python_bed_lookup/pyproject.toml at master · msk-access/python_bed_lookup · GitHub

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[build-system]
requires = ["setuptools>=64", "cython>=3,<4"]
build-backend = "setuptools.build_meta"

[project]
name = "bed_lookup"
version = "2.0.1"
description = "Lookup a gene or SNP by genomic coordinate from a BED file, fast."
readme = "README.rst"
requires-python = ">=3.11"
license = { text = "MIT" }
authors = [
    { name = "Michael Dacre", email = "mike.dacre@gmail.com" },
]
keywords = ["bed", "genomics", "bioinformatics", "snp", "lookup"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Environment :: Console",
    "Natural Language :: English",
    "License :: OSI Approved :: MIT License",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Software Development :: Libraries",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
]
# typer + rich power the `bed_location_lookup` CLI (a first-class feature). They are kept out
# of the library import path — `import bed_lookup` never imports them.
dependencies = [
    "typer>=0.12",
    "rich>=13",
]

[project.optional-dependencies]
# lookup_df / lookup_series need pandas; the core lookup does not.
dataframe = ["pandas>=2.0"]
test = ["pytest>=8", "pandas>=2.0"]

[project.urls]
Homepage = "https://github.com/msk-access/python_bed_lookup"
Source = "https://github.com/msk-access/python_bed_lookup"

[project.scripts]
bed_location_lookup = "bed_lookup.cli:app"

[tool.setuptools]
packages = ["bed_lookup"]

[tool.ruff]
line-length = 100
target-version = "py311"

[tool.ruff.lint]
select = ["E", "F", "I", "UP", "B", "W"]
# The Cython .pyx is not linted by ruff (it is not valid Python).

[tool.pytest.ini_options]
testpaths = ["tests"]

[tool.cibuildwheel]
# Build CPython 3.11-3.14 only. `cp314-*` does not match free-threaded `cp314t-*`, so those
# are excluded automatically.
build = "cp311-* cp312-* cp313-* cp314-*"
# Skip musllinux, 32-bit, and win32 to keep the matrix focused on common targets.
skip = "*-musllinux_* *_i686 *-win32"
# Smoke-test each built wheel against the real test suite.
test-requires = ["pytest", "pandas"]
test-command = "pytest {project}/tests -q"

[tool.cibuildwheel.macos]
# Build both macOS architectures from the arm64 runner: arm64 natively (tested) and x86_64
# via cross-compile (cibuildwheel skips tests for the cross build). This ships Intel wheels
# without needing a separate macos-13 Intel runner.
archs = ["x86_64", "arm64"]