Merge pull request #20284 from migueldiascosta/eb491

prepare release notes for EasyBuild v4.9.1 + bump version to 4.9.1
easybuilders · Apr 4, 2024 · 04b386c · 04b386c
2 parents 9a653b4 + 16f61a2
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diff --git a/RELEASE_NOTES b/RELEASE_NOTES
@@ -3,10 +3,199 @@ 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 18,752 easyconfig files, for 3,369 different software packages,
+The latest version of easybuild-easyconfig provides 19,487 easyconfig files, for 3,470 different software packages,
 incl. 40 different (compiler) toolchains.
 
 
+v4.9.1 (5 April 2024)
+---------------------
+
+update/bugfix release
+
+- added example easyconfig files for 101 new software packages:
+  - AMICA (#19842), AreTomo2 (#19681), btllib (#19779), bwa-mem2 (#20217), CENSO (#19826), Circlator (#19847), Clarabel.rs (#20149),
+    code-cli (#19645), Concorde (#19768), contextily (#19807), CUTLASS (#19304), DeepLoc (#19514), Delft3D (#19869), DeltaLake (#19758),
+    denseweight (#20139), desktop-file-utils (#19701), devbio-napari (#19586), DjVuLibre (#19701), Elmer (#19448),
+    EnergyPlus (#19565), EpiSCORE (#18618), evince (#19701), ExpressBetaDiversity (#19938), ExtremeLy (#19870), f90nml (#19171),
+    FFAVES (#19822), fugue (#19694), gcsfs (#20042), GenomeComb (#19749), GI-DocGen (#19701), GKlib-METIS (#20096), GRASP-suite (#19665),
+    gspell (#19701), GUIDANCE (#20063), hdWGCNA (#20124), HF-Datasets (#20166), IDG (#18924), igvShiny (#19714), inflection (#20036),
+    InterOp (#19303), IonQuant (#19812), Lab-Streaming-Layer (#19945), Levenshtein (#19771), libfyaml (#19856), libgxps (#19701),
+    libhandy (#19701), libspectre (#19701), lit (#20252), lmoments3 (#19870), Markdown (#20239), MetaDecoder (#20123), mfqe (#19781),
+    Miniforge3 (#20227), MLflow (#19893), MODFLOW (#20142), morphosamplers (#20000), MotionCor3 (#19681), MSFragger (#19811),
+    multiprocess (#19986), nf-core (#19107), noise (#20048), OpenMEEG (#19853), OpenSlide-Java (#19962), PAGAN2 (#19618), PASA (#19570),
+    pblat (#19570), PBZIP2 (#19677), PDM (#20012), Philosopher (#19383), phyluce (#19779), poppunk (#17402), PSASS (#20160), psycopg (#19107),
+    PyInstaller (#19519), PyQt-builder (#16703), pytest-workflow (#19107), python-casacore (#20089), pytorch-3dunet (#19290), pyXDF (#19916),
+    q2-krona (#19633), QuPath (#19962), radian (#19484), remake (#19581), rethinking (#19755), RHEIA (#19496), s3fs (#19576),
+    safestringlib (#20217), scikit-extremes (#19870), SemiBin (#19767), semla (#19747), Sentence-Transformers (#19509), sinto (#13846),
+    sktime (#19692), SQLAlchemy (#20242), tiny-cuda-nn (#19304), tox (#16178), Vamb (#17457), xpdf (#20024), yt (#20263), Zeo++ (#19555),
+    zUMIs (#19949)
+- added additional easyconfigs for various supported software packages, including:
+  - Abseil 20240116.1, ABySS 2.3.7, AMS 2023.104, Anaconda3 2024.02, anndata 0.10.5.post1, anvio 8, ArchR 1.0.2,
+    archspec 0.2.2, Armadillo 12.8.0, arpack-ng 3.9.1, arrow-R 14.0.0.2, ASAP3 3.13.3, assimp 5.3.1, autopep8 2.0.4,
+    basemap 1.3.9, BerkeleyGW 3.1.0 + 4.0, BiG-SCAPE 1.1.5, Biopython 1.83, Blosc 1.21.5, Blosc2 2.13.2, Boost.MPI 1.82.0,
+    Boost.Python 1.83.0, Braindecode 0.8.1, Brotli-python 1.1.0, build 1.0.3, buildenv-default foss-2023b + intel-2023b,
+    bx-python 0.10.0, CapnProto 1.0.1.1, c-ares 1.27.0, Cartopy 0.22.0, casacore 3.5.0, Cbc 2.10.11, ccache 4.9, cclib 1.8,
+    CellBender 0.3.1, CellTypist 1.6.2, CFITSIO 4.3.1, Cgl 0.60.8, Clang-Python-bindings 16.0.6, Clp 1.17.9, CmdStanR 0.7.1,
+    COBRApy 0.29.0, code-server 4.22.1, CoinUtils 2.11.10, CoordgenLibs 3.0.2, CREST 2.12, cryoCARE 0.3.0, CSBLAST 2.2.4,
+    CUDA 12.3.2 + 12.4.0, cuDNN 8.9.7.29, CuPy 13.0.0, cuSPARSELt 0.6.0.6, cuTENSOR 2.0.1.2, CVXPY 1.4.2, Cython 3.0.8,
+    dask 2023.12.1, datalad 0.19.5, DB_File 1.859, deepdiff 6.7.1, DeepLabCut 2.3.6, DendroPy 4.6.1, Deprecated 1.2.14,
+    DFT-D4 3.6.0, DIAMOND 2.1.9, Dice 20240101, dlb 3.4, DLPack 0.8, dorado 0.5.1, EggLib 3.3.0, einops 0.7.0, ELPA 2023.11.001,
+    enchant-2 2.6.5, ESMF 8.4.2, eSpeak-NG 1.51, ETE 3.1.3, expecttest 0.2.1, fastjet 3.4.2, fastjet-contrib 1.053, FDS 6.8.0,
+    fineRADstructure 20210514, fio 3.36, Fiona 1.9.5, Flask 3.0.0, FLINT 3.1.1, Flye 2.9.3, fmt 10.2.0, freebayes 1.3.7,
+    GATK 4.5.0.0, gawk 5.3.0, geocube 0.4.3, geopandas 0.14.2, geopy 2.4.1, GHC 9.4.6, Ghostscript 10.02.1, GIMIC 2.2.1,
+    git-lfs 3.5.1, GitPython 3.1.42, GLFW 3.4, Go 1.22.1, GPAW 24.1.0, GPAW-setups 24.1.0, gperftools 2.14, Gradle 8.6,
+    graph-tool 2.55, Greenlet 3.0.3, GROMACS 2024.1, gRPC 1.62.1, GTK3 3.24.39, Gurobi 11.0.0, HDF5 1.14.3, HeFFTe 2.4.0,
+    HepMC3 3.2.6, hunspell 1.7.2, igraph 0.10.10, infercnvpy 0.4.3, iperf 3.16, IQ-TREE 2.2.2.7, ISA-L 2.31.0, Java/19 (19.0.2),
+    Java/21 (21.0.2), json-c 0.17, Julia 1.10.0, KaHIP 3.16, LAMMPS 2Aug2023_update2, LASTZ 1.04.22, LDC 1.36.0, leidenalg 0.10.2,
+    libcint 5.5.0, libgit2 1.7.2, librosa 0.10.1, librsvg 2.58.0, libSBML 5.19.7, libsigsegv 2.14, libtirpc 1.3.4,
+    libxml2-python 2.11.4, likwid 5.3.0, LLVM 14.0.6, MACS3 3.0.1, maeparser 1.3.1, Mamba 23.11.0-0, MATIO 1.5.26,
+    matplotlib 3.8.2, maturin 1.5.0, MCR R2023a, MDAnalysis 2.7.0, MDI 1.4.26, medaka 1.11.3, Meson 1.3.1, MiXCR 4.6.0,
+    MNE-Python-1.6., MOABB 1.0.0, molmod 1.4.8, MONAI 1.3.0, mpi4py 3.1.5, mrcfile 1.5.0, NCCL 2.20.5, NCO 5.1.9, NECI 20230620,
+    netcdf4-python-1.6.5, networkx 3.2.1, NGSpeciesID 0.3.0, NiBabel 5.2.0, nichenetr 2.0.4, Nilearn 0.10.3,
+    nlohmann_json 3.11.3, NLTK 3.8.1, ntCard 1.2.2, numba 0.58.1, NVHPC 24.1, OBITools3 3.0.1b26, OCaml 4.14.0, occt 7.8.0,
+    onedrive 2.4.25, ONNX 1.15.0, ONNX-Runtime 1.16.3, ont-fast5-api 4.1.2, OPARI2 2.0.8, OpenFOAM v2306 + v2312, OpenSSL/3,
+    Optuna 3.5.0, Osi 0.108.9, PAPI 7.1.0, Parallel-Hashmap 1.3.12, ParaView 5.12.0, PDT 3.25.2, PETSc 3.20.3, PGPLOT 5.2.2,
+    phonemizer 3.2.1, phono3py 2.7.0, Pillow 10.2.0, Pint 0.23, plotly.py 5.18.0, poetry 1.7.1, presto-1.0.0 20230501,
+    PROJ 9.3.1, prompt-toolkit 3.0.36, protobuf 25.3, protobuf-python 4.25.3, psmc 0.6.5_20221121, pstoedit 3.78,
+    psycopg2 2.9.9, PuLP 2.8.0, PyCheMPS2 1.8.12, pycodestyle 2.11.1, pydantic 1.10.13 + 2.5.3 2.6.4, pydicom 2.4.4, pydot 2.0.0,
+    pyfaidx 0.8.1.1, PyFrag 2023-dev.20240220, pymatgen 2023.12.18, PyOpenCL 2023.1.4, PyOpenGL 3.1.7, pyparsing 3.1.1,
+    PyQt5 5.15.10, Pysam 0.22.0, PySCF 2.4.0, pyspoa 0.2.1, PyTables 3.9.2, pytest-rerunfailures 14.0, python-igraph 0.11.4,
+    python-irodsclient 2.0.0, python-isal 1.6.1, python-libsbml 5.20.2, python-xxhash 3.4.1, PyTorch-Ignite 0.4.13,
+    PyTorch-Lightning 2.2.1, PyZMQ 25.1.2, QIIME2 2023.7.0, Qt5 5.15.13, Qt6 6.6.3, Qtconsole 5.5.1, QtPy 2.4.1,
+    QuantumESPRESSO 7.3, R 4.3.3, rasterio 1.3.9, R-bundle-Bioconductor 3.18, rclone 1.66.0, RE2 2024-03-01, Redis 7.2.4,
+    redis-py 5.0.1, rioxarray 0.15.0, Rivet 3.1.9, rMATS-turbo 4.2.0, RNA-Bloom 2.0.1, rocm-smi 5.6.0, rpy2 3.5.15,
+    ruamel.yaml 0.18.6, Ruby 3.3.0, Rust 1.75.0 + 1.76.0, Salmon 1.10.1, Sambamba 1.0.1, Saxon-HE 12.4, SBCL 2.4.1,
+    ScaFaCoS 1.0.4, Scalene 1.5.35, scanpy 1.9.8, scib 1.1.4, scikit-bio 0.5.9, scikit-learn 1.4.0, scikit-lego 0.7.4,
+    scikit-misc 0.3.1, SCons 4.6.0, Score-P 8.4, scVelo 0.3.1, Seaborn 0.13.2, SentencePiece 0.1.99, Seqmagick 0.8.6,
+    Seurat 5.0.1, SIP 6.8.1, siscone 3.0.6, skorch 0.15.0, SLEPc 3.20.1, snakemake 8.4.2, SNAPE-pooled 20150707,
+    SOAPdenovo-Trans 1.0.5, Spark 3.5.1, spdlog 1.12.0, spoa 4.1.0, SRA-Toolkit 3.0.10, Stack 2.13.1, STAR 2.7.11b,
+    statsmodels 0.14.1, tensorboard 2.15.1, tensorboardX 2.6.2.2, tensorflow-probability 0.20.0, texinfo 7.1, timm 0.9.7,
+    torchvision 0.16.0, tqdm 4.66.2, TRIQS 3.2.0, TRIQS-cthyb 3.2.1, TRIQS-dft_tools 3.2.0, TRIQS-tprf 3.2.1,
+    typing-extensions 4.9.0, UCX 1.16.0, UDUNITS 2.2.28, umap-learn 0.5.5, UMI-tools 1.1.4, Vala 0.56.14, VEP 111,
+    Vim 9.1.0004, vsc-mympirun 5.4.0, WFA2 2.3.4, wget 1.21.4, WhatsHap 2.2, WIEN2k 23.2, wrf-python 1.3.4.1,
+    Xerces-C++ 3.2.5, XlsxWriter 3.1.9, XML-LibXML v2.0209, xxHash 0.8.2, yaff 1.6.0, YAXT 0.10.0, Yices 2.6.4, YODA 1.9.9
+- minor enhancements, including:
+  - add build info message to easyconfig for NLTK 3.7 (#18550)
+  - enable KLU and CUDA solvers in SUNDIALS v6.6.0 (#19490)
+  - add extensions to R-bundle-CRAN v2023.12: tidybayes (#19712), spdep (#19729), fixest (#20055)
+  - add plyranges extension to R-bundle-Bioconductor (for zUMIs) (#19949)
+  - add PyOpenGL-accelerate extension to PyOpenGL v3.1.7 (#20007)
+  - use system architecture template in DB_File (#20014), GD (#20015), and GDGraph (#20016)
+  - add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency (#20069)
+  - add MODIStsp extension (+ required dependencies) to R 4.2.2 (#20113)
+  - enable LittleCMS2 and WebP support in recent Pillow (#20195)
+  - improve test for validity of easyconfig files (#20205)
+  - add easyconfig test that checks if backdoored XZ versions are introduced (#20267)
+- various bug fixes, including:
+  - add patch for Bison 3.7.1 to fix build error on old OS versions (#12291)
+  - add missing pkg-config build dependency for recent p11-kit easyconfigs (#16318)
+  - fix dependencies and configure flags of GnuTLS 3.7.x (#19070)
+  - remove numa configure option from hwloc 2.5+ (#19085)
+  - add patches for OpenBLAS v0.3.21 to disable -ftree-vectorize for netlib LAPACK (#19280)
+  - add patch to fix flaky scipy build in SciPy-bundle v2023.11 (#19481)
+  - add missing SciPy-bundle dependency to TensorRT easyconfig (#19486)
+  - fix lapack test failures in OpenBLAS 0.3.23/24 (#19495)
+  - add patch for Arrow v8.0.0 - v11.0.0 to add missing `__arrow_ext_class__` method to `BaseExtensionType` class (#19532)
+  - change homepage for argtable (#19551)
+  - add patches for PyTorch v2.1.2 with `foss/2022a` (#19571), `foss/2022b` (#19572), and `foss/2023a` (#19573) to fix test failures on non-x86 platforms
+  - use pocl with CUDA support as dependency for PyOpenCL v2023.1.4 (#19584)
+  - remove `osdependencies` from ccache easyconfigs using GCCcore toolchain (#19600)
+  - use https source URL for alsa-lib (#19628)
+  - add missing dm-tree dependency for dm-reverb 0.2.0 (#19653)
+  - add libyaml import check to PyYAML and fix builds since split to minimal Python (#19662)
+  - demote meson-python to a build dependency in recent matplotlib easyconfigs (#19670)
+  - add patch to fix upb CopyFrom error in protobuf-python 4.24.0 (#19671)
+  - demote poetry to build dep in expecttest (#19675)
+  - add zlib dependency to YODA and Rivet (#19679)
+  - fix missing spaces in Graphviz configure options (#19687)
+  - strip iconv from pkgconfig file for libarchive v3.6.2 (#19698)
+  - use separate bcrypt easyconfig (using CargoPythonPackage) as dependency for JupyterHub v4.0.2 (#19703)
+  - use maturin easyconfig using CargoPythonPackage as a dependency for fastparquet v2023.4.0 (#19704)
+  - add patches for Perl-bundle-CPAN v5.36.1 to fix installation of `Sys::Info::Driver::Linux*` extensions on Debian Bookworm (#19727)
+  - explicitly specify Fortran compiler for recent CDO versions to fix issues on non-x86_64 architectures (#19735)
+  - add patch for `jupyter_core` extension in `jupyter-server` to set jupyter path by `$EB_ENV_JUPYTER_ROOT` (#19737)
+  - add Python build dependency to 1.9.x Doxygen (#19743)
+  - fix Arrow v14.0.1 to install pyarrow as an extension (#19758)
+  - fix homepage + source URL for Gblocks 0.91b (#19797)
+  - make sure that Brunsli libraries are installed into `lib` (#19805)
+  - fix dependency with `libidn.so.11` in tbl2asn v20220427 and v20230713 easyconfigs (#19821)
+  - add missing dependencies for fslpy in easyconfig for FSL v6.0.5.1 (#19829)
+  - remove numa configure option from hwloc 2+ (#19833)
+  - avoid spurious test failure when enabling RPATH for Perl (#19835)
+  - add missing Python deps and packages in PSI4 1.7 (#19836)
+  - add patch to fix `MS_RDONLY` error in OpenMPI 3.1.x and 4.0.0 (#20140), 4.0.3 (#19944), and 4.0.5 (#19837)
+  - demote meson-python to build dependency for matplotlib v3.7.2 w/ `iimkl/2023a` (#19892)
+  - demote hatchling to build dependency in easyconfig for einops 0.7.0 (#19915)
+  - add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs (#19940)
+  - stop using non-existent `--disable-libdeflate` option for LibTIFF 4.1.0 (#19951)
+  - add patch to remove git version check and fix test command for molmod 1.4.8 (#19952)
+  - replace SYSTEM-level GCC dependency in git-annex with binutils (#19956)
+  - stop using non-existing `--with-doc` configure option for groff 1.23 (#19969)
+  - fix test failures of Perl-bundle-CPAN-5.38 in non-English locales (#19971)
+  - add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 13.2.0 for ARM architectures with SVE support (#19974, #20218)
+  - drop checksum from easyconfig for VSCode 1.85.0 since tarball are not stable (#19995)
+  - respect `sysroot` in recent Pillow-SIMD easyconfigs, when in use (#19996)
+  - remove `--disable-docs` configure option from FriBidi 1.0.5+ (#19998)
+  - fix geotiff configure option in GDAL (#19999)
+  - unpack SCG database to 'db' subdirectory for DAS_Tool (#20008)
+  - remove Jasper dependency and configure option from GDAL 3.5+ (#20009)
+  - update homepage and source URLs for SPAdes (#20018)
+  - fix GDAL 3.5.0 install on high-core-count machines (#20027)
+  - remove disable-visibility configure flag from GTK3 (#20028)
+  - remove mpi configure option from libfdf 0.2.2 (#20034)
+  - add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs (#20035)
+  - fix invocation typo and unneeded folder change on invocation in fgbio 1.3.0 easyconfig (#20039)
+  - remove hdf5 configure option from MDSplus 7.96.12 (#20041)
+  - fix python configure option of MEME (#20043)
+  - fix configure options of FFLAS-FFPACK (#20052)
+  - find the correct Python in xtensor (#20056)
+  - fix geotiff configure option in GDAL 2.2.3 (#20057)
+  - fix configure option and remove gperftools dependency for MIRA 5.0 (#20061)
+  - fix confgure options in GRASS (#20062)
+  - fix configure of LinBox 1.7.0 (#20064)
+  - remove unknown configure option from GnuTLS 3.7.2 (#20065)
+  - use 32-bit indexing for SUNDIALS 6.6.0 (with foss/2023a) to enable sunmatrix-cusparse (#20075)
+  - find correct Python for MDI (#20083)
+  - add `pixman` and `FriBidi` dependencies to recent ImageMagick easyconfigs (#20086)
+  - add patch to fix failing tests with OpenSSL 3.x for Net-SSLeay v1.92 extension in Perl-bundle-CPAN v5.36.1 (#20090) and v5.38.0 (#20118)
+  - add patches for minimus2 in AMOS-3.1.0 (#20114)
+  - fix download url for cuSPARSELt 0.3.0.3 (#20129)
+  - add patches to fix test issues for PyTorch 2.1.2 with `foss/2023a` + CUDA 12.1.1 (#20156)
+  - remove easyconfig for UCX-CUDA 1.15.0 using incompatible combo of CUDA 12.3.0 + GCC 13.2.0 (#20158)
+  - remove flake8 suppressions for invalid escape sequences (#20161)
+  - fix post-install command for SuperLU_DIST in case library prefix is `lib` instead of `lib64` (#20162)
+  - switch to gitlab source URL for libxc + add alternative checksum (#20163)
+  - enable `download_dep_fail` in Pythonpackage easyconfigs where it was wrongly disabled (#20174)
+  - add patch to fix PyTorch 1.12.x and 1.13.x for Linux 6+ (#20176, #20177, #20178, #20179, #20180, #20181, #20182)
+  - disable tests for `Time::HiRes` extension in Perl-bundle-CPAN v5.36.1 (#20187)
+  - fix several typos in GlobalArrays 5.8 configure step (#20188)
+  - fix broken homepage from older SCOTCH easyconfigs (#20192)
+  - remove dead URL for ISL from `source_urls` in easyconfigs for GCCcore 10.3.0, 11.1.0, 11.2.0 (#20193)
+  - fix package installation in easyconfigs for Python 2.7.15 and 3.7.2 (using `GCCcore/8.2.0`) (#20194)
+  - add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency (#20214)
+  - fix cuSPARSELt easyconfigs for aarch64 (#20216)
+  - fix python shebang in napari easyconfigs (#20219)
+  - add patch to fix scipy test failure for SciPy-bundle 2023.02 with `gfbf/2022b` (#20235)
+  - fix `incompatible types` errors when building the R extension `dbarts` on Arm (#20238)
+  - add patch to fix for libarchive to fix error reporting in tar (#20254)
+  - add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin (#20260)
+  - fix download for python-parasail 1.3.4 by adding missing source URL (#20263)
+- other changes:
+  - update DualSPHysics easyconfig to use custom easyblock (#19400)
+  - fix name for DETONATE in existing easyconfig (was `detonate`) (#19569)
+  - rename `VSCode` to `code-cli` (to match with existing `code-server`) (#19585, #19645)
+  - remove urllib3 extension from wandb easyconfig, not neeed since Python-bundle-PyPI dependency already provides it (#19725)
+  - stop using custom easyblock for Doxygen (#19742)
+  - move `setuptools_scm` extension from hatchling to Python easyconfig (#19777, #20200)
+  - move xtb v6.6.1 to gfbf/2023a (#19826)
+  - unify Z3 4.12.2 easyconfigs into a single one with Python bindings (and fix Z3 dependency for PyTorch 2.1.2 accordingly) (#20050)
+  - use GPAW-setups v24.1.0 in existing GPAW easyconfigs (#20117)
+  - fix duplicate dict entries and enable fatal error checking for easyconfigs via `flake8` (#20173)
+  - move Greenlet 2.0.2 to GCCcore toolchain (#20241)
+  - update Java/8 wrapper to Java 8.402 (#20261)
+  - update copyright lines to 2024 (#20276)
+
+
 v4.9.0 (30 December 2023)
 -------------------------
 

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 = '4.9.1.dev0'
+VERSION = '4.9.1'
 
 MAJ_VER = VERSION.split('.')[0]
 MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])