Skip to content

Latest commit

 

History

History
179 lines (149 loc) · 7.21 KB

CHANGELOG.md

File metadata and controls

179 lines (149 loc) · 7.21 KB

Change Log

Unreleased

Infrastructure

  • Add user roles to database_settings.py. #832

0.5.0 (February 9, 2024)

Infrastructure

  • Docs:
    • Additional documentation. #690
    • Add overview of Spyglass to docs. #779
    • Update docs to reflect new notebooks. #776
  • Mixin:
    • 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
      • More robust caching of join to downstream tables. #806
      • Overwrite datajoint delete method to use cautious_delete. #806
      • Reverse join order for session summary. #821
      • Add temporary logging of use to common_usage. #811, #821
  • Merge Tables:
    • UUIDs: Revise Merge table uuid generation to include source. #824
    • UUIDs: Remove mutual exclusivity logic due to new UUID generation. #824
    • Add method for merge_populate. #824
  • Linting:
    • Clean up following pre-commit checks. #688
    • Update linting for Black 24. #808
  • Misc:
    • Add deprecation_factory to facilitate table migration. #717
    • Add Spyglass logger. #730
    • Increase pytest coverage for common, lfp, and utils. #743
    • Steamline dependency management. #822

Pipelines

  • Common:
    • IntervalList: Add secondary key pipeline #742
    • Add common_usage table. #811, #821, #824
    • Add catch errors during populate_all_common. #824
  • Spike sorting:
    • Add SpikeSorting V1 pipeline. #651
    • Move modules into spikesorting.v0 #807
  • LFP:
    • Minor fixes to LFPBandV1 populator and make. #706, #795
    • LFPV1: Fix error for multiple lfp settings on same data #775
  • 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
    • Fix in place column bug #752
  • Decoding:
    • Add decoding pipeline V1. #731, #769, #819
    • 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 clusterless decoding #731
    • Reorder notebooks #731
    • Add fetch class functionality to Merge table. #783, #786
    • Add ability to filter sorted units in decoding #807
    • Rename SortedSpikesGroup.SortGroup to SortedSpikesGroup.Units #807
    • Change methods with load_... to fetch_... for consistency #807
    • Use merge table methods to access part methods #807
  • MUA
    • Add MUA pipeline V1. #731, #819
  • Ripple
    • Add figurl to Ripple pipeline #819

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