requirements.in

# dev-deps, still placed in the same requirements file
ruff==0.6.3 # in sync with pre-commit-hook
mypy
pytest
pre-commit

# types/stubs are required by mypy
pandas-stubs
types-pyyaml
types-tqdm
typing-extensions
types-requests

# CLI, administrator tools
typer~=0.12        # CLI generator
# pydantic~=2.5      # serialization/deserialization of configs

# notebooks, plotting
ipykernel~=6.27    # needed by vs code to run notebooks in devcontainer
# seaborn
matplotlib

# misc
tqdm~=4.66

# data import/export, application-specific
gemmi~=0.6.3       # pdb/mmcif parsing
rdkit==2023.9.5    # parsing of ligands. 2023.9.6 has broken type stubs
biopython>=1.83    # parsing, data access
antipickle==0.2.0  # save/load heterogeneous python structures
tmtools>=0.0.3     # Python bindings for the TM-align algorithm
modelcif>=1.0      # mmcif writing, confirmed to work currently latest 1.0

# commented out following optional dependencies for release on pypi
# dockq metric for comparing predicted pdbs and ground truth pdbs
# dockq @ git+https://github.com/bjornwallner/DockQ.git@v2.1.1
# pip-compatible minimized version of anarci
# anarci @ git+https://github.com/arogozhnikov/microANARCI@d81823395d0c3532d6e033d80b036b4aa4a4565e

# computing, dl
numpy~=1.21
pandas[parquet,gcp,aws]~=2.1 
pandera
numba>=0.59
# polars              
einops~=0.8
jaxtyping>=0.2.25   # versions <0.2.25 do not easily support runtime typechecking
beartype>=0.18      # compatible typechecker to use with jaxtyping
# do not use 2.2 because https://github.com/pytorch/pytorch/issues/122385
torch~=2.3.1
transformers~=4.44  # for esm inference