WaterFlow/pyproject.toml at main · diff-use/WaterFlow · GitHub

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[project]
name = "waterflow"
version = "0.1.0"
requires-python = ">=3.12,<3.13"
dependencies = [
  "torch==2.8.0",
  "torch-geometric",
  "torch-scatter",
  "torch-cluster",
  "pyg-lib",
  "e3nn",
  "esm",
  "biotite",
  "pymol-open-source",
  "scipy",
  "pandas",
  "numpy",
  "matplotlib",
  "pillow",
  "loguru",
  "tqdm",
  "wandb",
  "jaxtyping",
]

[dependency-groups]
dev = ["pytest", "pytest-cov", "ty", "prek", "ruff"]

# PyTorch CUDA 12.6 index (so `torch` comes from the right place)
[[tool.uv.index]]
name = "pytorch-cu126"
url = "https://download.pytorch.org/whl/cu126"
explicit = true

# PyG “find-links” page as a flat index (equivalent to pip -f ...)
[[tool.uv.index]]
name = "pyg-cu126"
url = "https://data.pyg.org/whl/torch-2.8.0+cu126.html"
format = "flat"
explicit = true

[tool.uv.sources]
torch = { index = "pytorch-cu126" }

torch-scatter = { index = "pyg-cu126" }
torch-cluster = { index = "pyg-cu126" }
pyg-lib = { index = "pyg-cu126" }

[tool.mypy]
disallow_untyped_defs = false
ignore_missing_imports = true
python_version = "3.12"
warn_return_any = true
warn_unused_configs = true

[tool.ty.rules]
# uvx runs ty in isolation without project dependencies - ignore missing imports
unresolved-import = "ignore"
# PyTorch Geometric has incomplete type stubs - dynamic attributes on Batch/Data
unresolved-attribute = "ignore"
# PyG's MessagePassing.message() override pattern is intentional
invalid-method-override = "ignore"
# PyG's propagate() uses **kwargs which ty doesn't understand
missing-argument = "ignore"
# Dict.get() returns union types that don't narrow well
invalid-argument-type = "ignore"

[tool.ruff.lint]
fixable = ["I001", "F401", "UP"]
ignore = ["E402", "E501", "E721", "E731", "E741", "F722", "F821", "UP015", "UP037"]
select = ["E", "F", "I001", "UP"]

[tool.ruff.lint.flake8-import-conventions.extend-aliases]
"collections" = "co"
"functools" = "ft"
"itertools" = "it"

[tool.ruff.lint.isort]
combine-as-imports = true
extra-standard-library = ["typing_extensions"]
lines-after-imports = 2
order-by-type = false