[build-system]
requires = ["setuptools >= 77.0.3"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
include = ["hairpin2*"]

[project]
name = "hairpin2"
version = "3.0.2"
description = "CLI for running read-aware artefactual variant flagging algorithms over VCFs"
authors = [
  {name = "Alex Byrne"}
]
license = "MIT"
readme = "README.md"
dependencies = [
  "pysam>=0.22, ==0.*",
  "pydantic>=2.11.7, ==2.*",
  "click>=8.2.1, ==8.*",
  "click-option-group>=0.5.7, ==0.*"
]
requires-python = ">= 3.12"

[project.optional-dependencies]
dev = [
  "pytest==9.*",
  "pytest-cov==7.*",
  "ruff"
]
docs = [
  "sphinx",
  "sphinx-autobuild",
  "sphinx_rtd_theme",
  "myst-parser"
]

[project.scripts]
hairpin2 = "hairpin2.infrastructure.cli:hairpin2_cli"
hp2-utils = "hairpin2.hp2_utils.cli:hp2_utils"

[tool.ruff]
line-length = 100
extend-exclude = ["scratch-api.py"]

[tool.ruff.lint]
select = [
    # Default rules
    "E4",
    "E7",
    "E9",
    "F",
    # Additional rules
    "I",    # Import order
    "D",    # Docstrings
    "D401", # First line should be in imperative mood
    "D213", # Multi-line docstring summary should start at the second line
    "C",    # Complexity
]
ignore = [
    "D100", # Missing docstring in public module
    "D101", # Missing docstring in public class
    "D102", # Missing docstring in public method
    "D103", # Missing docstring in public function
    "D105", # Missing docstring in magic method
    "D107", # Missing docstring in __init__
    "D200", # One-line docstring should fit on one line with quotes
    "D417", # Missing argument descriptions in the docstring
]

[tool.ruff.lint.pydocstyle]
convention = "pep257"

[tool.ruff.lint.per-file-ignores]
"tests/*" = ["D"]
"**/*/__init__.py" = ["D"]


[tool.pyright]  # basedpyright recommended
failOnWarnings = false
ignore = ["scratch-api.py", 'examples/*']
reportAny = false
reportExplicitAny = false
reportUnnecessaryIsInstance = false
reportUnnecessaryComparison = false
reportUnknownLambdaType = false