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

[Horea Christian]

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>gentoo@×××××××.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@g.o</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
+}