diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 45d27a2e696..e687bf442f8 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,130 @@ 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 19,487 easyconfig files, for 3,470 different software packages, +The latest version of easybuild-easyconfig provides 19,985 easyconfig files, for 3,552 different software packages, incl. 40 different (compiler) toolchains. +v4.9.2 (12 June 2024) +--------------------- + +update/bugfix release + +- added easyconfigs for foss/2024.05 toolchain (candidate for foss/2024a) (#20646) +- added example easyconfig files for 82 new software packages: + - AEDT (#20357), amdahl (#20346), AMGX (#20255), assembly-stats (#20281), Bio-FeatureIO (#20461), + bitshuffle (#20661), Cassiopeia (#20289), CCCL (#20255), charm-gems (#20327), CheckM2 (#20399), + chromVARmotifs (#20402), cmph (#20278), COMEBin (#20717), Compass (#20500), ctffind5 (#20669), currentNe (#20791), + CVX (#20231), deepfold (#20247), dotNET-Core (#20256), EasyMocap (#20446), ensmallen (#20485), EVcouplings (#20744), + Faiss (#19669), FDMNES (#20321), gnupg-bundle (#20406), grpcio (#20191), hatch-jupyter-builder (#20606), + hevea (#20597), HiGHS (#20186), hmmcopy_utils (#20472), HOMER (#20590), ICON (#20573), jiter (#20746), + LangChain (#20746), langchain-anthropic (#20746), libabigail (#20539), libbraiding (#20655), libhomfly (#20482), + libsupermesh (#20470), LIBSVM-MATLAB (#20752), Lightning (#19964), lil-aretomo (#20696), makefun (#20619), + MetalWalls (#20403), MICOM (#20186), ml-collections (#20247), ml_dtypes (#20707), mlpack (#20485), MOFA2 (#20538), + mumott (#20719), nvitop (#20512), ocamlbuild (#20552), optiSLang (#20320), orthAgogue (#20278), pdf2docx (#20416), + planarity (#20753), plantri (#20467), plmc (#20744), PortAudio (#20307), premailer (#20348), ProteinMPNN (#20705), + PRRTE (#20698), PSM2 (#20496), PyAEDT (#20357), pybind11-stubgen (#20518), PyEXR (#19983), pyGAM (#20385), + PyHMMER (#20544), pyseer (#20502), PyVista (#20649), qmflows (#20384), SciTools-Iris (#20767), SCReadCounts (#20455), + SDL2_gfx (#20466), subunit (#20412), TF-COMB (#20666), tiktoken (#20336), TorchIO (#20648), t-SNE-CUDA (#19669), + VAMPIRE-ASM (#20368), wfdb (#20521), WGDgc (#20367) +- added additional easyconfigs for various supported software packages, including: + - 4ti2 1.6.10, AFNI 24.0.02, Autoconf 2.72, Autotools 20231222, adjustText 1.1.1, aiohttp 3.9.5, alevin-fry 0.9.0, + alsa-lib 1.2.9, atropos 1.1.32, autopep8 2.2.0, BCFtools 1.19, BLIS 1.0, BWA 0.7.18, Boost 1.85.0, bcrypt 4.1.3, + binutils 2.42, bokeh 3.4.1, CGAL 5.6.1, CREST 3.0.1, CellRanger-ARC 2.0.2, CellRanger 8.0.1, CellRank 2.0.2, + Clang 17.0.6, CoCoALib 0.99850, Cython 3.0.10, cURL 8.7.1, cffi 1.16.0, code-server 4.89.1, + configurable-http-proxy 4.6.1, coverage 7.4.4, cpio 2.15, cppyy 3.1.2, cysignals 1.11.4, Doxygen 1.11.0, + dask-labextension 7.0.0, dask 2024.5.1, deal.II 9.5.2, dorado 0.5.3, dotNET-Core 8.0.203, E-ANTIC 2.0.2, + ECL 24.5.10, ESPResSo 4.2.2, eclib 20240408, expat 2.6.2, FLTK 1.3.9, FMM3D 1.0.4, FlexiBLAS 3.4.4, f90wrap 0.2.13, + fgbio 2.2.1, fontconfig 2.15.0, freetype-py 2.4.0, GAMESS-US 20220930-R2 + 20230930-R2, GCC 13.3.0 + 14.1.0, + GDB 14.2, GDRCopy 2.4.1, GOATOOLS 1.4.5, GTDB-Tk 2.4.0, Giza 1.4.1, gc 8.2.6, gcloud 472.0.0, gemmi 0.6.5, + gettext 0.22.5, giac 1.9.0-99, git 2.45.1, gmsh 4.12.2, gsutil 5.29, HDDM 0.9.9, HTSlib 1.19.1, HyPhy 2.5.60, + h5py 3.11.0, hwloc 2.10.0, ICU 75.1, IOR 4.0.0, imagecodecs 2024.1.1, imgaug 0.4.1, ipympl 0.9.4, + Jupyter-bundle 20240522, JupyterHub 4.1.5, JupyterLab 4.2.0, JupyterNotebook 7.2.0, jupyter-matlab-proxy 0.12.2, + jupyter-resource-usage 1.0.2, jupyter-rsession-proxy 2.2.0, jupyter-server-proxy 4.1.2, jupyter-server 2.14.0, + Kalign 3.4.0, KrakenUniq 1.0.4, kallisto 0.50.1, LAPACK 3.12.0, libarchive 3.7.4, libde265 1.0.15, libdeflate 1.20, + libdwarf 0.9.2, libfabric 1.21.0, libffi 3.4.5, libgcrypt 1.10.3, libgpg-error 1.48, libheif 1.17.6, libidn2 2.3.7, + libnsl 2.0.1, libpciaccess 0.18.1, libpng 1.6.43, libuv 1.48.0, libxml2 2.12.7, line_profiler 4.1.2, MATSim 15.0, + MDTraj 1.9.9, Mako 1.3.5, Meson 1.4.0, MetaMorpheus 1.0.5, Molpro 2024.1.0, MuJoCo 3.1.4, matlab-proxy 0.18.1, + mold 2.31.0, mpmath 1.3.0, NASM 2.16.03, NanoPlot 1.42.0, Nextflow 24.04.2, Ninja 1.12.1, nanoget 1.19.1, + napari 0.4.19.post1, nauty 2.8.8, ncurses 6.5, nghttp2 1.58.0, nghttp3 1.3.0, nglview 3.1.2, ngtcp2 1.2.0, + nodejs 20.13.1, numactl 2.0.18, nvtop 3.1.0, OCaml 5.1.1, OSU-Micro-Benchmarks 7.4, OpenBLAS 0.3.27, OpenMPI 5.0.3, + PARI-GP 2.15.5, PCRE2 10.43, PMIx 5.0.2, Perl 5.38.2, PhyML 3.3.20220408, PnetCDF 1.13.0, PyAMG 5.1.0, + PyQtGraph 0.13.7, PyTorch-Geometric 2.5.0, PyTorch-bundle 2.1.2, PycURL 7.45.3, Pysam 0.22.0, Python 3.12.3, + p11-kit 0.25.3, p4est 2.8.6, parallel 20240322, pauvre 0.2.3, petsc4py 3.20.3, pkgconf 2.2.0, plc 3.10, polars 0.20.2, + poppler 24.04.0, psutil 5.9.8, py3Dmol 2.1.0, pybedtools 0.9.1, pygame 2.5.2, pyiron 0.5.1, pyro-ppl 1.9.0, + python-mujoco 3.1.4, ROOT 6.30.06, RPostgreSQL 0.7-6, RStudio-Server 2023.12.1+402, Rtree 1.2.0, Rust 1.78.0, + SAMtools 1.19.2, SCOTCH 7.0.4, SDL2_image 2.8.2, SDL2_mixer 2.8.0, SDL2_ttf 2.22.0, SQLite 3.45.3, SWIG 4.2.1, + SentencePiece 0.2.0, Seurat 5.1.0, SeuratDisk 20231104, SimNIBS 4.0.1, Singular 4.4.0, Spack 0.21.2, Squidpy 1.4.1, + SymEngine-python 0.11.0, SymEngine 0.11.2, sbt 1.6.2, scikit-build-core 0.9.3, scikit-learn 1.4.2, TOBIAS 0.16.1, + Tcl 8.6.14, TensorFlow 2.15.1, Transformers 4.39.3, texlive 20230313, tmux 3.4, tokenizers 0.15.2, 0.2.5.20231120, + tornado 6.4, UCC 1.3.0, UCX 1.16.0, util-linux 2.40, VSCode 1.88.1, Valgrind 3.23.0, VisPy 0.14.1, wget 1.24.5, + XZ 5.4.5, xorg-macros 1.20.1, xprop 1.2.7, xtb 6.7.0, xxd 9.1.0307, yaml-cpp 0.8.0, zarr 2.17.1, zfp 1.0.1, + zlib-ng 2.1.6, zlib 1.3.1, zstd 1.5.6 +- minor enhancements, including: + - add missing (optional) dependency pyproject-metadata to scikit-build-core (#20391) + - add hatch-requirements-txt extension to hatchling easyconfigs (#20389) + - install pkg-config files for ncurses 6.4 when using GCCcore toolchain (#20405) + - use regular 'configure' instead of wrapper script for recent UCX easyconfigs (#20428) + - add RISC-V support to UCX 1.15.0 (#20429), UCC 1.2.0 (#20432), BLIS 0.9.0 (#20468), PAPI 7.1.0 (20659) + - add extensions to R-bundle-CRAN v2023.12: cmna (#20445), rhandsontable (#20614), XBRL (#20506) + - add checksum for RISC-V version to easyconfig for Java 21.0.2 (#20495) + - remove 'TORCHVISION_INCLUDE' from PyTorch-bundle easyconfigs, now handled by custom easyblock for torchvision (#20504) + - add dependencies required for GUI in Cellpose 2.2.2 easyconfigs (#20620) + - add 'build_info_msg' about kernel modules to GDRCopy (#20641) + - build both static and shared libs for Brotli 1.1.0 (#20757) +- various bug fixes, including: + - add missing dependencies for funannotate (#17690) + - fix path to SuiteSparse include/lib in easyconfig for CVXopt v1.3.1 (#20232) + - fix Highway 1.0.3 on some systems by disabling 'AVX3_DL' (#20298) + - replace incorrect scikit-bio 0.5.9 with scikit-bio 0.6.0 as dependency for scCODA (#20300) + - add alternate checksum to OpenMolcas v23.06 (#20301) + - change arrow-R dependency of Bioconductor v3.18 to v14.0.1 (which depends on required matching Arrow v14.0.1) (#20324) + - fix hardcoded '/bin/mv' path in Rhdf5lib extension included in R-bundle-Bioconductor v3.16 + v3.18 (#20378) + - remove dependency on HDF5 in recent Bioconductor easyconfigs (#20379) + - make sure that libjpeg-turbo libraries are installed in 'lib' subdirectory (#20386) + - add patch for Libint 2.7.2 to fix compiler error with glibc >= 2.34 (#20396) + - use 'bash' rather than 'sh' to run PLINK-2.00a3.7 tests (#20404) + - add patch to fix 'UNPACK-OPAL-VALUE: UNSUPPORTED TYPE 33 FOR KEY' error in OpenMPI 4.1.5 (#20422) + - add patch to increase compatibility with AVX512 platforms for bwa-mem2 v2.2.1 (#20434) + - add patch for GROMACS 2024.1 to fix filesystem race in tests (#20439) + - demote poetry to build dependency for nanocompore (#20453) + - add patch to fix CVE-2024-27322 in R v3.6.x (#20464), v4.0.x (#20463), and v4.1.x + v4.2.x + v4.3.x (#20462) + - disable test that fetches from the web for torchtext extension in PyTorch-bundle v2.1.2 (#20484) + - fix sanity check paths for JupyterLab 4.0.5 (#20514) + - fix detection of CC/CXX compilers for 'wmake' in OpenFOAM v2306 + v2312 (#20517) + - use the included gmxapi for GROMACS 2024.1 (#20522) + - add new checksum for signal_1.8-0 to R-bundle-CRAN-2023.12 (#20527) + - fix test in Cwd extension of Perl-bundle-CPAN 5.36.1 (#20536) + - fix patch name in easyconfig for Perl-bundle-CPAN 5.36.1 + add also use it for Perl-bundle-CPAN 5.38.0 (#20540) + - fix cwd_enoent test in Perl (#20541) + - move dependency on BeasutifulSoup in IPython v8.14.0 to jupyter-server (#20547) + - remove dependency on BeasutifulSoup from IPython v8.17.2 (#20548) + - add alternative checksum for source tarball of MONAI 1.3.0 (#20618) + - add cpio as build dependency to recent BLAST+ versions (#20674) + - add --disable-htmlpages to recent FFmpeg easyconfigs (#20686) + - remove duplicate crates from easyconfig for timm-0.9.7 (#20687) + - add missing HDF5 dependency in recent Armadillo easyconfigs (>= 11.4.3) (#20710) + - add patches for failing LAPACK tests and RISC-V test segfaults to OpenBLAS 0.3.27 (#20745) + - move all easyconfigs for libavif to GCCcore toolchain + fix dependencies (#20747) + - make sure mummerplot can use gnuplot if available for recent MUMmer (#20749) + - prevent configure script of recent BLAST+ versions from prepending system paths to $PATH (#20751) + - fix fastparquet v2023.4.0 using CargoPythonBundle easyblock (#20775) + - remove --with-64 from configopts for recent BLAST+ versions (#20784) + - add patch to fix build of pdsh 2.34 with Slurm 23.x (#20795) +- other changes: + - move 'build' from extensions to dependencies in easyconfig for napari 0.4.18 (#20433) + - update version of fsspec extension in easyconfig for Squidpy 1.4.1 to be compatible with s3fs provided via PyTorch-bundle (#20477) + - add commented out PSM2 dependency, relevant for x86_64 systems with OmniPath, to recent libfabric easyconfigs (#20501, #20585, #20794) + - replace SQLAlchemy extension with regular dependency in easyconfig for Optuna v3.5.0 (#20510) + - replace SQLAlchemy extension in JupyterHub v4.0.2 easyconfig with regular dependency (#20511) + - bump Cython to v3.0.8 in Cartopy v0.22.0 easyconfig for foss/2023a toolchain, to avoid dependency version conflict with sckit-learn v1.4.2, which requires Cython >= v3.0.8 (#20525) + - change dependency on hatchling of BeautifulSoup v4.12.2 to a build dependency (#20546) + - bump async-timeout to 4.0.3 in aiohttp 3.8.5 (#20553) + - stick to gfbf/2023a as toolchain for ipympl v0.9.3 (#20586) + - rename tornado-timeouts.patch to tornado-6.1_increase-default-timeouts.patch + add missing authorship (#20587) + - remove easyconfigs for CellBender v0.3.1, since this version has been redacted due to a serious bug (#20722) + + v4.9.1 (5 April 2024) --------------------- diff --git a/setup.py b/setup.py index 58cbb040c4c..3aa9a822208 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 = '4.9.2.dev0' +VERSION = '4.9.2' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])