content: [build-system]
  requires = ["setuptools >= 61.0", "setuptools_scm>=8"]
  build-backend = "setuptools.build_meta"
  
  [project]
  name = "snakePipes"
  description = 'Snakemake workflows and wrappers for NGS data processing from the MPI-IE'
  readme = "README.md"
  version = "3.3.0"
  keywords = [
      "DNAmapping",
      "ChIPSeq",
      "mRNAseq",
      "ncRNAseq",
      "ATACseq",
      "scRNAseq",
      "WGBS / Bisulfite seq",
      "epigenetics workflows",
      "Illumina"
  ]
  
  authors = [
    {name = "Bioinfo-Core MPI-IE"}
  ]
  
  classifiers = [
      "Intended Audience :: Science/Research",
      "License :: OSI Approved :: MIT License",
      "Programming Language :: Python :: 3",   
  ]
  
  requires-python = ">= 3.11"
  
  dependencies = [
      "snakemake >= 8,<9.10.0",
      "pandas",
      "thefuzz",
  #    "pyyaml >= 5.1",
      "ruamel.yaml",
      "snakemake-executor-plugin-cluster-generic >= 1.0.9",
      "graphviz"
  ]
  
  [project.optional-dependencies]
  actions = [
      "pytest",
      "ruff",
      "ruamel.yaml",
      "pytest-xdist"
  ]
  
  docs = [
      "sphinx >= 7.1.2",
      "sphinx-rtd-theme >= 2.0.0",
      "readthedocs-sphinx-search >= 0.3.2",
      "sphinx-argparse >= 0.4.0",
      "mock==5.1.0"
  ]
  build = [
      "build"
  ]
  
  [tool.setuptools.package-data]
  snakePipes = ["**/*.yaml", "**/*.R", "**/*.Rmd", "**/*snakefile", "**/*Snakefile", "**/*sh"]
  
  [project.scripts]
  ATACseq = "snakePipes.workflows.ATACseq.ATACseq:main"
  ChIPseq = "snakePipes.workflows.ChIPseq.ChIPseq:main"
  createIndices = "snakePipes.workflows.createIndices.createIndices:main"
  DNAmapping = "snakePipes.workflows.DNAmapping.DNAmapping:main"
  HiC = "snakePipes.workflows.HiC.HiC:main"
  makePairs = "snakePipes.workflows.makePairs.makePairs:main"
  mRNAseq = "snakePipes.workflows.mRNAseq.mRNAseq:main"
  ncRNAseq = "snakePipes.workflows.ncRNAseq.ncRNAseq:main"
  preprocessing = "snakePipes.workflows.preprocessing.preprocessing:main"
  scRNAseq = "snakePipes.workflows.scRNAseq.scRNAseq:main"
  WGBS = "snakePipes.workflows.WGBS.WGBS:main"
  snakePipes = "snakePipes.snakePipes:main"
  
  [tool.ruff]
  exclude = [
      "build"
  ]
  lint.select = ["E", "F", "W", "B"]
  lint.ignore = [
      "E722", # bare excepts
      "E501", # line length
      "B006", # Do not use mutable data structures for argument defaults
  ]
  