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[WIP] Standardize schema names, add ImportedSS, revamp SortGroup #372

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@rly rly commented Oct 26, 2022

Breaking up the changes in #334 into smaller PRs...

credit to @khl02007 for most of these changes

Breaking changes:

  • Rename the following tables/classes:
    • ArtifactDetectionParameters -> ArtifactDetectionParameter
    • AutomaticCuration -> MetricAutomaticCuration
    • AutomaticCurationParameters -> MetricAutomaticCurationParameters
    • AutomaticCurationSelection -> MetricAutomaticCurationSelection
    • MetricParameters -> MetricParameter
    • QualityMetrics -> QualityMetric
    • UnitInclusionParameters -> UnitInclusionParameter
    • WaveformParameters -> WaveformParameter
    • Waveforms -> Waveform
    • SpikeSortingPreprocessingParameters -> SpikeSortingPreprocessingParameter
    • SpikeSorterParameters -> SpikeSorterParameter
  • Move sortingview_helper_fn to utils/sortingview_helper_fn
  • Remove deprecated channel field from SortingviewWorkspace
  • Remove option to pass description to SortingviewWorkspace.insert_manual_curation. It is now hardcoded as “from SortingviewWorkspace”
  • Make Curation.SpikeSorting and Curation.ImportedSpikeSorting part tables instead of having SpikeSorting as part of the primary key of Curation
  • Make MetricAutomaticCuration not have a auto_curation_key blob field but instead a output_curation_id uuid field.
  • MetricAutomaticCuration.make would:
    • generate a random UUID output_curation_id
    • insert a new row in MetricAutomaticCuration
    • insert a new row in the Curation part table with many of the same values plus the output_curation_id
  • SortGroup now has a Probe.Shank field
  • SortGroup.set_group_by_shank was updated
    • Previously, all sort groups for this file were deleted. Then, complex code was used to identify the probe shank and the reference electrodes for each electrode group.
    • TODO: @rly fill this out more
  • Comment out SortGroup.set_group_by_electrode_group
  • Comment out SortGroup.get_geometry

Non-breaking changes:

  • Add new table spyglass.spikesorting.spikesorting_sorting.ImportedSpikeSorting
  • Add type hints to various functions

@rly rly changed the base branch from master to 0.2.0 October 26, 2022 21:14
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@khl02007 khl02007 deleted the branch target_0.3.0 July 28, 2023 22:14
@khl02007 khl02007 closed this Jul 28, 2023
@khl02007 khl02007 deleted the update_spikesorting branch July 28, 2023 22:14
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