Gentoo Packages

# Copyright 1999-2025 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2

EAPI=8

DISTUTILS_USE_PEP517=hatchling
PYTHON_COMPAT=( python3_{12..13} )
export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}

inherit distutils-r1

DESCRIPTION="Handling annotated data matrices in memory and on disk"
HOMEPAGE="http://anndata.readthedocs.io/"
SRC_URI="https://github.com/scverse/anndata/archive/${PV}.tar.gz -> ${P}.gh.tar.gz"

LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64"

RDEPEND="
	dev-python/array-api-compat[${PYTHON_USEDEP}]
	dev-python/h5py[${PYTHON_USEDEP}]
	dev-python/natsort[${PYTHON_USEDEP}]
	dev-python/numpy[${PYTHON_USEDEP}]
	dev-python/pandas[${PYTHON_USEDEP}]
	dev-python/scipy[${PYTHON_USEDEP}]
"
DEPEND="
	test? (
		dev-python/awkward[${PYTHON_USEDEP}]
		dev-python/boltons[${PYTHON_USEDEP}]
		dev-python/dask[${PYTHON_USEDEP}]
		dev-python/joblib[${PYTHON_USEDEP}]
		dev-python/numba[${PYTHON_USEDEP}]
		dev-python/pyarrow[${PYTHON_USEDEP}]
		dev-python/scikit-learn[${PYTHON_USEDEP}]
		<dev-python/zarr-3[${PYTHON_USEDEP}]
		dev-python/pytest-xdist[${PYTHON_USEDEP}]
	)
"

PATCHES=( "${FILESDIR}/${P}-testargs.patch" )

distutils_enable_tests pytest
RESTRICT="test" # dev-python/scanpy ebuild not available

EPYTEST_DESELECT=(
	# requires dask[distributed], not included in dask ebuild
	tests/test_dask.py::test_dask_distributed_write
	tests/test_io_elementwise.py::test_read_lazy_h5_cluster
	# requires openpyxl
	tests/test_readwrite.py::test_read_excel
	# https://github.com/dask/dask/issues/11752 + https://github.com/scverse/anndata/pull/1862
	tests/test_views.py::test_modify_view_component
	tests/test_views.py::test_not_set_subset_X_dask
	tests/test_concatenate.py::test_concat_dask_sparse_matches_memory
	tests/test_concatenate.py::test_concatenate_layers_misaligned
	tests/test_concatenate.py::test_nan_merge
	tests/test_concatenate.py::test_transposed_concat
	tests/test_concatenate.py::test_concat_dask_sparse_matches_memory
	tests/test_views.py::test_set_scalar_subset_X
	tests/test_views.py::test_set_scalar_subset_X_dask
)