pyproject.toml

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

[project]
name = "bioemu"
version = "0.1.0"
description = "Biomolecular emulator"
authors = [
]
requires-python = ">=3.10"
dependencies = [
    "mdtraj==1.9.9",
    "torch_geometric==2.6.1",
    "torch==2.4.0",
    "torchvision",
    "modelcif==0.7",
    "bio==1.7.1",
    "fire==0.7.0",
    "huggingface-hub",
    "hydra-core",
    "dm-tree",
    "stackprinter",
]

[project.optional-dependencies]
dev = [
    "pytest", # For developers
    "pytest-cov",
    "pre-commit",
]
md = [
    "openmm==8.2.0",
    "pdb2pqr==3.4.1"
]

[tool.black]
line-length = 100
include = '\.pyi?$'
exclude = '''
/(
    \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | _build
  | buck-out
  | build
  | dist
  | bioemu/openfold
)/
'''

[tool.isort]
profile = "black"
line_length = 100
known_first_party = [
    "bioemu",
]

[tool.mypy]
verbosity = 0

[[tool.mypy.overrides]]
module = [
    "Bio.*",
    "git.*",
    "hydra.*",
    "IPython.*",
    "matplotlib.*",
    "mdtraj.*",
    "numpy.*",
    "openmm.*",
    "tqdm.*",
    "torch.*",
    "torch_geometric.*",
    "torch_scatter.*",
    "pandas.*",
    "pdbfixer.*",
    "pytest.*",
    "omegaconf.*",
    "scipy.*",
    "sklearn.*",
]
ignore_missing_imports = true




[tool.ruff]
line-length = 100

[tool.ruff.lint]
# Check https://beta.ruff.rs/docs/rules/ for full list of rules
select = [
  "E", "W",  # pycodestyle
  "F",  # Pyflakes
  # "C90",  # mccabe
  # "I",  # isort
  # "N",  # pep8-naming
  # "D",  # pydocstyle
  "UP",  # pyupgrade
  # "YTT",  # flake8-2020
  # "ANN",  # flake8-annotations
  # "S",  # flake8-bandit
  # "BLE",  # flake8-blind-except
  # "FBT",  # flake8-boolean-trap
  # "B",  # flake8-bugbear
  # "A",  # flake8-builtins
  # "COM",  # flake8-commas
  # "C4",  # flake8-comprehensions
  # "DTZ",  # flake8-datetimez
  # "T10",  # flake8-debugger
  # "DJ",  # flake8-django
  # "EM",  # flake8-errmsg
  # "EXE",  # flake8-executable
  # "ISC",  # flake8-implicit-str-concat
  # "ICN",  # flake8-import-conventions
  # "G",  # flake8-logging-format
  # "INP",  # flake8-no-pep420
  # "PIE",  # flake8-pie
  # "T20",  # flake8-print
  # "PYI",  # flake8-pyi
  # "PT",  # flake8-pytest-style
  # "Q",  # flake8-quotes
  # "RSE",  # flake8-raise
  # "RET",  # flake8-return
  # "SLF",  # flake8-self
  # "SIM",  # flake8-simplify
  # "TID",  # flake8-tidy-imports
  # "TCH",  # flake8-type-checking
  # "ARG",  # flake8-unused-arguments
  # "PTH",  # flake8-use-pathlib
  # "ERA",  # eradicate
  # "PD",  # pandas-vet
  # "PGH",  # pygrep-hooks
  # "PLC",  # pylint-convention
  "PLE",  # pylint-error
  # "PLR",  # pylint-refactor
  # "PLW",  # pylint-warning
  # "TRY",  # tryceratops
  # "NPY",  # numpy
  # "RUF",  # ruff
]
ignore = [
  # W605: invalid escape sequence -- triggered by pseudo-LaTeX in comments
  "W605",
  # E501: Line too long -- triggered by comments and such. black deals with shortening.
  "E501",
  # E402: Module level import not at top of file -- triggered by python path manipulations
  "E402",
  # E741:  Do not use variables named 'l', 'o', or 'i' -- disagree with PEP8
  "E741",
]
extend-safe-fixes = [
  "UP"
]
exclude=["openfold"]

[tool.setuptools]
include-package-data = true

[tool.setuptools.packages.find]
where = ["src"]