pyproject.toml

[project]
name = "test-workflows-shared"
version = "0.1.0"
description = "Add your description here"
readme = "README.md"
requires-python = ">=3.10,<3.11"
dependencies = [
    "analysis-runner>=3.2.2",
    "cpg-utils>=5.1.1",
    "hail>=0.2.133",
]

[tool.uv]
dev-dependencies = [
    "black>=24.10.0",
    "pip-audit>=2.7.3",
    "pre-commit>=4.0.1",
]

[tool.uv.sources]

[project.urls]
Repository = "https://github.com/populationgenomics/test_workflows_shared"

[tool.ruff]
line-length = 120

extend-exclude = ["venv", ".mypy_cache", ".tox", ".venv", "build", "dist"]

[tool.ruff.format]
quote-style = "single"

[tool.ruff.lint]
# 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",
    "PYI",
    "RET",
    "RSE",
    "RUF",
    "SIM",
    "SLF",
    "TCH",
    "TID",
    "UP",
    "YTT",
]

fixable = ["ALL"]

ignore = [
    "ANN201",  # Missing return type annotation for public function
    "ANN204",  # Missing type annotation for special method `__init__`
    "ANN401",  # Dynamically typed expressions (typing.Any) are disallowed in `**kwargs`
    "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
    "SLF001",  # Private member accessed: `_preemptible`

    "ARG001", # Unused function argument
    "ARG002", # Unused method argument

    "PLR2004", # Magic value used

    "ANN001",
    "ANN202",
    "C408",
    "TID252",
    "RET504",
    "ERA001",
    "UP032",
    "RUF100",
    "ISC001",
    "PIE804",
    "F401",
    "C901",
    "W605",
    "RET505",
    "ANN003",
    "RUF013",
    "UP031",
    "RUF010",
    "B006",
    "ANN002",
    "B023",
    "EXE001",
    "G001",
    "SIM108",
    "RUF005",
    "G002",
    "PD901",
    "N999",
    "SIM118",
    "SIM102",
    "PLW2901",
    "S603",
    "ARG005",
    "PGH003",
    "B904",
    "N802",
    "ISC003",
    "ANN205",
    "S607",
    "RUF015",
    "E701",
    "N818",
    "PIE790",
    "N803",
    "A002",
    "RUF012",
    "W291",
    "S113",
    "S311",
    "N806",
    "PLR5501",
    "F403",
    "SIM115",
    "B007",
    "F841",
    "C405",
    "C419",
    "SIM300",
    "PD011",
    "UP015",
    "S602",
    "Q002",
    "ISC002",
    "COM819",
    "C416",
    "DTZ005",
    "G003",
    "S608",
    "PIE808",
    "B008",
    "S108",
    "E402",
    "S605",
    "F821",
    "RET507",
    "RET503",
    "UP030",
    "UP026",
    "PLR1714",
    "C403",
    "PLR1711",
    "PIE810",
    "DTZ011",
    "S105",
    "BLE001",
    "C401",
    "C400",
    "PLR0402",
    "SIM201",
    "RET506",
    "C417",
    "PD010",
    "PLW1510",
    "A001",
    "W292",
    "PYI024",
    "Q003",
    "S301",
    "RET501",
    "PD003",
    "SIM117",
    "RUF002",
    "SIM105",
    "E713",
    "S324",
    "S310",
    "Q001",
    "UP020",
    "S506",
    "N805",
    "E712",
    "E401",
    "SIM212",
    "DTZ002",
    "UP007",
]