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Preparing for the Release 1.5.0 (#115)
* Fix Elements Database Editor bug (#33) * Correct bug and change sizer and panel usage * Clean up code to PEP8 standard * Reorganise changed code to match the previous style Co-authored-by: Turanyi <[email protected]> * Correct macro name (#37) Co-authored-by: Turanyi <[email protected]> * Update AUTHORS * Update AUTHORS * Use forces instead of gradients (#39) Co-authored-by: Turanyi <[email protected]> * Implement rdf and tcf inside pdf (#40) Co-authored-by: Turanyi <[email protected]> * Fix normalisation in GACF and PACF (#36) * Fix gacf and pacf normalisation * Use normalize funtion in gacf and pacf * Fix bug by removing intermediary variable Co-authored-by: Turanyi <[email protected]> * only the congiguration (and velocities and gradients when available) are written in the output trajectory * bug fixed with the output of a few trajectory converters * added info method to NetCDFInputData added info about the variables stored in a trajectory in MMTKTrajectoryInputData * added time to the variables to be written in output trajectory * bug fix with missing time as output variable for a few converters * Add time to Gromacs and fix typo * 42 improve pane layout in plotter (#55) * Added a splitter window between the dataset and data list of the data panel * added a minimum size for the dataset and data panels of the splitter windows of the plotter * Removed frame sizing * Set back code to previous state Co-authored-by: eric pellegrini <[email protected]> * 28 enhance simple help (#54) * Replaced plain text window by an HTML window for better reading experience of the simple help * Add superscipts * added a missing superscript in simple help html file Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Add User Guide DOI to GUI help menu (#49) Co-authored-by: Turanyi <[email protected]> * Replace outputData reference with correct variables * Remove ability to plot non-meaningful data (#34) * Catch the TypeError and abort autofit * Notification is shown when user initiates invalid autofit * Handle TypeError in add_offset method * Partially clean up code to increase PEP8 compliance * Revert and instead stop before plotting * Remove certain variables from plotting * Fix Elements Database Editor bug (#33) * Correct bug and change sizer and panel usage * Clean up code to PEP8 standard * Reorganise changed code to match the previous style Co-authored-by: Turanyi <[email protected]> * Correct macro name (#37) Co-authored-by: Turanyi <[email protected]> * Update AUTHORS * Update AUTHORS * Use forces instead of gradients (#39) Co-authored-by: Turanyi <[email protected]> * Implement rdf and tcf inside pdf (#40) Co-authored-by: Turanyi <[email protected]> * Fix normalisation in GACF and PACF (#36) * Fix gacf and pacf normalisation * Use normalize funtion in gacf and pacf * Fix bug by removing intermediary variable Co-authored-by: Turanyi <[email protected]> * Prevent plotting of new variables * only the congiguration (and velocities and gradients when available) are written in the output trajectory * bug fixed with the output of a few trajectory converters * added info method to NetCDFInputData added info about the variables stored in a trajectory in MMTKTrajectoryInputData * added time to the variables to be written in output trajectory * bug fix with missing time as output variable for a few converters * Add time to Gromacs and fix typo * 42 improve pane layout in plotter (#55) * Added a splitter window between the dataset and data list of the data panel * added a minimum size for the dataset and data panels of the splitter windows of the plotter * Removed frame sizing * Set back code to previous state Co-authored-by: eric pellegrini <[email protected]> * filtered out the variables which are not of numeric type * Forbid remaining trajectory variables Co-authored-by: Turanyi <[email protected]> Co-authored-by: Sanghamitra Mukhopadhyay <[email protected]> Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: eurydice76 <[email protected]> * Update headers (#47) * Update copyright information inside headers * Revert ILL copyright to 2013-now Co-authored-by: Turanyi <[email protected]> * Implement velocity reading in Gromacs converter via TRR files (#44) * Implement velocity reading from trr * Update .gitignore to exclude trr.c and xtc.c after build * Remove problematic double import and unpack correctly * Fix read method by redefining a constant * Enable reading trr files not containing vels/forces * Remove unused parts of trr module * Change gui label to 'xtc and trr file' * Fix Elements Database Editor bug (#33) * Correct bug and change sizer and panel usage * Clean up code to PEP8 standard * Reorganise changed code to match the previous style Co-authored-by: Turanyi <[email protected]> * Correct macro name (#37) Co-authored-by: Turanyi <[email protected]> * Update AUTHORS * Update AUTHORS * Use forces instead of gradients (#39) Co-authored-by: Turanyi <[email protected]> * Implement rdf and tcf inside pdf (#40) Co-authored-by: Turanyi <[email protected]> * Fix normalisation in GACF and PACF (#36) * Fix gacf and pacf normalisation * Use normalize funtion in gacf and pacf * Fix bug by removing intermediary variable Co-authored-by: Turanyi <[email protected]> * Add tests * only the congiguration (and velocities and gradients when available) are written in the output trajectory * bug fixed with the output of a few trajectory converters * added info method to NetCDFInputData added info about the variables stored in a trajectory in MMTKTrajectoryInputData * added time to the variables to be written in output trajectory * bug fix with missing time as output variable for a few converters * Add time to Gromacs and fix typo * Implement velocity reading from trr * Update .gitignore to exclude trr.c and xtc.c after build * Remove problematic double import and unpack correctly * Fix read method by redefining a constant * Enable reading trr files not containing vels/forces * Remove unused parts of trr module * Add tests * The coords, velocities and forces arrays are now casted to float64 * Clean up Gromacs.py of git dif lines * Update tests to check gradients Co-authored-by: Turanyi <[email protected]> Co-authored-by: Sanghamitra Mukhopadhyay <[email protected]> Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: eurydice76 <[email protected]> * Use existing vars to calculate tcf and rdf * Fixed bug in writing quaternions,com and fit variables in rbt job * Write units in trajectory files (#72) * Fixed typo in Converter.py file * Fixed typo in Converter.py file * Securized the code for writing units in the trajectory file Co-authored-by: eric pellegrini <[email protected]> * Added better securization around the adding of units in Converter.finalize method (#73) Co-authored-by: eric pellegrini <[email protected]> * MD compliant plotter (#61) * Added a new mode for viewing 3D data * Added brand new plugin for viewing trajectory related variables * Added support for unit in TrajectoryViewer plugin cosmetic change in DCDConverter file * Fix bug with 2D slice * Fixed windows-specific bug when doing scalar plot * Added the possibility to remove lines for the TrajectoryViewer plugin * Fixed buggy behavior with the legend Co-authored-by: eric pellegrini <[email protected]> * Make the names of output files more descriptive (#60) * Change output file default name in GUI * Implement incrementing filename for job output * Modified the algorithm for checking already existing filename * Added a mechanism for guessing the output filename for converter analysis * Removed print * Added a new configuration/widget for setting single output file * Update headers of new files to comply with #47 * Update configurator docstrings * Removed useless checking of datakey in set_data method * Renamed OutputFile configurator and widgets to SingleOutputFile Co-authored-by: eric pellegrini <[email protected]> * Add continuous integration using GitHub actions (#20) * Replace buggy py2app qt recipes with correct ones * Change the replacement qt files to always return None * Change qt5.py into a dummy function * Make qt6 a dummy too * Truly make qt6 a dummy too and add netcdf investigation * Place change_dylib_path.sh code into deploy_old.sh * Add investigation and ' to deploy_old.sh * Add more investigation * Add more investigation * Try using -fv with problematic command * Stop using wildcard with cp * Deploy for different ubuntus separately * Deploy for different ubuntus separately * Correct artifact name * Increase investigation * Copy libhdf5 files into artifacts * Try removing arguments from build.py * Restore arguments to build.py * Search ubuntu for libsz * Copy the whole x86_64-linux-gnu file * Use argparse in build.py * Only parse known arguments * Revert, instead hardcode py2app arg and change depends for deb * Try several things and fix syntax error * Correct paths and try sudo * Use source and include parameters * Add osx sphinx investigation and copy libnetcdf on ubuntu * Add more investigation about sphinx * Correct syntax and upload log * Fix yaml indentation * Correct path to sphinx logs * Add further investigation * Always run the copy of sphinx log * Disable the failing sphinx usage for now * Place ' around args * Remove args completely from build.py * Specify version of docutils * Move scripts to the same run as build.py * Create different installers for different versions of ubuntu * Enable ubuntu * Correct ubuntu and use getenv * Enable ubuntu * Use sys.argv * Try solutions to the build.py issue * Try using --argv-inject * Try ways to use --argv-inject correctly * Print sys.argv * Use argv correctly * Remove the extra MDANSE from icon path * Correct path to icons * Create directory before creating file inside it * Add postinst and create installer for ubuntu 21 * Correct postinst path and remove rm * Correct artifact name for ubuntu 21 * Add mising su privilege * Add missing su privileges * Correct ubuntu version, sed permanently and correct postinst * Create Contents/MacOS directory before symlinking into it * Add missing files * Expand amount of places where env vars are exported on ubuntu * Add missing ' * Correct postinst type of ' on ubuntu * Correct env var name * Copy dylibs * Add investigation * Add investigation and add files for fake osx deploy * Correct mistakes and add investigation * Correct path * Copy libwx * Correct typo and dist dir path * Remove unmounting and add sudo * Provide correct permissions and investigate * Add investigation * Add sudo everywhere in old * Use mv -T to force rename * Remove -T * Use matrix for osx CI and add investigation * Create bin in resources first * Add missing sudo * Add more sudos * Change python link name * Add more sudos * Add investigation and use the list rather than ls list * Use full path with GITHUB_WORKSPACE for wx dylibs * Remove quotes around the dylib path * Add investigation * Use complete full path * Use sudo inside script rather than sudo script * Add investigation and use * instead of @ * Use cd and then get the list * Add investigation, add files to fake and add sudo * Remove sudo and investigation and use more complete path * Correct paths * Correct paths * Add investigation * Use sudo hdiutil create * Remove unmount and -debug * Increase projected dmg size and remove untarred artifacts * Try ways to decrease disk size * Upload dist folder * Delete instead of uninstall and use df -h * Remove upload * Add investigation to create_dmg * Move dylibs rather than copy * Set -size to be 200 larger than expected * Add sudos * Remove deploy_osx and investigation and export mdanse_dmg * Search for libint* * Dont copy python dylib * Include libint dylib and deploy on macos 11 too * Correct yaml syntax * Correct artifact names * Change libintl path in libpython2.7.dylib * Comment out _boot_multiprocessing in __boot__ and add investigation * Correct python dylib pointer on macos11 * Relink dylibs amond each other, add investigation and cp not mv * Replace ls with find for investigation * Also change wx dylib links. Add investigation * Change dylib link for all wx dylibs * Remove ' from cp with wildcard * Change dylib links for libwx in lib-dynload * Search for libz and libc++ * Include missing dylibs and change rpath to executable path * Correct typos in dylib names * Actually correct typos in dylib names * Investigate hashlib and don't copy libz and libc++ on 11 * Try unlinking openssl and correct paths * Only unlink on macos10.15 * Correct placements of conditional statement * Investigate openssl on mac11 * Try specifying openssl version * Link more dylibs and try copying libssl * Add investigation and try buildin app with --includes openssl * Investigate ssl locations * Relink _hashlib.so to correct dylibs * Relink vtk so files inside lib-dynload * Change vtk rpath instead * Try relinking other files, remove extra python and link dylibs rather than copy * Correct issue * Try different source for wxpython * Try different source for conda wx * Revert to previous provider and correct cp paths * Correct path * Revert to original provider * Investigate wx version * Use -r to copy egg info * Build wxpython from source * Use sudo * Only build from source on 10.15 * Try wx from travis on mac11 * Disable fail fast * Copy over files on mac11 * Move vtk and wx installation to deploy and use conda wx3 * Correct yaml syntax * Remove wx installation from ci_osx * Replace mdanse_gui test with running the app at the end of deploy * Correct copying and remove ln * Relink .so files in lib-dynload/wx * Make PlatformError in create_directory more descriptive * Correct yaml syntax * Test bundled python and add bash script to run it * Correct sed command syntax * Use echo >> instead of sed -i * Improve script and make executable and bundle bin/python * Remove extension from script * Correct script name * Make python2 behave like an actual python * Correct script and remove bin/python * Correct windows desktip shortcut icon path * Delete unused files * Try using for links in windows nsi * Copy the MDANSE shortcut to desktop * Clean up yaml and scripts * Try out cache action for vs2008 * Try removing ' from around path * Remove ' from around paths * Set VS90CMNTOOLS * Append PATH and use cmd * Cache sdk 5.0 too * Cache sdk 5 and 6 and set windowssdkdir * Correct mistakes and search for mingw * Correct yaml syntax * Use cmd for test * Use powershell ls for test * Try using mingw and editing vcvarsamd64 * Use custom vcvarsamd.bat and set env vars manually * Correct mistake and set python vars * Try vs for python2.7 * Add investigation * Cache separately * Correct yaml issues * Correct yaml issues * Run restore after retrieving from cache * Try full install after restoring cache * Try vc for python2.7 * Try using setuptools * Run vcvarsall too * Add paths * Remove restoring VS2008 * Correct name * Save the msi to github workspace * Remove id * Restore vs2008 from cache * Bring the experimental win CI to be official * Try removing .net framework from caching * Add postrm script for ubuntu * Run vcvars before scientific and cache CI result * Try replacing distutils with setuptools in scientific * Replace scientific setup.py with edited one * Install VS2008 if python could not be restored * Correct != into == * Change key name from python to mdanse * Remove old step * Use full path to python * Use ' * Put the problematic line on a separate line * Fix the yaml syntax * Use full path to all pythons * Try running macos tests directly * Unpack list for os.path.join in BuildJobTests * Correct BuildJobTests.py to get right path to ref data * Make AllTests.py be able to be run from anywhere * Use different approach * Create the test files inside Jobs/ * Put test file name as full path * Use os.chdir inside all test scripts * Add usage instructions to mac * Bring the README to workspace * Correct readme path and try different logic * Correct yaml indentation * Correct yaml syntax * Remove extra MDANSE build install step * Make mdanse scripts able to be run by themselves * Correct ubuntu dependencies and ensure LD_LIBRARY_PATH is set * Correct sed syntax * Remove superfluous netcdf caching * Correct python syntax edited into mdanse scripts * Correct windows netcdf download url * Use older py2app and try != true instead of == false * Fix CASTEP test by removing gradients variable * Temporarily disable pdf tests * Add sudo apt-get update on ubuntus * Update maintainer/publisher information * Remove this branch from deploy list * Remove dangerous MacOS parse_command_line.py * Remove the copying of removed script * Remove deployment on this branch * Fixed regression due to recent merge * Don't subtract 1 from pdf during tcf_intra calculation * Regenerate test reference file using current code * Fixed buggy DL_POLY trajectory * Added mdanse_job application for running a job through a stand-alone dialog (#65) * Added mdanse_job application for running a job through a stand-alone dialog * Added more info to mdanse_job script help Fixed typo with Doc/conf_api.py file * Revert changes to Doc Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Fix broken tests (#66) * Fix CASTEP test by removing gradients variable * Temporarily disable pdf tests * Change BuildJobTests to ignore T and KE * Use try finally when opening NetCDF files * Don't compare velocities in DFTB and Forcite * Make DFTB and Forcite tests proper by generating new references * Delete copies even when exception occurs * Fix issues due to output_file vs output_files * Fix bug with triclinic unit cells * Fixed regression in ConfigurationPanel (#84) Co-authored-by: eric pellegrini <[email protected]> * Use netCDF4 as the NetCDF dependency instead of Scientific.IO/NetCDF (#81) * Replaced Scientific.IO.NetCDF dep by netCDF4 * Fixed regression * Replaced Scientific.IO.NetCDF dep by netCDF4 * Fixed regression * Install netCDF4 during CI/CD pipeline * Correct windows netCDF4 path * Copy netCDF4 contents on ubuntu ci * Add investigation to CI/CD * Set HOME env var before using it on win * Correct netCDF4 path on ubuntu and mac * Copy .so libraries on unixes * Add investigation to windows pipeline * Investigate RUNNER_TOOL_CACHE on win CI * Correct netCDF4 destination path on win * Separate conda calls on win and copy libmfhdf on unix * Copy over libdf.so on unix pipelines * Remove leadin \ from xcopy source on win pipeline * Create destination dirs on windows pipeline * Edit paths on ubuntu * Investigate KeyError on win pipeline * Copy netcdf and hdf5 libs on ubuntu * Try importing problematic configurator directly * Add investigation to pipelines * Correct yaml syntax * Correct yaml syntax * Copy msvc dlls from conda to main on win * Copy netcdf dlls into python\DLLs on win * Copy netcdf dlls into netCDF4 directory * Clean up pipelines * Fix broken tests * Handle possible IOError in tests * Handle IOError on monoprocessor too * Run AllTests.py with sudo * Relocate test output file for Test_dp * Add forgotten \n to BuildJobTests * Correct test generation for dp on linux * Use repo directory for dp output path on linux * Alter BuildJobTests to output to reference dir * Clean up pipeline and BuildJobTests * Use context manager in test_gromacs_trr * Use context manager in PlotterPlugin * Add forgotten context managers to test_trr Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Fixed bug when closing partial charges plugin (#85) Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Add advanced units manipulation and definition options (#78) * Added Units module for handling units * Advances in integration of Units module in the plotter * Added Units module for handling units * Advances in integration of Units module in the plotter * Added app for editing units The plotter accepts now equivalent units (e.g. THz/eV) Added icon ofr units * Removed external dependencyy to magnitude project * Fixed conflicts * Added the possibility to add an unit from the units editor * Fixed bug when closing the UnitsEditor dialog * Install pyyaml on CI/CD pipeline * Added docstrings and more unit tests to Units module * Added new equivalences Added warning when adding unit in the unit editor * Added new equivalences * Updated the units editor dialog * Big fixed when multiplying or dividing unit by another * Added J_per_mole unit * Change q unit from inv_nm to 1/nm Big fixed in the unit parser * Bug fix with inv_nm factor in Units.yml * Added unit test for prefixes * Bug fixed in __ipow__ function * Removed old dependencies to magnitude * Fixed regression in Forcite converter * Fixed bug in SFFSF analysis * Added akma_time in available units Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Fix script installation (#82) * Remove setuptools and enable CD * Correct branch name in CI.yml and try running VS9 vcvars * Call correct vcvars on CD too * Use setuptools on runners only, keep only distutils in default setup * Remove this branch from contains() calls * Add abstraction for plotter data (#86) * Added abstraction layer for NetCDF data * Added missing method for closing data properly * Added missing module * Added _IPlotterVariable interface and NetCDFPlotterVariable concrete class * Added comments to PlotterData module Fixed bug in load_data * Fixed bug with axis names * Fixed regression in PlotterPlugin.py * Flattened the name of the variable in PlotterData Added Path columns to datalist in Plotter * Implement context manager for PlotterData classes * Removed __del__ method of _IPlotterData class Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Update apt-get on ubuntu CD (#77) * Make MacOS CI fail when tests fail (#88) * Move MacOS tests to yaml * Add bug to test changes * Remove testing bug * Fix the installation of netCDF4 on MacOS CI/CD (#90) * Investigate the issue * Remove leading / when copying netcdf4 * Remove investigation * Correct MacOS CI artifact upload mechanism (#92) * Alter yaml syntax for MacOS if * Try different syntax change on MacOS CI * Use the working syntax everywhere * Add interpolation to ccf (#35) * Add interpolation to ccf * Bug fixed with velocities array * Use a sparse array for setting the velocities in case when interpolation is set * Bug fix when setting the velocities sparse array * Start rewriting * Implement slower but memory-efficient interpolation * Implement disk interpolation * Add another disk interpolation implementation * Introduce chunking * Add vel preloading to disk interpolation * Error out if 'preload' == 0 * Delete self._velocities at start of finalize() * Close netcdf at start of finalize() * Handle os.path.join error * Use unique name for each ccf instance * Improve name readability and change defaults * Fix bug caused by using old name * Add mode that selects appropriate mode Co-authored-by: eric pellegrini <[email protected]> * Fix lm and lux units (#96) * Fix AtomsListPlugin (#100) * Correct AtomsListWidget method name * Disable SpinCtrl instead of hiding it * Remove default value from msg_set_ud (#101) * Added support for HDF5 format for output files (#94) * Addd support for HDF5 format for output files * Install h5py and enable deploy win * Copy conda hdf dlls, libs etc * Alter PATH in win launcher.bat * Correct path in .bat and try setting path * Copy all conda dlls etc * Use conda only for win CD * Correct numpy installation on win CD * Use conda numpy in win CD * Add testing to win CD * Add more testing to win CD * Set paths on win CD * Use setup-miniconda action in win CD * Adapt win CD to setup-miniconda action * Add vcvars to PATH on win CD * Call vcvars in win CD * Use setuptools in ScientificPython win CD * Use setuptools for mmtk on win CD * Added hardcoded netcdf.h path to mmtk setup.py * Add investigation to win CD * Copy netcdf.h directly to include on win CD * Try copying Scientific\* to include * Look for missing header files * Try setuptools and distutils for Scientific * Remove investigations from win CD * Rework win CI/CD to use conda * Only use conda netcdf-c files * Alter Scientific setup.py to correct lib path * Split windows CI tests * Use full python path to run tests * Use setuptools and distutils for mmtk * Use different trajectory in TestConfigurator.py * Change caching key * Add investigation to win CD * Add investigation to windows CI * Try setting use-only-tar-bz2 on conda setup * Change setup-miniconda interaction with caching * Add investigation to windows CI * Try running 'conda activate' * Try different setup-miniconda configuration * Try different setup-miniconda configuration * Replace conda with mamba * Specifiy python 2.7.18 for mamba * Change conda and cache interaction * Cache only packages * Cache all of site-packages * Hardoce conda path for cache * Use conda only for h5py and netcdf4 * Change cache key * Remove python caching on Windows * Correct artifact name on win CD * Correct wrong shell usage * Clean up environment before packaging * Use -y with pip uninstall * Disable windows CD on this branch * Enable MacOS and Ubuntu CI Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Use only centre of masses selection for COM calculation (#102) * Use distutils in Ubuntu CI/CD * Restore if statements in CI.yml * Fix MacOS CD (#103) * Fix type in MacOS deploy.sh * Correct order of MacOS deploy instructions * Use -y with pip uninstall * Fix Toggle toolbar option (#108) * Use ToolBar.IsShown() * Keep the main window size constant * Update CHANGELOG (#104) * Update CHANGELOG * Update CHANGELOG to include #48 * Fixed bug when building clusters in XTD parser (#106) Co-authored-by: eric pellegrini <[email protected]> * Install psutil in CI/CD (#109) * Update authors information (#112) * Add path information to NetCDFInputData (#114) * Create Path column only in standalone plotter * Implement recursive var search in netcdf * Refactor to use variable wrappers * Refactor into multiple files * Set .nc and .h5 formats as default for browsing in plotter (#116) Co-authored-by: RastislavTuranyi <[email protected]> Co-authored-by: Turanyi <[email protected]> Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: eurydice76 <[email protected]> Co-authored-by: gonzalezma <[email protected]> Co-authored-by: franzlang <[email protected]>
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