ci: bump pynwb from 4.1.0 to 4.2.0 in /+tests

[dependabot]

Bumps pynwb from 4.1.0 to 4.2.0.

Release notes

Sourced from pynwb's releases.

4.2.0

Changed

• The array-valued fields TimeSeries.control and control_description, ImageSeries.dimension and starting_frame, TwoPhotonSeries.field_of_view, AbstractFeatureSeries.features and feature_units, Clustering.peak_over_rms, and ClusterWaveforms.waveform_mean and waveform_sd accept zarr arrays. They no longer accept non-array iterables such as str, set, range, and generators. @​rly #2235
• TimeSeries.get_timestamps raises a ValueError when timestamps must be generated but the number of samples in the data cannot be determined. @​rly #2235
• Added support for NWB Schema 2.11.0
  • The unit attribute of Units.waveform_mean, Units.waveform_sd, and Units.waveforms now has a default value of "volts" instead of a fixed value of "volts".
  • Units.waveform_mean, Units.waveform_sd, and Units.waveforms have a new optional time_before_peak_in_ms attribute, exposed as the waveform_time_before_peak_in_ms argument and field of Units. It holds the time, in milliseconds, from the start of each waveform to the spike peak, i.e., the alignment point used during spike sorting. @​rly #2237
  • Incorporates HDMF Common Schema 1.10.0, which changes MeaningsTable.target from a link to an object-reference attribute. @​rly #2244
• Raised the minimum HDMF requirement to 6.2.0, which bundles the HDMF Common Schema 1.10.0 required by NWB Schema 2.11.0. @​rly #2244

Added

• Added a section to the "How to Configure Term Validations" tutorial showing how to populate a HERD from the fields that a loaded type configuration wraps with a TermSetWrapper. @​oruebel #2251
• Added model and serial_number parameters to mock_Device. Passing a DeviceModel as model together with an nwbfile also places that DeviceModel in the NWBFile, so the link resolves when the file is written. @​rly #2238

Fixed

• Fixed FeatureExtraction.times and Clustering.peak_over_rms being copied into a Python list on construction, which was slow for data read from a file. @​cboulay #2253
• Fixed ElectricalSeries.__init__, TimeSeries.get_timestamps, and TimeSeries.num_samples failing on data backed by a zarr array. @​rly #2235
• Fixed TimeSeries.num_samples returning None when the data or timestamps are backed by a DataChunkIterator that wraps an array. @​rly #2235
• Fixed Units.waveform_unit having no effect on the written file. It is now written to the unit attribute of the waveform_mean, waveform_sd, and waveforms columns, and still defaults to "volts". Reading a file whose waveform columns carry different unit or sampling_rate attributes now warns, since Units keeps a single value for each. @​rly #2237
• Fixed mock_DeviceModel defaulting manufacturer to None. The mock now defaults it to "manufacturer". @​HugoFara #2232
• Fixed reading a file whose dates carry a sub-minute UTC offset (e.g. 1900-10-01T00:00:00-05:50:36). @​h-mayorquin #2230
• Fixed wide pandas DataFrames in the tutorials spilling out of the content column and into the right margin. @​bendichter #2236
• Fixed the experimenter check in the "Annotating Multiple Streamed NWB Files with a Single HERD" example testing for "Chen, Tsai-Wen" while dandiset 000015 stores "Tsai-Wen Chen", so the ORCID reference was never added. The example also streams the first 5 assets of the dandiset rather than all 210. @​rly #2246
• Fixed set_data_io being silently ignored on NWBData subclasses (GrayscaleImage, RGBImage, RGBAImage, ExternalImage, ImageReferences, and ScratchData), so requested chunking and compression were dropped. @​h-mayorquin #2233
• Fixed ImageSeries (and its subclasses) writing a derived num_samples dataset that the user never set. @​adityasingh2400 #2239
• Fixed OpticalSeries, OnePhotonSeries, and TwoPhotonSeries not accepting num_samples, which made them impossible to construct with format="external" and rate. @​rly #2248
• Fixed ImageSeries.num_samples returning None instead of len(timestamps) for an external-file series timed with timestamps, which also made get_starting_time and get_duration return None. @​rly #2250
• Fixed TimeSeriesReference.timestamps returning incorrect times for a TimeSeries that has starting_time and rate instead of timestamps. @​h-mayorquin @​rly #2245

Changelog

Sourced from pynwb's changelog.

PyNWB 4.2.0 (September 2, 2026)

Changed

• The array-valued fields TimeSeries.control and control_description, ImageSeries.dimension and starting_frame, TwoPhotonSeries.field_of_view, AbstractFeatureSeries.features and feature_units, Clustering.peak_over_rms, and ClusterWaveforms.waveform_mean and waveform_sd accept zarr arrays. They no longer accept non-array iterables such as str, set, range, and generators. @​rly #2235
• TimeSeries.get_timestamps raises a ValueError when timestamps must be generated but the number of samples in the data cannot be determined. @​rly #2235
• Added support for NWB Schema 2.11.0
  • The unit attribute of Units.waveform_mean, Units.waveform_sd, and Units.waveforms now has a default value of "volts" instead of a fixed value of "volts".
  • Units.waveform_mean, Units.waveform_sd, and Units.waveforms have a new optional time_before_peak_in_ms attribute, exposed as the waveform_time_before_peak_in_ms argument and field of Units. It holds the time, in milliseconds, from the start of each waveform to the spike peak, i.e., the alignment point used during spike sorting. @​rly #2237
  • Incorporates HDMF Common Schema 1.10.0, which changes MeaningsTable.target from a link to an object-reference attribute. @​rly #2244
• Raised the minimum HDMF requirement to 6.2.0, which bundles the HDMF Common Schema 1.10.0 required by NWB Schema 2.11.0. @​rly #2244

Added

• Added a section to the "How to Configure Term Validations" tutorial showing how to populate a HERD from the fields that a loaded type configuration wraps with a TermSetWrapper. @​oruebel #2251
• Added model and serial_number parameters to mock_Device. Passing a DeviceModel as model together with an nwbfile also places that DeviceModel in the NWBFile, so the link resolves when the file is written. @​rly #2238

Fixed

• Fixed FeatureExtraction.times and Clustering.peak_over_rms being copied into a Python list on construction, which was slow for data read from a file. @​cboulay #2253
• Fixed ElectricalSeries.__init__, TimeSeries.get_timestamps, and TimeSeries.num_samples failing on data backed by a zarr array. @​rly #2235
• Fixed TimeSeries.num_samples returning None when the data or timestamps are backed by a DataChunkIterator that wraps an array. @​rly #2235
• Fixed Units.waveform_unit having no effect on the written file. It is now written to the unit attribute of the waveform_mean, waveform_sd, and waveforms columns, and still defaults to "volts". Reading a file whose waveform columns carry different unit or sampling_rate attributes now warns, since Units keeps a single value for each. @​rly #2237
• Fixed mock_DeviceModel defaulting manufacturer to None. The mock now defaults it to "manufacturer". @​HugoFara #2232
• Fixed reading a file whose dates carry a sub-minute UTC offset (e.g. 1900-10-01T00:00:00-05:50:36). @​h-mayorquin #2230
• Fixed wide pandas DataFrames in the tutorials spilling out of the content column and into the right margin. @​bendichter #2236
• Fixed the experimenter check in the "Annotating Multiple Streamed NWB Files with a Single HERD" example testing for "Chen, Tsai-Wen" while dandiset 000015 stores "Tsai-Wen Chen", so the ORCID reference was never added. The example also streams the first 5 assets of the dandiset rather than all 210. @​rly #2246
• Fixed set_data_io being silently ignored on NWBData subclasses (GrayscaleImage, RGBImage, RGBAImage, ExternalImage, ImageReferences, and ScratchData), so requested chunking and compression were dropped. @​h-mayorquin #2233
• Fixed ImageSeries (and its subclasses) writing a derived num_samples dataset that the user never set. @​adityasingh2400 #2239
• Fixed OpticalSeries, OnePhotonSeries, and TwoPhotonSeries not accepting num_samples, which made them impossible to construct with format="external" and rate. @​rly #2248
• Fixed ImageSeries.num_samples returning None instead of len(timestamps) for an external-file series timed with timestamps, which also made get_starting_time and get_duration return None. @​rly #2250
• Fixed TimeSeriesReference.timestamps returning incorrect times for a TimeSeries that has starting_time and rate instead of timestamps. @​h-mayorquin @​rly #2245

Commits

• 8676056 Prepare for release of PyNWB 4.2.0 (take two) (#2261)
• ddcbee3 Fix PyPI upload rejecting metadata 2.5 and gate it in CI (#2260)
• 00faa03 Prepare for release of PyNWB 4.2.0 (#2246)
• b5c3b81 Only write ImageSeries.num_samples when it was explicitly provided (#2239)
• f378275 Illustrate usage of add_ref_container in HERD tutorial (#2251)
• d1ad531 Store FeatureExtraction.times and Clustering.peak_over_rms as given, instead ...
• a4f0c96 Accept num_samples in OpticalSeries, OnePhotonSeries, and TwoPhotonSeries (#2...
• 7249083 Derive ImageSeries.num_samples from timestamps for external-file series (#2250)
• ff2e9dc Fix TimeSeriesReference.timestamps for series that store starting_time an...
• 7ea33bb Accept zarr arrays in array-valued fields and when determining data lengths (...
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[ehennestad]

Needs #859 - Support nwb-schema 2.11.0