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pyproject.toml
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[tool.poetry]
name = "pybwa"
version = "1.4.3"
description = "Python bindings for BWA"
authors = ["Nils Homer"]
license = "MIT"
readme = "README.md"
homepage = "https://github.com/fulcrumgenomics/pybwa"
repository = "https://github.com/fulcrumgenomics/pybwa"
keywords = ["bioinformatics"]
packages = [{ include = "pybwa" }]
classifiers = [
"Development Status :: 3 - Alpha",
"Environment :: Console",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Software Development :: Documentation",
"Topic :: Software Development :: Libraries :: Python Modules",
]
include = [
"LICENSE",
{ path = "pybwa/**/*.so", format = "wheel" },
{ path = "**/*.so", format = "wheel" },
{ path = "*.so", format = "wheel" },
{ path = "bwa/*.h", format = ["sdist", "wheel"] },
{ path = "bwa/*.c", format = ["sdist", "wheel"] },
{ path = "patches/*patch", format = ["sdist", "wheel"] },
{ path = "tests", format = "sdist" },
]
exclude = [
"pybwa/**/*.so",
"**/*.so",
"*.so",
]
[tool.poetry.build]
generate-setup-file = false
script = "build.py"
[tool.poetry.dependencies]
fgpyo = ">=0.7.0"
python = ">=3.9.0,<4.0"
pysam = ">=0.22.1"
typing_extensions = { version = ">=3.7.4", python = "<3.12" }
[tool.poetry.group.dev.dependencies]
# dependencies for linting, style checking, and unit testing
mypy = ">=1.7.0"
pytest = ">=7.4.0"
pytest-cov = ">=2.8.1"
ruff = "0.4.8"
setuptools = ">=68.0.0"
black = ">=24.8.0" # for readthedocs
cython = "^3.0.11"
coverage = {extras = ["toml"], version = "^7.6.10"}
[tool.poetry.group.docs.dependencies]
# dependencies for building docs
sphinx = { version = ">=7.0.0"}
enum-tools = "^0.12.0"
sphinx-toolbox = "^3.8.1"
sphinx-jinja2-compat = "^0.3.0"
sphinx-rtd-theme = "^3.0.2"
sphinx-autodoc-typehints = "2"
[build-system]
requires = ["poetry-core>=1.0.0", "cython>=3.0.11", "setuptools>=75.1.0"]
build-backend = "poetry.core.masonry.api"
[tool.ruff]
line-length = 100
target-version = "py39"
output-format = "full"
[tool.ruff.lint]
select = ["C901", "B", "E", "F", "I", "W", "Q"]
ignore = ["E203", "E701"]
unfixable = ["B"]
[tool.ruff.lint.isort]
force-single-line = true
[tool.mypy]
strict_optional = true
check_untyped_defs = true
disallow_incomplete_defs = true
disallow_untyped_calls = true
disallow_untyped_decorators = true
disallow_untyped_defs = true
no_implicit_optional = true
warn_no_return = true
warn_redundant_casts = true
warn_return_any = true
warn_unreachable = true
warn_unused_configs = true
warn_unused_ignores = true
enable_error_code = "ignore-without-code"
exclude = ["site/", "docs/"]
[tool.coverage.run]
plugins = ["Cython.Coverage"]
branch = true