NeurodataWithoutBorders/pynwb: 4.2.0

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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

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