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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
[project]
name = "bioframe"
version = "0.8.0"
description = "Operations and utilities for Genomic Interval Dataframes."
license = {text = "MIT"}
authors = [
{name = "Open2C", email = "open.chromosome.collective@gmail.com"},
]
keywords = [
"pandas",
"dataframe",
"genomics",
"epigenomics",
"bioinformatics",
"interval operations",
"genomic ranges",
"bedtools",
"bedframe",
"viewframe",
"bed",
]
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"
requires-python = ">=3.8"
dependencies = [
"matplotlib",
"numpy>=1.10, <3",
"pandas>=1.3",
"pyyaml",
"requests",
"typing-extensions ; python_version<'3.9'",
"importlib-metadata ; python_version<'3.8'",
"importlib-resources ; python_version<'3.9'",
]
[project.optional-dependencies]
dev = [
"biopython",
"pre-commit",
"pysam",
"pybbi",
"pytest",
"ruff",
]
test = [
"pytest",
]
docs = [
"autodocsumm",
"myst_nb",
"jinja2",
"Sphinx",
"sphinx-autobuild",
"sphinx_rtd_theme",
]
[project.urls]
homepage = "https://github.com/open2c/bioframe"
documentation = "https://bioframe.readthedocs.io/en/latest"
repository = "https://github.com/open2c/bioframe"
changelog = "https://github.com/open2c/bioframe/blob/main/CHANGES.md"
[tool.ruff]
target-version = "py37"
exclude = [
".venv",
]
[tool.ruff.lint]
extend-select = [
"B", # bugbear
# "C", # mccabe 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 = ["bioframe"]
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.pytest.ini_options]
minversion = "7"
log_cli_level = "info"
xfail_strict = true
addopts = [
"-ra",
"--showlocals",
"--strict-config",
"--strict-markers",
]
filterwarnings = ["ignore::PendingDeprecationWarning"]
testpaths = ["tests"]
[tool.hatch.envs.default]
features = ["dev", "test", "docs"]
[tool.hatch.envs.default.scripts]
fix = "ruff check --fix ."
lint = "ruff check bioframe tests"
format = "ruff format bioframe tests"
test = "pytest ."
docs = "sphinx-autobuild docs docs/_build/html"
[tool.hatch.envs.test]
features = ["dev", "test"]
[[tool.hatch.envs.test.matrix]]
python = ["3.9", "3.10", "3.11", "3.12"]
|
