Merge pull request #19103 from easybuilders/4.8.x

release EasyBuild v4.8.2

Author: boegel

.github/workflows/unit_tests.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.6]
+        python: [3.6, '3.11']
         modules_tool: [Lmod-7.8.22, Lmod-8.6.8]
         module_syntax: [Lua, Tcl]
         # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 3.6
@@ -147,10 +147,6 @@ jobs:
           eb --search '^foss-2019b.eb' | tee eb_search_foss.out
           grep '/foss-2019b.eb$' eb_search_foss.out
 
-          # make sure CVS easyconfigs are included in installation (cfr. issue #10325)
-          echo "Searching for CVS easyconfigs..."
-          eb --search '^CVS-' | grep '/CVS-'
-
           # try installing M4 with system toolchain (requires ConfigureMake easyblock + easyconfig)
           # use /tmp/sources because that has cached downloads (see cache step above)
           eb --prefix /tmp/$USER/$GITHUB_SHA --sourcepath /tmp/sources M4-1.4.18.eb
@@ -159,7 +155,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.6]
+        python: [3.6, '3.11']
     steps:
     - uses: actions/checkout@v2
 
@@ -184,12 +180,3 @@ jobs:
           else
             echo "No .git folders found in source tarball: OK"
           fi
-
-          # CVS easyconfigs must be included in source tarball,
-          # see https://github.com/easybuilders/easybuild-easyconfigs/issues/10325
-          cvs_easyconfigs=$(find . -name 'CVS-*.eb')
-          if [ -z "$cvs_easyconfigs" ]; then
-            echo "CVS easyconfigs not found" && false
-          else
-            echo "Found CVS easyconfigs: $cvs_easyconfigs"
-          fi

.gitignore

@@ -11,3 +11,4 @@ dist/
 *.ropeproject/
 eb-*.log
 /MANIFEST
+/easybuild/easyconfigs/.eb-path-index

RELEASE_NOTES

@@ -3,10 +3,89 @@ 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 18,021 easyconfig files, for 3,224 different software packages,
+The latest version of easybuild-easyconfig provides 18,407 easyconfig files, for 3,292 different software packages,
 incl. 40 different (compiler) toolchains.
 
 
+v4.8.2 (29 October 2023)
+------------------------
+
+update/bugfix release
+- added example easyconfig files for 48 new software packages:
+  - ALL (#18971), anadama2 (#18688), AOFlagger (#19010), bases2fastq (#18866), BgeeCall (#18784), 
+    biobakery-workflows (#18688), BMTK (#18863), CIRIquant (#18815), Clair3 (#18748), CLEAR (#16357), 
+    cpio (#14728), DP3 (#19010), EveryBeam (#19010), fasta-reader (#18936), git-annex (#18673), GSD (#6453),
+    imutils (#18920), Jblob (#18478), Jmol (#18988), kneaddata (#18688), libbaseencode (#12319), 
+    libcotp (#12319), MACS3 (#18354), Mashtree (#19019), mpath (#5029), MUSCLE3 (#18287), plotutils (#16196),
+    ProBiS  (#18830), PyMC (#10399), PyPy (#18847), PyTensor (#18928), Qt6 (#18683), QuickTree (#19019),
+    Raptor (#18919), RCall (#18933), ResistanceGA (#18933), scCODA (#18949), scikit-build-core (#18777),
+    segmentation-models-pytorch (#18930), SNAP-ESA (#19031), SNAP-ESA-python (#19031), starparser (#18965),
+    synapseclient (#19016), uncertainties (#18923), WSClean (#19010), XBeach (#18849), XOOPIC (#15269),
+    zeus-mcmc (#19033)
+- added additional easyconfigs for various supported software packages, including:
+  - alleleCount 4.3.0, Amber 22.4, ant 1.10.14, ArviZ 0.16.1, ASAP3 3.13.2, biobambam2 2.0.185, BLAST+ 2.14.1,
+    bokeh 3.2.2, Brotli 1.1.0, Cantera 3.0.0, CapnProto 1.0.1, casacore 3.5.0, Catch2 2.13.9, CGAL 5.6,
+    Chemaxon-Marvin 23.9, CMake 3.27.6, code-server 4.16.1, Coot 0.9.8.92, CSBDeep 0.7.4, CUDA-Samples 12.1.1,
+    CuPy 12.1.0, cURL 8.3.0, dask 2023.9.2, DL_POLY_4 5.1.0, DoubletFinder 2.0.3-20230131, Doxygen 1.9.8, dxpy 0.345.0,
+    EDirect 20.5.20231006, FastANI 1.34, FastME 2.1.6.3, Flask 2.3.3, Flye 2.9.2, fmt 10.1.0, foss/2023.09,
+    freetype 2.13.2, GDAL 3.7.1, GDRCopy 2.4, git 2.42.0, GMP 6.3.0, Go 1.21.1, googletest 1.14.0, GPAW 23.9.1,
+    groff 1.23.0, GTDB-Tk 2.3.2, GTK4 4.13.1, gzip 1.13, harmony 0.1.0, HDF 4.2.16, HighFive 2.7.1, Highway 1.0.7,
+    HMMER 3.4, hmmlearn 0.3.0, Imath 3.1.9, Inspector 2023.2.0, intel/2023.07, IsoSeq 4.0.0, itac 2021.10.0, 
+    JupyterNotebook 7.0.3, libarchive 3.7.2, libcint 5.4.0, libdeflate 1.19, libdrm 2.4.117, libglvnd 1.7.0,
+    libjpeg-turbo 3.0.1, libmaus2 2.0.813, libpng 1.6.40, libsigc++ 2.12.1, libsodium 1.0.19, LibTIFF 4.6.0,
+    libwebp 1.3.2, libxc 6.2.2, line_profiler 4.1.1, LMDB 0.9.31, MAFFT 7.520, makeinfo 7.1, MATLAB 2023b,
+    MEGAN 6.25.3, Mesa 23.1.9, Meson 1.2.3, mold 2.3.1, MPFR 4.2.1, msgpack-c 6.0.0, nanopolish 0.14.0,
+    NBO 7.0.10, netcdf4-python 1.6.4, OpenBLAS 0.3.24, OpenCV 4.8.1, OpenEXR 3.2.0, OpenMolcas 23.06, OpenMPI 4.1.6,
+    openslide-python 1.3.1, OrthoFinder 2.5.5, OSU-Micro-Benchmarks 7.2, ParaView 5.11.2, Perl-bundle-CPAN 5.38.0,
+    PETSc 3.19.2, PMIx 4.2.6, poppler 23.09.0, preCICE 2.5.0, pretty-yaml 23.9.5, PyCairo 1.25.0, pyEGA3 5.0.2,
+    PyGObject 3.46.0, pygraphviz 1.11, pytest-rerunfailures 12.0, Python 3.11.5, PyTorch 2.0.1, PyTorch-bundle 1.13.1,
+    PyTorch-Ignite 0.4.12, PyYAML 6.0.1, RagTag 2.1.0, rapidcsv 8.62, rasterstats 0.19.0, RAxML-NG 1.2.0,
+    RDFlib 7.0.0, RDKit 2023.03.3, ReFrame 4.3.3, RMBlast 2.14.0, ruamel.yaml 0.17.32, Rust 1.73.0, scikit-learn 1.3.1,
+    SCons 4.5.2, SHAP 0.42.1, SignalP 6.0h, SMRT-Link 12.0.0.177059, spglib-python 2.1.0, SQLite 3.43.1,
+    TensorRT 8.6.1, texlive 20230313, Tkinter 3.11.5, UCX 1.15.0, VBZ-Compression 1.0.3, VCFtools 0.1.16,
+    VTune 2023.2.0, X11 20231019, x264 20231019, xarray 2023.9.0, XlsxWriter 3.1.3, xtb 6.6.0, ZeroMQ 4.3.5
+- minor enhancements, including:
+  - also run easyconfigs test suite with Python 3.11 (#18009)
+  - don't disable building of third and fourth derivates in libxc 6.1.0 (#18467)
+  - add easyconfigs cache file to `.gitignore` (#18797)
+  - add patch to improve CUDA 11 compatibility of `GCCcore/12.2.0` and `GCCcore/12.3.0` (#18854)
+  - also build Python bindings for ITK 5.2.1 with `foss/2022a` (#18922)
+  - add ridge extension to R 4.2.2 (#18924)
+  - add MSstatsLiP (#19009)and escape (#19027) to Bioconductor 3.16 bundle
+  - add patches to build Qt5 5.15.10 with Python 3 instead of Python 2.7 (#19045)
+- various bug fixes, including:
+  - rename ACT to Artemis (#18382)
+  - backport lchown patch to PMIx 3.1.x + 3.2.x (#18759)
+  - also copy scripts directory for Clair3 (#18783)
+  - rename isoseq3 after download for IsoSeq 3.8.2 + fix permissions (#18785)
+  - add missing required extensions + fix wrong version of extensions in recent Perl easyconfigs (#18789)
+  - add patch for OpenBLAS 0.3.23 to fix hanging tests (#18790)
+  - add patch to fix Open MPI 4.1.5 with PMIx >= 4.2.3 (#18833)
+  - fix permission issues when copying xvfb-run script in Xvfb easyconfigs (#18834)
+  - statically link Boost 1.75 in Cufflinks v20190706 installed with `GCC/11.2.0`, so Boost can be changed to build dependency (#18843)
+  - add missing required PyPy dependency for Clair3, also copy preprocess and shared subdirectories, and enhance sanity check for provided libclair3 Python package (#18847)
+  - add patch to fix build of util-linux 2.39 on CentOS 7 (#18855)
+  - add patch to fix finding of tk.tcl for Tk 8.6.13 (#18864)
+  - add patch to fix issue with automatic detection of NeoverseV1 CPU architecture in OpenBLAS v0.3.20 (#18870)
+  - fix source URL for segemehl 0.3.4 (#18878)
+  - avoid use of hardcoded paths for Pillow by using `--disable-platform-guessing` option (#18881)
+  - add patch to disable flaky DDRGES3 LAPACK test in OpenBLAS 0.3.23 + 0.3.24 (#18887)
+  - add alternate checksum for NCCL v2.18.3 (#18906)
+  - add missing dependencies for MONAI to support extras required by MONAI-Label (#18921)
+  - make sure Python dependency included for ESPResSo is actually used by specifying `-DPYTHON_EXECUTABLE` (#18963)
+  - only add tbb as dependency in recent LAMMPS easyconfigs when installing on x86_64 (#19000)
+  - detect the correct Python for vcflib (#19001)
+  - fix invalid pointer access in UCX 1.11-1.14 (#19023)
+  - disable threadedmpi in recent SCOTCH easyconfigs using gompi toolchain (#19024)
+  - add missing GSL dependency for casacore 3.4.0 (#19042)
+  - fix pybind11 incompatibility with some CUDA versions and add Catch2 dependency for tests (#19047)
+  - enable `-fPIC` in easyconfig for libwebp 1.3.2 (#19098)
+- other changes:
+  - remove 'cstd': 'c++17' as that's the default in GCC 11 (#18941, #18942, #18943, #18944, #18945, #18946)
+  - rename CVS to ConcurrentVersionsSystem, to avoid problems with recent setuptools versions (#18985)
+  - use sysroot template in wget easyconfigs to define PKG_CONFIG_PATH (#19080)
+
+
 v4.8.1 (11 September 2023)
 --------------------------
 

easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.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': '2022b'}
+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', '3.24.3'),
+    ('Boost', '1.81.0'),  # only needed for tests
+]
+
+dependencies = [
+    ('VTK', '9.2.6'),
+]
+
+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/ACT/ACT-18.0.3-Java-11.eb

@@ -0,0 +1,42 @@
+easyblock = 'CMakeMake'
+
+name = 'AOFlagger'
+version = '3.4.0'
+
+homepage = 'https://aoflagger.readthedocs.io/'
+description = """The AOFlagger is a tool that can find and remove radio-frequency interference (RFI)
+in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible,
+and the tools are applicable to a wide set of telescopes."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [{
+    'source_urls': ['https://gitlab.com/aroffringa/aoflagger/-/package_files/96704214/'],
+    'filename': '%(namelower)s-v%(version)s.tar.bz2',
+    'download_filename': 'download'  # provided source tarball is not versioned...
+}]
+checksums = ['9560b7381b68f37d842599f222a8aa2a5d3d3d501d1277471e1a0ba3d7b2aeba']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+dependencies = [
+    ('casacore', '3.5.0'),
+    ('Boost', '1.79.0'),
+    ('CFITSIO', '4.2.0'),
+    ('GSL', '2.7'),
+    ('HDF5', '1.12.2'),
+    ('Python', '3.10.4'),
+    ('Lua', '5.4.4'),
+    ('libpng', '1.6.37'),
+    ('libxml2', '2.9.13'),
+]
+
+sanity_check_paths = {
+    'files': ['include/aoflagger.h', 'bin/aoflagger'],
+    'dirs': ['bin'],
+}
+
+sanity_check_commands = [('aoflagger', '-v')]
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb

@@ -0,0 +1,36 @@
+easyblock = "PythonPackage"
+
+name = 'ASAP3'
+version = '3.13.2'
+
+homepage = 'https://wiki.fysik.dtu.dk/asap/'
+description = """ASAP is a calculator for doing large-scale classical molecular
+dynamics within the Campos Atomic Simulation Environment (ASE)."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True, 'usempi': True, 'openmp': False}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['c2e6f0570de8037be45afd9bf35f6b4e76e1f518a0af0207c6bf5809ddb1abb8']
+
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('ASE', '3.22.1'),
+    ('kim-api', '2.3.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+moduleclass = 'phys'

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

@@ -0,0 +1,30 @@
+easyblock = 'RPackage'
+
+name = 'ASCAT'
+version = '3.1.2'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/VanLoo-lab/ascat'
+description = """ASCAT is a method to derive copy number profiles of tumor cells,
+ accounting for normal cell admixture and tumor aneuploidy."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://github.com/VanLoo-lab/ascat/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['5d65aef417ad12ea0e638b4179def5a9b8f25e1ccd757e41a6509534fe20eb17']
+
+dependencies = [
+    ('R', '4.2.2'),
+    ('R-bundle-Bioconductor', '3.16', versionsuffix),
+    ('alleleCount', '4.3.0'),
+]
+
+start_dir = '%(name)s'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['%(name)s']
+}
+
+moduleclass = 'bio'