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pyproject.toml
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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
[project]
name = "cooler"
description = "Sparse binary format for genomic interaction matrices."
requires-python = ">=3.6"
license = {text = "BSD-3-Clause"}
authors = [
{name = "Nezar Abdennur", email = "nabdennur@gmail.com"},
]
maintainers = [
{name = "Open2C", email = "open.chromosome.collective@gmail.com"}
]
keywords = [
"genomics",
"bioinformatics",
"Hi-C",
"contact",
"matrix",
"sparse",
"format",
"hdf5"
]
classifiers = [
"Development Status :: 4 - Beta",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
]
readme = "README.md"
dependencies = [
"numpy>=1.9",
"scipy>=0.16",
"pandas>1.0",
"h5py>=2.5",
"click>=7",
"cytoolz",
"multiprocess",
"pyfaidx",
"asciitree",
"pyyaml",
"simplejson",
]
dynamic = ["version"]
[project.optional-dependencies]
test = [
"coverage[toml]",
"isort",
"pytest",
"pytest-cov",
"ruff",
]
docs = [
"autodocsumm",
"m2r",
"recommonmark",
"Sphinx>=1.6",
"sphinx-autobuild",
"sphinx_rtd_theme",
]
complete = [
"biopython",
"dask[array,dataframe]",
"ipytree>=0.2.2",
"ipywidgets>=8.0.0",
"matplotlib",
"pypairix",
"psutil",
"pysam",
]
dev = [
"cooler[complete,test]",
]
[project.urls]
homepage = "https://open2c.github.io/cooler"
documentation = "https://cooler.readthedocs.io"
repository = "https://github.com/open2c/cooler"
changelog = "https://github.com/open2c/cooler/blob/master/CHANGES.md"
[project.scripts]
cooler = "cooler.cli:cli"
[tool.hatch.version]
path = "src/cooler/_version.py"
[tool.ruff]
exclude = [
"__init__.py",
"__main__.py",
]
extend-select = [
"E", # style errors
# "D", # pydocstyle
"F", # pyflakes
"I", # isort
"RUF", # ruff-specific rules
"UP", # pyupgrade
"W", # style warnings
]
[tool.isort]
profile = "black"
skip_gitignore = true
known_first_party = "cooler"
[tool.pytest.ini_options]
addopts = "--cov cooler --cov-config pyproject.toml --cov-report term-missing --cov-report html --cov-report=xml"
filterwarnings = ["ignore::PendingDeprecationWarning"]
testpaths = ["tests"]
[tool.coverage.run]
source = ["cooler"]
omit = [
"*/cooler/__main__.py",
"*/cooler/_version.py",
"*/cooler/sandbox/*",
"*/cooler/cli/csort.py"
]
[tool.coverage.report]
exclude_lines = [
"pragma: no cover",
"return NotImplemented",
"raise NotImplementedError"
]
[tool.hatch.envs.default.scripts]
fix = "ruff --fix ."
lint = "ruff src/cooler" #tests
test = "pytest ."
docs = "sphinx-autobuild docs docs/_build/html"