pyproject.toml

[project]
name = "bonsai-prp"
dynamic = ["version"]
authors = [
  {name = "Markus Johansson", email = "markus.h.johansson@skane.se"},
  {name = "Ryan Kennedy", email = "Ryan.Kennedy@skane.se"},
]
description = "Pipline result processing program for the JASEN pipeline and Bonsai tool."
readme = "README.md"
requires-python = ">=3.10"
classifiers = [
    "Development Status :: 3 - Alpha",
    "Natural Language :: English",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
]
dependencies = [
    "setuptools",
    "wheel",
    "click==8.1.7",
    "pydantic==2.5.2",
    "pandas==2.1.3",
    "Biopython==1.83",
    "cyvcf2",
    "pysam",
    "pyyaml",
    "requests"
]

[project.urls]
Repository = "https://github.com/Clinical-Genomics-Lund/"
Issues = "https://github.com/Clinical-Genomics-Lund/bonsai-prp/issues"
Changelog = "https://github.com/Clinical-Genomics-Lund/CHANGELOG.md"

[project.scripts]
prp = "prp.cli:cli"

[project.optional-dependencies]
dev = [
    "pylint ~=3.0.2",
    "black ~=23.11.0",
    "isort ~=5.12.0",
]
test = [
    "pytest-cov ~=4.1.0",
]

[build-system]
requires = ["setuptools>=61.0"]
build-backend = "setuptools.build_meta"

[tool.setuptools.dynamic]
version = {attr = "prp.VERSION"}

[tool.isort]
profile = "black"

[tool.pylint]
max-line-length = 88

[tool.pytest.ini_options]
addopts = "--cov --cov-report html --cov-report term-missing --cov-fail-under 95"

[tool.coverage.run]
source = ["prp"]

[tool.pylint.TYPECHECK]
generated-members = "pysam.asTuple,pysam.TabixFile,pysam.AlignmentFile"