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",
    "pyyaml",
    # style
    "pre-commit>=4.0.1",
    "pylint",
    "yapf",
    # 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.yapf]
based_on_style = "pep8"
column_limit = 120
spaces_before_comment = 4
split_before_logical_operator = true
split_before_named_assigns = true