From 3c310184fd6b6795771deb106655ea32c9be2001 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 1 Feb 2023 10:00:50 -0500 Subject: [PATCH] dev-python/spikeinterface: pushed to Gentoo ::science https://gitweb.gentoo.org/proj/sci.git/commit/?id=bdf4308195544e9082598647943e18e1fe6ee262 --- dev-python/spikeinterface/Manifest | 2 - dev-python/spikeinterface/metadata.xml | 19 ---- .../spikeinterface-0.91.0.ebuild | 54 ----------- .../spikeinterface-0.96.1.ebuild | 93 ------------------- 4 files changed, 168 deletions(-) delete mode 100644 dev-python/spikeinterface/Manifest delete mode 100644 dev-python/spikeinterface/metadata.xml delete mode 100644 dev-python/spikeinterface/spikeinterface-0.91.0.ebuild delete mode 100644 dev-python/spikeinterface/spikeinterface-0.96.1.ebuild diff --git a/dev-python/spikeinterface/Manifest b/dev-python/spikeinterface/Manifest deleted file mode 100644 index 7c3a0e5..0000000 --- a/dev-python/spikeinterface/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST spikeinterface-0.91.0.tar.gz 1226833 BLAKE2B a7c1404297216b552b400128cec48eaf6d78f71885a7810ce734af758ac079d6e58851f3e06d4f7cdb413a1f6757d7cbbd67c2578948334ef37db657d8bc3dc0 SHA512 bce2e6919238445d6209112f5ea0177476c5b4b025fbdf02d695bc5da56a9c6404d8d8d8e7dd9f7ec9c702b6752ab12b8b3efebe1e3c0141dd3a03cd16722912 -DIST spikeinterface-0.96.1.tar.gz 1596455 BLAKE2B 52b5d4f0b435433396e7d06b9a2ed83646280ebefb1f62f179f068a060f43898a822e41bf1500ec53087ad5410ee060806f415988606b0197d13d7a671a5603a SHA512 12de90a8d27e900489d36d0ca14edaac3d1abab1a29f0c41ff1d1648fbf11be09c6c01cb0bd1cc4e1d00a81303fab5ffcb4de596ae69be9508e0503edab768ef diff --git a/dev-python/spikeinterface/metadata.xml b/dev-python/spikeinterface/metadata.xml deleted file mode 100644 index b9d1b48..0000000 --- a/dev-python/spikeinterface/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ - - - - - gentoo@chymera.eu - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - support for all extractors - support for all optional processing features - - - SpikeInterface/spikeinterface - - diff --git a/dev-python/spikeinterface/spikeinterface-0.91.0.ebuild b/dev-python/spikeinterface/spikeinterface-0.91.0.ebuild deleted file mode 100644 index fce486a..0000000 --- a/dev-python/spikeinterface/spikeinterface-0.91.0.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 2021-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) -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="test" -RESTRICT="test" -# Tests fail, checking with upstream -# https://github.com/SpikeInterface/spikeinterface/issues/307 - -DEPEND=" - ${RDEPEND} - test? ( - dev-python/loky[${PYTHON_USEDEP}] - dev-python/numba[${PYTHON_USEDEP}] - dev-python/tridesclous[${PYTHON_USEDEP}] - sci-libs/spyking-circus[${PYTHON_USEDEP}] - dev-vcs/datalad - ) -" -RDEPEND=" - dev-python/joblib[${PYTHON_USEDEP}] - dev-python/neo[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/probeinterface[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] -" -# also needs: -# dev-python/PyQt5 -# hbdscan -# shybird -# herdingspikes -# might also need: -# dev-vcs/git-annex -# dev-python/matplotlib[${PYTHON_USEDEP}] -# sci-libs/scikit-learn[${PYTHON_USEDEP}] -# dev-python/networkx[${PYTHON_USEDEP}] -# dev-python/pybind11[${PYTHON_USEDEP}] -# dev-python/pillow[${PYTHON_USEDEP}] -# dev-python/pandas[${PYTHON_USEDEP}] -# dev-python/h5py[${PYTHON_USEDEP}] -BDEPEND="" - -distutils_enable_tests pytest diff --git a/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild deleted file mode 100644 index 6dae8d1..0000000 --- a/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild +++ /dev/null @@ -1,93 +0,0 @@ -# Copyright 2021-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) -DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 - -DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines." -HOMEPAGE="https://github.com/SpikeInterface/spikeinterface" -SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${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 -}