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Merge branch 'develop' of https://github.com/easybuilders/easybuild-easyconfigs into 20260108150318_new_pr_scvi-tools141
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‎easybuild/easyconfigs/a/AITW-microstructures/AITW-microstructures-1.0.0-foss-2023a.eb‎

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easyblock = 'PythonBundle'
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name = 'AITW-microstructures'
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version = '1.0.0'
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homepage = 'https://www.ai-transpwood-project.eu/'
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description = """AI-TranspWood - Generate realistic microstructure models of wood (birch, spruce, etc.) from a set of
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given parameters. This is a port of the original MATLAB code to Python.
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"""
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toolchain = {'name': 'foss', 'version': '2023a'}
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builddependencies = [
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('poetry', '1.7.1'), # Needed to install textual
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]
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dependencies = [
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('Python', '3.11.3'),
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('Python-bundle-PyPI', '2023.06'),
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('SciPy-bundle', '2023.07'),
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('Pillow', '10.0.0'),
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('PyTorch', '2.1.2')
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]
24+
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exts_list = [
26+
('nptyping', '2.5.0', {
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'checksums': ['e3d35b53af967e6fb407c3016ff9abae954d3a0568f7cc13a461084224e8e20a'],
28+
}),
29+
('pynrrd', '1.0.0', {
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'modulename': 'nrrd',
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'checksums': ['4eb4caba03fbca1b832114515e748336cb67bce70c7f3ae36bfa2e135fc990d2'],
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}),
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('textual', '0.61.0', {
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'checksums': ['91c83a659da40b227eced4fa749026a236b493cc5911a9bedd990ad5f0786be2'],
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}),
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('trogon', '0.6.0', {
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'checksums': ['fd1abfeb7b15d79d6e6cfc9e724aad2a2728812e4713a744d975f133e7ec73a4'],
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}),
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(name, version, {
40+
'modulename': 'wood_microstructure',
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'source_urls': ['https://github.com/AI-TranspWood/AITW_microstructures/archive/refs/tags'],
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'sources': [{
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'filename': SOURCE_TAR_GZ,
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'download_filename': 'v%(version)s.tar.gz'
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}],
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'checksums': ['5e7bd9a4333617f7e3783e307d088e13d643d3ae5514f4035ec5e766db8df534'],
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'click_autocomplete_bins': ['wood_ms'],
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}),
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]
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sanity_check_commands = [
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'wood_ms --help',
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]
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moduleclass = 'chem'

‎easybuild/easyconfigs/a/AITW-stiffness/AITW-stiffness-1.0.0-foss-2023a.eb‎

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easyblock = 'PythonBundle'
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name = 'AITW-stiffness'
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version = '1.0.0'
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homepage = 'https://www.ai-transpwood-project.eu/'
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description = """AI-TranspWood - Neural network surrogate model for computing macroscopic stiffness parameters of
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wood fibers from given microscopic parameters.
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"""
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toolchain = {'name': 'foss', 'version': '2023a'}
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dependencies = [
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('Python', '3.11.3'),
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('Python-bundle-PyPI', '2023.06'),
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('SciPy-bundle', '2023.07'),
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('h5py', '3.9.0'),
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('TensorFlow', '2.13.0'),
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('tensorflow-probability', '0.20.0'),
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]
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exts_list = [
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(name, version, {
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'modulename': 'aitw_stiffness_surrogate',
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'source_urls': ['https://github.com/AI-TranspWood/biocomposite-surrogate/archive/refs/tags'],
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'sources': [{
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'filename': SOURCE_TAR_GZ,
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'download_filename': 'v%(version)s.tar.gz'
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}],
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'checksums': ['5f708e9bdef6679d8db096068b1a62558b74d40caf6f686e942aeba7bfc3a413'],
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'click_autocomplete_bins': ['aitw-stiffness'],
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}),
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]
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sanity_check_commands = [
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'aitw-stiffness --help',
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]
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moduleclass = 'chem'

‎easybuild/easyconfigs/a/AITW-viscosity/AITW-viscosity-1.0.0-foss-2023a.eb‎

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easyblock = 'PythonBundle'
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name = 'AITW-viscosity'
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version = '1.0.0'
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homepage = 'https://www.ai-transpwood-project.eu/'
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description = """AI-TranspWood - AiiDA workchain to compute the shear viscosity of molecular liquids,
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starting from a SMILES string of a molecule and using GROMACS to perform the molecular dynamics simulations.
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"""
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toolchain = {'name': 'foss', 'version': '2023a'}
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builddependencies = [
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('poetry', '1.7.1'), # Needed to install textual
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]
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dependencies = [
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('Python', '3.11.3'),
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('Python-bundle-PyPI', '2023.06'),
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('SciPy-bundle', '2023.07'),
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('aiida-core', '2.7.2'),
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('aiida-shell', '0.8.2'),
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('RDKit', '2024.03.3'),
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('matplotlib', '3.7.2'),
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('PyQt5', '5.15.10'),
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]
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exts_list = [
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('textual', '0.61.0', {
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'checksums': ['91c83a659da40b227eced4fa749026a236b493cc5911a9bedd990ad5f0786be2'],
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}),
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('trogon', '0.6.0', {
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'checksums': ['fd1abfeb7b15d79d6e6cfc9e724aad2a2728812e4713a744d975f133e7ec73a4'],
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}),
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(name, version, {
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'modulename': 'aitw_aiida_viscosity',
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'source_urls': ['https://github.com/AI-TranspWood/Molecular-liquid-shear-viscosity/archive/refs/tags'],
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'sources': [{
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'filename': SOURCE_TAR_GZ,
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'download_filename': 'v%(version)s.tar.gz'
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}],
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'checksums': ['fc0201716c4afe9f96c9583b705373395a943bb2796e2705e8eee07ef4a8dc2a'],
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'click_autocomplete_bins': ['aitw-viscosity'],
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}),
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]
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sanity_check_commands = [
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'aitw-viscosity --help',
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]
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moduleclass = 'chem'

‎easybuild/easyconfigs/a/AOCL-LAPACK/AOCL-LAPACK-5.1-GCC-14.3.0.eb‎

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easyblock = 'Bundle'
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name = 'AOCL-LAPACK'
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version = '5.1'
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homepage = 'https://github.com/amd/libflame'
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description = """AOCL-LAPACK is AMD's optimized version of
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LAPACK targeted for AMD EPYC and Ryzen CPUs."""
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toolchain = {'name': 'GCC', 'version': '14.3.0'}
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builddependencies = [
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('CMake', '4.0.3'),
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('Python', '3.13.5'),
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('Perl', '5.40.2'),
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]
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dependencies = [
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('AOCL-BLAS', '%(version)s'),
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]
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default_component_specs = {'sources': [{'download_filename': '%(version)s.tar.gz',
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'filename': SOURCELOWER_TAR_GZ}]}
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sanity_check_all_components = True
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components = [
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('AOCL-Utils', version, {
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'easyblock': 'CMakeMake',
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'source_urls': ['https://github.com/amd/aocl-utils/archive/refs/tags'],
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'checksums': ['68d75e04013abe90ea8308a9bc99b99532233b6c7f937f35381563f4124c20a5'],
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'start_dir': '%(namelower)s-%(version)s',
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'sanity_check_paths': {
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'files': ['lib/libaoclutils.%s' % SHLIB_EXT, 'include/Capi/au/cpuid/cpuid.h'],
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'dirs': [],
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},
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}),
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(name, version, {
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'source_urls': ['https://github.com/amd/libflame/archive/refs/tags'],
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'patches': ['AOCL-LAPACK-5.1_support-shlib-netlib-tests.patch'],
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'checksums': [
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{SOURCELOWER_TAR_GZ: '25524ba78b5952303369fa0859d217e44071144fd122a9dc3f72ed0bd73e3b2d'},
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{'AOCL-LAPACK-5.1_support-shlib-netlib-tests.patch':
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'8a5ab79f9120511e93708919050a1cc575fc6df9fa9cff994ecbe068955958fe'},
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],
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'start_dir': 'libflame-%(version)s',
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'runtest': True,
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'run_lapack_tests': True,
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'max_failing_lapack_tests_num_errors': 250,
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}),
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]
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sanity_check_paths = {
53+
'dirs': ['include', 'lib'],
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'files': [],
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}
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moduleclass = 'numlib'

‎easybuild/easyconfigs/a/AOCL-LAPACK/AOCL-LAPACK-5.1_support-shlib-netlib-tests.patch‎

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Support the Netlib test with shared library for AOCL-LAPACK
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Bart Oldeman <bart.oldeman@calculquebec.ca>
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diff -ur libflame-5.1.orig/CMakeLists.txt libflame-5.1/CMakeLists.txt
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--- libflame-5.1.orig/CMakeLists.txt 2025-05-06 07:29:28.000000000 +0000
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+++ libflame-5.1/CMakeLists.txt 2026-01-14 18:42:04.010934344 +0000
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@@ -1347,10 +1347,6 @@
8+
9+
if (BUILD_NETLIB_TEST)
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11+
- if (BUILD_SHARED_LIBS)
12+
- message(FATAL_ERROR "Netlib test is not supported for shared library build")
13+
- endif()
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-
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if(WIN32)
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add_subdirectory(netlib-test)
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else()
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diff -ur libflame-5.1.orig/netlib-test/run-netlib-test.sh libflame-5.1/netlib-test/run-netlib-test.sh
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--- libflame-5.1.orig/netlib-test/run-netlib-test.sh 2025-05-06 07:29:28.000000000 +0000
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+++ libflame-5.1/netlib-test/run-netlib-test.sh 2026-01-14 18:43:44.422513485 +0000
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@@ -8,7 +8,7 @@
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LAPACK_LIB=libflame.a
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LAPACK_LIB_PATH=
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AOCLUTILS_LIB_PATH=
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-AOCLUTILS_LIB=libaoclutils.a
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+AOCLUTILS_LIB=libaoclutils.so
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DTL_LIB=libaocldtl.a
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DTL_LIB_PATH=
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ILP64=0
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@@ -112,7 +112,7 @@
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ulimit -s unlimited
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FORTRAN_FLAGS="gfortran -fopenmp"
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-TESTLAPACKLIB="$PWD/liblapack.a $AOCLUTILS_LIB_PATH/$AOCLUTILS_LIB"
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+TESTLAPACKLIB="$LAPACK_LIB_PATH/$LAPACK_LIB $AOCLUTILS_LIB_PATH/$AOCLUTILS_LIB"
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if [[ $ILP64 =~ ("1"|"ON") ]]
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then
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@@ -130,7 +130,7 @@
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GCOV_FLAGS="-lgcov --coverage"
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fi
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-OMP_NUM_THREADS=1 make FC="$FORTRAN_FLAGS" LDFLAGS+="-lstdc++ -lpthread -fopenmp $GCOV_FLAGS" LAPACKLIB="$TESTLAPACKLIB" -j
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+OMP_NUM_THREADS=1 make FC="$FORTRAN_FLAGS" LDFLAGS+="-Wl,-rpath=$LAPACK_LIB_PATH -lstdc++ -lpthread -fopenmp $GCOV_FLAGS" LAPACKLIB="$TESTLAPACKLIB" BLASLIB="$BLAS_LIB_PATH/$BLAS_LIB" -j
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if [[ $AOCL_LAPACK_SUMMARY = "1" ]]
47+
then

‎easybuild/easyconfigs/a/accelerate/accelerate-1.11.0-foss-2024a-CUDA-12.6.0.eb‎

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easyblock = 'PythonBundle'
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name = 'accelerate'
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version = '1.11.0'
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versionsuffix = '-CUDA-%(cudaver)s'
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homepage = 'https://github.com/huggingface/accelerate'
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description = """A simple way to launch, train, and use PyTorch models on almost any device and
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distributed configuration, automatic mixed precision (including fp8),
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and easy-to-configure FSDP and DeepSpeed support."""
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toolchain = {'name': 'foss', 'version': '2024a'}
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dependencies = [
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('Python', '3.12.3'),
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('SciPy-bundle', '2024.05'),
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('CUDA', '12.6.0', '', SYSTEM),
18+
('PyTorch', '2.7.1', '-CUDA-%(cudaver)s'),
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('PyYAML', '6.0.2'),
20+
('Safetensors', '0.6.2'),
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('huggingface_hub', '0.34.4'),
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]
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exts_list = [
25+
(name, version, {
26+
'checksums': ['bb1caf2597b4cd632b917b5000c591d10730bb024a79746f1ee205bba80bd229'],
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}),
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]
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sanity_check_commands = ['accelerate test']
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moduleclass = 'ai'

‎easybuild/easyconfigs/a/aiida-core/aiida-core-2.5.1-foss-2023a.eb‎

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@@ -106,6 +106,7 @@ exts_list = [
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{'aiida_core-2.5.1.tar.gz': '9a5898ca355f0494d07ec4d2f714d17abef43e2e6c0b938cc2263db0115c33b4'},
107107
{'aiida_core-2.5.1-psycopg.patch': '8ca8799ca053d830832ffd3f0cbc8fd9e5f67cfafdf02f53f81f4de66a3b2f25'},
108108
],
109+
'click_autocomplete_bins': ['verdi'],
109110
}),
110111
]
111112

@@ -114,20 +115,3 @@ sanity_check_commands = [
114115
]
115116

116117
moduleclass = 'tools'
117-
118-
modluafooter = """
119-
local shell = myShellName()
120-
121-
if (shell == "bash") or (shell == "sh") then
122-
execute{cmd="eval \\"$(_VERDI_COMPLETE=bash_source verdi)\\"", modeA={"load"}}
123-
execute{cmd="complete -r verdi && unset _verdi_completion_setup && unset _verdi_completion", modeA={"unload"}}
124-
elseif (shell == "zsh") then
125-
execute{cmd="eval \\"$(_VERDI_COMPLETE=zsh_source verdi)\\"", modeA={"load"}}
126-
execute{cmd="unset '_comps[verdi]' && unset -f _verdi_completion", modeA={"unload"}}
127-
elseif (shell == "fish") then
128-
execute{cmd="eval (env _VERDI_COMPLETE=fish_source verdi)", modeA={"load"}}
129-
execute{cmd="complete -e verdi && functions --erase _verdi_completion", modeA={"unload"}}
130-
else
131-
LmodMessage("Autocompletion cannot be setup automatically for shell: " .. shell)
132-
end
133-
"""

‎easybuild/easyconfigs/a/aiida-core/aiida-core-2.7.2-foss-2023a.eb‎

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@@ -113,6 +113,7 @@ exts_list = [
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{'aiida_core-2.7.2.tar.gz': 'bd3c2734affb3a41832d5bafaca0775732e302ff7353259aa0049a42781acc96'},
114114
{'aiida_core-2.7.2-unfix_deps.patch': 'c26e6441a269a1cb944bcbe42b38bb5dff4057d2312f6fcfcae153afdffcc953'},
115115
],
116+
'click_autocomplete_bins': ['verdi'],
116117
}),
117118
]
118119

@@ -121,20 +122,3 @@ sanity_check_commands = [
121122
]
122123

123124
moduleclass = 'tools'
124-
125-
modluafooter = """
126-
local shell = myShellName()
127-
128-
if (shell == "bash") or (shell == "sh") then
129-
execute{cmd="eval \\"$(_VERDI_COMPLETE=bash_source verdi)\\"", modeA={"load"}}
130-
execute{cmd="complete -r verdi && unset _verdi_completion_setup && unset _verdi_completion", modeA={"unload"}}
131-
elseif (shell == "zsh") then
132-
execute{cmd="eval \\"$(_VERDI_COMPLETE=zsh_source verdi)\\"", modeA={"load"}}
133-
execute{cmd="unset '_comps[verdi]' && unset -f _verdi_completion", modeA={"unload"}}
134-
elseif (shell == "fish") then
135-
execute{cmd="eval (env _VERDI_COMPLETE=fish_source verdi)", modeA={"load"}}
136-
execute{cmd="complete -e verdi && functions --erase _verdi_completion", modeA={"unload"}}
137-
else
138-
LmodMessage("Autocompletion cannot be setup automatically for shell: " .. shell)
139-
end
140-
"""

‎easybuild/easyconfigs/a/aiida-pseudo/aiida-pseudo-1.5.0-foss-2023a.eb‎

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easyblock = 'PythonBundle'
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name = 'aiida-pseudo'
4+
version = '1.5.0'
5+
6+
homepage = 'https://aiida-pseudo.readthedocs.io/en/latest/'
7+
description = """The aiida-pseudo package is an AiiDA plugin that simplifies working with pseudopotentials when
8+
running calculations or workflows using AiiDA."""
9+
10+
toolchain = {'name': 'foss', 'version': '2023a'}
11+
toolchainopts = {'pic': True}
12+
13+
dependencies = [
14+
('Python', '3.11.3'),
15+
('aiida-core', '2.5.1'),
16+
('xmlschema', '2.5.1'),
17+
('jsonschema', '4.22.0'),
18+
]
19+
20+
exts_list = [
21+
('pint', '0.23', {
22+
'sources': ['Pint-%(version)s.tar.gz'],
23+
'checksums': ['e1509b91606dbc52527c600a4ef74ffac12fff70688aff20e9072409346ec9b4'],
24+
}),
25+
(name, version, {
26+
'sources': ['aiida_pseudo-%(version)s.tar.gz'],
27+
'checksums': ['6fa7bc257e66c0d3fb96b229888eb762378aa21f896ec4a2c1981919cfd707fd'],
28+
'click_autocomplete_bins': ['aiida-pseudo'],
29+
}),
30+
]
31+
32+
sanity_check_commands = [
33+
'aiida-pseudo --help',
34+
]
35+
36+
moduleclass = 'tools'

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