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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "drive-ibd"
version = "2.7.6"
description = "cli tool to identify networks of individuals who share IBD segments overlapping loci of interest"
authors = ["James Baker <[email protected]>", "Hung-Hsin Chen <[email protected]>", "Jennifer E. Below <[email protected]>"]
maintainers = ["James Baker <[email protected]>", "Hung-Hsin Chen <[email protected]>"]
repository = "https://github.com/belowlab/drive"
homepage = "https://drive-ibd.readthedocs.io/en/latest/"
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",
]
packages = [
{include = "drive"}
]
[tool.poetry.scripts]
drive = 'drive.drive:main'
[tool.poetry.dependencies]
python = ">=3.9,<3.11.0 || >3.11.0,<3.12"
pandas = "^1.5.3"
numpy = "^1.24.2"
igraph = "^0.10.4"
scipy = "^1.10.1"
rich-argparse = "^1.3.0"
[tool.poetry.group.dev.dependencies]
commitizen = "^2.42.1"
black = "^23.1.0"
mypy = "^1.1.1"
data-science-types = "^0.2.23"
pytest = "^7.2.2"
pydocstyle = "^6.3.0"
ipykernel = "^6.22.0"
isort = "^5.12.0"
ruff = "^0.4.4"
scalene = "^1.5.35"
[tool.poetry.group.notebook.dependencies]
ipykernel = "^6.22.0"
[tool.poetry.group.docs.dependencies]
sphinx = "<7.0.0"
sphinx-autobuild = "^2021.3.14"
sphinx-autodocgen = "^1.3"
sphinx-copybutton = "^0.5.2"
sphinx-book-theme = "^1.0.1"
[tool.commitizen]
name = "cz_conventional_commits"
version = "2.0.2"
tag_format = "$version"
update_changelog_on_bump = true
[build-system]
requires = ["poetry-core>=1.8.3"]
build-backend = "poetry.core.masonry.api"
[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"