pyproject.toml

[build-system]
requires = ['setuptools', 'setuptools_scm', 'wheel', 'pytoml']
build-backend = 'setuptools.build_meta'

# uses the format of tool.flit.metadata because we’ll move to it anyway
[tool.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'

[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/.*
|/scanpy/(
    get
    |__init__
    |logging
    |_utils
    |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
        |_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'''