Merge pull request easybuilders#21413 from boegel/develop

sync with main + bump version to 4.9.4dev
boegel · Sep 14, 2024 · ce06eb4 · ce06eb4
2 parents 1cdd815 + 1f37456
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diff --git a/RELEASE_NOTES b/RELEASE_NOTES
@@ -3,8 +3,145 @@ 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 19,985 easyconfig files, for 3,552 different software packages,
-incl. 40 different (compiler) toolchains.
+The latest version of easybuild-easyconfig provides 20,561 easyconfig files, for 3,656 different software packages,
+incl. 41 different (compiler) toolchains.
+
+
+v4.9.3 (14 September 2024)
+--------------------------
+
+update/bugfix release
+
+- added easyconfigs for foss/2024a (#21100) and intel/2024a (#21101) common toolchains
+- new toolchain: gmpflf/2024.06 (#20882)
+- added example easyconfig files for 107 new software packages:
+  - absl-py (#21039), accelerate (#21107), affogato (#20636), APOST3D (#21133), bayesian-optimization (#21301),
+    BayesOpt (#21261), BGEN-enkre (#15752), bitsandbytes (#21248), bliss (#21206), cfgrib (#21113), CLANS (#21099),
+    colorize (#20964), CORSIKA (#20693), COSTA (#20989), coxeter (#21254), Critic2 (#20833), crypt4gh (#20870),
+    dblatex (#21207), dictys (#21166), DL_POLY_Classic_GUI (#20819), EGA-QuickView (#20870, #20888), EMMAX (#21174),
+    empanada-dl (#20454), empanada-napari (#20454), ESIpy (#21006), fastfilters (#21003), fish (#21345, #21381),
+    flash-attention (#21083), Flax (#21039), fonttools (#21363), fsm-lite (#20503), GDMA (#21171), GeoDict (#20650),
+    GPflow (#21172), gtk-doc (#21207), Gubbins (#20413), Gymnasium (#20420), HERRO (#21252), IEntropy (#20808),
+    ilastik-napari (#21003), IMAGE (#20994), junos-eznc (#21166), jupyter-collaboration (#20741),
+    jupyter-vscode-proxy (#20876), langchain-mistralai (#20759), langchain-openai (#20711), LRBinner (#21310),
+    lrcalc (#21339), MAGIC (#20900), mallard-ducktype (#21127), MATES (#21229), MBX (#21155), mcqd (#21283),
+    MeshLab (#20806), meteogrid (#20921), micro-sam (#20636), miniprot (#21157), napari-denoiseg (#20934),
+    NECAT (#21359), nellie (#21267), NextPolish (#21265), nifty (#20636), ome-types (#21256), openai-python (#20711),
+    OpenForceField-Toolkit (#20852), orjson (#20880), PEcAn (#21227), PretextMap (#20790), PyBEL (#20953),
+    pyMBE (#21034), pystencils (#20889), python-blosc (#20636), python-elf (#20636), rankwidth (#20788), Rasqal (#21207),
+    Redland (#21227), Regenie (#15752), rMATS-long (#20916), Sagemath (#21365), scCustomize (#20907), SCENICplus (#21085),
+    scFEA (#20777), sdsl-lite (#20503), SharedMeatAxe (#21303), Single-cell-python-bundle (#20116), SIRIUS (#20989),
+    sirocco (#21304), SKA2 (#20411), SpFFT (#20989), spla (#11607), Stable-Baselines3 (#20884), submitit (#21103),
+    SVDSS2 (#20855), tdlib (#21305), torch-em (#20636), Umpire (#20989), Uni-Core (#21182), vigra (#20636),
+    Visit (#20981), weblogo (#20800), wradlib (#21110), xtb-IFF (#20783), yell (#20964), yelp-tools (#21127),
+    yelp-xsl (#21127), z5py (#20636), Zoltan (#21324)
+- added additional easyconfigs for various supported software packages, including:
+  - AGAT 1.4.0, ASE 3.23.0, Abseil 20240722.0, Albumentations 1.4.0, AlphaPulldown 2.0.0b4, AlphaPulldown 2.0.0b4,
+    AmberTools 26.3, Arrow 16.1.0, alsa-lib 1.2.11, archspec 0.2.4, attr 2.5.2, BayesTraits 4.1.2, BeautifulSoup 4.12.3,
+    Biopython 1.84, Boost.MPI 1.83.0, bcl-convert 4.2.7-2, beagle-lib 4.0.1, biom-format 2.1.16, byacc 2.0.20240109,
+    CDO 2.3.0, CFITSIO 4.4.1, CUDA-Samples 12.2, CUDA 12.5.0 + 12.6.0, CUTLASS 3.4.0, Catch2 2.13.10, CellOracle 0.18.0,
+    Clang 18.1.8, Coreutils 9.5, chewBBACA 3.3.9, code-server 4.90.2, connected-components-3d 3.14.1, cooler 0.10.2, 
+    cryptography 42.0.8, cutadapt 4.9, cyvcf2 0.31.1, dorado 0.7.3, dtcmp 1.1.5, ESMF 8.6.1, EvidentialGene 2023.07.15,
+    Extrae 4.2.0, ecBuild 3.8.5, elfutils 0.191, FFmpeg 7.0.2, FLAC 1.4.3, FUSE 3.16.2, Flask 3.0.3, Flye 2.9.4,
+    FriBidi 1.0.15, ffnvcodec 12.2.72.0, flatbuffers-python 24.3.25, flatbuffers 24.3.25, fmt 10.2.1, fpylll 0.6.1,
+    GCC 14.2.0, GDAL 3.9.0, GEOS 3.12.1, GHC 9.10.1, GLM 1.0.1, GLib 2.80.4, GLibmm 2.72.1 + 2.75.0 + 2.77.0 + 2.78.1,
+    GPAW 24.6.0, GetOrganelle 1.7.7.1, Guile 2.0.14 + 3.0.10, Gurobi 11.0.2, gap 4.13.0, genomepy 0.16.1, gensim 4.3.2,
+    gffutils 0.13, gh 2.52.0, git-annex 10.20240731, gmpy2 2.2.0, googletest 1.15.2, graph-tool 2.59, HDBSCAN 0.8.38.post1,
+    HOMER 4.11.1, HTSeq 2.0.7, HiCMatrix 17.2, Highway 1.2.0, Hypre 2.31.0, hatchling 1.24.2, histolab 0.7.0,
+    hypothesis 6.103.1, IQ-TREE 2.3.5, ImageMagick 7.1.1-34, Imath 3.1.11, IsoQuant 3.5.0, igraph 0.10.12, imageio 2.34.1,
+    imbalanced-learn 0.12.3, inferCNV 1.21.0, intervaltree 0.1, JsonCpp 1.9.5, Julia 1.10.4, jax 0.4.25, json-fortran 8.5.2,
+    Kent_tools 468, LLVM 18.1.8, LittleCMS 2.16, libdrm 2.4.122, libdwarf 0.10.1, libedit 20240517, libgeotiff 1.7.3,
+    libgit2 1.8.1, libopus 1.5.2, libsigc++ 3.6.0, libspatialindex 2.0.0, libunistring 1.2, libunwind 1.8.1, libwebp 1.4.0,
+    libxslt 1.1.42, libzip 1.10.1, lwgrp 1.0.6, lxml 5.3.0, MCR R2024a, MPICH 4.2.1, MUMPS 5.7.2, MariaDB 11.6.0,
+    Maven 3.9.7, Mercurial 6.8.1, Mesa 24.1.3, Miniconda3 23.10.0-1, MultiQC 1.22.3, makedepend 1.0.9, matplotlib 3.9.2,
+    maturin 1.6.0, medaka 1.12.1, meshio 5.3.5, meson-python 0.16.0, mm-common 1.0.6, NanoCaller 3.6.0, Normaliz 3.10.3,
+    n2v 0.3.3, nano 8.1, ncbi-vdb 3.1.1, nettle 3.10, nsync 1.29.2, numexpr 2.9.0, ORCA 6.0.0, OpenEXR 3.2.4, OpenFOAM 12,
+    OpenFOAM v2406, OpenJPEG 2.5.2, Optax 0.2.2, Optuna 3.6.1, PaStiX 6.3.2, Perl-bundle-CPAN 5.38.2, Pillow-SIMD 10.4.0,
+    Pint 0.24, Platypus-Opt 1.2.0, PostgreSQL 16.4, PyAEDT 0.9.9, PyCharm 2024.1.6, PyRosetta 4.release-384,
+    PyWavelets 1.7.0, PyYAML 6.0.2, Pygments 2.18.0, Pylint 3.2.5, Pyomo 6.7.3, Python-bundle-PyPI 2024.06, packmol 20.14.4,
+    pagmo 2.19.0, parallel 20240722, pixman 0.43.4, pod5-file-format 0.3.10, poetry 1.8.3, popt 1.19, pretty-yaml 24.7.0,
+    primecount 7.14, psycopg 3.2.1, pyGenomeTracks 3.9, pybind11 2.12.0, pycocotools 2.0.7, pydantic 2.7.4, pygmo 2.19.5,
+    pyperf 2.7.0, pyseer 1.3.12, pysteps 1.10.0, QuantumESPRESSO 7.3.1, Qwt 6.3.0, R-bundle-CRAN 2024.06, R 4.4.1,
+    RDKit 2024.03.3, RapidJSON 1.1.0-20240409, Ray-project 2.9.1, ReFrame 4.6.2, Rust 1.79.0, redis-py 5.0.9,
+    regionmask 0.12.1, rjags 4-15, rpmrebuild 2.18, SDL2 2.30.6, SHAP 0.43.0, SIP 6.8.3, SRA-Toolkit 3.1.1,
+    STAR 2.7.11b_alpha_2024-02-09, STRUMPACK 7.1.0, SVDSS2 2.0.0-alpha.3, Safetensors 0.4.3, Salmon 1.10.3,
+    SciPy-bundle 2024.05, SeqKit 2.8.2, SingleM 0.16.0, Sphinx-RTD-Theme 2.0.0, Stack 3.1.1, SuiteSparse 7.7.0,
+    SuperLU 6.0.1, SuperLU_DIST 8.2.1, scArches 0.6.1, scib-metrics 0.5.1, scvi-tools 1.1.2, sdsl-lite 2.0.3,
+    setuptools-rust 1.9.0, sirocco 2.1.0, slepc4py 3.20.2, smafa 0.8.0, snpEff 5.2c, spaCy 3.7.4, spektral 1.2.0,
+    spglib-python 2.5.0, spglib 2.5.0, TELEMAC-MASCARET 8p5r0, Tk 8.6.14, Tkinter 3.12.3, Trycycler 0.5.5, tiktoken 0.7.0,
+    timm 1.0.8, UCX-CUDA 1.16.0, unixODBC 2.3.12, utf8proc 2.9.0, VSEARCH 2.28.1, virtualenv 20.26.2, WRF 4.5.1,
+    Wayland 1.23.0, X11 20240607, XGBoost 2.1.1, XML-LibXML 2.0210, x264 20240513, x265 3.6, xarray 2024.5.0, xtb-IFF 1.1,
+    xtb 6.7.1, xtensor 0.24.7, yelp-xsl 42.1
+- minor enhancements, including:
+  - add internal CUDA header patch for PSM2 v12.0.1 (#20804)
+  - add patch for JupyterHub support to recent tensorboard easyconfigs (#20823)
+  - make sure that recent ImageMagick versions pick up the right pkgconf + improve sanity check for ImageMagick (#20900)
+  - also install utilities for recent versions of FUSE 3.x (#20918)
+  - add RISC-V support to x264 v20231019 (#20968)
+  - add RISC-v support to recent LAME easyconfigs by removing workaround for finding libncurses (#20970)
+  - enable PIC in recent x265 easyconfigs to solve compilation errors on RISC-V (#20971)
+  - add extensions to R-bundle-CRAN: missmDA (#21167, #21183). insight (#21260), performance + datwizard + bayestestR (#21272, #21285)
+  - add Qt support to VTK 9.3.0 (#21221)
+  - add `helper_scripts` to `$PATH` in easyconfig for ProteinMPNN v1.0.1-20230627 (#21289)
+  - also build & install the plugins with OpenFOAM v2406 (#21332)
+- various bug fixes, including:
+  - fix easyconfigs for recent versions of QuantumESPRESSO (#20070)
+  - add wrapper for Julia with linking safeguards and delegate environment setup to JuliaPackage (#20103)
+  - fix typo in description of SuiteSparse v7.7.0 (#20567)
+  - add 'pic' flag to IML (#20789)
+  - add patch to recent SciPy-bundle easyconfigs to fix build error with numpy with some Fortran compilers (#20817)
+  - rename unpacked sources for components of EasyBuild v4.9.2, to ensure that '`--install-latest-eb-release`' works with older EasyBuild versions (#20818)
+  - fix build of OpenBLAS 0.3.24 on A64FX (#20820)
+  - remove maturin build dependency from langchain-antropic (#20825)
+  - add GMP and MPFR as dependencies to OpenFOAM v2306 and v2312 (#20841)
+  - add patch to SciPy-bundle 2024.05 that fixes numpy test failures on RISC-V (#20847)
+  - skip unreliable memory leak test in PyTorch 2.1.2 (#20874)
+  - use PyYAML 6.0.1 instead of 6.0 for recent ReFrame versions to fix problem with Cython 3.x (#20879)
+  - use PyPI source tarball and gfbf/2023a toolchain for pyBigWig (#20881)
+  - add fix for failing test on zen4 to Highway 1.0.4 (#20942)
+  - add patch to fix implicit function declaration in OpenMPI 4.1.4 (#20949)
+  - only use libxsmm as dependency for CP2K 2023.1 w/ `foss/2023a` on x86_64 (#20951)
+  - copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command (#20956)
+  - set `$SATSUMA2_PATH` so Satsuma2 can locate executables (#20957)
+  - disable auto-vectorizer (`-ftree-vectorize`) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11 (#20958)
+  - disable test step for WIEN2k 23.2 because files required by it can no longer be downloaded (#20969)
+  - add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection (#21002)
+  - update homepage in phonopy easyconfigs (#21014)
+  - make libunwind dependency architecture specific in Extrae 4.2.0 easyconfig (#21017)
+  - add `OPENSSL_ENABLE_SHA1_SIGNATURES` for building `ansys-pythonnet` (#21028)
+  - fix download URLs for old Intel software (2018-2023) by using `IRC_NAS` instead of `irc_nas` (#21108)
+  - update source and homepage URLs in Szip easyconfigs (#21129)
+  - rename source URL in HDF v4.2.16-2 easyconfig (#21130)
+  - consistently fix homeage + source URL for `HDF` + `h4toh5` (#21134)
+  - ensure that recent BioPerl easyconfigs use `Bundle` easyblock (#21136)
+  - fix checksum checks for easyconfigs using a `Bundle`-like easyblock in easyconfigs test suite (#21143)
+  - add pkgconf build dependency to scikit-misc v0.3.1 (#21144)
+  - explicitly disable use of MySQL in recent GDAL easyconfigs (#21156)
+  - fix easyconfig tensorflow-probability v0.20.0 to pass `pip check` (#21172)
+  - stop RStudio-Server 2023.09 from installing R packages (+ move to `foss/2023a` toolchain) (#21175)
+  - remove `Time::HiRes` from `Perl-bundle-CPAN` since there's newer version in `Perl` (#21198)
+  - fix build of STAR 2.7.11a + 2.7.11b on non-x86 architectures by avoiding use of `-maxv2` + add missing `xxd` build dependency (#21200)
+  - add missing cairo dependency for python-igraph v0.10.6 (#21211)
+  - add patch for xtb 6.7.0 to fix build failure due to changes in tblite (#21255)
+  - add patch for HDF5 v1.14.3 to suppress fp exceptions (#21280)
+  - update easyconfig for dorado 0.7.3 to properly use provided OpenSSL dependency, and not install external libraries into its own lib directory (#21297)
+  - use proper Python dependency for OTF2 (#21325)
+  - use source tarballs from GitHub for recent libdap easyconfigs (#21334)
+  - remove Highway build dependency in Brunsli easyconfigs, since it's not actually required at all (#21366)
+  - add alternative checksum for bold 1.3.0 extension in R-bundle-CRAN (#21370)
+- other changes:
+  - archive outdated example easyconfigs for Fujitsu toolchain (#20781)
+  - upgrade rpmrebuild build dependency to version 2.18 in bcl-convert 4.2.7 easyconfig (#20861)
+  - use proper dependency for Safetensors in easyconfig for Transformers v4.39.3 (#20864)
+  - remove CMake Arrow flag as there is no Arrow dependency in recent GDAL easyconfigs (#20905)
+  - whitelist `ConfigureMakePythonPackage` for `sanity_check_paths` CI check (#20963)
+  - rename `gubbins-2.4.0.eb` to `Gubbins-2.4.0.eb` (#20995)
+  - make pytest v7.4.2 independent of Python-bundle-PyPI (#21004)
+  - reorganize Flax/JAX stack in 2023a: move `jax` + `Optax` to `gfbf/2023a` toolchain + use standalone `Flax` + `absl-py` as dependencies (#21038)
+  - use stand-alone absl-py as dependency for jax w/ `gfbf/2023a` (#21039)
+  - remove Cython dependency from Python-bundle-PyPI 2024.06 + add standalone easyconfig for Cython 3.0.10 (#21233)
+  - add Cython build dependency for SciPy-bundle v2024.05 (#21235)
+  - use top-level parameters for `use_pip` & co instead of `exts_default_options` for `PythonBundle` easyconfigs (#21292)
 
 
 v4.9.2 (12 June 2024)

diff --git 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 = '4.9.3.dev0'
+VERSION = '4.9.4.dev0'
 
 MAJ_VER = VERSION.split('.')[0]
 MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])