content: [build-system]
  requires = ["flit_core >=3.2,<4"]
  build-backend = "flit_core.buildapi"
  
  [project]
  name = "metacoag"
  authors = [{name = "Vijini Mallawaarachchi", email = "viji.mallawaarachchi@gmail.com"}]
  keywords = ["metagenomics", "binning", "contigs", "bioinformatics"]
  readme = "README.md"
  license = {file = "LICENSE"}
  requires-python = ">=3.9,<3.13"
  classifiers=[
      "Development Status :: 5 - Production/Stable",
      "Programming Language :: Python :: 3",
      "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
      "Natural Language :: English",
      "Topic :: Scientific/Engineering :: Bio-Informatics",
      "Operating System :: MacOS",
      "Operating System :: POSIX",
  ]
  
  dependencies=[
      "biopython",
      "igraph",
      "networkx",
      "scipy",
      "numpy",
      "tqdm",
      "pandas",
      "click",
  ]
  # the following are inferred from the source code
  dynamic = ["version", "description"]
  
  [project.sdist]
  include = ["doc/", "requirements.txt", "src/*", "pyproject.toml"]
  exclude = ["doc/*.html"]
  
  [project.urls]
  Home = "https://metacoag.readthedocs.io"
  
  [project.scripts]
  metacoag = "metacoag.cli:main"
  combine_cov = "metacoag.metacoag_utils.support.combine_cov:main"
  
  [project.optional-dependencies]
  test = [
      "nox",
      "pytest",
      "pytest-cov",
      "pytest-xdist",
  ]
  dev = [
      "black",
      "click",
      "docformatter",
      "flit",
      "nox",
      "isort",
      "pytest",
      "pytest-cov",
      "pytest-xdist",
  ]
  
  [tool.flit.sdist]
  include = ["docs/", "requirements.txt", "src/*", "pyproject.toml"]
  exclude = ["docs/*.html"]
  
  [tool.pytest.ini_options]
  addopts = ["--strict-config", "-ra"]
  testpaths = "tests"
  
  [tool.black]
  line-length = 88
  target-version = ['py39', 'py310', 'py311', 'py312']
  exclude = '''
  /(
      \.eggs
    | \.git
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | _build
    | build
    | doc
    | dist
    | tests/data
  )/
  '''
  
  [tool.isort]
  atomic=true
  force_grid_wrap=0
  include_trailing_comma=true
  lines_after_imports=2
  lines_between_types=1
  multi_line_output=3
  use_parentheses=true
  