From 291deba625e76de62d778248e9076b73f23a131e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 May 2023 11:18:58 +0200 Subject: [PATCH] prepare release notes for EasyBuild v4.7.2 + bump version to 4.7.2 --- RELEASE_NOTES | 94 ++++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 94 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index f4454f0b91e..26d8721fa48 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,102 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 16,628 easyconfig files, for 2,995 different software packages, +The latest version of easybuild-easyconfig provides 17,098 easyconfig files, for 3,085 different software packages, incl. 39 different (compiler) toolchains. +v4.7.2 (27 May 2023) +-------------------- + +update/bugfix release + +- added easyconfigs for intel/2023.03 (#17676) +- added example easyconfig files for 89 new software packages: + - AGeNT (#17864), anndata (#17677), Annocript (#17910), avro-cpp (#17527), batchgenerators (#17833), + BoltzTraP2 (#17742), Braindecode (#17913), build (#17776), casacore (#15499), Casanovo (#17735, #17736), + CASPR (#17606), CellChat (#17856), CellOracle (#17507), CLIP (#17782), CodingQuarry (#17682), ColabFold (#17751), + CopyKAT (#17646), CPC2 (#17849), cppzmq (#17601), dask-labextension (#17882), DIALOGUE (#17696), DiCE-ML (#17591), + ESPResSo (#17709), Evcxr-REPL (#17831), EZC3D (#17832), funannotate (#17588), FunGAP (#17652), GATB-Core (#17635), + GenMap (#17746), GimmeMotifs (#17507), GLI (#17793), GOBNILP (#17639), h5netcdf (#17835), HD-BET (#17833), + HTSplotter (#17369, #17586), ipympl (#17613), IsoSeq (#17791), KrakenUniq (#17569), LIANA (#17928), + libWallModelledLES (#17480), LoRDEC (#17635), M3GNet (#17555), mandrake (#17394), mctc-lib (#16760), MOABB (#17913), + MRPRESSO (#17925), ont-guppy (#17477, #17828), OptaDOS (#17777), PALEOMIX (#17912), PGPLOT (#15496), + PICI-LIGGGHTS (#17710), pod5-file-format (#17776), powerlaw (#17647), pp-sketchlib (#17397), + py3Dmol (#17752), pytesseract (#17898), pytest-cpp (#17966), pytest-flakefinder (#17966), Python-bundle (#17626), + python-xxhash (#17844), PyTorch-bundle (#17540), qnorm (#17507), R-MXM (#17667), R-transport (#17642, #17968), + Raven (#15833), ReaxFF (#17780), ripunzip (#17959), RPostgreSQL (#17739), rustworkx (#17857), Scalene (#16472), + sceasy (#17677), SCIP (#17639), Simple-DFTD3 (#16760), SMAP (#17672), SoPlex (#17639), SoupX (#17851), + spektral (#15551), synthcity (#17623), sysbench (#17643), tantan (#17681), thirdorder (#17703), TOPAS (#17553), + Triplexator (#17866), tRNAscan-SE (#17680, #17800), turbinesFoam (#17917), unicore-uftp (#17665), vispr (#17606), + WCSLIB (#15497), ZIMPL (#17639) +- added additional easyconfigs for various supported software packages, including: + - Abseil v20230125.2, AlphaFold v2.3.1 + v2.3.4, Arrow v11.0.0, arrow-R v11.0.0.3, astropy v5.2.2, awscli v2.11.21, + Bismark v0.24.0, biom-format v2.1.14, Blender v3.5.0, Blosc2 v2.8.0, Bottleneck v1.3.7, breseq v0.38.1, + bwa-meth v0.2.6, buildenv default for foss/2022b + CUDA 12.0.0, Cantera v2.6.0, CapnProto v0.10.3, CASTEP v22.11, + Clang v15.0.5, CLHEP v2.4.6.4, CMake v3.26.3, CMSeq v1.0.4, coverage v7.2.3, CP2K v9.1 + v2022.1, CPLEX v22.1.1, + CREST v2.11.2, cURL v8.0.1, CuPy v11.4.0, DBus v1.15.4, DBG2OLC v20200724, dlb v3.3.1, double-conversion v3.3.0, + Doxygen v1.9.7, expat v2.5.0, FASTA v36.3.8i, FHI-aims v221103, fio v3.34, Fiona v1.9.2, Flask v2.2.3, fmt v10.0.0, + freeglut v3.4.0, FUSE v3.14.1, GapFiller v2.1.2, GCC 12.3.0 + 13.1.0, GDCM v3.0.21, GitPython v3.1.31, Go v1.20.4, + googletest v1.13.0, gpustat v1.1, Guile v3.0.9, Gurobi v10.0.1, Harminv v1.4.2, Highway v1.0.4, IgBlast v1.21.0, + Imath v3.1.7, infercnvpy v0.4.2, IQ-TREE v2.2.2.3, jax v0.3.25, jupyterlmod v4.0.3, Kalign v3.3.5, + L_RNA_scaffolder v20190530, libaio v0.3.113, libarchive v3.6.2, libctl v4.5.1, libdeflate v1.8, libgcrypt v1.10.1, + libGridXC v1.1.0, libjpeg-turbo v2.1.5.1, libmaus2 v2.0.499, libopus v1.4, libpng v1.6.39, libPSML v1.1.12, + libRmath v4.2.1, libsigc++ v3.4.0, LibTIFF v4.5.0, libunistring v1.1, libxc v6.1.0, libxml2 v2.11.4, + libxslt v1.1.38, lifelines v0.27.4, lxml v4.9.2, make v4.4.1, MariaDB v10.11.2, Meep v1.26.0, MetaPhlAn v4.0.6, + mold v1.11.0, MPB v1.11.1, muParser v2.3.4, NAG v7.1, NAGfor v7.1, nano v7.2, NASM v2.16.01, ncurses v6.4, + netcdf4-python v1.6.3, networkx v2.8.8, NSS v3.89.1, numexpr v2.8.4, nvtop v3.0.1, OpenEXR v3.1.7, OpenMM v8.0.0, + Pandoc v3.1.2, ParaView v5.11.0, PCRE2 v10.42, PhyloPhlAn v3.0.3, phyx v1.3, picard v3.0.0, Pint v0.20.1, + pkgconf v1.9.5, PostgreSQL v15.2, PROJ v9.2.0, Proteinortho v6.2.3, protobuf v23.0, protobuf-python v4.23.0, + pydantic v1.10.4, pyFFTW v0.13.1, PyGEOS v0.14, Pyomo v6.5.0, pyparsing v3.0.9, pyperf v2.6.0, pyproj v3.5.0, + pytest v7.2.2, PYTHIA v8.309, Qtconsole v5.4.0, R-bundle-Bioconductor v3.16, R-tesseract v5.1.0, RE2 v2023-03-01, + ReFrame v4.2.0, RepeatMasker v4.1.5, RevBayes v1.2.1, rgdal v1.6-6, rioxarray v0.14.0, rocm-smi v5.4.4, + ROOT v6.26.10, Rtree v1.0.1, scib v1.1.3, scikit-build v0.17.2, Seaborn v0.12.2, SHAP v0.41.0, Shapely v2.0.1, + ShengBTE v1.5.0, SLiM v4.0.1, snappy v1.1.10, spdlog v1.11.0, spglib v2.0.2, spglib-python v2.0.2, SQLite v3.42.0, + Subread v2.0.4, Tcl v8.6.13, tcsh v6.24.05, torchtext v0.14.1, trimesh v3.21.5, UCC-CUDA v1.1.0, utf8proc v2.8.0, + Vim v9.0.1434, vsc-mympirun v5.3.1, WRF v4.4.1, xmlf90 v1.5.6, xxHash v0.8.1, XZ v5.4.2, zsh v5.9, zstd v1.5.5 +- minor enhancements, including: + - add local::lib extension to Perl 5.34.0 (#17679) + - install shared libraries for tesseract (#17721) + - add additional extensions to recent R easyconfigs: word2vec, tau, quanteda, ... (#17738) + - add extensions to R-bundle-Bioconductor 3.15: deepSNV (#17852) + - add extensions to R 4.2.x: dlm (#17640), PMA + unikn + ppcor (#17695), tvem (#17729), epitools (#17852) +- various bug fixes, including: + - add patch for UCC 1.1.0 for multiple component paths (#17255) + - fix configure step for ELSI 2.5.0+ (#17288) + - switch bamtofastq to Cargo easyblock (#17595) + - add missing OpenJPEG dependency for recent GDAL versions (#17599) + - fix CodAn bin/* executable permissions for all users #(#17607) + - upgrade traitlets, ipywidgets, and widgetsnbextension + downgrade jupyterlab_widgets extensions in IPython v8.5.0 to fix known issues (#17612) + - add patch for GPAW-22.8.0 with 2022a toolchain to make test tolerance a bit less strict (#17618) + - add alternative checksum for MONAI 1.0.1 (#17628) + - fix paths to Perl modules in MAKER v3.01.04 (#17629) + - add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6 (#17631) + - explicitely disable mpi/python in Boost (intel-compilers/2021.4.0) (#17638) + - remove LLVM build dependency from TensorFlow easyconfigs (#17641) + - update easyconfig for Longshot 0.4.5 to use Cargo easyblock (#17666) + - fix homepage in ELPA easyconfigs (due to switch to new domain) (#17697) + - add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test (#17713) + - use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0 (#17717) + - exclude flaky test_optim for PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent (#17726, #17730, #17731, #17737) + - add missing PCRE dependency for InterProScan 5.55-88.0 (#17762) + - fix building Python bindings of DGL, requires static libs (#17764) + - only use QEF gitlab source url for QuantumESPRESSO itself (#17766) + - add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file (#17779) + - fix broken source URL for AOCC 4.0.0 (#17794) + - specify source_urls inside exts_default_options in Seurat easyconfigs to ensure correct name expansion for the archived packages (#17830) + - add Doxygen build dependency to X11 (#17842) + - FLINT needs BLAS so move it up from GCC level (#17868) + - fix broken tarball links for ispc 1.6, 1.10, and 1.12 easyconfigs (#17875) + - add dependency on PycURL to JupyterHub-3.0.0-GCCcore-11.3.0.eb (#17887) + - add historical repo paths to install cmd for old versions of texlive (#17893) + - add missing FastTreeMP binary for FastTree (#17897) + - add checksum for arm64 source tarball for Go 1.18.3 (#17903) + - add patch to fix test_quantization in PyTorch 1.12.1 (#17908) + - add make 4.3 as build dependency for recent OpenBLAS versions (#17924) +- other changes: + - bump versions in Java wrappers to latest builds that include ppc64le: Java/8.362, Java/11.0.8, Java/17.0.6 (#17775) + - move Arb and polymake to gfbf/foss since FLINT is now at gfbf/foss (#17869) + v4.7.1 (March 20th 2023) ------------------------ diff --git a/setup.py b/setup.py index 1e5caaddac1..70004ce1b12 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.7.2.dev0' +VERSION = '4.7.2' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])