pyproject.toml

[build-system]
requires = [
    'flit_core >=2,<4',
    'setuptools_scm',
    'pytoml',
    'importlib_metadata>=0.7; python_version < "3.8"',
]
build-backend = 'flit_core.buildapi'

[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'
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',
    # 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 dev version
    'setuptools_scm',
    'pytoml',
    # 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']
scvi = ['scvi>=0.6.5']
rapids = ['cudf>=0.9', 'cuml>=0.9', 'cugraph>=0.9']
magic = ['magic-impute>=2.0']
skmisc = ['scikit-misc>=0.1.3']
harmony = ['harmonypy']
doc = [
    'sphinx<3.1, >3',
    'sphinx-rtd-theme>=0.3.1',
    'sphinx-autodoc-typehints',
    'scanpydoc>=0.5',
    'typing_extensions; python_version < "3.8"',  # for `Literal`
]
test = [
    'pytest>=4.4',
    'dask[array]!=2.17.0',
    'fsspec',
    'zappy',
    'zarr',
    'black',
    'profimp',
    'docutils',  # for rst2html.py
]

[tool.flit.metadata.urls]
Documentation = 'https://scanpy.readthedocs.io/'

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

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

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

[tool.black]
line-length = 88
target-version = ['py36']
skip-string-normalization = true
exclude = '''
/build/.*
|/scanpy/(
    get
    |__init__
    |logging
    |_utils
    |_settings
    |neighbors/__init__
    |api/(__init__|pp|pl|datasets)
    |external/(exporting|tl/_palantir)
    |preprocessing/(
        _qc
        |_simple
        |_normalization
        |_highly_variable_genes
        |_deprecated/highly_variable_genes
    )
    |tools/(
        _dpt
        |_sim
        |_paga
        |_umap
        |_utils
        |_leiden
        |_louvain
        |_tsne_fix
        |_top_genes
        |_score_genes
        |_utils_clustering
        |_rank_genes_groups
    )
    |plotting/(
        __init__
        |palettes
        |_tools/(__init__|paga)
    )
    |tests/(
        test_get
        |test_neighbors
        |test_readwrite
        |test_clustering
        |test_preprocessing
        |test_rank_genes_groups
        |test_marker_gene_overlap
        |test_highly_variable_genes
        |test_rank_genes_groups_logreg
        |notebooks/(test_paga_paul15_subsampled|test_pbmc3k)
    )
).py'''