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pyproject.toml
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pyproject.toml
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[project]
name = "bioutils"
authors = [
{ name="biocommons contributors", email="[email protected]" },
]
description = "miscellaneous simple bioinformatics utilities and lookup tables"
readme = "README.rst"
license = { file="LICENSE.txt" }
requires-python = ">=3.10"
classifiers = [
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"License :: OSI Approved :: Apache Software License",
"Operating System :: OS Independent",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Medical Science Apps."
]
keywords = [
"biocommons",
"bioinformatics",
"genomics",
"HGVS",
"variation"
]
dynamic = ["version"]
dependencies = [
"attrs",
"requests",
]
[project.optional-dependencies]
dev = [
"bandit~=1.7",
"build~=0.8",
"flake8~=4.0",
"ipython~=8.4",
"isort~=5.10",
"mypy",
"pylint~=2.14",
"ruff == 0.4.4",
]
test = [
"pytest~=7.1",
"pytest-cov~=4.0",
"pytest-optional-tests",
"tox~=3.25",
"vcrpy",
]
docs = ["mkdocs"]
[project.urls]
"Homepage" = "https://github.com/biocommons/bioutils"
"Bug Tracker" = "https://github.com/biocommons/bioutils/issues"
[build-system]
requires = ["setuptools >= 70.1", "setuptools_scm[toml] ~= 8.1"]
build-backend = "setuptools.build_meta"
[tool.setuptools.package-data]
"*" = ["_data/*/*.json.gz"]
[tool.setuptools_scm]
[tool.pytest.ini_options]
addopts = "-s -v -x --strict-markers -m 'not extra' --doctest-modules --cov=src"
doctest_optionflags = [
"ALLOW_BYTES",
"ALLOW_UNICODE",
"ELLIPSIS",
"IGNORE_EXCEPTION_DETAIL",
"NORMALIZE_WHITESPACE",
]
markers = [
"network: tests that require network connectivity",
"slow: slow tests that should be run infrequently",
]
testpaths = [
"tests"
]
[tool.coverage.run]
branch = true
source = ["biocommons.example"]
omit = ["*_test.py", "*/tests/*"]
[tool.coverage.report]
show_missing = true
exclude_lines = [
# Have to re-enable the standard pragma
"pragma: no cover",
# Don't complain about missing debug-only code:
"def __repr__",
"if self.debug",
# Don't complain if tests don't hit defensive assertion code:
"raise AssertionError",
"raise NotImplementedError",
# Don't complain if non-runnable code isn't run:
"if __name__ == .__main__.:",
]
[tool.isort]
profile = "black"
# [tool.flake8]
# flake8 does not support configuration in pyproject.toml
# https://github.com/PyCQA/flake8/issues/234#issuecomment-812800832
# The config in setup.cfg
[tool.pylint.'MESSAGES CONTROL']
disable = "R0913"
[tool.pylint.format]
max-line-length = "120"
[tool.ruff]
src = ["src", "tests"]
line-length = 120