commit: efd779b9c71210ac035d5299dd8024054cbf597f
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Mar 2 16:52:39 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Mar 2 16:52:39 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=efd779b9
dev-python/spikeinterface: add 0.97.0
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
.../spikeinterface/spikeinterface-0.97.0.ebuild | 93 ++++++++++++++++++++++
1 file changed, 93 insertions(+)
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..5c4e65481
--- /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..10} )
+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
+}
