sm-vcf-annotation/pyproject.toml at main · scholl-lab/sm-vcf-annotation · GitHub

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# =============================================================================
# pyproject.toml — tool configuration for sm-vcf-annotation
# =============================================================================
# Centralises settings for ruff, mypy, snakefmt, and shellcheck.
# Install dev tools:  pip install ruff mypy snakefmt shellcheck-py

[project]
name = "sm-vcf-annotation"
requires-python = ">=3.10"

# ---------------------------------------------------------------------------
# Ruff  (linter + formatter for Python)
# ---------------------------------------------------------------------------
[tool.ruff]
target-version = "py310"
line-length = 99
src = ["scripts", "workflow/rules", "workflow/scripts", "tests"]

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort
    "UP",  # pyupgrade
    "B",   # flake8-bugbear
    "SIM", # flake8-simplify
    "RUF", # ruff-specific
]
ignore = [
    "E501",   # line too long — handled by formatter
    "SIM108", # ternary operator — readability preference
    "SIM102", # nested if — keep for readability with comments
]

[tool.ruff.lint.per-file-ignores]
"workflow/scripts/*.py" = ["F821"]  # `snakemake` global is injected at runtime

[tool.ruff.lint.isort]
known-first-party = ["scripts"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
line-ending = "lf"

# ---------------------------------------------------------------------------
# Mypy  (type checker)
# ---------------------------------------------------------------------------
[tool.mypy]
python_version = "3.10"
ignore_missing_imports = true
warn_unused_configs = true
warn_return_any = true
warn_unused_ignores = true
check_untyped_defs = true
exclude = ["workflow/scripts/"]  # `snakemake` global is injected at runtime

# ---------------------------------------------------------------------------
# Pytest
# ---------------------------------------------------------------------------
[tool.pytest.ini_options]
testpaths = ["tests"]
markers = ["dryrun: snakemake subprocess tests (may require snakemake installed)"]

# ---------------------------------------------------------------------------
# Snakefmt  (Snakemake formatter)
# ---------------------------------------------------------------------------
[tool.snakefmt]
line_length = 99
include = 'workflow/.*\.(smk|rules)$|workflow/Snakefile$'