ConfoState/pyproject.toml at main · Becksteinlab/ConfoState · GitHub

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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "confostate"
version = "0.1.0"
description = "Classify membrane protein structures into conformational states"
readme = "README.md"
requires-python = ">=3.9"
license = {text = "MIT"}
authors = [
    {name = "ConfoState Contributors"}
]

dependencies = [
    "pandas>=1.3.0",
    "numpy>=1.21.0",
    "scikit-learn>=1.2.0",
    "MDAnalysis>=2.4.0",
    "scipy>=1.7.0",
    "requests",
    "openai",
    "pypaperretriever",
    "pymupdf",
    "joblib>=1.2.0",
]

[project.optional-dependencies]
test = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
]
docs = [
    "sphinx>=7.0",
    "myst-parser>=2.0",
    "furo>=2024.1.0",
    "sphinx-copybutton>=0.5",
]
lint = [
    "ruff>=0.9",
    "pre-commit>=3.0",
]
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "sphinx>=7.0",
    "myst-parser>=2.0",
    "furo>=2024.1.0",
    "sphinx-copybutton>=0.5",
    "ruff>=0.9",
    "pre-commit>=3.0",
]

[tool.setuptools.packages.find]
where = ["."]
include = ["confostate*"]

[tool.setuptools.package-data]
confostate = ["data/**/*"]

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "-ra"

[tool.coverage.run]
source = ["confostate"]
branch = true

# All code-style settings live here (ruff lint + format).
[tool.ruff]
line-length = 79
target-version = "py39"
include = ["*.py", "*.pyi"]
extend-exclude = [
    "docs/_build",
    "Plans",
]

[tool.ruff.lint]
# Flake8-compatible core rules (pycodestyle + pyflakes).
select = ["E", "F", "W"]

[tool.ruff.lint.per-file-ignores]
# Example scripts may adjust sys.path before importing the package.
"examples/*" = ["E402"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"