Merge pull request #24021 from easybuilders/5.1.x

release EasyBuild v5.1.2

Author: boegel

RELEASE_NOTES

@@ -3,10 +3,136 @@ 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 9,901 easyconfig files, for 2,835 different software packages,
+The latest version of easybuild-easyconfig provides 10,735 easyconfig files, for 2,917 different software packages,
 incl. 41 different (compiler) toolchains.
 
 
+v5.1.2 (26 Sept 2025)
+---------------------
+
+update/bugfix release
+
+- add easyconfigs for `foss/2025b` and `intel/2025b` common toolchains (#23480, #23468, #23586, #23589, #23708)
+- added example easyconfig files for 81 new software packages:
+   - aiida-core (#20456), asv (#23724), autoCAS (#23201), BigStitcher-Spark (#23726), BPCells (#23441), cargo-c (#23437), Chargemol (#20885),
+     CHARM++ (#22281), Cling (#23388), CPCM-X (#23575), dpcpp (#22418), Eclipse-IDE-java (#19621), Eclipse-SDK (#19621), Elixir (#20441),
+     ErlangOTP (#20441), EvtGen (#19135), flit-core (#23306), Flux (#22979), GAlib (#23862), glslang-SPIRV (#23171), GoPeaks (#20932),
+     gpaw-data (#23666), heat (#23857), hpc-container-wrapper (#23701), HPCToolkit (#23830), huggingface_hub (#23656), iGUIDE (#23467),
+     IMAS-Validator (#23052), ipp (#23691), ipyparallel (#23300), LCov (#23752), libecpint (#16172), libGDSII (#23456), libneurosim (#23481),
+     libosmium (#23768, #23788), libspng (#23485), libtecla (#19874), libtommath (#23570), libvpx (#23486), lru-dict (#20593), luaposix (#22979),
+     Ludwig (#23348), MACE (#23210), mcpl (#23224), McXtrace (#22834), MDSplus (#23531), MFEM (#21023), minizip-ng (#23522), mirtrace (#18781),
+     MongoDB (#17366), mpiP (#16796), numdifftools (#23342), numsa (#23575), nvbandwidth (#23653), NVPL (#20456), OpenColorIO (#23522), OpenQP (#22739),
+     opt-einsum (#23322), OSM-Express (#23771), osmium-tool (#23768, #23788), PennCNV (#21827), Planet (#21302), plumpy (#23469), PPM (#23225),
+     protozero (#23768, #23788), pyOpenRiverCam (#23540), pyrosm (#23771), pystring (#23522), QCMaquis (#23201, #23980), r5py (#23345),
+     RabbitMQ (#20441), RDP (#23344), rkcommon (#23504), RSAT (#23706), schemdraw (#23265), simplification (#23344), SnapATAC2 (#23314),
+     starfile (#20634), websockify (#23596), wxMacMolPlt (#22187), xmlto (#20441)
+- added additional easyconfigs for various supported software packages, including (but not limited to):
+  - AmberTools 24.10 + 25.2, ASE 3.26.0, BLIS 2.0, CASTEP 25.1.2, CDO 2.5.3, CENSO 2.1.4, CGAL 6.0.1, CUDA 12.9.1 + 13.0.0, CUDA-Python 12.8.0,
+    CUDA-Samples 12.9, CUTLASS 4.1.0, deepdiff 8.5.0, DualSPHysics 5.4.0, ecCodes 2.43.0, ELPA 2025.06.001, Emacs 30.1, GATE 10.0.2, GCC 15.2.0,
+    GDAL 3.11.1, Go 1.25.0, GPAW 25.7.0, GROMACS 2025.2, GTK4 4.17.1, Highway 1.3.0, HTSlib 1.22.1, iomkl 2023b/2024a/2025a, jax 0.6.2 + 0.7.0,
+    libxc 7.0.0, likwid 5.4.1, LLVM 20.1.8, lxml 6.0.0, magma 2.9.0, matplotlib 3.10.5, MixMHC2pred 2.0, modkit 0.5.0, MUST 1.11.1, NAMD 3.0.2,
+    networkx 3.5, NLTK 3.9.1, numba 0.62.0, NVSHMEM 3.3.20, Octave 10.1.0, ollama 0.11.10, OpenCV 4.11.0, OpenMM 8.3.0, ORCA 6.1.0,
+    Perl-bundle-CPAN 5.40.2, PETSc 3.23.5, pocl 7.0, PyStan 3.10.0, PYTHIA 8.2.45, Python-bundle-PyPI 2025.07, PyTorch 2.6.0, pytorch-3dunet 1.9.1,
+    QuantumESPRESSO 7.5, ROOT 6.32.10, SAMtools 1.22.1, scikit-learn 1.7.0, SciPy-bundle 2025.07, Score-P 9.2, segmentation-models-pytorch 0.5.0,
+    SeqKit 2.10.1, Siesta 5.4.1, SLEPc 3.23.2, SLiM 5.0, SUNDIALS 7.0.0, torchvision 0.21.0, X11 20250608, xarray 2025.7.0
+  - add CodePlay CUDA SYCL plug-in variants for oneAPI 2023.0.0 to 2025.0.0 (#21582)
+- minor enhancements, including:
+  - also install Python bindings in recent tblite 0.4.0 easyconfigs (#23998)
+- various bug fixes, including:
+  - switch to `CargoPythonBundle` easyblock for orjson 3.9.15 (#21392)
+  - run the tests in the test step for OpenMolcas (#22230)
+  - add patch to enable installing GLib typelibs for GObject-Introspection 1.80.1 (#22309, #23444)
+  - use patch to fix pkgconfig file for GraphicsMagick 1.3.45 (#22930)
+  - remove default `separate_build_dir = True` from various easyconfigs (#23296, #23303, #23315, #23317, #23327, #23328, #23329, #23332, #23334, #23335, #23336)
+  - fix setting of `PYSCF_INC_DIR` in build options and Python packages in `PySCF` easyconfigs (#23325)
+  - fix `source_urls` for `FLINT` (#23333)
+  - add libiconv build dependency to libarchive 3.8.1 (#23353)
+  - add patch to build versioned shared libraries in ecCodes v2.38.3 (#23360)
+  - fix missing `-lm -lpthread` for SQLite 3.50.1 by setting `$LIBS` to empty string value (#23374)
+  - add patch to re-enable `-rpath-link` for builds with Meson 1.8.2 (#23375)
+  - replace broken source URL with download instructions in easyconfigs for bcl2fastq2 2.20.0 (#23427)
+  - add pkgconf build dependency for Tkinter (#23428)
+  - add missing libxml2, libffi, zstd dependencies for LLVM (#23429, #23555, #23603, #23608, #23609, #23610, #23611, #23612, #23613)
+  - fix outdated source URL for `occt` v7.5.0p1 (#23430)
+  - add patch to EasyBuild 5.1.1 easyconfig for bug that causes failures when copying readonly patches (#23442)
+  - add `pkgconf` build dep for `SentencePiece` (#23444)
+  - restore easyconfig for ADMIXTURE v1.3.0 (#23449)
+  - add `Perl` and `pkgconf` build dependencies to easyconfigs for PMIx 5.x (#23495)
+  - fix broken source URLs for Mesa versions 23.x  (#23516)
+  - explicitly disable libgsasl support in cURL easyconfigs avoid picking up system library (#23519)
+  - add missing dependencies libxml2 & zstd to libarchive easyconfigs (#23520)
+  - fix hardcoded path to java binary in canu v2.3 + add OpenSSL dependency (#23529)
+  - add patch for ESM-2 2.0.0 (#23532)
+  - add additional patches for OpenMPI 5.0.7 (#23556)
+  - disable flaky `LWP::Simple` test in `Perl` * `Perl-bundle-CPAN` (#23564, #23565)
+  - add libtommath dependency to Tcl v9.0.1 (#23568)
+  - fix installation of xtb 6.7.1 w/ `gfbf/2023b` by adding missing dependencies (mctc-lib, tblite, mstore, numsa, CPCM-X, dftd4, Simple-DFTD3) (#23575)
+  - disable `lseq` tests when building Tcl 9.0.1 on Arm and RISC-V systems (to avoid hang in test step) (#23617, #23619)
+  - fix version information for `cppy` (#23625)
+  - add patch for dask v2024.9.1 to fix incorrect indexing with boolean arrays (#23634)
+  - skip flaky sanitizer tests in easyconfig for LLVM 18.1.8 (#23636)
+  - ignore failing time formatter tests for LLVM 20.1.8 (#23637)
+  - add missing ASE versionsuffix for MACE and remove redundant ASE exception from easyconfigs test suite (#23660)
+  - fix source for PARI-GP 2.15.x + add missing Bison build dependency (#23662)
+  - update extensions for OCaml 4.14.0 and 5.1.1 to nearest version that is still available (#23664)
+  - install `strmap.h` in easyconfig for mpifileutils 0.12 (#23676)
+  - fix homepage in easyconfigs for `intel` toolchain (#23695)
+  - update `source_urls` for `WCSLIB` (#23722)
+  - fix incorrect configopts for GOTCHA (#23732)
+  - apply small fix in `simnibs_segmentation_utils.py` of SimNIBS v4.0.1 (#23748)
+  - add patch to git easyconfigs to fix CVE-2025-48384 (#23769)
+  - update source URL for CFITSIO v4.3.0 to use `https://` (#23775)
+  - add patch to allow SymEngine v0.7 to compile with `glibc` >= 2.34 (#23817)
+  - fix build of ncurses 5.9 with system compiler on RHEL9 (#23820)
+  - fix patch for torchtext to use system libraries, to fix linking of RE2 in both PyTorch-bundle and torchtext (#23823)
+  - add Simple-DFTD3 as dependency for CREST to avoid it being downloaded during the build (#23831)
+  - use `%%(source)s` in `STREAM` easyconfigs (#23841)
+  - add patch to fix UCX-18.0.0 compatibility with CUDA 12.9 (R575) (#23843)
+  - fix typo in `%(version)s` template in easyconfig for AlphaFold v2.3.2 w/ CUDA 12.1.1 (#23850)
+  - fix SuiteSparse options for CVXOPT 1.2.6 w/ `foss/2021a` (#23864)
+  - fix specifying meson options to pass via `--config-settings` in `pip install` for matplotlib 3.9+ (#23872)
+  - replace broken source URL with download instructions in easyconfigs for bcl-convert 4.3.13 (#23878)
+  - add patch for Boost 1.85.0 to fix UB on flat_map/multimap containers (#23890)
+  - add missing ICU dependency to Xerces-C++ (#23896)
+  - consistently apply patch for OpenMPI 5.x to fix compatibility with recent GPFS versions (#23908)
+  - add patch to fix compatibility of OpenMPI 4.x >= 4.1.1 with recent GPFS (#23911, #23916, #23917)
+  - fix sources for librttopo 1.1.0 (#23921)
+  - add patch to LLVM 20.1.8 to better support CUDA 13 and Blackwell GPUs (#23940)
+  - add patch to fix failing tests for `Net::SSLeay` 1.92 and `IO::Socket::SSL` 2.083 in Perl-bundle-CPAN easyconfigs (#23967)
+  - add missing zlib + zstd dependencies for Clang 18.1.8 (#23983)
+- enhancements and fixes for test suite:
+  - add RISC-V support to R-bundle-CRAN easyconfigs by adding/improving patches for `liquidSVM` and `ff` extensions (#21726)
+  - add patches for LLVM 20.1.5 required for RISC-V compatibility (#22656)
+  - include `intel-compilers` in the toolchain multi-variant checks (#23187, #23594)
+  - remove unused whitelist items for non HTTPS URLs in test suite (#23235)
+  - add RISC-V checksum to Java 17.0.15 easyconfig (#23448)
+  - add NVPL backend to FlexiBLAS v3.4.5 (#23563)
+  - add RTree module to SQLite 3.50.1, required by GDAL-3.11.3 (#23765)
+  - enhance patch file to show output when LAMMPS Python package failed to install (#23774)
+  - add patch for ESPResSo v4.2.2 to allow specifying target CUDA architectures (#23795)
+- other changes:
+  - remove redundant `default_easyblock` in PyQt5 and ml-dtypes easyconfigs (#22449)
+  - add InterProScan_data dependency to easyconfig for InterProScan 5.73-104.0 (#22747)
+  - use LLVM easyblock for Clang 18 easyconfigs (#23055)
+  - add explicit `R-bundle-CRAN` dependency to `R-bundle-Bioconductor` (#23127)
+  - switch to `CMakeMake` easyblock and remove unused dependencies in `Armadillo/14.0.3-foss-2024a` (#23261)
+  - cleanup `icc`, `iccifort`, and `ifort` directories (#23230)
+  - remove final links to gforge (#23233)
+  - use minimal Graphviz as dependency for MUST v1.10.0 + also install prebuilds (#23308)
+  - use available custom easyblock for DualSPHysics v5.0.175 w/ CUDA 11.4.1 (#23382)
+  - remove `'sanity_pip_check': True` from easyconfig templates (#23418)
+  - remove `max_failed_tests` in PyTorch easyconfigs where the used value was less or equal to the default (#23577)
+  - update Java/21 wrapper to Java v21.0.8 (#23677)
+  - replace ASE v3.25.0 with v3.26.0 for 2025b generation of easyconfigs (#23758)
+  - remove duplicate Pygments package from Python-bundle-PyPI (#23801)
+  - move Biopython down to gfbf toolchain level (#23870)
+  - Unify system-lib options for matplotlib < 3.9 (#23873)
+  - explicitly disable building documentation in recent `HarfBuzz` easyconfigs (#23922)
+  - disable building of documentation for Waylandpp (#23968)
+  - remove deprecated license classifier in `setup.py` (#23991)
+  
+
+
 v5.1.1 (6 July 2025)
 --------------------
 

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

@@ -33,6 +33,5 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
 
 moduleclass = 'class_name'

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

@@ -30,6 +30,5 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
 
 moduleclass = 'class_name'

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

@@ -33,6 +33,5 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
 
 moduleclass = 'class_name'

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

@@ -29,6 +29,5 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
 
 moduleclass = 'class_name'

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

@@ -30,6 +30,5 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
 
 moduleclass = 'class_name'

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

@@ -33,6 +33,5 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
 
 moduleclass = 'class_name'

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

@@ -29,6 +29,5 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
 
 moduleclass = 'class_name'

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

@@ -30,6 +30,5 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
 
 moduleclass = 'class_name'

easybuild/easyconfigs/a/ABAQUS/ABAQUS-2024-hotfix-2450.eb

@@ -0,0 +1,40 @@
+name = 'ABAQUS'
+version = '2024'
+local_hotfix = '2450'
+versionsuffix = '-hotfix-%s' % local_hotfix
+
+homepage = 'https://www.simulia.com/products/abaqus_fea.html'
+description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit
+ dynamics FEA."""
+
+toolchain = SYSTEM
+
+with_tosca = True
+
+sources = [
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-6.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-6.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-6.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-6.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-6.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.6-6.tar',
+    # hotfixes
+    '%%(version)s.FP.CFA.%s.Part_SIMULIA_EstPrd.Linux64.tar' % local_hotfix,
+]
+checksums = [
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.1-6.tar': 'a8fcd10541a90177aefe68f0dee2a675a56cb97e1fdf4fb7d864b41d594f8b19'},
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.2-6.tar': '6caffc60ee34351203ac4205b4fcdc7e9975842e35d3ce689b831f94929ddac4'},
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.3-6.tar': '3d3bc97c686af0c87c4b6e46ae330983ed515bcc180dd30a834811c458774347'},
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.4-6.tar': 'c62596bd99125475e97bdeccd71baaf7cb36322e8da4d0dd1e4029bac677be16'},
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.5-6.tar': 'ee3349b2407b5d8a315108656590f39890d82c47085235b847103e22fba96fea'},
+    {'2024.AM_SIM_Abaqus_Extend.AllOS.6-6.tar': '482829b1c364966ae01a577233bddf6b377b8e3cd9b7f77dd95830d4636677d7'},
+    {'2024.FP.CFA.2450.Part_SIMULIA_EstPrd.Linux64.tar':
+     '0575392fea959309806c1716ca522c4688439a9555f113d73ce3313c06325fcf'},
+]
+
+download_instructions = f"""{name} requires manual download from https://www.3ds.com/support/software-downloads.
+
+Required downloads:\n{chr(10).join(sources)}"""
+
+
+moduleclass = 'cae'