pyproject.toml

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

[project]
name = "CalicoST"
version = "1.0.0"
authors = [
  { name="Cong Ma", email="congma@princeton.edu" },
  { name="Metin Balaban", email="metin@princeton.edu" },
  { name="Jingxian Liu", email="jingxian.liu@wustl.edu" },
  { name="Siqi Chen", email="siqichen@wustl.edu" },
  { name="Li Ding", email="lding@wustl.edu" },
  { name="Ben Raphael", email="braphael@cs.princeton.edu" },
]
description = "Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics"
readme = "README.md"
requires-python = ">=3.8"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
]
dependencies = [
  'numpy', 
  'scipy', 
  'pandas',
  'scikit-learn',
  'scanpy',
  'anndata',
  'numba',
  'tqdm',
  'statsmodels',
  'networkx',
  'matplotlib',
  'seaborn',
  'pysam',
  'ete3'
]

[project.optional-dependencies]
docs = [
    "ipython",
    "ipywidgets>=8.0.0",
    "sphinx>=5.3",
    "sphinx-autodoc-annotation",
    "sphinx-autodoc-typehints>=1.10.3",
    "sphinx_rtd_theme",
    "sphinxcontrib-bibtex>=2.3.0",
    "sphinxcontrib-spelling>=7.6.2",
    "nbsphinx>=0.8.1",
    "myst-nb>=0.17.1",
    "sphinx_copybutton>=0.5.0",
]

[project.urls]
"Homepage" = "https://github.com/raphael-group/CalicoST"

[tool.setuptools.packages.find]
where = ["src"]
include = ["calicost*"]