anndata2ri/pyproject.toml at main · theislab/anndata2ri · GitHub

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

[project]
name = "anndata2ri"
readme = "README.rst"
license = "GPL-3.0-or-later"
authors = [
    { name = "Philipp A.", email = "flying-sheep@web.de" },
]
requires-python = ">=3.11"
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Programming Language :: R",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dynamic = [ "version" ]
dependencies = [
    "anndata",
    "rpy2>=3.5.2", # first with get_conversion
    "tzlocal",     # for pandas2ri
]
urls."Issue Tracker" = "https://github.com/theislab/anndata2ri/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc"
urls."Source Code" = "https://github.com/theislab/anndata2ri"
urls.Documentation = "https://icb-anndata2ri.readthedocs-hosted.com/"

[dependency-groups]
dev = [ "pre-commit", "scipy-stubs" ]
test = [
    "pygments",
    "pytest",
    "pytest-faulthandler",
    "scanpy",
]
doc = [
    "ipython",
    "lxml",                       # For scraping the R link info
    "scanpydoc[theme,typehints]",
    "sphinx",
]

[tool.hatch]
version.source = "vcs"
version.raw-options = { local_scheme = "no-local-version" }  # be able to publish dev version
envs.default.installer = "uv"
envs.docs.scripts.build = "sphinx-build -M html docs docs/_build"
envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
envs.docs.scripts.open = "python3 -m webbrowser -t docs/_build/html/index.html"
envs.docs.dependency-groups = [ "doc" ]
envs.hatch-test.extra-dependencies = [ "ipykernel" ]
envs.hatch-test.dependency-groups = [ "test", "dev" ]

[tool.ruff]
line-length = 120
format.quote-style = "single"
lint.select = [ "ALL" ]
lint.ignore = [
    "C408",   # dict() calls are nice
    "COM812", # trailing commas handled by black
    "CPY001", # no need for copyright notices
    "D203",   # prefer 0 to 1 blank line before class members
    "D213",   # prefer docstring summary on first line
    "FIX002", # “TODO” comments
    "Q",      # handled by formatter
    "S101",   # asserts are fine
]
lint.per-file-ignores."**/*.ipynb" = [
    "F821", # `%%R -o` means that ruff doesn’t understand which variables exist
    "T201", # Allow print in notebooks
]
lint.per-file-ignores."docs/**/*.py" = [ "INP001" ]  # No __init__.py in docs
lint.per-file-ignores."src/**/*.py" = [ "PT" ]  # No Pytest checks
lint.per-file-ignores."tests/**/*.py" = [
    "D100",    # test modules don’t need docstrings
    "D103",    # tests don’t need docstrings
    "INP001",  # No __init__.py in tests
    "PLR0913", # many fixtures are OK
    "PLR2004", # magic numbers are fine in tests
]
lint.allowed-confusables = [ "×", "’" ]
lint.isort.known-first-party = [ "anndata2ri" ]
lint.isort.lines-after-imports = 2
lint.isort.required-imports = [ "from __future__ import annotations" ]
lint.pydocstyle.convention = "numpy"

[tool.pyproject-fmt]
indent = 4

[tool.pytest]
addopts = [
    "--import-mode=importlib",
    "-panndata2ri.test_utils",
    "-Werror",
]
strict = true