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Change Log

0.4.4 (Unreleased)

Infrastructure

  • Additional documentation. #690
  • Clean up following pre-commit checks. #688
  • Add Mixin class to centralize fetch_nwb functionality. #692, #734
  • Refactor restriction use in delete_downstream_merge #703
  • Add cautious_delete to Mixin class, initial implementation. #711, #762
  • Add deprecation_factory to facilitate table migration. #717
  • Add Spyglass logger. #730
  • IntervalList: Add secondary key pipeline #742
  • Increase pytest coverage for common, lfp, and utils. #743
  • Update docs to reflect new notebooks. #776
  • Add overview of Spyglass to docs. #779

Pipelines

  • Spike sorting: Add SpikeSorting V1 pipeline. #651
  • LFP: Minor fixes to LFPBandV1 populator. #706
  • Linearization:
    • Minor fixes to LinearizedPositionV1 pipeline #695
    • Rename position_linearization -> linearization. #717
    • Migrate tables: common_position -> linearization.v0. #717
  • Position:
    • Refactor input validation in DLC pipeline. #688
    • DLC path handling from config, and normalize naming convention. #722
  • Decoding:
    • Add decoding pipeline V1. #731, #769
    • Add a table to store the decoding results #731
    • Use the new non_local_detector package for decoding #731
    • Allow multiple spike waveform features for clusterelss decoding #731
    • Reorder notebooks #731

0.4.3 (November 7, 2023)

  • Migrate config helper scripts to Spyglass codebase. #662
  • Revise contribution guidelines. #655
  • Minor bug fixes. #656, #657, #659, #651, #671
  • Add setup instruction specificity.
  • Reduce primary key varchar allocation aross may tables. #664

0.4.2 (October 10, 2023)

Infrastructure / Support

  • Bumped Python version to 3.9. #583
  • Updated user management helper scripts for MySQL 8. #650
  • Centralized config/path handling to permit setting via datajoint config. #593
  • Fixed Merge Table deletes: error specificity and transaction context. #617

Pipelines

  • Common:
    • Added support multiple cameras per epoch. #557
    • Removed common_backup schema. #631
    • Added support for multiple position objects per NWB in common_behav via PositionSource.SpatialSeries and RawPosition.PosObject #628, #616. Note: Existing functions have been made compatible, but column labels for RawPosition.fetch1_dataframe may change.
  • Spike sorting:
    • Added pipeline populator. #637, #646, #647
    • Fixed curation functionality for nn_isolation. #597, #598
  • Position: Added position interval/epoch mapping via PositionIntervalMap. #620, #621, #627
  • LFP: Refactored pipeline. #594, #588, #605, #606, #607, #608, #615, #629

0.4.1 (June 30, 2023)

  • Add mkdocs automated deployment. #527, #537, #549, #551
  • Add class for Merge Tables. #556, #564, #565

0.4.0 (May 22, 2023)

  • Updated call to spikeinterface.preprocessing.whiten to use dtype np.float16. #446,
  • Updated default spike sorting metric parameters. #447
  • Updated whitening to be compatible with recent changes in spikeinterface when using mountainsort. #449
  • Moved LFP pipeline to src/spyglass/lfp/v1 and addressed related usability issues. #468, #478, #482, #484, #504
  • Removed whiten parameter for clusterless thresholder. #454
  • Added plot to plot all DIO events in a session. #457
  • Added file sharing functionality through kachery_cloud. #458, #460
  • Pinned numpy version to numpy<1.24
  • Added scripts to add guests and collaborators as users. #463
  • Cleaned up installation instructions in repo README. #467
  • Added checks in decoding visualization to ensure time dimensions are the correct length.
  • Fixed artifact removed valid times. #472
  • Added codespell workflow for spell checking and fixed typos. #471
  • Updated LFP code to save LFP as pynwb.ecephys.LFP type. #475
  • Added artifact detection to LFP pipeline. #473
  • Replaced calls to spikeinterface.sorters.get_default_params with spikeinterface.sorters.get_default_sorter_params. #486
  • Updated position pipeline and added functionality to handle pose estimation through DeepLabCut. #367, #505
  • Updated environment_position.yml. #502
  • Renamed FirFilter class to FirFilterParameters. #512

0.3.4 (March 30, 2023)

  • Fixed error in spike sorting pipeline referencing the "probe_type" column which is no longer accessible from the Electrode table. #437
  • Fixed error when inserting an NWB file that does not have a probe manufacturer. #433, #436
  • Fixed error when adding a new DataAcquisitionDevice and a new ProbeType. #436
  • Fixed inconsistency between capitalized/uncapitalized versions of "Intan" for DataAcquisitionAmplifier and DataAcquisitionDevice.adc_circuit. #430, #438

0.3.3 (March 29, 2023)

  • Fixed errors from referencing the changed primary key for Probe. #429

0.3.2 (March 28, 2023)

  • Fixed import of common_nwbfile. #424

0.3.1 (March 24, 2023)

  • Fixed import error due to sortingview.Workspace. #421

0.3.0 (March 24, 2023)

  • Refactor common for non Frank Lab data, allow file-based mods #420
  • Allow creation and linkage of device metadata from YAML #400
  • Move helper functions to utils directory #386