Implement data types from NWBEP001 by rly · Pull Request #2156 · NeurodataWithoutBorders/pynwb

rly · 2026-01-10T09:16:40Z

Motivation

Add new data types TimestampVectorData, DurationVectorData, EventsTable from NWBEP001.
Fix [Feature]: Implement NWBEP001 #2155
See Implement NWBEP001 (add EventsTable and more) nwb-schema#645
Dependent on new nwb schema release

How to test the behavior?

pytest

Checklist

Did you update CHANGELOG.md with your changes?
Have you checked our Contributing document?
Have you ensured the PR clearly describes the problem and the solution?
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Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

codecov · 2026-01-10T09:17:53Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.18%. Comparing base (a2d1efa) to head (75f052f).

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #2156      +/-   ##
==========================================
+ Coverage   95.10%   95.18%   +0.07%     
==========================================
  Files          29       30       +1     
  Lines        2943     2991      +48     
  Branches      443      444       +1     
==========================================
+ Hits         2799     2847      +48     
  Misses         86       86              
  Partials       58       58

Flag	Coverage Δ
integration	`73.05% <86.79%> (+0.20%)`	⬆️
unit	`85.59% <100.00%> (+0.23%)`	⬆️

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rly · 2026-01-10T09:19:09Z

~~TODO handle deprecations from NWBEP001:~~
~~- Deprecate the use of "instantaneous" for TimeSeries/data.continuity.~~
~~- Deprecate BehavioralEvents in favor of placing EventsTable tables in NWBFile/events.~~
~~- Deprecate AnnotationSeries in favor of creating an EventsTable with an annotation column.~~

rly · 2026-01-27T17:42:22Z

After discussion with @oruebel and @bendichter , we decided to not deprecate the "instantaneous" value for TimeSeries/data.continuity and instead make it a suggested best practice that is checked in the nwbinspector. I will make the change in nwb-schema and explain the rationale there.

Updated the docstring to clarify that timestamps are in seconds from the session start time and removed the default description.

Remove default description from DurationVectorData and update tests to always provide description, encouraging users to document their data. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

…Events/AnnotationSeries deprecation Bump nwb-schema submodule to nwbep001 (78af15e), which restores "instantaneous" as a valid TimeSeries.continuity value and recommends EventsTable instead. Switch BehavioralEvents and AnnotationSeries deprecations to warn on new instances and pass silently during read, via a new _warn_on_new_pass_on_construct helper. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Replace TODO placeholders with runnable EventsTable snippets: reward delivery events (with a custom amount column) in plot_behavior.py and video-scored behaviors (using the built-in duration and annotation columns) in plot_file.py. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

…ies to PR #2156 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

…n doc Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Pass meanings_tables (added in HDMF 5.1.0) through the docval of every DynamicTable subclass that already forwarded target_tables, so users can attach a MeaningsTable when constructing these tables. SweepTable is skipped because it is deprecated. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Adds export-roundtrip and file validation coverage via the standard testing mixin. Edge-case tests remain as plain TestCase methods. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

… CHANGELOG to 4.0.0 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

rly · 2026-04-14T08:08:35Z

Migration from ndx-events will be addressed in a separate PR.

Bump nwb-schema submodule to d69eba1 and mirror the new doc wording on the Python side. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

oruebel · 2026-04-20T19:00:20Z

 )
+behavior_events.add_event(timestamp=10.2, duration=1.4, annotation="grooming")
+behavior_events.add_event(timestamp=18.7, duration=0.6, annotation="rearing")
+behavior_events.add_event(timestamp=25.0, duration=2.1, annotation="grooming")


This can be a separate issue, but this seems like a great place to also introduce a Meanings table to define what "grooming" and "rearing" means.

oruebel

Overall, the PR looks good to me.

It looks like this PR also introduces MeaningsTable to PyNWB. While MeaningsTable is really an addition in HDMF, updating the nwb-schema also ends up exposing that change in NWB. For this it would be useful to:

Mention important changes (e.g., MeaningsTable) that have propagated from HDMF into the NWB schema also in the CHANGELOG (or at the very least point to where those additional changes are described)
Include MeaningsTable also in the tutorials in PyNWB. EventsTable seems like a great example use-case for MeaningsTable

rly requested a review from oruebel January 13, 2026 18:49

rly requested a review from bendichter January 27, 2026 17:27

bendichter reviewed Jan 27, 2026

View reviewed changes

Comment thread src/pynwb/event.py Outdated

rly marked this pull request as ready for review January 27, 2026 17:42