Olamide Isreal
f971fd0e21
- Nextflow pipeline using chai1 Docker image from Harbor - S3-based input/output paths (s3://omic/eureka/chai-lab/) - GPU-accelerated protein folding with MSA support Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
51 lines
1.6 KiB
Plaintext
Executable File
51 lines
1.6 KiB
Plaintext
Executable File
# dev-deps, still placed in the same requirements file
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ruff==0.6.3 # in sync with pre-commit-hook
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mypy
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pytest
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pre-commit
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# types/stubs are required by mypy
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pandas-stubs
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types-pyyaml
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types-tqdm
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typing-extensions
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types-requests
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# CLI, administrator tools
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typer~=0.12 # CLI generator
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# pydantic~=2.5 # serialization/deserialization of configs
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# notebooks, plotting
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ipykernel~=6.27 # needed by vs code to run notebooks in devcontainer
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# seaborn
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matplotlib
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# misc
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tqdm~=4.66
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# data import/export, application-specific
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gemmi~=0.6.3 # pdb/mmcif parsing
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rdkit==2023.9.5 # parsing of ligands. 2023.9.6 has broken type stubs
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biopython>=1.83 # parsing, data access
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antipickle==0.2.0 # save/load heterogeneous python structures
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tmtools>=0.0.3 # Python bindings for the TM-align algorithm
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modelcif>=1.0 # mmcif writing, confirmed to work currently latest 1.0
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# commented out following optional dependencies for release on pypi
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# dockq metric for comparing predicted pdbs and ground truth pdbs
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# dockq @ git+https://github.com/bjornwallner/DockQ.git@v2.1.1
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# pip-compatible minimized version of anarci
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# anarci @ git+https://github.com/arogozhnikov/microANARCI@d81823395d0c3532d6e033d80b036b4aa4a4565e
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# computing, dl
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numpy~=1.21
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pandas[parquet,gcp,aws]~=2.1
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pandera
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numba>=0.59
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# polars
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einops~=0.8
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jaxtyping>=0.2.25 # versions <0.2.25 do not easily support runtime typechecking
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beartype>=0.18 # compatible typechecker to use with jaxtyping
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# do not use 2.2 because https://github.com/pytorch/pytorch/issues/122385
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torch~=2.3.1
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transformers~=4.44 # for esm inference |