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Recent Releases of spyglass-neuro

spyglass-neuro - 0.5.5

What's Changed

  • Update URL for DANDI Docs by @kabilar in https://github.com/LorenFrankLab/spyglass/pull/1210
  • Ensure merge tables declared in new database by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1205
  • Fix missing pos interval map entry in pose estimation by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1208
  • Miscellaneous Fixes by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1220
  • Maintenance tool revision by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1226
  • Fix the bug for computing quality metrics in spikesorting v0 by @sytseng in https://github.com/LorenFrankLab/spyglass/pull/1212
  • Spike group v1 label compatability by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1238
  • Resolve different code and database state for merge table parts by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1237
  • Add email-on-fail to cron job by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1241
  • Export external tables by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1239
  • Moseq Pipeline by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1056
  • Import pose by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1225
  • Revert "Import pose" by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1245
  • Speedup get_sorting by @edeno in https://github.com/LorenFrankLab/spyglass/pull/1246
  • Fix filtering on labels by @edeno in https://github.com/LorenFrankLab/spyglass/pull/1249
  • Remove cli module by @edeno in https://github.com/LorenFrankLab/spyglass/pull/1250
  • Small fixes by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1256
  • Import pose edited by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1247
  • Add script for drive space check by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1257
  • Update jupysync by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1266
  • Fix mismatch in time_slice typing in SortedSpikesGroup.fetch_spike_data by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1261
  • Add v0.SpikeSortingRecording.cleanup by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1263
  • Revise cleanup scripts by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1271
  • Quickfix: Turn off transactions for CuratedSpikeSorting by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1288
  • Quickfix: spikesorting vo usetransaction by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1290
  • Misc old issues by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1281
  • Add fetch1_dataframe to sensor data by @edeno in https://github.com/LorenFrankLab/spyglass/pull/1291
  • Generalizations for nwb ingestion by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1278
  • LFP improvements by @edeno in https://github.com/LorenFrankLab/spyglass/pull/1280
  • Store arrays in AnalysisNwbfile by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1298
  • LFP Import fix by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1302
  • Cut down TODOs, part 1: 57 -> 43 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1304
  • Allow recompute via _make_file func by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1093
  • Add badge to tests README by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1305
  • Interval as object carries functions by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1293
  • Burst merge curation by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1209
  • Quickfix: Parse name for Session.Experimenter by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1306
  • Fix call to 'upper' in common_behav.py by @sophie-robertson in https://github.com/LorenFrankLab/spyglass/pull/1314
  • Fix recompute update_id by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1311
  • Spikeinterface channel_id ambiguity by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1310
  • Generate timestamps from rate and start time by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1322
  • Returned mergeid consistency for Merge.fetchnwb by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1320
  • Cleanup Update: exit on fail to chmod by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1328
  • Fix spikeinterface channel names by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1334
  • Import generalizations by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1318
  • DLC updates by @emreybroyles in https://github.com/LorenFrankLab/spyglass/pull/1339
  • adding function for plotting specific interval lists side by side by @gshvarts in https://github.com/LorenFrankLab/spyglass/pull/1330
  • Minor Issues by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1270
  • Add permissions to GitHub Actions workflows by @edeno in https://github.com/LorenFrankLab/spyglass/pull/1344
  • Skip empty timestamp objs by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1347
  • Improve position coverage by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1315
  • Fix DataJoint query errors with NaN values in probe geometry fields by @Copilot in https://github.com/LorenFrankLab/spyglass/pull/1346
  • Report table name in accept_divergence by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1350
  • Update kwargs in DLC config by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1352
  • Table chains cascade shortest path #1353 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1356
  • Allow return of Interval obj from to_indices method by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1357
  • More recompute fixes by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1340
  • Add long-distance example to doc by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1361
  • Bump version by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1316

New Contributors

  • @kabilar made their first contribution in https://github.com/LorenFrankLab/spyglass/pull/1210 🥳
  • @sytseng made their first contribution in https://github.com/LorenFrankLab/spyglass/pull/1212 🥳
  • @sophie-robertson made their first contribution in https://github.com/LorenFrankLab/spyglass/pull/1314 🥳
  • @gshvarts made their first contribution in https://github.com/LorenFrankLab/spyglass/pull/1330 🥳
  • @Copilot made their first contribution in https://github.com/LorenFrankLab/spyglass/pull/1346

Database Changes

To update your database to reflect these changes, we recommend running the following script. If you have any issues, please contact maintainers via our Discussions page.

```python

-- For TrackGraph --

from spyglass.linearization.v1.main import TrackGraph # noqa

TrackGraph.alter() # Add edge map parameter

-- For dropping deprecated tables --

import datajoint as dj

dj.FreeTable(dj.conn(), "commonnwbfile.analysisnwbfilelog").drop() dj.FreeTable(dj.conn(), "commonsession.session_group").drop()

-- For v0 recompute --

from spyglass.spikesorting.v0.spikesorting_recording import ( SpikeSortingRecording, SpikeSortingRecordingSelection, IntervalList, )

SpikeSortingRecording().alter() SpikeSortingRecording().update_ids()

-- For v1 recompute --

from spyglass.spikesorting.v1.recording import ( SpikeSortingRecording, SpikeSortingRecordingSelection, AnalysisNwbfile, )

SpikeSortingRecording().alter() SpikeSortingRecording().update_ids()

-- For LFP pipeline --

from spyglass.lfp.lfpimported import ImportedLFP from spyglass.lfp.lfpmerge import LFPOutput

if len(ImportedLFP()) or len(LFPOutput.ImportedLFP()): raise ValueError( "Existing entries found and would be dropped in update. Please delete " + "entries or start a GitHub discussion for migration assistance." + f"\nImportedLFP: {len(ImportedLFP())}" + f"\nLFPOutput.ImportedLFP: {len(LFPOutput.ImportedLFP())}" )

table = LFPOutput().ImportedLFP() tablename = table.fulltable_name

if len(droplist := table.connection.dependencies.descendants(tablename)) > 1: droplist = [x for x in droplist if x != tablename] raise ValueError( "Downstream tables exist and would be dropped in update." + "Please drop the following tables first: \n" + "\n ".join([str(t) for t in droplist]) )

LFPOutput().ImportedLFP().drop_quick() ImportedLFP().drop() ```

Full Changelog: https://github.com/LorenFrankLab/spyglass/compare/0.5.4...0.5.5

- Jupyter Notebook
Published by edeno 7 months ago

spyglass-neuro - 0.5.4

What's Changed

  • Allow disable transaction for select populates by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1067
  • Prevent error from unitless spike group by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1083
  • Add tests for spikesorting by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1078
  • Add docstrings by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1076
  • Bump dj dependency to 0.14.2 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1081
  • Fix #1094 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1096
  • Fix 1080 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1099
  • Add edge map parameter to track linearization by @edeno in https://github.com/LorenFrankLab/spyglass/pull/1091
  • Fix #1098 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1100
  • Fix #1101 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1103
  • Remove SessionGroup by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1106
  • Adjust no-transact pop hashing mechanism by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1108
  • Add objects to analysis file before insert by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1112
  • Apply restrictions on parent tables in fetch_nwb by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1086
  • Revise datajoint import name by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1116
  • Fix Curation primary key creation from spikesorting key by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1114
  • NWB ingestion fixes by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1074
  • speed up electrodes import by @magland in https://github.com/LorenFrankLab/spyglass/pull/1125
  • Switch to or logic when multiple merge ids in restriction by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1126
  • Fix null config_tasks value by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1120
  • Add password setting instruction to setup notebook by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1131
  • Fix waveform params in metric curation by @edeno in https://github.com/LorenFrankLab/spyglass/pull/1132
  • Convert string config settings to bool by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1117
  • Long distance restr fix by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1137
  • Update README.md to fix link by @bendichter in https://github.com/LorenFrankLab/spyglass/pull/1140
  • Update UsingNWB.md to fix typo by @bendichter in https://github.com/LorenFrankLab/spyglass/pull/1141
  • #1138, #1139 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1145
  • Update UsingNWB.md to fix task location in NWB file by @bendichter in https://github.com/LorenFrankLab/spyglass/pull/1143
  • Quickfix: typo in adding objects to nwb by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1148
  • Dandi export fixes by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1095
  • Fix test badge by @edeno in https://github.com/LorenFrankLab/spyglass/pull/1149
  • Additional export fixes by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1151
  • Remove stored hashes from tests by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1152
  • Remove mambaforge from tests by @edeno in https://github.com/LorenFrankLab/spyglass/pull/1153
  • DLC make_video minor fixes by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1150
  • Fix topological sort logic by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1162
  • Fix tests by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1165
  • Allow python <3.13 and remove numpy pin by @edeno in https://github.com/LorenFrankLab/spyglass/pull/1169
  • No transact insert v0 lfp by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1172
  • DLCPosVideo: Use provided epoch, multithread matplotlib by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1168
  • Expand Export logging abilities by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1164
  • No transact bug by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1178
  • VideoMaker trodes fixes and resume from fail by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1174
  • Quickfix: pass config_probe by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1179
  • Fix failing tests by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1181
  • No-credential data download by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1180
  • No transactions v0 spikesorting pipeline by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1187
  • Add pytests for decoding pipeline by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1155
  • Limit spikesorting artifacts to valid timestamps by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1196
  • Misc fixes by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1192
  • Decoding qol updates by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1198
  • Cleanup IntervalList orphans in weekly job only by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1195
  • fetch_nwb non-mixin compatability by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1201
  • Release 0.5.4 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1199

New Contributors

  • @bendichter made their first contribution in https://github.com/LorenFrankLab/spyglass/pull/1140

Full Changelog: https://github.com/LorenFrankLab/spyglass/compare/0.5.3...0.5.4

- Jupyter Notebook
Published by edeno about 1 year ago

spyglass-neuro - 0.5.3

Database Changes

This release (a) removes the old 'common' ripple pipeline in favor of the dedicated subpackage (see #1061), and (b) edits the definitions of PositionIntervalMap and PositionGroup (see #870, #1008). Users with existing databases should run the following:

```python import datajoint as dj from spyglass.common.common_behav import PositionIntervalMap from spyglass.decoding.v1.core import PositionGroup

dj.schema("common_ripple").drop() PositionIntervalMap.alter() PositionGroup.alter() ```

Software Changes

  • Add system requirements and typical installation time by @edeno in https://github.com/LorenFrankLab/spyglass/pull/945
  • Group part delete propagation by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/899
  • Fix bug report template html by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/955
  • QuickFix: Bug in curation v0 make by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/960
  • Fix tests/doc build by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/967
  • Fix relative pathing for mkdocstrings>=1.9.1 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/968
  • Long distance restrictions by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/949
  • Transaction on populate_all_common by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/957
  • Permit multiple restrict_by by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/969
  • Allow dlc pipeline to run without prior position tracking by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/970
  • Revert "Allow dlc pipeline to run without prior position tracking" by @edeno in https://github.com/LorenFrankLab/spyglass/pull/972
  • Fix test fails related to #957 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/971
  • Allow dlc pipeline to run without prior position tracking by @edeno in https://github.com/LorenFrankLab/spyglass/pull/973
  • Cleanup of dlc video by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/975
  • Replace old join call with cascade by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/982
  • Check existence of optional fields during Electrode table population by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/985
  • Add pytests to position by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/966
  • Don't insert lab member when creating lab team by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/983
  • Add ability to set smoothing sigma in getfiringrate by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/994
  • Add docstrings to SortedSpikesGroup and Decoding methods by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/996
  • Add Common Errors doc by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/997
  • Mua notebook by @denissemorales in https://github.com/LorenFrankLab/spyglass/pull/998
  • Dandi export and read by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/956
  • Minor fixes by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/999
  • Fix bug in change in analysisfile objectid by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1004
  • Remove classes for usused tables by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1003
  • Non-daemon parallel populate by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1001
  • Give UUID to artifact interval by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/993
  • Fix artifact list_triggers by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/1009
  • remove problem key in DLCPosV1 fetch_nwb attrs by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1011
  • Tidy position by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/870
  • Prevent delete orphans by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1002
  • Remove kachery_client dependency by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1014
  • Add upsampling option to PositionGroup by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1008
  • Implement adding data from config file by @calderast in https://github.com/LorenFrankLab/spyglass/pull/934
  • Fix broken link to Clusterless Decoding tutorial notebook from Sorted Spikes Decoding tutorial notebook by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/1018
  • #980 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1021
  • #1016 - Allow ModuleNotFoundError by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1023
  • Merge table efficiency by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1017
  • Disable AnalysisFile logging by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1024
  • Group integrity by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1026
  • Bugfixes from 870 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1034
  • Spike Unit Annotation by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1027
  • Reduce duplication 1 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1050
  • quick fix for issue 1045 by @MichaelCoulter in https://github.com/LorenFrankLab/spyglass/pull/1046
  • Quick fix for parralel populate and spike unit naming by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1052
  • Set sparse=False during waveform extraction by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/1039
  • Re-organize docs by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1029
  • Fix interpolation of nans in decoding position by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1033
  • Export updates by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1048
  • Revise getgroupby_shank by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1055
  • Remove common_ripple by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1061
  • Reduce duplication 2 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1053
  • #1053 bugfix by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1062
  • Spikesort artifact fixes by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1069
  • Add check threads util by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1063
  • fix fetch efficiency in insert_curation by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1072
  • Decode fixes by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/1073
  • Ban tables in distance restrict bugfix by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1066
  • Periph table fallback on TableChain for experimenter summary by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/1035

New Contributors

  • @calderast made their first contribution in https://github.com/LorenFrankLab/spyglass/pull/934

Full Changelog: https://github.com/LorenFrankLab/spyglass/compare/0.5.2...0.5.3

- Jupyter Notebook
Published by CBroz1 over 1 year ago

spyglass-neuro - 0.5.2

What's Changed

  • Bump version number by @edeno in https://github.com/LorenFrankLab/spyglass/pull/864
  • Fix failing chains pytests by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/867
  • Hhmi notebook check by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/876
  • Refine query of upstream tables on FigURL populate by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/871
  • Fix dlc video and kachery cloud config by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/882
  • Edits for docs by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/883
  • Hhmi notebook check by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/888
  • Update call to gettemplateextremum by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/893
  • Add spyglass version to created analysis nwb files by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/897
  • Quickfix: Change existing source script to spyglass version by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/900
  • Add pynapple support by @edeno in https://github.com/LorenFrankLab/spyglass/pull/898
  • Hot fixes for clusterless get_ahead_behind_distance and get_spike_times by @edeno in https://github.com/LorenFrankLab/spyglass/pull/904
  • Quickfix for fetch_nwb by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/913
  • Check for entry in merge part table prior to insert by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/922
  • Kachery fixes by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/918
  • Quickfix for removal of old kachery tables by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/925
  • Fix improper uses of strip by @edeno in https://github.com/LorenFrankLab/spyglass/pull/929
  • Misc Issues by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/903
  • Export logger by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/875
  • Spikesorting quality of life helpers by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/910
  • Add logging of AnalysisNwbfile creation time and file size by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/937
  • Log when file accessed by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/941
  • Fix bug on empty delete in merge table by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/940

Full Changelog: https://github.com/LorenFrankLab/spyglass/compare/0.5.1...0.5.2

- Jupyter Notebook
Published by edeno almost 2 years ago

spyglass-neuro - 0.5.1

What's Changed

  • Only apply include labels filter if include_labels not empty by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/827
  • gh-actions docs fixes by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/828
  • Proposed structure for user roles. by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/832
  • Fix test for update of position tools by @edeno in https://github.com/LorenFrankLab/spyglass/pull/835
  • Fix notebook name by @edeno in https://github.com/LorenFrankLab/spyglass/pull/840
  • Multicam DLC project support by @emreybroyles, @samuelbray32, @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/834
  • fix CuratedSpikeSorting insert with no curation by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/856
  • Revise dj_chains for table -> merge -> merge downstream deletes by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/846
  • Artifact interval bug by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/859
  • Pytests round 2 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/851
  • Update spike sorting V1 code and notebook to run sorters other than mountainsort4 by @donghoon-shin in https://github.com/LorenFrankLab/spyglass/pull/844
  • Make use of waveforms_dir consistent by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/857
  • Update spikeinterface version by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/852
  • Fix non-referencing option in lfp artifact detection by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/863

New Contributors

  • @donghoon-shin made their first contribution in https://github.com/LorenFrankLab/spyglass/pull/844

Full Changelog: https://github.com/LorenFrankLab/spyglass/compare/0.5.0...0.5.1

See also CHANGELOG.md

- Jupyter Notebook
Published by edeno almost 2 years ago

spyglass-neuro - 0.5.0

What's Changed

  • Add error message for single-led with wrong parameters by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/680
  • positionVideo debug by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/687
  • Limited scope docs PR by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/690
  • Make artifact interval a 2d array by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/691
  • Implement pre-commit, refactor input validation by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/688
  • Linearizationv1 debug and tutorial by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/695
  • Mixin class by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/692
  • Changed SpyglassMixin to be imported from djmixin rather than djhel… by @sharon-chiang in https://github.com/LorenFrankLab/spyglass/pull/696
  • added Path library to imports by @sharon-chiang in https://github.com/LorenFrankLab/spyglass/pull/697
  • Spike sorting v1 pipeline by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/651
  • Change CurationV1.insert_metric_curation to include metric_curation_id in description field to faciliate provenance checking by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/704
  • Lfp band fixes by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/706
  • Make sampling rate for LFP user-defined instead of hard-coded to 1000 Hz by @sharon-chiang in https://github.com/LorenFrankLab/spyglass/pull/705
  • Delete downstream restriction fix by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/703
  • Prevent Curation from re-adding an existing sorting key with a new cu… by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/670
  • Dlc debug by @emreybroyles in https://github.com/LorenFrankLab/spyglass/pull/702
  • add removeexistingfolder argument by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/708
  • Add cautious delete mixin by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/711
  • Hotfix for attrib error __ -> _nwb_table_dict by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/714
  • Fix ref channel append error by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/720
  • Avoid bug in spikeinterface for low spikecounts by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/721
  • Change method of defining base dir in getabspath by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/715
  • Env variables for DLC by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/722
  • Add mkdir to pass pytests by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/723
  • Priority for fetch_nwb function in merge tables by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/724
  • Handle single intervals in spike sorting by @edeno in https://github.com/LorenFrankLab/spyglass/pull/726
  • Handle sortings in which no units are detected (SpikeSortingV1) by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/728
  • Helper function for adding data to kachery by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/729
  • V0 migration model, revised by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/717
  • print -> logger by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/730
  • #732 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/734
  • Add detail to sharing notebook by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/735
  • Check for upsampled data in trodes fetch dataframe by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/741
  • Remove logger.info() without message by @edeno in https://github.com/LorenFrankLab/spyglass/pull/747
  • Fix PositionOutput.fetch1_dataframe bug by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/746
  • Remove old delete method from SpikeSorting table of V0 pipeline by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/751
  • Move figurl_views to spike sorting v0 by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/750
  • Decoding pipeline by @edeno in https://github.com/LorenFrankLab/spyglass/pull/731
  • Interval list types by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/742
  • Dlc debug: smoothing_duration fix by @emreybroyles in https://github.com/LorenFrankLab/spyglass/pull/753
  • restrict get position info by session name by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/757
  • Restrict UnitWaveformFeaturesGroup and SortedSpikesGroup by nwbfilename by @edeno in https://github.com/LorenFrankLab/spyglass/pull/758
  • Fix the length of object_id for ImportedSpikeSorting by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/760
  • Fix SpikeSortingOutput getrecording and getsorting by @edeno in https://github.com/LorenFrankLab/spyglass/pull/761
  • Print session/exp summary, fix lfp target sample fetch by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/762
  • Update LFP notebook by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/764
  • Use PositionOutput to get data in example notebook by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/765
  • Comment out video section for mini-rec in Update 20PositionTrodes.ipynb by @edeno in https://github.com/LorenFrankLab/spyglass/pull/767
  • Handle numpy arrays in create_lfp_electrode_group by @edeno in https://github.com/LorenFrankLab/spyglass/pull/766
  • Pytest revamp by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/743
  • Minor decoding fixes by @edeno in https://github.com/LorenFrankLab/spyglass/pull/769
  • DLC notebooks 21 and 22 by @emreybroyles in https://github.com/LorenFrankLab/spyglass/pull/772
  • Docs fixes for decoding pipeline by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/776
  • Add new function to retrieve spatial series from NWB file by @khl02007 in https://github.com/LorenFrankLab/spyglass/pull/777
  • Add overview to docs by @edeno in https://github.com/LorenFrankLab/spyglass/pull/779
  • LFPV1 interval insert by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/775
  • Proofing and minor edits to Tutorial notebooks 11-32 by @samuelbray32 in https://github.com/LorenFrankLab/spyglass/pull/796
  • Update 01InsertData.ipynb by @magland in https://github.com/LorenFrankLab/spyglass/pull/802
  • Decoding pipeline edits for imported data by @edeno in https://github.com/LorenFrankLab/spyglass/pull/782
  • Blackify 24.1.1 by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/808
  • More robust delete_downstream_merge by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/806
  • Address join-compatibility issue for long chains by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/811
  • Filtering units for decoding by @edeno in https://github.com/LorenFrankLab/spyglass/pull/807
  • Cautious delete bugfixes by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/821
  • Revise dependencies by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/822
  • Minor decoding fixes by @edeno in https://github.com/LorenFrankLab/spyglass/pull/819
  • Update waveform_features.py by @MichaelCoulter in https://github.com/LorenFrankLab/spyglass/pull/813
  • Fault-permit insert and remove mutual exclusivity protections on Merge by @CBroz1 in https://github.com/LorenFrankLab/spyglass/pull/824
  • Update CITATION.cff by @edeno in https://github.com/LorenFrankLab/spyglass/pull/826

New Contributors

  • @sharon-chiang made their first contribution in https://github.com/LorenFrankLab/spyglass/pull/696 🎉
  • @emreybroyles made their first contribution in https://github.com/LorenFrankLab/spyglass/pull/702 🎉

Full Changelog: https://github.com/LorenFrankLab/spyglass/compare/0.4.3...0.5.0

See also CHANGELOG.md

- Jupyter Notebook
Published by edeno about 2 years ago