pyproject.toml

[build-system]
build-backend = 'flit_core.buildapi'
requires = ['flit_core >=2,<4']

[tool.flit.metadata]
author = 'Xiaojie Qiu, Yan Zhang, Ke Ni'
author-email = 'xqiu.sc@gmail.com'
classifiers = [
  'License :: OSI Approved :: BSD License',
  'Development Status :: 5 - Production/Stable',
  'Intended Audience :: Science/Research',
  'Natural Language :: English',
  'Programming Language :: Python :: 3.6',
  'Programming Language :: Python :: 3.7',
  'Programming Language :: Python :: 3.8',
]
description-file = 'README.md'
home-page = 'https://github.com/aristoteleo/dynamo-release'
keywords = 'dynamo scslam-seq scrna-seq velocity rna protein vector-field potential-landscape'
license = 'BSD'
module = 'dynamo'
requires = [
  'numpy>=1.18.1',
  'pandas>=0.25.1',
  'scipy>=1.0',
  'scikit-learn>=0.19.1',
  'cvxopt>=1.2.3',
  'anndata==0.7.5',
  'loompy>=3.0.5',
  'matplotlib>=3.1.0',
  'trimap>=1.0.11',
  'setuptools',
  'numdifftools>=0.9.39',
  'umap-learn>=0.5.1',
  'hdbscan>=0.8.26',
  'PATSY>=0.5.1',
  'statsmodels>=0.9.0',
  'numba>=0.46.0',
  'seaborn>=0.9.0',
  'colorcet>=2.0.1',
  'networkx',
  'tqdm',
  'python-igraph>=0.7.1',
  'pynndescent>=0.5.2',
  'joblib',
  'setuptools',
]
requires-python = '>=3.8'

[tool.flit.metadata.requires-extra]
bigdata_visualization = ["datashader>=0.9.0", "bokeh>=1.4.0", "holoviews>=1.9.2"]
dev = ['pytest']
dimension_reduction = ['fitsne>=1.0.1']
docs = [
  'docutils',
  'setuptools',
  'sphinx',
  'sphinx-rtd-theme',
  'sphinx_autodoc_typehints',
  'nbsphinx',
  'mock',
  'readthedocs-sphinx-ext',
]
network = ["networkx", "nxviz", "hiveplotlib", "python-igraph", "leidenalg", "wurlitzer"]
spatial = ['pysal>2.0.0']
test = ['pytest', 'sympy>=1.4']

[tool.flit.sdist]
exclude = [
  'dynamo/tests',
  'setup.py',
]

[tool.coverage.run]
omit = ['*/tests/*']
source = ['dynamo']

[tool.black]
exclude = '''
/(
    \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | _build
  | buck-out
  | build
  | dist
)/
'''
include = '\.pyi?$'
line-length = 80