OptiType/pyproject.toml at master · FRED-2/OptiType · GitHub

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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "optitype"
version = "1.5.0"
description = "Precision HLA typing from next-generation sequencing data"
readme = "README.md"
license = {text = "BSD-3-Clause"}
requires-python = ">=3.10"
authors = [
    {name = "Andras Szolek"},
    {name = "Benjamin Schubert"},
    {name = "Christopher Mohr"},
    {name = "Jonas Scheid"},
]
maintainers = [
    {name = "OptiType Contributors"}
]
keywords = [
    "HLA",
    "typing",
    "bioinformatics",
    "NGS",
    "next-generation-sequencing",
    "immunogenetics",
]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    "click>=8.0",
    "numpy>=1.23",
    "pandas>=2.0",
    "pyarrow>=12.0",
    "pyomo>=6.6",
    "pysam>=0.21",
    "matplotlib>=3.5",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "ruff>=0.1.0",
    "mypy>=1.0",
    "build>=1.0",
    "twine>=4.0",
]

[project.scripts]
optitype = "optitype.cli:main"

[project.urls]
Homepage = "https://github.com/FRED-2/OptiType"
Documentation = "https://github.com/FRED-2/OptiType#readme"
Repository = "https://github.com/FRED-2/OptiType"
Issues = "https://github.com/FRED-2/OptiType/issues"

[tool.hatch.build.targets.wheel]
packages = ["src/optitype"]

[tool.hatch.build.targets.sdist]
include = [
    "/src",
    "/data",
    "/tests",
    "/README.md",
    "/LICENSE",
]

[tool.hatch.build.targets.wheel.shared-data]
"data/alleles" = "share/optitype/data/alleles"
"data/hla_reference_dna.fasta" = "share/optitype/data/hla_reference_dna.fasta"
"data/hla_reference_rna.fasta" = "share/optitype/data/hla_reference_rna.fasta"

[tool.ruff]
target-version = "py310"
line-length = 100
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort
    "B",   # flake8-bugbear
    "UP",  # pyupgrade
]
ignore = [
    "E501",  # line too long - handled by formatter
]

[tool.ruff.isort]
known-first-party = ["optitype"]

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
ignore_missing_imports = true

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_functions = ["test_*"]
addopts = "-v --tb=short"