commit: 2197df0e3de174258d330058ca961121c538784c Author: Horea Christian <chr <AT> chymera <DOT> eu> AuthorDate: Tue Jan 31 09:57:44 2023 +0000 Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> CommitDate: Tue Jan 31 09:57:44 2023 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2197df0e
dev-python/tridesclous: new package, add 1.6.4, 1.6.6 Signed-off-by: Horea Christian <chr <AT> chymera.eu> dev-python/tridesclous/metadata.xml | 16 ++++ dev-python/tridesclous/tridesclous-1.6.4.ebuild | 101 ++++++++++++++++++++++++ dev-python/tridesclous/tridesclous-1.6.6.ebuild | 101 ++++++++++++++++++++++++ 3 files changed, 218 insertions(+) diff --git a/dev-python/tridesclous/metadata.xml b/dev-python/tridesclous/metadata.xml new file mode 100644 index 000000000..819340cd1 --- /dev/null +++ b/dev-python/tridesclous/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>[email protected]</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">tridesclous/tridesclous</remote-id> + <remote-id type="pypi">tridesclous</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/tridesclous/tridesclous-1.6.4.ebuild b/dev-python/tridesclous/tridesclous-1.6.4.ebuild new file mode 100644 index 000000000..a65c30298 --- /dev/null +++ b/dev-python/tridesclous/tridesclous-1.6.4.ebuild @@ -0,0 +1,101 @@ +# 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="offline/online spike sorting" +HOMEPAGE="https://github.com/tridesclous/tridesclous"; +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="gui test" + +RDEPEND=" + <dev-python/numpy-1.24.0[${PYTHON_USEDEP}] + dev-python/cython[${PYTHON_USEDEP}] + dev-python/hdbscan[${PYTHON_USEDEP}] + dev-python/loky[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] + dev-python/numba + dev-python/openpyxl[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/seaborn[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] + gui? ( + dev-python/PyQt5[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +# Network sandboxing, this is sadly more than half the test suite :( +EPYTEST_DESELECT=( + tridesclous/tests/test_cleancluster.py::test_auto_split + tridesclous/tests/test_cleancluster.py::test_trash_not_aligned + tridesclous/tests/test_cleancluster.py::test_auto_merge + tridesclous/tests/test_cleancluster.py::test_trash_low_extremum + tridesclous/tests/test_cleancluster.py::test_trash_small_cluster + tridesclous/tests/test_cluster.py::test_sawchaincut + tridesclous/tests/test_cluster.py::test_pruningshears + tridesclous/tests/test_decomposition.py::test_all_decomposition + tridesclous/tests/test_export.py::test_export + tridesclous/tests/test_export.py::test_export_catalogue_spikes + tridesclous/tests/test_jobtools.py::test_run_parallel_signalprocessor + tridesclous/tests/test_matplotlibplot.py::test_plot_probe_geometry + tridesclous/tests/test_matplotlibplot.py::test_plot_signals + tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms_with_geometry + tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms + tridesclous/tests/test_matplotlibplot.py::test_plot_features_scatter_2d + tridesclous/tests/test_metrics.py::test_all_metrics + tridesclous/tests/test_metrics.py::test_cluster_ratio + tridesclous/tests/test_peeler.py::test_peeler_geometry + tridesclous/tests/test_peeler.py::test_peeler_geometry_cl + tridesclous/tests/test_peeler.py::test_peeler_empty_catalogue + tridesclous/tests/test_peeler.py::test_peeler_several_chunksize + tridesclous/tests/test_peeler.py::test_peeler_with_and_without_preprocessor + tridesclous/tests/test_peeler.py::test_export_spikes + tridesclous/tests/test_report.py::test_summary_catalogue_clusters + tridesclous/tests/test_report.py::test_summary_noise + tridesclous/tests/test_report.py::test_summary_after_peeler_clusters + tridesclous/tests/test_report.py::test_generate_report + tridesclous/tests/test_autoparams.py::test_get_auto_params + tridesclous/tests/test_catalogueconstructor.py::test_catalogue_constructor + tridesclous/tests/test_catalogueconstructor.py::test_make_catalogue + tridesclous/tests/test_catalogueconstructor.py::test_ratio_amplitude + tridesclous/tests/test_catalogueconstructor.py::test_create_savepoint_catalogue_constructor + tridesclous/tests/test_catalogueconstructor.py::test_feature_with_lda_selection + tridesclous/tests/test_cataloguetools.py::test_apply_all_catalogue_steps + tridesclous/tests/test_dataio.py::test_DataIO + tridesclous/tests/test_dataio.py::test_DataIO_probes + tridesclous/tests/test_datasets.py::test_download_dataset + tridesclous/tests/test_datasets.py::test_get_dataset + tridesclous/tests/test_datasource.py::test_RawDataSource + tridesclous/tests/test_datasource.py::test_NeoRawIOAggregator + tridesclous/tests/test_peakdetector.py::test_compare_offline_online_engines + tridesclous/tests/test_peakdetector.py::test_detect_geometrical_peaks + tridesclous/tests/test_peakdetector.py::test_peak_sign_symetry + tridesclous/tests/test_signalpreprocessor.py::test_compare_offline_online_engines + tridesclous/tests/test_signalpreprocessor.py::test_auto_pad_width + tridesclous/tests/test_tools.py::test_fix_prb_file_py2 +) + +python_test() { + local EPYTEST_IGNORE=( + tridesclous/online/tests/* + ) + if use !gui ; then + local EPYTEST_IGNORE+=( + tridesclous/gui/* + ) + fi + epytest +} diff --git a/dev-python/tridesclous/tridesclous-1.6.6.ebuild b/dev-python/tridesclous/tridesclous-1.6.6.ebuild new file mode 100644 index 000000000..13697e657 --- /dev/null +++ b/dev-python/tridesclous/tridesclous-1.6.6.ebuild @@ -0,0 +1,101 @@ +# 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="offline/online spike sorting" +HOMEPAGE="https://github.com/tridesclous/tridesclous"; +SRC_URI="https://github.com/tridesclous/tridesclous/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="gui test" + +RDEPEND=" + <dev-python/numpy-1.24.0[${PYTHON_USEDEP}] + dev-python/cython[${PYTHON_USEDEP}] + dev-python/hdbscan[${PYTHON_USEDEP}] + dev-python/loky[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] + dev-python/numba + dev-python/openpyxl[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/seaborn[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] + gui? ( + dev-python/PyQt5[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +# Network sandboxing, this is sadly more than half the test suite :( +EPYTEST_DESELECT=( + tridesclous/tests/test_cleancluster.py::test_auto_split + tridesclous/tests/test_cleancluster.py::test_trash_not_aligned + tridesclous/tests/test_cleancluster.py::test_auto_merge + tridesclous/tests/test_cleancluster.py::test_trash_low_extremum + tridesclous/tests/test_cleancluster.py::test_trash_small_cluster + tridesclous/tests/test_cluster.py::test_sawchaincut + tridesclous/tests/test_cluster.py::test_pruningshears + tridesclous/tests/test_decomposition.py::test_all_decomposition + tridesclous/tests/test_export.py::test_export + tridesclous/tests/test_export.py::test_export_catalogue_spikes + tridesclous/tests/test_jobtools.py::test_run_parallel_signalprocessor + tridesclous/tests/test_matplotlibplot.py::test_plot_probe_geometry + tridesclous/tests/test_matplotlibplot.py::test_plot_signals + tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms_with_geometry + tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms + tridesclous/tests/test_matplotlibplot.py::test_plot_features_scatter_2d + tridesclous/tests/test_metrics.py::test_all_metrics + tridesclous/tests/test_metrics.py::test_cluster_ratio + tridesclous/tests/test_peeler.py::test_peeler_geometry + tridesclous/tests/test_peeler.py::test_peeler_geometry_cl + tridesclous/tests/test_peeler.py::test_peeler_empty_catalogue + tridesclous/tests/test_peeler.py::test_peeler_several_chunksize + tridesclous/tests/test_peeler.py::test_peeler_with_and_without_preprocessor + tridesclous/tests/test_peeler.py::test_export_spikes + tridesclous/tests/test_report.py::test_summary_catalogue_clusters + tridesclous/tests/test_report.py::test_summary_noise + tridesclous/tests/test_report.py::test_summary_after_peeler_clusters + tridesclous/tests/test_report.py::test_generate_report + tridesclous/tests/test_autoparams.py::test_get_auto_params + tridesclous/tests/test_catalogueconstructor.py::test_catalogue_constructor + tridesclous/tests/test_catalogueconstructor.py::test_make_catalogue + tridesclous/tests/test_catalogueconstructor.py::test_ratio_amplitude + tridesclous/tests/test_catalogueconstructor.py::test_create_savepoint_catalogue_constructor + tridesclous/tests/test_catalogueconstructor.py::test_feature_with_lda_selection + tridesclous/tests/test_cataloguetools.py::test_apply_all_catalogue_steps + tridesclous/tests/test_dataio.py::test_DataIO + tridesclous/tests/test_dataio.py::test_DataIO_probes + tridesclous/tests/test_datasets.py::test_download_dataset + tridesclous/tests/test_datasets.py::test_get_dataset + tridesclous/tests/test_datasource.py::test_RawDataSource + tridesclous/tests/test_datasource.py::test_NeoRawIOAggregator + tridesclous/tests/test_peakdetector.py::test_compare_offline_online_engines + tridesclous/tests/test_peakdetector.py::test_detect_geometrical_peaks + tridesclous/tests/test_peakdetector.py::test_peak_sign_symetry + tridesclous/tests/test_signalpreprocessor.py::test_compare_offline_online_engines + tridesclous/tests/test_signalpreprocessor.py::test_auto_pad_width + tridesclous/tests/test_tools.py::test_fix_prb_file_py2 +) + +python_test() { + local EPYTEST_IGNORE=( + tridesclous/online/tests/* + ) + if use !gui ; then + local EPYTEST_IGNORE+=( + tridesclous/gui/* + ) + fi + epytest +}
