From 7ab0505036df5d0f641f7809839cdd89df49e88c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 7 Aug 2024 12:58:47 +0200 Subject: [PATCH 1/9] adding easyconfigs: synthcity-0.2.10-foss-2022b.eb, DECAF-synthetic-data-0.1.6-foss-2022b.eb, PyTorch-Lightning-1.8.4-foss-2022b.eb, torchtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb, fastai-2.7.15-foss-2022b.eb, spaCy-3.7.4-foss-2022b.eb, Optuna-3.5.0-foss-2022b.eb, redis-py-5.0.1-GCCcore-12.2.0.eb, Redis-7.2.3-GCCcore-12.2.0.eb, lifelines-0.27.7-foss-2022b.eb, SHAP-0.43.0-foss-2022b.eb, XGBoost-1.7.2-foss-2022b.eb, imbalanced-learn-0.12.3-gfbf-2022b.eb, pycodestyle-2.11.1-foss-2022b.eb --- .../DECAF-synthetic-data-0.1.6-foss-2022b.eb | 42 +++ .../f/fastai/fastai-2.7.15-foss-2022b.eb | 42 +++ .../imbalanced-learn-0.12.3-gfbf-2022b.eb | 27 ++ .../lifelines/lifelines-0.27.7-foss-2022b.eb | 45 ++++ .../o/Optuna/Optuna-3.5.0-foss-2022b.eb | 50 ++++ .../PyTorch-Lightning-1.8.4-foss-2022b.eb | 121 +++++++++ .../pycodestyle-2.11.1-foss-2022b.eb | 22 ++ .../r/Redis/Redis-7.2.3-GCCcore-12.2.0.eb | 37 +++ .../redis-py/redis-py-5.0.1-GCCcore-12.2.0.eb | 33 +++ .../s/SHAP/SHAP-0.43.0-foss-2022b.eb | 37 +++ .../s/spaCy/spaCy-3.7.4-foss-2022b.eb | 81 ++++++ .../synthcity/synthcity-0.2.10-foss-2022b.eb | 239 ++++++++++++++++++ ...chtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb | 45 ++++ .../x/XGBoost/XGBoost-1.7.2-foss-2022b.eb | 29 +++ 14 files changed, 850 insertions(+) create mode 100644 easybuild/easyconfigs/d/DECAF-synthetic-data/DECAF-synthetic-data-0.1.6-foss-2022b.eb create mode 100644 easybuild/easyconfigs/f/fastai/fastai-2.7.15-foss-2022b.eb create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/l/lifelines/lifelines-0.27.7-foss-2022b.eb create mode 100644 easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2022b.eb create mode 100644 easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/d/DECAF-synthetic-data/DECAF-synthetic-data-0.1.6-foss-2022b.eb b/easybuild/easyconfigs/d/DECAF-synthetic-data/DECAF-synthetic-data-0.1.6-foss-2022b.eb new file mode 100644 index 00000000000..a46a26ae49d --- /dev/null +++ b/easybuild/easyconfigs/d/DECAF-synthetic-data/DECAF-synthetic-data-0.1.6-foss-2022b.eb @@ -0,0 +1,42 @@ +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': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('PyTorch-Lightning', '1.8.4'), + ('PyTorch', '1.13.1'), + ('XGBoost', '1.7.2'), + ('scikit-learn', '1.2.1'), + ('torchtext', '0.14.1', '-PyTorch-1.13.1'), +] + +use_pip = True +sanity_pip_check = True + +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'], + }), +] + +sanity_check_commands = ["python -c 'from decaf import DECAF, DataModule'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastai/fastai-2.7.15-foss-2022b.eb b/easybuild/easyconfigs/f/fastai/fastai-2.7.15-foss-2022b.eb new file mode 100644 index 00000000000..20e8dcdf96d --- /dev/null +++ b/easybuild/easyconfigs/f/fastai/fastai-2.7.15-foss-2022b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'fastai' +version = '2.7.15' + +homepage = 'https://www.fast.ai/' +description = """The fastai deep learning library.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +use_pip = True + +dependencies = [ + ('Python', '3.10.8'), + ('PyTorch', '1.13.1'), + ('matplotlib', '3.7.0'), + ('SciPy-bundle', '2023.02'), + ('PyYAML', '6.0'), + ('Pillow', '9.4.0'), + ('scikit-learn', '1.2.1'), + ('spaCy', '3.7.4'), + ('torchvision', '0.14.1'), +] + +exts_list = [ + ('fastdownload', '0.0.7', { + 'checksums': ['20507edb8e89406a1fbd7775e6e2a3d81a4dd633dd506b0e9cf0e1613e831d6a'], + }), + ('fastcore', '1.5.54', { + 'checksums': ['3f23dfadd77428be99558fdad66bf04c79a9c626e694c7404ede816ed8372987'], + }), + ('fastprogress', '1.0.3', { + 'checksums': ['7a17d2b438890f838c048eefce32c4ded47197ecc8ea042cecc33d3deb8022f5'], + }), + (name, version, { + 'checksums': ['f2cc20fd18cdf5ec738cc56d29d54de75887d48ad15f9d35cf50c38d3a856923'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2022b.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2022b.eb new file mode 100644 index 00000000000..10e219da604 --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'imbalanced-learn' +version = '0.12.3' + +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': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('scikit-learn', '1.2.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'imblearn', + 'checksums': ['5b00796a01419e9102bd425e27c319d58d1f6cf2dfa751e02ed7f4edf67c3c1b'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.27.7-foss-2022b.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.27.7-foss-2022b.eb new file mode 100644 index 00000000000..69b35bc787f --- /dev/null +++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.27.7-foss-2022b.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'lifelines' +version = '0.27.7' + +homepage = "https://lifelines.readthedocs.io/en/latest/" +description = """lifelines is a complete survival analysis library, written in pure Python.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('wrapt', '1.16.0', { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('interface_meta', '1.3.0', { + 'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'], + }), + ('autograd', '1.6.2', { + 'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'], + }), + ('autograd-gamma', '0.5.0', { + 'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'], + }), + ('formulaic', '1.0.1', { + 'checksums': ['64dd7992a7aa5bbceb1e40679d0f01fc6f0ba12b7d23d78094a88c2edc68fba1'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['44d60171f5abe85506b55cdf754b4ba769f61a5f8f18a9d05491009c6cee5803'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2022b.eb b/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2022b.eb new file mode 100644 index 00000000000..26185a5afe2 --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2022b.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '3.5.0' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2023.02'), + ('tqdm', '4.64.1'), + ('matplotlib', '3.7.0'), # optional + ('plotly.py', '5.13.1'), # optional + ('redis-py', '5.0.1'), # optional + ('scikit-learn', '1.2.1'), # optional + ('SQLAlchemy', '2.0.29'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cmaes', '0.10.0', { + 'checksums': ['48afc70df027114739872b50489ae6b32461c307b92d084a63c7090a9742faf9'], + }), + ('colorlog', '6.8.0', { + 'checksums': ['fbb6fdf9d5685f2517f388fb29bb27d54e8654dd31f58bc2a3b217e967a95ca6'], + }), + ('optuna', version, { + 'use_pip_extras': 'optional', + 'checksums': ['ca9e1ce16aa6c6a5af0e1cc1d0cbcd98eb1c75b6a2f06be6bd9c0c5ab0698724'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022b.eb new file mode 100644 index 00000000000..acec48e2187 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022b.eb @@ -0,0 +1,121 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.8.4' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + # dependencies from requirements/app/base.txt + ('aiohttp', '3.8.5'), + ('BeautifulSoup', '4.11.1'), + ('deepdiff', '6.7.1'), + # dependencies from requirements/pytorch/base.txt + ('PyTorch', '1.13.1'), + ('tqdm', '4.64.1'), + ('tensorboardX', '2.6.2.2'), +] + +use_pip = True + +# dependencies from requirements/app/base.txt and requirements/pytorch/base.txt +exts_list = [ + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.5.1', { + 'checksums': ['63a5c5ce3673d3d5fbbf23cd87e11ab84b6b451436f1b7f19ec54b6bc36ed7ca'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), + ('starlette', '0.19.1', { + 'checksums': ['c6d21096774ecb9639acad41b86b7706e52ba3bf1dc13ea4ed9ad593d47e24c7'], + }), + ('fastapi', '0.79.1', { + 'checksums': ['006862dec0f0f5683ac21fb0864af2ff12a931e7ba18920f28cc8eceed51896b'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + ('lightning_cloud', '0.5.12', { + 'checksums': ['5b0cf53ecfb512f9476eec3a7f425c0e174ca9d0e726673605d5e1e57074eb0c'], + }), + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('starsessions', '1.3.0', { + 'checksums': ['8d3b509d4e6d235655f7dd495fcf0afc1bd86da84de3a8d434e6f82137ebcde8'], + }), + ('fsspec', '2022.7.1', { + 'checksums': ['7f9fb19d811b027b97c4636c6073eb53bc4cbee2d3c4b33fa88b9f26906fd7d7'], + }), + ('croniter', '1.3.8', { + 'checksums': ['32a5ec04e97ec0837bcdf013767abd2e71cceeefd3c2e14c804098ce51ad6cd9'], + }), + ('traitlets', '5.2.0', { + 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('lightning-utilities', '0.4.2', { + 'checksums': ['dc6696ab180117f7e97b5488dac1d77765ab891022f7521a97a39e10d362bdb8'], + }), + ('blessed', '1.19.1', { + 'checksums': ['9a0d099695bf621d4680dd6c73f6ad547f6a3442fbdbe80c4b1daa1edbc492fc'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('readchar', '4.0.3', { + 'checksums': ['1d920d0e9ab76ec5d42192a68d15af2562663b5dfbf4a67cf9eba520e1ca57e6'], + }), + ('inquirer', '2.10.1', { + 'checksums': ['e9876258183e24f6e8c44136b04f6f2e18dd6684aee59b86a8057c50601a6523'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('botocore', '1.24.21', { + 'checksums': ['7e976cfd0a61601e74624ef8f5246b40a01f2cce73a011ef29cf80a6e371d0fa'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('aiobotocore', '2.3.4', { + 'checksums': ['6554ebea5764f66f4be544a4fcaa0953ee80e600dd7bd818ba4893d72bf12bfb'], + }), + ('s3fs', '2022.7.1', { + 'checksums': ['4883d682cb96b769fca568dbbcaa33ff457ac8077a03af221e6f253adac05771'], + }), + ('torchmetrics', '0.9.3', { + 'checksums': ['4ebfd2466021db26397636966ee1a195d3b340ba5d71bb258e764340dfc2476f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['c2771f966fc1b909cdfd1d603a87b8c84a3d5ff7aacf35b2c0260f697ec0c8be'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022b.eb b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022b.eb new file mode 100644 index 00000000000..562cc2adea8 --- /dev/null +++ b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022b.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'pycodestyle' +version = '2.11.1' + +homepage = "https://pycodestyle.readthedocs.io" +description = """pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f'] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..823ff30517e --- /dev/null +++ b/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Redis' +version = '7.2.3' + +homepage = 'https://redis.io' +description = """Redis is an open source (BSD licensed), in-memory data structure store, used as +a database, cache, and message broker. Redis provides data structures such as +strings, hashes, lists, sets, sorted sets with range queries, bitmaps, +hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, +Lua scripting, LRU eviction, transactions, and different levels of on-disk +persistence, and provides high availability via Redis Sentinel and automatic +partitioning with Redis Cluster.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://download.redis.io/releases'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3e2b196d6eb4ddb9e743088bfc2915ccbb42d40f5a8a3edd8cb69c716ec34be7'] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('binutils', '2.39'), +] + +skipsteps = ['configure'] + +installopts = 'PREFIX="%(installdir)s"' + +sanity_check_paths = { + 'files': ['bin/redis-cli', 'bin/redis-server'], + 'dirs': [], +} + +sanity_check_commands = [('redis-server', '--version')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..3c71c6c7190 --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'redis-py' +version = '5.0.1' + +homepage = 'https://github.com/redis/redis-py' +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] +dependencies = [ + ('Python', '3.10.8'), + ('typing-extensions', '4.9.0'), + ('Redis', '7.2.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['0a40afc824a5a3b465db4ba868a056a83779482f22d7d003c48fca230d9fe93a'], + }), +] + +moduleclass = "data" diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb new file mode 100644 index 00000000000..25053fc5fd3 --- /dev/null +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'SHAP' +version = '0.43.0' + +homepage = "https://github.com/shap/shap" +description = """SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any + machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley + values from game theory and their related extensions.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('scikit-learn', '1.2.1'), + ('tqdm', '4.64.1'), + ('numba', '0.58.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('slicer', '0.0.7', { + 'checksums': ['f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['1eabe01444a24e181ef6a7c9593b4d7c7143eefaeb1fa4d97bd5d9fdc96c4c1e'], + }), +] + +moduleclass = 'data' \ No newline at end of file diff --git a/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2022b.eb b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2022b.eb new file mode 100644 index 00000000000..825f9f573c3 --- /dev/null +++ b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2022b.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'spaCy' +version = '3.7.4' + +homepage = 'https://spacy.io/' +description = "Industrial-strength Natural Language Processing (NLP) in Python." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('tqdm', '4.64.1'), + ('pydantic', '2.5.3'), +] + +use_pip = True + +exts_list = [ + ('spacy-legacy', '3.0.12', { + 'checksums': ['b37d6e0c9b6e1d7ca1cf5bc7152ab64a4c4671f59c85adaf7a3fcb870357a774'], + }), + ('spacy-loggers', '1.0.5', { + 'checksums': ['d60b0bdbf915a60e516cc2e653baeff946f0cfc461b452d11a4d5458c6fe5f24'], + }), + ('cymem', '2.0.8', { + 'checksums': ['8fb09d222e21dcf1c7e907dc85cf74501d4cea6c4ed4ac6c9e016f98fb59cbbf'], + }), + ('murmurhash', '1.0.10', { + 'checksums': ['5282aab1317804c6ebd6dd7f69f15ba9075aee671c44a34be2bde0f1b11ef88a'], + }), + ('preshed', '3.0.9', { + 'checksums': ['721863c5244ffcd2651ad0928951a2c7c77b102f4e11a251ad85d37ee7621660'], + }), + ('blis', '0.7.11', { + 'checksums': ['cec6d48f75f7ac328ae1b6fbb372dde8c8a57c89559172277f66e01ff08d4d42'], + }), + ('confection', '0.1.4', { + 'checksums': ['e80f22fd008b5231a2e8852fac6de9e28f2276a04031d0536cff74fe4a990c8f'], + }), + ('thinc', '8.2.3', { + 'checksums': ['f5afc5222912a80bda8bdcec958362a2ba538d7027dc8db6154845d2859dca76'], + }), + ('ml_datasets', '0.2.0', { + 'checksums': ['3f9c8901f8d6be3dab5b23ec3a6c01e619a60d0184696b1030cde2e3086943f1'], + }), + ('wasabi', '1.1.2', { + 'checksums': ['1aaef3aceaa32edb9c91330d29d3936c0c39fdb965743549c173cb54b16c30b5'], + }), + ('srsly', '2.4.8', { + 'checksums': ['b24d95a65009c2447e0b49cda043ac53fecf4f09e358d87a57446458f91b8a91'], + }), + ('catalogue', '2.0.10', { + 'checksums': ['4f56daa940913d3f09d589c191c74e5a6d51762b3a9e37dd53b7437afd6cda15'], + }), + ('typer', '0.9.0', { + 'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'], + }), + ('smart-open', '6.4.0', { + 'source_tmpl': 'smart_open-%(version)s.tar.gz', + 'checksums': ['be3c92c246fbe80ebce8fbacb180494a481a77fcdcb7c1aadb2ea5b9c2bee8b9'], + }), + ('langcodes', '3.3.0', { + 'checksums': ['794d07d5a28781231ac335a1561b8442f8648ca07cd518310aeb45d6f0807ef6'], + }), + ('weasel', '0.3.4', { + 'checksums': ['eb16f92dc9f1a3ffa89c165e3a9acd28018ebb656e0da4da02c0d7d8ae3f6178'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['525f2ced2e40761562c8cace93ef6a1e6e8c483f27bd564bc1b15f608efbe85b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb new file mode 100644 index 00000000000..105a486ab07 --- /dev/null +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -0,0 +1,239 @@ +easyblock = 'PythonBundle' + +name = 'synthcity' +version = '0.2.10' + +local_pytorch_version = '1.13.1' + +homepage = 'https://github.com/vanderschaarlab/synthcity' +description = """A library for generating and evaluating synthetic tabular data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [('hypothesis', '6.68.2')] # for numpy 1.23.5 +dependencies = [ + ('Python', '3.10.8'), + ('lifelines', '0.27.7'), + ('SciPy-bundle', '2023.02'), + ('pydantic', '2.5.3'), + ('Redis', '7.2.3'), + ('scikit-learn', '1.2.1'), + ('SHAP', '0.43.0'), + ('PyTorch', local_pytorch_version), + ('XGBoost', '1.7.2'), + ('tqdm', '4.64.1'), + ('HF-Datasets', '2.14.4'), + ('Transformers', '4.30.2'), + ('fastai', '2.7.15'), + ('h5py', '3.8.0'), + ('Brotli-python', '1.0.9'), + ('statsmodels', '0.14.0'), + ('imbalanced-learn', '0.12.3'), + ('Optuna', '3.5.0'), + ('MONAI', '1.3.0'), + ('DECAF-synthetic-data', '0.1.6'), + ('PyTorch-Lightning', '1.8.4'), + # TESTS + ('JupyterNotebook', '7.0.3'), + ('python-igraph', '0.10.6'), + ('coverage', '7.2.3'), + ('py-cpuinfo', '9.0.0'), + ('pycodestyle', '2.11.1'), +] + +# unpin pydantic version restriction +local_preinstallopts = "sed -i 's/pydantic<2.0/pydantic/' %(builddir)s/%(name)s/%(name)s-%(version)s/setup.cfg && " + +# ignore the failing part of ddpm test - seems constraints are wrong +# https://github.com/vanderschaarlab/synthcity/blob/v0.2.10/tests/plugins/generic/test_ddpm.py#L114 +local_pretestopts = ( + "sed -i '138,144d' %(builddir)s/%(name)s/%(name)s-%(version)s/tests/plugins/generic/test_ddpm.py && " +) + +# fix invalid syntax of xgbse/setup.py +local_xgbse_preinstallopts = "sed -i -e '45,49d' -e 's/pandas>=1.0.\*/pandas>=1.0.0/' setup.py && " + +exts_list = [ + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pyflakes', '3.2.0', { + 'checksums': ['1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f'], + }), + ('mccabe', '0.7.0', { + 'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'], + }), + ('restructuredtext_lint', '1.4.0', { + 'checksums': ['1b235c0c922341ab6c530390892eb9e92f90b9b75046063e047cacfb0f050c45'], + }), + ('stevedore', '5.2.0', { + 'checksums': ['46b93ca40e1114cea93d738a6c1e365396981bb6bb78c27045b7587c9473544d'], + }), + ('nodeenv', '1.9.1', { + 'checksums': ['6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f'], + }), + ('identify', '2.6.0', { + 'checksums': ['cb171c685bdc31bcc4c1734698736a7d5b6c8bf2e0c15117f4d469c8640ae5cf'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('pytest-cov', '5.0.0', { + 'checksums': ['5837b58e9f6ebd335b0f8060eecce69b662415b16dc503883a02f45dfeb14857'], + }), + ('bandit', '1.7.9', { + 'checksums': ['7c395a436743018f7be0a4cbb0a4ea9b902b6d87264ddecf8cfdc73b4f78ff61'], + }), + ('black', '22.12.0', { + 'checksums': ['229351e5a18ca30f447bf724d007f890f97e13af070bb6ad4c0a441cd7596a2f'], + }), + ('black-nb', '0.7', { + 'checksums': ['8742a4f7c728302c91954325168d779f9444f8e3c31b19598ee8e98fc4bf4782'], + }), + ('darglint', '1.8.1', { + 'checksums': ['080d5106df149b199822e7ee7deb9c012b49891538f14a11be681044f0bb20da'], + }), + ('doc8', '1.1.1', { + 'checksums': ['d97a93e8f5a2efc4713a0804657dedad83745cca4cd1d88de9186f77f9776004'], + }), + ('flake8', '7.0.0', { + 'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'], + }), + ('isort', '5.13.2', { + 'checksums': ['48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109'], + }), + ('pytest-benchmark', '4.0.0', { + 'checksums': ['fb0785b83efe599a6a956361c0691ae1dbb5318018561af10f3e915caa0048d1'], + }), + ('pytest-xprocess', '1.0.2', { + 'modulename': 'xprocess', + 'checksums': ['15e270637586eabc56755ee5fcc81c48bdb46ba7ef7c0d5b1b64302d080cc60f'], + }), + ('pre_commit', '3.7.1', { + 'checksums': ['8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a'], + }), + ('typing_extensions', '4.9.0', { + 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], + }), + ('fflows', '0.0.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['18de7a7b98e3708ff2d5ae9f10fad625740230c4de6447906b7ca477667b78fb'], + }), + ('geomloss', '0.2.6', { + 'checksums': ['491c47085c5001b2cb6128ea541fd2d0a8808ae50e88a0798c7853c9d995faeb'], + }), + ('nflows', '0.14', { + 'checksums': ['6299844a62f9999fcdf2d95cb2d01c091a50136bd17826e303aba646b2d11b55'], + }), + ('opt_einsum', '3.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['2455e59e3947d3c275477df7f5205b30635e266fe6dc300e3d9f9646bfcea147'], + }), + ('opacus', '1.4.0', { + 'checksums': ['7a41d49c34af8e4308189bc8c2b22e65cf1edc0373477a02a43ccd957bac970d'], + }), + ('pgmpy', '0.1.25', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['7c4fb15e4c0fd0310160a6a77297d6db382bd18f6ff35fcd0458c3cbd42caf78'], + }), + ('feather-format', '0.4.1', { + 'modulename': 'feather', + 'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'], + }), + ('inflate64', '1.0.0', { + 'checksums': ['3278827b803cf006a1df251f3e13374c7d26db779e5a33329cc11789b804bc2d'], + }), + ('multivolumefile', '0.2.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['237f4353b60af1703087cf7725755a1f6fcaeeea48421e1896940cd1c920d678'], + }), + ('pybcj', '1.0.2', { + 'modulename': 'bcj', + 'checksums': ['c7f5bef7f47723c53420e377bc64d2553843bee8bcac5f0ad076ab1524780018'], + }), + ('pycryptodomex', '3.20.0', { + 'modulename': 'Crypto', + 'checksums': ['7a710b79baddd65b806402e14766c721aee8fb83381769c27920f26476276c1e'], + }), + ('pyppmd', '1.0.0', { + 'checksums': ['075c9bd297e3b0a87dd7aeabca7fee668218acbe69ecc1c6511064558de8840f'], + }), + ('pyzstd', '0.16.0', { + 'checksums': ['fd43a0ae38ae15223fb1057729001829c3336e90f4acf04cf12ebdec33346658'], + }), + ('texttable', '1.7.0', { + 'checksums': ['2d2068fb55115807d3ac77a4ca68fa48803e84ebb0ee2340f858107a36522638'], + }), + ('py7zr', '0.20.6', { + 'checksums': ['d036dee11fce69ad8d4fa86025ccfc4a3511ec27ee1c6b5bd8d6759313dbd077'], + }), + ('torchtuples', '0.2.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['186625230a149cc09f64116d51b203ffefe78160f5a0445adad195893663f55b'], + }), + ('pycox', '0.2.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['9ea3c64a4a650ccf6c96cf512712de330f2d75de32122d86995c7cd37ff105d1'], + }), + ('keopscore', '2.2.3', { + 'checksums': ['64d5dad1e8c806d7070cdc60e48fd5bbf006f2bf1afd39ad3fa5e9fb213517d2'], + }), + ('pykeops', '2.2.3', { + 'checksums': ['2e2cba1de5e05c35559957a14f41cb5165dc667cc51b3b2118d7e0027eb435a1'], + }), + ('pyts', '0.13.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['b49608267b686ea693dba31316ef2b22ad73ea29b27144696c347809ecd5ad62'], + }), + ('tsai', '0.3.9', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['0e6460e9ff075176c8af25ef90444ef2e287bc5fe5510e2a0f427e4d0b37ebc0'], + }), + ('accelerate', '0.31.0', { + 'checksums': ['b5199865b26106ccf9205acacbe8e4b3b428ad585e7c472d6a46f6fb75b6c176'], + }), + ('be_great', '0.0.7', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['824f10482581f5211d3a435d8b14adcc6c21b38d952f00b6a792fc7c089788b1'], + }), + ('xgbse', '0.2.3', { + 'preinstallopts': local_xgbse_preinstallopts, + 'source_urls': ['https://github.com/loft-br/xgboost-survival-embeddings/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['9e6b71539b2b533c00eddfe7681cdd541f393d9573594eca358d263b141c127d'], + }), + ('arfpy', '0.1.1', { + 'checksums': ['88170d5e72638b0dbfec28cfbdfee02e97bd6a06d5a636e960acd5d90d480707'], + }), + ('numpy', '1.23.5', { + 'patches': [ + 'numpy-1.20.3_fix-fortran-compiler-error.patch', + 'numpy-1.22.3_disable-broken-override-test.patch', + ], + 'checksums': [ + {'numpy-1.23.5.tar.gz': '1b1766d6f397c18153d40015ddfc79ddb715cabadc04d2d228d4e5a8bc4ded1a'}, + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + 'f12a49a754cb4c01a39691f8a7470bfa0e56c70139d78ca8b188f049010e7647'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '0d894fa9592ba9855397bc89fd4408bd911d49e6b6449d1693f87d2e5fcac486'}, + ], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/vanderschaarlab/synthcity/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'testinstall': True, + 'runtest': local_pretestopts + 'cd tests && pytest -vvvs -m "not slow" --durations=50', + 'checksums': ['122a8546cad35e3ac5c74cf81281252dec4dd3c7b1d7afe0f45ef785f89cc682'], + }), +] + +sanity_pip_check = True +use_pip = True + +sanity_check_commands = [ + "python -c 'from synthcity.plugins import Plugins'", + "python -c 'from decaf import DECAF, DataModule'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb new file mode 100644 index 00000000000..7903b8102f8 --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022b-PyTorch-1.13.1.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.14.1' +local_pytorch_version = '1.13.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'foss', 'version': '2022b'} + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +patches = ['torchtext-0.14.1_deps_fix.patch'] +checksums = [ + {'torchtext-0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, + {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'}, +] + +builddependencies = [ + ('RE2', '2023-03-01'), + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('SentencePiece', '0.1.99'), + ('tqdm', '4.64.1'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.2.1'), + ('utf8proc', '2.8.0'), +] + +download_dep_fail = True, +use_pip = True +sanity_pip_check = True, + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && " + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022b.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022b.eb new file mode 100644 index 00000000000..937201a36b5 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '1.7.2' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f1a749aedb9330afc48007cc78b8bbbbea35ce372f48a2735f9c71bbc7b8dcfb'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# use the parallel parameter from EB instead of total procs in the system +preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&" + +moduleclass = 'lib' From e1847a481007b496eb5344be4ba6449e432bb1a1 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 7 Aug 2024 13:09:59 +0200 Subject: [PATCH 2/9] Update synthcity-0.2.10-foss-2022b.eb try raw string --- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index 105a486ab07..bc1eeafab12 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -51,7 +51,7 @@ local_pretestopts = ( ) # fix invalid syntax of xgbse/setup.py -local_xgbse_preinstallopts = "sed -i -e '45,49d' -e 's/pandas>=1.0.\*/pandas>=1.0.0/' setup.py && " +local_xgbse_preinstallopts = r"sed -i -e '45,49d' -e 's/pandas>=1.0.\*/pandas>=1.0.0/' setup.py && " exts_list = [ ('cfgv', '3.4.0', { From 51357fa5cc27149e7f4ded01b61be58a2b3257b5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 7 Aug 2024 13:26:25 +0200 Subject: [PATCH 3/9] Update easyconfigs.py - PyTorch-Lightning exception for synthcity --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d228333cca6..231863a7c76 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -625,6 +625,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'NGSpeciesID-0.1.1.1-']), ('0.18.0;', ['medaka-1.6.0-', 'NGSpeciesID-0.1.2.1-', 'WhatsHap-1.4-']), ], + # PyTorch-Lightning-1.8.4 is requiered in synthcity-0.2.10 and DECAF-synthetic-data-0.1.6 + 'PyTorch-Lightning': [('1.8.4;', ['synthcity-0.2.10-', 'DECAF-synthetic-data-0.1.6-'])], # OPERA requires SAMtools 0.x 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], From eaf2389064b30227f13f2f2f55927db34ef92a2a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 7 Aug 2024 15:22:06 +0200 Subject: [PATCH 4/9] fix new line and comment indent --- easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb | 2 +- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb index 25053fc5fd3..cca163e6ee4 100644 --- a/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2022b.eb @@ -34,4 +34,4 @@ exts_list = [ }), ] -moduleclass = 'data' \ No newline at end of file +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index bc1eeafab12..7ef97fcc743 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -10,7 +10,7 @@ description = """A library for generating and evaluating synthetic tabular data. toolchain = {'name': 'foss', 'version': '2022b'} -builddependencies = [('hypothesis', '6.68.2')] # for numpy 1.23.5 +builddependencies = [('hypothesis', '6.68.2')] # for numpy 1.23.5 dependencies = [ ('Python', '3.10.8'), ('lifelines', '0.27.7'), From 5e0f098c80e611b193c8d198768a1efb99bad7c6 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 7 Aug 2024 16:05:42 +0200 Subject: [PATCH 5/9] add HF-Datasets ec --- .../HF-Datasets-2.14.4-gfbf-2022b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.14.4-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.14.4-gfbf-2022b.eb b/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.14.4-gfbf-2022b.eb new file mode 100644 index 00000000000..e92ec85db93 --- /dev/null +++ b/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.14.4-gfbf-2022b.eb @@ -0,0 +1,44 @@ +easyblock = "PythonBundle" + +name = 'HF-Datasets' +version = '2.14.4' + +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': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('aiohttp', '3.8.5'), + ('dill', '0.3.7'), + ('Arrow', '11.0.0'), + ('PyYAML', '6.0'), + ('tqdm', '4.64.1'), + ('python-xxhash', '3.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyarrow_hotfix', '0.6', { + 'checksums': ['79d3e030f7ff890d408a100ac16d6f00b14d44a502d7897cd9fc3e3a534e9945'], + }), + ('multiprocess', '0.70.15', { + 'checksums': ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'], + }), + ('huggingface-hub', '0.15.1', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['a61b7d1a7769fe10119e730277c72ab99d95c48d86a3d6da3e9f3d0f632a4081'], + }), + ('datasets', version, { + 'checksums': ['ef29c2b5841de488cd343cfc26ab979bff77efa4d2285af51f1ad7db5c46a83b'], + }), +] + +moduleclass = 'data' From 2a64e21cbba6f6090a6ef38ccef7bef367aa7810 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 13 Aug 2024 15:08:09 +0200 Subject: [PATCH 6/9] add alt_location for numpy patches --- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index 7ef97fcc743..7d53f08dd4e 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -207,8 +207,8 @@ exts_list = [ }), ('numpy', '1.23.5', { 'patches': [ - 'numpy-1.20.3_fix-fortran-compiler-error.patch', - 'numpy-1.22.3_disable-broken-override-test.patch', + {'name': 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'alt_location': 'Scipy-bundle'}, + {'name': 'numpy-1.22.3_disable-broken-override-test.patch', 'alt_location': 'Scipy-bundle'}, ], 'checksums': [ {'numpy-1.23.5.tar.gz': '1b1766d6f397c18153d40015ddfc79ddb715cabadc04d2d228d4e5a8bc4ded1a'}, From 324d07c96588cce54592662ad90a2e95ddb271ec Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Mon, 19 Aug 2024 12:33:12 +0200 Subject: [PATCH 7/9] Update easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb - SciPy typo Co-authored-by: Kenneth Hoste --- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index 7d53f08dd4e..522830f8f40 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -207,8 +207,8 @@ exts_list = [ }), ('numpy', '1.23.5', { 'patches': [ - {'name': 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'alt_location': 'Scipy-bundle'}, - {'name': 'numpy-1.22.3_disable-broken-override-test.patch', 'alt_location': 'Scipy-bundle'}, + {'name': 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'alt_location': 'SciPy-bundle'}, + {'name': 'numpy-1.22.3_disable-broken-override-test.patch', 'alt_location': 'SciPy-bundle'}, ], 'checksums': [ {'numpy-1.23.5.tar.gz': '1b1766d6f397c18153d40015ddfc79ddb715cabadc04d2d228d4e5a8bc4ded1a'}, From f2f5962754e38c655d63c4358f071e8772052d25 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 19 Aug 2024 14:35:24 +0200 Subject: [PATCH 8/9] update patches checksums --- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index 522830f8f40..29a94b22448 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -213,9 +213,9 @@ exts_list = [ 'checksums': [ {'numpy-1.23.5.tar.gz': '1b1766d6f397c18153d40015ddfc79ddb715cabadc04d2d228d4e5a8bc4ded1a'}, {'numpy-1.20.3_fix-fortran-compiler-error.patch': - 'f12a49a754cb4c01a39691f8a7470bfa0e56c70139d78ca8b188f049010e7647'}, + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, {'numpy-1.22.3_disable-broken-override-test.patch': - '0d894fa9592ba9855397bc89fd4408bd911d49e6b6449d1693f87d2e5fcac486'}, + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, ], }), (name, version, { From 4164dcb9de87e0309e22831e0a5e24140d0289a6 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 18 Oct 2024 11:38:58 +0200 Subject: [PATCH 9/9] fix SLURM NTASK in test step --- .../easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb index 29a94b22448..cd64d6ed49a 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.10-foss-2022b.eb @@ -45,10 +45,13 @@ dependencies = [ local_preinstallopts = "sed -i 's/pydantic<2.0/pydantic/' %(builddir)s/%(name)s/%(name)s-%(version)s/setup.cfg && " # ignore the failing part of ddpm test - seems constraints are wrong -# https://github.com/vanderschaarlab/synthcity/blob/v0.2.10/tests/plugins/generic/test_ddpm.py#L114 +# see https://github.com/vanderschaarlab/synthcity/blob/v0.2.10/tests/plugins/generic/test_ddpm.py#L114 local_pretestopts = ( "sed -i '138,144d' %(builddir)s/%(name)s/%(name)s-%(version)s/tests/plugins/generic/test_ddpm.py && " ) +# solve problem with PyTorch-Lightning _validate_srun_variables method +# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21141#issuecomment-2318854045 +local_pretestopts += "export SLURM_NTASKS_PER_NODE=$SLURM_NTASKS && " # fix invalid syntax of xgbse/setup.py local_xgbse_preinstallopts = r"sed -i -e '45,49d' -e 's/pandas>=1.0.\*/pandas>=1.0.0/' setup.py && "