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Change Log

0.5.6 (Unreleased)

Release Notes

Running draft to be removed immediately prior to release. When altering tables, import all foreign key references.

# Alter Decoding v1 table
from spyglass.common.common_filter import FirFilterParameters
from spyglass.decoding.v1.core import DecodingParameters

FirFilterParameters().alter()
DecodingParameters().alter()

# Alter v0 recompute table
from spyglass.spikesorting.v0.spikesorting_recompute import (
    RecordingRecompute,
    RecordingRecomputeSelection,
    RecordingRecomputeVersions,  # noqa F401
    UserEnvironment,  # noqa F401
)

RecordingRecomputeSelection().alter()
RecordingRecompute().alter()

# Alter v1 recompute table
from spyglass.spikesorting.v1.recompute import (
    RecordingRecompute,
    RecordingRecomputeSelection,
    RecordingRecomputeVersions,  # noqa F401
    UserEnvironment,  # noqa F401
)

RecordingRecomputeSelection().alter()
RecordingRecompute().alter()


# Fix LFPBandV1 issue #1481
from spyglass.lfp.analysis.v1 import LFPBandV1

LFPBandV1().fix_1481()

# Increase DLCProject.config_path length
from spyglass.position.v1.position_dlc_project import DLCProject

DLCProject().alter()

Breaking Changes

LFPBandV1 Fix

If you were using a pre-release version of Spyglass 0.5.6 LFPBandV1 after April 2025, you may have stored inaccurate interval list times due to #1481. To fix these, please run LFPBandV1().fix_1481() as shown in the release notes.

Decoding Results Structure

The intervals dimension has been removed from decoding results. Results from multiple decoding intervals are now concatenated along the time dimension with an interval_labels coordinate tracking which interval each time point belongs to.

Why: Eliminates NaN padding when intervals have different lengths, reducing memory usage significantly.

Migration guide:

# OLD (before v0.5.6):
results.isel(intervals=0)  # Get first interval
for i in range(results.sizes["intervals"]):  # Iterate intervals
    interval_data = results.isel(intervals=i)

# NEW (v0.5.6+):
results.where(results.interval_labels == 0, drop=True)  # Get first interval
for label in np.unique(results.interval_labels.values):  # Iterate intervals
    if (
        label >= 0
    ):  # Skip -1 (outside intervals, only with estimate_decoding_params=True)
        interval_data = results.where(results.interval_labels == label, drop=True)

# Or use groupby:
for label, interval_data in results.groupby("interval_labels"):
    if label >= 0:
        # process interval_data
        pass

interval_labels values:

  • 0, 1, 2, ... - Sequential interval indices (0-indexed)
  • -1 - Time points outside any decoding interval (only when estimate_decoding_params=True)

Documentation

  • Delete extra pyscripts that were renamed # 1363
  • Add note on fetching changes to setup notebook #1371
  • Revise table field docstring heading and mermaid diagram generation #1402
  • Add pages for custom analysis tables and class inheritance structure #1435
  • Add support for bandstop filter type #1464

Infrastructure

  • Add cross-platform installer script with Docker support, input validation, and automated environment setup #1414
  • Set default codecov threshold for test fail, disable patch check #1370, #1372
  • Simplify PR template #1370
  • Allow email send on space check success, clean up maintenance logging #1381, #1544
  • Update pynwb pin to >=2.5.0 for TimeSeries.get_timestamps #1385
  • Sort UserEnvironment dict objects by key for consistency #1380
  • Fix typo in VideoFile.make #1427
  • Fix bug in TaskEpoch.make so that it correctly handles multi-row task tables from NWB #1433
  • Split SpyglassMixin into task-specific mixins #1435 #1451
  • Auto-load within-Spyglass tables for graph operations #1368
  • Add explicit kachery-cloud dependency #1430
  • Default to globally saved config #1430
  • Allow rechecking of recomputes #1380, #1413
  • Add SpyglassIngestion class to centralize functionality #1377, #1423, #1465, #1484, #1489, #1507
  • Pin ndx-optogenetics to 0.2.0 #1458
  • Cleanup bug when fetching raw files from DANDI #1469
  • Refactor pytests for speed, run fast tests on push #1440
  • Allow for permissive name selection when identifying objects in ingestion nwb #1490
  • Update fixes for accessing files from DANDI #1477
  • Deprecate populate transaction workaround with tripart make calls #1422 #1505
  • Improve export process for speed and generalization #1387
  • Additional methods for updating files for DANDI standards #1387
  • Implementation of union and intersect methods for restriction graphs #1387
  • Add file issue checks to AnalysisNwbfile cleanup steps #1431
  • Update to latest black and jupytext versions #1508
  • Update minimum Python version to 3.10 #1508
  • Remove outdated cli scripts #1508
  • Pin datajoint version < 2.0 #1516
  • Log expected recompute failures #1470
  • Track file created/deletion status of recomputes #1470
  • Upgrade to pynwb>=3.1 #1506
  • Remove imports of ndx extensions in main package to prevent errors in nwb io #1506
  • Add analysis_table property to mixin for custom pipelines #1525
  • Quiet pytest output for expected warnings in test runs #1534
  • Fix update bug in _resolve_external_tables #1536

Pipelines

  • Behavior

    • Add methods for calling moseq visualization functions #1374
    • Ensure latent moseq dimension is compatible with dataset #1511

  • Common

    • Add tables for storing optogenetic experiment information #1312
    • Remove wildcard matching in Nwbfile().get_abs_path #1382
    • Change IntervalList.insert to cautious_insert #1423
    • Allow email send on space check success, clean up maintenance logging #1381
    • Update pynwb pin to >=2.5.0 for TimeSeries.get_timestamps #1385
    • Fix error from unlinked object in AnalysisNwbfile.create #1396
    • Sort UserEnvironment dict objects by key for consistency #1380
    • Fix typo in VideoFile.make #1427
    • Fix bug in TaskEpoch.make so that it correctly handles multi-row task tables from NWB #1433
    • Add custom/dynamic AnalysisNwbfile creation #1435, #1496, #1498
    • Allow nullable DataAcquisitionDevice foreign keys #1455
    • Remove pre-existing Units from created analysis nwb files #1453
    • Allow multiple VideoFile entries during ingestion #1462
    • Handle epoch formats with varying zero-padding #1459, #1492
    • Reduce lock conflicts between users during ingestion #1483
    • Add the table RawCompassDirection for importing orientation data from NWB files #1466
    • Allow ingestion of nwb files without behavior module #1441
    • Warn when ingesting ImageSeries without TaskEpoch #1461
    • Support ingestion of multi-epoch video files #1548
    • Fix bug with sgc.LabTeam().create_new_team when google_user_name is not available #1546
    • Fix bug from overlapping intervals in interval union #1520

  • Decoding

    • Ensure results directory is created if it doesn't exist #1362
    • Change BLOB fields to LONGBLOB in DecodingParameters #1463
    • Fix PositionGroup.fetch_position_info() returning empty DataFrame when merge IDs are fetched in non-chronological order #1471
    • Separate ClusterlessDecodingV1 to tri-part make #1467
    • BREAKING: Remove intervals dimension from decoding results. Results from multiple intervals are now concatenated along the time dimension with an interval_labels coordinate to track interval membership. This eliminates NaN padding and reduces memory usage. See migration guide above.
    • Fix fetching position df in SortedSpikesDecodingV1.get_ahead_behind_distance() #1540

  • LFP

    • LFPBandV1: fix bug that inserted LFP times instead of LFP band times #1482
    • Update artifact detection algorithms to return times #1553

  • Position

    • Ensure video files are properly added to DLCProject # 1367
    • DLC parameter handling improvements and default value corrections #1379
    • Fix ingestion nwb files with position objects but no spatial series #1405
    • Ignore percent_frames when using limit in DLCPosVideo #1418
    • Increase DLCProject.config_path length #1534

  • Spikesorting

    • Implement short-transaction SpikeSortingRecording.make for v0 #1338
    • Fix FigURLCuration.make. Postpone fetch of unhashable items #1505
    • Improve get_recording efficiency #1522
    • Raise error if FigURLCurationSelection finds no curation label #1531
    • Allow CurationV1 to save without any spikes #1533

0.5.5 (Aug 6, 2025)

Infrastructure

  • Ensure merge tables are declared during file insertion #1205
  • Update URL for DANDI Docs #1210
  • Add common method get_position_interval_epoch #1056
  • Improve cron job documentation and script #1226, #1241, #1257, #1328
  • Update export process to include ~external tables #1239
  • Only add merge parts to source_class_dict if present in codebase #1237
  • Remove cli module #1250
  • Fix column error in check_threads method #1256
  • Export python env and store in newly created analysis files #1270
  • Enforce single table entry in fetch1_dataframe calls #1270
  • Add recompute ability for SpikeSortingRecording for both v0 and v1 #1093, #1311, #1340
  • Track Spyglass version in dedicated table for enforcing updates #1281
  • Pin to datajoint>=0.14.4 for dj.Top and long make call fix #1281
  • Remove outdated code comments #1304
  • Add code coverage badge, and increase position coverage #1305, #1315
  • Force TableChain to follow shortest path #1356

Documentation

  • Add documentation for custom pipeline #1281
  • Add developer note on initializing hatch #1281
  • Add concrete example for long-distance restrictions #1361

Pipelines

  • Common
    • Default AnalysisNwbfile.create permissions are now 777 #1226
    • Make Nwbfile.fetch_nwb functional # 1256
    • Calculate mode of timestep size in log scale when estimating sampling rate #1270
    • Ingest all ImageSeries objects in nwb file to VideoFile #1278
    • Allow ingestion of multi-row task epoch tables #1278
    • Add SensorData to populate_all_common #1281
    • Add fetch1_dataframe to SensorData #1291
    • Allow storage of numpy arrays using AnalysisNwbfile.add_nwb_object #1298
    • IntervalList.fetch_interval now returns Interval object #1293, #1357
    • Correct name parsing in Session.Experimenter insertion #1306
    • Allow insert with dio events but no e-series data #1318
    • Prompt user to verify compatibility between new insert and existing table entries # 1318, #1350
    • Skip empty timeseries ingestion (PositionSource, DioEvents) #1347
  • Position
    • Allow population of missing PositionIntervalMap entries during population of DLCPoseEstimation #1208
    • Enable import of existing pose data to ImportedPose in position pipeline #1247
    • Change key value position_source to "imported" during ingestion #1270
    • Define orientation as nan for single-led data #1270
    • Sanitize new project names for unix file system #1247
    • Add arg to return percent below threshold in get_subthresh_inds #1304, #1305
    • Accept imported timestamps defined by rate and start_time #1322
    • Fix bug preventing DLC config updates #1352
  • Spikesorting
    • Fix compatibility bug between v1 pipeline and SortedSpikesGroup unit filtering #1238, #1249
    • Speedup get_sorting on CurationV1 #1246
    • Add cleanup for v0.SpikeSortingRecording #1263
    • Revise cleanup for v0.SpikeSorting #1271
    • Fix type compatibility of time_slice in SortedSpikesGroup.fetch_spike_data #1261
    • Update transaction and parallel make settings for v0 and v1 SpikeSorting tables #1270
    • Disable make transactionsfor CuratedSpikeSorting #1288
    • Refactor SpikeSortingOutput.get_restricted_merge_ids #1304
    • Add burst merge curation #1209
    • Reconcile spikeinterface value for channel_id when channel_name column present in nwb file electrodes table #1310, #1334
    • Ensure matching order of returned merge_ids and nwb files in SortedSpikesGroup.fetch_spike_data #1320
  • Behavior
    • Implement pipeline for keypoint-moseq extraction of behavior syllables #1056
  • LFP
    • Implement ImportedLFP.make() for ingestion from nwb files #1278
    • Adding a condition in the MAD detector to replace zero, NaN, or infinite MAD values with 1.0. #1280
    • Refactoring the creation of LFPElectrodeGroup with added input validation and transactional insertion. #1280, #1302
    • Updating the LFPBandSelection logic with comprehensive validation and batch insertion for electrodes and references. #1280
    • Implement ImportedLFP.make() for ingestion from nwb files #1278, #1302
    • Skip empty timeseries ingestion for ImportedLFP #1347

0.5.4 (December 20, 2024)

Infrastructure

  • Disable populate transaction protection for long-populating tables #1066, #1108, #1172, #1187
  • Add docstrings to all public methods #1076
  • Update DataJoint to 0.14.2 #1081
  • Remove AnalysisNwbfileLog #1093
  • Allow restriction based on parent keys in Merge.fetch_nwb() #1086, #1126
  • Import datajoint.dependencies.unite_master_parts -> topo_sort #1116, #1137, #1162
  • Fix bool settings imported from dj config file #1117
  • Allow definition of tasks and new probe entries from config #1074, #1120, #1179
  • Enforce match between ingested nwb probe geometry and existing table entry #1074
  • Update DataJoint install and password instructions #1131
  • Fix dandi upload process for nwb's with video or linked objects #1095, #1151
  • Minor docs fixes #1145
  • Add Nwb hashing tool #1093
  • Test fixes
    • Remove stored hashes from pytests #1152
    • Remove mambaforge from tests #1153
    • Remove debug statement #1164
    • Add testing for python versions 3.9, 3.10, 3.11, 3.12 #1169
    • Initialize tables in pytests #1181
    • Download test data without credentials, trigger on approved PRs #1180
    • Add coverage of decoding pipeline to pytests #1155
  • Allow python < 3.13 #1169
  • Remove numpy version restriction #1169
  • Merge table delete removes orphaned master entries #1164
  • Edit merge_fetch to expect positional before keyword arguments #1181
  • Allow part restriction SpyglassMixinPart.delete #1192
  • Move cleanup of IntervalList orphan entries to cron job cleanup process #1195
  • Add mixin method get_fully_defined_key #1198

Pipelines

  • Common

    • Drop SessionGroup table #1106
    • Improve electrodes import efficiency #1125
    • Fix logger method call in common_task #1132
    • Export fixes #1164
      • Allow get_abs_path to add selection entry. #1164
      • Log restrictions and joins. #1164
      • Check if querying table inherits mixin in fetch_nwb. #1192, #1201
      • Ensure externals entries before adding to export. #1192
    • Error specificity in LabMemberInfo #1192

  • Decoding

    • Fix edge case errors in spike time loading #1083
    • Allow fetch of partial key from DecodingParameters #1198
    • Allow data fetching with partial but unique key #1198

  • Linearization

    • Add edge_map parameter to LinearizedPositionV1 #1091

  • Position

    • Fix video directory bug in DLCPoseEstimationSelection #1103
    • Restore #973, allow DLC without position tracking #1100
    • Minor fix to DLCCentroid make function order #1112, #1148
    • Video creator tools:
      • Pass output path as string to cv2.VideoWriter #1150
      • Set DLCPosVideo default processor to matplotlib, remove support for open-cv #1168
      • VideoMaker class to process frames in multithreaded batches #1168, #1174
      • TrodesPosVideo updates for matplotlib processor #1174
    • User prompt if ambiguous insert in DLCModelSource #1192

  • Spike Sorting

    • Fix bug in get_group_by_shank #1096
    • Fix bug in _compute_metric #1099
    • Fix bug in insert_curation returned key #1114
    • Add fields to SpikeSortingRecording to allow recompute #1093
    • Fix handling of waveform extraction sparse parameter #1132
    • Limit Artifact detection intervals to valid times #1196

0.5.3 (August 27, 2024)

Infrastructure

  • Create class SpyglassGroupPart to aid delete propagations #899
  • Fix bug report template #955
  • Add rollback option to populate_all_common #957, #971
  • Add long-distance restrictions via << and >> operators. #943, #969
  • Fix relative pathing for mkdocstring-python=>1.9.1. #967, #968
  • Add method to export a set of files to Dandi. #956
  • Add fetch_nwb fallback to stream files from Dandi. #956
  • Clean up old TableChain.join call in mixin delete. #982
  • Add pytests for position pipeline, various test_mode exceptions #966
  • Migrate pip dependencies from environment.ymls to pyproject.toml #966
  • Add documentation for common error messages #997
  • Expand delete_downstream_merge -> delete_downstream_parts. #1002
  • cautious_delete now ...
    • Checks IntervalList and externals tables. #1002
    • Ends early if called on empty table. #1055
  • Allow mixin tables with parallelization in make to run populate with processes > 1 #1001, #1052, #1068
  • Speed up fetch_nwb calls through merge tables #1017
  • Allow ModuleNotFoundError or ImportError for optional dependencies #1023
  • Ensure integrity of group tables #1026
  • Convert list of LFP artifact removed interval list to array #1046
  • Merge duplicate functions in decoding and spikesorting #1050, #1053, #1062, #1066, #1069
  • Reivise docs organization.
    • Misc -> Features/ForDevelopers. #1029
    • Installation instructions -> Setup notebook. #1029
  • Migrate SQL export tools to utils to support exporting DandiPath #1048
  • Add tool for checking threads for metadata locks on a table #1063
  • Use peripheral tables as fallback in TableChains #1035
  • Ignore non-Spyglass tables during descendant check for part_masters #1035

Pipelines

  • Common

    • PositionVideo table now inserts into self after make #966
    • Don't insert lab member when creating lab team #983
    • Files created by AnalysisNwbfile.create() receive new object_id #999
    • Remove unused ElectrodeBrainRegion table #1003
    • Files created by AnalysisNwbfile.create() receive new object_id #999, #1004
    • Remove redundant calls to tables in populate_all_common #870
    • Improve logging clarity in populate_all_common #870
    • PositionIntervalMap now inserts null entries for missing intervals #870
    • AnalysisFileLog now truncates table names that exceed field length #1021
    • Disable logging with AnalysisFileLog #1024
    • Remove common_ripple schema #1061

  • Decoding:

    • Default values for classes on ImportError #966
    • Add option to upsample data rate in PositionGroup #1008
    • Avoid interpolating over large nan intervals in position #1033
    • Minor code calling corrections #1073

  • Position

    • Allow dlc without pre-existing tracking data #973, #975
    • Raise KeyError for missing input parameters across helper funcs #966
    • DLCPosVideo table now inserts into self after make #966
    • Remove unused PositionVideoSelection and PositionVideo tables #1003
    • Fix SQL query error in DLCPosV1.fetch_nwb #1011
    • Add keyword args to all calls of convert_to_pixels #870
    • Unify make_video logic across DLCPosVideo and TrodesVideo #870
    • Replace OutputLogger context manager with decorator #870
    • Rename check_videofile -> find_mp4 and get_video_path -> get_video_info to reflect actual use #870
    • Fix red_led_bisector np.nan handling issue from #870. Fixed in #1034
    • Fix one_pt_centoid np.nan handling issue from #870. Fixed in #1034

  • Spikesorting

    • Allow user to set smoothing timescale in SortedSpikesGroup.get_firing_rate #994
    • Update docstrings #996
    • Remove unused UnitInclusionParameters table from spikesorting.v0 #1003
    • Fix bug in identification of artifact samples to be zeroed out in spikesorting.v1.SpikeSorting #1009
    • Remove deprecated dependencies on kachery_client #1014
    • Add UnitAnnotation table and naming convention for units #1027, #1052
    • Set sparse parameter to waveform extraction step in spikesorting.v1 #1039
    • Efficiency improvement to v0.Curation.insert_curation #1072
    • Add pytests for spikesorting.v1 #1078

0.5.2 (April 22, 2024)

Infrastructure

  • Refactor TableChain to include _searched attribute. #867
  • Fix errors in config import #882
  • Save current spyglass version in analysis nwb files to aid diagnosis #897
  • Add functionality to export vertical slice of database. #875
  • Add pynapple support #898
  • Update PR template checklist to include db changes. #903
  • Avoid permission check on personnel tables. #903
  • Add documentation for SpyglassMixin. #903
  • Add helper to identify merge table by definition. #903
  • Prioritize datajoint filepath entry for defining abs_path of analysis nwbfile #918
  • Fix potential duplicate entries in Merge part tables #922
  • Add logging of AnalysisNwbfile creation time and size #937
  • Fix error on empty delete call in merge table. #940
  • Add log of AnalysisNwbfile creation time, size, and access count #937, #941

Pipelines

  • Spikesorting
    • Update calls in v0 pipeline for spikeinterface>=0.99 #893
    • Fix method type of get_spike_times #904
    • Add helper functions for restricting spikesorting results and linking to probe info #910
  • Decoding
    • Handle dimensions of clusterless get_ahead_behind_distance #904
    • Fix improper handling of nwb file names with .strip #929

0.5.1 (March 7, 2024)

Infrastructure

  • Add user roles to database_settings.py. #832
  • Fix redundancy in waveforms_dir #857
  • Revise dj_chains to permit undirected paths for paths with multiple Merge Tables. #846

Pipelines

  • Common:
    • Add ActivityLog to common_usage to track unreferenced utilities. #870
  • Position:
    • Fixes to environment-dlc.yml restricting tensortflow #834
    • Video restriction for multicamera epochs #834
    • Fixes to _convert_mp4 #834
    • Replace deprecated calls to yaml.safe_load() #834
    • Refactoring to reduce redundancy #870
    • Migrate OutputLogger behavior to decorator #870
  • Spikesorting:
    • Increasespikeinterface version to >=0.99.1, <0.100 #852
    • Bug fix in single artifact interval edge case #859
    • Bug fix in FigURL #871
  • LFP
    • In LFPArtifactDetection, only apply referencing if explicitly selected #863

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