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