pyproject.toml

[build-system]
build-backend = "flit_core.buildapi"
requires = ["flit_core >=3.8.0,<4"]

[project]
name = "CytoSimplex"
description = "Simplex Visualization of Cell Fate Similarity in Single-Cell Data"
version = "0.1.0"
requires-python = ">=3.10"
license = {file = "LICENSE"}
authors = [
    {name = "Yichen Wang"},
    {name = "Jialin Liu"},
    {name = "Joshua D. Welch"}
]
maintainers = [
    {name = "Yichen Wang", email = "wayichen@umich.edu"}
]
readme = {file = "README.md", content-type="text/markdown"}
classifiers = [
    'Development Status :: 5 - Production/Stable',
    'Intended Audience :: Developers',
    'Intended Audience :: Science/Research',
    'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
    'Programming Language :: Python :: 3.10',
    'Natural Language :: English',
    'Operating System :: MacOS',
    'Operating System :: Microsoft :: Windows',
    'Operating System :: POSIX :: Linux',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
    'Topic :: Scientific/Engineering :: Visualization',
]
dependencies = [
    'scikit-learn',
    'numpy',
    'anndata',
    'scipy',
    'pandas',
    'matplotlib',
    'mpltern',
    'scanpy'
]

[project.urls]
Documentation = "https://cytosimplex.readthedocs.io/en/latest/"
Source = "https://github.com/welch-lab/pyCytoSimplex"

[project.optional-dependencies]
test-min = [
    "pytest>=4.4",
    "pytest-nunit",
    "pytest-mock",
    # "profimp",
]
test = [
    "CytoSimplex[test-min]"
]
doc = [
    "sphinx>=4.4,<5", # remove upper bound when theme supports dark mode
    "sphinx-book-theme",
    "sphinx_design",
    "scanpydoc>=0.9.5",
    "sphinx-autodoc-typehints",
    "myst-parser",
    "myst-nb",
    "sphinx-design",
    "sphinxext-opengraph", # for nice cards when sharing on social
    "sphinx-copybutton",
    "nbsphinx",
    "matplotlib!=3.6.1",
]

[tool.pytest.ini_options]
addopts = "--cov --cov-report html --cov-fail-under 95"
testpaths = ["src/CytoSimplex/tests"]
xfail_strict = true
markers = [
    "internet: tests which rely on internet resources (enable with `--internet-tests`)",
]

[tool.coverage.run]
source = ["src"]

[tool.pylint]
disable = [
    # module imported but unused
    "W0611",
]