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commit: bdf4308195544e9082598647943e18e1fe6ee262 |
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Author: Horea Christian <chr <AT> chymera <DOT> eu> |
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AuthorDate: Wed Feb 1 14:55:11 2023 +0000 |
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Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> |
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CommitDate: Wed Feb 1 14:55:11 2023 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bdf43081 |
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|
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dev-python/spikeinterface: new package, add 0.96.1 |
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|
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Signed-off-by: Horea Christian <chr <AT> chymera.eu> |
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|
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dev-python/spikeinterface/metadata.xml | 19 +++++ |
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.../spikeinterface/spikeinterface-0.96.1.ebuild | 93 ++++++++++++++++++++++ |
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2 files changed, 112 insertions(+) |
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|
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diff --git a/dev-python/spikeinterface/metadata.xml b/dev-python/spikeinterface/metadata.xml |
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new file mode 100644 |
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index 000000000..f91c7a26c |
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--- /dev/null |
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+++ b/dev-python/spikeinterface/metadata.xml |
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@@ -0,0 +1,19 @@ |
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+<?xml version='1.0' encoding='UTF-8'?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <maintainer type="person"> |
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+ <email>gentoo@×××××××.eu</email> |
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+ <name>Horea Christian</name> |
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+ </maintainer> |
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+ <maintainer type="project"> |
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+ <email>sci@g.o</email> |
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+ <name>Gentoo Science Project</name> |
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+ </maintainer> |
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+ <use> |
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+ <flag name="extractors">support for all extractors</flag> |
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+ <flag name="full">support for all optional processing features</flag> |
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+ </use> |
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+ <upstream> |
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+ <remote-id type="github">SpikeInterface/spikeinterface</remote-id> |
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+ </upstream> |
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+</pkgmetadata> |
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|
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diff --git a/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild |
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new file mode 100644 |
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index 000000000..6dae8d191 |
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--- /dev/null |
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+++ b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild |
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@@ -0,0 +1,93 @@ |
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+# Copyright 2021-2023 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=8 |
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+ |
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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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+ |
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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 -> ${P}.tar.gz" |
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+ |
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+LICENSE="MIT" |
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+SLOT="0" |
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+KEYWORDS="~amd64" |
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+IUSE="extractors full test" |
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+ |
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+RDEPEND=" |
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+ dev-python/joblib[${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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+ |
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+distutils_enable_tests pytest |
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+ |
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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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+} |