pyproject.toml

[project]
name = "seqr-loading-pipeline"
dynamic = ['version']
requires-python = ">=3.10"

[tool.setuptools]
include-package-data = false

[tool.setuptools.dynamic]
version = {attr = "v03_pipeline.__version__"}

[tool.setuptools.packages.find]
include = ["v03_pipeline*"]
exclude = ["v03_pipeline.bin", "v03_pipeline.deploy", "v03_pipeline*test*"]
namespaces = false

[tool.mypy]
packages = 'v03_pipeline'
python_version = "3.10"
ignore_missing_imports = true
strict = true

[tool.ruff]
extend-exclude = [
    'download_and_create_reference_datasets/v02/*',
    'gcloud_dataproc/*',
    'hail_scripts/*',
    'kubernetes/*',
    'luigi_pipeline/lib/*',
    'luigi_pipeline/seqr*.py',
    'luigi_pipeline/tests/data/*',
]
ignore = [
    # Individual Rules
    "E501",  # Black is less aggressive here when touching comments and strings, we're going to let those through.
    "G004",  # logging-f-string, these are fine for now

    # Rule Groupings
    "D",     # pydocstyle is for docs... we have none
    "FBT",   # flake-boolean-trap... disallows boolean args to functions... fixing this code will require refactors.
    "ANN",   # flake8-annotations is for typed code
    "DJ",    # django specific
    "PYI",   # pyi is typing stub files
    "PT",    # pytest specific
    "PTH",   # pathlib is preferred, but we're not using it yet
    "PD",    # pandas specific
    "NPY",   # numpy specific
    "TD",    # todos
    "FIX",   # fixmes
]
line-length = 88
select = [
    "ALL"
]
target-version = "py310"

[tool.ruff.flake8-quotes]
inline-quotes = "single"

[tool.ruff.per-file-ignores]
'*test*' = [
    'ARG002', # allow unused method arguments
    'SLF001', # allow private access
    'PLR0913', # allow high arity functions
]
'*migration*' = [
    'N999', # allow invalid module names
]

[tool.ruff.pylint]
max-args = 6

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