Merge pull request #21463 from easybuilders/4.9.x

release EasyBuild v4.9.4

Author: boegel

.gitignore

@@ -1,12 +1,15 @@
 .pydevproject
 .project
 LICENSE_HEADER
+*.eb.bak_*
 *.pyc
 *.pyo
 *.nja
+*.out
 build/
 dist/
 *egg-info/
+.venv/
 *.swp
 *.ropeproject/
 eb-*.log

RELEASE_NOTES

@@ -3,10 +3,43 @@ 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 20,561 easyconfig files, for 3,656 different software packages,
+The latest version of easybuild-easyconfig provides 20,670 easyconfig files, for 3,670 different software packages,
 incl. 41 different (compiler) toolchains.
 
 
+v4.9.4 (22 september 2024)
+--------------------------
+
+update/bugfix release
+
+- added example easyconfig files for 14 new software packages:
+  - Biotite (#21026), chopper (#21418), CLUMPP (#21329), cramino (#21382), dub (#21378), ESM3 (#21026), GOMC (#21008),
+    MOKIT (#21352), nanoQC (#21371), phasius (#21389), PyBullet (#21356), rnamotif (#21336), versioningit (#21424),
+    xskillscore (#21351)
+- added additional easyconfigs for various supported software packages, including:
+  - awscli 2.17.54, BiG-SCAPE-1.1.9, ccache 4.10.2, CLHEP 2.4.7.1, CREST 3.0.2, decona 1.4-2024073, dftd4 3.7.0,
+    GATE 9.4, Gdk-Pixbuf 2.42.11, Geant4 11.2.2, Geant4-data 11.2, Ghostscript 10.03.1, GitPython 3.1.43,
+    GObject-Introspection 1.80.1, HarfBuzz 9.0.0, ImageMagick 7.1.1-38, JasPer 4.2.4, joypy 0.2.6, Julia 1.10.4,
+    LDC 1.39.0, Leptonica 1.84.1, Markdown 3.7, MPICH 4.2.2, NanoComp 1.24.0, nanoget 1.19.3, nanomath 1.4.0,
+    NanoPlot 1.43.0, Pango 1.54.0, PCAngsd 1.2, Pillow 10.4.0, python-isal 1.7.0, pocl 6.0, PROJ 9.4.1, protobuf 28.0,
+    protobuf-python 5.28.0, R-tesseract 5.2.1, RepeatMasker 4.1.7-p1, RHEIA 1.1.11, RMBlast 2.14.1,
+    scikit-build-core 0.10.6, sleuth 0.30.1, SNAP-ESA 10.0.0, tesseract 5.3.4, Triton 2.1.0, TurboVNC 3.1.2,
+    VirtualGL 3.1.1, zlib-ng 2.2.1
+- minor enhancements, including:
+  - enable support for Apache ORC to Arrow v14.0.1 and v16.1.0 (#21056)
+  - use proper dependency for tensorboard in easyconfigs for TensorFlow v2.15.1 (#21337)
+- various bug fixes, including:
+  - account for crates for easyconfigs using Cargo-based easyblock when determining checksums for patches in easyconfigs test suite (#21419)
+  - avoid missing symbol in mclust extension of R-4.0.3 w/ foss/2020b (#21429)
+  - fix build of librosa 0.10.1 in some environments by removing "python -m build" for soxr extension (#21434)
+  - fix repeated sanity check runs in manta easyconfigs (#21435)
+  - fix test_easyconfig_locations when easyconfigs index is present (#21394)
+  - use proper dependency for libnsl in git-annex (#21441)
+  - avoid writing into ~/.stack directory during build for git-annex (#21452)
+- other changes:
+  - remove exts_default_options from TensorFlow 2.3.1 (#21290)
+
+
 v4.9.3 (14 September 2024)
 --------------------------
 

easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.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': '13.3.0'}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Meson', '1.4.0'),
+    ('Ninja', '1.12.1'),
+    ('pkgconf', '2.2.0'),
+    ('GObject-Introspection', '1.80.1'),
+]
+
+dependencies = [
+    ('GLib', '2.80.4'),
+]
+
+configopts = "--buildtype=release --default-library=both "
+configopts += "-Dintrospection=true "
+
+sanity_check_paths = {
+    'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'vis'

easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb

@@ -39,10 +39,10 @@ dependencies = [
 start_dir = 'cpp'
 
 # see https://arrow.apache.org/docs/developers/python.html
-configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON "
+configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON "
 configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON "
-configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON "
-configopts += "-DZSTD_ROOT=$EBROOTZSTD "
+configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON "
+configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD "
 
 # install Python bindings
 _pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && "
@@ -52,7 +52,7 @@ _pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && "
 _pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && "
 _pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON "
 _pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT
-_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 "
+_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 "
 
 exts_defaultclass = 'PythonPackage'
 exts_default_options = {
@@ -81,6 +81,7 @@ sanity_check_commands = [
     "python -c 'import pyarrow'",
     "python -c 'import pyarrow.dataset'",
     "python -c 'import pyarrow.parquet'",
+    "python -c 'import pyarrow.orc'",
 ]
 
 moduleclass = 'data'

easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb

@@ -39,10 +39,10 @@ dependencies = [
 start_dir = 'cpp'
 
 # see https://arrow.apache.org/docs/developers/python.html
-configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON "
+configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON "
 configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON "
-configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON "
-configopts += "-DZSTD_ROOT=$EBROOTZSTD "
+configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON "
+configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD "
 
 # install Python bindings
 _pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && "
@@ -52,7 +52,7 @@ _pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && "
 _pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && "
 _pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON "
 _pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT
-_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 "
+_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 "
 
 exts_defaultclass = 'PythonPackage'
 exts_default_options = {
@@ -81,6 +81,7 @@ sanity_check_commands = [
     "python -c 'import pyarrow'",
     "python -c 'import pyarrow.dataset'",
     "python -c 'import pyarrow.parquet'",
+    "python -c 'import pyarrow.orc'",
 ]
 
 moduleclass = 'data'

easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb

@@ -0,0 +1,73 @@
+easyblock = 'PythonBundle'
+
+name = 'awscli'
+version = '2.17.54'
+
+homepage = 'https://pypi.python.org/pypi/awscli'
+description = 'Universal Command Line Environment for AWS'
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),  # required for awscrt
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('PyYAML', '6.0.1'),
+    ('ruamel.yaml', '0.18.6'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('jmespath', '1.0.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980'],
+    }),
+    ('botocore', '1.35.22', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['d9bc656e7dde0b3e3f3080fc54bacff6a97fd7806b98acbcc21c7f9d4d0102b9'],
+    }),
+    ('s3transfer', '0.10.2', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['eca1c20de70a39daee580aef4986996620f365c4e0fda6a86100231d62f1bf69'],
+    }),
+    ('prompt_toolkit', '3.0.47', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['0d7bfa67001d5e39d02c224b663abc33687405033a8c422d0d675a5a13361d10'],
+    }),
+    ('distro', '1.9.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['7bffd925d65168f85027d8da9af6bddab658135b840670a223589bc0c8ef02b2'],
+    }),
+    ('awscrt', '0.21.5', {
+        'preinstallopts': "export AWS_CRT_BUILD_USE_SYSTEM_LIBCRYPTO=1 && ",
+        'checksums': ['7ec2a67af30fbf386494df00bbdf996f7024000df6b01ab160014afef2b91005'],
+    }),
+    # older version of `urllib3` to avoid `ImportError: cannot import name 'DEFAULT_CIPHERS' from 'urllib3.util.ssl_'`
+    # see https://github.com/aws/aws-cli/issues/7905#issuecomment-1559817550
+    ('urllib3', '1.26.20', {
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['0ed14ccfbf1c30a9072c7ca157e4319b70d65f623e91e7b32fadb2853431016e'],
+    }),
+    (name, version, {
+        # version requirements are too strict
+        'preinstallopts': """sed -i 's/>[^"]*//g' pyproject.toml && """,
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/aws/aws-cli/archive/'],
+        'checksums': ['c0a37eeb52b7df336e117667b67a275929701e9f6dad0ddb7de59a6f834e5b48'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/aws'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/'],
+}
+
+sanity_check_commands = ["aws help"]
+
+moduleclass = 'tools'

easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb

@@ -0,0 +1,68 @@
+easyblock = 'PythonPackage'
+
+name = 'BiG-SCAPE'
+version = '1.1.9'
+
+homepage = 'https://bigscape-corason.secondarymetabolites.org/index.html'
+description = """BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters 
+(BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene 
+cluster families, and exploring gene cluster diversity linked to enzyme phylogenies."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+github_account = 'medema-group'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'BiG-SCAPE-1.1.5_use_env_var_for_html.patch',
+    'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch',
+]
+checksums = [
+    {'v1.1.9.tar.gz': 'ef0ddb5b433e0b1467ae5f96037fd6d23ebcba6bc08201d1421eba35d072e534'},
+    {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'},
+    {'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch':
+     'e1572e4134c6163a3927ac32bd2a39b7f87cf01109f7913b3c55126e2381a771'},
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Biopython', '1.84'),
+    ('scikit-learn', '1.4.0'),
+    ('networkx', '3.2.1'),
+    ('HMMER', '3.4'),
+    ('FastTree', '2.1.11'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+options = {'modulename': 'bigscape'}
+
+local_lib_py_bigscape_path = 'lib/python%(pyshortver)s/site-packages/bigscape'
+
+sanity_check_paths = {
+    'files': ['bin/bigscape'],
+    'dirs': [local_lib_py_bigscape_path],
+}
+
+sanity_check_commands = [
+    'bigscape --help',
+]
+
+modextravars = {
+    'BIG_SCAPE_HTML_PATH': '%(installdir)s/' + local_lib_py_bigscape_path,
+}
+
+modloadmsg = "%(name)s needs processed Pfam database to work properly.\n"
+modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website "
+modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), "
+modloadmsg += "uncompress it and process it using the `hmmpress` command.\n"
+modloadmsg += "For data files, like the domains_color_file.tsv and domain_includelist.txt, "
+modloadmsg += "one can set the environment variable BIG_SCAPE_DATA_PATH, if that is not set "
+modloadmsg += "it will use the directory where the bigscape command is started from.\n"
+modloadmsg += "One can copy the domains_color_file.tsv from "
+modloadmsg += "%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/domains_color_file.tsv\n"
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb

@@ -0,0 +1,32 @@
+easyblock = 'PythonBundle'
+
+name = 'Biotite'
+version = '0.41.0'
+
+homepage = 'https://www.biotite-python.org/'
+description = """Biotite is your Swiss army knife for bioinformatics. Whether you want to
+identify homologous sequence regions in a protein family or you would like to
+find disulfide bonds in a protein structure: Biotite has the right tool for
+you. This package bundles popular tasks in computational molecular biology into
+a uniform Python library."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('networkx', '3.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('biotite', version, {
+        'checksums': ['a5fddb4d738291772735cf04dfa8b642e0bdd6b4c2c0c71e2db727c0a66bd106'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb

@@ -0,0 +1,54 @@
+easyblock = 'ConfigureMake'
+
+name = 'CAMPARI'
+version = '4.0'
+_date = '12202020'
+
+homepage = 'http://campari.sourceforge.net/V4/index.html'
+description = """
+CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological
+relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte
+Carlo and molecular dynamics in seamless fashion."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['campari_v%s_%s.zip' % (version.split('.')[0], _date)]
+checksums = ['bc627fb286b5461a5c68aa3e1a551ecd81016495163685800163c734f7c4f1bd']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+]
+
+dependencies = [
+    ('netCDF-Fortran', '4.6.1'),
+    ('libtirpc', '1.3.3'),
+]
+
+start_dir = 'source'
+
+# remove hardcoded paths in configure script
+preconfigopts = 'sed -i "s|/usr/share|$EBROOTAUTOMAKE/share|" configure &&'
+# ignore default compiler settings and use EB build environment
+local_fcflags = '$FCFLAGS -fallow-argument-mismatch $CPPFLAGS'
+configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="%s" ' % local_fcflags
+configopts += '--enable-mpi=auto '
+configopts += 'LIBS="$LIBS $LIBFFT $LIBBLAS -ltirpc"'
+
+buildopts = 'all'
+
+maxparallel = 10
+
+postinstallcmds = ['cp -a %(builddir)s/campari/{data,doc,examples,params,tools,LICENSE} %(installdir)s/']
+
+_binaries = ['campari', 'campari_mpi', 'campari_mpi_threads', 'campari_threads', 'camp_ncminer', 'camp_ncminer_threads']
+_libraries = ['lcampari.a', 'lcampari_mpi.a', 'lcampari_mpi_threads.a', 'lcampari_threads.a', 'libxdrf.a']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _binaries] + ['lib/%s' % x for x in _libraries],
+    'dirs': [],
+}
+
+sanity_check_commands = ['campari -h | grep "USAGE: CAMPARI"']
+
+moduleclass = 'bio'