* [gentoo-commits] proj/sci:master commit in: dev-python/spikeinterface/
@ 2023-02-01 14:55 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2023-02-01 14:55 UTC (permalink / raw
To: gentoo-commits
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
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-python/spikeinterface/
@ 2023-03-02 16:52 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2023-03-02 16:52 UTC (permalink / raw
To: gentoo-commits
commit: efd779b9c71210ac035d5299dd8024054cbf597f
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Mar 2 16:52:39 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Mar 2 16:52:39 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=efd779b9
dev-python/spikeinterface: add 0.97.0
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
.../spikeinterface/spikeinterface-0.97.0.ebuild | 93 ++++++++++++++++++++++
1 file changed, 93 insertions(+)
diff --git a/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild
new file mode 100644
index 000000000..5c4e65481
--- /dev/null
+++ b/dev-python/spikeinterface/spikeinterface-0.97.0.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-0.2.16[${PYTHON_USEDEP}]
+ dev-python/threadpoolctl[${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
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-python/spikeinterface/
@ 2023-05-02 12:44 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:44 UTC (permalink / raw
To: gentoo-commits
commit: 7deed86a843e45007093edc9893212aa7587c6b9
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:43:50 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:43:50 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7deed86a
dev-python/spikeinterface: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
dev-python/spikeinterface/metadata.xml | 19 -----
.../spikeinterface/spikeinterface-0.96.1.ebuild | 93 ----------------------
.../spikeinterface/spikeinterface-0.97.0.ebuild | 93 ----------------------
3 files changed, 205 deletions(-)
diff --git a/dev-python/spikeinterface/metadata.xml b/dev-python/spikeinterface/metadata.xml
deleted file mode 100644
index f91c7a26c..000000000
--- a/dev-python/spikeinterface/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?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
deleted file mode 100644
index 6dae8d191..000000000
--- 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
-}
diff --git a/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild
deleted file mode 100644
index 5c4e65481..000000000
--- a/dev-python/spikeinterface/spikeinterface-0.97.0.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-0.2.16[${PYTHON_USEDEP}]
- dev-python/threadpoolctl[${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
-}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-python/spikeinterface/
@ 2023-05-02 22:12 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2023-05-02 22:12 UTC (permalink / raw
To: gentoo-commits
commit: c69efcc0dc70418ddcfdcf5b059cbb30ca804ce8
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue May 2 21:55:15 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue May 2 22:12:09 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c69efcc0
dev-python/spikeinterface: brought back
This reverts commit 7deed86a843e45007093edc9893212aa7587c6b9.
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
dev-python/spikeinterface/metadata.xml | 19 +++++
.../spikeinterface/spikeinterface-0.96.1.ebuild | 93 ++++++++++++++++++++++
.../spikeinterface/spikeinterface-0.97.0.ebuild | 93 ++++++++++++++++++++++
3 files changed, 205 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
+}
diff --git a/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild
new file mode 100644
index 000000000..5c4e65481
--- /dev/null
+++ b/dev-python/spikeinterface/spikeinterface-0.97.0.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-0.2.16[${PYTHON_USEDEP}]
+ dev-python/threadpoolctl[${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
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-python/spikeinterface/
@ 2023-05-02 23:01 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2023-05-02 23:01 UTC (permalink / raw
To: gentoo-commits
commit: 6c3f47bd802cd5b2aa1d504109165eb3536ec8da
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue May 2 22:51:10 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue May 2 22:51:10 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6c3f47bd
dev-python/spikeinterface: enable py3.11
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
dev-python/spikeinterface/spikeinterface-0.96.1.ebuild | 2 +-
dev-python/spikeinterface/spikeinterface-0.97.0.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild
index 6dae8d191..ef6a472f4 100644
--- a/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild
+++ b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
diff --git a/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild
index 5c4e65481..2a25d4eee 100644
--- a/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild
+++ b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-python/spikeinterface/
@ 2023-12-14 19:31 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2023-12-14 19:31 UTC (permalink / raw
To: gentoo-commits
commit: 9ae7b9a12b89ec8fcb4473bd6912343c99f0f260
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Dec 14 19:31:22 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Dec 14 19:31:22 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ae7b9a1
dev-python/spikeinterface: add 0.99.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
.../spikeinterface/spikeinterface-0.99.1.ebuild | 53 ++++++++++++++++++++++
1 file changed, 53 insertions(+)
diff --git a/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild
new file mode 100644
index 000000000..a428775eb
--- /dev/null
+++ b/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+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 -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="extractors full test"
+# Reported upstream:
+# https://github.com/SpikeInterface/spikeinterface/issues/2339
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/joblib[${PYTHON_USEDEP}]
+ dev-python/neo[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ >=dev-python/probeinterface-0.2.16[${PYTHON_USEDEP}]
+ dev-python/threadpoolctl[${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
^ permalink raw reply related [flat|nested] 6+ messages in thread
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