[gentoo-commits] proj/sci:master commit in: dev-python/spikeinterface/

["Horea Christian" <horea.christ@gmail.com>]

commit:     bdf4308195544e9082598647943e18e1fe6ee262
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed Feb  1 14:55:11 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Feb  1 14:55:11 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bdf43081

dev-python/spikeinterface: new package, add 0.96.1

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 dev-python/spikeinterface/metadata.xml             | 19 +++++
 .../spikeinterface/spikeinterface-0.96.1.ebuild    | 93 ++++++++++++++++++++++
 2 files changed, 112 insertions(+)

diff --git a/dev-python/spikeinterface/metadata.xml b/dev-python/spikeinterface/metadata.xml
new file mode 100644
index 000000000..f91c7a26c
--- /dev/null
+++ b/dev-python/spikeinterface/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<use>
+		<flag name="extractors">support for all extractors</flag>
+		<flag name="full">support for all optional processing features</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">SpikeInterface/spikeinterface</remote-id>
+	</upstream>
+</pkgmetadata>

diff --git a/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild
new file mode 100644
index 000000000..6dae8d191
--- /dev/null
+++ b/dev-python/spikeinterface/spikeinterface-0.96.1.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[${PYTHON_USEDEP}]
+	dev-python/threadpoolctl[${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
+}