_free*/ - 0, /*tp_is_gc*/ - 0, /*tp_bases*/ - 0, /*tp_mro*/ - 0, /*tp_cache*/ - 0, /*tp_subclasses*/ - 0, /*tp_weaklist*/ - 0, /*tp_del*/ - 0, /*tp_version_tag*/ - #if PY_VERSION_HEX >= 0x030400a1 - 0, /*tp_finalize*/ - #endif - #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) - 0, /*tp_vectorcall*/ - #endif - #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 - 0, /*tp_print*/ - #endif - #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 - 0, /*tp_pypy_flags*/ - #endif -}; -static struct __pyx_vtabstruct__memoryviewslice __pyx_vtable__memoryviewslice; - 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- __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } else if (unlikely(PyErr_Occurred())) { - return NULL; - } -#else - result = PyDict_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } -#endif -#else - result = PyObject_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } - PyErr_Clear(); -#endif - return __Pyx_GetBuiltinName(name); -} - -/* GetItemInt */ -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { - PyObject *r; - if (!j) return NULL; - r = PyObject_GetItem(o, j); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyList_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyTuple_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } - else if (PyTuple_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } else { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_item)) { - if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { - Py_ssize_t l = m->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return NULL; - PyErr_Clear(); - } - } - return m->sq_item(o, i); - } - } -#else - if (is_list || PySequence_Check(o)) { - return PySequence_GetItem(o, i); - } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -} - -/* RaiseException */ -#if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* BytesEquals */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { - const char *ps1, *ps2; - Py_ssize_t length = PyBytes_GET_SIZE(s1); - if (length != PyBytes_GET_SIZE(s2)) - return (equals == Py_NE); - ps1 = PyBytes_AS_STRING(s1); - ps2 = PyBytes_AS_STRING(s2); - if (ps1[0] != ps2[0]) { - return (equals == Py_NE); - } else if (length == 1) { - return (equals == Py_EQ); - } else { - int result; -#if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000) - Py_hash_t hash1, hash2; - hash1 = ((PyBytesObject*)s1)->ob_shash; - hash2 = ((PyBytesObject*)s2)->ob_shash; - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - return (equals == Py_NE); - } -#endif - result = memcmp(ps1, ps2, (size_t)length); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -#endif -} - -/* UnicodeEquals */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else -#if PY_MAJOR_VERSION < 3 - PyObject* owned_ref = NULL; -#endif - int s1_is_unicode, s2_is_unicode; - if (s1 == s2) { - goto return_eq; - } - s1_is_unicode = PyUnicode_CheckExact(s1); - s2_is_unicode = PyUnicode_CheckExact(s2); -#if PY_MAJOR_VERSION < 3 - if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { - owned_ref = PyUnicode_FromObject(s2); - if (unlikely(!owned_ref)) - return -1; - s2 = owned_ref; - s2_is_unicode = 1; - } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { - owned_ref = PyUnicode_FromObject(s1); - if (unlikely(!owned_ref)) - return -1; - s1 = owned_ref; - s1_is_unicode = 1; - } else if (((!s2_is_unicode) & (!s1_is_unicode))) { - return __Pyx_PyBytes_Equals(s1, s2, equals); - } -#endif - if (s1_is_unicode & s2_is_unicode) { - Py_ssize_t length; - int kind; - void *data1, *data2; - if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) - return -1; - length = __Pyx_PyUnicode_GET_LENGTH(s1); - if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { - goto return_ne; - } -#if CYTHON_USE_UNICODE_INTERNALS - { - Py_hash_t hash1, hash2; - #if CYTHON_PEP393_ENABLED - hash1 = ((PyASCIIObject*)s1)->hash; - hash2 = ((PyASCIIObject*)s2)->hash; - #else - hash1 = ((PyUnicodeObject*)s1)->hash; - hash2 = ((PyUnicodeObject*)s2)->hash; - #endif - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - goto return_ne; - } - } -#endif - kind = __Pyx_PyUnicode_KIND(s1); - if (kind != __Pyx_PyUnicode_KIND(s2)) { - goto return_ne; - } - data1 = __Pyx_PyUnicode_DATA(s1); - data2 = __Pyx_PyUnicode_DATA(s2); - if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { - goto return_ne; - } else if (length == 1) { - goto return_eq; - } else { - int result = memcmp(data1, data2, (size_t)(length * kind)); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & s2_is_unicode) { - goto return_ne; - } else if ((s2 == Py_None) & s1_is_unicode) { - goto return_ne; - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -return_eq: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ); -return_ne: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_NE); -#endif -} - -/* RaiseTooManyValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -/* RaiseNeedMoreValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -/* IterFinish */ -static CYTHON_INLINE int __Pyx_IterFinish(void) { -#if CYTHON_FAST_THREAD_STATE - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* exc_type = tstate->curexc_type; - if (unlikely(exc_type)) { - if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) { - PyObject *exc_value, *exc_tb; - exc_value = tstate->curexc_value; - exc_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; - Py_DECREF(exc_type); - Py_XDECREF(exc_value); - Py_XDECREF(exc_tb); - return 0; - } else { - return -1; - } - } - return 0; -#else - if (unlikely(PyErr_Occurred())) { - if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { - PyErr_Clear(); - return 0; - } else { - return -1; - } - } - return 0; -#endif -} - -/* UnpackItemEndCheck */ -static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { - if (unlikely(retval)) { - Py_DECREF(retval); - __Pyx_RaiseTooManyValuesError(expected); - return -1; - } - return __Pyx_IterFinish(); -} - -/* ExtTypeTest */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(__Pyx_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* PyIntBinop */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, int inplace, int zerodivision_check) { - (void)inplace; - (void)zerodivision_check; - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - const long b = intval; - long x; - long a = PyInt_AS_LONG(op1); - x = (long)((unsigned long)a - b); - if (likely((x^a) >= 0 || (x^~b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_subtract(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - default: return PyLong_Type.tp_as_number->nb_subtract(op1, op2); - } - } - x = a - b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla - llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("subtract", return NULL) - result = ((double)a) - (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceSubtract : PyNumber_Subtract)(op1, op2); -} -#endif - -/* ObjectGetItem */ -#if CYTHON_USE_TYPE_SLOTS -static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { - PyObject *runerr = NULL; - Py_ssize_t key_value; - PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; - if (unlikely(!(m && m->sq_item))) { - PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); - return NULL; - } - key_value = __Pyx_PyIndex_AsSsize_t(index); - if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { - return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); - } - if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { - PyErr_Clear(); - PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); - } - return NULL; -} -static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { - PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; - if (likely(m && m->mp_subscript)) { - return m->mp_subscript(obj, key); - } - return __Pyx_PyObject_GetIndex(obj, key); -} -#endif - -/* GetTopmostException */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* PyErrExceptionMatches */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* GetException */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* ArgTypeTest */ -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) -{ - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - else if (exact) { - #if PY_MAJOR_VERSION == 2 - if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; - #endif - } - else { - if (likely(__Pyx_TypeCheck(obj, type))) return 1; - } - PyErr_Format(PyExc_TypeError, - "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", - name, type->tp_name, Py_TYPE(obj)->tp_name); - return 0; -} - -/* IsLittleEndian */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) -{ - union { - uint32_t u32; - uint8_t u8[4]; - } S; - S.u32 = 0x01020304; - return S.u8[0] == 4; -} - -/* BufferFormatCheck */ -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type) { - stack[0].field = &ctx->root; - stack[0].parent_offset = 0; - ctx->root.type = type; - ctx->root.name = "buffer dtype"; - ctx->root.offset = 0; - ctx->head = stack; - ctx->head->field = &ctx->root; - ctx->fmt_offset = 0; - ctx->head->parent_offset = 0; - ctx->new_packmode = '@'; - ctx->enc_packmode = '@'; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->is_complex = 0; - ctx->is_valid_array = 0; - ctx->struct_alignment = 0; - while (type->typegroup == 'S') { - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = 0; - type = type->fields->type; - } -} -static int __Pyx_BufFmt_ParseNumber(const char** ts) { - int count; - const char* t = *ts; - if (*t < '0' || *t > '9') { - return -1; - } else { - count = *t++ - '0'; - while (*t >= '0' && *t <= '9') { - count *= 10; - count += *t++ - '0'; - } - } - *ts = t; - return count; -} -static int __Pyx_BufFmt_ExpectNumber(const char **ts) { - int number = __Pyx_BufFmt_ParseNumber(ts); - if (number == -1) - PyErr_Format(PyExc_ValueError,\ - "Does not understand character buffer dtype format string ('%c')", **ts); - return number; -} -static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { - PyErr_Format(PyExc_ValueError, - "Unexpected format string character: '%c'", ch); -} -static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { - switch (ch) { - case '?': return "'bool'"; - case 'c': return "'char'"; - case 'b': return "'signed char'"; - case 'B': return "'unsigned char'"; - case 'h': return "'short'"; - case 'H': return "'unsigned short'"; - case 'i': return "'int'"; - case 'I': return "'unsigned int'"; - case 'l': return "'long'"; - case 'L': return "'unsigned long'"; - case 'q': return "'long long'"; - case 'Q': return "'unsigned long long'"; - case 'f': return (is_complex ? "'complex float'" : "'float'"); - case 'd': return (is_complex ? "'complex double'" : "'double'"); - case 'g': return (is_complex ? "'complex long double'" : "'long double'"); - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - case 's': case 'p': return "a string"; - case 0: return "end"; - default: return "unparseable format string"; - } -} -static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return 2; - case 'i': case 'I': case 'l': case 'L': return 4; - case 'q': case 'Q': return 8; - case 'f': return (is_complex ? 8 : 4); - case 'd': return (is_complex ? 16 : 8); - case 'g': { - PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); - return 0; - } - case 'O': case 'P': return sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(short); - case 'i': case 'I': return sizeof(int); - case 'l': case 'L': return sizeof(long); - #ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(PY_LONG_LONG); - #endif - case 'f': return sizeof(float) * (is_complex ? 2 : 1); - case 'd': return sizeof(double) * (is_complex ? 2 : 1); - case 'g': return sizeof(long double) * (is_complex ? 2 : 1); - case 'O': case 'P': return sizeof(void*); - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -typedef struct { char c; short x; } __Pyx_st_short; -typedef struct { char c; int x; } __Pyx_st_int; -typedef struct { char c; long x; } __Pyx_st_long; -typedef struct { char c; float x; } __Pyx_st_float; -typedef struct { char c; double x; } __Pyx_st_double; -typedef struct { char c; long double x; } __Pyx_st_longdouble; -typedef struct { char c; void *x; } __Pyx_st_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_st_float) - sizeof(float); - case 'd': return sizeof(__Pyx_st_double) - sizeof(double); - case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -/* These are for computing the padding at the end of the struct to align - on the first member of the struct. This will probably the same as above, - but we don't have any guarantees. - */ -typedef struct { short x; char c; } __Pyx_pad_short; -typedef struct { int x; char c; } __Pyx_pad_int; -typedef struct { long x; char c; } __Pyx_pad_long; -typedef struct { float x; char c; } __Pyx_pad_float; -typedef struct { double x; char c; } __Pyx_pad_double; -typedef struct { long double x; char c; } __Pyx_pad_longdouble; -typedef struct { void *x; char c; } __Pyx_pad_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); - case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); - case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { - switch (ch) { - case 'c': - return 'H'; - case 'b': case 'h': case 'i': - case 'l': case 'q': case 's': case 'p': - return 'I'; - case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': - return 'U'; - case 'f': case 'd': case 'g': - return (is_complex ? 'C' : 'R'); - case 'O': - return 'O'; - case 'P': - return 'P'; - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { - if (ctx->head == NULL || ctx->head->field == &ctx->root) { - const char* expected; - const char* quote; - if (ctx->head == NULL) { - expected = "end"; - quote = ""; - } else { - expected = ctx->head->field->type->name; - quote = "'"; - } - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected %s%s%s but got %s", - quote, expected, quote, - __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); - } else { - __Pyx_StructField* field = ctx->head->field; - __Pyx_StructField* parent = (ctx->head - 1)->field; - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", - field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), - parent->type->name, field->name); - } -} -static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { - char group; - size_t size, offset, arraysize = 1; - if (ctx->enc_type == 0) return 0; - if (ctx->head->field->type->arraysize[0]) { - int i, ndim = 0; - if (ctx->enc_type == 's' || ctx->enc_type == 'p') { - ctx->is_valid_array = ctx->head->field->type->ndim == 1; - ndim = 1; - if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { - PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %zu", - ctx->head->field->type->arraysize[0], ctx->enc_count); - return -1; - } - } - if (!ctx->is_valid_array) { - PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", - ctx->head->field->type->ndim, ndim); - return -1; - } - for (i = 0; i < ctx->head->field->type->ndim; i++) { - arraysize *= ctx->head->field->type->arraysize[i]; - } - ctx->is_valid_array = 0; - ctx->enc_count = 1; - } - group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); - do { - __Pyx_StructField* field = ctx->head->field; - __Pyx_TypeInfo* type = field->type; - if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { - size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); - } else { - size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); - } - if (ctx->enc_packmode == '@') { - size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); - size_t align_mod_offset; - if (align_at == 0) return -1; - align_mod_offset = ctx->fmt_offset % align_at; - if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; - if (ctx->struct_alignment == 0) - ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, - ctx->is_complex); - } - if (type->size != size || type->typegroup != group) { - if (type->typegroup == 'C' && type->fields != NULL) { - size_t parent_offset = ctx->head->parent_offset + field->offset; - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = parent_offset; - continue; - } - if ((type->typegroup == 'H' || group == 'H') && type->size == size) { - } else { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - } - offset = ctx->head->parent_offset + field->offset; - if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; - } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } - } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; -} -static PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number, ndim; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ndim = ctx->head->field->type->ndim; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; - } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; - } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; - } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; -} -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; - } - break; - case '}': - { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } - } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; - } - CYTHON_FALLTHROUGH; - case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && - (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - CYTHON_FALLTHROUGH; - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: - { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; - } - } - } -} - -/* BufferGetAndValidate */ - static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { - if (unlikely(info->buf == NULL)) return; - if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; - __Pyx_ReleaseBuffer(info); -} -static void __Pyx_ZeroBuffer(Py_buffer* buf) { - buf->buf = NULL; - buf->obj = NULL; - buf->strides = __Pyx_zeros; - buf->shape = __Pyx_zeros; - buf->suboffsets = __Pyx_minusones; -} -static int __Pyx__GetBufferAndValidate( - Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, - int nd, int cast, __Pyx_BufFmt_StackElem* stack) -{ - buf->buf = NULL; - if (unlikely(__Pyx_GetBuffer(obj, buf, flags) == -1)) { - __Pyx_ZeroBuffer(buf); - return -1; - } - if (unlikely(buf->ndim != nd)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - nd, buf->ndim); - goto fail; - } - if (!cast) { - __Pyx_BufFmt_Context ctx; - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; - } - if (unlikely((size_t)buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", - buf->itemsize, (buf->itemsize > 1) ? "s" : "", - dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; - return 0; -fail:; - __Pyx_SafeReleaseBuffer(buf); - return -1; -} - -/* MemviewSliceInit */ - static int -__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference) -{ - __Pyx_RefNannyDeclarations - int i, retval=-1; - Py_buffer *buf = &memview->view; - __Pyx_RefNannySetupContext("init_memviewslice", 0); - if (unlikely(memviewslice->memview || memviewslice->data)) { - PyErr_SetString(PyExc_ValueError, - "memviewslice is already initialized!"); - goto fail; - } - if (buf->strides) { - for (i = 0; i < ndim; i++) { - memviewslice->strides[i] = buf->strides[i]; - } - } else { - Py_ssize_t stride = buf->itemsize; - for (i = ndim - 1; i >= 0; i--) { - memviewslice->strides[i] = stride; - stride *= buf->shape[i]; - } - } - for (i = 0; i < ndim; i++) { - memviewslice->shape[i] = buf->shape[i]; - if (buf->suboffsets) { - memviewslice->suboffsets[i] = buf->suboffsets[i]; - } else { - memviewslice->suboffsets[i] = -1; - } - } - memviewslice->memview = memview; - memviewslice->data = (char *)buf->buf; - if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { - Py_INCREF(memview); - } - retval = 0; - goto no_fail; -fail: - memviewslice->memview = 0; - memviewslice->data = 0; - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} -#ifndef Py_NO_RETURN -#define Py_NO_RETURN -#endif -static void __pyx_fatalerror(const char *fmt, ...) Py_NO_RETURN { - va_list vargs; - char msg[200]; -#if PY_VERSION_HEX >= 0x030A0000 || defined(HAVE_STDARG_PROTOTYPES) - va_start(vargs, fmt); -#else - va_start(vargs); -#endif - vsnprintf(msg, 200, fmt, vargs); - va_end(vargs); - Py_FatalError(msg); -} -static CYTHON_INLINE int -__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)++; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE int -__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)--; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE void -__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) -{ - int first_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) - return; - if (unlikely(__pyx_get_slice_count(memview) < 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - first_time = __pyx_add_acquisition_count(memview) == 0; - if (unlikely(first_time)) { - if (have_gil) { - Py_INCREF((PyObject *) memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_INCREF((PyObject *) memview); - PyGILState_Release(_gilstate); - } - } -} -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, - int have_gil, int lineno) { - int last_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) { - memslice->memview = NULL; - return; - } - if (unlikely(__pyx_get_slice_count(memview) <= 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - last_time = __pyx_sub_acquisition_count(memview) == 1; - memslice->data = NULL; - if (unlikely(last_time)) { - if (have_gil) { - Py_CLEAR(memslice->memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_CLEAR(memslice->memview); - PyGILState_Release(_gilstate); - } - } else { - memslice->memview = NULL; - } -} - -/* SliceObject */ - static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, - Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, - int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { -#if CYTHON_USE_TYPE_SLOTS - PyMappingMethods* mp; -#if PY_MAJOR_VERSION < 3 - PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; - if (likely(ms && ms->sq_slice)) { - if (!has_cstart) { - if (_py_start && (*_py_start != Py_None)) { - cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); - if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstart = 0; - } - if (!has_cstop) { - if (_py_stop && (*_py_stop != Py_None)) { - cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); - if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstop = PY_SSIZE_T_MAX; - } - if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { - Py_ssize_t l = ms->sq_length(obj); - if (likely(l >= 0)) { - if (cstop < 0) { - cstop += l; - if (cstop < 0) cstop = 0; - } - if (cstart < 0) { - cstart += l; - if (cstart < 0) cstart = 0; - } - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - goto bad; - PyErr_Clear(); - } - } - return ms->sq_slice(obj, cstart, cstop); - } -#endif - mp = Py_TYPE(obj)->tp_as_mapping; - if (likely(mp && mp->mp_subscript)) -#endif - { - PyObject* result; - PyObject *py_slice, *py_start, *py_stop; - if (_py_slice) { - py_slice = *_py_slice; - } else { - PyObject* owned_start = NULL; - PyObject* owned_stop = NULL; - if (_py_start) { - py_start = *_py_start; - } else { - if (has_cstart) { - owned_start = py_start = PyInt_FromSsize_t(cstart); - if (unlikely(!py_start)) goto bad; - } else - py_start = Py_None; - } - if (_py_stop) { - py_stop = *_py_stop; - } else { - if (has_cstop) { - owned_stop = py_stop = PyInt_FromSsize_t(cstop); - if (unlikely(!py_stop)) { - Py_XDECREF(owned_start); - goto bad; - } - } else - py_stop = Py_None; - } - py_slice = PySlice_New(py_start, py_stop, Py_None); - Py_XDECREF(owned_start); - Py_XDECREF(owned_stop); - if (unlikely(!py_slice)) goto bad; - } -#if CYTHON_USE_TYPE_SLOTS - result = mp->mp_subscript(obj, py_slice); -#else - result = PyObject_GetItem(obj, py_slice); -#endif - if (!_py_slice) { - Py_DECREF(py_slice); - } - return result; - } - PyErr_Format(PyExc_TypeError, - "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name); -bad: - return NULL; -} - -/* DivInt[Py_ssize_t] */ - static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { - Py_ssize_t q = a / b; - Py_ssize_t r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* GetAttr */ - static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { -#if CYTHON_USE_TYPE_SLOTS -#if PY_MAJOR_VERSION >= 3 - if (likely(PyUnicode_Check(n))) -#else - if (likely(PyString_Check(n))) -#endif - return __Pyx_PyObject_GetAttrStr(o, n); -#endif - return PyObject_GetAttr(o, n); -} - -/* decode_c_string */ - static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { - Py_ssize_t length; - if (unlikely((start < 0) | (stop < 0))) { - size_t slen = strlen(cstring); - if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { - PyErr_SetString(PyExc_OverflowError, - "c-string too long to convert to Python"); - return NULL; - } - length = (Py_ssize_t) slen; - if (start < 0) { - start += length; - if (start < 0) - start = 0; - } - if (stop < 0) - stop += length; - } - if (unlikely(stop <= start)) - return __Pyx_NewRef(__pyx_empty_unicode); - length = stop - start; - cstring += start; - if (decode_func) { - return decode_func(cstring, length, errors); - } else { - return PyUnicode_Decode(cstring, length, encoding, errors); - } -} - -/* GetAttr3 */ - static PyObject *__Pyx_GetAttr3Default(PyObject *d) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - return NULL; - __Pyx_PyErr_Clear(); - Py_INCREF(d); - return d; -} -static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { - PyObject *r = __Pyx_GetAttr(o, n); - return (likely(r)) ? r : __Pyx_GetAttr3Default(d); -} - -/* RaiseNoneIterError */ - static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); -} - -/* SwapException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = *type; - exc_info->exc_value = *value; - exc_info->exc_traceback = *tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = *type; - tstate->exc_value = *value; - tstate->exc_traceback = *tb; - #endif - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); - PyErr_SetExcInfo(*type, *value, *tb); - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#endif - -/* Import */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* FastTypeChecks */ - #if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; - if (a == b) - return 1; - } - return b == &PyBaseObject_Type; -} -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { - PyObject *mro; - if (a == b) return 1; - mro = a->tp_mro; - if (likely(mro)) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(mro); - for (i = 0; i < n; i++) { - if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) - return 1; - } - return 0; - } - return __Pyx_InBases(a, b); -} -#if PY_MAJOR_VERSION == 2 -static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { - PyObject *exception, *value, *tb; - int res; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&exception, &value, &tb); - res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - if (!res) { - res = PyObject_IsSubclass(err, exc_type2); - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - } - __Pyx_ErrRestore(exception, value, tb); - return res; -} -#else -static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { - int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; - if (!res) { - res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); - } - return res; -} -#endif -static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - assert(PyExceptionClass_Check(exc_type)); - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; i= 0 || (x^b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - default: return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - } - x = a + b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla + llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("add", return NULL) - result = ((double)a) + (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); -} -#endif - -/* None */ - static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { - PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); -} - -/* DivInt[long] */ - static CYTHON_INLINE long __Pyx_div_long(long a, long b) { - long q = a / b; - long r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* ImportFrom */ - static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { - PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); - if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_Format(PyExc_ImportError, - #if PY_MAJOR_VERSION < 3 - "cannot import name %.230s", PyString_AS_STRING(name)); - #else - "cannot import name %S", name); - #endif - } - return value; -} - -/* HasAttr */ - static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { - PyObject *r; - if (unlikely(!__Pyx_PyBaseString_Check(n))) { - PyErr_SetString(PyExc_TypeError, - "hasattr(): attribute name must be string"); - return -1; - } - r = __Pyx_GetAttr(o, n); - if (unlikely(!r)) { - PyErr_Clear(); - return 0; - } else { - Py_DECREF(r); - return 1; - } -} - -/* PyObject_GenericGetAttrNoDict */ - #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { - PyErr_Format(PyExc_AttributeError, -#if PY_MAJOR_VERSION >= 3 - "'%.50s' object has no attribute '%U'", - tp->tp_name, attr_name); -#else - "'%.50s' object has no attribute '%.400s'", - tp->tp_name, PyString_AS_STRING(attr_name)); -#endif - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { - PyObject *descr; - PyTypeObject *tp = Py_TYPE(obj); - if (unlikely(!PyString_Check(attr_name))) { - return PyObject_GenericGetAttr(obj, attr_name); - } - assert(!tp->tp_dictoffset); - descr = _PyType_Lookup(tp, attr_name); - if (unlikely(!descr)) { - return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); - } - Py_INCREF(descr); - #if PY_MAJOR_VERSION < 3 - if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) - #endif - { - descrgetfunc f = Py_TYPE(descr)->tp_descr_get; - if (unlikely(f)) { - PyObject *res = f(descr, obj, (PyObject *)tp); - Py_DECREF(descr); - return res; - } - } - return descr; -} -#endif - -/* PyObject_GenericGetAttr */ - #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { - if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { - return PyObject_GenericGetAttr(obj, attr_name); - } - return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); -} -#endif - -/* SetVTable */ - static int __Pyx_SetVtable(PyObject *dict, void *vtable) { -#if PY_VERSION_HEX >= 0x02070000 - PyObject *ob = PyCapsule_New(vtable, 0, 0); -#else - PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); -#endif - if (!ob) - goto bad; - if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) - goto bad; - Py_DECREF(ob); - return 0; -bad: - Py_XDECREF(ob); - return -1; -} - -/* PyObjectGetAttrStrNoError */ - static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - __Pyx_PyErr_Clear(); -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { - PyObject *result; -#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 - PyTypeObject* tp = Py_TYPE(obj); - if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { - return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); - } -#endif - result = __Pyx_PyObject_GetAttrStr(obj, attr_name); - if (unlikely(!result)) { - __Pyx_PyObject_GetAttrStr_ClearAttributeError(); - } - return result; -} - -/* SetupReduce */ - static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { - int ret; - PyObject *name_attr; - name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2); - if (likely(name_attr)) { - ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); - } else { - ret = -1; - } - if (unlikely(ret < 0)) { - PyErr_Clear(); - ret = 0; - } - Py_XDECREF(name_attr); - return ret; -} -static int __Pyx_setup_reduce(PyObject* type_obj) { - int ret = 0; - PyObject *object_reduce = NULL; - PyObject *object_getstate = NULL; - PyObject *object_reduce_ex = NULL; - PyObject *reduce = NULL; - PyObject *reduce_ex = NULL; - PyObject *reduce_cython = NULL; - PyObject *setstate = NULL; - PyObject *setstate_cython = NULL; - PyObject *getstate = NULL; -#if CYTHON_USE_PYTYPE_LOOKUP - getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate); -#else - getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate); - if (!getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (getstate) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate); -#else - object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate); - if (!object_getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (object_getstate != getstate) { - goto __PYX_GOOD; - } - } -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; - if (reduce_ex == object_reduce_ex) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; - if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); - if (likely(reduce_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (reduce == object_reduce || PyErr_Occurred()) { - goto __PYX_BAD; - } - setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); - if (!setstate) PyErr_Clear(); - if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); - if (likely(setstate_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (!setstate || PyErr_Occurred()) { - goto __PYX_BAD; - } - } - PyType_Modified((PyTypeObject*)type_obj); - } - } - goto __PYX_GOOD; -__PYX_BAD: - if (!PyErr_Occurred()) - PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); - ret = -1; -__PYX_GOOD: -#if !CYTHON_USE_PYTYPE_LOOKUP - Py_XDECREF(object_reduce); - Py_XDECREF(object_reduce_ex); - Py_XDECREF(object_getstate); - Py_XDECREF(getstate); -#endif - Py_XDECREF(reduce); - Py_XDECREF(reduce_ex); - Py_XDECREF(reduce_cython); - Py_XDECREF(setstate); - Py_XDECREF(setstate_cython); - return ret; -} - -/* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* CLineInTraceback */ - #ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ - #include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - if ((0)) {} - view->obj = NULL; - Py_DECREF(obj); -} -#endif - - - /* MemviewSliceIsContig */ - static int -__pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim) -{ - int i, index, step, start; - Py_ssize_t itemsize = mvs.memview->view.itemsize; - if (order == 'F') { - step = 1; - start = 0; - } else { - step = -1; - start = ndim - 1; - } - for (i = 0; i < ndim; i++) { - index = start + step * i; - if (mvs.suboffsets[index] >= 0 || mvs.strides[index] != itemsize) - return 0; - itemsize *= mvs.shape[index]; - } - return 1; -} - -/* OverlappingSlices */ - static void -__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, - void **out_start, void **out_end, - int ndim, size_t itemsize) -{ - char *start, *end; - int i; - start = end = slice->data; - for (i = 0; i < ndim; i++) { - Py_ssize_t stride = slice->strides[i]; - Py_ssize_t extent = slice->shape[i]; - if (extent == 0) { - *out_start = *out_end = start; - return; - } else { - if (stride > 0) - end += stride * (extent - 1); - else - start += stride * (extent - 1); - } - } - *out_start = start; - *out_end = end + itemsize; -} -static int -__pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize) -{ - void *start1, *end1, *start2, *end2; - __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); - __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); - return (start1 < end2) && (start2 < end1); -} - -/* Capsule */ - static CYTHON_INLINE PyObject * -__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) -{ - PyObject *cobj; -#if PY_VERSION_HEX >= 0x02070000 - cobj = PyCapsule_New(p, sig, NULL); -#else - cobj = PyCObject_FromVoidPtr(p, NULL); -#endif - return cobj; -} - -/* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* TypeInfoCompare */ - static int -__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) -{ - int i; - if (!a || !b) - return 0; - if (a == b) - return 1; - if (a->size != b->size || a->typegroup != b->typegroup || - a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { - if (a->typegroup == 'H' || b->typegroup == 'H') { - return a->size == b->size; - } else { - return 0; - } - } - if (a->ndim) { - for (i = 0; i < a->ndim; i++) - if (a->arraysize[i] != b->arraysize[i]) - return 0; - } - if (a->typegroup == 'S') { - if (a->flags != b->flags) - return 0; - if (a->fields || b->fields) { - if (!(a->fields && b->fields)) - return 0; - for (i = 0; a->fields[i].type && b->fields[i].type; i++) { - __Pyx_StructField *field_a = a->fields + i; - __Pyx_StructField *field_b = b->fields + i; - if (field_a->offset != field_b->offset || - !__pyx_typeinfo_cmp(field_a->type, field_b->type)) - return 0; - } - return !a->fields[i].type && !b->fields[i].type; - } - } - return 1; -} - -/* MemviewSliceValidateAndInit */ - static int -__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) -{ - if (buf->shape[dim] <= 1) - return 1; - if (buf->strides) { - if (spec & __Pyx_MEMVIEW_CONTIG) { - if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { - if (unlikely(buf->strides[dim] != sizeof(void *))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly contiguous " - "in dimension %d.", dim); - goto fail; - } - } else if (unlikely(buf->strides[dim] != buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_FOLLOW) { - Py_ssize_t stride = buf->strides[dim]; - if (stride < 0) - stride = -stride; - if (unlikely(stride < buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - } else { - if (unlikely(spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1)) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not contiguous in " - "dimension %d", dim); - goto fail; - } else if (unlikely(spec & (__Pyx_MEMVIEW_PTR))) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not indirect in " - "dimension %d", dim); - goto fail; - } else if (unlikely(buf->suboffsets)) { - PyErr_SetString(PyExc_ValueError, - "Buffer exposes suboffsets but no strides"); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) -{ - if (spec & __Pyx_MEMVIEW_DIRECT) { - if (unlikely(buf->suboffsets && buf->suboffsets[dim] >= 0)) { - PyErr_Format(PyExc_ValueError, - "Buffer not compatible with direct access " - "in dimension %d.", dim); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_PTR) { - if (unlikely(!buf->suboffsets || (buf->suboffsets[dim] < 0))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly accessible " - "in dimension %d.", dim); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) -{ - int i; - if (c_or_f_flag & __Pyx_IS_F_CONTIG) { - Py_ssize_t stride = 1; - for (i = 0; i < ndim; i++) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not fortran contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { - Py_ssize_t stride = 1; - for (i = ndim - 1; i >- 1; i--) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not C contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } - return 1; -fail: - return 0; -} -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj) -{ - struct __pyx_memoryview_obj *memview, *new_memview; - __Pyx_RefNannyDeclarations - Py_buffer *buf; - int i, spec = 0, retval = -1; - __Pyx_BufFmt_Context ctx; - int from_memoryview = __pyx_memoryview_check(original_obj); - __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); - if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) - original_obj)->typeinfo)) { - memview = (struct __pyx_memoryview_obj *) original_obj; - new_memview = NULL; - } else { - memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - original_obj, buf_flags, 0, dtype); - new_memview = memview; - if (unlikely(!memview)) - goto fail; - } - buf = &memview->view; - if (unlikely(buf->ndim != ndim)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - ndim, buf->ndim); - goto fail; - } - if (new_memview) { - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (unlikely(!__Pyx_BufFmt_CheckString(&ctx, buf->format))) goto fail; - } - if (unlikely((unsigned) buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " - "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", - buf->itemsize, - (buf->itemsize > 1) ? "s" : "", - dtype->name, - dtype->size, - (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->len > 0) { - for (i = 0; i < ndim; i++) { - spec = axes_specs[i]; - if (unlikely(!__pyx_check_strides(buf, i, ndim, spec))) - goto fail; - if (unlikely(!__pyx_check_suboffsets(buf, i, ndim, spec))) - goto fail; - } - if (unlikely(buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))) - goto fail; - } - if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, - new_memview != NULL) == -1)) { - goto fail; - } - retval = 0; - goto no_fail; -fail: - Py_XDECREF(new_memview); - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_nn___pyx_t_5numpy_float32_t(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_FOLLOW), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 2, - &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_int64_t(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 1, - &__Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* MemviewDtypeToObject */ - static CYTHON_INLINE PyObject *__pyx_memview_get_nn___pyx_t_5numpy_float32_t(const char *itemp) { - return (PyObject *) PyFloat_FromDouble(*(__pyx_t_5numpy_float32_t *) itemp); -} -static CYTHON_INLINE int __pyx_memview_set_nn___pyx_t_5numpy_float32_t(const char *itemp, PyObject *obj) { - __pyx_t_5numpy_float32_t value = __pyx_PyFloat_AsFloat(obj); - if ((value == ((npy_float32)-1)) && PyErr_Occurred()) - return 0; - *(__pyx_t_5numpy_float32_t *) itemp = value; - return 1; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_nn___pyx_t_10MDAnalysis_3lib_7formats_9libmdaxdr_DTYPE_T(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_FOLLOW), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 2, - &__Pyx_TypeInfo_nn___pyx_t_10MDAnalysis_3lib_7formats_9libmdaxdr_DTYPE_T, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* MemviewSliceCopyTemplate */ - static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object) -{ - __Pyx_RefNannyDeclarations - int i; - __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; - struct __pyx_memoryview_obj *from_memview = from_mvs->memview; - Py_buffer *buf = &from_memview->view; - PyObject *shape_tuple = NULL; - PyObject *temp_int = NULL; - struct __pyx_array_obj *array_obj = NULL; - struct __pyx_memoryview_obj *memview_obj = NULL; - __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); - for (i = 0; i < ndim; i++) { - if (unlikely(from_mvs->suboffsets[i] >= 0)) { - PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " - "indirect dimensions (axis %d)", i); - goto fail; - } - } - shape_tuple = PyTuple_New(ndim); - if (unlikely(!shape_tuple)) { - goto fail; - } - __Pyx_GOTREF(shape_tuple); - for(i = 0; i < ndim; i++) { - temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); - if(unlikely(!temp_int)) { - goto fail; - } else { - PyTuple_SET_ITEM(shape_tuple, i, temp_int); - temp_int = NULL; - } - } - array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); - if (unlikely(!array_obj)) { - goto fail; - } - __Pyx_GOTREF(array_obj); - memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - (PyObject *) array_obj, contig_flag, - dtype_is_object, - from_mvs->memview->typeinfo); - if (unlikely(!memview_obj)) - goto fail; - if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) - goto fail; - if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, - dtype_is_object) < 0)) - goto fail; - goto no_fail; -fail: - __Pyx_XDECREF(new_mvs.memview); - new_mvs.memview = NULL; - new_mvs.data = NULL; -no_fail: - __Pyx_XDECREF(shape_tuple); - __Pyx_XDECREF(temp_int); - __Pyx_XDECREF(array_obj); - __Pyx_RefNannyFinishContext(); - return new_mvs; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int64_t) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int64_t, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int64_t) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int64_t) 0; - case 1: __PYX_VERIFY_RETURN_INT(int64_t, digit, digits[0]) - case 2: - if (8 * sizeof(int64_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) >= 2 * PyLong_SHIFT) { - return (int64_t) (((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int64_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) >= 3 * PyLong_SHIFT) { - return (int64_t) (((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int64_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) >= 4 * PyLong_SHIFT) { - return (int64_t) (((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int64_t) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int64_t) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int64_t) 0; - case -1: __PYX_VERIFY_RETURN_INT(int64_t, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int64_t, digit, +digits[0]) - case -2: - if (8 * sizeof(int64_t) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { - return (int64_t) (((int64_t)-1)*(((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int64_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { - return (int64_t) ((((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { - return (int64_t) (((int64_t)-1)*(((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int64_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { - return (int64_t) ((((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT) { - return (int64_t) (((int64_t)-1)*(((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int64_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT) { - return (int64_t) ((((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int64_t) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int64_t, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int64_t, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int64_t val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int64_t) -1; - } - } else { - int64_t val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int64_t) -1; - val = __Pyx_PyInt_As_int64_t(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int64_t"); - return (int64_t) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int64_t"); - return (int64_t) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int64_t) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int64_t) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int64_t) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int64_t), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const char neg_one = (char) -1, const_zero = (char) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(char) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (char) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (char) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(char) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) - case -2: - if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - } -#endif - if (sizeof(char) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - char val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (char) -1; - } - } else { - char val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (char) -1; - val = __Pyx_PyInt_As_char(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to char"); - return (char) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to char"); - return (char) -1; -} - -/* CheckBinaryVersion */ - static int __Pyx_check_binary_version(void) { - char ctversion[5]; - int same=1, i, found_dot; - const char* rt_from_call = Py_GetVersion(); - PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); - found_dot = 0; - for (i = 0; i < 4; i++) { - if (!ctversion[i]) { - same = (rt_from_call[i] < '0' || rt_from_call[i] > '9'); - break; - } - if (rt_from_call[i] != ctversion[i]) { - same = 0; - break; - } - } - if (!same) { - char rtversion[5] = {'\0'}; - char message[200]; - for (i=0; i<4; ++i) { - if (rt_from_call[i] == '.') { - if (found_dot) break; - found_dot = 1; - } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') { - break; - } - rtversion[i] = rt_from_call[i]; - } - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* FunctionImport */ - #ifndef __PYX_HAVE_RT_ImportFunction -#define __PYX_HAVE_RT_ImportFunction -static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig) { - PyObject *d = 0; - PyObject *cobj = 0; - union { - void (*fp)(void); - void *p; - } tmp; - d = PyObject_GetAttrString(module, (char *)"__pyx_capi__"); - if (!d) - goto bad; - cobj = PyDict_GetItemString(d, funcname); - if (!cobj) { - PyErr_Format(PyExc_ImportError, - "%.200s does not export expected C function %.200s", - PyModule_GetName(module), funcname); - goto bad; - } -#if PY_VERSION_HEX >= 0x02070000 - if (!PyCapsule_IsValid(cobj, sig)) { - PyErr_Format(PyExc_TypeError, - "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)", - PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj)); - goto bad; - } - tmp.p = PyCapsule_GetPointer(cobj, sig); -#else - {const char *desc, *s1, *s2; - desc = (const char *)PyCObject_GetDesc(cobj); - if (!desc) - goto bad; - s1 = desc; s2 = sig; - while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; } - if (*s1 != *s2) { - PyErr_Format(PyExc_TypeError, - "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)", - PyModule_GetName(module), funcname, sig, desc); - goto bad; - } - tmp.p = PyCObject_AsVoidPtr(cobj);} -#endif - *f = tmp.fp; - if (!(*f)) - goto bad; - Py_DECREF(d); - return 0; -bad: - Py_XDECREF(d); - return -1; -} -#endif - -/* InitStrings */ - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - if (PyObject_Hash(*t->p) == -1) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT -#if !CYTHON_PEP393_ENABLED -static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); - return NULL; - } - } - } -#endif - *length = PyBytes_GET_SIZE(defenc); - return defenc_c; -} -#else -static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (likely(PyUnicode_IS_ASCII(o))) { - *length = PyUnicode_GET_LENGTH(o); - return PyUnicode_AsUTF8(o); - } else { - PyUnicode_AsASCIIString(o); - return NULL; - } -#else - return PyUnicode_AsUTF8AndSize(o, length); -#endif -} -#endif -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { - return __Pyx_PyUnicode_AsStringAndSize(o, length); - } else -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - if (PyByteArray_Check(o)) { - *length = PyByteArray_GET_SIZE(o); - return PyByteArray_AS_STRING(o); - } else -#endif - { - char* result; - int r = PyBytes_AsStringAndSize(o, &result, length); - if (unlikely(r < 0)) { - return NULL; - } else { - return result; - } - } -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - int is_true = x == Py_True; - if (is_true | (x == Py_False) | (x == Py_None)) return is_true; - else return PyObject_IsTrue(x); -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) { - int retval; - if (unlikely(!x)) return -1; - retval = __Pyx_PyObject_IsTrue(x); - Py_DECREF(x); - return retval; -} -static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { -#if PY_MAJOR_VERSION >= 3 - if (PyLong_Check(result)) { - if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, - "__int__ returned non-int (type %.200s). " - "The ability to return an instance of a strict subclass of int " - "is deprecated, and may be removed in a future version of Python.", - Py_TYPE(result)->tp_name)) { - Py_DECREF(result); - return NULL; - } - return result; - } -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - type_name, type_name, Py_TYPE(result)->tp_name); - Py_DECREF(result); - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS - PyNumberMethods *m; -#endif - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x) || PyLong_Check(x))) -#else - if (likely(PyLong_Check(x))) -#endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS - m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = m->nb_int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = m->nb_long(x); - } - #else - if (likely(m && m->nb_int)) { - name = "int"; - res = m->nb_int(x); - } - #endif -#else - if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) { - res = PyNumber_Int(x); - } -#endif - if (likely(res)) { -#if PY_MAJOR_VERSION < 3 - if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) { -#else - if (unlikely(!PyLong_CheckExact(res))) { -#endif - return __Pyx_PyNumber_IntOrLongWrongResultType(res, name); - } - } - else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_TypeError, - "an integer is required"); - } - return res; -} -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { - Py_ssize_t ival; - PyObject *x; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(b); - } -#endif - if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - if (size == -1) ival = -ival; - return ival; - } else { - switch (size) { - case 2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - } - } - #endif - return PyLong_AsSsize_t(b); - } - x = PyNumber_Index(b); - if (!x) return -1; - ival = PyInt_AsSsize_t(x); - Py_DECREF(x); - return ival; -} -static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) { - if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) { - return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o); -#if PY_MAJOR_VERSION < 3 - } else if (likely(PyInt_CheckExact(o))) { - return PyInt_AS_LONG(o); -#endif - } else { - Py_ssize_t ival; - PyObject *x; - x = PyNumber_Index(o); - if (!x) return -1; - ival = PyInt_AsLong(x); - Py_DECREF(x); - return ival; - } -} -static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) { - return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False); -} -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { - return PyInt_FromSize_t(ival); -} - - -#endif /* Py_PYTHON_H */ diff --git a/package/MDAnalysis/lib/nsgrid.cpp b/package/MDAnalysis/lib/nsgrid.cpp deleted file mode 100644 index e090c359487..00000000000 --- a/package/MDAnalysis/lib/nsgrid.cpp +++ /dev/null @@ -1,29962 +0,0 @@ -/* Generated by Cython 0.29.33 */ - -/* BEGIN: Cython Metadata -{ - "distutils": { - "depends": [ - "C:\\Users\\USER\\Desktop\\MDA_analysis\\mdanalysis\\package\\MDAnalysis\\lib\\include\\calc_distances.h" - ], - "extra_compile_args": [ - "-ffast-math", - "-O3", - "-funroll-loops", - "-fsigned-zeros", - "-std=c++11" - ], - "include_dirs": [ - "C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python311\\Lib\\site-packages\\numpy\\core\\include", - "C:\\Users\\USER\\Desktop\\MDA_analysis\\mdanalysis\\package\\MDAnalysis/lib/include" - ], - "language": "c++", - "name": "MDAnalysis.lib.nsgrid", - "sources": [ - "MDAnalysis/lib/nsgrid.pyx" - ] - }, - "module_name": "MDAnalysis.lib.nsgrid" -} -END: Cython Metadata */ - -#ifndef PY_SSIZE_T_CLEAN -#define PY_SSIZE_T_CLEAN -#endif /* PY_SSIZE_T_CLEAN */ -#include "Python.h" -#ifndef Py_PYTHON_H - #error Python headers needed to compile C extensions, please install development version of Python. -#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) - #error Cython requires Python 2.6+ or Python 3.3+. -#else -#define CYTHON_ABI "0_29_33" -#define CYTHON_HEX_VERSION 0x001D21F0 -#define CYTHON_FUTURE_DIVISION 1 -#include -#ifndef offsetof - #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) -#endif -#if !defined(WIN32) && !defined(MS_WINDOWS) - #ifndef __stdcall - #define __stdcall - #endif - #ifndef __cdecl - #define __cdecl - #endif - #ifndef __fastcall - #define __fastcall - #endif -#endif -#ifndef DL_IMPORT - #define DL_IMPORT(t) t -#endif -#ifndef DL_EXPORT - #define DL_EXPORT(t) t -#endif -#define __PYX_COMMA , -#ifndef HAVE_LONG_LONG - #if PY_VERSION_HEX >= 0x02070000 - #define HAVE_LONG_LONG - #endif -#endif -#ifndef PY_LONG_LONG - #define PY_LONG_LONG LONG_LONG -#endif -#ifndef Py_HUGE_VAL - #define Py_HUGE_VAL HUGE_VAL -#endif -#ifdef PYPY_VERSION - #define CYTHON_COMPILING_IN_PYPY 1 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 0 - #undef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 0 - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #if PY_VERSION_HEX < 0x03050000 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #undef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 0 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #undef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 1 - #undef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 0 - #undef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 0 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #undef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 0 - #undef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 0 - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 - #endif -#elif defined(PYSTON_VERSION) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 1 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #undef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 0 - #undef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 0 - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 - #endif -#elif defined(PY_NOGIL) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #define CYTHON_COMPILING_IN_NOGIL 1 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #ifndef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT 1 - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE 1 - #endif - #undef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS 0 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 -#else - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 1 - #define CYTHON_COMPILING_IN_NOGIL 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYTYPE_LOOKUP - #define CYTHON_USE_PYTYPE_LOOKUP 0 - #elif !defined(CYTHON_USE_PYTYPE_LOOKUP) - #define CYTHON_USE_PYTYPE_LOOKUP 1 - #endif - #if PY_MAJOR_VERSION < 3 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #elif !defined(CYTHON_USE_PYLONG_INTERNALS) - #define CYTHON_USE_PYLONG_INTERNALS 1 - #endif - #ifndef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 1 - #endif - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #elif !defined(CYTHON_USE_UNICODE_WRITER) - #define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #elif !defined(CYTHON_FAST_THREAD_STATE) - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000) - #endif - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000) - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) - #endif - #ifndef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1) - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #elif !defined(CYTHON_USE_EXC_INFO_STACK) - #define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3) - #endif - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 - #endif -#endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #if PY_MAJOR_VERSION < 3 - #include "longintrepr.h" - #endif - #undef SHIFT - #undef BASE - #undef MASK - #ifdef SIZEOF_VOID_P - enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) }; - #endif -#endif -#ifndef __has_attribute - #define __has_attribute(x) 0 -#endif -#ifndef __has_cpp_attribute - #define __has_cpp_attribute(x) 0 -#endif -#ifndef CYTHON_RESTRICT - #if defined(__GNUC__) - #define CYTHON_RESTRICT __restrict__ - #elif defined(_MSC_VER) && _MSC_VER >= 1400 - #define CYTHON_RESTRICT __restrict - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_RESTRICT restrict - #else - #define CYTHON_RESTRICT - #endif -#endif -#ifndef CYTHON_UNUSED -# if defined(__GNUC__) -# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -#endif -#ifndef CYTHON_MAYBE_UNUSED_VAR -# if defined(__cplusplus) - template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } -# else -# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) -# endif -#endif -#ifndef CYTHON_NCP_UNUSED -# if CYTHON_COMPILING_IN_CPYTHON -# define CYTHON_NCP_UNUSED -# else -# define CYTHON_NCP_UNUSED CYTHON_UNUSED -# endif -#endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) -#ifdef _MSC_VER - #ifndef _MSC_STDINT_H_ - #if _MSC_VER < 1300 - typedef unsigned char uint8_t; - typedef unsigned int uint32_t; - #else - typedef unsigned __int8 uint8_t; - typedef unsigned __int32 uint32_t; - #endif - #endif -#else - #include -#endif -#ifndef CYTHON_FALLTHROUGH - #if defined(__cplusplus) && __cplusplus >= 201103L - #if __has_cpp_attribute(fallthrough) - #define CYTHON_FALLTHROUGH [[fallthrough]] - #elif __has_cpp_attribute(clang::fallthrough) - #define CYTHON_FALLTHROUGH [[clang::fallthrough]] - #elif __has_cpp_attribute(gnu::fallthrough) - #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] - #endif - #endif - #ifndef CYTHON_FALLTHROUGH - #if __has_attribute(fallthrough) - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - #else - #define CYTHON_FALLTHROUGH - #endif - #endif - #if defined(__clang__ ) && defined(__apple_build_version__) - #if __apple_build_version__ < 7000000 - #undef CYTHON_FALLTHROUGH - #define CYTHON_FALLTHROUGH - #endif - #endif -#endif - -#ifndef __cplusplus - #error "Cython files generated with the C++ option must be compiled with a C++ compiler." -#endif -#ifndef CYTHON_INLINE - #if defined(__clang__) - #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) - #else - #define CYTHON_INLINE inline - #endif -#endif -template -void __Pyx_call_destructor(T& x) { - x.~T(); -} -template -class __Pyx_FakeReference { - public: - __Pyx_FakeReference() : ptr(NULL) { } - __Pyx_FakeReference(const T& ref) : ptr(const_cast(&ref)) { } - T *operator->() { return ptr; } - T *operator&() { return ptr; } - operator T&() { return *ptr; } - template bool operator ==(U other) { return *ptr == other; } - template bool operator !=(U other) { return *ptr != other; } - private: - T *ptr; -}; - -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - if (type) { - PyErr_Restore(type, value, traceback); - } - return co; - } -#else - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_STACKLESS - #define METH_STACKLESS 0 -#endif -#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) - #ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - #endif - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); - typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast - #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1 - #define PyMem_RawMalloc(n) PyMem_Malloc(n) - #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) - #define PyMem_RawFree(p) PyMem_Free(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#elif PY_VERSION_HEX >= 0x03060000 - #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() -#elif PY_VERSION_HEX >= 0x03000000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#else - #define __Pyx_PyThreadState_Current _PyThreadState_Current -#endif -#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) -#include "pythread.h" -#define Py_tss_NEEDS_INIT 0 -typedef int Py_tss_t; -static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { - *key = PyThread_create_key(); - return 0; -} -static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { - Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); - *key = Py_tss_NEEDS_INIT; - return key; -} -static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { - PyObject_Free(key); -} -static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { - return *key != Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { - PyThread_delete_key(*key); - *key = Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { - return PyThread_set_key_value(*key, value); -} -static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { - return PyThread_get_key_value(*key); -} -#endif -#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) -#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) -#else -#define __Pyx_PyDict_NewPresized(n) PyDict_New() -#endif -#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION - #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) -#else - #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS -#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) -#else -#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_READY(op) (0) - #else - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #endif - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) - #else - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? 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-value : value) -#endif -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); -static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); -#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) -#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) -#define __Pyx_PyBytes_FromString PyBytes_FromString -#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); -#if PY_MAJOR_VERSION < 3 - #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString - #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize -#else - #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString - #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize -#endif -#define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s)) -#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) -#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) -#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) -#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) -#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) -static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { - const Py_UNICODE *u_end = u; - while (*u_end++) ; - return (size_t)(u_end - u - 1); -} -#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) -#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode -#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode -#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) -#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); -static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*); -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); -#define __Pyx_PySequence_Tuple(obj)\ - (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj)) -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); -static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*); -#if CYTHON_ASSUME_SAFE_MACROS -#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) -#else -#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) -#endif -#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) -#else -#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) -#endif -#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII -static int __Pyx_sys_getdefaultencoding_not_ascii; -static int __Pyx_init_sys_getdefaultencoding_params(void) { - PyObject* sys; - PyObject* default_encoding = NULL; - PyObject* ascii_chars_u = NULL; - PyObject* ascii_chars_b = NULL; - const char* default_encoding_c; - sys = PyImport_ImportModule("sys"); - if (!sys) goto bad; - default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); - Py_DECREF(sys); - if (!default_encoding) goto bad; - default_encoding_c = PyBytes_AsString(default_encoding); - if (!default_encoding_c) goto bad; - if (strcmp(default_encoding_c, "ascii") == 0) { - __Pyx_sys_getdefaultencoding_not_ascii = 0; - } else { - char ascii_chars[128]; - int c; - for (c = 0; c < 128; c++) { - ascii_chars[c] = c; - } - __Pyx_sys_getdefaultencoding_not_ascii = 1; - ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); - if (!ascii_chars_u) goto bad; - ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); - if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { - PyErr_Format( - PyExc_ValueError, - "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", - default_encoding_c); - goto bad; - } - Py_DECREF(ascii_chars_u); - Py_DECREF(ascii_chars_b); - } - Py_DECREF(default_encoding); - return 0; -bad: - Py_XDECREF(default_encoding); - Py_XDECREF(ascii_chars_u); 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(PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ - __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, - int is_list, int wraparound, int boundscheck); - -/* RaiseException.proto */ -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); - -/* PyFloatBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyFloat_EqObjC(PyObject *op1, PyObject *op2, double floatval, int inplace, int zerodivision_check); -#else -#define __Pyx_PyFloat_EqObjC(op1, op2, floatval, inplace, zerodivision_check)\ - (PyObject_RichCompare(op1, op2, Py_EQ)) - #endif - -/* SliceObject.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice( - PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** py_start, PyObject** py_stop, PyObject** py_slice, - int has_cstart, int has_cstop, int wraparound); - -/* PyObjectCallNoArg.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); -#else -#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) -#endif - -/* MemviewSliceInit.proto */ -#define __Pyx_BUF_MAX_NDIMS %(BUF_MAX_NDIMS)d -#define __Pyx_MEMVIEW_DIRECT 1 -#define __Pyx_MEMVIEW_PTR 2 -#define __Pyx_MEMVIEW_FULL 4 -#define __Pyx_MEMVIEW_CONTIG 8 -#define __Pyx_MEMVIEW_STRIDED 16 -#define __Pyx_MEMVIEW_FOLLOW 32 -#define __Pyx_IS_C_CONTIG 1 -#define __Pyx_IS_F_CONTIG 2 -static int __Pyx_init_memviewslice( - struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference); -static CYTHON_INLINE int __pyx_add_acquisition_count_locked( - __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); -static CYTHON_INLINE int __pyx_sub_acquisition_count_locked( - __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); -#define __pyx_get_slice_count_pointer(memview) (memview->acquisition_count_aligned_p) -#define __pyx_get_slice_count(memview) (*__pyx_get_slice_count_pointer(memview)) -#define __PYX_INC_MEMVIEW(slice, have_gil) __Pyx_INC_MEMVIEW(slice, have_gil, __LINE__) -#define __PYX_XDEC_MEMVIEW(slice, have_gil) __Pyx_XDEC_MEMVIEW(slice, have_gil, __LINE__) -static CYTHON_INLINE void __Pyx_INC_MEMVIEW(__Pyx_memviewslice *, int, int); -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *, int, int); - -/* Import.proto */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); - -/* ImportFrom.proto */ -static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); - -/* PyFloatBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyFloat_TrueDivideCObj(PyObject *op1, PyObject *op2, double floatval, int inplace, int zerodivision_check); -#else -#define __Pyx_PyFloat_TrueDivideCObj(op1, op2, floatval, inplace, zerodivision_check)\ - (inplace ? PyNumber_InPlaceTrueDivide(op1, op2) : PyNumber_TrueDivide(op1, op2)) -#endif - -/* IncludeStringH.proto */ -#include - -/* PySequenceContains.proto */ -static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) { - int result = PySequence_Contains(seq, item); - return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); -} - -/* HasAttr.proto */ -static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); - -/* ListCompAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len)) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) -#endif - -/* GetTopmostException.proto */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate); -#endif - -/* SaveResetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -#else -#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) -#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) -#endif - -/* ArgTypeTest.proto */ -#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\ - ((likely((Py_TYPE(obj) == type) | (none_allowed && (obj == Py_None)))) ? 1 :\ - __Pyx__ArgTypeTest(obj, type, name, exact)) -static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact); - -/* BytesEquals.proto */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); - -/* UnicodeEquals.proto */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); - -/* StrEquals.proto */ -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals -#else -#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals -#endif - -/* UnaryNegOverflows.proto */ -#define UNARY_NEG_WOULD_OVERFLOW(x)\ - (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) - -static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *); /*proto*/ -/* ObjectGetItem.proto */ -#if CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key); -#else -#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key) -#endif - -/* decode_c_string_utf16.proto */ -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = 0; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16LE(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = -1; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} -static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16BE(const char *s, Py_ssize_t size, const char *errors) { - int byteorder = 1; - return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); -} - -/* decode_c_string.proto */ -static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); - -/* RaiseTooManyValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); - -/* RaiseNeedMoreValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); - -/* RaiseNoneIterError.proto */ -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); - -/* ExtTypeTest.proto */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); - -/* GetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* SwapException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* FastTypeChecks.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type); -static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2); -#else -#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) -#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type) -#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2)) -#endif -#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) - -static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); -#else -#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace, zerodivision_check)\ - (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) -#endif - -/* ListExtend.proto */ -static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { -#if CYTHON_COMPILING_IN_CPYTHON - PyObject* none = _PyList_Extend((PyListObject*)L, v); - if (unlikely(!none)) - return -1; - Py_DECREF(none); - return 0; -#else - return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); -#endif -} - -/* ListAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - __Pyx_SET_SIZE(list, len + 1); - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) -#endif - -/* None.proto */ -static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); - -/* PyObject_GenericGetAttrNoDict.proto */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); -#else -#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr -#endif - -/* PyObject_GenericGetAttr.proto */ -#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name); -#else -#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr -#endif - -/* SetVTable.proto */ -static int __Pyx_SetVtable(PyObject *dict, void *vtable); - -/* PyObjectGetAttrStrNoError.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name); - -/* SetupReduce.proto */ -static int __Pyx_setup_reduce(PyObject* type_obj); - -/* CLineInTraceback.proto */ -#ifdef CYTHON_CLINE_IN_TRACEBACK -#define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) -#else -static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line); -#endif - -/* CodeObjectCache.proto */ -typedef struct { - PyCodeObject* code_object; - int code_line; -} __Pyx_CodeObjectCacheEntry; -struct __Pyx_CodeObjectCache { - int count; - int max_count; - __Pyx_CodeObjectCacheEntry* entries; -}; -static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); -static PyCodeObject *__pyx_find_code_object(int code_line); -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); - -/* AddTraceback.proto */ -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename); - -/* None.proto */ -#include - -#if PY_MAJOR_VERSION < 3 - static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); - static void __Pyx_ReleaseBuffer(Py_buffer *view); -#else - #define __Pyx_GetBuffer PyObject_GetBuffer - #define __Pyx_ReleaseBuffer PyBuffer_Release -#endif - - -/* BufferStructDeclare.proto */ -typedef struct { - Py_ssize_t shape, strides, suboffsets; -} __Pyx_Buf_DimInfo; -typedef struct { - size_t refcount; - Py_buffer pybuffer; -} __Pyx_Buffer; -typedef struct { - __Pyx_Buffer *rcbuffer; - char *data; - __Pyx_Buf_DimInfo diminfo[8]; -} __Pyx_LocalBuf_ND; - -/* MemviewSliceIsContig.proto */ -static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim); - -/* OverlappingSlices.proto */ -static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize); - -/* Capsule.proto */ -static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); - -/* GCCDiagnostics.proto */ -#if defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6)) -#define __Pyx_HAS_GCC_DIAGNOSTIC -#endif - -/* MemviewDtypeToObject.proto */ -static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp); -static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj); - -/* IsLittleEndian.proto */ -static CYTHON_INLINE int __Pyx_Is_Little_Endian(void); - -/* BufferFormatCheck.proto */ -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type); - -/* TypeInfoCompare.proto */ -static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); - -/* MemviewSliceValidateAndInit.proto */ -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_float(PyObject *, int writable_flag); - -/* MemviewDtypeToObject.proto */ -static CYTHON_INLINE PyObject *__pyx_memview_get_int(const char *itemp); -static CYTHON_INLINE int __pyx_memview_set_int(const char *itemp, PyObject *obj); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_int(PyObject *, int writable_flag); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *, int writable_flag); - -/* CppExceptionConversion.proto */ -#ifndef __Pyx_CppExn2PyErr -#include -#include -#include -#include -static void __Pyx_CppExn2PyErr() { - try { - if (PyErr_Occurred()) - ; // let the latest Python exn pass through and ignore the current one - else - throw; - } catch (const std::bad_alloc& exn) { - PyErr_SetString(PyExc_MemoryError, exn.what()); - } catch (const std::bad_cast& exn) { - PyErr_SetString(PyExc_TypeError, exn.what()); - } catch (const std::bad_typeid& exn) { - PyErr_SetString(PyExc_TypeError, exn.what()); - } catch (const std::domain_error& exn) { - PyErr_SetString(PyExc_ValueError, exn.what()); - } catch (const std::invalid_argument& exn) { - PyErr_SetString(PyExc_ValueError, exn.what()); - } catch (const std::ios_base::failure& exn) { - PyErr_SetString(PyExc_IOError, exn.what()); - } catch (const std::out_of_range& exn) { - PyErr_SetString(PyExc_IndexError, exn.what()); - } catch (const std::overflow_error& exn) { - PyErr_SetString(PyExc_OverflowError, exn.what()); - } catch (const std::range_error& exn) { - PyErr_SetString(PyExc_ArithmeticError, exn.what()); - } catch (const std::underflow_error& exn) { - PyErr_SetString(PyExc_ArithmeticError, exn.what()); - } catch (const std::exception& exn) { - PyErr_SetString(PyExc_RuntimeError, exn.what()); - } - catch (...) - { - PyErr_SetString(PyExc_RuntimeError, "Unknown exception"); - } -} -#endif - -/* MemviewSliceCopyTemplate.proto */ -static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); - -/* CIntFromPy.proto */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); - -/* CIntFromPy.proto */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); - -/* CopyContentsUtility.proto */ -#define __pyx_memoryview_copy_slice_d_dc_float_c(slice)\ - __pyx_memoryview_copy_new_contig(&slice, "c", 2,\ - sizeof(float), (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT),\ - 0) - -/* CopyContentsUtility.proto */ -#define __pyx_memoryview_copy_slice_dcd__float_f(slice)\ - __pyx_memoryview_copy_new_contig(&slice, "fortran", 2,\ - sizeof(float), (PyBUF_F_CONTIGUOUS | PyBUF_FORMAT),\ - 0) - -/* CIntFromPy.proto */ -static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *); - -/* CIntFromPy.proto */ -static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); - -/* CheckBinaryVersion.proto */ -static int __Pyx_check_binary_version(void); - -/* InitStrings.proto */ -static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); - -static void __pyx_f_10MDAnalysis_3lib_6nsgrid_9NSResults_add_neighbors(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_v_self, int __pyx_v_beadid_i, int __pyx_v_beadid_j, double __pyx_v_distance2); /* proto*/ -static float __pyx_f_10MDAnalysis_3lib_6nsgrid_6FastNS__prepare_box(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, PyObject *__pyx_v_box, int __pyx_v_pbc); /* proto*/ -static void __pyx_f_10MDAnalysis_3lib_6nsgrid_6FastNS__pack_grid(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, __Pyx_memviewslice __pyx_v_coords); /* proto*/ -static int __pyx_f_10MDAnalysis_3lib_6nsgrid_6FastNS_coord2cellid(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, float const *__pyx_v_coord); /* proto*/ -static void __pyx_f_10MDAnalysis_3lib_6nsgrid_6FastNS_coord2cellxyz(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, float const *__pyx_v_coord, int *__pyx_v_xyz); /* proto*/ -static int __pyx_f_10MDAnalysis_3lib_6nsgrid_6FastNS_cellxyz2cellid(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, int __pyx_v_cx, int __pyx_v_cy, int __pyx_v_cz); /* proto*/ -static double __pyx_f_10MDAnalysis_3lib_6nsgrid_6FastNS_calc_distsq(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, float const *__pyx_v_a, float const *__pyx_v_b); /* proto*/ -static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *__pyx_v_self); /* proto*/ -static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto*/ -static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj); /* proto*/ -static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_dst, PyObject *__pyx_v_src); /* proto*/ -static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memoryview_obj *__pyx_v_self, struct __pyx_memoryview_obj *__pyx_v_dst, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ -static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ -static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ - -/* Module declarations from 'libcpp.vector' */ - -/* Module declarations from 'libc' */ - -/* Module declarations from 'libc.math' */ - -/* Module declarations from 'MDAnalysis.lib.nsgrid' */ -static PyTypeObject *__pyx_ptype_10MDAnalysis_3lib_6nsgrid_NSResults = 0; -static PyTypeObject *__pyx_ptype_10MDAnalysis_3lib_6nsgrid_FastNS = 0; -static PyTypeObject *__pyx_array_type = 0; -static PyTypeObject *__pyx_MemviewEnum_type = 0; -static PyTypeObject *__pyx_memoryview_type = 0; -static PyTypeObject *__pyx_memoryviewslice_type = 0; -static PyObject *generic = 0; -static PyObject *strided = 0; -static PyObject *indirect = 0; -static PyObject *contiguous = 0; -static PyObject *indirect_contiguous = 0; -static int __pyx_memoryview_thread_locks_used; -static PyThread_type_lock __pyx_memoryview_thread_locks[8]; -static CYTHON_INLINE float __pyx_f_10MDAnalysis_3lib_6nsgrid_fmax(float, float); /*proto*/ -static CYTHON_INLINE float __pyx_f_10MDAnalysis_3lib_6nsgrid_fmin(float, float); /*proto*/ -static CYTHON_INLINE float __pyx_f_10MDAnalysis_3lib_6nsgrid_degsin(float); /*proto*/ -static PyObject *__pyx_f_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_NSResults__set_state(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *, PyObject *); /*proto*/ -static PyObject *__pyx_f_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_FastNS__set_state(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *, PyObject *); /*proto*/ -static PyObject *__pyx_convert_vector_to_py_double(const std::vector &); /*proto*/ -static std::vector __pyx_convert_vector_from_py_double(PyObject *); /*proto*/ -static PyObject *__pyx_convert_vector_to_py_int(const std::vector &); /*proto*/ -static std::vector __pyx_convert_vector_from_py_int(PyObject *); /*proto*/ -static CYTHON_INLINE PyObject *__Pyx_carray_to_py_int(int *, Py_ssize_t); /*proto*/ -static CYTHON_INLINE PyObject *__Pyx_carray_to_tuple_int(int *, Py_ssize_t); /*proto*/ -static int __Pyx_carray_from_py_int(PyObject *, int *, Py_ssize_t); /*proto*/ -static CYTHON_INLINE PyObject *__Pyx_carray_to_py_double(double *, Py_ssize_t); /*proto*/ -static CYTHON_INLINE PyObject *__Pyx_carray_to_tuple_double(double *, Py_ssize_t); /*proto*/ -static int __Pyx_carray_from_py_double(PyObject *, double *, Py_ssize_t); /*proto*/ -static CYTHON_INLINE PyObject *__Pyx_carray_to_py_float(float *, Py_ssize_t); /*proto*/ -static CYTHON_INLINE PyObject *__Pyx_carray_to_tuple_float(float *, Py_ssize_t); /*proto*/ -static int __Pyx_carray_from_py_float(PyObject *, float *, Py_ssize_t); /*proto*/ -static CYTHON_INLINE PyObject *__Pyx_carray_to_py_Py_ssize_t(Py_ssize_t *, Py_ssize_t); /*proto*/ -static CYTHON_INLINE PyObject *__Pyx_carray_to_tuple_Py_ssize_t(Py_ssize_t *, Py_ssize_t); /*proto*/ -static struct __pyx_array_obj *__pyx_array_new(PyObject *, Py_ssize_t, char *, char *, char *); /*proto*/ -static void *__pyx_align_pointer(void *, size_t); /*proto*/ -static PyObject *__pyx_memoryview_new(PyObject *, int, int, __Pyx_TypeInfo *); /*proto*/ -static CYTHON_INLINE int __pyx_memoryview_check(PyObject *); /*proto*/ -static PyObject *_unellipsify(PyObject *, int); /*proto*/ -static PyObject *assert_direct_dimensions(Py_ssize_t *, int); /*proto*/ -static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_obj *, PyObject *); /*proto*/ -static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int, int); /*proto*/ -static char *__pyx_pybuffer_index(Py_buffer *, char *, Py_ssize_t, Py_ssize_t); /*proto*/ -static int __pyx_memslice_transpose(__Pyx_memviewslice *); /*proto*/ -static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice, int, PyObject *(*)(char *), int (*)(char *, PyObject *), int); /*proto*/ -static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/ -static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/ -static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/ -static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/ -static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/ -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/ -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/ -static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/ -static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/ -static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/ -static int __pyx_memoryview_err(PyObject *, char *); /*proto*/ -static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/ -static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/ -static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/ -static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ -static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ -static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ -static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ -static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *, PyObject *); /*proto*/ -static __Pyx_TypeInfo __Pyx_TypeInfo_float = { "float", NULL, sizeof(float), { 0 }, 0, 'R', 0, 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_int = { "int", NULL, sizeof(int), { 0 }, 0, IS_UNSIGNED(int) ? 'U' : 'I', IS_UNSIGNED(int), 0 }; -#define __Pyx_MODULE_NAME "MDAnalysis.lib.nsgrid" -extern int __pyx_module_is_main_MDAnalysis__lib__nsgrid; -int __pyx_module_is_main_MDAnalysis__lib__nsgrid = 0; - -/* Implementation of 'MDAnalysis.lib.nsgrid' */ -static PyObject *__pyx_builtin_ValueError; -static PyObject *__pyx_builtin_range; -static PyObject *__pyx_builtin_TypeError; -static PyObject *__pyx_builtin_OverflowError; -static PyObject *__pyx_builtin_enumerate; -static PyObject *__pyx_builtin_IndexError; -static PyObject *__pyx_builtin_MemoryError; -static PyObject *__pyx_builtin_Ellipsis; -static PyObject *__pyx_builtin_id; -static const char __pyx_k_C[] = "C"; -static const char __pyx_k_O[] = "O"; -static const char __pyx_k_c[] = "c"; -static const char __pyx_k_id[] = "id"; -static const char __pyx_k_np[] = "np"; -static const char __pyx_k_any[] = "any"; -static const char __pyx_k_box[] = "box"; -static const char __pyx_k_new[] = "__new__"; -static const char __pyx_k_obj[] = "obj"; -static const char __pyx_k_pbc[] = "pbc"; -static const char __pyx_k_base[] = "base"; -static const char __pyx_k_dict[] = "__dict__"; -static const char __pyx_k_full[] = "full"; -static const char __pyx_k_intp[] = "intp"; -static const char __pyx_k_main[] = "__main__"; -static const char __pyx_k_mode[] = "mode"; -static const char __pyx_k_name[] = "name"; -static const char __pyx_k_ndim[] = "ndim"; -static const char __pyx_k_pack[] = "pack"; -static const char __pyx_k_size[] = "size"; -static const char __pyx_k_sqrt[] = "sqrt"; -static const char __pyx_k_step[] = "step"; -static const char __pyx_k_stop[] = "stop"; -static const char __pyx_k_test[] = "__test__"; -static const char __pyx_k_ASCII[] = "ASCII"; -static const char __pyx_k_class[] = "__class__"; -static const char __pyx_k_dtype[] = "dtype"; -static const char __pyx_k_error[] = "error"; -static const char __pyx_k_flags[] = "flags"; -static const char __pyx_k_int32[] = "int32"; -static const char __pyx_k_numpy[] = "numpy"; -static const char __pyx_k_order[] = "order"; -static const char __pyx_k_range[] = "range"; -static const char __pyx_k_shape[] = "shape"; -static const char __pyx_k_start[] = "start"; -static const char __pyx_k_FastNS[] = "FastNS"; -static const char __pyx_k_coords[] = "coords"; -static const char __pyx_k_cutoff[] = "cutoff"; -static const char __pyx_k_encode[] = "encode"; -static const char __pyx_k_format[] = "format"; -static const char __pyx_k_import[] = "__import__"; -static const char __pyx_k_name_2[] = "__name__"; -static const char __pyx_k_pickle[] = "pickle"; -static const char __pyx_k_reduce[] = "__reduce__"; -static const char __pyx_k_struct[] = "struct"; -static const char __pyx_k_unpack[] = "unpack"; -static const char __pyx_k_update[] = "update"; -static const char __pyx_k_asarray[] = "asarray"; -static const char __pyx_k_fortran[] = "fortran"; -static const char __pyx_k_memview[] = "memview"; -static const char __pyx_k_reshape[] = "reshape"; -static const char __pyx_k_Ellipsis[] = "Ellipsis"; -static const char __pyx_k_getstate[] = "__getstate__"; -static const char __pyx_k_itemsize[] = "itemsize"; -static const char __pyx_k_pyx_type[] = "__pyx_type"; -static const char __pyx_k_setstate[] = "__setstate__"; -static const char __pyx_k_NSResults[] = "NSResults"; -static const char __pyx_k_TypeError[] = "TypeError"; -static const char __pyx_k_enumerate[] = "enumerate"; -static const char __pyx_k_pyx_state[] = "__pyx_state"; -static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; -static const char __pyx_k_IndexError[] = "IndexError"; -static const char __pyx_k_ValueError[] = "ValueError"; -static const char __pyx_k_pyx_result[] = "__pyx_result"; -static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; -static const char __pyx_k_MemoryError[] = "MemoryError"; -static const char __pyx_k_PickleError[] = "PickleError"; -static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; -static const char __pyx_k_stringsource[] = "stringsource"; -static const char __pyx_k_OverflowError[] = "OverflowError"; -static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; -static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; -static const char __pyx_k_View_MemoryView[] = "View.MemoryView"; -static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; -static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; -static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; -static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; -static const char __pyx_k_pyx_unpickle_Enum[] = "__pyx_unpickle_Enum"; -static const char __pyx_k_triclinic_vectors[] = "triclinic_vectors"; -static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; -static const char __pyx_k_strided_and_direct[] = ""; -static const char __pyx_k_pyx_unpickle_FastNS[] = "__pyx_unpickle_FastNS"; -static const char __pyx_k_strided_and_indirect[] = ""; -static const char __pyx_k_MDAnalysis_lib_nsgrid[] = "MDAnalysis.lib.nsgrid"; -static const char __pyx_k_contiguous_and_direct[] = ""; -static const char __pyx_k_MDAnalysis_lib_mdamath[] = "MDAnalysis.lib.mdamath"; -static const char __pyx_k_MemoryView_of_r_object[] = ""; -static const char __pyx_k_pyx_unpickle_NSResults[] = "__pyx_unpickle_NSResults"; -static const char __pyx_k_Cutoff_must_be_positive[] = "Cutoff must be positive"; -static const char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; -static const char __pyx_k_contiguous_and_indirect[] = ""; -static const char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; -static const char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; -static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; -static const char __pyx_k_Cutoff_too_large_for_box_max[] = "Cutoff {} too large for box (max {})"; -static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; -static const char __pyx_k_strided_and_direct_or_indirect[] = ""; -static const char __pyx_k_Box_must_be_a_numpy_array_of_lx[] = "Box must be a numpy array of [lx, ly, lz, alpha, beta, gamma], got {}"; -static const char __pyx_k_Neighbor_search_library_mod_MDA[] = "\nNeighbor search library --- :mod:`MDAnalysis.lib.nsgrid`\n========================================================\n\nAbout the code\n--------------\n\nThis Neighbor search library is a serialized Cython version greatly\ninspired by the NS grid search implemented in\n`GROMACS `_ .\n\nGROMACS 4.x code (more precisely\n`nsgrid.c `_\nand `ns.c `_ )\nwas used as reference to write this file.\n\nGROMACS 4.x code is released under the GNU Public Licence v2.\n\nAbout the algorithm\n-------------------\n\nThe neighbor search implemented here is based on\n`cell lists `_ which allow\ncomputation of pairs [#]_ with a cost of :math:`O(N)`, instead\nof :math:`O(N^2)`. The basic algorithm is described in\nAppendix F, Page 552 of\n``Understanding Molecular Dynamics: From Algorithm to Applications`` by Frenkel and Smit.\n\nIn brief, the algorithm divides the domain into smaller subdomains called `cells`\nand distributes every particle to these cells based on their positions. Subsequently,\nany distance based query first identifies the corresponding cell position in the\ndomain followed by distance evaluations within the identified cell and\nneighboring cells only. Care must be taken to ensure that `cellsize` is\ngreater than the desired search distance, otherwise all of the neighbours might\nnot reflect in the results.\n\n.. [#] a pair correspond to two particles that are considered as neighbors .\n\n.. versionadded:: 0.19.0\n.. versionchanged:: 1.0.2\n Rewrote module\n.. versionchanged:: 2.1.0\n Capped max grid dimension to 1290, which when cubed is the max value of\n a 32 bit signed integer.\n\nClasses\n-------\n"; -static const char __pyx_k_coords_must_have_a_shape_of_n_3[] = "coords must have a shape of (n, 3), got {}."; -static const char __pyx_k_search_coords_must_have_a_shape[] = "search_coords must have a shape of (n, 3), got {}."; -static const char __pyx_k_Any_of_the_box_dimensions_cannot[] = "Any of the box dimensions cannot be 0"; -static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; -static const char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; -static const char __pyx_k_Cannot_assign_to_read_only_memor[] = "Cannot assign to read-only memoryview"; -static const char __pyx_k_Cannot_create_writable_memory_vi[] = "Cannot create writable memory view from read-only memoryview"; -static const char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; -static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0x9689e9e, 0xa2ae72e, 0xf30f62a) = (distances2, pairs))"; -static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; -static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; -static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; -static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; -static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; -static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; -static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; -static const char __pyx_k_Incompatible_checksums_0x_x_vs_0_2[] = "Incompatible checksums (0x%x vs (0x42b468a, 0x904c588, 0x52c6edf) = (cell_offsets, cellsize, coords_bbox, cutoff, dimensions, half_dimensions, head_id, inverse_dimensions, ncells, next_id, pbc, periodic, triclinic, triclinic_dimensions))"; -static const char __pyx_k_Incompatible_checksums_0x_x_vs_0_3[] = "Incompatible checksums (0x%x vs (0xb068931, 0x82a3537, 0x6ae9995) = (name))"; -static PyObject *__pyx_n_s_ASCII; -static PyObject *__pyx_kp_u_Any_of_the_box_dimensions_cannot; -static PyObject *__pyx_kp_u_Box_must_be_a_numpy_array_of_lx; -static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; -static PyObject *__pyx_n_u_C; -static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; -static PyObject *__pyx_kp_s_Cannot_assign_to_read_only_memor; -static PyObject *__pyx_kp_s_Cannot_create_writable_memory_vi; -static PyObject *__pyx_kp_s_Cannot_index_with_type_s; -static PyObject *__pyx_kp_u_Cutoff_must_be_positive; 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/* proto */ -static int __pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS___init__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, PyObject *__pyx_v_cutoff, PyObject *__pyx_v_coords, PyObject *__pyx_v_box, PyObject *__pyx_v_pbc); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, __Pyx_memviewslice __pyx_v_search_coords); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_6cutoff___get__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_6__reduce_cython__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_8__setstate_cython__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_NSResults(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_2__pyx_unpickle_FastNS(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__len__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_12__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ -static PyObject *__pyx_pf___pyx_array___reduce_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_array_2__setstate_cython__(CYTHON_UNUSED struct __pyx_array_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_MemviewEnum_2__setstate_cython__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ -static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); 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/* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_memoryview___reduce_cython__(CYTHON_UNUSED struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_memoryview_2__setstate_cython__(CYTHON_UNUSED struct __pyx_memoryview_obj *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ -static void __pyx_memoryviewslice___pyx_pf_15View_dot_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf___pyx_memoryviewslice___reduce_cython__(CYTHON_UNUSED struct __pyx_memoryviewslice_obj *__pyx_v_self); 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- - /* "MDAnalysis/lib/nsgrid.pyx":336 - * max_cutoff = fmin(max_cutoff, self.triclinic_dimensions[ZZ] * degsin(self.dimensions[4])) - * # gamma - * max_cutoff = fmin(max_cutoff, self.triclinic_dimensions[XX] * degsin(self.dimensions[5])) # <<<<<<<<<<<<<< - * max_cutoff = fmin(max_cutoff, self.triclinic_dimensions[YY] * degsin(self.dimensions[5])) - * max_cutoff /= 2 - */ - __pyx_v_max_cutoff = __pyx_f_10MDAnalysis_3lib_6nsgrid_fmin(__pyx_v_max_cutoff, ((__pyx_v_self->triclinic_dimensions[0]) * __pyx_f_10MDAnalysis_3lib_6nsgrid_degsin((__pyx_v_self->dimensions[5])))); - - /* "MDAnalysis/lib/nsgrid.pyx":337 - * # gamma - * max_cutoff = fmin(max_cutoff, self.triclinic_dimensions[XX] * degsin(self.dimensions[5])) - * max_cutoff = fmin(max_cutoff, self.triclinic_dimensions[YY] * degsin(self.dimensions[5])) # <<<<<<<<<<<<<< - * max_cutoff /= 2 - * - */ - __pyx_v_max_cutoff = __pyx_f_10MDAnalysis_3lib_6nsgrid_fmin(__pyx_v_max_cutoff, ((__pyx_v_self->triclinic_dimensions[4]) * __pyx_f_10MDAnalysis_3lib_6nsgrid_degsin((__pyx_v_self->dimensions[5])))); 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Limit the number - * # of cells in any dimension to the cube root of the maximum of 32 bit integer values. - * self.ncells[0] = min(math.floor(self.triclinic_dimensions[XX] / min_cellsize), MAX_GRID_DIM) # <<<<<<<<<<<<<< - * self.ncells[1] = min(math.floor(self.triclinic_dimensions[YY] / min_cellsize), MAX_GRID_DIM) - * self.ncells[2] = min(math.floor(self.triclinic_dimensions[ZZ] / min_cellsize), MAX_GRID_DIM) - */ - __pyx_t_13 = 0x50A; - __pyx_t_12 = floor(((__pyx_v_self->triclinic_dimensions[0]) / __pyx_v_min_cellsize)); - if (((__pyx_t_13 < __pyx_t_12) != 0)) { - __pyx_t_10 = __pyx_t_13; - } else { - __pyx_t_10 = __pyx_t_12; - } - (__pyx_v_self->ncells[0]) = ((int)__pyx_t_10); - - /* "MDAnalysis/lib/nsgrid.pyx":354 - * # of cells in any dimension to the cube root of the maximum of 32 bit integer values. - * self.ncells[0] = min(math.floor(self.triclinic_dimensions[XX] / min_cellsize), MAX_GRID_DIM) - * self.ncells[1] = min(math.floor(self.triclinic_dimensions[YY] / min_cellsize), MAX_GRID_DIM) # <<<<<<<<<<<<<< - * self.ncells[2] = min(math.floor(self.triclinic_dimensions[ZZ] / min_cellsize), MAX_GRID_DIM) - * - */ - __pyx_t_13 = 0x50A; 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- - /* "MDAnalysis/lib/nsgrid.pyx":444 - * # Make sure cell coordinate indices are within the primary unit cell - * # (better safe than sorry): - * xyz[0] %= self.ncells[0] # <<<<<<<<<<<<<< - * xyz[1] %= self.ncells[1] - * xyz[2] %= self.ncells[2] - */ - __pyx_t_1 = 0; - (__pyx_v_xyz[__pyx_t_1]) = ((__pyx_v_xyz[__pyx_t_1]) % (__pyx_v_self->ncells[0])); - - /* "MDAnalysis/lib/nsgrid.pyx":445 - * # (better safe than sorry): - * xyz[0] %= self.ncells[0] - * xyz[1] %= self.ncells[1] # <<<<<<<<<<<<<< - * xyz[2] %= self.ncells[2] - * - */ - __pyx_t_1 = 1; - (__pyx_v_xyz[__pyx_t_1]) = ((__pyx_v_xyz[__pyx_t_1]) % (__pyx_v_self->ncells[1])); - - /* "MDAnalysis/lib/nsgrid.pyx":446 - * xyz[0] %= self.ncells[0] - * xyz[1] %= self.ncells[1] - * xyz[2] %= self.ncells[2] # <<<<<<<<<<<<<< - * - * cdef int cellxyz2cellid(self, int cx, int cy, int cz) nogil: - */ - __pyx_t_1 = 2; - (__pyx_v_xyz[__pyx_t_1]) = ((__pyx_v_xyz[__pyx_t_1]) % (__pyx_v_self->ncells[2])); - - /* "MDAnalysis/lib/nsgrid.pyx":435 - * return xyz[0] + xyz[1] * self.cell_offsets[1] + xyz[2] * self.cell_offsets[2] - * - * cdef void coord2cellxyz(self, const float* coord, int* xyz) nogil: # <<<<<<<<<<<<<< - * """Calculate cell coordinate for coord""" - * # This assumes coordinate is inside the primary unit cell - */ - - /* function exit code */ -} - -/* "MDAnalysis/lib/nsgrid.pyx":448 - * xyz[2] %= self.ncells[2] - * - * cdef int cellxyz2cellid(self, int cx, int cy, int cz) nogil: # <<<<<<<<<<<<<< - * """Convert cell coordinate to cell id, END for out of bounds""" - * if cx < 0: - */ - -static int __pyx_f_10MDAnalysis_3lib_6nsgrid_6FastNS_cellxyz2cellid(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, int __pyx_v_cx, int __pyx_v_cy, int __pyx_v_cz) { - int __pyx_r; - int __pyx_t_1; - - /* "MDAnalysis/lib/nsgrid.pyx":450 - * cdef int cellxyz2cellid(self, int cx, int cy, int cz) nogil: - * """Convert cell coordinate to cell id, END for out of bounds""" - * if cx < 0: # <<<<<<<<<<<<<< - * if self.periodic[0]: - * cx = self.ncells[0] - 1 - */ - __pyx_t_1 = ((__pyx_v_cx < 0) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":451 - * """Convert cell coordinate to cell id, END for out of bounds""" - * if cx < 0: - * if self.periodic[0]: # <<<<<<<<<<<<<< - * cx = self.ncells[0] - 1 - * else: - */ - __pyx_t_1 = ((__pyx_v_self->periodic[0]) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":452 - * if cx < 0: - * if self.periodic[0]: - * cx = self.ncells[0] - 1 # <<<<<<<<<<<<<< - * else: - * return END - */ - __pyx_v_cx = ((__pyx_v_self->ncells[0]) - 1); - - /* "MDAnalysis/lib/nsgrid.pyx":451 - * """Convert cell coordinate to cell id, END for out of bounds""" - * if cx < 0: - * if self.periodic[0]: # <<<<<<<<<<<<<< - * cx = self.ncells[0] - 1 - * else: - */ - goto __pyx_L4; - } - - /* "MDAnalysis/lib/nsgrid.pyx":454 - * cx = self.ncells[0] - 1 - * else: - * return END # <<<<<<<<<<<<<< - * elif cx == self.ncells[0]: - * if self.periodic[0]: - */ - /*else*/ { - __pyx_r = -1; - goto __pyx_L0; - } - __pyx_L4:; - - /* "MDAnalysis/lib/nsgrid.pyx":450 - * cdef int cellxyz2cellid(self, int cx, int cy, int cz) nogil: - * """Convert cell coordinate to cell id, END for out of bounds""" - * if cx < 0: # <<<<<<<<<<<<<< - * if self.periodic[0]: - * cx = self.ncells[0] - 1 - */ - goto __pyx_L3; - } - - /* "MDAnalysis/lib/nsgrid.pyx":455 - * else: - * return END - * elif cx == self.ncells[0]: # <<<<<<<<<<<<<< - * if self.periodic[0]: - * cx = 0 - */ - __pyx_t_1 = ((__pyx_v_cx == (__pyx_v_self->ncells[0])) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":456 - * return END - * elif cx == self.ncells[0]: - * if self.periodic[0]: # <<<<<<<<<<<<<< - * cx = 0 - * else: - */ - __pyx_t_1 = ((__pyx_v_self->periodic[0]) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":457 - * elif cx == self.ncells[0]: - * if self.periodic[0]: - * cx = 0 # <<<<<<<<<<<<<< - * else: - * return END - */ - __pyx_v_cx = 0; - - /* "MDAnalysis/lib/nsgrid.pyx":456 - * return END - * elif cx == self.ncells[0]: - * if self.periodic[0]: # <<<<<<<<<<<<<< - * cx = 0 - * else: - */ - goto __pyx_L5; - } - - /* "MDAnalysis/lib/nsgrid.pyx":459 - * cx = 0 - * else: - * return END # <<<<<<<<<<<<<< - * if cy < 0: - * if self.periodic[1]: - */ - /*else*/ { - __pyx_r = -1; - goto __pyx_L0; - } - __pyx_L5:; - - /* "MDAnalysis/lib/nsgrid.pyx":455 - * else: - * return END - * elif cx == self.ncells[0]: # <<<<<<<<<<<<<< - * if self.periodic[0]: - * cx = 0 - */ - } - __pyx_L3:; - - /* "MDAnalysis/lib/nsgrid.pyx":460 - * else: - * return END - * if cy < 0: # <<<<<<<<<<<<<< - * if self.periodic[1]: - * cy = self.ncells[1] - 1 - */ - __pyx_t_1 = ((__pyx_v_cy < 0) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":461 - * return END - * if cy < 0: - * if self.periodic[1]: # <<<<<<<<<<<<<< - * cy = self.ncells[1] - 1 - * else: - */ - __pyx_t_1 = ((__pyx_v_self->periodic[1]) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":462 - * if cy < 0: - * if self.periodic[1]: - * cy = self.ncells[1] - 1 # <<<<<<<<<<<<<< - * else: - * return END - */ - __pyx_v_cy = ((__pyx_v_self->ncells[1]) - 1); - - /* "MDAnalysis/lib/nsgrid.pyx":461 - * return END - * if cy < 0: - * if self.periodic[1]: # <<<<<<<<<<<<<< - * cy = self.ncells[1] - 1 - * else: - */ - goto __pyx_L7; - } - - /* "MDAnalysis/lib/nsgrid.pyx":464 - * cy = self.ncells[1] - 1 - * else: - * return END # <<<<<<<<<<<<<< - * elif cy == self.ncells[1]: - * if self.periodic[1]: - */ - /*else*/ { - __pyx_r = -1; - goto __pyx_L0; - } - __pyx_L7:; - - /* "MDAnalysis/lib/nsgrid.pyx":460 - * else: - * return END - * if cy < 0: # <<<<<<<<<<<<<< - * if self.periodic[1]: - * cy = self.ncells[1] - 1 - */ - goto __pyx_L6; - } - - /* "MDAnalysis/lib/nsgrid.pyx":465 - * else: - * return END - * elif cy == self.ncells[1]: # <<<<<<<<<<<<<< - * if self.periodic[1]: - * cy = 0 - */ - __pyx_t_1 = ((__pyx_v_cy == (__pyx_v_self->ncells[1])) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":466 - * return END - * elif cy == self.ncells[1]: - * if self.periodic[1]: # <<<<<<<<<<<<<< - * cy = 0 - * else: - */ - __pyx_t_1 = ((__pyx_v_self->periodic[1]) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":467 - * elif cy == self.ncells[1]: - * if self.periodic[1]: - * cy = 0 # <<<<<<<<<<<<<< - * else: - * return END - */ - __pyx_v_cy = 0; - - /* "MDAnalysis/lib/nsgrid.pyx":466 - * return END - * elif cy == self.ncells[1]: - * if self.periodic[1]: # <<<<<<<<<<<<<< - * cy = 0 - * else: - */ - goto __pyx_L8; - } - - /* "MDAnalysis/lib/nsgrid.pyx":469 - * cy = 0 - * else: - * return END # <<<<<<<<<<<<<< - * if cz < 0: - * if self.periodic[2]: - */ - /*else*/ { - __pyx_r = -1; - goto __pyx_L0; - } - __pyx_L8:; - - /* "MDAnalysis/lib/nsgrid.pyx":465 - * else: - * return END - * elif cy == self.ncells[1]: # <<<<<<<<<<<<<< - * if self.periodic[1]: - * cy = 0 - */ - } - __pyx_L6:; - - /* "MDAnalysis/lib/nsgrid.pyx":470 - * else: - * return END - * if cz < 0: # <<<<<<<<<<<<<< - * if self.periodic[2]: - * cz = self.ncells[2] - 1 - */ - __pyx_t_1 = ((__pyx_v_cz < 0) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":471 - * return END - * if cz < 0: - * if self.periodic[2]: # <<<<<<<<<<<<<< - * cz = self.ncells[2] - 1 - * else: - */ - __pyx_t_1 = ((__pyx_v_self->periodic[2]) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":472 - * if cz < 0: - * if self.periodic[2]: - * cz = self.ncells[2] - 1 # <<<<<<<<<<<<<< - * else: - * return END - */ - __pyx_v_cz = ((__pyx_v_self->ncells[2]) - 1); - - /* "MDAnalysis/lib/nsgrid.pyx":471 - * return END - * if cz < 0: - * if self.periodic[2]: # <<<<<<<<<<<<<< - * cz = self.ncells[2] - 1 - * else: - */ - goto __pyx_L10; - } - - /* "MDAnalysis/lib/nsgrid.pyx":474 - * cz = self.ncells[2] - 1 - * else: - * return END # <<<<<<<<<<<<<< - * elif cz == self.ncells[2]: - * if self.periodic[2]: - */ - /*else*/ { - __pyx_r = -1; - goto __pyx_L0; - } - __pyx_L10:; - - /* "MDAnalysis/lib/nsgrid.pyx":470 - * else: - * return END - * if cz < 0: # <<<<<<<<<<<<<< - * if self.periodic[2]: - * cz = self.ncells[2] - 1 - */ - goto __pyx_L9; - } - - /* "MDAnalysis/lib/nsgrid.pyx":475 - * else: - * return END - * elif cz == self.ncells[2]: # <<<<<<<<<<<<<< - * if self.periodic[2]: - * cz = 0 - */ - __pyx_t_1 = ((__pyx_v_cz == (__pyx_v_self->ncells[2])) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":476 - * return END - * elif cz == self.ncells[2]: - * if self.periodic[2]: # <<<<<<<<<<<<<< - * cz = 0 - * else: - */ - __pyx_t_1 = ((__pyx_v_self->periodic[2]) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":477 - * elif cz == self.ncells[2]: - * if self.periodic[2]: - * cz = 0 # <<<<<<<<<<<<<< - * else: - * return END - */ - __pyx_v_cz = 0; - - /* "MDAnalysis/lib/nsgrid.pyx":476 - * return END - * elif cz == self.ncells[2]: - * if self.periodic[2]: # <<<<<<<<<<<<<< - * cz = 0 - * else: - */ - goto __pyx_L11; - } - - /* "MDAnalysis/lib/nsgrid.pyx":479 - * cz = 0 - * else: - * return END # <<<<<<<<<<<<<< - * - * return cx + cy * self.cell_offsets[1] + cz * self.cell_offsets[2] - */ - /*else*/ { - __pyx_r = -1; - goto __pyx_L0; - } - __pyx_L11:; - - /* "MDAnalysis/lib/nsgrid.pyx":475 - * else: - * return END - * elif cz == self.ncells[2]: # <<<<<<<<<<<<<< - * if self.periodic[2]: - * cz = 0 - */ - } - __pyx_L9:; - - /* "MDAnalysis/lib/nsgrid.pyx":481 - * return END - * - * return cx + cy * self.cell_offsets[1] + cz * self.cell_offsets[2] # <<<<<<<<<<<<<< - * - * cdef double calc_distsq(self, const float* a, const float* b) nogil: - */ - __pyx_r = ((__pyx_v_cx + (__pyx_v_cy * (__pyx_v_self->cell_offsets[1]))) + (__pyx_v_cz * (__pyx_v_self->cell_offsets[2]))); - goto __pyx_L0; - - /* "MDAnalysis/lib/nsgrid.pyx":448 - * xyz[2] %= self.ncells[2] - * - * cdef int cellxyz2cellid(self, int cx, int cy, int cz) nogil: # <<<<<<<<<<<<<< - * """Convert cell coordinate to cell id, END for out of bounds""" - * if cx < 0: - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "MDAnalysis/lib/nsgrid.pyx":483 - * return cx + cy * self.cell_offsets[1] + cz * self.cell_offsets[2] - * - * cdef double calc_distsq(self, const float* a, const float* b) nogil: # <<<<<<<<<<<<<< - * cdef double dx[3] - * - */ - -static double __pyx_f_10MDAnalysis_3lib_6nsgrid_6FastNS_calc_distsq(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_FastNS *__pyx_v_self, float const *__pyx_v_a, float const *__pyx_v_b) { - double __pyx_v_dx[3]; - double __pyx_r; - int __pyx_t_1; - - /* "MDAnalysis/lib/nsgrid.pyx":486 - * cdef double dx[3] - * - * dx[0] = a[0] - b[0] # <<<<<<<<<<<<<< - * dx[1] = a[1] - b[1] - * dx[2] = a[2] - b[2] - */ - (__pyx_v_dx[0]) = ((__pyx_v_a[0]) - (__pyx_v_b[0])); - - /* "MDAnalysis/lib/nsgrid.pyx":487 - * - * dx[0] = a[0] - b[0] - * dx[1] = a[1] - b[1] # <<<<<<<<<<<<<< - * dx[2] = a[2] - b[2] - * - */ - (__pyx_v_dx[1]) = ((__pyx_v_a[1]) - (__pyx_v_b[1])); - - /* "MDAnalysis/lib/nsgrid.pyx":488 - * dx[0] = a[0] - b[0] - * dx[1] = a[1] - b[1] - * dx[2] = a[2] - b[2] # <<<<<<<<<<<<<< - * - * if self.pbc: - */ - (__pyx_v_dx[2]) = ((__pyx_v_a[2]) - (__pyx_v_b[2])); - - /* "MDAnalysis/lib/nsgrid.pyx":490 - * dx[2] = a[2] - b[2] - * - * if self.pbc: # <<<<<<<<<<<<<< - * if self.triclinic: - * minimum_image_triclinic(dx, &self.triclinic_dimensions[0]) - */ - __pyx_t_1 = (__pyx_v_self->pbc != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":491 - * - * if self.pbc: - * if self.triclinic: # <<<<<<<<<<<<<< - * minimum_image_triclinic(dx, &self.triclinic_dimensions[0]) - * else: - */ - __pyx_t_1 = (__pyx_v_self->triclinic != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/nsgrid.pyx":492 - * if self.pbc: - * if self.triclinic: - * minimum_image_triclinic(dx, &self.triclinic_dimensions[0]) # <<<<<<<<<<<<<< - * else: - * _minimum_image_ortho_lazy(dx, &self.dimensions[0], - */ - minimum_image_triclinic(__pyx_v_dx, (&(__pyx_v_self->triclinic_dimensions[0]))); - - /* "MDAnalysis/lib/nsgrid.pyx":491 - * - * if self.pbc: - * if self.triclinic: # <<<<<<<<<<<<<< - * minimum_image_triclinic(dx, &self.triclinic_dimensions[0]) - * else: - */ - goto __pyx_L4; - } - - /* "MDAnalysis/lib/nsgrid.pyx":494 - * minimum_image_triclinic(dx, &self.triclinic_dimensions[0]) - * else: - * _minimum_image_ortho_lazy(dx, &self.dimensions[0], # <<<<<<<<<<<<<< - * &self.half_dimensions[0]) - * - */ - /*else*/ { - - /* "MDAnalysis/lib/nsgrid.pyx":495 - * else: - * _minimum_image_ortho_lazy(dx, &self.dimensions[0], - * &self.half_dimensions[0]) # <<<<<<<<<<<<<< - * - * return dx[0]*dx[0] + dx[1]*dx[1] + dx[2]*dx[2] - */ - _minimum_image_ortho_lazy(__pyx_v_dx, (&(__pyx_v_self->dimensions[0])), (&(__pyx_v_self->half_dimensions[0]))); - } - __pyx_L4:; - - /* "MDAnalysis/lib/nsgrid.pyx":490 - * dx[2] = a[2] - b[2] - * - * if self.pbc: # <<<<<<<<<<<<<< - * if self.triclinic: - * minimum_image_triclinic(dx, &self.triclinic_dimensions[0]) - */ - } - - /* "MDAnalysis/lib/nsgrid.pyx":497 - * &self.half_dimensions[0]) - * - * return dx[0]*dx[0] + dx[1]*dx[1] + dx[2]*dx[2] # <<<<<<<<<<<<<< - * - * def search(self, float[:, :] search_coords): - */ - __pyx_r = ((((__pyx_v_dx[0]) * (__pyx_v_dx[0])) + ((__pyx_v_dx[1]) * (__pyx_v_dx[1]))) + ((__pyx_v_dx[2]) * (__pyx_v_dx[2]))); - goto __pyx_L0; - - /* "MDAnalysis/lib/nsgrid.pyx":483 - * return cx + cy * self.cell_offsets[1] + cz * self.cell_offsets[2] - * - * cdef double calc_distsq(self, const float* a, const float* b) nogil: # <<<<<<<<<<<<<< - * cdef double dx[3] - * - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "MDAnalysis/lib/nsgrid.pyx":499 - * return dx[0]*dx[0] + dx[1]*dx[1] + dx[2]*dx[2] - * - * def search(self, float[:, :] search_coords): # <<<<<<<<<<<<<< - * """Search a group of atoms against initialized coordinates - * - */ - -/* Python wrapper */ -static PyObject *__pyx_pw_10MDAnalysis_3lib_6nsgrid_6FastNS_3search(PyObject *__pyx_v_self, PyObject *__pyx_arg_search_coords); /*proto*/ -static char __pyx_doc_10MDAnalysis_3lib_6nsgrid_6FastNS_2search[] = "FastNS.search(self, float[:, :] search_coords)\nSearch a group of atoms against initialized coordinates\n\n Creates a new grid with the query atoms and searches\n against the initialized coordinates. 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} - __pyx_t_3 = (__pyx_t_2 != 0); - __pyx_t_1 = __pyx_t_3; - __pyx_L5_bool_binop_done:; - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - if (__pyx_t_1) { - - /* "View.MemoryView":1157 - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent))); - - /* "View.MemoryView":1155 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - goto __pyx_L4; - } - - /* "View.MemoryView":1159 - * memcpy(dst_data, src_data, itemsize * dst_extent) - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - __pyx_t_5 = __pyx_t_4; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1160 - * else: - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< - * src_data += src_stride - * dst_data += dst_stride - */ - (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize)); - - /* "View.MemoryView":1161 - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * else: - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1162 - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L4:; - - /* "View.MemoryView":1154 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1164 - * dst_data += dst_stride - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * _copy_strided_to_strided(src_data, src_strides + 1, - * dst_data, dst_strides + 1, - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - __pyx_t_5 = __pyx_t_4; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1165 - * else: - * for i in range(dst_extent): - * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< - * dst_data, dst_strides + 1, - * src_shape + 1, dst_shape + 1, - */ - _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - - /* "View.MemoryView":1169 - * src_shape + 1, dst_shape + 1, - * ndim - 1, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1170 - * ndim - 1, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L3:; - - /* "View.MemoryView":1142 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - - /* function exit code */ -} - -/* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - -static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - - /* "View.MemoryView":1175 - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< - * src.shape, dst.shape, ndim, itemsize) - * - */ - _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - - /* "View.MemoryView":1172 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - - /* function exit code */ -} - -/* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { - Py_ssize_t __pyx_v_shape; - Py_ssize_t __pyx_v_size; - Py_ssize_t __pyx_r; - Py_ssize_t __pyx_t_1; - Py_ssize_t *__pyx_t_2; - Py_ssize_t *__pyx_t_3; - Py_ssize_t *__pyx_t_4; - - /* "View.MemoryView":1181 - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize # <<<<<<<<<<<<<< - * - * for shape in src.shape[:ndim]: - */ - __pyx_t_1 = __pyx_v_src->memview->view.itemsize; - __pyx_v_size = __pyx_t_1; - - /* "View.MemoryView":1183 - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - * - * for shape in src.shape[:ndim]: # <<<<<<<<<<<<<< - * size *= shape - * - */ - __pyx_t_3 = (__pyx_v_src->shape + __pyx_v_ndim); - for (__pyx_t_4 = __pyx_v_src->shape; __pyx_t_4 < __pyx_t_3; __pyx_t_4++) { - __pyx_t_2 = __pyx_t_4; - __pyx_v_shape = (__pyx_t_2[0]); - - /* "View.MemoryView":1184 - * - * for shape in src.shape[:ndim]: - * size *= shape # <<<<<<<<<<<<<< - * - * return size - */ - __pyx_v_size = (__pyx_v_size * __pyx_v_shape); - } - - /* "View.MemoryView":1186 - * size *= shape - * - * return size # <<<<<<<<<<<<<< - * - * @cname('__pyx_fill_contig_strides_array') - */ - __pyx_r = __pyx_v_size; - goto __pyx_L0; - - /* "View.MemoryView":1179 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef Py_ssize_t shape, size = src.memview.view.itemsize - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1189 - * - * @cname('__pyx_fill_contig_strides_array') - * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< - * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, - * int ndim, char order) nogil: - */ - -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { - int __pyx_v_idx; - Py_ssize_t __pyx_r; - int __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - int __pyx_t_4; - - /* "View.MemoryView":1198 - * cdef int idx - * - * if order == 'F': # <<<<<<<<<<<<<< - * for idx in range(ndim): - * strides[idx] = stride - */ - __pyx_t_1 = ((__pyx_v_order == 'F') != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1199 - * - * if order == 'F': - * for idx in range(ndim): # <<<<<<<<<<<<<< - * strides[idx] = stride - * stride *= shape[idx] - */ - __pyx_t_2 = __pyx_v_ndim; - __pyx_t_3 = __pyx_t_2; - for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { - __pyx_v_idx = __pyx_t_4; - - /* "View.MemoryView":1200 - * if order == 'F': - * for idx in range(ndim): - * strides[idx] = stride # <<<<<<<<<<<<<< - * stride *= shape[idx] - * else: - */ - (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - - /* "View.MemoryView":1201 - * for idx in range(ndim): - * strides[idx] = stride - * stride *= shape[idx] # <<<<<<<<<<<<<< - * else: - * for idx in range(ndim - 1, -1, -1): - */ - __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); - } - - /* "View.MemoryView":1198 - * cdef int idx - * - * if order == 'F': # <<<<<<<<<<<<<< - * for idx in range(ndim): - * strides[idx] = stride - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1203 - * stride *= shape[idx] - * else: - * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< - * strides[idx] = stride - * stride *= shape[idx] - */ - /*else*/ { - for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { - __pyx_v_idx = __pyx_t_2; - - /* "View.MemoryView":1204 - * else: - * for idx in range(ndim - 1, -1, -1): - * strides[idx] = stride # <<<<<<<<<<<<<< - * stride *= shape[idx] - * - */ - (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - - /* "View.MemoryView":1205 - * for idx in range(ndim - 1, -1, -1): - * strides[idx] = stride - * stride *= shape[idx] # <<<<<<<<<<<<<< - * - * return stride - */ - __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); - } - } - __pyx_L3:; - - /* "View.MemoryView":1207 - * stride *= shape[idx] - * - * return stride # <<<<<<<<<<<<<< - * - * @cname('__pyx_memoryview_copy_data_to_temp') - */ - __pyx_r = __pyx_v_stride; - goto __pyx_L0; - - /* "View.MemoryView":1189 - * - * @cname('__pyx_fill_contig_strides_array') - * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< - * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, - * int ndim, char order) nogil: - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1210 - * - * @cname('__pyx_memoryview_copy_data_to_temp') - * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *tmpslice, - * char order, - */ - -static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_tmpslice, char __pyx_v_order, int __pyx_v_ndim) { - int __pyx_v_i; - void *__pyx_v_result; - size_t __pyx_v_itemsize; - size_t __pyx_v_size; - void *__pyx_r; - Py_ssize_t __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - struct __pyx_memoryview_obj *__pyx_t_4; - int __pyx_t_5; - int __pyx_t_6; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - - /* "View.MemoryView":1221 - * cdef void *result - * - * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< - * cdef size_t size = slice_get_size(src, ndim) - * - */ - __pyx_t_1 = __pyx_v_src->memview->view.itemsize; - __pyx_v_itemsize = __pyx_t_1; - - /* "View.MemoryView":1222 - * - * cdef size_t itemsize = src.memview.view.itemsize - * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<< - * - * result = malloc(size) - */ - __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim); - - /* "View.MemoryView":1224 - * cdef size_t size = slice_get_size(src, ndim) - * - * result = malloc(size) # <<<<<<<<<<<<<< - * if not result: - * _err(MemoryError, NULL) - */ - __pyx_v_result = malloc(__pyx_v_size); - - /* "View.MemoryView":1225 - * - * result = malloc(size) - * if not result: # <<<<<<<<<<<<<< - * _err(MemoryError, NULL) - * - */ - __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1226 - * result = malloc(size) - * if not result: - * _err(MemoryError, NULL) # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(1, 1226, __pyx_L1_error) - - /* "View.MemoryView":1225 - * - * result = malloc(size) - * if not result: # <<<<<<<<<<<<<< - * _err(MemoryError, NULL) - * - */ - } - - /* "View.MemoryView":1229 - * - * - * tmpslice.data = result # <<<<<<<<<<<<<< - * tmpslice.memview = src.memview - * for i in range(ndim): - */ - __pyx_v_tmpslice->data = ((char *)__pyx_v_result); - - /* "View.MemoryView":1230 - * - * tmpslice.data = result - * tmpslice.memview = src.memview # <<<<<<<<<<<<<< - * for i in range(ndim): - * tmpslice.shape[i] = src.shape[i] - */ - __pyx_t_4 = __pyx_v_src->memview; - __pyx_v_tmpslice->memview = __pyx_t_4; - - /* "View.MemoryView":1231 - * tmpslice.data = result - * tmpslice.memview = src.memview - * for i in range(ndim): # <<<<<<<<<<<<<< - * tmpslice.shape[i] = src.shape[i] - * tmpslice.suboffsets[i] = -1 - */ - __pyx_t_3 = __pyx_v_ndim; - __pyx_t_5 = __pyx_t_3; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1232 - * tmpslice.memview = src.memview - * for i in range(ndim): - * tmpslice.shape[i] = src.shape[i] # <<<<<<<<<<<<<< - * tmpslice.suboffsets[i] = -1 - * - */ - (__pyx_v_tmpslice->shape[__pyx_v_i]) = (__pyx_v_src->shape[__pyx_v_i]); - - /* "View.MemoryView":1233 - * for i in range(ndim): - * tmpslice.shape[i] = src.shape[i] - * tmpslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< - * - * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, - */ - (__pyx_v_tmpslice->suboffsets[__pyx_v_i]) = -1L; - } - - /* "View.MemoryView":1235 - * tmpslice.suboffsets[i] = -1 - * - * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, # <<<<<<<<<<<<<< - * ndim, order) - * - */ - (void)(__pyx_fill_contig_strides_array((&(__pyx_v_tmpslice->shape[0])), (&(__pyx_v_tmpslice->strides[0])), __pyx_v_itemsize, __pyx_v_ndim, __pyx_v_order)); - - /* "View.MemoryView":1239 - * - * - * for i in range(ndim): # <<<<<<<<<<<<<< - * if tmpslice.shape[i] == 1: - * tmpslice.strides[i] = 0 - */ - __pyx_t_3 = __pyx_v_ndim; - __pyx_t_5 = __pyx_t_3; - for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; - - /* "View.MemoryView":1240 - * - * for i in range(ndim): - * if tmpslice.shape[i] == 1: # <<<<<<<<<<<<<< - * tmpslice.strides[i] = 0 - * - */ - __pyx_t_2 = (((__pyx_v_tmpslice->shape[__pyx_v_i]) == 1) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1241 - * for i in range(ndim): - * if tmpslice.shape[i] == 1: - * tmpslice.strides[i] = 0 # <<<<<<<<<<<<<< - * - 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* for i in range(ndim): - * if src.shape[i] != dst.shape[i]: - * if src.shape[i] == 1: # <<<<<<<<<<<<<< - * broadcasting = True - * src.strides[i] = 0 - */ - goto __pyx_L7; - } - - /* "View.MemoryView":1299 - * src.strides[i] = 0 - * else: - * _err_extents(i, dst.shape[i], src.shape[i]) # <<<<<<<<<<<<<< - * - * if src.suboffsets[i] >= 0: - */ - /*else*/ { - __pyx_t_6 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(1, 1299, __pyx_L1_error) - } - __pyx_L7:; - - /* "View.MemoryView":1294 - * - * for i in range(ndim): - * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< - * if src.shape[i] == 1: - * broadcasting = True - */ - } - - /* "View.MemoryView":1301 - * _err_extents(i, dst.shape[i], src.shape[i]) - * - * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - */ - __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1302 - * - * if src.suboffsets[i] >= 0: - * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<< - * - * if slices_overlap(&src, &dst, ndim, itemsize): - */ - __pyx_t_6 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(1, 1302, __pyx_L1_error) - - /* "View.MemoryView":1301 - * _err_extents(i, dst.shape[i], src.shape[i]) - * - * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - */ - } - } - - /* "View.MemoryView":1304 - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< - * - * if not slice_is_contig(src, order, ndim): - */ - __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1306 - * if slices_overlap(&src, &dst, ndim, itemsize): - * - * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< - * order = get_best_order(&dst, ndim) - * - */ - __pyx_t_2 = ((!(__pyx_memviewslice_is_contig(__pyx_v_src, __pyx_v_order, __pyx_v_ndim) != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1307 - * - * if not slice_is_contig(src, order, ndim): - * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<< - * - * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) - */ - __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim); - - /* "View.MemoryView":1306 - * if slices_overlap(&src, &dst, ndim, itemsize): - * - * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< - * order = get_best_order(&dst, ndim) - * - */ - } - - /* "View.MemoryView":1309 - * order = get_best_order(&dst, ndim) - * - * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<< - * src = tmp - * - */ - __pyx_t_7 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_7 == ((void *)NULL))) __PYX_ERR(1, 1309, __pyx_L1_error) - __pyx_v_tmpdata = __pyx_t_7; - - /* "View.MemoryView":1310 - * - * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) - * src = tmp # <<<<<<<<<<<<<< - * - * if not broadcasting: - */ - __pyx_v_src = __pyx_v_tmp; - - /* "View.MemoryView":1304 - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< - * - * if not slice_is_contig(src, order, ndim): - */ - } - - /* "View.MemoryView":1312 - * src = tmp - * - * if not broadcasting: # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1315 - * - * - * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - */ - __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'C', __pyx_v_ndim) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1316 - * - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) # <<<<<<<<<<<<<< - * elif slice_is_contig(src, 'F', ndim): - * direct_copy = slice_is_contig(dst, 'F', ndim) - */ - __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'C', __pyx_v_ndim); - - /* "View.MemoryView":1315 - * - * - * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - */ - goto __pyx_L12; - } - - /* "View.MemoryView":1317 - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - */ - __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'F', __pyx_v_ndim) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1318 - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - * direct_copy = slice_is_contig(dst, 'F', ndim) # <<<<<<<<<<<<<< - * - * if direct_copy: - */ - __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'F', __pyx_v_ndim); - - /* "View.MemoryView":1317 - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - */ - } - __pyx_L12:; - - /* "View.MemoryView":1320 - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - * if direct_copy: # <<<<<<<<<<<<<< - * - * refcount_copying(&dst, dtype_is_object, ndim, False) - */ - __pyx_t_2 = (__pyx_v_direct_copy != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1322 - * if direct_copy: - * - * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) - * refcount_copying(&dst, dtype_is_object, ndim, True) - */ - __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - - /* "View.MemoryView":1323 - * - * refcount_copying(&dst, dtype_is_object, ndim, False) - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< - * refcount_copying(&dst, dtype_is_object, ndim, True) - * free(tmpdata) - */ - (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim))); - - /* "View.MemoryView":1324 - * refcount_copying(&dst, dtype_is_object, ndim, False) - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) - * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< - * free(tmpdata) - * return 0 - */ - __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - - /* "View.MemoryView":1325 - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) - * refcount_copying(&dst, dtype_is_object, ndim, True) - * free(tmpdata) # <<<<<<<<<<<<<< - * return 0 - * - */ - free(__pyx_v_tmpdata); - - /* "View.MemoryView":1326 - * refcount_copying(&dst, dtype_is_object, ndim, True) - * free(tmpdata) - * return 0 # <<<<<<<<<<<<<< - * - * if order == 'F' == get_best_order(&dst, ndim): - */ - __pyx_r = 0; - goto __pyx_L0; - - /* "View.MemoryView":1320 - 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PyDict_Size(kwargs) : 0; - if (Py_EnterRecursiveCall((char*)" while calling a Python object")) { - return NULL; - } - if ( -#if PY_MAJOR_VERSION >= 3 - co->co_kwonlyargcount == 0 && -#endif - likely(kwargs == NULL || nk == 0) && - co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { - if (argdefs == NULL && co->co_argcount == nargs) { - result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); - goto done; - } - else if (nargs == 0 && argdefs != NULL - && co->co_argcount == Py_SIZE(argdefs)) { - /* function called with no arguments, but all parameters have - a default value: use default values as arguments .*/ - args = &PyTuple_GET_ITEM(argdefs, 0); - result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); - goto done; - } - } - if (kwargs != NULL) { - Py_ssize_t pos, i; - kwtuple = PyTuple_New(2 * nk); - if (kwtuple == NULL) { - result = NULL; - goto done; - } - k = &PyTuple_GET_ITEM(kwtuple, 0); - pos = i = 0; - while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { - Py_INCREF(k[i]); - Py_INCREF(k[i+1]); - i += 2; - } - nk = i / 2; - } - else { - kwtuple = NULL; - k = NULL; - } - closure = PyFunction_GET_CLOSURE(func); -#if PY_MAJOR_VERSION >= 3 - kwdefs = PyFunction_GET_KW_DEFAULTS(func); -#endif - if (argdefs != NULL) { - d = &PyTuple_GET_ITEM(argdefs, 0); - nd = Py_SIZE(argdefs); - } - else { - d = NULL; - nd = 0; - } -#if PY_MAJOR_VERSION >= 3 - result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, kwdefs, closure); -#else - result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, closure); -#endif - Py_XDECREF(kwtuple); -done: - Py_LeaveRecursiveCall(); - return result; -} -#endif -#endif - -/* PyObjectCall2Args */ -static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { - PyObject *args, *result = NULL; - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyFunction_FastCall(function, args, 2); - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyCFunction_FastCall(function, args, 2); - } - #endif - args = PyTuple_New(2); - if (unlikely(!args)) goto done; - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 0, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 1, arg2); - Py_INCREF(function); - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); -done: - return result; -} - -/* PyObjectCallMethO */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { - PyObject *self, *result; - PyCFunction cfunc; - cfunc = PyCFunction_GET_FUNCTION(func); - self = PyCFunction_GET_SELF(func); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = cfunc(self, arg); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallOneArg */ -#if CYTHON_COMPILING_IN_CPYTHON -static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_New(1); - if (unlikely(!args)) return NULL; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif - if (likely(PyCFunction_Check(func))) { - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (__Pyx_PyFastCFunction_Check(func)) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } - } - return __Pyx__PyObject_CallOneArg(func, arg); -} -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -#endif - -/* PyErrExceptionMatches */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* GetAttr */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { -#if CYTHON_USE_TYPE_SLOTS -#if PY_MAJOR_VERSION >= 3 - if (likely(PyUnicode_Check(n))) -#else - if (likely(PyString_Check(n))) -#endif - return __Pyx_PyObject_GetAttrStr(o, n); -#endif - return PyObject_GetAttr(o, n); -} - -/* GetAttr3 */ -static PyObject *__Pyx_GetAttr3Default(PyObject *d) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - return NULL; - __Pyx_PyErr_Clear(); - Py_INCREF(d); - return d; -} -static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { - PyObject *r = __Pyx_GetAttr(o, n); - return (likely(r)) ? r : __Pyx_GetAttr3Default(d); -} - -/* RaiseArgTupleInvalid */ -static void __Pyx_RaiseArgtupleInvalid( - const char* func_name, - int exact, - Py_ssize_t num_min, - Py_ssize_t num_max, - Py_ssize_t num_found) -{ - Py_ssize_t num_expected; - const char *more_or_less; - if (num_found < num_min) { - num_expected = num_min; - more_or_less = "at least"; - } else { - num_expected = num_max; - more_or_less = "at most"; - } - if (exact) { - more_or_less = "exactly"; - } - PyErr_Format(PyExc_TypeError, - "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", - func_name, more_or_less, num_expected, - (num_expected == 1) ? "" : "s", num_found); -} - -/* RaiseDoubleKeywords */ -static void __Pyx_RaiseDoubleKeywordsError( - const char* func_name, - PyObject* kw_name) -{ - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION >= 3 - "%s() got multiple values for keyword argument '%U'", func_name, kw_name); - #else - "%s() got multiple values for keyword argument '%s'", func_name, - PyString_AsString(kw_name)); - #endif -} - -/* ParseKeywords */ -static int __Pyx_ParseOptionalKeywords( - PyObject *kwds, - PyObject **argnames[], - PyObject *kwds2, - PyObject *values[], - Py_ssize_t num_pos_args, - const char* function_name) -{ - PyObject *key = 0, *value = 0; - Py_ssize_t pos = 0; - PyObject*** name; - PyObject*** first_kw_arg = argnames + num_pos_args; - while (PyDict_Next(kwds, &pos, &key, &value)) { - name = first_kw_arg; - while (*name && (**name != key)) name++; - if (*name) { - values[name-argnames] = value; - continue; - } - name = first_kw_arg; - #if PY_MAJOR_VERSION < 3 - if (likely(PyString_Check(key))) { - while (*name) { - if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) - && _PyString_Eq(**name, key)) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - if ((**argname == key) || ( - (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) - && _PyString_Eq(**argname, key))) { - goto arg_passed_twice; - } - argname++; - } - } - } else - #endif - if (likely(PyUnicode_Check(key))) { - while (*name) { - int cmp = (**name == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**name, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - int cmp = (**argname == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**argname, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) goto arg_passed_twice; - argname++; - } - } - } else - goto invalid_keyword_type; - if (kwds2) { - if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; - } else { - goto invalid_keyword; - } - } - return 0; -arg_passed_twice: - __Pyx_RaiseDoubleKeywordsError(function_name, key); - goto bad; -invalid_keyword_type: - PyErr_Format(PyExc_TypeError, - "%.200s() keywords must be strings", function_name); - goto bad; -invalid_keyword: - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION < 3 - "%.200s() got an unexpected keyword argument '%.200s'", - function_name, PyString_AsString(key)); - #else - "%s() got an unexpected keyword argument '%U'", - function_name, key); - #endif -bad: - return -1; -} - -/* PyIntCompare */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_NeObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED long inplace) { - if (op1 == op2) { - Py_RETURN_FALSE; - } - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - const long b = intval; - long a = PyInt_AS_LONG(op1); - if (a != b) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - int unequal; - unsigned long uintval; - Py_ssize_t size = Py_SIZE(op1); - const digit* digits = ((PyLongObject*)op1)->ob_digit; - if (intval == 0) { - if (size != 0) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } else if (intval < 0) { - if (size >= 0) - Py_RETURN_TRUE; - intval = -intval; - size = -size; - } else { - if (size <= 0) - Py_RETURN_TRUE; - } - uintval = (unsigned long) intval; -#if PyLong_SHIFT * 4 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 4)) { - unequal = (size != 5) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[4] != ((uintval >> (4 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif -#if PyLong_SHIFT * 3 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 3)) { - unequal = (size != 4) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif -#if PyLong_SHIFT * 2 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 2)) { - unequal = (size != 3) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif -#if PyLong_SHIFT * 1 < SIZEOF_LONG*8 - if (uintval >> (PyLong_SHIFT * 1)) { - unequal = (size != 2) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) - | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); - } else -#endif - unequal = (size != 1) || (((unsigned long) digits[0]) != (uintval & (unsigned long) PyLong_MASK)); - if (unequal != 0) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - if ((double)a != (double)b) Py_RETURN_TRUE; else Py_RETURN_FALSE; - } - return ( - PyObject_RichCompare(op1, op2, Py_NE)); -} - -/* GetItemInt */ -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { - PyObject *r; - if (!j) return NULL; - r = PyObject_GetItem(o, j); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyList_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyTuple_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } - else if (PyTuple_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } else { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_item)) { - if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { - Py_ssize_t l = m->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return NULL; - PyErr_Clear(); - } - } - return m->sq_item(o, i); - } - } -#else - if (is_list || PySequence_Check(o)) { - return PySequence_GetItem(o, i); - } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -} - -/* RaiseException */ -#if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* PyFloatBinop */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyFloat_EqObjC(PyObject *op1, PyObject *op2, double floatval, int inplace, int zerodivision_check) { - const double b = floatval; - double a; - (void)inplace; - (void)zerodivision_check; - if (op1 == op2) { - Py_RETURN_TRUE; - } - if (likely(PyFloat_CheckExact(op1))) { - a = PyFloat_AS_DOUBLE(op1); - - } else - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - a = (double) PyInt_AS_LONG(op1); - - } else - #endif - if (likely(PyLong_CheckExact(op1))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - switch (size) { - case 0: a = 0.0; break; - case -1: a = -(double) digits[0]; break; - case 1: a = (double) digits[0]; break; - case -2: - case 2: - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (1 * PyLong_SHIFT < 53))) { - a = (double) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - if ((8 * sizeof(unsigned long) < 53) || (2 * PyLong_SHIFT < 53) || (a < (double) ((PY_LONG_LONG)1 << 53))) { - if (size == -2) - a = -a; - break; - } - } - CYTHON_FALLTHROUGH; - case -3: - case 3: - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (2 * PyLong_SHIFT < 53))) { - a = (double) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - if ((8 * sizeof(unsigned long) < 53) || (3 * PyLong_SHIFT < 53) || (a < (double) ((PY_LONG_LONG)1 << 53))) { - if (size == -3) - a = -a; - break; - } - } - CYTHON_FALLTHROUGH; - case -4: - case 4: - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (3 * PyLong_SHIFT < 53))) { - a = (double) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - if ((8 * sizeof(unsigned long) < 53) || (4 * PyLong_SHIFT < 53) || (a < (double) ((PY_LONG_LONG)1 << 53))) { - if (size == -4) - a = -a; - break; - } - } - CYTHON_FALLTHROUGH; - default: - #else - { - #endif - return ( - PyFloat_Type.tp_richcompare(op2, op1, Py_EQ)); - } - } else { - return ( - PyObject_RichCompare(op1, op2, Py_EQ)); - } - if (a == b) { - Py_RETURN_TRUE; - } else { - Py_RETURN_FALSE; - } -} -#endif - -/* SliceObject */ - static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, - Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, - int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { -#if CYTHON_USE_TYPE_SLOTS - PyMappingMethods* mp; -#if PY_MAJOR_VERSION < 3 - PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; - if (likely(ms && ms->sq_slice)) { - if (!has_cstart) { - if (_py_start && (*_py_start != Py_None)) { - cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); - if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstart = 0; - } - if (!has_cstop) { - if (_py_stop && (*_py_stop != Py_None)) { - cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); - if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstop = PY_SSIZE_T_MAX; - } - if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { - Py_ssize_t l = ms->sq_length(obj); - if (likely(l >= 0)) { - if (cstop < 0) { - cstop += l; - if (cstop < 0) cstop = 0; - } - if (cstart < 0) { - cstart += l; - if (cstart < 0) cstart = 0; - } - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - goto bad; - PyErr_Clear(); - } - } - return ms->sq_slice(obj, cstart, cstop); - } -#endif - mp = Py_TYPE(obj)->tp_as_mapping; - if (likely(mp && mp->mp_subscript)) -#endif - { - PyObject* result; - PyObject *py_slice, *py_start, *py_stop; - if (_py_slice) { - py_slice = *_py_slice; - } else { - PyObject* owned_start = NULL; - PyObject* owned_stop = NULL; - if (_py_start) { - py_start = *_py_start; - } else { - if (has_cstart) { - owned_start = py_start = PyInt_FromSsize_t(cstart); - if (unlikely(!py_start)) goto bad; - } else - py_start = Py_None; - } - if (_py_stop) { - py_stop = *_py_stop; - } else { - if (has_cstop) { - owned_stop = py_stop = PyInt_FromSsize_t(cstop); - if (unlikely(!py_stop)) { - Py_XDECREF(owned_start); - goto bad; - } - } else - py_stop = Py_None; - } - py_slice = PySlice_New(py_start, py_stop, Py_None); - Py_XDECREF(owned_start); - Py_XDECREF(owned_stop); - if (unlikely(!py_slice)) goto bad; - } -#if CYTHON_USE_TYPE_SLOTS - result = mp->mp_subscript(obj, py_slice); -#else - result = PyObject_GetItem(obj, py_slice); -#endif - if (!_py_slice) { - Py_DECREF(py_slice); - } - return result; - } - PyErr_Format(PyExc_TypeError, - "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name); -bad: - return NULL; -} - -/* PyObjectCallNoArg */ - #if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, NULL, 0); - } -#endif -#if defined(__Pyx_CyFunction_USED) && defined(NDEBUG) - if (likely(PyCFunction_Check(func) || __Pyx_CyFunction_Check(func))) -#else - if (likely(PyCFunction_Check(func))) -#endif - { - if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { - return __Pyx_PyObject_CallMethO(func, NULL); - } - } - return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL); -} -#endif - -/* MemviewSliceInit */ - static int -__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference) -{ - __Pyx_RefNannyDeclarations - int i, retval=-1; - Py_buffer *buf = &memview->view; - __Pyx_RefNannySetupContext("init_memviewslice", 0); - if (unlikely(memviewslice->memview || memviewslice->data)) { - PyErr_SetString(PyExc_ValueError, - "memviewslice is already initialized!"); - goto fail; - } - if (buf->strides) { - for (i = 0; i < ndim; i++) { - memviewslice->strides[i] = buf->strides[i]; - } - } else { - Py_ssize_t stride = buf->itemsize; - for (i = ndim - 1; i >= 0; i--) { - memviewslice->strides[i] = stride; - stride *= buf->shape[i]; - } - } - for (i = 0; i < ndim; i++) { - memviewslice->shape[i] = buf->shape[i]; - if (buf->suboffsets) { - memviewslice->suboffsets[i] = buf->suboffsets[i]; - } else { - memviewslice->suboffsets[i] = -1; - } - } - memviewslice->memview = memview; - memviewslice->data = (char *)buf->buf; - if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { - Py_INCREF(memview); - } - retval = 0; - goto no_fail; -fail: - memviewslice->memview = 0; - memviewslice->data = 0; - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} -#ifndef Py_NO_RETURN -#define Py_NO_RETURN -#endif -static void __pyx_fatalerror(const char *fmt, ...) Py_NO_RETURN { - va_list vargs; - char msg[200]; -#if PY_VERSION_HEX >= 0x030A0000 || defined(HAVE_STDARG_PROTOTYPES) - va_start(vargs, fmt); -#else - va_start(vargs); -#endif - vsnprintf(msg, 200, fmt, vargs); - va_end(vargs); - Py_FatalError(msg); -} -static CYTHON_INLINE int -__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)++; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE int -__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)--; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE void -__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) -{ - int first_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) - return; - if (unlikely(__pyx_get_slice_count(memview) < 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - first_time = __pyx_add_acquisition_count(memview) == 0; - if (unlikely(first_time)) { - if (have_gil) { - Py_INCREF((PyObject *) memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_INCREF((PyObject *) memview); - PyGILState_Release(_gilstate); - } - } -} -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, - int have_gil, int lineno) { - int last_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (unlikely(!memview || (PyObject *) memview == Py_None)) { - memslice->memview = NULL; - return; - } - if (unlikely(__pyx_get_slice_count(memview) <= 0)) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - last_time = __pyx_sub_acquisition_count(memview) == 1; - memslice->data = NULL; - if (unlikely(last_time)) { - if (have_gil) { - Py_CLEAR(memslice->memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_CLEAR(memslice->memview); - PyGILState_Release(_gilstate); - } - } else { - memslice->memview = NULL; - } -} - -/* Import */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* ImportFrom */ - static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { - PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); - if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_Format(PyExc_ImportError, - #if PY_MAJOR_VERSION < 3 - "cannot import name %.230s", PyString_AS_STRING(name)); - #else - "cannot import name %S", name); - #endif - } - return value; -} - -/* PyFloatBinop */ - #if !CYTHON_COMPILING_IN_PYPY -#define __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(operand) if (unlikely(zerodivision_check && ((operand) == 0))) {\ - PyErr_SetString(PyExc_ZeroDivisionError, "float division by zero");\ - return NULL;\ -} -static PyObject* __Pyx_PyFloat_TrueDivideCObj(PyObject *op1, PyObject *op2, double floatval, int inplace, int zerodivision_check) { - const double a = floatval; - double b, result; - (void)inplace; - (void)zerodivision_check; - if (likely(PyFloat_CheckExact(op2))) { - b = PyFloat_AS_DOUBLE(op2); - __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(b) - } else - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op2))) { - b = (double) PyInt_AS_LONG(op2); - __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(b) - } else - #endif - if (likely(PyLong_CheckExact(op2))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)op2)->ob_digit; - const Py_ssize_t size = Py_SIZE(op2); - switch (size) { - case 0: __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(0) break; - case -1: b = -(double) digits[0]; break; - case 1: b = (double) digits[0]; break; - case -2: - case 2: - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (1 * PyLong_SHIFT < 53))) { - b = (double) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - if ((8 * sizeof(unsigned long) < 53) || (2 * PyLong_SHIFT < 53) || (b < (double) ((PY_LONG_LONG)1 << 53))) { - if (size == -2) - b = -b; - break; - } - } - CYTHON_FALLTHROUGH; - case -3: - case 3: - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (2 * PyLong_SHIFT < 53))) { - b = (double) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - if ((8 * sizeof(unsigned long) < 53) || (3 * PyLong_SHIFT < 53) || (b < (double) ((PY_LONG_LONG)1 << 53))) { - if (size == -3) - b = -b; - break; - } - } - CYTHON_FALLTHROUGH; - case -4: - case 4: - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (3 * PyLong_SHIFT < 53))) { - b = (double) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - if ((8 * sizeof(unsigned long) < 53) || (4 * PyLong_SHIFT < 53) || (b < (double) ((PY_LONG_LONG)1 << 53))) { - if (size == -4) - b = -b; - break; - } - } - CYTHON_FALLTHROUGH; - default: - #else - { - #endif - b = PyLong_AsDouble(op2); - if (unlikely(b == -1.0 && PyErr_Occurred())) return NULL; - __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(b) - } - } else { - return (inplace ? PyNumber_InPlaceTrueDivide : PyNumber_TrueDivide)(op1, op2); - } - __Pyx_PyFloat_TrueDivideCObj_ZeroDivisionError(b) - PyFPE_START_PROTECT("divide", return NULL) - result = a / b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); -} -#endif - -/* HasAttr */ - static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { - PyObject *r; - if (unlikely(!__Pyx_PyBaseString_Check(n))) { - PyErr_SetString(PyExc_TypeError, - "hasattr(): attribute name must be string"); - return -1; - } - r = __Pyx_GetAttr(o, n); - if (unlikely(!r)) { - PyErr_Clear(); - return 0; - } else { - Py_DECREF(r); - return 1; - } -} - -/* GetTopmostException */ - #if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* ArgTypeTest */ - static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) -{ - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - else if (exact) { - #if PY_MAJOR_VERSION == 2 - if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; - #endif - } - else { - if (likely(__Pyx_TypeCheck(obj, type))) return 1; - } - PyErr_Format(PyExc_TypeError, - "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", - name, type->tp_name, Py_TYPE(obj)->tp_name); - return 0; -} - -/* BytesEquals */ - static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { - const char *ps1, *ps2; - Py_ssize_t length = PyBytes_GET_SIZE(s1); - if (length != PyBytes_GET_SIZE(s2)) - return (equals == Py_NE); - ps1 = PyBytes_AS_STRING(s1); - ps2 = PyBytes_AS_STRING(s2); - if (ps1[0] != ps2[0]) { - return (equals == Py_NE); - } else if (length == 1) { - return (equals == Py_EQ); - } else { - int result; -#if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000) - Py_hash_t hash1, hash2; - hash1 = ((PyBytesObject*)s1)->ob_shash; - hash2 = ((PyBytesObject*)s2)->ob_shash; - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - return (equals == Py_NE); - } -#endif - result = memcmp(ps1, ps2, (size_t)length); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -#endif -} - -/* UnicodeEquals */ - static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else -#if PY_MAJOR_VERSION < 3 - PyObject* owned_ref = NULL; -#endif - int s1_is_unicode, s2_is_unicode; - if (s1 == s2) { - goto return_eq; - } - s1_is_unicode = PyUnicode_CheckExact(s1); - s2_is_unicode = PyUnicode_CheckExact(s2); -#if PY_MAJOR_VERSION < 3 - if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { - owned_ref = PyUnicode_FromObject(s2); - if (unlikely(!owned_ref)) - return -1; - s2 = owned_ref; - s2_is_unicode = 1; - } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { - owned_ref = PyUnicode_FromObject(s1); - if (unlikely(!owned_ref)) - return -1; - s1 = owned_ref; - s1_is_unicode = 1; - } else if (((!s2_is_unicode) & (!s1_is_unicode))) { - return __Pyx_PyBytes_Equals(s1, s2, equals); - } -#endif - if (s1_is_unicode & s2_is_unicode) { - Py_ssize_t length; - int kind; - void *data1, *data2; - if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) - return -1; - length = __Pyx_PyUnicode_GET_LENGTH(s1); - if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { - goto return_ne; - } -#if CYTHON_USE_UNICODE_INTERNALS - { - Py_hash_t hash1, hash2; - #if CYTHON_PEP393_ENABLED - hash1 = ((PyASCIIObject*)s1)->hash; - hash2 = ((PyASCIIObject*)s2)->hash; - #else - hash1 = ((PyUnicodeObject*)s1)->hash; - hash2 = ((PyUnicodeObject*)s2)->hash; - #endif - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - goto return_ne; - } - } -#endif - kind = __Pyx_PyUnicode_KIND(s1); - if (kind != __Pyx_PyUnicode_KIND(s2)) { - goto return_ne; - } - data1 = __Pyx_PyUnicode_DATA(s1); - data2 = __Pyx_PyUnicode_DATA(s2); - if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { - goto return_ne; - } else if (length == 1) { - goto return_eq; - } else { - int result = memcmp(data1, data2, (size_t)(length * kind)); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & s2_is_unicode) { - goto return_ne; - } else if ((s2 == Py_None) & s1_is_unicode) { - goto return_ne; - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -return_eq: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ); -return_ne: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_NE); -#endif -} - -/* ObjectGetItem */ - #if CYTHON_USE_TYPE_SLOTS -static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { - PyObject *runerr = NULL; - Py_ssize_t key_value; - PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; - if (unlikely(!(m && m->sq_item))) { - PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); - return NULL; - } - key_value = __Pyx_PyIndex_AsSsize_t(index); - if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { - return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); - } - if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { - PyErr_Clear(); - PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); - } - return NULL; -} -static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { - PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; - if (likely(m && m->mp_subscript)) { - return m->mp_subscript(obj, key); - } - return __Pyx_PyObject_GetIndex(obj, key); -} -#endif - -/* decode_c_string */ - static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { - Py_ssize_t length; - if (unlikely((start < 0) | (stop < 0))) { - size_t slen = strlen(cstring); - if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { - PyErr_SetString(PyExc_OverflowError, - "c-string too long to convert to Python"); - return NULL; - } - length = (Py_ssize_t) slen; - if (start < 0) { - start += length; - if (start < 0) - start = 0; - } - if (stop < 0) - stop += length; - } - if (unlikely(stop <= start)) - return __Pyx_NewRef(__pyx_empty_unicode); - length = stop - start; - cstring += start; - if (decode_func) { - return decode_func(cstring, length, errors); - } else { - return PyUnicode_Decode(cstring, length, encoding, errors); - } -} - -/* RaiseTooManyValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -/* RaiseNeedMoreValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -/* RaiseNoneIterError */ - static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); -} - -/* ExtTypeTest */ - static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(__Pyx_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* GetException */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* SwapException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = *type; - exc_info->exc_value = *value; - exc_info->exc_traceback = *tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = *type; - tstate->exc_value = *value; - tstate->exc_traceback = *tb; - #endif - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); - PyErr_SetExcInfo(*type, *value, *tb); - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#endif - -/* FastTypeChecks */ - #if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; - if (a == b) - return 1; - } - return b == &PyBaseObject_Type; -} -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { - PyObject *mro; - if (a == b) return 1; - mro = a->tp_mro; - if (likely(mro)) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(mro); - for (i = 0; i < n; i++) { - if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) - return 1; - } - return 0; - } - return __Pyx_InBases(a, b); -} -#if PY_MAJOR_VERSION == 2 -static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { - PyObject *exception, *value, *tb; - int res; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&exception, &value, &tb); - res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - if (!res) { - res = PyObject_IsSubclass(err, exc_type2); - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - } - __Pyx_ErrRestore(exception, value, tb); - return res; -} -#else -static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { - int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; - if (!res) { - res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); - } - return res; -} -#endif -static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - assert(PyExceptionClass_Check(exc_type)); - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; i= 0 || (x^b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - CYTHON_FALLTHROUGH; - default: return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - } - x = a + b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla + llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("add", return NULL) - result = ((double)a) + (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); -} -#endif - -/* None */ - static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { - PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); -} - -/* PyObject_GenericGetAttrNoDict */ - #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { - PyErr_Format(PyExc_AttributeError, -#if PY_MAJOR_VERSION >= 3 - "'%.50s' object has no attribute '%U'", - tp->tp_name, attr_name); -#else - "'%.50s' object has no attribute '%.400s'", - tp->tp_name, PyString_AS_STRING(attr_name)); -#endif - return NULL; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { - PyObject *descr; - PyTypeObject *tp = Py_TYPE(obj); - if (unlikely(!PyString_Check(attr_name))) { - return PyObject_GenericGetAttr(obj, attr_name); - } - assert(!tp->tp_dictoffset); - descr = _PyType_Lookup(tp, attr_name); - if (unlikely(!descr)) { - return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); - } - Py_INCREF(descr); - #if PY_MAJOR_VERSION < 3 - if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) - #endif - { - descrgetfunc f = Py_TYPE(descr)->tp_descr_get; - if (unlikely(f)) { - PyObject *res = f(descr, obj, (PyObject *)tp); - Py_DECREF(descr); - return res; - } - } - return descr; -} -#endif - -/* PyObject_GenericGetAttr */ - #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 -static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { - if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { - return PyObject_GenericGetAttr(obj, attr_name); - } - return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); -} -#endif - -/* SetVTable */ - static int __Pyx_SetVtable(PyObject *dict, void *vtable) { -#if PY_VERSION_HEX >= 0x02070000 - PyObject *ob = PyCapsule_New(vtable, 0, 0); -#else - PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); -#endif - if (!ob) - goto bad; - if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) - goto bad; - Py_DECREF(ob); - return 0; -bad: - Py_XDECREF(ob); - return -1; -} - -/* PyObjectGetAttrStrNoError */ - static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) - __Pyx_PyErr_Clear(); -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { - PyObject *result; -#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 - PyTypeObject* tp = Py_TYPE(obj); - if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { - return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); - } -#endif - result = __Pyx_PyObject_GetAttrStr(obj, attr_name); - if (unlikely(!result)) { - __Pyx_PyObject_GetAttrStr_ClearAttributeError(); - } - return result; -} - -/* SetupReduce */ - static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { - int ret; - PyObject *name_attr; - name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2); - if (likely(name_attr)) { - ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); - } else { - ret = -1; - } - if (unlikely(ret < 0)) { - PyErr_Clear(); - ret = 0; - } - Py_XDECREF(name_attr); - return ret; -} -static int __Pyx_setup_reduce(PyObject* type_obj) { - int ret = 0; - PyObject *object_reduce = NULL; - PyObject *object_getstate = NULL; - PyObject *object_reduce_ex = NULL; - PyObject *reduce = NULL; - PyObject *reduce_ex = NULL; - PyObject *reduce_cython = NULL; - PyObject *setstate = NULL; - PyObject *setstate_cython = NULL; - PyObject *getstate = NULL; -#if CYTHON_USE_PYTYPE_LOOKUP - getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate); -#else - getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate); - if (!getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (getstate) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate); -#else - object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate); - if (!object_getstate && PyErr_Occurred()) { - goto __PYX_BAD; - } -#endif - if (object_getstate != getstate) { - goto __PYX_GOOD; - } - } -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; -#endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; - if (reduce_ex == object_reduce_ex) { -#if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; -#endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; - if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); - if (likely(reduce_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (reduce == object_reduce || PyErr_Occurred()) { - goto __PYX_BAD; - } - setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); - if (!setstate) PyErr_Clear(); - if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); - if (likely(setstate_cython)) { - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; - } else if (!setstate || PyErr_Occurred()) { - goto __PYX_BAD; - } - } - PyType_Modified((PyTypeObject*)type_obj); - } - } - goto __PYX_GOOD; -__PYX_BAD: - if (!PyErr_Occurred()) - PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); - ret = -1; -__PYX_GOOD: -#if !CYTHON_USE_PYTYPE_LOOKUP - Py_XDECREF(object_reduce); - Py_XDECREF(object_reduce_ex); - Py_XDECREF(object_getstate); - Py_XDECREF(getstate); -#endif - Py_XDECREF(reduce); - Py_XDECREF(reduce_ex); - Py_XDECREF(reduce_cython); - Py_XDECREF(setstate); - Py_XDECREF(setstate_cython); - return ret; -} - -/* CLineInTraceback */ - #ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ - #include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); - if (__Pyx_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - if ((0)) {} - view->obj = NULL; - Py_DECREF(obj); -} -#endif - - - /* MemviewSliceIsContig */ - static int -__pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, char order, int ndim) -{ - int i, index, step, start; - Py_ssize_t itemsize = mvs.memview->view.itemsize; - if (order == 'F') { - step = 1; - start = 0; - } else { - step = -1; - start = ndim - 1; - } - for (i = 0; i < ndim; i++) { - index = start + step * i; - if (mvs.suboffsets[index] >= 0 || mvs.strides[index] != itemsize) - return 0; - itemsize *= mvs.shape[index]; - } - return 1; -} - -/* OverlappingSlices */ - static void -__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, - void **out_start, void **out_end, - int ndim, size_t itemsize) -{ - char *start, *end; - int i; - start = end = slice->data; - for (i = 0; i < ndim; i++) { - Py_ssize_t stride = slice->strides[i]; - Py_ssize_t extent = slice->shape[i]; - if (extent == 0) { - *out_start = *out_end = start; - return; - } else { - if (stride > 0) - end += stride * (extent - 1); - else - start += stride * (extent - 1); - } - } - *out_start = start; - *out_end = end + itemsize; -} -static int -__pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize) -{ - void *start1, *end1, *start2, *end2; - __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); - __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); - return (start1 < end2) && (start2 < end1); -} - -/* Capsule */ - static CYTHON_INLINE PyObject * -__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) -{ - PyObject *cobj; -#if PY_VERSION_HEX >= 0x02070000 - cobj = PyCapsule_New(p, sig, NULL); -#else - cobj = PyCObject_FromVoidPtr(p, NULL); -#endif - return cobj; -} - -/* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* MemviewDtypeToObject */ - static CYTHON_INLINE PyObject *__pyx_memview_get_float(const char *itemp) { - return (PyObject *) PyFloat_FromDouble(*(float *) itemp); -} -static CYTHON_INLINE int __pyx_memview_set_float(const char *itemp, PyObject *obj) { - float value = __pyx_PyFloat_AsFloat(obj); - if ((value == (float)-1) && PyErr_Occurred()) - return 0; - *(float *) itemp = value; - return 1; -} - -/* IsLittleEndian */ - static CYTHON_INLINE int __Pyx_Is_Little_Endian(void) -{ - union { - uint32_t u32; - uint8_t u8[4]; - } S; - S.u32 = 0x01020304; - return S.u8[0] == 4; -} - -/* BufferFormatCheck */ - static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type) { - stack[0].field = &ctx->root; - stack[0].parent_offset = 0; - ctx->root.type = type; - ctx->root.name = "buffer dtype"; - ctx->root.offset = 0; - ctx->head = stack; - ctx->head->field = &ctx->root; - ctx->fmt_offset = 0; - ctx->head->parent_offset = 0; - ctx->new_packmode = '@'; - ctx->enc_packmode = '@'; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->is_complex = 0; - ctx->is_valid_array = 0; - ctx->struct_alignment = 0; - while (type->typegroup == 'S') { - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = 0; - type = type->fields->type; - } -} -static int __Pyx_BufFmt_ParseNumber(const char** ts) { - int count; - const char* t = *ts; - if (*t < '0' || *t > '9') { - return -1; - } else { - count = *t++ - '0'; - while (*t >= '0' && *t <= '9') { - count *= 10; - count += *t++ - '0'; - } - } - *ts = t; - return count; -} -static int __Pyx_BufFmt_ExpectNumber(const char **ts) { - int number = __Pyx_BufFmt_ParseNumber(ts); - if (number == -1) - PyErr_Format(PyExc_ValueError,\ - "Does not understand character buffer dtype format string ('%c')", **ts); - return number; -} -static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { - PyErr_Format(PyExc_ValueError, - "Unexpected format string character: '%c'", ch); -} -static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { - switch (ch) { - case '?': return "'bool'"; - case 'c': return "'char'"; - case 'b': return "'signed char'"; - case 'B': return "'unsigned char'"; - case 'h': return "'short'"; - case 'H': return "'unsigned short'"; - case 'i': return "'int'"; - case 'I': return "'unsigned int'"; - case 'l': return "'long'"; - case 'L': return "'unsigned long'"; - case 'q': return "'long long'"; - case 'Q': return "'unsigned long long'"; - case 'f': return (is_complex ? "'complex float'" : "'float'"); - case 'd': return (is_complex ? "'complex double'" : "'double'"); - case 'g': return (is_complex ? "'complex long double'" : "'long double'"); - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - case 's': case 'p': return "a string"; - case 0: return "end"; - default: return "unparseable format string"; - } -} -static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return 2; - case 'i': case 'I': case 'l': case 'L': return 4; - case 'q': case 'Q': return 8; - case 'f': return (is_complex ? 8 : 4); - case 'd': return (is_complex ? 16 : 8); - case 'g': { - PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); - return 0; - } - case 'O': case 'P': return sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(short); - case 'i': case 'I': return sizeof(int); - case 'l': case 'L': return sizeof(long); - #ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(PY_LONG_LONG); - #endif - case 'f': return sizeof(float) * (is_complex ? 2 : 1); - case 'd': return sizeof(double) * (is_complex ? 2 : 1); - case 'g': return sizeof(long double) * (is_complex ? 2 : 1); - case 'O': case 'P': return sizeof(void*); - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -typedef struct { char c; short x; } __Pyx_st_short; -typedef struct { char c; int x; } __Pyx_st_int; -typedef struct { char c; long x; } __Pyx_st_long; -typedef struct { char c; float x; } __Pyx_st_float; -typedef struct { char c; double x; } __Pyx_st_double; -typedef struct { char c; long double x; } __Pyx_st_longdouble; -typedef struct { char c; void *x; } __Pyx_st_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_st_float) - sizeof(float); - case 'd': return sizeof(__Pyx_st_double) - sizeof(double); - case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -/* These are for computing the padding at the end of the struct to align - on the first member of the struct. This will probably the same as above, - but we don't have any guarantees. - */ -typedef struct { short x; char c; } __Pyx_pad_short; -typedef struct { int x; char c; } __Pyx_pad_int; -typedef struct { long x; char c; } __Pyx_pad_long; -typedef struct { float x; char c; } __Pyx_pad_float; -typedef struct { double x; char c; } __Pyx_pad_double; -typedef struct { long double x; char c; } __Pyx_pad_longdouble; -typedef struct { void *x; char c; } __Pyx_pad_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); - case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); - case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { - switch (ch) { - case 'c': - return 'H'; - case 'b': case 'h': case 'i': - case 'l': case 'q': case 's': case 'p': - return 'I'; - case '?': case 'B': case 'H': case 'I': case 'L': case 'Q': - return 'U'; - case 'f': case 'd': case 'g': - return (is_complex ? 'C' : 'R'); - case 'O': - return 'O'; - case 'P': - return 'P'; - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { - if (ctx->head == NULL || ctx->head->field == &ctx->root) { - const char* expected; - const char* quote; - if (ctx->head == NULL) { - expected = "end"; - quote = ""; - } else { - expected = ctx->head->field->type->name; - quote = "'"; - } - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected %s%s%s but got %s", - quote, expected, quote, - __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); - } else { - __Pyx_StructField* field = ctx->head->field; - __Pyx_StructField* parent = (ctx->head - 1)->field; - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", - field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), - parent->type->name, field->name); - } -} -static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { - char group; - size_t size, offset, arraysize = 1; - if (ctx->enc_type == 0) return 0; - if (ctx->head->field->type->arraysize[0]) { - int i, ndim = 0; - if (ctx->enc_type == 's' || ctx->enc_type == 'p') { - ctx->is_valid_array = ctx->head->field->type->ndim == 1; - ndim = 1; - if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { - PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %zu", - ctx->head->field->type->arraysize[0], ctx->enc_count); - return -1; - } - } - if (!ctx->is_valid_array) { - PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", - ctx->head->field->type->ndim, ndim); - return -1; - } - for (i = 0; i < ctx->head->field->type->ndim; i++) { - arraysize *= ctx->head->field->type->arraysize[i]; - } - ctx->is_valid_array = 0; - ctx->enc_count = 1; - } - group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); - do { - __Pyx_StructField* field = ctx->head->field; - __Pyx_TypeInfo* type = field->type; - if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { - size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); - } else { - size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); - } - if (ctx->enc_packmode == '@') { - size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); - size_t align_mod_offset; - if (align_at == 0) return -1; - align_mod_offset = ctx->fmt_offset % align_at; - if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; - if (ctx->struct_alignment == 0) - ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, - ctx->is_complex); - } - if (type->size != size || type->typegroup != group) { - if (type->typegroup == 'C' && type->fields != NULL) { - size_t parent_offset = ctx->head->parent_offset + field->offset; - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = parent_offset; - continue; - } - if ((type->typegroup == 'H' || group == 'H') && type->size == size) { - } else { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - } - offset = ctx->head->parent_offset + field->offset; - if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; - } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } - } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; -} -static PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number, ndim; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ndim = ctx->head->field->type->ndim; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; - } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; - } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; - } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; -} -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; - } - break; - case '}': - { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } - } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; - } - CYTHON_FALLTHROUGH; - case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && - (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - CYTHON_FALLTHROUGH; - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: - { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; - } - } - } -} - -/* TypeInfoCompare */ - static int -__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) -{ - int i; - if (!a || !b) - return 0; - if (a == b) - return 1; - if (a->size != b->size || a->typegroup != b->typegroup || - a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { - if (a->typegroup == 'H' || b->typegroup == 'H') { - return a->size == b->size; - } else { - return 0; - } - } - if (a->ndim) { - for (i = 0; i < a->ndim; i++) - if (a->arraysize[i] != b->arraysize[i]) - return 0; - } - if (a->typegroup == 'S') { - if (a->flags != b->flags) - return 0; - if (a->fields || b->fields) { - if (!(a->fields && b->fields)) - return 0; - for (i = 0; a->fields[i].type && b->fields[i].type; i++) { - __Pyx_StructField *field_a = a->fields + i; - __Pyx_StructField *field_b = b->fields + i; - if (field_a->offset != field_b->offset || - !__pyx_typeinfo_cmp(field_a->type, field_b->type)) - return 0; - } - return !a->fields[i].type && !b->fields[i].type; - } - } - return 1; -} - -/* MemviewSliceValidateAndInit */ - static int -__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) -{ - if (buf->shape[dim] <= 1) - return 1; - if (buf->strides) { - if (spec & __Pyx_MEMVIEW_CONTIG) { - if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { - if (unlikely(buf->strides[dim] != sizeof(void *))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly contiguous " - "in dimension %d.", dim); - goto fail; - } - } else if (unlikely(buf->strides[dim] != buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_FOLLOW) { - Py_ssize_t stride = buf->strides[dim]; - if (stride < 0) - stride = -stride; - if (unlikely(stride < buf->itemsize)) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - } else { - if (unlikely(spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1)) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not contiguous in " - "dimension %d", dim); - goto fail; - } else if (unlikely(spec & (__Pyx_MEMVIEW_PTR))) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not indirect in " - "dimension %d", dim); - goto fail; - } else if (unlikely(buf->suboffsets)) { - PyErr_SetString(PyExc_ValueError, - "Buffer exposes suboffsets but no strides"); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) -{ - if (spec & __Pyx_MEMVIEW_DIRECT) { - if (unlikely(buf->suboffsets && buf->suboffsets[dim] >= 0)) { - PyErr_Format(PyExc_ValueError, - "Buffer not compatible with direct access " - "in dimension %d.", dim); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_PTR) { - if (unlikely(!buf->suboffsets || (buf->suboffsets[dim] < 0))) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly accessible " - "in dimension %d.", dim); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) -{ - int i; - if (c_or_f_flag & __Pyx_IS_F_CONTIG) { - Py_ssize_t stride = 1; - for (i = 0; i < ndim; i++) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not fortran contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { - Py_ssize_t stride = 1; - for (i = ndim - 1; i >- 1; i--) { - if (unlikely(stride * buf->itemsize != buf->strides[i] && buf->shape[i] > 1)) { - PyErr_SetString(PyExc_ValueError, - "Buffer not C contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } - return 1; -fail: - return 0; -} -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj) -{ - struct __pyx_memoryview_obj *memview, *new_memview; - __Pyx_RefNannyDeclarations - Py_buffer *buf; - int i, spec = 0, retval = -1; - __Pyx_BufFmt_Context ctx; - int from_memoryview = __pyx_memoryview_check(original_obj); - __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); - if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) - original_obj)->typeinfo)) { - memview = (struct __pyx_memoryview_obj *) original_obj; - new_memview = NULL; - } else { - memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - original_obj, buf_flags, 0, dtype); - new_memview = memview; - if (unlikely(!memview)) - goto fail; - } - buf = &memview->view; - if (unlikely(buf->ndim != ndim)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - ndim, buf->ndim); - goto fail; - } - if (new_memview) { - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (unlikely(!__Pyx_BufFmt_CheckString(&ctx, buf->format))) goto fail; - } - if (unlikely((unsigned) buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " - "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", - buf->itemsize, - (buf->itemsize > 1) ? "s" : "", - dtype->name, - dtype->size, - (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->len > 0) { - for (i = 0; i < ndim; i++) { - spec = axes_specs[i]; - if (unlikely(!__pyx_check_strides(buf, i, ndim, spec))) - goto fail; - if (unlikely(!__pyx_check_suboffsets(buf, i, ndim, spec))) - goto fail; - } - if (unlikely(buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))) - goto fail; - } - if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, - new_memview != NULL) == -1)) { - goto fail; - } - retval = 0; - goto no_fail; -fail: - Py_XDECREF(new_memview); - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_d_dc_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_FOLLOW), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 2, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* MemviewDtypeToObject */ - static CYTHON_INLINE PyObject *__pyx_memview_get_int(const char *itemp) { - return (PyObject *) __Pyx_PyInt_From_int(*(int *) itemp); -} -static CYTHON_INLINE int __pyx_memview_set_int(const char *itemp, PyObject *obj) { - int value = __Pyx_PyInt_As_int(obj); - if ((value == (int)-1) && PyErr_Occurred()) - return 0; - *(int *) itemp = value; - return 1; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_int(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT) | writable_flag, 1, - &__Pyx_TypeInfo_int, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *obj, int writable_flag) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, - PyBUF_RECORDS_RO | writable_flag, 2, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* MemviewSliceCopyTemplate */ - static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object) -{ - __Pyx_RefNannyDeclarations - int i; - __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; - struct __pyx_memoryview_obj *from_memview = from_mvs->memview; - Py_buffer *buf = &from_memview->view; - PyObject *shape_tuple = NULL; - PyObject *temp_int = NULL; - struct __pyx_array_obj *array_obj = NULL; - struct __pyx_memoryview_obj *memview_obj = NULL; - __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); - for (i = 0; i < ndim; i++) { - if (unlikely(from_mvs->suboffsets[i] >= 0)) { - PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " - "indirect dimensions (axis %d)", i); - goto fail; - } - } - shape_tuple = PyTuple_New(ndim); - if (unlikely(!shape_tuple)) { - goto fail; - } - __Pyx_GOTREF(shape_tuple); - for(i = 0; i < ndim; i++) { - temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); - if(unlikely(!temp_int)) { - goto fail; - } else { - PyTuple_SET_ITEM(shape_tuple, i, temp_int); - temp_int = NULL; - } - } - array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); - if (unlikely(!array_obj)) { - goto fail; - } - __Pyx_GOTREF(array_obj); - memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - (PyObject *) array_obj, contig_flag, - dtype_is_object, - from_mvs->memview->typeinfo); - if (unlikely(!memview_obj)) - goto fail; - if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) - goto fail; - if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, - dtype_is_object) < 0)) - goto fail; - goto no_fail; -fail: - __Pyx_XDECREF(new_mvs.memview); - new_mvs.memview = NULL; - new_mvs.data = NULL; -no_fail: - __Pyx_XDECREF(shape_tuple); - __Pyx_XDECREF(temp_int); - __Pyx_XDECREF(array_obj); - __Pyx_RefNannyFinishContext(); - return new_mvs; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const size_t neg_one = (size_t) -1, const_zero = (size_t) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(size_t) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(size_t, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (size_t) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (size_t) 0; - case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, digits[0]) - case 2: - if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) >= 2 * PyLong_SHIFT) { - return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) >= 3 * PyLong_SHIFT) { - return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) >= 4 * PyLong_SHIFT) { - return (size_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (size_t) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(size_t) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (size_t) 0; - case -1: __PYX_VERIFY_RETURN_INT(size_t, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, +digits[0]) - case -2: - if (8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { - return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { - return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { - return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { - return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { - return (size_t) (((size_t)-1)*(((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) { - return (size_t) ((((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); - } - } - break; - } -#endif - if (sizeof(size_t) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(size_t) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - size_t val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (size_t) -1; - } - } else { - size_t val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (size_t) -1; - val = __Pyx_PyInt_As_size_t(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to size_t"); - return (size_t) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to size_t"); - return (size_t) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const char neg_one = (char) -1, const_zero = (char) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(char) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (char) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (char) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(char) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) - case -2: - if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - } -#endif - if (sizeof(char) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - char val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (char) -1; - } - } else { - char val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (char) -1; - val = __Pyx_PyInt_As_char(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to char"); - return (char) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to char"); - return (char) -1; -} - -/* CheckBinaryVersion */ - static int __Pyx_check_binary_version(void) { - char ctversion[5]; - int same=1, i, found_dot; - const char* rt_from_call = Py_GetVersion(); - PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); - found_dot = 0; - for (i = 0; i < 4; i++) { - if (!ctversion[i]) { - same = (rt_from_call[i] < '0' || rt_from_call[i] > '9'); - break; - } - if (rt_from_call[i] != ctversion[i]) { - same = 0; - break; - } - } - if (!same) { - char rtversion[5] = {'\0'}; - char message[200]; - for (i=0; i<4; ++i) { - if (rt_from_call[i] == '.') { - if (found_dot) break; - found_dot = 1; - } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') { - break; - } - rtversion[i] = rt_from_call[i]; - } - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* InitStrings */ - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); 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#define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #elif !defined(CYTHON_FAST_THREAD_STATE) - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000) - #endif - #ifndef CYTHON_PEP489_MULTI_PHASE_INIT - #define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000) - #endif - #ifndef CYTHON_USE_TP_FINALIZE - #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) - #endif - #ifndef CYTHON_USE_DICT_VERSIONS - #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1) - #endif - #if PY_VERSION_HEX >= 0x030B00A4 - #undef CYTHON_USE_EXC_INFO_STACK - #define CYTHON_USE_EXC_INFO_STACK 0 - #elif !defined(CYTHON_USE_EXC_INFO_STACK) - #define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3) - #endif - #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC - #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 - #endif -#endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #if PY_MAJOR_VERSION < 3 - #include "longintrepr.h" - #endif - #undef SHIFT - #undef BASE - #undef MASK - #ifdef SIZEOF_VOID_P - enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) }; - #endif -#endif -#ifndef __has_attribute - #define __has_attribute(x) 0 -#endif -#ifndef __has_cpp_attribute - #define __has_cpp_attribute(x) 0 -#endif -#ifndef CYTHON_RESTRICT - #if defined(__GNUC__) - #define CYTHON_RESTRICT __restrict__ - #elif defined(_MSC_VER) && _MSC_VER >= 1400 - #define CYTHON_RESTRICT __restrict - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_RESTRICT restrict - #else - #define CYTHON_RESTRICT - #endif -#endif -#ifndef CYTHON_UNUSED -# if defined(__GNUC__) -# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -#endif -#ifndef CYTHON_MAYBE_UNUSED_VAR -# if defined(__cplusplus) - template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } -# else -# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) -# endif -#endif -#ifndef CYTHON_NCP_UNUSED -# if CYTHON_COMPILING_IN_CPYTHON -# define CYTHON_NCP_UNUSED -# else -# define CYTHON_NCP_UNUSED CYTHON_UNUSED -# endif -#endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) -#ifdef _MSC_VER - #ifndef _MSC_STDINT_H_ - #if _MSC_VER < 1300 - typedef unsigned char uint8_t; - typedef unsigned int uint32_t; - #else - typedef unsigned __int8 uint8_t; - typedef unsigned __int32 uint32_t; - #endif - #endif -#else - #include -#endif -#ifndef CYTHON_FALLTHROUGH - #if defined(__cplusplus) && __cplusplus >= 201103L - #if __has_cpp_attribute(fallthrough) - #define CYTHON_FALLTHROUGH [[fallthrough]] - #elif __has_cpp_attribute(clang::fallthrough) - #define CYTHON_FALLTHROUGH [[clang::fallthrough]] - #elif __has_cpp_attribute(gnu::fallthrough) - #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] - #endif - #endif - #ifndef CYTHON_FALLTHROUGH - #if __has_attribute(fallthrough) - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - #else - #define CYTHON_FALLTHROUGH - #endif - #endif - #if defined(__clang__ ) && defined(__apple_build_version__) - #if __apple_build_version__ < 7000000 - #undef CYTHON_FALLTHROUGH - #define CYTHON_FALLTHROUGH - #endif - #endif -#endif - -#ifndef CYTHON_INLINE - #if defined(__clang__) - #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) - #elif defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline - #else - #define CYTHON_INLINE - #endif -#endif - -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_DefaultClassType PyType_Type -#if PY_VERSION_HEX >= 0x030B00A1 - static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f, - PyObject *code, PyObject *c, PyObject* n, PyObject *v, - PyObject *fv, PyObject *cell, PyObject* fn, - PyObject *name, int fline, PyObject *lnos) { - PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; - PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; - const char *fn_cstr=NULL; - const char *name_cstr=NULL; - PyCodeObject* co=NULL; - PyObject *type, *value, *traceback; - PyErr_Fetch(&type, &value, &traceback); - if (!(kwds=PyDict_New())) goto end; - if (!(argcount=PyLong_FromLong(a))) goto end; - if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; - if (!(posonlyargcount=PyLong_FromLong(0))) goto end; - if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; - if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; - if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; - if (!(nlocals=PyLong_FromLong(l))) goto end; - if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; - if (!(stacksize=PyLong_FromLong(s))) goto end; - if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; - if (!(flags=PyLong_FromLong(f))) goto end; - if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; - if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; - if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; - if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; - if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; - if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; - if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here - if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; - Py_XDECREF((PyObject*)co); - co = (PyCodeObject*)call_result; - call_result = NULL; - if (0) { - cleanup_code_too: - Py_XDECREF((PyObject*)co); - co = NULL; - } - end: - Py_XDECREF(kwds); - Py_XDECREF(argcount); - Py_XDECREF(posonlyargcount); - Py_XDECREF(kwonlyargcount); - Py_XDECREF(nlocals); - Py_XDECREF(stacksize); - Py_XDECREF(replace); - Py_XDECREF(call_result); - Py_XDECREF(empty); - if (type) { - PyErr_Restore(type, value, traceback); - } - return co; - } -#else - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_STACKLESS - #define METH_STACKLESS 0 -#endif -#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) - #ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - #endif - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); - typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast - #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1 - #define PyMem_RawMalloc(n) PyMem_Malloc(n) - #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) - #define PyMem_RawFree(p) PyMem_Free(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#elif PY_VERSION_HEX >= 0x03060000 - #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() -#elif PY_VERSION_HEX >= 0x03000000 - #define __Pyx_PyThreadState_Current PyThreadState_GET() -#else - #define __Pyx_PyThreadState_Current _PyThreadState_Current -#endif -#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) -#include "pythread.h" -#define Py_tss_NEEDS_INIT 0 -typedef int Py_tss_t; -static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { - *key = PyThread_create_key(); - return 0; -} -static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { - Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); - *key = Py_tss_NEEDS_INIT; - return key; -} -static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { - PyObject_Free(key); -} -static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { - return *key != Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { - PyThread_delete_key(*key); - *key = Py_tss_NEEDS_INIT; -} -static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { - return PyThread_set_key_value(*key, value); -} -static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { - return PyThread_get_key_value(*key); -} -#endif -#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized) -#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) -#else -#define __Pyx_PyDict_NewPresized(n) PyDict_New() -#endif -#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION - #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) -#else - #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) -#endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS -#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) -#else -#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_READY(op) (0) - #else - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #endif - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #if PY_VERSION_HEX >= 0x030C0000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) - #else - #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000 - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) - #else - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) - #endif - #endif -#else - #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 - #define __Pyx_PyUnicode_READY(op) (0) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) - #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) - #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) - #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) -#endif -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) -#else - #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ - PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) -#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) -#if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) -#else - #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) -#endif -#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII) - #define PyObject_ASCII(o) PyObject_Repr(o) -#endif -#if PY_MAJOR_VERSION >= 3 - #define PyBaseString_Type PyUnicode_Type - #define PyStringObject PyUnicodeObject - #define PyString_Type PyUnicode_Type - #define PyString_Check PyUnicode_Check - #define PyString_CheckExact PyUnicode_CheckExact -#ifndef PyObject_Unicode - #define PyObject_Unicode PyObject_Str -#endif -#endif -#if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) - #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) -#else - #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) - #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) -#endif -#ifndef PySet_CheckExact - #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) -#endif -#if PY_VERSION_HEX >= 0x030900A4 - #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt) - #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size) -#else - #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt) - #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size) -#endif -#if CYTHON_ASSUME_SAFE_MACROS - #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) -#else - #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq) -#endif -#if PY_MAJOR_VERSION >= 3 - #define PyIntObject PyLongObject - #define PyInt_Type PyLong_Type - #define PyInt_Check(op) PyLong_Check(op) - #define PyInt_CheckExact(op) PyLong_CheckExact(op) - #define PyInt_FromString PyLong_FromString - #define PyInt_FromUnicode PyLong_FromUnicode - #define PyInt_FromLong PyLong_FromLong - #define PyInt_FromSize_t PyLong_FromSize_t - #define PyInt_FromSsize_t PyLong_FromSsize_t - #define PyInt_AsLong PyLong_AsLong - #define PyInt_AS_LONG PyLong_AS_LONG - #define PyInt_AsSsize_t PyLong_AsSsize_t - #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask - #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask - #define PyNumber_Int PyNumber_Long -#endif -#if PY_MAJOR_VERSION >= 3 - #define PyBoolObject PyLongObject -#endif -#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY - #ifndef PyUnicode_InternFromString - #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) - #endif -#endif -#if PY_VERSION_HEX < 0x030200A4 - typedef long Py_hash_t; - #define __Pyx_PyInt_FromHash_t PyInt_FromLong - #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsHash_t -#else - #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t - #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsSsize_t -#endif -#if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyMethod_New(func, self, klass) ((self) ? 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- default_encoding_c = PyBytes_AsString(default_encoding); - if (!default_encoding_c) goto bad; - if (strcmp(default_encoding_c, "ascii") == 0) { - __Pyx_sys_getdefaultencoding_not_ascii = 0; - } else { - char ascii_chars[128]; - int c; - for (c = 0; c < 128; c++) { - ascii_chars[c] = c; - } - __Pyx_sys_getdefaultencoding_not_ascii = 1; - ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); - if (!ascii_chars_u) goto bad; - ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); - if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { - PyErr_Format( - PyExc_ValueError, - "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", - default_encoding_c); - goto bad; - } - Py_DECREF(ascii_chars_u); - Py_DECREF(ascii_chars_b); - } - Py_DECREF(default_encoding); - return 0; -bad: - Py_XDECREF(default_encoding); - Py_XDECREF(ascii_chars_u); 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-static const char __pyx_k_cite_module[] = "cite_module"; -static const char __pyx_k_description[] = "description"; -static const char __pyx_k_InnerProduct[] = "InnerProduct"; -static const char __pyx_k_SyzSzymSyySzz2[] = "SyzSzymSyySzz2"; -static const char __pyx_k_Sxy2Sxz2Syx2Szx2[] = "Sxy2Sxz2Syx2Szx2"; -static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; -static const char __pyx_k_Sxx2Syy2Szz2Syz2Szy2[] = "Sxx2Syy2Szz2Syz2Szy2"; -static const char __pyx_k_MDAnalysis_lib_qcprot[] = "MDAnalysis.lib.qcprot"; -static const char __pyx_k_QCProt_implementation[] = "QCProt implementation"; -static const char __pyx_k_FastCalcRMSDAndRotation[] = "FastCalcRMSDAndRotation"; -static const char __pyx_k_CalcRMSDRotationalMatrix[] = "CalcRMSDRotationalMatrix"; -static const char __pyx_k_10_1107_s0108767305015266[] = "10.1107/s0108767305015266"; -static const char __pyx_k_MDAnalysis_lib_qcprot_pyx[] = "MDAnalysis\\lib\\qcprot.pyx"; -static const char __pyx_k_Fast_QCP_RMSD_structure_alignme[] = "\nFast QCP RMSD structure alignment --- :mod:`MDAnalysis.lib.qcprot`\n==================================================================\n\n:Author: Joshua L. Adelman, University of Pittsburgh\n:Author: Robert R. Delgado, Cornell University and Arizona State University\n:Contact: jla65@pitt.edu\n:Year: 2011, 2016\n:Licence: BSD\n\nPyQCPROT_ is a python/cython implementation of Douglas Theobald's QCP\nmethod for calculating the minimum RMSD between two structures\n[Theobald2005]_ and determining the optimal least-squares rotation\nmatrix [Liu2010]_.\n\nA full description of the method, along with the original C implementation can\nbe found at http://theobald.brandeis.edu/qcp/\n\nSee Also\n--------\nMDAnalysis.analysis.align:\n Align structures using :func:`CalcRMSDRotationalMatrix`\nMDAnalysis.analysis.rms.rmsd:\n Calculate the RMSD between two structures using\n :func:`CalcRMSDRotationalMatrix`\n\n\n.. versionchanged:: 0.16.0\n Call signatures were changed to directly interface with MDAnalysis\n coordinate arrays: shape (N, 3)\n\nReferences\n----------\n\nIf you use this QCP rotation calculation method in a publication, please\nreference:\n\n.. [Theobald2005] Douglas L. Theobald (2005)\n \"Rapid calculation of RMSD using a quaternion-based characteristic\n polynomial.\" Acta Crystallographica A 61(4):478-480.\n\n.. [Liu2010] Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2010)\n \"Fast determination of the optimal rotational matrix for macromolecular\n superpositions.\" J. Comput. Chem. 31, 1561-1563.\n\n.. _PyQCPROT: https://github.com/synapticarbors/pyqcprot\n\n\nFunctions\n---------\n\nUsers will typically use the :func:`CalcRMSDRotationalMatrix` function.\n\n.. autofunction:: CalcRMSDRotationalMatrix\n\n.. autofunction:: InnerProduct\n\n.. autofunction:: FastCalcRMSDAndRotation\n\n"; -static const char __pyx_k_article_qcprot2_author_Pu_Liu_a[] = "@article{qcprot2,\nauthor = {Pu Liu and Dimitris K. Agrafiotis and Douglas L. 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- - /* "MDAnalysis/lib/qcprot.pyx":464 - * # uncommented, but it is most likely unnecessary. - * - * if (qsqr < evecprec): # <<<<<<<<<<<<<< - * q1 = a12*a3344_4334 - a13*a3244_4234 + a14*a3243_4233 - * q2 = -a11*a3344_4334 + a13*a3144_4134 - a14*a3143_4133 - */ - __pyx_t_11 = ((__pyx_v_qsqr < __pyx_v_evecprec) != 0); - if (__pyx_t_11) { - - /* "MDAnalysis/lib/qcprot.pyx":465 - * - * if (qsqr < evecprec): - * q1 = a12*a3344_4334 - a13*a3244_4234 + a14*a3243_4233 # <<<<<<<<<<<<<< - * q2 = -a11*a3344_4334 + a13*a3144_4134 - a14*a3143_4133 - * q3 = a11*a3244_4234 - a12*a3144_4134 + a14*a3142_4132 - */ - __pyx_v_q1 = (((__pyx_v_a12 * __pyx_v_a3344_4334) - (__pyx_v_a13 * __pyx_v_a3244_4234)) + (__pyx_v_a14 * __pyx_v_a3243_4233)); - - /* "MDAnalysis/lib/qcprot.pyx":466 - * if (qsqr < evecprec): - * q1 = a12*a3344_4334 - a13*a3244_4234 + a14*a3243_4233 - * q2 = -a11*a3344_4334 + a13*a3144_4134 - a14*a3143_4133 # <<<<<<<<<<<<<< - * q3 = a11*a3244_4234 - a12*a3144_4134 + a14*a3142_4132 - * q4 = -a11*a3243_4233 + a12*a3143_4133 - a13*a3142_4132 - */ - __pyx_v_q2 = ((((-__pyx_v_a11) * __pyx_v_a3344_4334) + (__pyx_v_a13 * __pyx_v_a3144_4134)) - (__pyx_v_a14 * __pyx_v_a3143_4133)); - - /* "MDAnalysis/lib/qcprot.pyx":467 - * q1 = a12*a3344_4334 - a13*a3244_4234 + a14*a3243_4233 - * q2 = -a11*a3344_4334 + a13*a3144_4134 - a14*a3143_4133 - * q3 = a11*a3244_4234 - a12*a3144_4134 + a14*a3142_4132 # <<<<<<<<<<<<<< - * q4 = -a11*a3243_4233 + a12*a3143_4133 - a13*a3142_4132 - * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 - */ - __pyx_v_q3 = (((__pyx_v_a11 * __pyx_v_a3244_4234) - (__pyx_v_a12 * __pyx_v_a3144_4134)) + (__pyx_v_a14 * __pyx_v_a3142_4132)); - - /* "MDAnalysis/lib/qcprot.pyx":468 - * q2 = -a11*a3344_4334 + a13*a3144_4134 - a14*a3143_4133 - * q3 = a11*a3244_4234 - a12*a3144_4134 + a14*a3142_4132 - * q4 = -a11*a3243_4233 + a12*a3143_4133 - a13*a3142_4132 # <<<<<<<<<<<<<< - * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 - * - */ - __pyx_v_q4 = ((((-__pyx_v_a11) * __pyx_v_a3243_4233) + (__pyx_v_a12 * __pyx_v_a3143_4133)) - (__pyx_v_a13 * __pyx_v_a3142_4132)); - - /* "MDAnalysis/lib/qcprot.pyx":469 - * q3 = a11*a3244_4234 - a12*a3144_4134 + a14*a3142_4132 - * q4 = -a11*a3243_4233 + a12*a3143_4133 - a13*a3142_4132 - * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 # <<<<<<<<<<<<<< - * - * if (qsqr < evecprec): - */ - __pyx_v_qsqr = ((((__pyx_v_q1 * __pyx_v_q1) + (__pyx_v_q2 * __pyx_v_q2)) + (__pyx_v_q3 * __pyx_v_q3)) + (__pyx_v_q4 * __pyx_v_q4)); 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- if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; - } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } - } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; -} -static PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number, ndim; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ndim = ctx->head->field->type->ndim; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; - } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; - } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; - } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; -} -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_Is_Little_Endian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; - } - break; - case '}': - { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } - } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; - } - CYTHON_FALLTHROUGH; - case '?': case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if ((ctx->enc_type == *ts) && (got_Z == ctx->is_complex) && - (ctx->enc_packmode == ctx->new_packmode) && (!ctx->is_valid_array)) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - CYTHON_FALLTHROUGH; - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: - { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; - } - } - } -} - -/* BufferGetAndValidate */ - static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { - if (unlikely(info->buf == NULL)) return; - if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; - __Pyx_ReleaseBuffer(info); -} -static void __Pyx_ZeroBuffer(Py_buffer* buf) { - buf->buf = NULL; - buf->obj = NULL; - buf->strides = __Pyx_zeros; - buf->shape = __Pyx_zeros; - buf->suboffsets = __Pyx_minusones; -} -static int __Pyx__GetBufferAndValidate( - Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, - int nd, int cast, __Pyx_BufFmt_StackElem* stack) -{ - buf->buf = NULL; - if (unlikely(__Pyx_GetBuffer(obj, buf, flags) == -1)) { - __Pyx_ZeroBuffer(buf); - return -1; - } - if (unlikely(buf->ndim != nd)) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - nd, buf->ndim); - goto fail; - } - if (!cast) { - __Pyx_BufFmt_Context ctx; - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; - } - if (unlikely((size_t)buf->itemsize != dtype->size)) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", - buf->itemsize, (buf->itemsize > 1) ? "s" : "", - dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; - return 0; -fail:; - __Pyx_SafeReleaseBuffer(buf); - return -1; -} - -/* PyErrFetchRestore */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -} -#endif - -/* PyDictVersioning */ - #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; -} -static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) { - PyObject **dictptr = NULL; - Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset; - if (offset) { -#if CYTHON_COMPILING_IN_CPYTHON - dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj); -#else - dictptr = _PyObject_GetDictPtr(obj); -#endif - } - return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; -} -static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) - return 0; - return obj_dict_version == __Pyx_get_object_dict_version(obj); -} -#endif - -/* GetModuleGlobalName */ - #if CYTHON_USE_DICT_VERSIONS -static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value) -#else -static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name) -#endif -{ - PyObject *result; -#if !CYTHON_AVOID_BORROWED_REFS -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 - result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } else if (unlikely(PyErr_Occurred())) { - return NULL; - } -#else - result = PyDict_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } -#endif -#else - result = PyObject_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } - PyErr_Clear(); -#endif - return __Pyx_GetBuiltinName(name); -} - -/* PyObjectCall */ - #if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { - PyObject *result; - ternaryfunc call = Py_TYPE(func)->tp_call; - if (unlikely(!call)) - return PyObject_Call(func, arg, kw); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = (*call)(func, arg, kw); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* ExtTypeTest */ - static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(__Pyx_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* PyFunctionFastCall */ - #if CYTHON_FAST_PYCALL -static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, - PyObject *globals) { - PyFrameObject *f; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject **fastlocals; - Py_ssize_t i; - PyObject *result; - assert(globals != NULL); - /* XXX Perhaps we should create a specialized - PyFrame_New() that doesn't take locals, but does - take builtins without sanity checking them. - */ - assert(tstate != NULL); - f = PyFrame_New(tstate, co, globals, NULL); - if (f == NULL) { - return NULL; - } - fastlocals = __Pyx_PyFrame_GetLocalsplus(f); - for (i = 0; i < na; i++) { - Py_INCREF(*args); - fastlocals[i] = *args++; - } - result = PyEval_EvalFrameEx(f,0); - ++tstate->recursion_depth; - Py_DECREF(f); - --tstate->recursion_depth; - return result; -} -#if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { - PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); - PyObject *globals = PyFunction_GET_GLOBALS(func); - PyObject *argdefs = PyFunction_GET_DEFAULTS(func); - PyObject *closure; -#if PY_MAJOR_VERSION >= 3 - PyObject *kwdefs; -#endif - PyObject *kwtuple, **k; - PyObject **d; - Py_ssize_t nd; - Py_ssize_t nk; - PyObject *result; - assert(kwargs == NULL || PyDict_Check(kwargs)); - nk = kwargs ? PyDict_Size(kwargs) : 0; - if (Py_EnterRecursiveCall((char*)" while calling a Python object")) { - return NULL; - } - if ( -#if PY_MAJOR_VERSION >= 3 - co->co_kwonlyargcount == 0 && -#endif - likely(kwargs == NULL || nk == 0) && - co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { - if (argdefs == NULL && co->co_argcount == nargs) { - result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); - goto done; - } - else if (nargs == 0 && argdefs != NULL - && co->co_argcount == Py_SIZE(argdefs)) { - /* function called with no arguments, but all parameters have - a default value: use default values as arguments .*/ - args = &PyTuple_GET_ITEM(argdefs, 0); - result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); - goto done; - } - } - if (kwargs != NULL) { - Py_ssize_t pos, i; - kwtuple = PyTuple_New(2 * nk); - if (kwtuple == NULL) { - result = NULL; - goto done; - } - k = &PyTuple_GET_ITEM(kwtuple, 0); - pos = i = 0; - while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { - Py_INCREF(k[i]); - Py_INCREF(k[i+1]); - i += 2; - } - nk = i / 2; - } - else { - kwtuple = NULL; - k = NULL; - } - closure = PyFunction_GET_CLOSURE(func); -#if PY_MAJOR_VERSION >= 3 - kwdefs = PyFunction_GET_KW_DEFAULTS(func); -#endif - if (argdefs != NULL) { - d = &PyTuple_GET_ITEM(argdefs, 0); - nd = Py_SIZE(argdefs); - } - else { - d = NULL; - nd = 0; - } -#if PY_MAJOR_VERSION >= 3 - result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, kwdefs, closure); -#else - result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, closure); -#endif - Py_XDECREF(kwtuple); -done: - Py_LeaveRecursiveCall(); - return result; -} -#endif -#endif - -/* PyCFunctionFastCall */ - #if CYTHON_FAST_PYCCALL -static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) { - PyCFunctionObject *func = (PyCFunctionObject*)func_obj; - PyCFunction meth = PyCFunction_GET_FUNCTION(func); - PyObject *self = PyCFunction_GET_SELF(func); - int flags = PyCFunction_GET_FLAGS(func); - assert(PyCFunction_Check(func)); - assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))); - assert(nargs >= 0); - assert(nargs == 0 || args != NULL); - /* _PyCFunction_FastCallDict() must not be called with an exception set, - because it may clear it (directly or indirectly) and so the - caller loses its exception */ - assert(!PyErr_Occurred()); - if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) { - return (*((__Pyx_PyCFunctionFastWithKeywords)(void*)meth)) (self, args, nargs, NULL); - } else { - return (*((__Pyx_PyCFunctionFast)(void*)meth)) (self, args, nargs); - } -} -#endif - -/* PyObjectCall2Args */ - static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { - PyObject *args, *result = NULL; - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyFunction_FastCall(function, args, 2); - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyCFunction_FastCall(function, args, 2); - } - #endif - args = PyTuple_New(2); - if (unlikely(!args)) goto done; - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 0, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 1, arg2); - Py_INCREF(function); - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); -done: - return result; -} - -/* PyObjectCallMethO */ - #if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { - PyObject *self, *result; - PyCFunction cfunc; - cfunc = PyCFunction_GET_FUNCTION(func); - self = PyCFunction_GET_SELF(func); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = cfunc(self, arg); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallOneArg */ - #if CYTHON_COMPILING_IN_CPYTHON -static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_New(1); - if (unlikely(!args)) return NULL; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif - if (likely(PyCFunction_Check(func))) { - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (__Pyx_PyFastCFunction_Check(func)) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } - } - return __Pyx__PyObject_CallOneArg(func, arg); -} -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -#endif - -/* BufferIndexError */ - static void __Pyx_RaiseBufferIndexError(int axis) { - PyErr_Format(PyExc_IndexError, - "Out of bounds on buffer access (axis %d)", axis); -} - -/* GetTopmostException */ - #if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* PyErrExceptionMatches */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; icurexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - if (unlikely(PyTuple_Check(err))) - return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); - return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* GetException */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* RaiseException */ - #if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - if (cause) { - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType -#define __PYX_HAVE_RT_ImportType -static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name, - size_t size, enum __Pyx_ImportType_CheckSize check_size) -{ - PyObject *result = 0; - char warning[200]; - Py_ssize_t basicsize; -#ifdef Py_LIMITED_API - PyObject *py_basicsize; -#endif - result = PyObject_GetAttrString(module, class_name); - if (!result) - goto bad; - if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, - "%.200s.%.200s is not a type object", - module_name, class_name); - goto bad; - } -#ifndef Py_LIMITED_API - basicsize = ((PyTypeObject *)result)->tp_basicsize; -#else - py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); - if (!py_basicsize) - goto bad; - basicsize = PyLong_AsSsize_t(py_basicsize); - Py_DECREF(py_basicsize); - py_basicsize = 0; - if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) - goto bad; -#endif - if ((size_t)basicsize < size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) { - PyErr_Format(PyExc_ValueError, - "%.200s.%.200s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - goto bad; - } - else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. " - "Expected %zd from C header, got %zd from PyObject", - module_name, class_name, size, basicsize); - if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - } - return (PyTypeObject *)result; -bad: - Py_XDECREF(result); - return NULL; -} -#endif - -/* Import */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_MAJOR_VERSION < 3 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_MAJOR_VERSION < 3 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* ImportFrom */ - static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { - PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); - if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_Format(PyExc_ImportError, - #if PY_MAJOR_VERSION < 3 - "cannot import name %.230s", PyString_AS_STRING(name)); - #else - "cannot import name %S", name); - #endif - } - return value; -} - -/* CLineInTraceback */ - #ifndef CYTHON_CLINE_IN_TRACEBACK -static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { - PyObject *use_cline; - PyObject *ptype, *pvalue, *ptraceback; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject **cython_runtime_dict; -#endif - if (unlikely(!__pyx_cython_runtime)) { - return c_line; - } - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); -#if CYTHON_COMPILING_IN_CPYTHON - cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); - if (likely(cython_runtime_dict)) { - __PYX_PY_DICT_LOOKUP_IF_MODIFIED( - use_cline, *cython_runtime_dict, - __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) - } else -#endif - { - PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); - if (use_cline_obj) { - use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; - Py_DECREF(use_cline_obj); - } else { - PyErr_Clear(); - use_cline = NULL; - } - } - if (!use_cline) { - c_line = 0; - (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); - } - else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { - c_line = 0; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - return c_line; -} -#endif - -/* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ - #include "compile.h" -#include "frameobject.h" -#include "traceback.h" -#if PY_VERSION_HEX >= 0x030b00a6 - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = NULL; - PyObject *py_funcname = NULL; - #if PY_MAJOR_VERSION < 3 - PyObject *py_srcfile = NULL; - py_srcfile = PyString_FromString(filename); - if (!py_srcfile) goto bad; - #endif - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - if (!py_funcname) goto bad; - funcname = PyUnicode_AsUTF8(py_funcname); - if (!funcname) goto bad; - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - if (!py_funcname) goto bad; - #endif - } - #if PY_MAJOR_VERSION < 3 - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - #else - py_code = PyCode_NewEmpty(filename, funcname, py_line); - #endif - Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline - return py_code; -bad: - Py_XDECREF(py_funcname); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(py_srcfile); - #endif - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject *ptype, *pvalue, *ptraceback; - if (c_line) { - c_line = __Pyx_CLineForTraceback(tstate, c_line); - } - py_code = __pyx_find_code_object(c_line ? -c_line : py_line); - if (!py_code) { - __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) { - /* If the code object creation fails, then we should clear the - fetched exception references and propagate the new exception */ - Py_XDECREF(ptype); - Py_XDECREF(pvalue); - Py_XDECREF(ptraceback); - goto bad; - } - __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); - __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); - } - py_frame = PyFrame_New( - tstate, /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - if ((0)) {} - view->obj = NULL; - Py_DECREF(obj); -} -#endif - - - /* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return ::std::complex< float >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - return x + y*(__pyx_t_float_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { - __pyx_t_float_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = (float)(1.0) / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = (float)(1.0) / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { - __pyx_t_float_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrtf(z.real*z.real + z.imag*z.imag); - #else - return hypotf(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - __pyx_t_float_complex z; - float r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - float denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_float(a, a); - case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); - case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_float(a); - theta = atan2f(a.imag, a.real); - } - lnr = logf(r); - z_r = expf(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cosf(z_theta); - z.imag = z_r * sinf(z_theta); - return z; - } - #endif -#endif - -/* Declarations */ - #if CYTHON_CCOMPLEX - #ifdef __cplusplus - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return ::std::complex< double >(x, y); - } - #else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - return x + y*(__pyx_t_double_complex)_Complex_I; - } - #endif -#else - static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { - __pyx_t_double_complex z; - z.real = x; - z.imag = y; - return z; - } -#endif - -/* Arithmetic */ - #if CYTHON_CCOMPLEX -#else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - return (a.real == b.real) && (a.imag == b.imag); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real + b.real; - z.imag = a.imag + b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real - b.real; - z.imag = a.imag - b.imag; - return z; - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - z.real = a.real * b.real - a.imag * b.imag; - z.imag = a.real * b.imag + a.imag * b.real; - return z; - } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = (double)(1.0) / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = (double)(1.0) / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } - } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = -a.real; - z.imag = -a.imag; - return z; - } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { - return (a.real == 0) && (a.imag == 0); - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { - __pyx_t_double_complex z; - z.real = a.real; - z.imag = -a.imag; - return z; - } - #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { - #if !defined(HAVE_HYPOT) || defined(_MSC_VER) - return sqrt(z.real*z.real + z.imag*z.imag); - #else - return hypot(z.real, z.imag); - #endif - } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - __pyx_t_double_complex z; - double r, lnr, theta, z_r, z_theta; - if (b.imag == 0 && b.real == (int)b.real) { - if (b.real < 0) { - double denom = a.real * a.real + a.imag * a.imag; - a.real = a.real / denom; - a.imag = -a.imag / denom; - b.real = -b.real; - } - switch ((int)b.real) { - case 0: - z.real = 1; - z.imag = 0; - return z; - case 1: - return a; - case 2: - return __Pyx_c_prod_double(a, a); - case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); - case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); - } - } - if (a.imag == 0) { - if (a.real == 0) { - return a; - } else if ((b.imag == 0) && (a.real >= 0)) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0.0, -1.0); - } - } else { - r = __Pyx_c_abs_double(a); - theta = atan2(a.imag, a.real); - } - lnr = log(r); - z_r = exp(lnr * b.real - theta * b.imag); - z_theta = theta * b.real + lnr * b.imag; - z.real = z_r * cos(z_theta); - z.imag = z_r * sin(z_theta); - return z; - } - #endif -#endif - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const int neg_one = (int) -1, const_zero = (int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE unsigned int __Pyx_PyInt_As_unsigned_int(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const unsigned int neg_one = (unsigned int) -1, const_zero = (unsigned int) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(unsigned int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(unsigned int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (unsigned int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (unsigned int) 0; - case 1: __PYX_VERIFY_RETURN_INT(unsigned int, digit, digits[0]) - case 2: - if (8 * sizeof(unsigned int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(unsigned int) >= 2 * PyLong_SHIFT) { - return (unsigned int) (((((unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(unsigned int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(unsigned int) >= 3 * PyLong_SHIFT) { - return (unsigned int) (((((((unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(unsigned int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(unsigned int) >= 4 * PyLong_SHIFT) { - return (unsigned int) (((((((((unsigned int)digits[3]) << PyLong_SHIFT) | (unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (unsigned int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(unsigned int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(unsigned int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(unsigned int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(unsigned int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (unsigned int) 0; - case -1: __PYX_VERIFY_RETURN_INT(unsigned int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(unsigned int, digit, +digits[0]) - case -2: - if (8 * sizeof(unsigned int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(unsigned int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(unsigned int) - 1 > 2 * PyLong_SHIFT) { - return (unsigned int) (((unsigned int)-1)*(((((unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(unsigned int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(unsigned int) - 1 > 2 * PyLong_SHIFT) { - return (unsigned int) ((((((unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(unsigned int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(unsigned int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(unsigned int) - 1 > 3 * PyLong_SHIFT) { - return (unsigned int) (((unsigned int)-1)*(((((((unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(unsigned int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(unsigned int) - 1 > 3 * PyLong_SHIFT) { - return (unsigned int) ((((((((unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(unsigned int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(unsigned int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(unsigned int) - 1 > 4 * PyLong_SHIFT) { - return (unsigned int) (((unsigned int)-1)*(((((((((unsigned int)digits[3]) << PyLong_SHIFT) | (unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(unsigned int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(unsigned int) - 1 > 4 * PyLong_SHIFT) { - return (unsigned int) ((((((((((unsigned int)digits[3]) << PyLong_SHIFT) | (unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(unsigned int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(unsigned int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(unsigned int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(unsigned int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - unsigned int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (unsigned int) -1; - } - } else { - unsigned int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (unsigned int) -1; - val = __Pyx_PyInt_As_unsigned_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to unsigned int"); - return (unsigned int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to unsigned int"); - return (unsigned int) -1; -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* FastTypeChecks */ - #if CYTHON_COMPILING_IN_CPYTHON -static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { - while (a) { - a = a->tp_base; - if (a == b) - return 1; - } - return b == &PyBaseObject_Type; -} -static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { - PyObject *mro; - if (a == b) return 1; - mro = a->tp_mro; - if (likely(mro)) { - Py_ssize_t i, n; - n = PyTuple_GET_SIZE(mro); - for (i = 0; i < n; i++) { - if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) - return 1; - } - return 0; - } - return __Pyx_InBases(a, b); -} -#if PY_MAJOR_VERSION == 2 -static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { - PyObject *exception, *value, *tb; - int res; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&exception, &value, &tb); - res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - if (!res) { - res = PyObject_IsSubclass(err, exc_type2); - if (unlikely(res == -1)) { - PyErr_WriteUnraisable(err); - res = 0; - } - } - __Pyx_ErrRestore(exception, value, tb); - return res; -} -#else -static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { - int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; - if (!res) { - res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); - } - return res; -} -#endif -static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { - Py_ssize_t i, n; - assert(PyExceptionClass_Check(exc_type)); - n = PyTuple_GET_SIZE(tuple); -#if PY_MAJOR_VERSION >= 3 - for (i=0; i '9'); - break; - } - if (rt_from_call[i] != ctversion[i]) { - same = 0; - break; - } - } - if (!same) { - char rtversion[5] = {'\0'}; - char message[200]; - for (i=0; i<4; ++i) { - if (rt_from_call[i] == '.') { - if (found_dot) break; - found_dot = 1; - } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') { - break; - } - rtversion[i] = rt_from_call[i]; - } - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* InitStrings */ - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - if (PyObject_Hash(*t->p) == -1) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT -#if !CYTHON_PEP393_ENABLED -static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); 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J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, -# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. -# MDAnalysis: A Python package for the rapid analysis of molecular dynamics -# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th -# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. -# doi: 10.25080/majora-629e541a-00e -# -# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. -# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. -# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 -# -from contextlib import contextmanager - -import MDAnalysis as mda -import MDAnalysis.analysis.align as align -import MDAnalysis.analysis.rms as rms -import os -import numpy as np -import pytest -from MDAnalysis import SelectionError, SelectionWarning -from MDAnalysisTests import executable_not_found -from MDAnalysisTests.datafiles import (PSF, DCD, CRD, FASTA, ALIGN_BOUND, - ALIGN_UNBOUND, PDB_helix) -from numpy.testing import ( - assert_almost_equal, - assert_equal, - assert_array_equal, - assert_array_almost_equal, - assert_allclose, -) - -#Function for Parametrizing conditional raising -@contextmanager -def does_not_raise(): - yield - -class TestRotationMatrix(object): - a = np.array([[0.1, 0.2, 0.3], [1.1, 1.1, 1.1]]) - b = np.array([[0.1, 0.1, 0.1], [1.1, 1.1, 1.1]]) - w = np.array([1.3, 2.3]) - - @pytest.mark.parametrize('a, b, weights', ( - (a, b, None), - (a, b, w), - (a.astype(int), b.astype(int), w.astype(np.float32)) - )) - def test_rotation_matrix_input(self, a, b, weights): - rot, rmsd = align.rotation_matrix(a, b, weights) - assert_equal(rot, np.eye(3)) - assert rmsd is None - - def test_list_args(self): - a = [[0.1, 0.2, 0.3], [1.1, 1.1, 1.1]] - b = [[0.1, 0.1, 0.1], [1.1, 1.1, 1.1]] - w = [1.3, 2.3] - rot, rmsd = align.rotation_matrix(a, b, w) - assert_equal(rot, np.eye(3)) - assert rmsd is None - - def test_exception(self): - a = [[0.1, 0.2, 0.3], - [1.1, 1.1, 1.1], - [2, 2, 2]] - b = [[0.1, 0.1, 0.1], - [1.1, 1.1, 1.1]] - with pytest.raises(ValueError): - align.rotation_matrix(a, b) - - -class TestGetMatchingAtoms(object): - @staticmethod - @pytest.fixture() - def universe(): - return mda.Universe(PSF, DCD) - - @staticmethod - @pytest.fixture() - def reference(): - return mda.Universe(PSF, DCD) - - @staticmethod - @pytest.fixture() - def reference_small(reference): - return mda.Merge(reference.select_atoms( - "not name H* and not atom 4AKE 1 CA")) - - @pytest.mark.parametrize("strict", (True, False)) - def test_match(self, universe, reference, strict, - selection="protein and backbone"): - ref = reference.select_atoms(selection) - mobile = universe.select_atoms(selection) - groups = align.get_matching_atoms(ref, mobile, strict=strict) - assert_equal(groups[0].names, groups[1].names) - - @pytest.mark.parametrize("strict", (True, False)) - def test_nomatch_atoms_raise(self, universe, reference, - strict, selection="protein and backbone"): - # one atom less but same residues; with strict=False should try - # to get selections (but current code fails, so we also raise SelectionError) - ref = reference.select_atoms(selection).atoms[1:] - mobile = universe.select_atoms(selection) - if strict: - with pytest.raises(SelectionError): - groups = align.get_matching_atoms(ref, mobile, strict=strict) - else: - with pytest.warns(SelectionWarning): - with pytest.raises(SelectionError): - groups = align.get_matching_atoms(ref, mobile, strict=strict) - - @pytest.mark.parametrize("strict", (True, False)) - def test_nomatch_residues_raise_empty(self, universe, reference_small, - strict, selection="protein and backbone"): - # one atom less and all residues different: will currently create - # empty selections with strict=False, see also - # https://gist.github.com/orbeckst/2686badcd15031e6c946baf9164a683d - ref = reference_small.select_atoms(selection) - mobile = universe.select_atoms(selection) - if strict: - with pytest.raises(SelectionError): - groups = align.get_matching_atoms(ref, mobile, strict=strict) - else: - with pytest.warns(SelectionWarning): - with pytest.raises(SelectionError): - groups = align.get_matching_atoms(ref, mobile, strict=strict) - - def test_toggle_atom_mismatch_default_error(self, universe, reference): - selection = ('resname ALA and name CA', 'resname ALA and name O') - with pytest.raises(SelectionError): - rmsd = align.alignto(universe, reference, select=selection) - - def test_toggle_atom_mismatch_kwarg_error(self, universe, reference): - selection = ('resname ALA and name CA', 'resname ALA and name O') - with pytest.raises(SelectionError): - rmsd = align.alignto(universe, reference, select=selection, match_atoms=True) - - def test_toggle_atom_nomatch(self, universe, reference): - selection = ('resname ALA and name CA', 'resname ALA and name O') - rmsd = align.alignto(universe, reference, select=selection, match_atoms=False) - assert rmsd[0] > 0.01 - - def test_toggle_atom_nomatch_mismatch_atoms(self, universe, reference): - # mismatching number of atoms, but same number of residues - u = universe.select_atoms('resname ALA and name CA') - u += universe.select_atoms('resname ALA and name O')[-1] - ref = reference.select_atoms('resname ALA and name CA') - with pytest.raises(SelectionError): - align.alignto(u, ref, select='all', match_atoms=False) - - @pytest.mark.parametrize('subselection, expectation', [ - ('resname ALA and name CA', does_not_raise()), - (mda.Universe(PSF, DCD).select_atoms('resname ALA and name CA'), does_not_raise()), - (1234, pytest.raises(TypeError)), - ]) - def test_subselection_alignto(self, universe, reference, subselection, expectation): - - with expectation: - rmsd = align.alignto(universe, reference, subselection=subselection) - assert_almost_equal(rmsd[1], 0.0, decimal=9) - - def test_no_atom_masses(self, universe): - #if no masses are present - u = mda.Universe.empty(6, 2, atom_resindex=[0, 0, 0, 1, 1, 1], trajectory=True) - with pytest.warns(SelectionWarning): - align.get_matching_atoms(u.atoms, u.atoms) - - def test_one_universe_has_masses(self, universe): - u = mda.Universe.empty(6, 2, atom_resindex=[0, 0, 0, 1, 1, 1], trajectory=True) - ref = mda.Universe.empty(6, 2, atom_resindex=[0, 0, 0, 1, 1, 1], trajectory=True) - ref.add_TopologyAttr('masses') - with pytest.warns(SelectionWarning): - align.get_matching_atoms(u.atoms, ref.atoms) - -class TestAlign(object): - @staticmethod - @pytest.fixture() - def universe(): - return mda.Universe(PSF, DCD) - - @staticmethod - @pytest.fixture() - def reference(): - return mda.Universe(PSF, DCD) - - def test_rmsd(self, universe, reference): - universe.trajectory[0] # ensure first frame - bb = universe.select_atoms('backbone') - first_frame = bb.positions - universe.trajectory[-1] - last_frame = bb.positions - assert_almost_equal(rms.rmsd(first_frame, first_frame), 0.0, 5, - err_msg="error: rmsd(X,X) should be 0") - # rmsd(A,B) = rmsd(B,A) should be exact but spurious failures in the - # 9th decimal have been observed (see Issue 57 comment #1) so we relax - # the test to 6 decimals. - rmsd = rms.rmsd(first_frame, last_frame, superposition=True) - assert_almost_equal( - rms.rmsd(last_frame, first_frame, superposition=True), rmsd, 6, - err_msg="error: rmsd() is not symmetric") - assert_almost_equal(rmsd, 6.820321761927005, 5, - err_msg="RMSD calculation between 1st and last AdK frame gave wrong answer") - # test masses as weights - last_atoms_weight = universe.atoms.masses - A = universe.trajectory[0] - B = reference.trajectory[-1] - rmsd = align.alignto(universe, reference, weights='mass') - rmsd_sup_weight = rms.rmsd(A, B, weights=last_atoms_weight, center=True, - superposition=True) - assert_almost_equal(rmsd[1], rmsd_sup_weight, 6) - - def test_rmsd_custom_mass_weights(self, universe, reference): - last_atoms_weight = universe.atoms.masses - A = universe.trajectory[0] - B = reference.trajectory[-1] - rmsd = align.alignto(universe, reference, - weights=reference.atoms.masses) - rmsd_sup_weight = rms.rmsd(A, B, weights=last_atoms_weight, center=True, - superposition=True) - assert_almost_equal(rmsd[1], rmsd_sup_weight, 6) - - def test_rmsd_custom_weights(self, universe, reference): - weights = np.zeros(universe.atoms.n_atoms) - ca = universe.select_atoms('name CA') - weights[ca.indices] = 1 - rmsd = align.alignto(universe, reference, select='name CA') - rmsd_weights = align.alignto(universe, reference, weights=weights) - assert_almost_equal(rmsd[1], rmsd_weights[1], 6) - - def test_AlignTraj_outfile_default(self, universe, reference, tmpdir): - with tmpdir.as_cwd(): - reference.trajectory[-1] - x = align.AlignTraj(universe, reference) - try: - assert os.path.basename(x.filename) == 'rmsfit_adk_dims.dcd' - finally: - x._writer.close() - - def test_AlignTraj_outfile_default_exists(self, universe, reference, tmpdir): - reference.trajectory[-1] - outfile = str(tmpdir.join('align_test.dcd')) - align.AlignTraj(universe, reference, filename=outfile).run() - fitted = mda.Universe(PSF, outfile) - - # ensure default file exists - with mda.Writer(str(tmpdir.join("rmsfit_align_test.dcd")), - n_atoms=fitted.atoms.n_atoms) as w: - w.write(fitted.atoms) - - with tmpdir.as_cwd(): - align.AlignTraj(fitted, reference) - - # we are careful now. The default does nothing - with pytest.raises(IOError): - align.AlignTraj(fitted, reference, force=False) - - def test_AlignTraj_step_works(self, universe, reference, tmpdir): - reference.trajectory[-1] - outfile = str(tmpdir.join('align_test.dcd')) - # this shouldn't throw an exception - align.AlignTraj(universe, reference, filename=outfile).run(step=10) - - def test_AlignTraj_deprecated_attribute(self, universe, reference, tmpdir): - reference.trajectory[-1] - outfile = str(tmpdir.join('align_test.dcd')) - x = align.AlignTraj(universe, reference, filename=outfile).run(stop=2) - - wmsg = "The `rmsd` attribute was deprecated in MDAnalysis 2.0.0" - with pytest.warns(DeprecationWarning, match=wmsg): - assert_equal(x.rmsd, x.results.rmsd) - - def test_AlignTraj(self, universe, reference, tmpdir): - reference.trajectory[-1] - outfile = str(tmpdir.join('align_test.dcd')) - x = align.AlignTraj(universe, reference, filename=outfile).run() - fitted = mda.Universe(PSF, outfile) - - assert_almost_equal(x.results.rmsd[0], 6.9290, decimal=3) - assert_almost_equal(x.results.rmsd[-1], 5.2797e-07, decimal=3) - - # RMSD against the reference frame - # calculated on Mac OS X x86 with MDA 0.7.2 r689 - # VMD: 6.9378711 - self._assert_rmsd(reference, fitted, 0, 6.929083044751061) - self._assert_rmsd(reference, fitted, -1, 0.0) - - def test_AlignTraj_weighted(self, universe, reference, tmpdir): - outfile = str(tmpdir.join('align_test.dcd')) - x = align.AlignTraj(universe, reference, - filename=outfile, weights='mass').run() - fitted = mda.Universe(PSF, outfile) - assert_almost_equal(x.results.rmsd[0], 0, decimal=3) - assert_almost_equal(x.results.rmsd[-1], 6.9033, decimal=3) - - self._assert_rmsd(reference, fitted, 0, 0.0, - weights=universe.atoms.masses) - self._assert_rmsd(reference, fitted, -1, 6.929083032629219, - weights=universe.atoms.masses) - - def test_AlignTraj_custom_weights(self, universe, reference, tmpdir): - weights = np.zeros(universe.atoms.n_atoms) - ca = universe.select_atoms('name CA') - weights[ca.indices] = 1 - - outfile = str(tmpdir.join('align_test.dcd')) - - x = align.AlignTraj(universe, reference, - filename=outfile, select='name CA').run() - x_weights = align.AlignTraj(universe, reference, - filename=outfile, weights=weights).run() - - assert_array_almost_equal(x.results.rmsd, x_weights.results.rmsd) - - def test_AlignTraj_custom_mass_weights(self, universe, reference, tmpdir): - outfile = str(tmpdir.join('align_test.dcd')) - x = align.AlignTraj(universe, reference, - filename=outfile, - weights=reference.atoms.masses).run() - fitted = mda.Universe(PSF, outfile) - assert_almost_equal(x.results.rmsd[0], 0, decimal=3) - assert_almost_equal(x.results.rmsd[-1], 6.9033, decimal=3) - - self._assert_rmsd(reference, fitted, 0, 0.0, - weights=universe.atoms.masses) - self._assert_rmsd(reference, fitted, -1, 6.929083032629219, - weights=universe.atoms.masses) - - def test_AlignTraj_partial_fit(self, universe, reference, tmpdir): - outfile = str(tmpdir.join('align_test.dcd')) - # fitting on a partial selection should still write the whole topology - align.AlignTraj(universe, reference, select='resid 1-20', - filename=outfile, weights='mass').run() - mda.Universe(PSF, outfile) - - def test_AlignTraj_in_memory(self, universe, reference, tmpdir): - outfile = str(tmpdir.join('align_test.dcd')) - reference.trajectory[-1] - x = align.AlignTraj(universe, reference, filename=outfile, - in_memory=True).run() - assert x.filename is None - assert_almost_equal(x.results.rmsd[0], 6.9290, decimal=3) - assert_almost_equal(x.results.rmsd[-1], 5.2797e-07, decimal=3) - - # check in memory trajectory - self._assert_rmsd(reference, universe, 0, 6.929083044751061) - self._assert_rmsd(reference, universe, -1, 0.0) - - def _assert_rmsd(self, reference, fitted, frame, desired, weights=None): - fitted.trajectory[frame] - rmsd = rms.rmsd(reference.atoms.positions, fitted.atoms.positions, - superposition=True) - assert_almost_equal(rmsd, desired, decimal=5, - err_msg="frame {0:d} of fit does not have " - "expected RMSD".format(frame)) - - def test_alignto_checks_selections(self, universe, reference): - """Testing that alignto() fails if selections do not - match (Issue 143)""" - u = universe - - def different_size(): - a = u.atoms[10:100] - b = u.atoms[10:101] - return align.alignto(a, b) - - with pytest.raises(SelectionError): - different_size() - - def different_atoms(): - a = u.atoms[10:20] - b = u.atoms[10:17] + u.atoms[18:21] - return align.alignto(a, b) - - with pytest.raises(SelectionError): - different_atoms() - - def test_alignto_partial_universe(self, universe, reference): - u_bound = mda.Universe(ALIGN_BOUND) - u_free = mda.Universe(ALIGN_UNBOUND) - selection = 'segid B' - - segB_bound = u_bound.select_atoms(selection) - segB_free = u_free.select_atoms(selection) - segB_free.translate(segB_bound.centroid() - segB_free.centroid()) - - align.alignto(u_free, u_bound, select=selection) - assert_array_almost_equal(segB_bound.positions, segB_free.positions, - decimal=3) - - -def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs): - u = mda.Universe(*ref_files, in_memory=True) - prealigner = align.AlignTraj(u, ref, select=select, **kwargs).run() - ag = u.select_atoms(select) - reference_coordinates = u.trajectory.timeseries(asel=ag).mean(axis=1) - rmsd = sum(prealigner.results.rmsd/len(u.trajectory)) - return reference_coordinates, rmsd - -class TestAverageStructure(object): - - ref_files = (PSF, DCD) - - @pytest.fixture - def universe(self): - return mda.Universe(*self.ref_files) - - @pytest.fixture - def reference(self): - return mda.Universe(PSF, CRD) - - def test_average_structure_deprecated_attrs(self, universe, reference): - # Issue #3278 - remove in MDAnalysis 3.0.0 - avg = align.AverageStructure(universe, reference).run(stop=2) - - wmsg = "The `universe` attribute was deprecated in MDAnalysis 2.0.0" - with pytest.warns(DeprecationWarning, match=wmsg): - assert_equal(avg.universe.atoms.positions, - avg.results.universe.atoms.positions) - - wmsg = "The `positions` attribute was deprecated in MDAnalysis 2.0.0" - with pytest.warns(DeprecationWarning, match=wmsg): - assert_equal(avg.positions, avg.results.positions) - - wmsg = "The `rmsd` attribute was deprecated in MDAnalysis 2.0.0" - with pytest.warns(DeprecationWarning, match=wmsg): - assert avg.rmsd == avg.results.rmsd - - def test_average_structure(self, universe, reference): - ref, rmsd = _get_aligned_average_positions(self.ref_files, reference) - avg = align.AverageStructure(universe, reference).run() - assert_almost_equal(avg.results.universe.atoms.positions, ref, - decimal=4) - assert_almost_equal(avg.results.rmsd, rmsd) - - def test_average_structure_mass_weighted(self, universe, reference): - ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, weights='mass') - avg = align.AverageStructure(universe, reference, weights='mass').run() - assert_almost_equal(avg.results.universe.atoms.positions, ref, - decimal=4) - assert_almost_equal(avg.results.rmsd, rmsd) - - def test_average_structure_select(self, universe, reference): - select = 'protein and name CA and resid 3-5' - ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, select=select) - avg = align.AverageStructure(universe, reference, select=select).run() - assert_almost_equal(avg.results.universe.atoms.positions, ref, - decimal=4) - assert_almost_equal(avg.results.rmsd, rmsd) - - def test_average_structure_no_ref(self, universe): - ref, rmsd = _get_aligned_average_positions(self.ref_files, universe) - avg = align.AverageStructure(universe).run() - assert_almost_equal(avg.results.universe.atoms.positions, ref, - decimal=4) - assert_almost_equal(avg.results.rmsd, rmsd) - - def test_average_structure_no_msf(self, universe): - avg = align.AverageStructure(universe).run() - assert not hasattr(avg, 'msf') - - def test_mismatch_atoms(self, universe): - u = mda.Merge(universe.atoms[:10]) - with pytest.raises(SelectionError): - align.AverageStructure(universe, u) - - def test_average_structure_ref_frame(self, universe): - ref_frame = 3 - u = mda.Merge(universe.atoms) - - # change to ref_frame - universe.trajectory[ref_frame] - u.load_new(universe.atoms.positions) - - # back to start - universe.trajectory[0] - ref, rmsd = _get_aligned_average_positions(self.ref_files, u) - avg = align.AverageStructure(universe, ref_frame=ref_frame).run() - assert_almost_equal(avg.results.universe.atoms.positions, ref, - decimal=4) - assert_almost_equal(avg.results.rmsd, rmsd) - - def test_average_structure_in_memory(self, universe): - avg = align.AverageStructure(universe, in_memory=True).run() - reference_coordinates = universe.trajectory.timeseries().mean(axis=1) - assert_almost_equal(avg.results.universe.atoms.positions, - reference_coordinates, decimal=4) - assert avg.filename is None - - -class TestAlignmentProcessing(object): - seq = FASTA - error_msg = "selection string has unexpected length" - - def test_fasta2select_aligned(self): - """test align.fasta2select() on aligned FASTA (Issue 112)""" - sel = align.fasta2select(self.seq, is_aligned=True) - # length of the output strings, not residues or anything real... - assert len(sel['reference']) == 30623, self.error_msg - assert len(sel['mobile']) == 30623, self.error_msg - - @pytest.mark.skipif(executable_not_found("clustalw2"), - reason="Test skipped because clustalw2 executable not found") - def test_fasta2select_file(self, tmpdir): - """test align.fasta2select() on a non-aligned FASTA with default - filenames""" - with tmpdir.as_cwd(): - sel = align.fasta2select(self.seq, is_aligned=False, - alnfilename=None, treefilename=None) - assert len(sel['reference']) == 23080, self.error_msg - assert len(sel['mobile']) == 23090, self.error_msg - - @pytest.mark.skipif(executable_not_found("clustalw2"), - reason="Test skipped because clustalw2 executable not found") - def test_fasta2select_ClustalW(self, tmpdir): - """MDAnalysis.analysis.align: test fasta2select() with ClustalW - (Issue 113)""" - alnfile = str(tmpdir.join('alignmentprocessing.aln')) - treefile = str(tmpdir.join('alignmentprocessing.dnd')) - sel = align.fasta2select(self.seq, is_aligned=False, - alnfilename=alnfile, treefilename=treefile) - # numbers computed from alignment with clustalw 2.1 on Mac OS X - # [orbeckst] length of the output strings, not residues or anything - # real... - assert len(sel['reference']) == 23080, self.error_msg - assert len(sel['mobile']) == 23090, self.error_msg - - def test_fasta2select_resids(self, tmpdir): - """test align.fasta2select() when resids provided (Issue #3124)""" - resids = [x for x in range(705)] - sel = align.fasta2select(self.seq, is_aligned=True, - ref_resids=resids, target_resids=resids) - # length of the output strings, not residues or anything real... - assert len(sel['reference']) == 30621, self.error_msg - assert len(sel['mobile']) == 30621, self.error_msg - - -class TestSequenceAlignmentFunction: - # remove 3.0 - - @staticmethod - @pytest.fixture - def atomgroups(): - universe = mda.Universe(PSF) - reference = universe.atoms - mobile = universe.select_atoms("resid 122-159") - return reference, mobile - - @pytest.mark.filterwarnings("ignore:`sequence_alignment` is deprecated!") - def test_sequence_alignment(self, atomgroups): - reference, mobile = atomgroups - aln = align.sequence_alignment(mobile, reference) - - assert len(aln) == 5, "return value has wrong tuple size" - - seqA, seqB, score, begin, end = aln - assert_equal(seqA, reference.residues.sequence(format="string"), - err_msg="reference sequence mismatch") - assert mobile.residues.sequence( - format="string") in seqB, "mobile sequence mismatch" - assert score == pytest.approx(54.6) - assert_array_equal([begin, end], [0, reference.n_residues]) - - def test_sequence_alignment_deprecation(self, atomgroups): - reference, mobile = atomgroups - wmsg = ("`sequence_alignment` is deprecated!\n" - "`sequence_alignment` will be removed in release 3.0.") - with pytest.warns(DeprecationWarning, match=wmsg): - align.sequence_alignment(mobile, reference) - - -def test_alignto_reorder_atomgroups(): - # Issue 2977 - u = mda.Universe(PDB_helix) - mobile = u.atoms[:4] - ref = u.atoms[[3, 2, 1, 0]] - rmsd = align.alignto(mobile, ref, select='bynum 1-4') - assert_allclose(rmsd, (0.0, 0.0))