pyproject.toml

[project]
name = "prolif"
description = "Interaction Fingerprints for protein-ligand complexes and more"
authors = [
  { name = "Cédric Bouysset", email = "cedric@bouysset.net" },
]
readme = "README.rst"
requires-python = ">=3.9"
dynamic = ["version"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Operating System :: OS Independent",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Chemistry",
]
keywords = [
    "science",
    "chemistry",
    "drug-design",
    "cheminformatics",
    "chemoinformatics",
    "molecular-dynamics",
    "interaction-fingerprint",
]
dependencies = [
    "pandas>=1.1.0",
    "numpy>=1.13.3",
    "scipy>=1.3.0",
    "mdanalysis>=2.2.0",
    "tqdm",
    "multiprocess",
    "dill",
]

[project.license]
file = "LICENSE"

[project.optional-dependencies]
plots = [
    "py3Dmol",
    "matplotlib>=3.5",
]
tutorials = [
    "rdkit",
    "matplotlib>=3.7",
    "seaborn<1.0",
    "networkx",
    "pyvis",
    "prolif[plots]",
]
build = [
    "build",
]
tests = [
    "pytest>=6.1.2",
    "pytest-cov",
    "ipython",
    "prolif[plots]"
]
dev = [
    "prolif[build,tests]",
]

[project.urls]
Homepage = "https://github.com/chemosim-lab/ProLIF"
Documentation = "https://prolif.readthedocs.io/en/stable/"
Discussions = "https://github.com/chemosim-lab/ProLIF/discussions"
Issues = "https://github.com/chemosim-lab/ProLIF/issues"
Changelog = "https://github.com/chemosim-lab/ProLIF/blob/master/CHANGELOG.md"

[tool.setuptools]
zip-safe = false

[tool.setuptools.packages.find]
include = ["prolif*"]

[tool.setuptools.package-data]
"prolif.data" = ["*"]
"prolif.data.vina" = ["*"]

[tool.setuptools.dynamic]
version = { attr = "prolif._version.__version__" }

[tool.ruff]
line-length = 88
target-version = "py39"
exclude = [
    ".git",
    ".git-rewrite",
    ".ipynb_checkpoints",
    ".mypy_cache",
    ".pytest_cache",
    ".ruff_cache",
    ".vscode",
    "__pypackages__",
    "_build",
    "build",
    "dist",
    "site-packages",
]
extend-exclude = ["*.ipynb"]

[tool.ruff.lint]
select = [
    # pycodestyle
    "E",
    # Pyflakes
    "F",
    # Warning
    "W",
    # pyupgrade
    "UP",
    # flake8
    "B",  # bugbear
    "SIM",  # simplify
    "A",  # builtins
    "COM",  # commas
    "C4",  # comprehensions
    "ISC",  # implicit-str-concat
    "ICN",  # import-conventions
    "PIE",  # pie
    "T20",  # print
    "PT",  # pytest-style
    "Q",  # quotes
    "RET",  # return
    "ARG",  # unused-arguments
    "PTH",  # use-pathlib
    # pandas-vet
    "PD",
    # pylint
    "PLR",  # refactor
    "PLW",  # warning
    # numpy
    "NPY",
    # refurb
    "FURB",
    # ruff
    "RUF",
    # isort
    "I",
]
ignore = [
    "PLW1514", "PTH123", "PLR0904", "PLR0911", "PLR0913", "PLR0914", "PLR0915",
    "PLR0916", "PLR0917", "PLR2004", "PLR6301", "PD901", "PT001", "PT018", "FURB103",
    "COM812",
    # typing incompatible with 3.9
    "UP035", "UP006", "UP007",
]

[tool.isort]
profile = "black"

[tool.coverage.report]
include_namespace_packages = true
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "if __name__ == .__main__.:",
    "if .*TYPE_CHECKING:",
    "@.*abstractmethod",
]

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