From 16e88554ba259f4e876dc14331493cb77f333950 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 15 Jul 2024 17:48:30 +0200 Subject: [PATCH] #357 build ok + decaf + fastai --- 357_Synthcity/decaf_0.1.6.eb | 49 ++++ 357_Synthcity/decaf_origo_0.1.1.eb | 53 ++++ 357_Synthcity/fastai.eb | 41 +++ 357_Synthcity/lifelines.eb | 7 +- 357_Synthcity/synthcity.eb | 287 +++++++++++++++------ 357_Synthcity/synthcity_update_of_2022a.eb | 193 ++++++++++++++ 6 files changed, 542 insertions(+), 88 deletions(-) create mode 100644 357_Synthcity/decaf_0.1.6.eb create mode 100644 357_Synthcity/decaf_origo_0.1.1.eb create mode 100644 357_Synthcity/fastai.eb create mode 100644 357_Synthcity/synthcity_update_of_2022a.eb diff --git a/357_Synthcity/decaf_0.1.6.eb b/357_Synthcity/decaf_0.1.6.eb new file mode 100644 index 00000000..2b2ba86d --- /dev/null +++ b/357_Synthcity/decaf_0.1.6.eb @@ -0,0 +1,49 @@ +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': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyTorch-Lightning', '2.2.1'), + ('PyTorch-bundle', '2.1.2'), + ('XGBoost', '2.0.2'), + ('scikit-learn', '1.3.1'), + ('networkx', '3.1'), +] + +use_pip = True +sanity_pip_check = True + +# unpin dependencies versions +local_preinstallopts = ( + "sed -i" + " -e 's/networkx>=2.0,<3.0/networkx/'" + " -e 's/pytorch-lightning<2.0/pytorch-lightning/'" + " %(builddir)s/%(name)s/DECAF-%(version)s/requirements.txt && " +) + +exts_list = [ + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + (name, version, { + 'modulename': 'decaf', + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/vanderschaarlab/DECAF/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['8f34e99937d2ccc43bff97b310c371c450e27313c0801cdd36aa91664c8e3180'], + }), +] + +sanity_check_commands = ["python -c 'from decaf import DECAF, DataModule'"] + +moduleclass = 'bio' diff --git a/357_Synthcity/decaf_origo_0.1.1.eb b/357_Synthcity/decaf_origo_0.1.1.eb new file mode 100644 index 00000000..eeaeafd0 --- /dev/null +++ b/357_Synthcity/decaf_origo_0.1.1.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'DECAF-synthetic-data' +version = '0.1.1' +local_commit = "db6333a" + +homepage = 'https://github.com/trentkyono/DECAF' +description = """DEbiasing CAusal Fairness.""" + + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyTorch-Lightning', '2.2.1'), + ('PyTorch-bundle', '2.1.2'), + ('XGBoost', '2.0.2'), + ('scikit-learn', '1.3.1'), + ('networkx', '3.1'), +] + +use_pip = True +sanity_pip_check = True + +# unpin dependencies versions +local_preinstallopts = ( + "sed -i" + " -e 's/networkx == 2.\*/networkx/'" + " -e 's/numpy == 1.19.\*/numpy/'" + " -e 's/pytorch-lightning == 1.4.\*/pytorch-lightning/'" + " -e 's/torch == 1.9.\*/torch/'" + " -e 's/torchtext == 0.10.\*/torchtext/'" + " %(builddir)s/decaf_synthetic_data/DECAF-db6333aced375ef14961e06e805bf7412f378f29/requirements.txt && " +) + +exts_list = [ + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('decaf_synthetic_data', version, { + 'modulename': 'decaf', + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/trentkyono/DECAF/archive/'], + 'sources': [{'download_filename': 'db6333a.tar.gz', 'filename': '%(name)s-%(version)s-db6333a.tar.gz'}], + 'checksums': ['9df50a5b4ee96a6dcf53e2d845702ad48ebdbb0a31bb0cb2968b2217a1c8886e'], + }), +] + +sanity_check_commands = ["python -c 'from decaf import DECAF, DataModule'"] + +moduleclass = 'bio' diff --git a/357_Synthcity/fastai.eb b/357_Synthcity/fastai.eb new file mode 100644 index 00000000..a55f51d7 --- /dev/null +++ b/357_Synthcity/fastai.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'fastai' +version = '2.7.15' + +homepage = 'https://www.fast.ai/' +description = """The fastai deep learning library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +use_pip = True + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2'), + ('matplotlib', '3.7.2'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('Pillow', '10.0.0'), + ('scikit-learn', '1.3.1'), + ('spaCy', '3.7.4'), +] + +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/357_Synthcity/lifelines.eb b/357_Synthcity/lifelines.eb index 4aae5bca..4a7fb00e 100644 --- a/357_Synthcity/lifelines.eb +++ b/357_Synthcity/lifelines.eb @@ -1,21 +1,22 @@ easyblock = 'PythonBundle' name = 'lifelines' -version = '0.29.0' +version = '0.28.0' homepage = "https://lifelines.readthedocs.io/en/latest/" description = """lifelines is a complete survival analysis library, written in pure Python.""" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [('poetry', '1.5.1')] dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('matplotlib', '3.7.2'), ] -sanity_pip_check = True use_pip = True +sanity_pip_check = True exts_list = [ ('wrapt', '1.16.0', { @@ -37,7 +38,7 @@ exts_list = [ 'checksums': ['64dd7992a7aa5bbceb1e40679d0f01fc6f0ba12b7d23d78094a88c2edc68fba1'], }), (name, version, { - 'checksums': ['a82315a5daf2ad29eabefff38b8422364a8a721721136a501c30ff861cac8759'], + 'checksums': ['eecf726453fd409c94fef8a521f8e593bcd09337f920fe885131f01cfe58b25e'], }), ] diff --git a/357_Synthcity/synthcity.eb b/357_Synthcity/synthcity.eb index dcee5856..1e6fa79c 100644 --- a/357_Synthcity/synthcity.eb +++ b/357_Synthcity/synthcity.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} # scikit-learn>=1.2 OK # nflows>=0.14 ok exts # numpy>=1.20, <1.24 - v1.25.1 in scipy -> unpin - # lifelines>=0.27,!= 0.27.5, <0.27.8 -> NO -> create + # lifelines>=0.27,!= 0.27.5, <0.27.8 -> NO -> created OK # opacus>=1.3 ok exts # decaf-synthetic-data>=0.1.6 ok exts # optuna>=3.1 OK @@ -43,155 +43,272 @@ toolchain = {'name': 'foss', 'version': '2023a'} # tsai; python_version>"3.7" ok exts # be-great>=0.0.5;python_version>="3.9" ok exts # arfpy ok exts - + # + # opacus 1.4.1 requires opt-einsum, ok + # be-great 0.0.7 requires accelerate, ok + # be-great 0.0.7 requires datasets, OK (HF-Datasets) + # be-great 0.0.7 requires transformers, OK (Transformers) + # pgmpy 0.1.25 requires opt-einsum, ok + # pykeops 2.2.3 requires keopscore, ok + # tsai 0.3.9 requires fastai, -> UPDATE + # tsai 0.3.9 requires imbalanced-learn, OK + # tsai 0.3.9 requires pyts, ok + # decaf-synthetic-data 0.1.6 requires pytorch-lightning OK + # decaf-synthetic-data 0.1.6 requires torchtext -> add PyTorch-bundle instead of PyTorch -> has torchtext OK + # pycox 0.2.3 requires feather-format, ok + # pycox 0.2.3 requires h5py, OK + # pycox 0.2.3 requires py7zr, ok + # pycox 0.2.3 requires torchtuples, ok + # -> unpin in local_preinstallopts + # synthcity 0.2.10 has requirement lifelines!=0.27.5,<0.27.8,>=0.27, but you have lifelines 0.28 + # synthcity 0.2.10 has requirement numpy<1.24,>=1.20, but you have numpy 1.25.1. + # synthcity 0.2.10 has requirement pandas<2,>=1.4, but you have pandas 2.0.3. + # synthcity 0.2.10 has requirement pydantic<2.0, but you have pydantic 2.5.3. + # synthcity 0.2.10 has requirement torch<2.0,>=1.10.0, but you have torch 2.1.2. + # synthcity 0.2.10 has requirement xgboost<2.0.0, but you have xgboost 2.0.2. + # -> networkx v2.8.8 in exts + # decaf-synthetic-data 0.1.6 has requirement networkx<3.0,>=2.0, but you have networkx 3.1. + # -> use xgbse v0.2.3 + # xgbse 0.3.1 has requirement joblib<2.0.0,>=1.4.2, but you have joblib 1.2.0. + # xgbse 0.3.1 has requirement lifelines<0.30.0,>=0.29.0, but you have lifelines 0.28.0. + # xgbse 0.3.1 has requirement numpy<2.0.0,>=1.26.4, but you have numpy 1.25.1. + # xgbse 0.3.1 has requirement scikit-learn<2.0.0,>=1.5.0, but you have scikit-learn 1.3.1. + # xgbse 0.3.1 has requirement xgboost<3.0.0,>=2.1.0, but you have xgboost 2.0.2. + # py7zr 0.21.1 requires brotli, OK + # py7zr 0.21.1 requires inflate64, ok + # py7zr 0.21.1 requires multivolumefile, ok + # py7zr 0.21.1 requires pybcj, ok + # py7zr 0.21.1 requires pycryptodomex, ok + # py7zr 0.21.1 requires pyppmd, ok + # py7zr 0.21.1 requires pyzpyzstdstd, ok + # py7zr 0.21.1 requires texttable, ok + # decaf-synthetic-data 0.1.6 has requirement pytorch-lightning<2.0, but you have pytorch-lightning 2.2.1. + # -> create econfig for Decaf + # problem: decaf has only whl on pypi + no releases on GitHub + # fastapi 0.110.0 has requirement typing-extensions>=4.8.0, but you have typing-extensions 4.6.3. + # seems it goes from PyTorch-Lightning -> put it as the last dep + # py7zr 0.21.1 has requirement brotli>=1.1.0; platform_python_implementation == "CPython", but you have brotli 1.0.9. + # use v0.20.6 + # fastapi 0.110.0 has requirement typing-extensions>=4.8.0, but you have typing-extensions 4.6.3. + # -> add v typing-extensions v4.9.0 to exts + # py7zr 0.20.6 has requirement pyppmd<1.1.0,>=0.18.1, but you have pyppmd 1.1.0. -> add pyppmd v1.0.0 ok + +# builddependencies = [('poetry', '1.5.1')] dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), - # ('lifelines', '0.27.4'), + ('lifelines', '0.28.0'), ('SciPy-bundle', '2023.07'), ('pydantic', '2.5.3'), ('Redis', '7.2.3'), ('scikit-learn', '1.3.1'), ('SHAP', '0.43.0'), - ('PyTorch', local_pytorch_version), + ('PyTorch-bundle', local_pytorch_version), ('XGBoost', '2.0.2'), ('tqdm', '4.66.1'), + ('HF-Datasets', '2.18.0'), + ('Transformers', '4.39.3'), # ('Mako', '1.2.0'), # ('PyYAML', '6.0'), - # ('fastai', '2.7.10'), - # ('h5py', '3.7.0'), - ('networkx', '3.1'), + ('fastai', '2.7.15'), + ('h5py', '3.9.0'), + # ('networkx', '3.1'), # v2.8.8 in exts # ('protobuf', '3.19.4'), # ('Arrow', '8.0.0'), # ('pybind11', '2.9.2'), - # ('PyTorch-Lightning', '2.2.1'), # ('spaCy', '3.4.4'), # ('tensorboard', '2.10.0'), # ('torchvision', '0.13.1'), - # ('Brotli-python', '1.0.9'), + ('Brotli-python', '1.0.9'), ('statsmodels', '0.14.1'), - # ('imbalanced-learn', '0.10.1'), + ('imbalanced-learn', '0.12.3'), # ('Greenlet', '2.0.2'), ('Optuna', '3.5.0'), # ('Cython', '0.29.33'), # ('cython-blis', '0.9.1'), - # ('torchtext', '0.14.1', '-PyTorch-%s' % local_pytorch_version), # ('IPython', '8.5.0'), ('MONAI', '1.3.0'), + ('DECAF-synthetic-data', '0.1.6'), + ('PyTorch-Lightning', '2.2.1'), ] sanity_pip_check = True use_pip = True +# unpin deps restrictions +local_preinstallopts = ( + "sed -i" + " -e 's/pandas>=1.4,<2/pandas>=1.4/'" + " -e 's/torch>=1.10.0,<2.0/torch>=1.10.0/'" + " -e 's/numpy>=1.20, <1.24/numpy>=1.20/'" + " -e 's/pydantic<2.0/pydantic/'" + " -e 's/xgboost<2.0.0/xgboost/'" + " -e 's/lifelines>=0.27,!= 0.27.5, <0.27.8/lifelines>=0.27,!= 0.27.5/'" + " %(builddir)s/%(name)s/%(name)s-%(version)s/setup.cfg && " +) + +# 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 = [ - ('decaf_synthetic_data', '0.1.6', { - 'modulename': 'decaf', - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['dc51502f9f72b3fbdbef697238d72ae6b8457f76efc9763a747970ba543d4e0f'], + ('typing_extensions', '4.9.0', { + 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], }), - # ('feather-format', '0.4.1', { - # 'modulename': 'feather', - # 'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'], - # }), ('fflows', '0.0.3', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['18de7a7b98e3708ff2d5ae9f10fad625740230c4de6447906b7ca477667b78fb'], }), - # ('fsspec', '2022.7.1', { - # 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - # 'checksums': ['36c5a8e7c4fc20cf32ef6934ac0a122accc8a593ddc8478d30c3ca4dbbd95500'], - # }), - # ('functorch', '0.2.0', { - # 'source_urls': ['https://github.com/pytorch/%(name)s/archive/'], - # 'sources': ['v%(version)s.tar.gz'], - # 'checksums': ['ea6446b60d5e0847140e1a0dcb91d8a7de2b5844bba7c3f7560eb5020a05881f'], - # }), - ('geomloss', '0.2.6'), - # ('inflate64', '0.3.1', { - # 'checksums': ['b52dd8fefd2ba179e5dfa18d6eca7e2fc822584616271c039d5ef1f9ca90c71c'], - # }), - # ('keopscore', '2.1.1', { - # 'checksums': ['07b4d254a28a9d4a43153663856677263dd7112912efacbad83c2a76ea0836f0'], - # }), - ('loguru', '0.7.2', { - 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], - }), - # ('multivolumefile', '0.2.3', { - # 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - # 'checksums': ['237f4353b60af1703087cf7725755a1f6fcaeeea48421e1896940cd1c920d678'], - # }), + ('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', '1.4.1', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['8c46aff596bbbc6025ce9d169b49d5b3112cb958e3d74f8b77274134e7590890'], }), - # ('opt_einsum', '3.3.0', { - # 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - # 'checksums': ['2455e59e3947d3c275477df7f5205b30635e266fe6dc300e3d9f9646bfcea147'], - # }), ('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'], }), - # ('py7zr', '0.20.4', { - # 'checksums': ['1d01f98ea1e1f5c49940358691b2076f9a5848056426541e783de33834f59e21'], - # }), - # ('pybcj', '1.0.1', { - # 'modulename': 'bcj', - # 'checksums': ['8b682ed08caabfb7c042d4be083e28ddc692afb1deff5567111f8855071b75c3'], - # }), ('pycox', '0.2.3', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['9ea3c64a4a650ccf6c96cf512712de330f2d75de32122d86995c7cd37ff105d1'], }), - # ('pycryptodomex', '3.17', { - # 'modulename': 'Crypto', - # 'checksums': ['0af93aad8d62e810247beedef0261c148790c52f3cd33643791cc6396dd217c1'], - # }), - ('pykeops', '2.2.3'), - # ('pyppmd', '1.0.0', { - # 'checksums': ['075c9bd297e3b0a87dd7aeabca7fee668218acbe69ecc1c6511064558de8840f'], - # }), - # ('pyts', '0.12.0', { - # 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - # 'checksums': ['acd66b0cf1fd17d9ce6449335f5da30701f65fdee185d4b918726b62ca6af79d'], - # }), - # ('pyzstd', '0.15.4', { - # 'checksums': ['de07ac54f57642f186732075cdce2be3d4a30228c3b17a6d8c6053765dc6eec8'], - # }), - # ('texttable', '1.6.7', { - # 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - # 'checksums': ['b7b68139aa8a6339d2c320ca8b1dc42d13a7831a346b446cb9eb385f0c76310c'], - # }), - # ('thinc', '8.1.9', { - # 'checksums': ['8a1e65529c6d0796271d2a7e5ca6ea013fcb7dad69ec609d5093a25808107f51'], - # # we are using blis 0.9.1 - # # thinc has problems with blis>0.8.0 on Windows only (https://github.com/explosion/thinc/pull/772) - # 'preinstallopts': 'sed -i "s/blis>=0.7.8,<0.8.0/blis>=0.7.8/g" setup.cfg && ', - # }), - # ('torchtuples', '0.2.2', { - # 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - # 'checksums': ['186625230a149cc09f64116d51b203ffefe78160f5a0445adad195893663f55b'], - # }), + ('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', '0.32.1', { + 'checksums': ['3999acff0237cd0d4f9fd98b42d5a3163544777b53fc4f1eec886b77e992d177'], }), ('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': ['v%(version)s.tar.gz'], 'checksums': ['9e6b71539b2b533c00eddfe7681cdd541f393d9573594eca358d263b141c127d'], }), - ('arfpy', '0.1.1'), + ('arfpy', '0.1.1', { + 'checksums': ['88170d5e72638b0dbfec28cfbdfee02e97bd6a06d5a636e960acd5d90d480707'], + }), (name, version, { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/vanderschaarlab/synthcity/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['122a8546cad35e3ac5c74cf81281252dec4dd3c7b1d7afe0f45ef785f89cc682'], }), ] - + sanity_check_commands = [ "python -c 'from synthcity.plugins import Plugins'", + "python -c 'from decaf import DECAF, DataModule'" ] moduleclass = 'lib' + +# ERROR2: OK + # -> fix pandas version in setup.py by local_xgbse_preinstallopts + # == 2024-07-15 14:17:49,585 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd "sed -i '45,49d' setup.py && /apps/gent/RHEL8/zen2-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/zen2-ib/software/synthcity/0.2.10-foss-2023a --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 1 and output: + # Processing /tmp/vsc47063/easybuild/build/synthcity/0.2.10/foss-2023a/xgbse/xgboost-survival-embeddings-0.2.3 + # Preparing metadata (setup.py): started + # Preparing metadata (setup.py): finished with status 'error' + # error: subprocess-exited-with-error + + # python setup.py egg_info did not run successfully. + # exit code: 1 + # > [3 lines of output] + # error in xgbse setup command: 'install_requires' must be a string or list of strings containing valid project/version requirement specifiers; Expected end or semicolon (after version specifier) + # pandas>=1.0.* + # ~~~~~^ + # [end of output] + + # note: This error originates from a subprocess, and is likely not a problem with pip. + # error: metadata-generation-failed + + # Encountered error while generating package metadata. + # > See above for output. + + # note: This is an issue with the package mentioned above, not pip. + # hint: See above for details. +# ERROR1: OK + # -> add xgbse_preinstallopts to delete wrong part from setup.py + # -> seems like a problem with pip and setuptools version: https://stackoverflow.com/questions/77124879/pip-extras-require-must-be-a-dictionary-whose-values-are-strings-or-lists-of + # == 2024-07-15 13:57:09,544 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd " /apps/gent/RHEL8/zen2-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/zen2-ib/software/synthcity/0.2.10-foss-2023a --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 1 and output: + # Processing /tmp/vsc47063/easybuild/build/synthcity/0.2.10/foss-2023a/xgbse/xgboost-survival-embeddings-0.2.3 + # Preparing metadata (setup.py): started + # Preparing metadata (setup.py): finished with status 'error' + # error: subprocess-exited-with-error + + # python setup.py egg_info did not run successfully. + # exit code: 1 + # > [1 lines of output] + # error in xgbse setup command: 'extras_require' must be a dictionary whose values are strings or lists of strings containing valid project/version requirement specifiers. + # [end of output] + + # note: This error originates from a subprocess, and is likely not a problem with pip. + # error: metadata-generation-failed + + # Encountered error while generating package metadata. + # > See above for output. + + # note: This is an issue with the package mentioned above, not pip. + # hint: See above for details. diff --git a/357_Synthcity/synthcity_update_of_2022a.eb b/357_Synthcity/synthcity_update_of_2022a.eb new file mode 100644 index 00000000..4894339c --- /dev/null +++ b/357_Synthcity/synthcity_update_of_2022a.eb @@ -0,0 +1,193 @@ +easyblock = 'PythonBundle' + +name = 'synthcity' +version = '0.2.10' + +local_pytorch_version = '1.12.0' + +homepage = 'https://github.com/vanderschaarlab/synthcity' +description = """A library for generating and evaluating synthetic tabular data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('lifelines', '0.27.4'), + ('SciPy-bundle', '2022.05'), + ('pydantic', '1.10.4'), + ('Redis', '7.0.8'), + ('scikit-learn', '1.1.2'), + ('SHAP', '0.41.0'), + ('PyTorch', local_pytorch_version), + ('XGBoost', '1.7.2'), + ('tqdm', '4.64.0'), + ('Mako', '1.2.0'), + ('PyYAML', '6.0'), + ('fastai', '2.7.10'), + ('h5py', '3.7.0'), + ('networkx', '2.8.4'), + ('protobuf', '3.19.4'), + ('Arrow', '8.0.0'), + ('pybind11', '2.9.2'), + ('PyTorch-Lightning', '1.8.4'), + ('spaCy', '3.4.4'), + ('tensorboard', '2.10.0'), + ('torchvision', '0.13.1'), + ('Brotli-python', '1.0.9'), + ('statsmodels', '0.13.1'), + ('imbalanced-learn', '0.10.1'), + ('Greenlet', '2.0.2'), + ('Optuna', '3.1.0'), + ('Cython', '0.29.33'), + ('cython-blis', '0.9.1'), + ('torchtext', '0.14.1', '-PyTorch-%s' % local_pytorch_version), + ('IPython', '8.5.0'), + ('MONAI', '1.0.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('decaf_synthetic_data', '0.1.6', { + 'modulename': 'decaf', + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['dc51502f9f72b3fbdbef697238d72ae6b8457f76efc9763a747970ba543d4e0f'], + }), + ('feather-format', '0.4.1', { + 'modulename': 'feather', + 'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'], + }), + ('fflows', '0.0.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['18de7a7b98e3708ff2d5ae9f10fad625740230c4de6447906b7ca477667b78fb'], + }), + ('fsspec', '2022.7.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['36c5a8e7c4fc20cf32ef6934ac0a122accc8a593ddc8478d30c3ca4dbbd95500'], + }), + ('functorch', '0.2.0', { + 'source_urls': ['https://github.com/pytorch/%(name)s/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['ea6446b60d5e0847140e1a0dcb91d8a7de2b5844bba7c3f7560eb5020a05881f'], + }), + ('geomloss', '0.2.5', { + 'checksums': ['dcd851cc3c9625f384d4c18d235a790821162c34a2be503a61966b355b98456e'], + }), + ('inflate64', '0.3.1', { + 'checksums': ['b52dd8fefd2ba179e5dfa18d6eca7e2fc822584616271c039d5ef1f9ca90c71c'], + }), + ('keopscore', '2.1.1', { + 'checksums': ['07b4d254a28a9d4a43153663856677263dd7112912efacbad83c2a76ea0836f0'], + }), + ('loguru', '0.6.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['4e2414d534a2ab57573365b3e6d0234dfb1d84b68b7f3b948e6fb743860a77c3'], + }), + ('multivolumefile', '0.2.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['237f4353b60af1703087cf7725755a1f6fcaeeea48421e1896940cd1c920d678'], + }), + ('nflows', '0.14', { + 'checksums': ['6299844a62f9999fcdf2d95cb2d01c091a50136bd17826e303aba646b2d11b55'], + }), + ('opacus', '1.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ef5d6f2aab56901d714ee56fd177a3627d14d820b2ec49cb8bc8a6f52c326507'], + }), + ('opt_einsum', '3.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['2455e59e3947d3c275477df7f5205b30635e266fe6dc300e3d9f9646bfcea147'], + }), + ('pgmpy', '0.1.21', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3c442320e7822892813b4eb56e048729d3bde053a707b5bb032685af6b372246'], + }), + ('py7zr', '0.20.4', { + 'checksums': ['1d01f98ea1e1f5c49940358691b2076f9a5848056426541e783de33834f59e21'], + }), + ('pybcj', '1.0.1', { + 'modulename': 'bcj', + 'checksums': ['8b682ed08caabfb7c042d4be083e28ddc692afb1deff5567111f8855071b75c3'], + }), + ('pycox', '0.2.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['9ea3c64a4a650ccf6c96cf512712de330f2d75de32122d86995c7cd37ff105d1'], + }), + ('pycryptodomex', '3.17', { + 'modulename': 'Crypto', + 'checksums': ['0af93aad8d62e810247beedef0261c148790c52f3cd33643791cc6396dd217c1'], + }), + ('pykeops', '2.1.1', { + 'checksums': ['1931823c746345ce5a5805adad6baa1add772c6fe1800375f7f9a3ddb38b6f71'], + }), + ('pyppmd', '1.0.0', { + 'checksums': ['075c9bd297e3b0a87dd7aeabca7fee668218acbe69ecc1c6511064558de8840f'], + }), + ('pyts', '0.12.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['acd66b0cf1fd17d9ce6449335f5da30701f65fdee185d4b918726b62ca6af79d'], + }), + ('pyzstd', '0.15.4', { + 'checksums': ['de07ac54f57642f186732075cdce2be3d4a30228c3b17a6d8c6053765dc6eec8'], + }), + ('texttable', '1.6.7', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['b7b68139aa8a6339d2c320ca8b1dc42d13a7831a346b446cb9eb385f0c76310c'], + }), + ('thinc', '8.1.9', { + 'preinstallopts': 'sed -i "s/blis>=0.7.8,<0.8.0/blis>=0.7.8/g" setup.cfg && ', + 'checksums': ['8a1e65529c6d0796271d2a7e5ca6ea013fcb7dad69ec609d5093a25808107f51'], + }), + ('torchtuples', '0.2.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['186625230a149cc09f64116d51b203ffefe78160f5a0445adad195893663f55b'], + }), + ('tsai', '0.3.5', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['f5b888f7b968d1826a74eab3b8fa9559c6985d8532c017a4d85809e6c8e6cadd'], + }), + ('xgbse', '0.2.3', { + 'source_urls': ['https://github.com/loft-br/xgboost-survival-embeddings/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['9e6b71539b2b533c00eddfe7681cdd541f393d9573594eca358d263b141c127d'], + }), + ('be_great', '0.0.5', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['bb98c97abb08d611847c0a089c215a734f07a08500775e280d1e04e75f6a1efc'], + }), + ('arfpy', '0.1.0', { + 'checksums': ['18819df4e82aa4bb62750fca959642a63895ba7d6e092a419456704a3ba1a728'], + }), + ('scikit-learn', '1.2.1', { + 'modulename': 'sklearn', + 'checksums': ['fbf8a5c893c9b4b99bcc7ed8fb3e8500957a113f4101860386d06635520f7cfb'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['38ed176e190f1d8fca8299ae1f9b9d44498e33501fc0f1ea90ae55f56a473a1f'], + }), +] + +sanity_check_commands = [ + "python -c 'from synthcity.plugins import Plugins'", +] + +moduleclass = 'lib' + +# ERROR2: + # -> there is dep: be-great>=0.0.5;python_version>="3.9" -> seems this won`t work... + # be-great 0.0.5 requires accelerate, which is not installed. + # be-great 0.0.5 requires datasets, which is not installed. + # be-great 0.0.5 requires transformers, which is not installed. + # be-great 0.0.5 has requirement numpy>=1.24.2, but you have numpy 1.22.3. + # be-great 0.0.5 has requirement pandas>=1.4.4, but you have pandas 1.4.2. +# ERROR1: + # -> downgrade versions of be-great and arfpy + add scikit-learn 1.2.1 to exts + # be-great 0.0.7 requires accelerate, which is not installed. + # be-great 0.0.7 requires datasets, which is not installed. + # be-great 0.0.7 requires transformers, which is not installed. + # synthcity 0.2.10 has requirement scikit-learn>=1.2, but you have scikit-learn 1.1.2. -> add 1.2.1 to exts + # be-great 0.0.7 has requirement numpy>=1.23.1, but you have numpy 1.22.3. + # be-great 0.0.7 has requirement pandas>=1.4.4, but you have pandas 1.4.2. + # arfpy 0.1.1 has requirement pandas>=1.5, but you have pandas 1.4.2.