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77 lines
1.8 KiB
Plaintext
77 lines
1.8 KiB
Plaintext
# Core ML dependencies
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# NOTE: torch, torchvision, torchaudio are already included in NGC container
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lightning>=2.4.0,<2.5
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# Small molecule libraries
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rdkit>=2024.3.5
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# TODO: Remove OpenBabel dependency
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# openbabel will be installed via apt-get (pip installation fails due to C++ build dependencies)
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# Project-related dependencies
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# ... generic tools
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GitPython>=3.0.0,<4
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cython>=3.0.0,<4
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cytoolz>=0.12.3,<1
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assertpy>=1.1.0,<2 # TODO: remove this dependency
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tqdm>=4.65.0,<5
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rootutils>=1.0.7,<1.1
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dm-tree>=0.1.6,<1 # TODO: remove this dependency
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deepdiff>=8.0.0,<9 # TODO: remove this dependency
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# ... configuration & CLI
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fire>=0.6.0,<1
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hydra-core>=1.3.0,<1.4
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environs>=11.0.0,<12
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# ... linear algebra, maths & ml
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numpy>=1.25.0,<2
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scipy>=1.13.1,<2
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einops>=0.8.0,<1
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einx>=0.1.0,<1
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opt_einsum>=3.4.0,<4
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scikit-learn>=1.6.1,<2
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# ... kernels
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cuequivariance_ops_cu12>=0.5.0
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cuequivariance_ops_torch_cu12>=0.5.0
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cuequivariance_torch>=0.5.0
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# ... data tools
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pandas>=2.2,<2.3
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pyarrow>=17.0.0
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fastparquet>=2024.5.0
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seaborn>=0.13.0,<1
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# ... bioinformatics
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biopython>=1.83,<2
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py3Dmol>=2.2.1,<3
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pymol-remote>=0.0.5
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biotite==1.3.0 # Fixed version - updating may involve breaking changes
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hydride==1.2.3 # Fixed version - updating may involve breaking changes
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# ... logging
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wandb>=0.15.10,<1
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rich>=13.9.4,<14
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# Formatting & linting (only needed for development)
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ruff==0.8.3
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pre-commit==3.7.1
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# Debugger & interactive tools (only needed for development)
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debugpy>=1.8.5,<2
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ipykernel>=6.29.4,<7
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icecream>=2.0.0,<3
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pymol-remote>=0.1.0
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ipdb>=0.13.9
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# Pytest plugins (only needed for development)
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pytest>=8.2.0,<9
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pytest-testmon>=2.1.1,<3
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pytest-xdist>=3.6.1,<4
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pytest-dotenv>=0.5.2,<1
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pytest-cov>=4.1.0,<5
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pytest-benchmark>=5.0.0,<6
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# Typing & documentation (only needed for development)
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jaxtyping>=0.2.17,<1
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beartype>=0.18.0,<1 |