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pyproject.toml
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pyproject.toml
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[project]
name = "ga4gh.cat_vrs"
authors = [
{name = "Larry Babb", email = "[email protected]"},
{name = "Alex Wagner", email = "[email protected]"},
{name = "Daniel Puthawala", email = "[email protected]"},
]
readme = "README.md"
description = "GA4GH Categorical Variation Representation (Cat-VRS) reference implementation"
license = {file = "LICENSE"}
classifiers = [
"Development Status :: 3 - Alpha",
"Intended Audience :: Developers",
"Intended Audience :: Healthcare Industry",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: Apache Software License",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Medical Science Apps.",
]
keywords = [
"bioinformatics",
"ga4gh",
"genomics",
"variation"
]
requires-python = ">=3.10"
dynamic = ["version"]
dependencies = [
"ga4gh.vrs~=2.0.0a12",
"pydantic==2.*",
]
[project.optional-dependencies]
dev = [
"pre-commit",
"ruff==0.4.9",
]
tests = [
"pytest",
"pytest-cov",
]
[project.urls]
Homepage = "https://github.com/ga4gh/cat-vrs-python"
Documentation = "https://github.com/ga4gh/cat-vrs-python"
Changelog = "https://github.com/ga4gh/cat-vrs-python/releases"
Source = "https://github.com/ga4gh/cat-vrs-python"
"Bug Tracker" = "https://github.com/ga4gh/cat-vrs-python/issues"
[build-system]
requires = ["setuptools>=65.3", "setuptools_scm>=8"]
build-backend = "setuptools.build_meta"
[tool.ruff]
exclude = [
"submodules"
]
[tool.ruff.lint]
select = [
"F", # https://docs.astral.sh/ruff/rules/#pyflakes-f
"E", "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
"I", # https://docs.astral.sh/ruff/rules/#isort-i
"N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n
"D", # https://docs.astral.sh/ruff/rules/#pydocstyle-d
"UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up
"ANN", # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
"ASYNC", # https://docs.astral.sh/ruff/rules/#flake8-async-async
"S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
"B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
"A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
"C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
"DTZ", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
"T10", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
"EM", # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
"G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
"PIE", # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
"T20", # https://docs.astral.sh/ruff/rules/#flake8-print-t20
"PT", # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
"Q", # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
"RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
"RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret
"SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
"PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
"PGH", # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
"RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
]
fixable = [
"I",
"F401",
"D",
"UP",
"ANN",
"B",
"C4",
"G",
"PIE",
"PT",
"RSE",
"SIM",
"RUF"
]
# ANN101 - missing-type-self
# ANN003 - missing-type-kwargs
# D203 - one-blank-line-before-class
# D205 - blank-line-after-summary
# D206 - indent-with-spaces*
# D213 - multi-line-summary-second-line
# D300 - triple-single-quotes*
# D400 - ends-in-period
# D415 - ends-in-punctuation
# E111 - indentation-with-invalid-multiple*
# E114 - indentation-with-invalid-multiple-comment*
# E117 - over-indented*
# E501 - line-too-long*
# W191 - tab-indentation*
# S321 - suspicious-ftp-lib-usage
# *ignored for compatibility with formatter
ignore = [
"ANN101", "ANN003",
"D203", "D205", "D206", "D213", "D300", "D400", "D415",
"E111", "E114", "E117", "E501",
"W191",
"S321",
]
[tool.ruff.lint.per-file-ignores]
# ANN001 - missing-type-function-argument
# ANN2 - missing-return-type
# ANN102 - missing-type-cls
# S101 - assert
# B011 - assert-false
"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011"]
"src/ga4gh/cat_vrs/*models.py" = ["ANN102"]
[tool.setuptools.packages.find]
where = ["src"]
[tool.setuptools_scm]
[tool.pytest.ini_options]
addopts = "--cov-report=term-missing --cov=ga4gh"
testpaths = ["tests", "src"]
doctest_optionflags = "ALLOW_UNICODE ALLOW_BYTES ELLIPSIS IGNORE_EXCEPTION_DETAIL NORMALIZE_WHITESPACE"