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:

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

New Contributors

• @calderast made their first contribution in #934

Full Changelog: 0.5.2...0.5.3

0.5.2

What's Changed

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

Full Changelog: 0.5.1...0.5.2

0.5.1

What's Changed

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

New Contributors

• @donghoon-shin made their first contribution in #844

Full Changelog: 0.5.0...0.5.1

See also CHANGELOG.md

0.5.0

What's Changed

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

New Contributors

• @sharon-chiang made their first contribution in #696 🎉
• @emreybroyles made their first contribution in #702 🎉

Full Changelog: 0.4.3...0.5.0

See also CHANGELOG.md