2.1.0

PyNWB 2.1.0 (July 6, 2022)

Breaking changes:

• Updated TimeIntervals to use the new TimeSeriesReferenceVectorData type. This does not alter the overall
  structure of TimeIntervals in a major way aside from changing the value of the neurodata_type attribute of the
  TimeIntervals.timeseries column from VectorData to TimeSeriesReferenceVectorData. This change facilitates
  creating common functionality around TimeSeriesReferenceVectorData. For NWB files with version 2.4.0 and earlier,
  the TimeIntervals.timeseries column is automatically migrated on read in the TimeIntervalsMap
  object mapper class to use the TimeSeriesReferenceVectorData container class, so that users are presented a
  consistent API for existing and new files. This change affects all existing TimeIntervals tables
  e.g., NBWFile.epochs, NWBFile.trials, and NWBFile.invalid_times. While this is technically a breaking
  change, the impact user codes should be minimal as this change primarily adds functionality while the overall
  behavior of the API is largely consistent with existing behavior. @oruebel, @rly (#1390)

Enhancements and minor changes

• A warning is now raised if SpatialSeries.data has more than 3 columns. @bendichter, @rly (#1455, #1480)
• The arguments x, y, z, imp, location, filtering are no longer required in the electrodes table.
  @h-mayorquin, @rly (#1448)
• Added cell_id attribute to IntracellularElectrode. @bendichter (#1459)
• Added offset field to TimeSeries and its subtypes. @CodyCBakerPhD (#1424)
• Added support for NWB 2.5.0.
  • Added support for updated IndexSeries type, new order_of_images field in Images, and new neurodata_type
    ImageReferences. @rly (#1483)
• Added support for HDMF 3.3.1. This is now the minimum version of HDMF supported. Importantly, HDMF 3.3 introduces
  warnings when the constructor of a class mapped to an HDMF-common data type or an autogenerated data type class
  is passed positional arguments instead of all keyword arguments. @rly (#1484)
• Moved logic that checks the 0th dimension of TimeSeries data equals the length of timestamps to a private method in the
  TimeSeries class. This is to avoid raising a warning when an ImageSeries is used with external file.
  @weiglszonja (#1486)
• Improved warning text when dimensions are not matched in TimeSeries, ElectricalSeries, and RoiResponseSeries.
  @rly (#1491)

Documentation and tutorial enhancements:

• Added tutorial on annotating data via TimeIntervals. @oruebel (#1390)
• Added copy button to code blocks. @weiglszonja (#1460)
• Created behavioral tutorial. @weiglszonja (#1464)
• Enhanced display of icephys pandas tutorial by using dataframe_image to render and display large tables
  as images. @oruebel (#1469)
• Created tutorial about reading and exploring an existing NWBFile. @weiglszonja (#1453)
• Added new logo for PyNWB. @oruebel (#1461)
• Minor text fixes. @oruebel @bendichter (#1443, #1462, #1463, #1466, #1472, #1473)

Bug fixes:

• Fixed input data types to allow only float for fields conversion and offset in definition of
  TimeSeries. @CodyCBakerPhD (#1424)
• Fixed incorrect warning in RoiResponseSeries.__init__ about mismatch between the second dimension of data and
  the length of rois. @rly (#1491)