cgflow/pyproject.toml at main · tsa87/cgflow · GitHub

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[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "cgflow"
authors = [
  { name = "Tony Shen", email = "tony.z.shen@gmail.com" },
  { name = "Seonghwan Seo", email = "shwan0106@gmail.com" },
]
version = "0.1.0"
readme = "README.md"
classifiers = [
  "Operating System :: OS Independent",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3",
]
requires-python = ">=3.11,<3.13"
dependencies = [
  # torch, torch-geometric
  "torch>=2.5.0",
  "torch-geometric>=2.4.0",
  "torch-scatter>=2.1.2",
  "torch-sparse>=0.6.18",
  "torch-cluster>=1.6.3",
  # cgflow training
  "lightning",
  "torchmetrics",
  "lmdb",
  # cheminfo&bioinfo
  "rdkit",
  "biopython",
  "openbabel-wheel",
  "biotite==1.0.1",
  # additional
  "gitpython",
  "wandb",
  "tqdm",
  "omegaconf",
  "pandas>=2.2.2",
  "scikit-learn",
  "druglikeness @ git+https://github.com/SeonghwanSeo/drug-likeness.git",
  "pharmaconet @ git+https://github.com/SeonghwanSeo/PharmacoNet.git",
]

[project.optional-dependencies]
vina = [
  "meeko",
  "vina",
  "pdb2pqr",
  "AutoDockTools_py3 @ git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3",
]
unidock = [
  "unidock_tools @ git+https://github.com/dptech-corp/Uni-Dock.git@1.1.2#subdirectory=unidock_tools",
]
dev = ["pre-commit"]
extra = [
  "py3Dmol",
  "matplotlib",
  "jupyter",
  "ipykernel",
  "py3Dmol",
  "posecheck @ git+https://github.com/cch1999/posecheck.git",
  "MDAnalysis==2.7.0",
]

[tool.ruff]
target-version = "py311"
line-length = 120
[tool.ruff.lint]
select = ["E", "F", "B", "UP", "T203", "I"]
ignore = ["E501", "E722"]
[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401", "E402"]
[tool.ruff.lint.isort]
section-order = [
  "future",
  "standard-library",
  "third-party",
  "externals",
  "first-party",
  "local-folder",
]
[tool.ruff.lint.isort.sections]
externals = ['gflownet', 'rxnflow']