Merge pull request #22952 from easybuilders/5.1.x

release EasyBuild v5.1.0

Author: boegel

.github/workflows/unit_tests.yml

@@ -51,7 +51,7 @@ jobs:
       run: |
           cd $HOME
           # first determine which branch of easybuild-framework repo to install
-          BRANCH=5.0.x
+          BRANCH=develop
           if [ "x$GITHUB_BASE_REF" = 'xmain' ]; then BRANCH=main; fi
           if [ "x$GITHUB_BASE_REF" = 'x5.0.x' ]; then BRANCH=5.0.x; fi
           echo "Using easybuild-framework branch $BRANCH (\$GITHUB_BASE_REF $GITHUB_BASE_REF)"

.pre-commit-config.yaml

@@ -3,9 +3,117 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at https://docs.easybuild.io/release-notes .
 
-The latest version of easybuild-easyconfig provides 10,372 easyconfig files, for 2,835 different software packages,
+The latest version of easybuild-easyconfig provides 10,774 easyconfig files, for 2,899 different software packages,
 incl. 41 different (compiler) toolchains.
 
+
+v5.1.0 (26 May 2025)
+--------------------
+
+feature release
+
+- add easyconfigs for `foss/2025a` and `intel/2025a` common toolchains (#22879, #22941)
+- added example easyconfig files for 64 new software packages:
+  - ADMIXTURE (#22813), bcgTree (#22540), BOLT-LMM (#22771), Boltz-1 (#22473, #22475), bwtool (#22925), CAESES (#20542), cellsnp-lite (#22632),
+    clisops (#22635), compleasm (#21837), cooltools (#22536), cramjam (#22465), CrystFEL (#22863), Evo (#22746), FALL3D (#22610), fastStructure
+    (#22423), FCM (#17115), GCTB (#22710), grackle (#21185), greedy (#22755), HEEDS (#20545), jupyterlab-h5web (#22374), koopmans (#22372), koopmans-kcp (#22372),
+    koopmans-qe-utils (#22372), KrakenTools (#22617), Lep-MAP3 (#22794), libbeato (#22925), LM-Studio (#22712), lsb_release (#22721),
+    LST-AI (#22755), Mamba-SSM (#22670), MAQAO (#22860), momepy (#22131), MOPAC (#22662), ninja-python (#22669), pairix (#22600), PFLOTRAN_OGS (#18141),
+    porefoam (#22915), ProLaTherm (#22194), ProTstab2 (#22302), PyEphem (#22783), pyet (#22668), PySAL (#22316), PySide6 (#22906),
+    pytest-subtests (#22849), quaqc (#22872), RFdiffusion-models (#20019), RFdiffusion-schedules (#20019), SQUID (#22637), SQuIRE (#22356),
+    STITCH (#22525), stpipeline (#17127), tblite (#19219), TEtrimmer (#22252), THOP (#22762), timezonefinder (#22783), Tinker-HP (#22224),
+    tlparse (#20489), tree-sitter (#22776), TSEBRA (#21837), UFCG (#22223), uv (#21637), xclim (#22635), yacrd (#22812)
+- added additional easyconfigs for various supported software packages, including (but not limited to):
+  - AFNI 25.1.01, AlphaPulldown 2.0.3, Amber 24.0, AUGUSTUS 3.5.0, binutils 2.44, Bracken 3.1, CUDA 12.9.0, GCC 14.3.0 + 15.1.0,
+    geopandas 1.0.1, `iimkl/2024a`,
+    LLVM 20.1.5, metaWRAP 1.4-20230728, MPICH 4.3.0, MultiQC 1.28,
+    Nektar++ 5.7.0, NVHPC 25.3, nvtop 3.2.0, openCARP 17.0, OpenFold 2.0.0, OpenMolcas 24.10, PETSc 3.22.5, poetry 2.1.2, PyOpenGL 3.1.9, PyTensor 2.30.3, PyTorch
+    2.3.0, Python-bundle-PyPI 2025.04, RepeatModeler 2.0.6, Rust 1.85.1, QIIME2
+    2024.10.1, Qt5 5.15.16, scikit-learn 1.6.1, scikit-optimize 0.10.2, Score-P 9.0, StringTie
+    3.0.0, SuiteSparse 7.10.1, tiktoken 0.9.0, trimAl 1.5.0, Valgrind 3.25.0, VTK 9.3.1, WhatsHap 2.6
+- minor enhancements, including:
+  - add modsem extension + its dependencies to recent R-bundle-CRAN easyconfigs (#22594)
+  - add sgdGMF extension to recent R-bundle-CRAN easyconfigs (#22709)
+  - also build static libraries of Abseil (#22805)
+  - also install Python bindings for zlib-ng v2.1.6 (#22818)
+  - add patch to add zen5 support to OpenBLAS 0.3.27 (#22850)
+  - incorporate more detailed description in MAQAO easyconfig (#22864)
+  - add kableExtra extension to R-bundle-CRAN 2023.12 (#22874)
+  - add hiAnnotator extension to recent R-bundle-Bioconductor easyconfigs (#22873, #22897, #22898)
+- various bug fixes, including:
+  - add JsonCpp dependency to recent BamTools easyconfigs (#21612)
+  - add missing dependencies (TSEBRA, compleasm) + use more recent AUGUSTUS version for BRAKER v3.0.8 (#21837)
+  - add patch for OpenMPI v5.0.3 to fix C90 compliance (#22006)
+  - add an egg-info file to make RDKit findable by pip (#22018)
+  - disable check for RPATH section in git-lfs easyconfigs (#22346)
+  - add patch for astropy 7.0.0 to make one of the tests pass on ARM architectures (#22469)
+  - add patch to fix broken test for Siesta v5.2.2 (#22562)
+  - control number of parallel processes used by Ninja and add fix for aarch64 in easyconfig for Qt6 6.7.2 (#22588)
+  - add patch to fix regression in pytest 8.2.2 (#22602)
+  - remove Python 2.7 + Python 3.5 from classifiers in `setup.py` (#22605, #22621)
+  - update homepage and source URLs in libGLU easyconfigs (#22625)
+  - fix statsmodels 0.14.4 version by replacing incorrect patch with sed command in preinstallopts (#22628)
+  - use HTTP rather than FTP in source URLs of 'file' easyconfigs (#22685)
+  - add patch in occt easyconfig to fix OpenCASCADEConfig.cmake to correctly deal with `lib64` directory (#22689)
+  - add patch to fix OSHA1stream.H in OpenFOAM 6-20190620 w/ foss/2023a (#22694)
+  - make Python a dependency of GObject-Introspection 1.80.1 (#22701)
+  - update version of pRolocdata and RnBeads.hg38 extensions in R-bundle-Bioconductor 3.20 (since source tarball for previous versions are no longer available) (#22706)
+  - add patch to make bcgTree 1.2.1 compatible with MUSCLE 5 (#22707, #22852, #22861)
+  - re-add build of shared libs for LLVM (#22720)
+  - add lsb_release as build dependency to recent ABAQUS easyconfigs (#22721)
+  - add patch to fix dependency check in OPERA-MS (#22725)
+  - patch Siesta in order to let EasyBuild control optimization flags (#22731)
+  - add patch to avoid OpenCV searching for Python 2 (#22742)
+  - ensure `Infernal` is built with MPI support, and drop toolchain to gompi (#22753)
+  - ensure `Proteinortho` links against `FlexiBLAS`, and bump to `foss` (#22754)
+  - fix get_good_inter_pae.py script in AlphaPulldown v2.0.3 (#22758)
+  - use proper dependency for tokenizers in Uni-Core v0.0.3 (#22758)
+  - add patch to fix installation of MUSCLE 5.1.0 on aarch64 systems (#22780)
+  - use "standard" variant of RAxML dependency for bcgTree on aarch64 systems (#22781)
+  - add patch to fix bug in unittest-xml-reporting on Python 3.11+ (#22787)
+  - copy tests to minimap2 install dir to fix --sanity-check-only and --module only (#22791)
+  - fix installing recent `minimap2` easyconfigs on ARM (#22791)
+  - add groff build dependency to enchant-2 easyconfigs (#22804)
+  - set C standard to `c99` for ncurses 6.5 and M 1.4.19 with system toolchain (#22807, #22798)
+  - add optional patch file for OpenMPI 4.1.5 to disable OPAL path NFS test (#22817)
+  - add missing groff build dependency for Graphviz 12.2.0 (#22837)
+  - use `Java/21` wrapper instead of specific version for Bazel (#22839), Turbovnc (#22838), GraphViz (#22837)
+  - add patch to fix PyTorch 2.3 on systems with disabled SMT (#22843)
+  - use `modextravars` to set `$GENEMARK_PATH` in funannotate easyconfig (#22851)
+  - use `CargoPythonBundle` easyblock for Python-bundle-PyPI 2024.06 (#22853)
+  - don't update `$PYTHONPATH` via `modextrapaths` in easyconfig for OTF2 3.1.1 (#22854)
+  - add ICU dependency for Xerces-C++ 3.2.5 (#22866)
+  - use mimalloc instead of jemalloc for Arrow 17.0.0 (#22858)
+  - fix LM Studio AppImage permission (#22867)
+  - disable XPMEM in recent libfabric easyconfigs (v1.21.0, v2.0.0) (#22880)
+  - port ReFrame easyconfigs to EasyBuild 5 (#22883)
+  - fix MKL ILP64 flags for Global Arrays 5.8.2 w/ `intel/2024a` (#22894)
+  - disable libxpmem explicitely in OpenMPI 5 (#22902)
+  - stick to QIIME2 2024.2.0 with foss/2023a, since recent versions (like 2024.10.0) require a more recent version of `pandas` (#22904)
+  - add patch for PMIx 5.0.2 to fix support for IPv6 (#22909)
+  - don't fix shebang line in mympirun script, to make sure it uses system Python (#22916)
+  - define `$CONDA_PREFIX` via `modextravars` in QIIME2 (#22918)
+  - add patch to fix ml_dtypes 0.5.0 on AVX512 CPUs with FP16 support (#22919)
+  - stick to torchrl 0.3.0 in PyTorch-bundle 2.1.2 (#22937)
+- other changes:
+  - stick to `gfbf/2023b` toolchain for SuiteSparse 7.7.0 and remove `METIS` dependency + corresponding `versionsuffix` (#21199)
+  - change default data location in snpEff v5.2c to be a user-writable directory (#21910)
+  - update easyconfigs according to defaults in EasyBuild 5.x (#22629)
+  - improve failure message for download instruction CI check (#22648)
+  - delete `.pre-commit-config.yaml` (#22665)
+  - use `PythonPackage` easyblock for coverage v7.4.4 (#22672)
+  - use `SHLIB_EXT` in `TinyXML` (#22703)
+  - use Python rather than CMake as dependency in easyconfig templates for `PythonBundle` easyblock (#22760)
+  - replace `setenv` commands with environment variables in module footers with `modextravars` in easyconfigs for HIP, JupyterLab, mujoco-py, Triton (#22801)
+  - fix missing space in missing-patch CI error (#22826)
+  - update to latest Java versions for Java/8, Java/11, Java/17, Java/21, Java/23 (#22840)
+  - use Java 17 as default Java version in all 2024a generation easyconfigs (#22862)
+  - disable building documentation for jemalloc (#22869, #22870)
+  - add missing extension curly brackets and parentheses to template easyconfigs (#22892)
+  - update easyconfigs to use `Binary` instead of (deprecated) `JAR` easyblock (#22900)
+
+
+
 v5.0.0 (18 March 2025)
 ----------------------
 

RELEASE_NOTES

@@ -24,8 +24,10 @@ exts_list = [
     }),
     ('ext2-name-from-pypi', 'ext2_version', {
         'modulename': 'import_name',
+    }),
     ('wheel-name-from-pipy', 'ext3_version', {
         'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+    }),
     ('name-lower', 'version', {
         'use_pip_extras': 'extra',
     }),

contrib/easyconfig-templates/2022a/PythonBundle-minimal.eb.tmpl

@@ -21,8 +21,10 @@ exts_list = [
     }),
     ('ext2-name-from-pypi', 'ext2_version', {
         'modulename': 'import_name',
+    }),
     ('wheel-name-from-pipy', 'ext3_version', {
         'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+    }),
     ('name-lower', 'version', {
         'use_pip_extras': 'extra',
     }),

contrib/easyconfig-templates/2022a/PythonBundle-scipy.eb.tmpl

@@ -24,8 +24,10 @@ exts_list = [
     }),
     ('ext2-name-from-pypi', 'ext2_version', {
         'modulename': 'import_name',
+    }),
     ('wheel-name-from-pipy', 'ext3_version', {
         'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+    }),
     ('name-lower', 'version', {
         'use_pip_extras': 'extra',
     }),

contrib/easyconfig-templates/2023a/PythonBundle-minimal.eb.tmpl

@@ -21,8 +21,10 @@ exts_list = [
     }),
     ('ext2-name-from-pypi', 'ext2_version', {
         'modulename': 'import_name',
+    }),
     ('wheel-name-from-pipy', 'ext3_version', {
         'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+    }),
     ('name-lower', 'version', {
         'use_pip_extras': 'extra',
     }),

contrib/easyconfig-templates/2023a/PythonBundle-scipy.eb.tmpl

@@ -16,16 +16,18 @@ builddependencies = [
 ]
 
 dependencies = [
-    ('CMake', '3.12.3'),
+    ('Python', '3.12.3'),
 ]
 
 exts_list = [
     ('ext1-name-from-pypi', 'ext1_version', {
     }),
     ('ext2-name-from-pypi', 'ext2_version', {
         'modulename': 'import_name',
+    }),
     ('wheel-name-from-pipy', 'ext3_version', {
         'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+    }),
     ('name-lower', 'version', {
         'use_pip_extras': 'extra',
     }),

contrib/easyconfig-templates/2024a/PythonBundle-minimal.eb.tmpl

@@ -17,7 +17,7 @@ builddependencies = [
 ]
 
 dependencies = [
-    ('CMake', '3.12.3'),
+    ('Python', '3.12.3'),
 ]
 
 exts_list = [

contrib/easyconfig-templates/2024a/PythonBundle-pytest.eb.tmpl

@@ -9,10 +9,10 @@ description = """
 Description in 80 chars long column
 """
 
-toolchain = {'name': 'gfbf', 'version': '2023a'}
+toolchain = {'name': 'gfbf', 'version': '2024a'}
 
 dependencies = [
-    ('CMake', '3.12.3'),
+    ('Python', '3.12.3'),
     ('SciPy-bundle', '2024.05'),
 ]
 
@@ -21,8 +21,10 @@ exts_list = [
     }),
     ('ext2-name-from-pypi', 'ext2_version', {
         'modulename': 'import_name',
+    }),
     ('wheel-name-from-pipy', 'ext3_version', {
         'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+    }),
     ('name-lower', 'version', {
         'use_pip_extras': 'extra',
     }),