pyranges1/pyproject.toml at master · pyranges/pyranges1 · GitHub

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

[project]
name = "pyranges1"
version = "1.3.9"
description = "GenomicRanges for Python."
requires-python = ">=3.12.0"
readme = "README.md"
authors = [
    { name = "Endre Bakken Stovner", email = "endbak@hey.com" },
    { 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", "tabulate", "natsort", "ruranges>=0.1.4", "gtfreader>=0.2.0"]

[project.optional-dependencies]
add-ons = [
    "pyrle >= 0.0.43",
    "bamread",
    "pyfaidx",
    "pyBigWig",
    "joblib",
] #"fisher",
dev = [
    "tox",
    "ruff == 0.14.1",
    "pyright",
    "pandas-stubs",
    "types-tabulate",
    "pytest-watcher",
    "pytest-xdist",
]
docs = [
    "sphinx",
    "sphinx_rtd_theme",
    "sphinx-autoapi",
    "sphinxcontrib-napoleon",
]
cli = ["fire"]
all = [
    "pyranges1[add-ons]",
    "pyranges1[dev]",
    "pyranges1[docs]",
    "pyranges1[cli]",
]

[project.scripts]
# <script‐name> = "<module.path>:<callable>"
pyranger = "pyranges1.cli:main"

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

[tool.pytype]
inputs = ['pyranges1']

[project.urls]
Homepage = "http://github.com/pyranges/pyranges1"

[tool.tox] # Legacy tox configuration (to be replaced with native tox.ini when supported)
legacy_tox_ini = """
[tox]
envlist = py312, py313

[testenv]
basepython =
    py312: python3.12
    py313: python3.13
deps =
    pandas
    pyrle >= 0.0.41
    bamread
    pyBigWig
    pyfaidx
    tox
    ruff == 0.14.1
    pandas-stubs
    types-tabulate
    pytest
    pyright == 1.1.406
    joblib
    gtfreader >= 0.2.0
    ruranges >= 0.1.3
    # fisher
commands =
    pyright
    python tests/run_doctest_tutorial_howto.py
    pytest --doctest-modules pyranges1
    pytest tests/unit
    ruff format --check pyranges1
    ruff check pyranges1
"""

[tool.mypy]
python_version = "3.12"

[tool.ruff]

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

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

[tool.pytest-watcher]
now = true

[tool.pyright]
include = ["pyranges1"]
# typeCheckingMode = "strict"
pythonVersion = "3.12"

ignore = ["pyranges1/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",
]