pyproject.toml

[build-system]
requires = ["setuptools>=61.0.0", "wheel", "cython", "setuptools_scm[toml]>=6.2"]
build-backend = "setuptools.build_meta"

[project]
name = "pyranges1"
version = "1.0.3"
description = "GenomicRanges for Python."
requires-python = ">=3.12.0"
readme = "README.md"
authors = [
    { name = "Endre Bakken Stovner", email = "endbak@pm.me" },
    { name = "Marco Mariotti", email = "marco.mariotti@ub.edu" },
]
license = { text = "MIT" }
classifiers = [
    "Programming Language :: Python :: 3",
    "Development Status :: 4 - Beta", "Environment :: Other Environment",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS :: MacOS X",
    "Topic :: Scientific/Engineering"
]
keywords = ["bioinformatics", "genomicranges", "genomics"]
dependencies = ["pandas", "ncls>=0.0.63", "tabulate", "sorted_nearest>=0.0.33", "natsort"]

[project.optional-dependencies]
add-ons = ["pyrle >= 0.0.39", "bamread",  "pyfaidx", "pyBigWig", "joblib"] #"fisher",
dev = ["tox", "ruff == 0.3.0", "pyright", "pandas-stubs", "types-tabulate", "pytest-watcher", "pytest-xdist", "hypothesis>=6.92.1"]
docs = ["sphinx", "sphinx_rtd_theme", "sphinx-autoapi", "sphinxcontrib-napoleon"]
all = ["pyranges1[add-ons]", "pyranges1[dev]", "pyranges1[docs]"]

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

[tool.pytype]
inputs = ['pyranges']

[project.urls]
Homepage="http://github.com/pyranges/pyranges_1.x"

[tool.tox]  # TODO: replace with regular non-legacy entry when supported
legacy_tox_ini = """
[tox]
envlist = py312

[testenv]
deps =
    pyrle >= 0.0.39
    bamread
    pyBigWig
    pyfaidx
    tox
    ruff == 0.3.0
    pandas-stubs
    types-tabulate
    pytest
    pyright
    joblib
    hypothesis==6.92.1
    #fisher
commands =
    pytest --doctest-modules pyranges
    pytest tests/unit
    ruff format --check pyranges
    ruff check pyranges
    pyright
"""

[tool.mypy]
python_version = "3.12"

[tool.ruff]

target-version = "py312"
line-length = 120

[tool.ruff.lint]
select = ["ALL"]
ignore = [
    "E501", "ANN002", "ANN003", "ANN001", "ANN101", "ANN102", "ANN401", "PLR0913", "PLC0415",
    "PD901", "D101", "D100", "D107", "CPY", "D105", "D104", "D203", "D211", "D213", "COM812", "ISC001"
]

[tool.pytest-watcher]
now = true

[tool.pyright]
include = ["pyranges"]
# typeCheckingMode = "strict"
pythonVersion = "3.12"

ignore = ["pyranges/core/pyranges_groupby.py"]

# specific rules to disable
reportUnknownParameterType = false
reportUnknownMemberType = false
reportUnknownArgumentType = false
reportUnknownVariableType = false

[tool.pytest.ini_options]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "bedtools: marks tests that require bedtools",
]