pyproject.toml

[tool.black]
line-length = 88
skip-string-normalization = true

[tool.isort]
py_version = 311
profile = "black"
line_length = 88
sections = ["FUTURE", "STDLIB", "THIRDPARTY", "HAIL", "CPG", "FIRSTPARTY", "LOCALFOLDER"]
known_hail = [
    "hail",
    "hailtop",
]
# Adjust these for each repository, e.g., removing those that should be
# local rather than CPG. Also fill in extend_skip below if there are any
# subdirectories that should be ignored.
known_cpg = [
    "analysis_runner",
    "cpg_infra",
    "cpg_utils",
    "cpg_workflows",
    "gnomad",
    "hail_scripts",
    "metamist",
]
# extend_skip = ["list", "submodules", "etc", here"]

[tool.ruff]
line-length = 88

# ignore pydocstyle, flake8-boolean-trap (FBT)
select = ["A", "B", "C",  "E", "F", "G", "I", "N", "Q", "S", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]

fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "FBT", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]

ignore = [
    "ANN101",   # Missing type annotation for self in method
    "ANN201",   # Missing return type annotation for public function
    "E501",     # Line length too long
    "E731",     # Do not assign a lambda expression, use a def
    "E741",     # Ambiguous variable name
    "G004",     # Logging statement uses f-string
    "PLR0911",  # Too many return statements
    "PLR0912",  # Too many branches
    "PLR0913",  # Too many arguments to function call
    "PLR0915",  # Too many statements
    "PLW0603",  # Using the global statement to update `<VAR>` is discouraged
    "PT018",    # Assertion should be broken down into multiple parts
    "Q000",     # Single quotes found but double quotes preferred
    "S101",     # Use of assert detected
    "PT009",    # Use regular assert instead of unittest-style 'assertEqual'
    "I001",     # Import block is un-sorted (we use isort directly as ruff sort isn't fully supported)
]