Merge pull request #23339 from easybuilders/5.1.x

release EasyBuild v5.1.1

Author: boegel

RELEASE_NOTES

@@ -3,10 +3,120 @@ 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 10,774 easyconfig files, for 2,899 different software packages,
+The latest version of easybuild-easyconfig provides 9,901 easyconfig files, for 2,835 different software packages,
 incl. 41 different (compiler) toolchains.
 
 
+v5.1.1 (6 July 2025)
+--------------------
+  
+- added example easyconfig files for 105 new software packages:
+  - amdsmi (#23279), ANTx2 (#13819), ASAGI (#21065), bipartite (#21623), BLAKE3-C (#22476), btop (#21373), climate-indices (#22015),
+    ClustalW (#21973), cowsay (#22976), CrossMap (#22089), csvtk (#15305), DiffDRR (#20656), dssp (#22155), Dyninst (#22946),
+    easi (#21065), EMD (#22734), etils (#22642), evaluate (#22809), EvoDiff (#19939), Extra-P (#22907), FEBio (#22999),
+    fineSTRUCTURE (#19817), ForceBalance (#22978), FUNAERO (#23067), GADGET (#21625), GENESPACE (#21973), Gephi (#13231),
+    GIBBON (#23044), Ginkgo (#22719, #23078), googlebenchmark (#22641, #23176), GTKWave-GTK3 (#23020), h5glance (#23243), h5pyd (#21743),
+    HiCTools (#22528), huggingface-hub (#19991), IcarusVerilog (#23021), IMAS-Data-Dictionary (#22933), IMAS-Python (#22630),
+    ImpalaJIT (#21065), Infomap (#21296), intel-mbuild (#23189), intel-XED (#23189), ITK-SNAP (#13232), JACUSA2 (#23095),
+    Juicebox (#22530),KITE-Tools (#17138), Kornia (#22938), levmar (#22999), libbacktrace (#20738), libcifpp (#22155),
+    libetsf_io (#23170), libmcfp (#22155), MagicVLSI (#23018), MCScanX (#21973), mdocfile (#20610), MetaGeneMark-2 (#22531),
+    metaMDBG (#22014), MIGEC (#22989), Minimac3 (#22382), mOTUlizer (#22524), mrc (#22155), MRIcron (#13819), msgpack-cxx (#23098),
+    mumax3 (#20743), NAGlib (#22184), nanobind (#22414), Netgen (#23019), PeptideShaker (#23070), pybigtools (#22800),
+    Pychopper (#22943), pycomlink (#22974), pyiron-gpl (#23122, #23154, #23220), PyMDE (#19713, #19715), python-gdcm (#20664),
+    python-glfw (#22642), rmats2sashimiplot (#19659), robin-map (#22413), scalescape (#23038), scatac_fragment_tools (#22800),
+    SdfLib (#22642), SEACR (#22526), SearchGUI (#23309), SeisSol (#21065), SLICOT (#19860), snipit (#22266), snp-dists (#20996),
+    soapcheckr (#22939), spacyr (#22803), spin (#23023), TBProfiler (#23014), tdb (#22911), tinyobjloader (#22642), TinyXML-2 (#22642),
+    tinyxml2 (#22476), tmpi (#22949), trame (#20993), TRIQS-som (#23242), tueplots (#21335), USalign (#22463), vireoSNP (#22660),
+    WarpX (#19784), WebDataset (#22062), XeniumRanger (#20135, #20974, #21751), xschem (#23017), yMMSL-dot (#20906)
+- added additional easyconfigs for various supported software packages, including (but not limited to):
+  - Abseil 20250512.1, ABySS 2.3.10, Amber 24.3 + AmberTools 24.10, aria2 1.37.0, ASE 3.25.0, Autotools 20250527,
+    BindCraft 1.5.1, Blender 4.3.2, Boost 1.88.0, BUSCO 5.8.2, CMake 4.0.3, code-server 4.100.2, CUDA-Python 12.4.0,
+    cuDNN 9.10.1.4 , cutadapt 5.1, Dakota 6.22.0, DaliLite 5.0, datamash 1.9, DeltaLake 0.25.5, DFTB+ 24.1, DGL 1.1.3,
+    ELFIO 3.12, Embree 4.4.0, FFmpeg 7.1.1, FHI-aims 240920, Fiona 1.10.1, FLAC 1.5.0, flatbuffers-python 24.3.25,
+    Flink 2.0.0, FLTK 1.4.3, FLUENT 2024R1, GDB 16.3, Geant4 11.3.0, git-lfs 3.6.1, GLib 2.85.1, Globus-CLI 3.34.0,
+    googletest 1.17.0, gperf 3.3, GPyTorch 1.11, Gradle 8.14.2, h5py 3.14.0, HDF5 1.14.6, humann 3.9, intel-compilers 2025.2.0,
+    IPython 9.3.0, Jupyter-bundle 20250530, JupyterHub 5.3.0, Levenshtein 0.25.1, libfabric 2.1.0, libjpeg-turbo 3.1.0,
+    libpng 1.6.48, MAQAO 2025.1.0, matlab-proxy 0.25.1, matplotlib 3.10.3, MDAnalysis 2.9.0, Meson 1.8.2, mpi4py 4.1.0,
+    MUSCLE3 0.8.0, MUST 1.10.0, Nextflow 25.04.6, ngspice 44.2, Ninja 1.13.0, NLopt 2.10.0, nodejs 22.16.0, nsync 1.29.2,
+    openCARP 18.0, OpenFAST 3.5.2, OSPRay 3.2.0, OVITO 3.11.0, oxDNA 3.6.0, panaroo 1.5.1, PAPI 7.2.0, phonopy 2.40.0,
+    Pillow 11.3.0, pkgconf 2.4.3, polars 1.28.1, poppunk 2.6.7, PostgreSQL 17.5, preCICE 3.2.0, PROJ 9.5.1, py3Dmol 2.5.0,
+    Python 3.13.5, PyZMQ 27.0.0, Ray-project 2.47.1, RDKit 2025.03.3, re2c 4.2, RevBayes 1.3.0, rMATS-turbo 4.3.0,
+    rocm-smi 7.6.0 w/ ROCm 6.4.1, scNanoGPS 2.0, Siesta 5.4.0, SNAP-ESA 12.0.0, Sniffles 2.4, strace 6.14, Tcl 9.0.1,
+    TensorFlow 2.18.1, tensorflow-probability 0.23.0, Triton 3.1.0, ViennaRNA 2.7.0, X11 20250521, XZ 5.8.1
+- minor enhancements, including:
+  - add libheif dependency to JasPer easyconfigs (#22055)
+  - add ggpicrust2 and required dependencies to R-bundle-Bioconductor v3.20 and R-bundle-CRAN v2024.11 (#23026)
+- various bug fixes, including:
+  - use patch to fix finding libraries when linking ImageMagick (#21640)
+  - build CORSIKA v77550 in installation directory (#21868)
+  - add missing Python dependency to Bowtie easyconfigs (#22277)
+  - add patch for ParaView 5.12.0 to fix VTK HDF5 mangling (#22501)
+  - add patch for RISC-V architecture detection to easyconfig for ncbi-vdb 3.1.1 (#22543)
+  - fix beagle-lib dependency for MrBayes 3.2.7 (#22959)
+  - inject missing RPATH entries for QuPath (#22964)
+  - guide OpenFOAM to find the correct Python by patching `CMakeLists.txt` and setting `$Python3_ROOT_DIR` (#22969)
+  - use Rust with nightly channel as build dependency for polars 0.19.19 + 0.20.2 (#22984)
+  - add missing f-string in mixed component bundle easyconfig templates (#22996)
+  - fix build failure in M4 1.4.19 when C standard is set (#22998)
+  - add patch to fix failing OCSP stapling test for `IO::Socket::SSL` extension in Perl-bundle-CPAN easyconfigs (#23030)
+  - fix source URL for c-ares (#23057)
+  - ensure that configure step of Zoltan uses an up-to-date `config.guess` (#23068)
+  - add patch for porefoam 2023-12-01 to make sure that case directory has user write permissions after copying (#23071)
+  - add patch to fix support for non-x86_64 architectures for MEGAHIT 1.2.9 (#23073)
+  - fix failing contourpy installation in matplotlib-3.7.2-iimkl-2023a with RPATH (#23079)
+  - update colabdesign extension to required version 1.1.3 in easyconfig for BindCraft 1.5.1 + add modloadmsg (#23087)
+  - update homepage URL for IsoSeq to correct repository link (#23094)
+  - add missing zlib dependency to `Serf` (#23118)
+  - add Perl build dependency for groff 1.23.0 (#23123)
+  - add missing Perl dependency for OpenPGM + make sure Perl scripts use it (#23126)
+  - also make `dssp` and `DAlphaBall.gcc` scripts and binaries in functions subdirectory executable for BindCraft v1.5.1 (#23136, #23195)
+  - fix sanity check commands for MinPath 1.6 (#23151)
+  - update homepage for Pango 1.54.0 (#23185)
+  - enable `-fPIC` (and OpenMP) for phono3py 2.7.0 using standard `toolchainopts` (#23198, #23207)
+  - update `source_urls` in `PDT` easyconfigs (#23234)
+  - switch homepage for `libxml2`, `libxml2-python`, and `libxslt` (#23236)
+  - drop incorrect Java dependency from Gephi (#23241)
+  - add hwloc dependency to MPICH easyconfigs (#23260)
+  - switch to correct Pillow dep (non SIMD as its not actually updated) for matplotlib in 2024a (#23264)
+  - switch to using Pillow 10.2.0 instead of incorrect Pillow-SIMD 10.4.0 for 2023b easyconfigs (#23266)
+  - make Mesa 24.1.3 use standard LLVM to avoid dependency conflicts (#23267)
+  - add missing Python dependency to rocm-smi (#23301)
+  - add G4CHANNELING to Geant4-data v11.3 (#23321)
+- enhancements and fixes for test suite:
+  - improve check for multi-variant dependencies per generation of easyconfigs (#12687, #23177)
+  - improve output of styletest on failure (#22515)
+  - clean up `alt_dep_versions` in test to check for dependency variants (#23179)
+  - set a `User-Agent` for the https/http check (#23245)
+  - cleanup old items in whitelists in test suite (#23297)
+  - also check on post-install patches in easyconfigs test suite (#23331)
+- other changes:
+  - fix order of easyconfig parameters in enchant-2 easyconfigs (#22050)
+  - only build static libraries for googletest 1.14.0 and 1.15.2 (#22641)
+  - archive old easyconfigs (#22954, #22955, #22960, #23005)
+  - archive Java 1.8 (#22968)
+  - make Rust a build dependency for maturin (#22980, #22981, #22982, #22983, #22985)
+  - use `Binary` easyblock instead of `JAR` in `HiCTools` + `Juicebox` easyconfigs (#22995)
+  - migrate pre-2021 easyconfigs and Java 1.8 into archive repo (#23005)
+  - replace deprecated `usepolly` with `use_polly` in LLVM easyconfigs (#23033)
+  - update SuperLU_DIST easyconfigs to rely on updated SuperLU easyblock for configure options for ParMETIS (#23075)
+  - update `nvptx-tools` version to fix compatibility with CUDA 12 in easyconfigs for GCCcore 12.x and 13.x (#23077)
+  - use BLIS easyblock for recent BLIS and AOCL-BLAS easyconfigs (#23088)
+  - move toolchain from `foss` to `gfbf` for bx-python v0.13.0 (#23101)
+  - clarify use of download_instructions parameter in test_downloadable_or_instructions (#23103)
+  - remove dependency on Python-bundle-PyPI from pytest v8.3.3 (#23109)
+  - use `c-ares` 1.34.5 dependency for `tensorstore` 0.1.72 (#23132)
+  - use newer version of `pydantic` dependency in 2023b toolchain generation (#23137, #23138)
+  - switch `CESM-deps` to use latest `git-lfs` (#23115)
+  - delete all old `git-lfs` easyconfigs (CVE-2024-53263) (#23116)
+  - skip building the docs to avoid `ImageMagick` (`convert`) build dependency for `giflib` (#23182)
+  - clean up old patches (#23231, #23330)
+  - switch to https for homepage/source for ITSTool (#23237)
+  - update MPICH easyconfigs to rely on enhanced custom easyblock for MPICH (#23239)
+  - remove `packaging` extension from easyconfigs for `scikit-build` 0.17.6 (#23258, #23259)
+  - remove default `separate_build_dir = True` from various easyconfigs (#23273, #23274, #23275, #23277, #23278, #23284, #23285, #23286, #23287, #23294, #23310, #23311, #23316, #23318, #23319, #23324, #23326)
+  - update `dotNET-Core/8.0` to dotNET-Core v8.0.411 (#23289)
+
+
 v5.1.0 (26 May 2025)
 --------------------
 

contrib/easyconfig-templates/2022a/Bundle-mixed-components.eb.tmpl

@@ -46,7 +46,7 @@ components = [
 ]
 
 sanity_check_paths = {
-    'files': ['bin/{x}' for x in ['comp1', 'comp1_turbo', 'comp2']],
+    'files': [f'bin/{x}' for x in ['comp1', 'comp1_turbo', 'comp2']],
     'dirs': ['component2_data'],
 }
 

contrib/easyconfig-templates/2023a/Bundle-mixed-components.eb.tmpl

@@ -46,7 +46,7 @@ components = [
 ]
 
 sanity_check_paths = {
-    'files': ['bin/{x}' for x in ['comp1', 'comp1_turbo', 'comp2']],
+    'files': [f'bin/{x}' for x in ['comp1', 'comp1_turbo', 'comp2']],
     'dirs': ['component2_data'],
 }
 

contrib/easyconfig-templates/2024a/Bundle-mixed-components.eb.tmpl

@@ -46,7 +46,7 @@ components = [
 ]
 
 sanity_check_paths = {
-    'files': ['bin/{x}' for x in ['comp1', 'comp1_turbo', 'comp2']],
+    'files': [f'bin/{x}' for x in ['comp1', 'comp1_turbo', 'comp2']],
     'dirs': ['component2_data'],
 }