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pyproject.toml
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[project]
name = "drive-ibd"
version = "2.7.15a1"
description = "Python CLI using graph theory to identify networks of individuals who share IBD segments overlapping loci of interest"
authors = [
{name = "James Baker", email = "[email protected]"},
{name = "Hung-Hsin Chen", email = "[email protected]"},
{name = "Jennifer E. Below", email = "[email protected]"},
]
maintainers = [
{name = "James Baker", email = "[email protected]"},
{name = "Hung-Hsin Chen", email = "[email protected]"},
]
requires-python = "!=3.11.0,<3.12,>=3.9"
dependencies = [
"pandas<2.0.0,>=1.5.3",
"numpy<2.0.0,>=1.24.2",
"igraph<1.0.0,>=0.10.4",
"scipy<2.0.0,>=1.10.1",
"rich-argparse<2.0.0,>=1.3.0",
"modified-logger>=1.0.0",
]
readme = "README.md"
keywords = [
"python",
"genetics",
"identity by descent",
"relatedness",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Operating System :: Unix",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
]
[project.urls]
homepage = "https://drive-ibd.readthedocs.io/en/latest/"
repository = "https://github.com/belowlab/drive"
[project.license]
text = "Apache-2.0"
[project.scripts]
drive = "drive.drive:main"
[tool.pdm.dev-dependencies]
dev = [
"commitizen<3.0.0,>=2.42.1",
"black<24.0.0,>=23.1.0",
"mypy<2.0.0,>=1.1.1",
"data-science-types<1.0.0,>=0.2.23",
"pytest<8.0.0,>=7.2.2",
"pydocstyle<7.0.0,>=6.3.0",
"ipykernel<7.0.0,>=6.22.0",
"isort<6.0.0,>=5.12.0",
"ruff<1.0.0,>=0.4.4",
"scalene<2.0.0,>=1.5.35",
]
notebook = [
"ipykernel<7.0.0,>=6.22.0",
]
docs = [
"sphinx<7.0.0",
"sphinx-autobuild<2022.0.0,>=2021.3.14",
"sphinx-autodocgen<2.0,>=1.3",
"sphinx-copybutton<1.0.0,>=0.5.2",
"sphinx-book-theme<2.0.0,>=1.0.1",
]
[tool.pdm.build]
package-dir = "src"
[tool.pdm]
distribution = true
[build-system]
requires = ["pdm-backend"]
build-backend = "pdm.backend"
[tool.commitizen]
name = "cz_conventional_commits"
version = "2.0.2"
tag_format = "$version"
update_changelog_on_bump = true
[tool.pytest.ini_options]
markers = [
"integtest: marks test as integration test (deselected with '-m \"not integration\"')",
"unit: marks test as unit test (deslected with '-m \"not unit\"')",
"kcne1: marks test as testing backwards compatibility for kcne1 results (deselected with '-m \"not knce1\"')"
]
[tool.isort]
profile = "black"
[tool.pylint.format]
max-line-length = "88"
[tool.ruff]
exclude = [
".mypy_cache",
".git",
".ipynb_checkpoints",
".pytest_cache",
".venv",
".vscode",
"build",
"dist",
"venv",
"site-packages",
".github",
".ruff_cache",
]
[tool.ruff.lint]
ignore = ["E501"]
[tool.ruff.format]
# Like Black, use double quotes for strings.
quote-style = "double"