Latest (updated on 2025-01-29 17:01 UTC)

update default mock_NWBFile start time (#2018)

* update default mock_NWBFile start time

* Update src/pynwb/testing/mock/file.py

Co-authored-by: Ryan Ly <[email protected]>

---------

Co-authored-by: Ben Dichter <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>

3.0.0rc1

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 pynwb.read_nwb convenience method to simplify reading an NWBFile written with any backend @h-mayorquin #1994
• 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

2.8.3

Enhancements and minor changes

• Made gain an optional argument for PatchClampSeries to match the schema. @stephprince #1975
• Added warning when writing files with NWBHDF5IO without the .nwb extension. @stephprince #1978
• Added NWBHDF5IO.read_nwb convenience method to simplify reading an NWB file. @h-mayorquin #1979
• Removed unused references to region references and builders in preparation for changes in HDMF 4.0. @rly #1991

Documentation and tutorial enhancements

• Added documentation example for SpikeEventSeries. @stephprince #1983
• Added documentation example for AnnotationSeries. @stephprince #1989
• Added documentation example for DecompositionSeries. @stephprince #1981

Performance

• Cache global type map to speed import 3X. @sneakers-the-rat #1931

Bug fixes

• Fixed bug in how ElectrodeGroup.__init__ validates its position argument. @oruebel #1770
• Changed SpatialSeries.reference_frame from required to optional as specified in the schema. @rly #1986

2.8.2

Enhancements and minor changes

• Added support for numpy 2.0. @mavaylon1 #1956
• Make get_cached_namespaces_to_validate a public function @stephprince #1961

Documentation and tutorial enhancements

• Added pre-release pull request instructions to release process documentation @stephprince #1928
• Added section on how to use the family driver in h5py for splitting data across multiple files @oruebel #1949

Bug fixes

• Fixed can_read method to return False if no nwbfile version can be found @stephprince #1934
• Changed epoch_tags to be a NWBFile property instead of constructor argument. @stephprince #1935
• Exposed option to not cache the spec in NWBHDF5IO.export. @rly #1959

2.8.1

Documentation and tutorial enhancements

• Simplified the introduction to NWB tutorial. @rly #1914
• Simplified the ecephys and ophys tutorials. #1915
• Add comments to src/pynwb/io/file.py to improve developer documentation. @rly #1925

Bug fixes

• Fixed use of channel_conversion in TimeSeries get_data_in_units. @rohanshah 1923

2.8.0

Enhancements and minor changes

• Set rate default value inside mock_ElectricalSeries to avoid having to set rate=None explicitly when passing timestamps. @h-mayorquin #1894
• Integrate validation through the TypeConfigurator. @mavaylon1 #1829
• Exposed aws_region to NWBHDF5IO. @rly #1903

Bug fixes

• Revert changes in PyNWB 2.7.0 that allow datetimes without a timezone and without a time while issues with DANDI upload of NWB files missing timezone are resolved. @rly #1908

2.7.0

PyNWB 2.7.0 (May 2, 2024)

Enhancements and minor changes

• Added bounds field to SpatialSeries to set optional boundary range (min, max) for each dimension of data. @mavaylon1 #1869
• Added support for NWB schema 2.7.0. See 2.7.0 release notes for details
• Deprecated ImagingRetinotopy neurodata type. @rly #1813
• Modified OptogeneticSeries to allow 2D data, primarily in extensions of OptogeneticSeries. @rly #1812
• Support stimulus_template as optional predefined column in IntracellularStimuliTable. @stephprince #1815
• Support NWBDataInterface and DynamicTable in NWBFile.stimulus. @rly #1842
• Added support for python 3.12 and upgraded dependency versions. This also includes infrastructure updates for developers. @mavaylon1 #1853
• Added grid_spacing, grid_spacing_unit, origin_coords, origin_coords_unit to ImagingPlane fields. @h-mayorquin #1892
• Added mock_Units for generating Units tables. @h-mayorquin #1875 and #1883
• Allow datetimes without a timezone and without a time. @rly #1886
• No longer automatically set the timezone to the local timezone when not provided. #1886
• Updated testing to not install in editable mode and not run coverage by default. #1897

Bug fixes

• Fix bug with reading file with linked TimeSeriesReferenceVectorData @rly #1865
• Fix bug where extra keyword arguments could not be passed to NWBFile.add_{x}_column for use in custom VectorData classes. @rly #1861

2.6.0

PyNWB 2.6.0 (February 21, 2024)

Enhancements and minor changes

• For NWBHDF5IO(), change the default of arg load_namespaces from False to True. @bendichter #1748
• Add NWBHDF5IO.can_read(). @bendichter #1703
• Add pynwb.get_nwbfile_version(). @bendichter #1703
• Fix usage of the validate function in the pynwb.testing.testh5io classes and cache the spec by default in those classes. @rly #1782
• Updated timeseries data checks to warn instead of error when reading invalid files. @stephprince #1793 and #1809
• Expose the offset, conversion and channel conversion parameters in mock_ElectricalSeries. @h-mayorquin #1796
• Expose starting_time in mock_ElectricalSeries. @h-mayorquin #1805
• Enhance get_data_in_units() to work with objects that have a channel_conversion attribute like the ElectricalSeries. @h-mayorquin #1806
• Refactor validation CLI tests to use {sys.executable} -m coverage to use the same Python version and run correctly on Debian systems. @yarikoptic #1811
• Fixed tests to address newly caught validation errors. @rly #1839

Bug fixes

• Fix bug where namespaces were loaded in "w-" mode. @h-mayorquin #1795
• Fix bug where pynwb version was reported as "unknown" to readthedocs @stephprince #1810
• Fixed bug to allow linking of TimeSeries.data by setting the data constructor argument to another TimeSeries. @oruebel #1766
• Fix recursion error in html representation generation in jupyter notebooks. @stephprince #1831

Documentation and tutorial enhancements

• Add RemFile to streaming tutorial. @bendichter #1761
• Fix typos and improve clarify throughout tutorials. @zm711 #1825
• Fix internal links in docstrings and tutorials. @stephprince #1827
• Add Zarr IO tutorial @bendichter #1834

2.5.0

pynwb 2.5.0

2.4.0

PyNWB 2.4.0 (July 23, 2023)

Enhancements and minor changes

• Add support for ExternalResources. @mavaylon1 #1684
• Update links for making a release. @mavaylon1 #1720

Bug fixes

• Fixed sphinx-gallery setting to correctly display index in the docs with sphinx-gallery>=0.11. @oruebel #1733

Documentation and tutorial enhancements

• Added thumbnail for Optogentics tutorial. @oruebel #1729
• Update and fix errors in tutorials. @bendichter @oruebel