Merge pull request #19463 from easybuilders/4.9.x

release EasyBuild v4.9.0

Author: boegel

RELEASE_NOTES

@@ -3,10 +3,99 @@ 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 18,407 easyconfig files, for 3,292 different software packages,
+The latest version of easybuild-easyconfig provides 18,752 easyconfig files, for 3,369 different software packages,
 incl. 40 different (compiler) toolchains.
 
 
+v4.9.0 (30 December 2023)
+-------------------------
+
+feature release
+
+- added easyconfigs for foss/2023b (#19449) and intel/2023b (#19450) common toolchains
+- added example easyconfig files for 77 new software packages:
+  - AICSImageIO (#19315), ANTIC (#19203), BiasAdjustCXX (#19341), BOPTEST (#19295), BRiAl (#19208), castor (#19176),
+    CellBender (#19296), cliquer (#19210, #19323), CPMD (#19387), cppyy (#19204), CUDD (#19208), datalad (#18675),
+    Demystify (#17990), dftd4 (#19223), dialog (#17696), DIA-NN (#19454), dynesty (#19091), ebGSEA (#19447),
+    ECL (#19211), eclib (#19209), epct (#19298), EUKulele (#19217), FACE (#14840), fastml (#19357), forbear (#14840),
+    fplll (#19371), fpylll (#19371), ftfy (#19353), Gdspy (#19458), GFF3-toolkit (#19071), giac (#19323), GMP-ECM (#19323),
+    HepMC (#19139), hic-straw (#19309), HPCC (#18892), iced (#19309), IML (#19201), iperf (#19259), jedi (#19269),
+    jedi-language-server (#19269), jupyter-rsession-proxy (#19311), lcalc (#19329), libaed2 (#14840),
+    LoopTools (#19397), m4ri (#19208), m4rie (#19208), MDI (#19417), mdust (#19106), MitoHiFi (#19263), MPFI (#19323),
+    multicharge (#19221), OMERO.insight (#19337), OMERO.py (#19338), PFFT (#19255), primecount (#19370),
+    primecountpy (#19370), PyAV (#19359), pycubescd (#19302), pylipid (#19428), PySINDy (#19306),
+    pythermalcomfort (#19285), PyTorchVideo (#19359), R-bundle-CRAN (#19170), Restrander (#19232), scikit-lego (#19064),
+    scrublet (#19215), SEACells (#18724), simanneal (#19347), Simstrat (#14840), solo (#19216), SPEI (#19441),
+    SUPPA (#19181, #19275), SYMMETRICA (#19328), Triton (#19381), vaeda (#19214), VSCode (#19418), waLBerla (#18932)
+- added additional easyconfigs for various supported software packages, including:
+  - ANTs 2.5.0, Arriba 2.4.0, Arrow 14.0.1, at-spi2-core 2.50.0, Autoconf-archive 2023.02.20, awscli 2.15.2,
+    Blender 3.6.5 + 4.0.1, Boost 1.83.0, boto3 1.28.70, Bracken 2.9, BUStools 0.43.1, cairo 1.18.0, cairomm 1.16.2,
+    CASTEP 23.1, cddlib 0.94m, cdo-bindings 1.6.0, CellRanger 7.2.0, CoCoALib 0.99818, COMSOL 6.2.0.290, Coreutils 9.1,
+    cryptography 41.0.5, CubeLib 4.8.2, CubeWriter 4.8.2,  CUDA 12.3.0, CVXPY 1.3.0, cysignals 1.11.2, DBus 1.15.8,
+    dftd4 3.4.0, E-ANTIC 1.3.0, elfutils 0.190, f90wrap 0.2.11, FastQC 0.12.1, Ferret 7.6.0, FFLAS-FFPACK 2.5.0,
+    ffnvcodec 12.1.14.0, FPM 1.15.1, FriBidi 1.0.13, gap 4.12.2, git-lfs 3.4.0, GitPython 3.1.40, Givaro 4.2.0,
+    GLib 2.78.1, glog 0.6.0, GObject-Introspection 1.78.1, gperftools 2.13, GPyTorch 1.10, GROMACS 2023.3,
+    HarfBuzz 8.2.2, HiC-Pro 3.1.0, hifiasm 0.19.7, hypothesis 6.90.0, ICU 74.1, imageio 2.33.1, imkl 2024.0.0,
+    impi 2021.11.0, intel-compilers 2024.0.0, IPython 8.17.2, ITK 5.3.0, Kent_tools 457, KyotoCabinet 1.2.80,
+    LHAPDF 6.5.4, libfdf 0.5.0, libjxl 0.8.2, LinBox 1.7.0, lrslib 7.2, lxml 4.9.3, magma 2.7.2, maturin 1.3.1,
+    MEME 5.5.4, meson-python 0.15.0, Miniconda3 23.9.0, Mmg 5.7.2, Molden 7.3, mrcfile 1.4.3, nanoflann 1.5.0,
+    nauty 2.8.6, Nextflow 23.10.0, nodejs 20.9.0, Normaliz 3.10.1, NSS 3.94, NWChem 7.2.2, Oases 20180312, Pango 1.51.0,
+    Parallel-Hashmap 1.36, parameterized 0.9.0, phonopy 2.20.0, pigz 2.8, pmt 1.2.0, poetry 1.6.1, PostgreSQL 16.1,
+    pplpy 0.8.9, PyCairo 1.25.1, pypmt 1.2.0, PyQt5 5.15.7, pytest 7.4.2, pytest-xdist 3.3.1,
+    Python-bundle-PyPI 2023.10, PyTorch 2.1.2, R 4.3.2, RASPA2 2.0.47, SBCL 2.3.11, SCENIC 1.3.0, scikit-image 0.22.0,
+    SciPy-bundle 2023.11, SDL2 2.28.5, setuptools-rust 1.8.0, Seurat 4.4.0, SimpleITK 2.3.1, Singular 4.3.2p10,
+    Spark 3.5.0, STAR 2.7.11a, STAR-CCM+ 2310, strace 6.6, SuiteSparse 7.1.0, tbb 2021.11.0, TOML-Fortran 0.4.1,
+    TRAVIS-Analyzer 220729, UCX-CUDA 1.15.0, VirSorter 1.0.6, virtualenv 20.24.6, VSEARCH 2.25.0, VTK 9.3.0,
+    wandb 0.16.1, XGBoost 2.0.2, xprop 1.2.6, xtb 6.6.1, Xvfb 21.1.9, xxd 9.0.2112
+- minor enhancements, including:
+  - add sanity check commands for recent GDB versions (#19102)
+  - add aarch64 and ppc64le checksums to NVHPC 23.7 (#19249)
+  - allow Python version of Z3 to be used as a dependency (#19354)
+- various bug fixes, including:
+  - use `CargoPythonBundle` generic easyblock for timm to install required Rust packages in a controlled way (#18332)
+  - add alternate checksum for OpenImageIO v2.4.14.0 (#19090)
+  - only set flag `--enable-asmjit` for PLUMED when installing on `x86_64` (#19110)
+  - ensure right Python version is used in DP3, WSClean and dependencies by specifying `-DPython3_EXECUTABLE` CMake option (#19119)
+  - add patch to work around potential crash in PyTorch 1.13.1 caused by GCC 12 compiler bug (#19133)
+  - add patch to fix detection of newer Intel CPUs in OpenBLAS 0.3.20 through 0.3.23 (#19141)
+  - remove outdated `--disable-docs` configure option from FriBidi-1.0.12 (#19147)
+  - add libiconv dependency to gettext 0.22 (#19155)
+  - fix OpenBLAS 0.3.20+ on newer Intel CPUs (#19159)
+  - only use ScaFaCos as dependency for LAMMPS 23Jun2022 on `x86_64` (#19164)
+  - add patch to fix regression in GCC 12.x on AVX512 systems (#19180)
+  - add pkgconf build dependency to libGLU (#19186)
+  - sidestep some build issues with CUDA-Samples 12.1 (#19189)
+  - make Pillow easyconfigs aware of sysroot template (#19226, #19267)
+  - fix possible error/crash in NCCL on x86 due to cpuid (#19231)
+  - reduce timestep to fix sanity check commands in LAMMPS 23Jun2022 (#19246)
+  - add patch for GCC 12.x to fix miscompiling C++ code causing double-free in case of exceptions (#19253)
+  - replace format tag with explicit extension name in Optuna v3.0.3 (#19256)
+  - enhance easyconfigs for gnuplot 5.4.x to make sure that Lua dependency is always used (#19261)
+  - patch setup.py for grpcio extension in TensorFlow 2.13.0 easyconfigs to take into account alternate sysroot (#19268)
+  - avoid indirect dependency on old CMake version built with GCCcore/10.2.0 via Catch2 build dependency using system toolchain in recent pybind11 easyconfigs (#19270)
+  - use existing patch in pybind11 2.6.2 and 2.7.1 to fix failing test due to extra whitespace (#19279)
+  - change toolchain in `json-fortran` easyconfigs to `GCC`, since it includes Fortran modules (#19283)
+  - remove Unicode character in description of SMRT-Link easyconfigs (#19312)
+  - don't use `%(namelower)s` template in extension name in IPython v8.14.0 easyconfig (#19330)
+  - add patch to fix `[cz]asums` in OpenBLAS 0.3.24 (#19331)
+  - fix failing tokenizers with `CargoPythonPackage` easyblock (#19333)
+  - define `$GTKDOCIZE` as '`echo`' before generating configure script for new HarfBuzz versions (#19339)
+  - fix PAPI test step hanging on some systems (#19372)
+  - compile LERC test binary in `postinstallcmds` to fix sanity check error when RPATH linking is enabled (#19386)
+  - use `GCC` toolchain in `kim-api`, since it includes Fortran modules (#19399, #19401, #19402, #19403, #19404, #19405)
+  - fix wrong handling of floats in z3-solver (#19414)
+  - Fix numpy build on Sapphire Rapids CPUs in SciPy-bundle-2023.07-gfbf-2023a (#19419, #19425)
+  - allow ITK legacy code and Python wrappers in ITK v5.2.1 (#19431)
+  - link to xxHash library provided via EasyBuild in python-xxhash v3.2.0 (#19432)
+  - include MPFR 4.1.0 patch in MPFR 4.2.0 easyconfigs to fix failing tsprintf test with glibc >= 2.37 (#19438)
+  - skip `Test::Sys::Info` test that expects `/etc/fstab` in Perl-bundle-CPAN (#19440)
+  - exclude `cdp*` CUDA samples that fail to build on aarch64 in CUDA-Samples v12.1 (#19451)
+- other changes:
+  - let SuiteSparse easyblock set `CMAKE_OPTIONS` for SuiteSparse v7.1.0 (#19177)
+  - add versionsuffix `-param` to easyconfig for ReaxFF 2.0 (#19307)
+  - use `LooseVersion` from `easybuild.tools` (#19376)
+
+
 v4.8.2 (29 October 2023)
 ------------------------
 

easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb

@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = '4ti2'
+version = '1.6.9'
+
+homepage = 'https://4ti2.github.io/'
+description = """A software package for algebraic, geometric and combinatorial problems on linear spaces"""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+github_account = '4ti2'
+source_urls = [GITHUB_SOURCE]
+sources = ['Release_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['7b1015718102d8cd4dc2de64f69094fdba0bc69a1878ada5960979b171ff89e4']
+
+dependencies = [
+    ('GMP', '6.2.1'),
+    ('GLPK', '5.0'),
+]
+
+builddependencies = [('Autotools', '20220317')]
+
+preconfigopts = './autogen.sh && '
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['4ti2gmp', '4ti2int32', '4ti2int64']],
+    'dirs': ['include/4ti2', 'lib', 'share/4ti2']
+}
+
+moduleclass = 'math'

easybuild/easyconfigs/a/AICSImageIO/AICSImageIO-4.14.0-foss-2022a.eb

@@ -0,0 +1,64 @@
+easyblock = 'PythonBundle'
+
+name = 'AICSImageIO'
+version = '4.14.0'
+
+homepage = 'https://github.com/AllenCellModeling/aicsimageio'
+description = """Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('dask', '2022.10.0'),
+    ('imagecodecs', '2022.9.26'),
+    ('lxml', '4.9.1'),
+    ('SciPy-bundle', '2022.05'),
+    ('PyYAML', '6.0'),
+    ('wrapt', '1.15.0'),
+    ('xarray', '2022.6.0'),
+    ('zarr', '2.13.3'),
+    ('aiohttp', '3.8.3'),
+    ('scikit-image', '0.19.3'),
+    ('pydantic', '1.10.4'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('pydantic_compat', '0.1.2', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['37a4df48565a35aedc947f0fde5edbdff270a30836d995923287292bb59d5677'],
+    }),
+    ('xsdata', '23.8', {
+        'checksums': ['55f03d4c88236f047266affe550ba0dd19476adfce6a01f3e0aefac7c8078e56'],
+    }),
+    ('ome_types', '0.4.3', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['3d97ce595d0f2f9c37dce3dd359fb30c7dbcad8c8c806604c40f18f99be8c1b2'],
+    }),
+    # Overwrites installed version because aicsimageio 4.14.0 has requirement fsspec<2023.9.0,>=2022.8.0
+    ('fsspec', '2023.6.0', {
+        'checksums': ['d0b2f935446169753e7a5c5c55681c54ea91996cc67be93c39a154fb3a2742af'],
+    }),
+    ('ome-zarr', '0.8.3', {
+        'checksums': ['e98762e6a3cc82e8f6ef50c938e23fc579498d94d1991f3476ccf9726209997b'],
+    }),
+    ('resource_backed_dask_array', '0.1.0', {
+        'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'],
+    }),
+    ('elementpath', '4.1.5', {
+        'checksums': ['c2d6dc524b29ef751ecfc416b0627668119d8812441c555d7471da41d4bacb8d'],
+    }),
+    ('xmlschema', '2.5.0', {
+        'checksums': ['276a03e0fd3c94c148d528bff4d9482f9b99bf8c7b4056a2e8e703d28149d454'],
+    }),
+    ('%(namelower)s', version, {
+        'checksums': ['0f6684587b1d833ce5b10f3e81314e2a89269cd94bd09747fcd6460f3119855c'],
+    }),
+]
+
+sanity_check_commands = ["python -c 'from aicsimageio.writers import OmeTiffWriter'"]
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023a.eb

@@ -0,0 +1,41 @@
+easyblock = 'CMakeMake'
+
+name = 'ALL'
+version = '0.9.2'
+
+homepage = 'https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing'
+description = """A Load Balancing Library (ALL) aims to provide an easy way to include dynamic
+domain-based load balancing into particle based simulation codes. The library
+is developed in the Simulation Laboratory Molecular Systems of the Jülich
+Supercomputing Centre at Forschungszentrum Jülich."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ["https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing/-/archive/v%(version)s/"]
+sources = ['loadbalancing-v%(version)s.tar.gz']
+checksums = ['2b4ef52c604c3c0c467712d0912a33c82177610b67edc14df1e034779c6ddb71']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('Boost', '1.82.0'),  # only needed for tests
+]
+
+dependencies = [
+    ('VTK', '9.3.0'),
+]
+
+configopts = '-DCM_ALL_FORTRAN=ON -DCM_ALL_USE_F08=ON -DCM_ALL_VORONOI=ON -DCM_ALL_VTK_OUTPUT=ON '
+configopts += '-DCM_ALL_TESTS=ON -DCM_ALL_AUTO_DOC=OFF -DVTK_DIR=$EBROOTVTK '
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': [
+        'include/ALL.hpp', 'include/ALL_Voronoi.hpp', 'lib/all_module.mod',
+        'lib/libALL.a', 'lib/libALL_fortran.a'
+    ],
+    'dirs': ['lib/cmake'],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/ANTIC/ANTIC-0.2.5-gfbf-2022a.eb

@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'ANTIC'
+version = '0.2.5'
+
+homepage = 'https://github.com/flintlib/antic'
+description = "Antic is an algebraic number theory library."
+
+toolchain = {'name': 'gfbf', 'version': '2022a'}
+toolchainopts = {'pic': True}
+
+github_account = 'flintlib'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['7b236b6226d5730cf66d492f1562c34d4dcf1bdc8775fec2330f560332ab05c1']
+
+dependencies = [('FLINT', '2.9.0')]
+
+configopts = "--with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR --with-flint=$EBROOTFLINT "
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['lib/libantic.%s' % e for e in ['a', SHLIB_EXT]] +
+             ['include/antic/%s.h' % h for h in ['nf', 'nf_elem', 'qfb']],
+    'dirs': [],
+}
+
+moduleclass = 'math'

easybuild/easyconfigs/a/ANTs/ANTs-2.5.0-foss-2022b.eb

@@ -0,0 +1,37 @@
+easyblock = 'CMakeMake'
+
+name = 'ANTs'
+version = '2.5.0'
+
+homepage = 'https://stnava.github.io/ANTs/'
+description = """ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing,
+ interpreting and visualizing multidimensional data."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/ANTsX/ANTs/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['326efda09608a19752e802acc46ed808a4fdb62765f11a4f26402a5aa8bc70ac']
+
+builddependencies = [('CMake', '3.24.3')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('VTK', '9.2.6'),
+]
+
+configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
+configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON '
+configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF'
+
+preinstallopts = "cd ANTS-build && "
+
+sanity_check_paths = {
+    'files': ['bin/ANTS', 'bin/antsBrainExtraction.sh'],
+    'dirs': ['lib'],
+}
+
+modextravars = {'ANTSPATH': '%(installdir)s/bin'}
+
+moduleclass = 'data'

easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb

@@ -32,6 +32,11 @@ dependencies = [
     ('libxml2', '2.9.13'),
 ]
 
+# Without this, the wrong (system) python is picked up by cmake
+# in cases where the system python is newer than the one used in these EasyConfigs
+# See PR # 19119
+configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python '
+
 sanity_check_paths = {
     'files': ['include/aoflagger.h', 'bin/aoflagger'],
     'dirs': ['bin'],

easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb

@@ -0,0 +1,39 @@
+easyblock = 'MesonNinja'
+
+name = 'ATK'
+version = '2.38.0'
+
+homepage = 'https://developer.gnome.org/atk/'
+description = """
+ ATK provides the set of accessibility interfaces that are implemented by other
+ toolkits and applications. Using the ATK interfaces, accessibility tools have
+ full access to view and control running applications.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Meson', '1.2.3'),
+    ('Ninja', '1.11.1'),
+    ('pkgconf', '2.0.3'),
+    ('GObject-Introspection', '1.78.1'),
+]
+
+dependencies = [
+    ('GLib', '2.78.1'),
+]
+
+configopts = "--buildtype=release --default-library=both "
+configopts += "-Dintrospection=true "
+
+sanity_check_paths = {
+    'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'vis'