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pyproject.toml
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pyproject.toml
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[tool.ruff]
line-length = 99
indent-width = 4
target-version = "py312"
# Exclude a variety of commonly ignored directories.
exclude = [
".bzr",
".direnv",
".eggs",
".git",
".git-rewrite",
".hg",
".mypy_cache",
".nox",
".pants.d",
".pytype",
".ruff_cache",
".svn",
".tox",
".venv",
"__pypackages__",
"_build",
"buck-out",
"build",
"dist",
"node_modules",
"venv",
]
[tool.ruff.lint]
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 = [
# allow I, O, l as variable names -> I is the identity matrix
"E741",
# Missing docstring in public package
"D104",
# Missing docstring in public module
"D100",
# Missing docstring in __init__
"D107",
# Errors from function calls in argument defaults. These are fine when the result is immutable.
"B008",
# __magic__ methods are are often self-explanatory, allow missing docstrings
"D105",
# first line should end with a period [Bug: doesn't work with single-line docstrings]
"D400",
# First line should be in imperative mood; try rephrasing
"D401",
## Disable one in each pair of mutually incompatible rules
# We don’t want a blank line before a class docstring
"D203",
# We want docstrings to start immediately after the opening triple quote
"D213",
# Don't need module level imports at top of cell for notebooks
"E402",
# Don't need docstrings for public classes for notebooks
"D101",
# Don't need docstrings for public methods for notebooks
"D102",
# Don't need docstrings for public functions for notebooks
"D103",
]
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.ruff.lint.per-file-ignores]
"docs/*" = ["I", "BLE001"]
"tests/*" = ["D"]
"*/__init__.py" = ["F401"]
"src/scvi/__init__.py" = ["I"]
[tool.ruff.format]
# Like Black, use double quotes for strings.
quote-style = "double"
# Like Black, indent with spaces, rather than tabs.
indent-style = "space"
# Like Black, respect magic trailing commas.
skip-magic-trailing-comma = false
# Like Black, automatically detect the appropriate line ending.
line-ending = "auto"
[tool.jupytext]
formats = "ipynb,md"