pyproject.toml

[project]
name = "plinder"
dynamic = ["version"]
dependencies = [
    "biotite >= 1.0",
    "numpy<2",
    "pandas",
    "typing_extensions",
    "pydantic",
    "tqdm",
    "plotly",
    "nbformat",
    "google-cloud-storage",
    "gcsfs",
    "gemmi",
    "rdkit>=2023.9.5",
    "pyarrow",
    "omegaconf",
    "mmcif",
    "eval_type_backport",
    "posebusters",
    "duckdb",
    "cloudpathlib",
    "mols2grid",
    "six",
]
description = "PLINDER: The Protein-Ligand INteraction Dataset and Evaluation Resource"
readme = "README.md"
requires-python = ">=3.10"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: OS Independent",
]

[project.urls]
Homepage = "https://github.com/plinder-org/plinder"
Issues = "https://github.com/plinder-org/plinder/issues"

[project.scripts]
plinder_download = "plinder.core.index.utils:download_plinder_cmd"
plinder_eval = "plinder.eval.docking.write_scores:evaluate_cmd"
plinder_stratify = "plinder.eval.docking.stratify_test_set:stratify_cmd"
plinder_plot = "plinder.eval.docking.make_plots:plot_cmd"

[project.optional-dependencies]
lint = [
    "ruff == 0.1.2",
    "pre-commit == 2.21.0",
]
test = [
    "tox >= 4",
    "pytest == 7.2.0",
    "pytest-cov == 4.0.0",
    "pytest-xdist == 3.6.1",
    "build == 0.9.0",
    "setuptools_scm[toml] == 7.0.5",
]
type = [
    "mypy==1.2.0",
    "types-PyYAML",
    "types-requests",
]
dev = [
    "plinder[lint,test,type]",
]
loader = [
    "torch",
]
plots = [
    "matplotlib",
    "seaborn",
    "mols2grid",
    "matplotlib_venn",
    "scipy",
]
docs = [
    "itables",
    "jupyter-sphinx",
    "jupyterlab_myst",
    "jupytext",
    "myst-nb",
    "myst-parser[linkify]",
    "numpydoc",
    "pydata-sphinx-theme == 0.15.4",
    "sphinx",
    "sphinx-copybutton",
    "sphinx-design",
    "sphinx-gallery",
    "mols2grid",
    "matplotlib",
]

[build-system]
build-backend = "setuptools.build_meta"
requires = [
    "build == 0.9.0",
    "setuptools == 65.4.0",
    "setuptools_scm[toml] == 7.0.5",
]

[tool.setuptools_scm]
root = "."

[tool.setuptools.packages.find]
where = ["src"]
include = ["plinder*"]
namespaces = false

[tool.setuptools.package-data]
plinder = [
    "**.yaml",
    "**.tsv",
    "plinder/data/utils/annotations/static_files/artifacts_badlist.csv",
]

[tool.ruff]
line-length = 88
select = [
    "F",
    "I",
]
ignore = [
    "E",
    "W",
]
preview = true

[tool.ruff.flake8-tidy-imports]
ban-relative-imports = "all"

[tool.mypy]
ignore_missing_imports = true
strict = true
disallow_untyped_decorators = false

[[tool.mypy.overrides]]
module = "plinder._version"
ignore_errors = true