ruff.toml

# Ruff: fast linter + formatter. Owns style / imports / modernization / common
# refactors. Coexists with a slimmed pylint (config/pylint3.rc), which keeps only
# the inference-heavy checks + pylint_django that ruff can't replicate, and with
# mypy (mypy.ini) for type checking. Three complementary layers.

target-version = "py312"
line-length = 100

extend-exclude = [
    "**/migrations/**",
    "variantgrid/static_files",
    "variantgrid/sitestatic",
    "**/env/**",
]

[lint]
select = [
    "F",    # pyflakes - undefined names, unused imports/vars
    "E",    # pycodestyle errors
    "W",    # pycodestyle warnings (whitespace - replaces the autopep8 pass)
    "I",    # isort - import ordering
    "UP",   # pyupgrade - modern py312 syntax
    "B",    # flake8-bugbear - likely bugs
    "C4",   # flake8-comprehensions
    "DJ",   # flake8-django
    "TC",   # flake8-type-checking - move typing-only imports into TYPE_CHECKING
    "RUF",  # ruff-specific
]
ignore = [
    "E501",   # line-too-long - matches pylint (too many currently)
    "E741",   # ambiguous name l/I/O - pylint good-names allows i,j,k
    "B008",   # function call in arg default - common Django/DRF idiom (Depends-style)
    "B905",   # zip() without strict= - too noisy for now
    "RUF012", # mutable class attrs need ClassVar - clashes with Django model idiom
    "DJ001",  # null=True on string field - existing schema, not actionable in lint
    # PEP 604 union rewrites are NOT safe to auto-apply here: this codebase has
    # annotations where a name is shadowed (e.g. a dataclass field named `datetime`)
    # or is a non-type that Optional[...]/Union[...] silently tolerated. Converting to
    # `X | None` makes the annotation eager-evaluate and raise TypeError at import.
    # Re-enable per-file only after adding `from __future__ import annotations`.
    "UP007",  # Union[X, Y] -> X | Y
    "UP045",  # Optional[X]  -> X | None
]

[lint.per-file-ignores]
# __init__.py: re-exports are intentional (F401), and import order is frequently
# deliberate to manage circular dependencies, so do not sort imports here (I001).
"__init__.py" = ["F401", "I001"]
"**/tests/**" = ["F401", "F841"]    # unused fixtures/locals common in tests

[lint.isort]
known-first-party = [
    "analysis", "annotation", "classification", "eventlog", "flags", "genes",
    "library", "manual", "ontology", "pathtests", "patients", "pedigree",
    "seqauto", "snpdb", "sync", "uicore", "upload", "variantgrid", "variantopedia",
]