pyproject.toml

[project]
name = "ga4gh.vrs"
authors = [
    {name = "Larry Babb", email = "lbabb@broadinstitute.org"},
    {name = "Reece Hart", email = "reecehart@gmail.com"},
    {name = "Andreas Prlic", email = "andreas.prlic@gmail.com"},
    {name = "Alex Wagner", email = "alex.wagner@nationwidechildrens.org"},
]
readme = "README.md"
description = "GA4GH Variation Representation Specification (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",
    "hgvs",
    "spdi",
    "variation"
]
requires-python = ">=3.10"
dynamic = ["version"]
dependencies = [
    "pydantic~=2.1",
    "bioutils",
    "requests",
    "canonicaljson",
]

[project.optional-dependencies]
extras = [
    "psycopg2-binary",
    "biocommons.seqrepo>=0.5.1",
    "bioutils>=0.5.2",
    "hgvs>=1.4",
    "dill~=0.3.7",
    "click",
]
dev = [
    # tests
    "pytest",
    "pytest-cov",
    "pytest-vcr",
    "vcrpy>=7.0.0",
    "pyyaml",
    # style
    "pre-commit>=4.0.1",
    "ruff==0.9.4",
    # docs
    "sphinx",
    "sphinx_rtd_theme",
    "restview",
]
notebooks = [
    "jupyter",
    "tabulate",
    "pyyaml"
]

[project.urls]
Homepage = "https://github.com/ga4gh/vrs-python"
Documentation = "https://github.com/ga4gh/vrs-python"
Changelog = "https://github.com/ga4gh/vrs-python/releases"
Source = "https://github.com/ga4gh/vrs-python"
"Bug Tracker" = "https://github.com/ga4gh/vrs-python/issues"

[project.scripts]
vrs-annotate = "ga4gh.vrs.extras.vcf_annotation:_cli"

[build-system]
requires = ["setuptools>=65.3", "setuptools_scm>=8"]
build-backend = "setuptools.build_meta"

[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"

[tool.ruff]
src = ["src"]
exclude = ["docs", "misc", "notebooks", "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
    "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
    "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
    "INP",  # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
    "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
    "SLF",  # https://docs.astral.sh/ruff/rules/#flake8-self-slf
    "SLOT",  # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
    "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
    "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
    "PLC",  # https://docs.astral.sh/ruff/rules/#convention-c
    "PLE",  # https://docs.astral.sh/ruff/rules/#error-e_1
    "TRY",  # https://docs.astral.sh/ruff/rules/#tryceratops-try
    "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
    "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
]
fixable = ["ALL"]
# ANN002 - missing-type-args
# 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
# PLC0206 - dict-index-missing-items
# *ignored for compatibility with formatter
ignore = [
    "ANN002", "ANN003",
    "D203", "D205", "D206", "D213", "D300", "D400", "D415",
    "E111", "E114", "E117", "E501",
    "W191",
    "S321",
    "PLC0206",
]
exclude = [
    "src/ga4gh/vrs/models.py",  # there be monsters here
]

[tool.ruff.lint.per-file-ignores]
# ANN001 - missing-type-function-argument
# ANN2 - missing-return-type
# D100 - undocumented-public-module
# D102 - undocumented-public-class
# D103 - undocumented-public-function
# S101 - assert
# B011 - assert-false
# INP001 - implicit-namespace-package
# SLF001 - private-member-access
"tests/*" = [
    "ANN001",
    "ANN2",
    "D100",
    "D102",
    "D103",
    "S101",
    "B011",
    "INP001",
    "SLF001",
]
"src/ga4gh/vrs/utils/hgvs_tools.py" = [
    "ANN001",
    "ANN201",
    "ANN202",
    "D102",
]
"src/ga4gh/vrs/normalize.py" = [
    "ANN001",
    "ANN201",
    "ANN202",
]
"src/ga4gh/vrs/extras/vcf_annotation.py" = [
    "PTH123",  # see https://github.com/ga4gh/vrs-python/issues/482
]
"src/ga4gh/vrs/extras/translator.py" = [
    "ANN001",
    "ANN101",
    "ANN2",
]
"src/ga4gh/vrs/extras/object_store.py" = [
    "ANN",
    "D",
]
"src/ga4gh/vrs/enderef.py" = [
    "ANN",
    "D",
]
"src/ga4gh/vrs/dataproxy.py" = [
    "B019",
]
"src/ga4gh/core/pydantic.py" = [
    "ANN401",
]
"src/ga4gh/core/models.py" = [
    "UP007",
]

[tool.ruff.lint.flake8-annotations]
mypy-init-return = true

[tool.ruff.format]
docstring-code-format = true