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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
[project]
name = "cooler"
version = "0.10.2"
description = "Sparse binary format for genomic interaction matrices."
requires-python = ">=3.8"
license = {text = "BSD-3-Clause"}
authors = [
{name = "Nezar Abdennur", email = "[email protected]"},
]
maintainers = [
{name = "Open2C", email = "[email protected]"}
]
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 :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
readme = "README.md"
dependencies = [
"numpy>=1.9, <2",
"scipy>=0.16",
"pandas>1.5",
"h5py>=2.5",
"click>=7",
"cytoolz",
"multiprocess",
"pyfaidx",
"asciitree",
"pyyaml",
"simplejson",
]
[project.optional-dependencies]
all = [
"biopython",
"dask[array,dataframe]",
"ipytree>=0.2.2",
"ipywidgets>=8.0.0",
"matplotlib",
"pypairix; platform_system != 'Windows'",
"psutil",
"pysam; platform_system != 'Windows'",
]
test = [
"coverage[toml]",
"isort",
"pytest",
"pytest-cov",
"ruff",
]
dev = [
"cooler[all,test]",
"pre-commit"
]
docs = [
"autodocsumm",
"m2r",
"recommonmark",
"Sphinx>=1.6",
"sphinx-autobuild",
"sphinx_rtd_theme",
]
[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]
src = ["src"]
exclude = [
".venv",
"__main__.py",
]
[tool.ruff.lint]
extend-select = [
"B", # bugbear
# "C", # complexity
# "D", # pydocstyle
"E", # style errors
"F", # pyflakes
"I", # isort
"RUF", # ruff-specific rules
"UP", # pyupgrade
"W", # style warnings
]
[tool.ruff.lint.isort]
known-first-party = ["cooler"]
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.pytest.ini_options]
minversion = "7"
log_cli_level = "INFO"
xfail_strict = true
addopts = [
"-ra",
"--strict-config",
"--strict-markers",
"--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 check --fix src tests"
lint = "ruff check src tests"
test = "pytest ."
docs = "sphinx-autobuild docs docs/_build/html"
[tool.hatch.envs.test]
features = ["dev"]
[[tool.hatch.envs.test.matrix]]
python = ["3.8", "3.9", "3.10", "3.11", "3.12"]