3.0.0

Breaking changes

• The validation methods have been updated with multiple breaking changes. @stephprince #1911
  • The behavior of pynwb.validate(io=...) now matches the behavior of pynwb.validate(path=...). In previous pynwb versions, pynwb.validate(io=...) did not use the cached namespaces during validation. To obtain the same behavior as in previous versions, you can update the function call to pynwb.validate(io=..., use_cached_namespaces=False)
  • pynwb.validate will return only a list of validation errors instead of a tuple: (list of validation_errors, status code)
  • the pynwb.validate(path=...) argument has been added as a replacement for pynwb.validate(paths=[...]), which will be deprecated in a future major release #2024
  • The validate module has been renamed to validation.py. The validate method can be
    imported using import pynwb; pynwb.validate or from pynwb import validate

Deprecations

• The following deprecated classes will now raise errors when creating new instances of these classes: ClusteringWaveforms, Clustering, SweepTable. Reading files using these data types will continue to be supported.
• The following methods and arguments have been deprecated:
  • ProcessingModule.add_container and ProcessingModule.add_data_interface are replaced by ProcessingModule.add
  • ProcessingModule.get_container and ProcessingModule.get_data_interface are replaced by ProcessingModule.get
  • ScratchData.notes is deprecated. Use ScratchData.description instead.
  • NWBFile.ic_electrodes is deprecated. Use NWBFile.icephys_electrodes instead.
  • NWBFile.ec_electrodes is deprecated. Use NWBFile.electrodes instead.
  • NWBFile.icephys_filtering is deprecated. Use IntracellularElectrode.filtering instead.
  • NWBFile.modules is deprecated. Use NWBFile.processing instead.
  • ImageSeries.format is fixed to 'external' if an external file is provided.
  • ImageSeries.bits_per_pixel is deprecated.
  • ImagingPlane.manifold, ImagingPlane.conversion and ImagingPlane.unit are deprecated. Use ImagingPlane.origin_coords and ImagingPlane.grid_spacing instead.
  • IndexSeries.unit is fixed to "N\A".
  • IndexSeries.indexed_timeseries is deprecated. Use IndexSeries.indexed_images instead.
• The following deprecated methods have been removed:
  • NWBFile.add_ic_electrode is removed. Use NWBFile.add_icephys_electrode instead.
  • NWBFile.create_ic_electrode is removed. Use NWBFile.create_icephys_electrode instead.
  • NWBFile.get_ic_electrode is removed. Use NWBFile.get_icephys_electrode instead.
  • pynwb._get_resources is removed.

Enhancements and minor changes

• Added __all__ to modules. @bendichter #2021
• Added pynwb.read_nwb convenience method to simplify reading an NWBFile written with any backend @h-mayorquin #1994
• Constrained hdmf<5 to prevent future compatibility issues. #2040

Bug fixes

• Made distance, orientation, and field_of_view optional in OpticalSeries to match schema @bendichter #2023
• Added support for NWB schema 2.8.0. @rly #2001
  • Removed SpatialSeries.bounds field that was not functional. This will be fixed in a future release. @rly #1907, #1996
  • Added support for NWBFile.was_generated_by field. @stephprince #1924
  • Added support for model_number, model_name, and serial_number fields to Device. @stephprince #1997
  • Deprecated EventWaveform neurodata type. @rly #1940
  • Deprecated ImageMaskSeries neurodata type. @rly #1941
• Added enhancements to the validation CLI. @stephprince #1911
  • Added an entry point for the validation module. You can now use pynwb-validate "file.nwb".
  • Added the --json-outpath-path CLI argument to output validation results in a machine readable format.
• Removed python 3.8 support, added python 3.13 support. @stephprince #2007
• Added warnings when using positional arguments in Container constructor methods. Positional arguments will raise errors in the next major release. @stephprince #1972
• mock_ElectricalSeries. Make number of electrodes between data and electrode region agree when explicitly passing data @h-mayorquin #2019

Documentation and tutorial enhancements

• Updated SpikeEventSeries, DecompositionSeries, and FilteredEphys examples. @stephprince #2012
• Replaced deprecated scipy.misc.face dataset in the images tutorial with another example. @stephprince #2016
• Removed Allen Brain Observatory example which was unnecessary and difficult to maintain. @rly #2026