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Fix script and add main changes
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@alejoe91
alejoe91 committed Jul 9, 2024
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118 changes: 97 additions & 21 deletions doc/releases/0.101.0.rst
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Expand Up @@ -7,41 +7,89 @@ SpikeInterface 0.101.0 release notes

Main changes:

TODO
* Implementation of `SortingAnalyzer`` (#2398)
* Added framework for hybrid recording generation (#2436, #2769, #2857)
* Improved auto-merging functions and enable `SortingAnalyzer` to merge units and extensions (#2934, #3043, #3154)
* Refactored motion correction with addition of DREDGE AP and LFP (#2915, #3062)
* Better handling of time information (#3118, #3119, #3120)

core:

* Implement apply_merges_to_sorting() (#3154)
* Fix segment start/end frame None in `concatenate_recordings` (#3161)
* Implement `apply_merges_to_sorting()` (#3154)
* More explicit consistency checks for Channel aggregation (#3151)
* Round instead of int for `time_to_sample_index`. (#3119)
* Fix serializability in `save` function and `InjectDriftingTemplatesRecording` (#3130)
* Fix t_starts not propagated to `save_to_memory` (#3120)
* Round instead of int for `time_to_sample_index` (#3119)
* Add time vector case to `get_durations` (#3118)
* Reordering recording, sorting args (#3094)
* extractor_dict_iterator for solving path detection in object `kwargs` (#3089)
* Check start_frame/end_frame in `BaseRecording.get_traces()` (#3059)
* Relax numpy (#3056)
* Add `scale_to_uV` preprocessing (#3053)
* Add more helpful error when a non-existent id is passed to extractors (#3052)
* Propagate FrameSlice default behavior to frame_slice and time_slice (#3051)
* Propagate `FrameSlice` default behavior to `frame_slice` and `time_slice` (#3051)
* fix spike_vector_to_indices() (#3048)
* Skip loading `info.json` into `ext.data` (#3047)
* Proposal to implement a `sorting_analyzer.merge_units()` syntax (#3043)
* add recording.time_slice like recording.frame_slice (#3034)
* Numpy 2.0 cap Fix most egregorious deprecated behavior and cap version (#3032)
* Avoid redirection to not implemented method in `BaseRecording.select_channels` (#3002)
* Add documentation to `frame_slice` in recording and drop redundant inheritance (#3001)
* Add select chanel and select unit method for template objects (#2989)
* Missed `has_scaled` (#2979)
* Fixed `select_channels` (#2977)
* Make _set_probes private (#2949)
* Make `_set_probes` private (#2949)
* Add limit for `n_jobs` with a max of `os.cpu_count()` (#2940)
* API: switch `has_scaled` -> `has_scaleable_traces` (#2924)
* Making `chunk_size=None` behavior for n_jobs=1 explicit (#2902)
* Fix remaining verbose clashing (#2901)
* remove verbose from job_kwargs (#2898)
* Put get_extension (to trigger auto-import) before get_children_dependencies for deleting Analyzer extensions to prevent KeyError (#2888)
* Remove `verbose` from `job_kwargs` (#2898)
* Put get_extension (to trigger auto-import) before `get_children_dependencies` for deleting Analyzer extensions to prevent KeyError (#2888)
* Add peak_to_peak mode to get_templates_amplitude (#2885)
* Protect zarr properties of type object (#2884)
* Avoid returning std when asking for only mean/average with templates extension (#2868)
* Add binary suffixes to job tools memory specification (e.g. 1GiB vs 1GB) (#2858)
* **Implementation of `SortingAnalyzer` (#2398)**
* Possible fix for #2837 (#2854)
* Load `is_scaled` in from zarr Template representation (#2852)
* Use the `is_scaled` attribute inside of `template_tools` functions (#2848)
* Add extra check in fix_job_kwargs (#2829)
* Zarr: extract time vector once and for all! (#2828)
* Add html representation for recording objects (#2803)
* Remove SharedMemory from SortingAnalyzer and use NumpySorting instead. (#2801)
* Channel aggregation preserves names (#2797)
* Only assign memmap within boundaries for `write_binary` (#2796)
* Improve verbose of `ChunkRecordingExecutor` (#2795)
* Add `select_channels` method to base recording (#2786)
* Analyzer set recording (#2785)
* Add name as an extractor attribute for `__repr__` purposes (#2784)
* Compute quality metrics after pipeline nodes (#2773)
* Check for SortingAnalyzer `return_scaled` in template_tools (#2752)
* Template amplitude should not be returned as absolute value (#2750)
* Fix performance issue for `aggregate_channels` (#2736)
* Multiple verbose arguments fix (#2728)
* Fix pipelining of extensions (#2715)
* Seepd up random_spikes_selection() and put "all" method in it (#2700)
* Extend compute for extension kwargs and pipeline nodes (#2693)
* Add 'all' method for random_spikes (#2691)
* Move "return_scaled" options global to SortingAnalyzer. (#2684)
* Extend zarr compression options (#2643)
* Fast templates: compute `std` with and extend to widgets (#2623)
* SortingAnalyzer: `get_extension_default_params` (#2616)
* Load pca from waveform extractor and waveform from Zarr (#2613)
* Seeding silence periods (#2611)
* Implement `get_parent()` function (#2610)
* Fix analyzer sampling frequency check (#2606)
* Proposal to inject anisotropy while creating fake templates (#2600)
* Fix for sorting from_peaks with lexsort (handling multi segments) (#2594)
* Save extension class info. (#2585)
* Fix to impose sorting of the peaks in from_peaks() (#2584)
* Extension delete on recompute (#2579)
* Proposal for auto import extensions module. (#2571)
* Add `check_json` to `zarr` for `SortingAnalyzer` for sorting_provenance file writing (#2559)
* Add more backwards compatibly for MockWaveformExtractor (#2546)
* Make binary recording memmap efficient III (Avoiding spikes by only reserving memory equal to the trace) (#1781)
* Implementation of SortingAnalyzer (#2398)

extractors:

Expand Down Expand Up @@ -72,6 +120,7 @@ extractors:
* IBL extractors revived (#2617)
* Add strict_gap_mode in read_neuralynx to reflect neo. (#2550)
* Use `has_channel_location` instead of `get_property("contact_vector")` (#2475)
* Implementing read_spikeglx_event() (#2442)

sorters:

Expand Down Expand Up @@ -100,32 +149,35 @@ sorters:
* Simple sorter better params (#2547)
* Kilosort4 Wrapper (#2529)
* Fix singularity issue in deleting py_user_folder (#2493)
* Tridesclous2 update (#2267)

postprocessing:

* fix spike_vector_to_indices() (#3048)
* Fix `spike_vector_to_indices()` (#3048)
* Remove un-used argument (#3021)
* Optimize numba cross-correlation and extend `correlograms.py` docstrings and tests (#3017)
* Moving unit_localization into unit_locations for consistency (#2992)
* Template similarity lags (#2941)
* Fix isi_histograms when using numba (#2632)
* Revert change in set_params for unit locations (#2624)
* Revert change in `set_params` for unit locations (#2624)

qualitymetrics:

* Fix nn pca_metric computation and update tests (#3138)
* Add `peak_to_peak` mode to SNR (#3009)
* Add test to check unit structure in quality metric calculator output (#2973)
* Fix math error in `sd_ratio` (#2964)
* Remove "waveforms" dependency for compute_quality_metrics(). (#2707)
* compute_synchrony_metrics update (#2605)
* Remove "waveforms" dependency for `compute_quality_metrics()` (#2707)
* `compute_synchrony_metrics` update (#2605)

curation:

* Implement apply_merges_to_sorting() (#3154)
* Implement `apply_merges_to_sorting()` (#3154)
* Improve and benchmark auto-merging functions (#2934)
* Proposal of format to hold the manual curation information (#2933)
* Provide useful message if sorting used instead of analyzer for remove_duplicate_units (#2790)
* Provide useful message if sorting used instead of analyzer for `remove_duplicate_units` (#2790)
* Fix split in more than 2 units and extend curation docs and tests (#2775)
* Enhancing curation : get_potential_auto_merge() (#2753)
* Enhancing curation : `get_potential_auto_merge()` (#2753)
* Make sure `has_exceeding_spikes` also checks for negative spikes. (#2727)
* Allow for `remove_excess_spikes` to remove negative spike times (#2716)
* Add function in addition to class option for `MergeUnitsSorting`, `SplitUnitSorting`, and `CurationSorting` (#2659)
Expand All @@ -134,12 +186,13 @@ curation:
widgets:

* Since the gui now has curation we should allow users to set curation when making sorting summary (#3104)
* Add plot_drift_map widget (#3068)
* Fix bug in plot_potential_merges (#3044)
* Add peaks_on_probe widget. (#3022)
* Add `plot_drift_raster_map` widget (#3068)
* Fix bug in `plot_potential_merges` (#3044)
* Add `peaks_on_probe` widget. (#3022)
* Plot potential merges (#3003)
* Fix the new way of handling cmap in matpltolib. This fix the matplotib 3.9 problem related to this. (#2891)
* Extend plot waveforms/templates to Templates object (#2856)
* Fix bug in plot templates (#2850)
* Add errors to `ensure` functions in `Base` of widgets (#2791)
* Add `color_channels` option in in plot_probe_map (#2740)
* Extend capabilities of plot_traces and spikes_on_traces (#2737)
Expand All @@ -151,26 +204,35 @@ generation:

* Out-of-place multiply needed when using amplitude scaling in the drifty hybrid recording (#3115)
* Update tests against template library (#3000)
* Add select chanel and select unit method for template objects (#2989)
* Add select channel and select unit method for template objects (#2989)
* Template fetching methods (#2857)
* Load `is_scaled` in from zarr Template representation (#2852)
* Add `is_scaled` to `Templates` object (#2842)
* Add template `generate_recording_from_template_database` (#2769)
* Proposal to inject anisotropy while creating fake templates (#2600)
* Tools for Generation of Hybrid recordings (#2436)

sortingcomponents:

* Fix select peaks (#3132)
* Dredge lfp and dredge ap (#3062)
* Use "available" for memory caching (#3008)
* get_spike_prototype can have NaN sometimes (#2980)
* Benchmarks components: plotting utils (#2959)
* Internal motion API, aka `Motion` object (#2915)
* Components of SC2 (#2870)
* Benchmark sorting components + Tridesclous2 improvement (#2811)
* Change "idw" to "kriging" in spatial_interpolation_kernel parameters (#2708)
* Benchmarks for sorting components (#2586)
* Fix for template matching in circus (#2583)
* Circus2 improvements (#2574)
* Matched filtering to enhance peak detection (#2259)
* Benchmark matching (#2518)
* Initial benchmark components refactor (#2502)
* Remove WaveformExtractor from Templates matching (#2485)


docs:
documentation:

* analyse -> analyze in Neuropixels docs (#3143)
* Add pooch to docs extra (#3124)
Expand Down Expand Up @@ -202,6 +264,19 @@ docs:
* Fix example broken by #2684 (#2717)
* Add a "how to" for combining recordings (#2713)
* Fix SortingAnalyzer tutorial (#2648)
* Sync documentation with bug fixes (#2645)
* WaveformExtractor -> SortingAnalyzer doc page (#2633)
* Update get_started.rst with info for reloading saved binaries (#2622)
* Analyzer core extension: improve docstrings (#2608)
* Improve documentation for excess spikes error in `FrameSliceSorting`. (#2604)
* Put SortingAnalyzer in get started (#2582)
* Clarify status of main and Sortinganalyzer (#2580)
* Add note about recommendation not to change batch size in Kilosort1-3 (#2564)
* `SortingAnalyzer` core documentation (#2563)
* Cleanup of modules gallery docs (post SorterAnalyzer) (#2552)
* Add note to explain that Command Prompt is currently the only officially supported shell for Windows (#2494)
* Add documentation of preprocessing and sorting split by channel group. (#2316)
* `SortingAnalyzer` in "how to" analyze neuropixels (#2520)

continuous integration:

Expand All @@ -213,6 +288,7 @@ continuous integration:
* Update cron job for `installation_tips` (#3038)
* Improve profile imports test (#2955)
* Modify CI for new dev version criteria (#2636)
* update all CI actions (#2460)

packaging:

Expand Down Expand Up @@ -259,7 +335,7 @@ testing:
* Speed up test_sorting_s3_nwb_zarr (#2767)
* Fix full tests (#2665)
* Fix typo in fast templates test (#2651)

* update all CI actions (#2460)

Contributors:

Expand Down
12 changes: 9 additions & 3 deletions doc/scripts/auto-release-notes.sh
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@@ -1,14 +1,14 @@
#!/bin/bash
if [ $# -eq 0 ]; then
echo "Usage: $0 START_DATE END_DATE [LABEL] [BRANCH1,BRANCH2]"
echo "Usage: $0 START_DATE END_DATE [LABEL] [BRANCH1,BRANCH2] [LIMIT]"
exit 1
fi

START_DATE="$1"
END_DATE="$2"

if [ -z "$3" ] || [ "$3" = "all" ]; then
LABELS=("core" "extractors" "sorters" "postprocessing" "qualitymetrics" "curation" "widgets" "generation" "hybrid" "sortingcomponents" "documentation" "continuous integration" "packaging" "testing")
LABELS=("core" "extractors" "sorters" "postprocessing" "qualitymetrics" "curation" "widgets" "generation" "hybrid" "sortingcomponents" "motion correction" "documentation" "continuous integration" "packaging" "testing")
else
LABELS=("$3")
fi
Expand All @@ -17,11 +17,17 @@ if [ -n "$4" ]; then
IFS=',' read -ra BRANCHES <<< "$4"
fi

if [ -n "$5" ]; then
LIMIT=$5
else
LIMIT=300
fi

for LABEL in "${LABELS[@]}"; do
echo "$LABEL:"
echo ""
for BRANCH in "${BRANCHES[@]}"; do
gh pr list --repo SpikeInterface/spikeinterface --label "$LABEL" --base "$BRANCH" --state merged --json number,title,mergedAt \
gh pr list --repo SpikeInterface/spikeinterface --limit $LIMIT --label "$LABEL" --base "$BRANCH" --state merged --json number,title,mergedAt \
| jq -r --arg start_date "${START_DATE}T00:00:00Z" --arg end_date "${END_DATE}T00:00:00Z" \
'.[] | select(.mergedAt >= $start_date and .mergedAt <= $end_date) | "* \(.title) (#\(.number))"'
done
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10 changes: 6 additions & 4 deletions doc/whatisnew.rst
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Expand Up @@ -43,13 +43,15 @@ Release notes
releases/0.9.1.rst





Version 0.101.0
===============

TODO
* Implementation of `SortingAnalyzer`` (#2398)
* Added framework for hybrid recording generation (#2436, #2769, #2857)
* Improved auto-merging functions and enable `SortingAnalyzer` to merge units and extensions (#2934, #3043, #3154)
* Refactored motion correction with addition of DREDGE AP and LFP (#2915, #3062)
* Better handling of time information (#3118, #3119, #3120)


Version 0.100.8
===============
Expand Down

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