pyproject.toml

[project]
name = "DISCO"
version = "1.0.0"
description = "Diffusion for Sequence-Structure Co-design: a multimodal generative model that jointly co-designs protein sequences and 3D structures conditioned on arbitrary biomolecules"
readme = "README.md"
license = "Apache-2.0"
requires-python = ">=3.11,<3.13"
dependencies = [
    "accelerate>=1.12.0",
    "biopython==1.83",
    "biotite==1.4.0",
    "deepspeed>=0.18.3",
    "dm-tree>=0.1.8",
    "evaluate>=0.4.6",
    "fair-esm>=2.0.0",
    "fasteners>=0.20",
    "freesasa==2.2.1",
    "gemmi>=0.6.7",
    "hydra-core>=1.3.2",
    "icecream>=2.1.8",
    "ipdb>=0.13.13",
    "lightning>=2.6.0",
    "ml-collections>=1.1.0",
    "modelcif>=1.6",
    "multimolecule>=0.0.8",
    "ninja>=1.13.0",
    "numpy<2",
    "pandas>=2.3.3",
    "pdbeccdutils>=1.0.0",
    "pre-commit>=4.5.1",
    "prody>=2.6.1",
    "py3dmol>=2.5.3",
    "pyrootutils>=1.0.4",
    "rich>=14.2.0",
    "rootutils>=1.0.7",
    "scikit-learn>=1.8.0",
    "scipy>=1.16.3",
    "seaborn>=0.13.2",
    "sentencepiece>=0.2.1",
    "torch>=2.5",
    "torchdata>=0.11.0",
    "torchinfo>=1.8.0",
    "tos>=2.8.7",
    "tqdm>=4.67.1",
    "transformers>=4.50.0",
    "wandb>=0.23.1",
    "openfold",
    "LigandMPNN",
    "runner",
]
[tool.uv.workspace]
members = ["packages/LigandMPNN", "packages/openfold", "config", "runner"]
exclude = ["packages/TMscore"]

[tool.uv.sources]
openfold = { workspace = true }
LigandMPNN = { workspace = true }
configs = { workspace = true }
runner = { workspace = true }

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["disco"]

[tool.pytest.ini_options]
addopts = [
  "--color=yes",
  "--durations=0",
  "--strict-markers",
  "--doctest-modules",
]
filterwarnings = [
  "ignore::DeprecationWarning",
  "ignore::UserWarning",
]
log_cli = "True"
markers = [
  "slow: slow tests",
]
minversion = "6.0"
testpaths = "tests/"

[tool.coverage.report]
exclude_lines = [
    "pragma: nocover",
    "raise NotImplementedError",
    "raise NotImplementedError()",
    "if __name__ == .__main__.:",
]
# ----------------------------------------
# Ruff configuration
# ----------------------------------------
[tool.ruff]
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".ipynb_checkpoints",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pyenv",
    ".pytest_cache",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    ".vscode",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "site-packages",
    "venv",
    "outputs/",
    "packages/",
]

line-length = 99
indent-width = 4

target-version = "py311"

# ----------------------------------------
# Linting configuration
# ----------------------------------------
[tool.ruff.lint]
select = [
    "E",      # pycodestyle errors
    "F",      # pyflakes
    "W",      # pycodestyle warnings
    "B",      # flake8-bugbear
    "I",      # isort
    "UP",     # pyupgrade
    "N",      # pep8-naming
    "S",      # bandit (security)
    "COM",    # flake8-commas
    "ISC",    # implicit string concatenation
    "PT",     # pytest style
    "PTH",    # pathlib usage
    "T10",    # debugger detection
]

ignore = [
    "E203",   # whitespace before ':'
    "E731",   # lambda assignment
    "S101",   # use of assert
    "COM812", # trailing comma - conflicts with ruff formatter
]

fixable = ["ALL"]
unfixable = []

dummy-variable-rgx = "^(_.*|[ijk])$"

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["S"]

# ----------------------------------------
# Formatting (Black-compatible)
# ----------------------------------------
[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"