3.1.0

Breaking changes

• Removed unused functions prepend_string and _not_parent in core.py, _not_parent in file.py, and NWBBaseTypeMapper.get_nwb_file in io/core.py @oruebel #2036

Enhancements and minor changes

• Added support for NWB Schema 2.9.0.
  • Added BaseImage and ExternalImage as new neurodata types. The first so both Image and ExternalImage can inherit from it. The second to store external images. @rly #2079
  • Added new ElectrodesTable neurodata type. @mavaylon1 #1890
  • Formally defined and renamed ElectrodeTable as the ElectrodesTable neurodata type. @mavaylon1 #1890
  • Formally defined bands within DecompositionSeries as the neurodatatype FrequencyBandsTable. @mavaylon1 @rly #2063
  • Added new DeviceModel neurodata type to store device model information. @rly #2088
  • Deprecated Device.model_name, Device.model_number, and Device.manufacturer fields in favor of DeviceModel. @rly #2088
  • Added support for 2D EventDetection.source_index to indicate [time_index, channel_index]. @stephprince #2091
  • Made EventDetection.times optional. @stephprince #2091
  • Deprecated EventDetection.times. @stephprince #2101
• Automatically add timezone information to timestamps reference time if no timezone information is specified. @stephprince #2056
• Added option to disable typemap caching and updated type map cache location. @stephprince #2057
• Added dictionary-like operations directly on ProcessingModule objects (e.g., len(processing_module)). @bendichter #2020
• When an external file is detected when initializing an ImageSeries and no format is provided, automatically set format to "external" instead of raising an error. @stephprince #2060
• Added mask_type option to mock_PlaneSegmentation. @pauladkisson #2067
• Improved the documentation of the spike_times in the Units table methods @h-mayorquin #2085
• Removed core namespace warning unless cached version is newer. @stephprince #2077
• Bumped minimum HDMF version to 4.1.0. @stephprince #2077

Bug fixes

• Fixed add_data_interface functionality that was mistakenly removed in PyNWB 3.0. @stephprince #2052
• Fixed bug in IntracellularRecordingsTable.__init__ were IntracellularResponsesTable wasn't created correctly when custom category tables were provided @oruebel. #2031
• Fixed shape check in SpikeEventSeries.__init__ to support AbstractDataChunkIterator for timestamps/data. @oruebel #2031
• Added unit tests to enhance coverage of core.py, image.py, spec.py, icephys.py, epoch.py and others. @oruebel #2031
• Fixed missing IndexSeries.indexed_images. @rly #2074
• Fixed missing __nwbfields__ and _fieldsname for NWBData and its subclasses. @rly #2082
• Fixed caching of the type map when using HDMF 4.1.0. @rly #2087
• Removed use of complex numbers in scratch tutorial because of incompatibilities with HDMF 4.1.0. @stephprince #2090
• Made ImagingPlane.description optional to conform with the NWB Schema. @rly #2051

Documentation and tutorial enhancements

• Added NWB AI assistant to the home page of the documentation. @magland #2076