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"',
]

[tool.flit.metadata]
module = 'anndata'
author = 'Philipp Angerer, Alex Wolf, Isaac Virshup, Sergei Rybakov'
# We don’t need all emails, the main authors are sufficient.
author-email = 'phil.angerer@gmail.com, f.alex.wolf@gmx.de'
description-file = 'README.rst'
home-page = 'http://github.com/theislab/anndata'
urls = { Documentation = 'https://anndata.readthedocs.io/' }
classifiers = [
    'License :: OSI Approved :: BSD License',
    '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 = [
    'pandas>=1.1.1',  # pandas <1.1.1 has pandas/issues/35446
    'numpy>=1.16.5',  # required by pandas 1.x
    'scipy>1.4',
    'h5py',
    'natsort',
    'packaging>=20',
    'xlrd<2.0',  # xlsx format not support anymore from v2.0, see pandas/issues/38524
    # for getting the stable version
    'importlib_metadata>=0.7; python_version < "3.8"',
]

[tool.flit.metadata.requires-extra]
dev = [
    # dev version generation
    'setuptools_scm',
    'pytoml',
    # static checking
    'black>=20.8b1',
    'docutils',
]
doc = [
    'sphinx>=4.1',
    'sphinx-rtd-theme',
    'sphinx-autodoc-typehints>=1.11.0',
    'sphinx_issues',
    'scanpydoc>=0.7.3',
    'typing_extensions; python_version < "3.8"',
]
test = [
    'loompy>=3.0.5',
    'pytest>=6.0',
    'pytest-cov>=2.10',
    'zarr',
    'matplotlib',
    'sklearn',
    'openpyxl',
    'joblib',
    'boltons',
    'scanpy',
]

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

[tool.coverage.run]
source = ['anndata']
omit = [
	'setup.py',
	'versioneer.py',
	'anndata/_version.py',
	'**/test_*.py',
]

[tool.pytest.ini_options]
addopts = '--doctest-modules'
python_files = 'test_*.py'
testpaths = ['anndata', 'docs/concatenation.rst']
xfail_strict = true

[tool.black]
line-length = 88
target-version = ['py36']
exclude = '^/build/.*$'