pyproject.toml

# This template supports two use cases:
#   1. Scripts repo — linting/formatting only, no installation required.
#      Remove the [build-system], [tool.hatch.*], and [project] sections;
#      keep everything from [tool.ruff] onward.
#   2. Installable package — the default. Uses src/ layout with hatchling.
#      Replace "package_name" with your package name in [project], [tool.hatch.*],
#      and the src/ directory.

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["src/package_name"]

[tool.hatch.build.targets.wheel.sources]
"src" = ""

[project]
# TODO: replace with your project name
name = "package_name"
# TODO: replace with your project description
description = "TODO: project description"
readme = "README.md"
requires-python = ">=3.10"
version = "0.1.0"
license = { file = "LICENSE" }
classifiers = [
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Natural Language :: English",
    "Operating System :: Unix",
    "Programming Language :: Python",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = []

[project.optional-dependencies]
dev = ["pre-commit", "pytest", "bump-my-version"]
test = ["pytest"]

[project.urls]
# TODO: replace with your project repository URL
Repository = "https://github.com/populationgenomics/package_name"


[tool.pytest.ini_options]
testpaths = ["test"]

[tool.ruff]
line-length = 120

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

[tool.ruff.lint]
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 = ["ALL"]

ignore = [
    "ANN001",  # Missing type annotation for function argument
    "ANN201",  # Missing return type annotation for public function
    "ANN204",  # Missing type annotation for special method __init__
    "ANN401",  # Dynamically typed expressions (typing.Any) are disallowed
    "COM812",  # Trailing comma prohibited
    "G004",    # Logging statement uses f-string
    "PLR0913", # Too many arguments in function definition
    "PLR2004", # Magic value used in comparison
    "Q000",    # Single quotes found but double quotes preferred
    "S101",    # Use of assert detected
]

[tool.ruff.lint.isort]
section-order = ["future", "standard-library", "third-party", "hail", "cpg", "first-party", "local-folder"]

[tool.ruff.lint.isort.sections]
hail = ["hail", "hailtop"]
cpg = ["cpg_flow", "cpg_utils", "cpg_infra", "metamist", "analysis_runner"]

[tool.mypy]
ignore_missing_imports = true