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@nwb-bot nwb-bot released this 19 May 18:30
· 330 commits to dev since this release
1.5.0
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rly Ryan Ly
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Learn about vigilant mode.
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Learn about vigilant mode.

New features:

  • NWBFile.add_scratch(...) and ScratchData.__init__(...) now accept scalar data in addition to the currently
    accepted types. @rly (#1309)
  • Support pathlib.Path paths when opening files with NWBHDF5IO. @dsleiter (#1314)
  • Use HDMF 2.5.1. See the HDMF release notes for details.
  • Support driver='ros3' in NWBHDF5IO for streaming NWB files directly from s3. @bendichter (#1331)
  • Update documentation, CI GitHub processes. @oruebel @yarikoptic, @bendichter, @TomDonoghue, @rly
    (#1311, #1336, #1351, #1352, #1345, #1340, #1327)
  • Set default neurodata_type_inc for NWBGroupSpec, NWBDatasetSpec. @rly (#1295)
  • Block usage of h5py 3+ for now. h5py>=2.9, <3 is supported. (#1355)
  • Fix incompatibility issue with downstream github-release tool used to deploy releases to GitHub. @rly (#1245)
  • Fix issue with Sphinx gallery. @rly
  • Add citation information to documentation and support for duecredit tool. @rly
  • Remove use of ColoredTestRunner for more readable verbose test output. @rly
  • Add support for nwb-schema 2.3.0. @rly (#1245, #1330)
    • Add optional waveforms column to the Units table.
    • Add optional strain field to Subject.
    • Add to DecompositionSeries an optional DynamicTableRegion called source_channels.
    • Add to ImageSeries an optional link to Device.
    • Add optional continuity field to TimeSeries.
    • Add optional filtering attribute to ElectricalSeries.
    • Clarify documentation for electrode impedance and filtering.
    • Set the stimulus_description for IZeroCurrentClamp to have the fixed value "N/A".
    • See https://nwb-schema.readthedocs.io/en/latest/format_release_notes.html for full schema release notes.
  • Add support for HDMF 2.5.5 and upgrade HDMF requirement from 2.1.0 to 2.5.5. @rly @ajtritt
    (#1325, #1355, #1360, #1245, #1287). This includes several relevant features and bug fixes, including:
    • Fix issue where dependencies of included types were not being loaded in namespaces / extensions.
    • Add HDF5IO.get_namespaces(path=path, file=file) method which returns a dict of namespace name mapped to the
      namespace version (the largest one if there are multiple) for each namespace cached in the given HDF5 file.
    • Add methods for automatic creation of MultiContainerInterface classes.
    • Add ability to specify a custom class for new columns to a DynamicTable that are not VectorData,
      DynamicTableRegion, or VocabData using DynamicTable.__columns__ or DynamicTable.add_column(...).
    • Add support for creating and specifying multi-index columns in a DynamicTable using add_column(...).
    • Add capability to add a row to a column after IO.
    • Add method AbstractContainer.get_fields_conf.
    • Add functionality for storing external resource references.
    • Add method hdmf.utils.get_docval_macro to get a tuple of the current values for a docval_macro, e.g., 'array_data'
      and 'scalar_data'.
    • DynamicTable can be automatically generated using get_class. Now the HDMF API can read files with extensions
      that contain a DynamicTable without needing to import the extension first.
    • Add EnumData type for storing data that comes from a fixed set of values.
    • Add AlignedDynamicTable type which defines a DynamicTable that supports storing a collection of subtables.
    • Allow np.bool_ as a valid bool dtype when validating.
    • See https://github.com/hdmf-dev/hdmf/releases for full HDMF release notes.
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