hicstuff/pyproject.toml at master · koszullab/hicstuff · GitHub

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[build-system]
requires = ["setuptools>=64", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "hicstuff"
version = "3.2.5"
description = "General purpose stuff to generate and handle Hi-C data in its simplest form."
readme = "README.md"
requires-python = ">=3.8"
license = { text = "BSD-3-Clause" }
authors = [
    { name = "Jacques Serizay", email = "jacques.serizay@pasteur.fr" },
    { name = "Cyril Matthey-Doret", email = "cyril.matthey-doret@pasteur.fr" },
    { name = "Lyam Baudry", email = "lyam.baudry@pasteur.fr" },
]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Visualization",
    "Operating System :: POSIX",
    "Operating System :: Unix",
    "Operating System :: MacOS",
]
dependencies = [
    "numpy",
    "scipy",
    "pandas>=1.5.0",
    "matplotlib>=3.4.0",
    "rich-click>=1.7",
    "biopython",
    "requests",
    "scikit-learn",
    "pysam",
    "pyfastx",
    "cooler",
    "pairtools",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "ruff>=0.4",
    "pre-commit>=3.0",
    "sphinx",
    "sphinx-rtd-theme",
    "ipython>=8.12.3",
]

[project.urls]
Homepage = "https://github.com/koszullab/hicstuff"
Documentation = "https://hicstuff.readthedocs.io/en/latest"
Repository = "https://github.com/koszullab/hicstuff"

[project.scripts]
hicstuff = "hicstuff.cli:cli"

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
hicstuff = ["*"]

[tool.ruff]
line-length = 100
target-version = "py38"

[tool.ruff.lint]
select = ["E", "F", "W", "I", "UP", "B"]
ignore = [
    "E501",   # line-length handled by formatter
    "B008",   # function calls in default args
    "UP007",  # X | Y union syntax (py3.10+)
    "UP006",  # use `type` instead of `Type` (py3.9+)
]

[tool.ruff.format]
quote-style = "double"

[tool.pytest.ini_options]
testpaths = ["tests"]

[tool.coverage.run]
source = ["hicstuff"]
omit = ["*/tests/*"]

[tool.coverage.report]
show_missing = true
fail_under = 60