commit: a08147d6055164f0a98c973078488f3a84fb53ba Author: Michael Schubert <mschu.dev <AT> gmail <DOT> com> AuthorDate: Mon Apr 14 19:40:15 2025 +0000 Commit: Nowa Ammerlaan <nowa <AT> gentoo <DOT> org> CommitDate: Sat Apr 19 09:49:31 2025 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a08147d6
dev-python/anndata: add ebuild Signed-off-by: Michael Schubert <mschu.dev <AT> gmail.com> Closes: https://github.com/gentoo/sci/pull/1347 Signed-off-by: Nowa Ammerlaan <nowa <AT> gentoo.org> dev-python/anndata/anndata-0.11.4.ebuild | 63 ++++++++++++++++++++++ .../anndata/files/anndata-0.11.4-testargs.patch | 12 +++++ dev-python/anndata/metadata.xml | 12 +++++ 3 files changed, 87 insertions(+) diff --git a/dev-python/anndata/anndata-0.11.4.ebuild b/dev-python/anndata/anndata-0.11.4.ebuild new file mode 100644 index 000000000..85abbffd7 --- /dev/null +++ b/dev-python/anndata/anndata-0.11.4.ebuild @@ -0,0 +1,63 @@ +# 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_{11..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 +) diff --git a/dev-python/anndata/files/anndata-0.11.4-testargs.patch b/dev-python/anndata/files/anndata-0.11.4-testargs.patch new file mode 100644 index 000000000..87a1b0b04 --- /dev/null +++ b/dev-python/anndata/files/anndata-0.11.4-testargs.patch @@ -0,0 +1,12 @@ +diff --git a/pyproject.toml b/pyproject.toml +index c413510..600bc41 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -144,7 +144,6 @@ addopts = [ + "--doctest-modules", + "--pyargs", + "-ptesting.anndata._pytest", +- "--dist=loadgroup", + ] + filterwarnings = [ + "ignore::anndata._warnings.OldFormatWarning", diff --git a/dev-python/anndata/metadata.xml b/dev-python/anndata/metadata.xml new file mode 100644 index 000000000..e4c86cd99 --- /dev/null +++ b/dev-python/anndata/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>[email protected]</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">scverse/anndata</remote-id> + <remote-id type="pypi">anndata</remote-id> + </upstream> +</pkgmetadata>
