content: [build-system]
  requires = [
      "setuptools>=42",
      "setuptools_scm",
      "wheel",
      "numpy>=2"
  ]
  build-backend = "setuptools.build_meta"
  
  [tool.setuptools_scm]
  write_to = "tsinfer/_version.py"
  
  [project]
  name = "tsinfer"
  dynamic = ["version"]
  authors = [
      {name = "Tskit Developers", email = "admin@tskit.dev"},
  ]
  description = "Infer tree sequences from genetic variation data."
  readme = "README.md"
  requires-python = ">=3.10"
  license = {text = "GNU GPLv3+"}
  classifiers = [
      "Programming Language :: C",
      "Programming Language :: Python",
      "Programming Language :: Python :: 3",
      "Programming Language :: Python :: 3.10",
      "Programming Language :: Python :: 3.11",
      "Programming Language :: Python :: 3.12",
      "Programming Language :: Python :: 3.13",
      "Programming Language :: Python :: 3 :: Only",
      "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
      "Development Status :: 3 - Alpha",
      "Environment :: Other Environment",
      "Intended Audience :: Science/Research",
      "Operating System :: POSIX",
      "Operating System :: MacOS :: MacOS X",
      "Operating System :: Microsoft :: Windows",
      "Topic :: Scientific/Engineering",
      "Topic :: Scientific/Engineering :: Bio-Informatics",
  ]
  keywords = [
      "population genetics",
      "tree sequence",
      "ancestral recombination graph",
      "evolutionary tree",
      "inference",
      "tsinfer",
  ]
  dependencies = [
      "numpy>=1.23.5",
      "six",
      "tqdm",
      "humanize",
      "daiquiri",
      "tskit>=0.5.3",
      "numcodecs>=0.6,<0.15.1", #Pinned due to https://github.com/zarr-developers/numcodecs/issues/733
      "zarr>=2.2,!=2.11.0,!=2.11.1,!=2.11.2,<3",
      "lmdb",
      "sortedcontainers",
      "attrs>=19.2.0",
      "numba>=0.61.0",
      "psutil>=5.9.0",
  ]
  
  [project.urls]
  Homepage = "https://tskit.dev/tsinfer"
  Documentation = "https://tskit.dev/tsinfer/docs/stable"
  Changelog = "https://tskit.dev/tsinfer/docs/stable/CHANGELOG.html"
  "Bug Tracker" = "https://github.com/tskit-dev/tsinfer/issues"
  "Source Code" = "https://github.com/tskit-dev/tsinfer/"
  
  [project.scripts]
  tsinfer = "tsinfer.__main__:main"
  
  [project.optional-dependencies]
  test = [
      "build==1.2.2.post1",
      "colorama==0.4.6",
      "daiquiri==3.2.5.1",
      "humanize==4.12.1",
      "lmdb==1.6.2",
      "matplotlib==3.9.4",
      "meson==1.7.0",
      "msprime==1.3.4",
      "pytest==8.3.5",
      "pytest-cov==6.0.0",
      "seaborn==0.13.2",
      "sgkit[vcf]==0.9.0; sys_platform != 'win32'",
      "tskit==0.6.0",
      "tqdm==4.67.1",
      "twine==6.1.0"
  ]
  
  docs = [
      "jupyter-book==1.0.4.post1",
      "sphinx-issues==5.0.0",
      "sphinx-argparse==0.5.2",
      "humanize==4.12.1",
      "lmdb==1.6.2",
      "tqdm==4.67.1",
      "daiquiri==3.3.0",
      "msprime==1.3.3",
      "sgkit[vcf]==0.9.0",
      "ipywidgets==8.1.5",
      "Bio==1.7.1",
      "bio2zarr==0.1.4",
      "sphinx-book-theme",
      "pyfaidx==0.8.1.3"
  ]
  
  dev = [
      "attrs",
      "codecov",
      "coverage",
      "flake8",
      "six",
      "tqdm",
      "humanize",
      "daiquiri",
      "msprime>=1.0.0",
      "tskit>=0.5.3",
      "lmdb",
      "pre-commit",
      "pytest",
      "pytest-coverage",
      "h5py",
      "sortedcontainers",
      "python-prctl; sys_platform == 'linux'",
      "numa; sys_platform == 'linux'",
      "sphinx",
      "sphinx-argparse",
      "sphinx_rtd_theme",
      "setuptools>=45",
      "setuptools_scm",
      "matplotlib",
      "seaborn",
      "colorama",
      "sgkit[vcf]",
      "sphinx-book-theme",
      "jupyter-book",
      "sphinx-issues",
      "ipywidgets",
      "pyfaidx"
  ]
  
  [tool.setuptools]
  packages = ["tsinfer"]
  include-package-data = true
  
  [tool.pytest.ini_options]
  testpaths = ["tests"]
  filterwarnings = [
      'ignore:SampleData'
  ]