pyproject.toml

[project]
name = 'scanpydoc'
dynamic = ['version']
description = 'A series of Sphinx extensions to get maintainable numpydoc style documentation.'
authors = [
    { name = 'Philipp Angerer', email = 'phil.angerer@gmail.com' },
]
urls.Source = 'https://github.com/theislab/scanpydoc/'
urls.Documentation = 'https://icb-scanpydoc.readthedocs-hosted.com/'
readme = 'README.rst'
license = 'GPL-3.0-or-later'
classifiers = [
    'Intended Audience :: Developers',
    'Programming Language :: Python :: 3',
    'Topic :: Documentation :: Sphinx',
    'Topic :: Software Development :: Libraries :: Python Modules',
    'Framework :: Sphinx :: Extension',
    'Typing :: Typed',
]
requires-python = '>=3.10'
dependencies = [
    'sphinx>=7.0',
]

[project.optional-dependencies]
dev = ['pre-commit']
test = [
    'pytest',
    'coverage',
    'legacy-api-wrap',
    'defusedxml',  # sphinx[test] would also pull in cython
    'sphinx>=8.1.0' # https://github.com/sphinx-doc/sphinx/pull/12743
]
doc = [
    'scanpydoc[typehints,myst,theme]',
    'sphinx',
    'readthedocs-sphinx-search',
]
typehints = ['sphinx-autodoc-typehints>=1.15.2']
theme = ['sphinx-book-theme>=1.1.0']
myst = ['myst-parser']

[project.entry-points.'sphinx.html_themes']
scanpydoc = 'scanpydoc.theme'

[tool.ruff.lint]
select = ['ALL']
allowed-confusables = ['’', '×', 'l']
ignore = [
    'E741',   # Ambiguous variable name
    'C408',   # `dict` calls are useful
    'D203',   # No blank lines before class body
    'D213',   # Docstring summary on first line
    'D407',   # We’re not using Numpydoc style
    'FIX002', # TODOs are OK
    'PD',     # False positives
    'COM812', # Conflicts with formatting
    'ISC001', # Conflicts with formatting
]
[tool.ruff.lint.per-file-ignores]
'example.py' = ['ALL']
'docs/conf.py' = [
    'INP001', # `docs` is not a namespace package
]
'tests/**/*.py' = [
    'INP001', # test directories are not namespace packages
    'D103', # Test functions don’t need docstrings
    'S101', # Pytest tests use `assert`
    'RUF018', # Assignment expressions in assert are fine here
    'PLR0913', # Tests should be able to use as many fixtures as they want
]
[tool.ruff.lint.flake8-type-checking]
strict = true
exempt-modules = []
[tool.ruff.lint.isort]
length-sort = true
lines-after-imports = 2
known-first-party = ['scanpydoc']
required-imports = ['from __future__ import annotations']
[tool.ruff.lint.pydocstyle]
convention = 'numpy'

[tool.mypy]
strict = true
explicit_package_bases = true
disallow_untyped_defs = false  # handled by Ruff
mypy_path = ['$MYPY_CONFIG_FILE_DIR/src']

[tool.hatch.version]
source = 'vcs'
[tool.hatch.build.hooks.vcs]
version-file = 'src/scanpydoc/_version.py'

[tool.hatch.envs.default]
dependencies = ['types-docutils']
[tool.hatch.envs.docs]
python = '3.11'
features = ['doc']
[tool.hatch.envs.docs.scripts]
build = 'sphinx-build -M html docs docs/_build'
clean = 'git clean -fdX docs'

[tool.hatch.envs.hatch-test]
features = ['test', 'typehints', 'myst']

[tool.pytest.ini_options]
addopts = [
    '--import-mode=importlib',
    '-psphinx.testing.fixtures',
]
filterwarnings = [
    'error',
    'ignore:The frontend.Option:DeprecationWarning',
]

[tool.coverage.run]
source_pkgs = ['scanpydoc']
[tool.coverage.paths]
scanpydoc = ['src/scanpydoc']
[tool.coverage.report]
exclude_lines = [
  'no cov',
  'if __name__ == .__main__.:',
  'if TYPE_CHECKING:',
]

[build-system]
requires = ['hatchling', 'hatch-vcs']
build-backend = 'hatchling.build'