pyproject.toml

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

[project]
name = "StemCNV-check"
authors = [
  { name="Nicolai von Kügelgen", email="nicolai.von-kuegelgen@bih-charite.de" },
]
description = "CNV Based Quality Control Workflow for Stem Cell SNP Array Data"
readme = "README.md"
requires-python = ">=3.12"
keywords = ["bioinformatics"]
license = {text = "MIT License"}
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: R"
]
dynamic = ["version"]
dependencies = [
    "setuptools ~=68.1.2",
    # Nice, round-trip enabled YAML parsing
    "ruamel.yaml ~=0.18.6",
    # Snakemake is used for providing the actual wrapper calling functionality
    "snakemake ~=8.16.0",
    # Nicer logging
    "loguru ~=0.7.2",
    # native excel & tsv support
    "pandas ~=2.2",
    "openpyxl ~=3.1",
    "XlsxWriter ~=3.2",
    # Config validation & comparison
    "pydantic ~=2.8"  , 
    "deepdiff ~=8.0"
]

[project.urls]
Homepage = "https://github.com/bihealth/StemCNV-check"
Issues = "https://github.com/bihealth/StemCNV-check/issues"

[project.optional-dependencies]
test = [
    "pytest ~=7.2.0",
    "pyfakefs ~=5.6.0"
]
dev = [
    "vcfpy ~= 0.13.8"
]
all = [
    "stemcnv-check[test,dev]",
]

[project.scripts]
stemcnv-check = "stemcnv_check.__main__:main"

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

[tool.setuptools.dynamic]
version = {attr = "stemcnv_check.version.__version__"}


#[tool.coverage.run]
#omit = []
##relative_files = true
#
#[tool.coverage.report]
#exclude_lines = ["pragma: no cover", "def __repr__", "if __name__ == '__main__':"]


[tool.pytest.ini_options]
minversion = "6.0"
pythonpath = [
  "."
]
#addopts = "--cov=snappy_pipeline --cov-report=xml"
testpaths = [
    "tests",
]
norecursedirs = [
    "docs",
    "*.egg-info",
    ".git"
]
filterwarnings = [
    "error",
    "ignore::DeprecationWarning",
]