Merge branch 'easybuilders:develop' into 20250221133915_new_pr_PyTorc…

…h212

easybuild/easyconfigs/a/accelerate/accelerate-1.0.1-foss-2023b.eb

@@ -0,0 +1,38 @@
+easyblock = 'PythonBundle'
+
+name = 'accelerate'
+version = '1.0.1'
+
+homepage = 'https://github.com/huggingface/accelerate'
+description = """A simple way to launch, train, and use PyTorch models on almost any device and 
+distributed configuration, automatic mixed precision (including fp8), 
+and easy-to-configure FSDP and DeepSpeed support."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('PyTorch', '2.1.2'),
+    ('PyYAML', '6.0.1'),
+    ('Safetensors', '0.4.4'),
+    ('tqdm', '4.66.2'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('huggingface-hub', '0.26.2', {
+        'sources': ['huggingface_hub-%(version)s.tar.gz'],
+        'checksums': ['b100d853465d965733964d123939ba287da60a547087783ddff8a323f340332b'],
+    }),
+    (name, version, {
+        'checksums': ['e8f95fc2db14915dc0a9182edfcf3068e5ddb2fa310b583717ad44e5c442399c'],
+    }),
+]
+
+sanity_check_commands = ['accelerate test']
+
+moduleclass = 'ai'

easybuild/easyconfigs/d/DECAF-synthetic-data/DECAF-synthetic-data-0.1.6-foss-2023b.eb

@@ -0,0 +1,47 @@
+easyblock = 'PythonBundle'
+
+name = 'DECAF-synthetic-data'
+version = '0.1.6'
+
+homepage = 'https://github.com/vanderschaarlab/DECAF'
+description = """DEbiasing CAusal Fairness - 
+Generating Fair Synthetic Data Using Causally-Aware Generative Networks"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+local_pytorch_version = '2.1.2'
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('PyTorch-Lightning', '1.9.5'),
+    ('PyTorch', '2.1.2'),
+    ('XGBoost', '2.1.1'),
+    ('scikit-learn', '1.4.0'),
+    ('torchtext', '0.16.2', '-PyTorch-%s' % local_pytorch_version),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_pretestopts = "export SLURM_NTASKS_PER_NODE=$SLURM_NTASKS && "
+
+exts_list = [
+    ('networkx', '2.8.8', {
+        'checksums': ['230d388117af870fce5647a3c52401fcf753e94720e6ea6b4197a5355648885e'],
+    }),
+    ('loguru', '0.7.2', {
+        'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'],
+    }),
+    (name, version, {
+        'modulename': 'decaf',
+        'source_urls': ['https://github.com/vanderschaarlab/DECAF/archive/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['8f34e99937d2ccc43bff97b310c371c450e27313c0801cdd36aa91664c8e3180'],
+        'testinstall': True,
+        'runtest': local_pretestopts + 'pytest -vsx',
+    }),
+]
+
+sanity_check_commands = ["python -c 'from decaf import DECAF, DataModule'"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/f/fastai/fastai-2.7.18-foss-2023b.eb

@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'fastai'
+version = '2.7.18'
+
+homepage = 'https://www.fast.ai/'
+description = """The fastai deep learning library."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+use_pip = True
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('PyTorch', '2.1.2'),
+    ('matplotlib', '3.8.2'),
+    ('SciPy-bundle', '2023.11'),
+    ('PyYAML', '6.0.1'),
+    ('Pillow', '10.2.0'),
+    ('scikit-learn', '1.4.0'),
+    ('spaCy', '3.7.5'),
+    ('torchvision', '0.17.0'),
+]
+
+exts_list = [
+    ('fastdownload', '0.0.7', {
+        'checksums': ['20507edb8e89406a1fbd7775e6e2a3d81a4dd633dd506b0e9cf0e1613e831d6a'],
+    }),
+    ('fastcore', '1.7.19', {
+        'checksums': ['72ac75cf3f7a591966e24aa37a4283512a097a098b4794c944ce707f71ba0f02'],
+    }),
+    ('fastprogress', '1.0.3', {
+        'checksums': ['7a17d2b438890f838c048eefce32c4ded47197ecc8ea042cecc33d3deb8022f5'],
+    }),
+    (name, version, {
+        'checksums': ['b20593dbcae7522f1d77a8f5163d1fd60314f292640496804dc356e41cb36454'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-3.1.0-gfbf-2023b.eb

@@ -0,0 +1,46 @@
+easyblock = "PythonBundle"
+
+name = 'HF-Datasets'
+version = '3.1.0'
+
+homepage = 'https://github.com/huggingface/datasets'
+description = """
+The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient
+data manipulation tools.
+"""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),  # for fsspec
+    ('SciPy-bundle', '2023.11'),
+    ('aiohttp', '3.9.5'),
+    ('dill', '0.3.8'),
+    ('Arrow', '16.1.0'),
+    ('PyYAML', '6.0.1'),
+    ('tqdm', '4.66.2'),
+    ('python-xxhash', '3.4.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_preinstallopts = "sed -i s'/tqdm>=4.66.3/tqdm/' setup.py && "
+local_preinstallopts += "sed -i s'/requests>=2.32.2/requests/' setup.py && "
+
+exts_list = [
+    ('multiprocess', '0.70.16', {
+        'checksums': ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'],
+    }),
+    ('huggingface-hub', '0.26.2', {
+        'sources': ['huggingface_hub-%(version)s.tar.gz'],
+        'checksums': ['b100d853465d965733964d123939ba287da60a547087783ddff8a323f340332b'],
+    }),
+    ('datasets', version, {
+        'preinstallopts': local_preinstallopts,
+        'checksums': ['c92cac049e0f9f85b0dd63739c68e564c657b1624bc2b66b1e13489062832e27'],
+    }),
+]
+
+moduleclass = 'data'

easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.4-gfbf-2023b.eb

@@ -0,0 +1,27 @@
+easyblock = 'PythonBundle'
+
+name = 'imbalanced-learn'
+version = '0.12.4'
+
+homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn'
+description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in
+ datasets showing strong between-class imbalance."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('scikit-learn', '1.4.0'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'modulename': 'imblearn',
+        'checksums': ['8153ba385d296b07d97e0901a2624a86c06b48c94c2f92da3a5354827697b7a3'],
+    }),
+]
+
+moduleclass = 'tools'

easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-13.2.0-llvmlite.eb

@@ -0,0 +1,53 @@
+name = 'LLVM'
+version = '14.0.6'
+versionsuffix = '-llvmlite'
+
+homepage = "https://llvm.org/"
+description = """The LLVM Core libraries provide a modern source- and target-independent
+ optimizer, along with code generation support for many popular CPUs
+ (as well as some less common ones!) These libraries are built around a well
+ specified code representation known as the LLVM intermediate representation
+ ("LLVM IR"). The LLVM Core libraries are well documented, and it is
+ particularly easy to invent your own language (or port an existing compiler)
+ to use LLVM as an optimizer and code generator.
+
+ This version include patches for llvmlite / numba."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'cstd': 'gnu++11', 'pic': True}
+
+source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/']
+sources = ['llvm-%(version)s.src.tar.xz']
+patches = [
+    'LLVM-14.0.6-clear-gotoffsetmap.patch',
+    'LLVM-14.0.6-svml.patch',
+]
+checksums = [
+    {'llvm-14.0.6.src.tar.xz': '050922ecaaca5781fdf6631ea92bc715183f202f9d2f15147226f023414f619a'},
+    {'LLVM-14.0.6-clear-gotoffsetmap.patch': '690c96dcbd0a81e11d87f02e740c4ef34a0c578be741aaa6559cc00a5349fabf'},
+    {'LLVM-14.0.6-svml.patch': '59df18ea4af3479de42ecbc1c524d4106f4a55f23335a64c0f0d5433daaba1b7'},
+]
+
+# Patches from https://github.com/numba/llvmlite/raw/v0.41.1/conda-recipes/ but
+# renamed to follow EasyBuild conventions.
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+    ('Python', '3.11.5'),
+]
+
+dependencies = [
+    ('ncurses', '6.4'),
+    ('zlib', '1.2.13'),
+]
+
+build_shared_libs = True
+
+sanity_check_paths = {
+    'files': ['bin/llvm-ar', 'bin/FileCheck'],
+    'dirs': ['include/llvm', 'include/llvm-c'],
+}
+
+sanity_check_commands = ["llvm-ar --help"]
+
+moduleclass = 'compiler'

easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-14.2.0.eb

@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'libxslt'
+version = '1.1.42'
+
+homepage = 'http://xmlsoft.org/'
+description = """Libxslt is the XSLT C library developed for the GNOME project
+ (but usable outside of the Gnome platform)."""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['85ca62cac0d41fc77d3f6033da9df6fd73d20ea2fc18b0a3609ffb4110e1baeb']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.3.0'),
+]
+
+dependencies = [
+    ('zlib', '1.3.1'),
+    ('libxml2', '2.13.4'),
+]
+
+# Make sure it doesn't pick up OS installed libgcrypt or Python
+# enable building static libs
+configopts = '--with-crypto=no --with-python=no --enable-static=yes '
+
+sanity_check_paths = {
+    'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a',
+              'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a'],
+    'dirs': ['include/libxslt', 'include/libexslt'],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/l/lifelines/lifelines-0.29.0-gfbf-2023b.eb

@@ -0,0 +1,40 @@
+easyblock = 'PythonBundle'
+
+name = 'lifelines'
+version = '0.29.0'
+
+homepage = "https://lifelines.readthedocs.io/en/latest/"
+description = """lifelines is a complete survival analysis library, written in pure Python."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+builddependencies = [('poetry', '1.6.1')]
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('matplotlib', '3.8.2'),
+    ('wrapt', '1.16.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('interface_meta', '1.3.0', {
+        'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'],
+    }),
+    ('autograd', '1.7.0', {
+        'checksums': ['de743fd368d6df523cd37305dcd171861a9752a144493677d2c9f5a56983ff2f'],
+    }),
+    ('autograd-gamma', '0.5.0', {
+        'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'],
+    }),
+    ('formulaic', '1.0.2', {
+        'checksums': ['6eb65bedd1903c5381d8f2ae7a55b6ba13cb77d57bbaf6e4278f3b2c38e3660e'],
+    }),
+    (name, version, {
+        'checksums': ['a82315a5daf2ad29eabefff38b8422364a8a721721136a501c30ff861cac8759'],
+    }),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-14.2.0.eb

@@ -0,0 +1,28 @@
+easyblock = 'PythonPackage'
+
+name = 'lxml'
+version = '5.3.0'
+
+homepage = 'https://lxml.de/'
+description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt."""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['4e109ca30d1edec1ac60cdbe341905dc3b8f55b16855e03a54aaf59e51ec8c6f']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Python', '3.13.1'),
+    ('libxml2', '2.13.4'),
+    ('libxslt', '1.1.42'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'

easybuild/easyconfigs/m/Miniforge3/Miniforge3-24.1.2-0.eb

@@ -18,7 +18,7 @@ checksums = [
             'dbadb808edf4da00af35d888d3eeebbfdce71972b60bf4b16dbacaee2ab57f28',
         '%(name)s-%(version)s-Linux-ppc64le.sh':
             '858b9acbcca1e3f67298a56095f547f2c540d79e1020918cf0d8d6a8af407542',
-        '%(name)s-py312_%(version)s-Linux-aarch64.sh':
+        '%(name)s-%(version)s-Linux-aarch64.sh':
             'f881e2fa24aa898c25fac3250ccb213e8b892fdd95851f000dce93c419e8f89a',
     }
 ]