pyproject.toml

[build-system]
build-backend = 'flit_core.buildapi'
requires = [
    'flit_core >=3.1,<4',
    'setuptools_scm',
    'pytoml',
    'importlib_metadata>=0.7; python_version < "3.8"',
    # setup.py stuff
    'packaging',
]

[tool.flit.metadata]
module = 'scanpy'
author = """\
Alex Wolf, Philipp Angerer, Fidel Ramirez, Isaac Virshup, \
Sergei Rybakov, Gokcen Eraslan, Tom White, Malte Luecken, \
Davide Cittaro, Tobias Callies, Marius Lange, Andrés R. Muñoz-Rojas\
"""
# We don’t need all emails, the main authors are sufficient.
author-email = 'f.alex.wolf@gmx.de, philipp.angerer@helmholtz-muenchen.de'
description-file = 'README.rst'
home-page = 'http://github.com/theislab/scanpy'
urls = { Documentation = 'https://scanpy.readthedocs.io/' }
classifiers = [
    'License :: OSI Approved :: BSD License',
    'Development Status :: 5 - Production/Stable',
    'Environment :: Console',
    'Framework :: Jupyter',
    'Intended Audience :: Developers',
    'Intended Audience :: Science/Research',
    'Natural Language :: English',
    'Operating System :: MacOS :: MacOS X',
    'Operating System :: Microsoft :: Windows',
    'Operating System :: POSIX :: Linux',
    'Programming Language :: Python :: 3',
    'Programming Language :: Python :: 3.6',
    'Programming Language :: Python :: 3.7',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
    'Topic :: Scientific/Engineering :: Visualization',
]
requires-python = '>=3.6'
requires = [
    'anndata>=0.7.4',
    # numpy needs a version due to #1320
    'numpy>=1.17.0',
    # Matplotlib 3.1 causes an error in 3d scatter plots (https://github.com/matplotlib/matplotlib/issues/14298)
    # But matplotlib 3.0 causes one in heatmaps
    'matplotlib>=3.1.2',
    'pandas>=0.21',
    'scipy>=1.4',
    'seaborn',
    'h5py>=2.10.0',
    'tables',
    'tqdm',
    'scikit-learn>=0.21.2',
    'statsmodels>=0.10.0rc2',
    'patsy',
    'networkx>=2.3',
    'natsort',
    'joblib',
    'numba>=0.41.0',
    'umap-learn>=0.3.10',
    'legacy-api-wrap',
    'packaging',
    'sinfo',
    # for getting the stable version
    'importlib_metadata>=0.7; python_version < "3.8"',
]

[tool.flit.metadata.requires-extra]
louvain = ['python-igraph', 'louvain>=0.6,!=0.6.2']
leiden = ['python-igraph', 'leidenalg']
bbknn = ['bbknn']
rapids = ['cudf>=0.9', 'cuml>=0.9', 'cugraph>=0.9']
magic = ['magic-impute>=2.0']
skmisc = ['scikit-misc>=0.1.3']
harmony = ['harmonypy']
scanorama = ['scanorama']
scrublet = ['scrublet']
dev = [
    # getting the dev version
    'setuptools_scm',
    'pytoml',
    # static checking
    'black>=20.8b1',
    'docutils',
]
doc = [
    'sphinx>=3.2',
    'sphinx-rtd-theme>=0.3.1',
    'sphinx-autodoc-typehints',
    'readthedocs-sphinx-search',
    'scanpydoc>=0.5',
    'typing_extensions; python_version < "3.8"',  # for `Literal`
]
test = [
    'pytest>=4.4',
    'pytest-nunit',
    'dask[array]!=2.17.0',
    'fsspec',
    'zappy',
    'zarr',
    'profimp',
    # Test the metadata while this exists: https://github.com/takluyver/flit/issues/387
    'flit_core',
]

[tool.flit.scripts]
scanpy = 'scanpy.cli:console_main'

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

[tool.pytest.ini_options]
python_files = 'test_*.py'
testpaths = 'scanpy/tests/'
xfail_strict = true
nunit_attach_on = 'fail'
markers = [
    'internet: tests which rely on internet resources (enable with `--internet-tests`)',
]

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

[tool.black]
line-length = 88
target-version = ['py36']
skip-string-normalization = true
exclude = '''
/build/.*
'''