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Diffstat (limited to 'dev-python/spikeinterface/spikeinterface-0.97.0.ebuild')
| -rw-r--r-- | dev-python/spikeinterface/spikeinterface-0.97.0.ebuild | 93 |
1 files changed, 93 insertions, 0 deletions
diff --git a/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild new file mode 100644 index 000000000..2a25d4eee --- /dev/null +++ b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild @@ -0,0 +1,93 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines." +HOMEPAGE="https://github.com/SpikeInterface/spikeinterface" +SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="extractors full test" + +RDEPEND=" + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + >=dev-python/probeinterface-0.2.16[${PYTHON_USEDEP}] + dev-python/threadpoolctl[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + extractors? ( + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/lxml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ) + full? ( + dev-python/distinctipy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/xarray[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] + ) +" +# Also wants: +# # Extractors: +# MEArec +# pyedflib +# sonpy +# dev-python/hdf5storage (in ::science, masked) + +distutils_enable_tests pytest + +# Test failures reported upstream: +# https://github.com/SpikeInterface/spikeinterface/issues/307 +python_test() { + # Network sandboxing, mostly (?) + local EPYTEST_DESELECT=( + spikeinterface/core/tests/test_datasets.py::test_download_dataset + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_motion_functions + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_rigid + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_non_rigid + spikeinterface/comparison/tests/test_multisortingcomparison.py::test_compare_multiple_sorters + spikeinterface/curation/tests/test_sortingview_curation.py::test_sortingview_curation + spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy + spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy_by_sparsity + spikeinterface/exporters/tests/test_report.py::test_export_report + spikeinterface/extractors/tests/test_neoextractors.py + spikeinterface/sorters/tests/test_launcher.py::test_run_sorters_with_dict + spikeinterface/sorters/tests/test_launcher.py::test_sorter_installation + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_local + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_docker + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_singularity + spikeinterface/sorters/tests/test_si_based_sorters.py::SpykingCircus2SorterCommonTestSuite + spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_class + spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_run + spikeinterface/sortingcomponents/tests/test_clustering.py::test_find_cluster_from_peaks + spikeinterface/sortingcomponents/tests/test_features_from_peaks.py::test_features_from_peaks + spikeinterface/sortingcomponents/tests/test_peak_detection.py::test_detect_peaks + spikeinterface/sortingcomponents/tests/test_peak_localization.py::test_localize_peaks + spikeinterface/sortingcomponents/tests/test_peak_pipeline.py::test_run_peak_pipeline + spikeinterface/sortingcomponents/tests/test_peak_selection.py::test_detect_peaks + spikeinterface/sortingcomponents/tests/test_template_matching.py::test_find_spikes_from_templates + spikeinterface/widgets/tests/test_widgets.py::TestWidgets + ) + # Reported upstream: + # https://github.com/SpikeInterface/spikeinterface/issues/307#issuecomment-1410840998 + EPYTEST_DESELECT+=( + spikeinterface/sorters/tests/test_launcher.py::test_collect_sorting_outputs + ) + local EPYTEST_IGNORE=( + spikeinterface/widgets/_legacy_mpl_widgets/tests/* + ) + epytest +} |