pyproject.toml

[tool.black]
line-length = 89

[tool.ruff]
line-length = 89
select = [
    "F",  # Errors detected by Pyflakes
    "E",  # Error detected by Pycodestyle
    "W",  # Warning detected by Pycodestyle
    "I",  # isort
    "D",  # pydocstyle
    "B",  # flake8-bugbear
    "TID",  # flake8-tidy-imports
    "C4",  # flake8-comprehensions
    "BLE",  # flake8-blind-except
    "UP",  # pyupgrade
    "RUF100",  # Report unused noqa directives
]
ignore = [
    # Missing docstring in public package
    "D104",
    # Missing docstring in public module
    "D100",
    # Missing docstring in __init__
    "D107",
    # We don’t want a blank line before a class docstring
    "D203",
    # We want docstrings to start immediately after the opening triple quote
    "D213",
]

[tool.ruff.isort]
force-single-line = true

[tool.ruff.pydocstyle]
convention = "numpy"

[tool.ruff.per-file-ignores]
"docs/*" = ["I"]
"tests/*" = ["D"]
# Ignore errors linked to sphinx gallery syntax
"examples/*" = ["D205", "B018", "D400"]
# Ignore unused imports in __init__.py files
"*/__init__.py" = ["F401"]

# pyproject.toml
[tool.pytest.ini_options]
filterwarnings = [
    "error",
    '''ignore:\s*Pyarrow will become a required dependency of pandas:DeprecationWarning''',
    # ignore Pyarrow deprecation warnings
    "ignore::FutureWarning", # Ignore AnnData FutureWarning about implicit conversion
]