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pyproject.toml
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pyproject.toml
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[project]
name = "ga4gh.vrs"
authors = [
{name = "Larry Babb", email = "[email protected]"},
{name = "Reece Hart", email = "[email protected]"},
{name = "Andreas Prlic", email = "[email protected]"},
{name = "Alex Wagner", email = "[email protected]"},
]
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