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