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

Latest (updated on 2024-05-03 00:05 UTC)

Update SpatialSeries to have bounds field (#1869)

Co-authored-by: Ryan Ly <rly@lbl.gov>

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

2.3.3

PyNWB 2.3.3 (June 26, 2023)

Enhancements and minor changes

• Add testing support for Python 3.11. @rly #1687
• Add CI testing of NWB files on DANDI. @rly #1695

Bug fixes

• Remove unused, deprecated codecov package from dev installation requirements. @rly
  #1688
• Remove references to discontinued requires.io service in documentation. @rly
  #1690
• Update requirements-doc.txt to resolve Python 3.7 incompatibility. @rly
  #1694
• Fixed test battery to show and check for warnings appropriately. @rly
  #1698

2.3.2

PyNWB 2.3.2 (April 10, 2023)

Enhancements and minor changes

• Fixed typos and added codespell GitHub action to check spelling in the future. @yarikoptic #1648

Documentation and tutorial enhancements

• Added OnePhotonSeries to calcium imaging tutorial. @bendichter #1658
• Add tutorial for optogenetics. @bendichter #1657
• Update testing of gallery examples and disable testing of the allensdk tutorial.
  #1680
• Updated tutorials to follow best practices. @bendichter #1656

Bug fixes

• Fixed bug when initializing OnePhotonSeries with no value for binning. @bendichter #1660
• Fixed bug in NWBHDF5IO.nwb_version property to support files written by third-party software with a fixed-length nwb_version attribute. @oruebel #1669
• Fixed search bar and missing jquery in ReadTheDocs documentation. @rly #1671
• Requires HDMF 3.5.4 which includes bug fixes. @rly #1672
• Fixed issue with deprecated pkg_resources. @rly #1678

2.3.1

PyNWB 2.3.1 (February 24, 2023)

Bug fixes

• Fixed an issue where NWB files with version "2.0b" could not be read.
  @rly #1651

2.3.0

PyNWB 2.3.0 (February 23, 2023)

Enhancements and minor changes

• Added support for NWB Schema 2.6.0. @mavaylon1 #1636
• Added a class and tests for the OnePhotonSeries new in NWB v2.6.0. @CodyCBakerPhD #1593(see also NWB Schema #523
• Subject.age can be input as a timedelta type. @bendichter #1590
• Added Subject.age__reference field. @bendichter (#1540)
• IntracellularRecordingsTable.add_recording: the electrode arg is now optional, and is automatically populated from the stimulus or response.
  #1597
• Added module pynwb.testing.mock.icephys and corresponding tests. @bendichter
  1595
• Removed redundant object mapper code. @rly #1600
• Fixed pending deprecations and issues in CI. @rly #1594
• Added NWBHDF5IO.nwb_version property to get the NWB version from an NWB HDF5 file @oruebel #1612
• Updated NWBHDF5IO.read to check NWB version before read and raise more informative error if an unsupported version is found @oruebel #1612
• Added the driver keyword argument to the pynwb.validate function as well as the corresponding namespace caching. @CodyCBakerPhD #1588
• Updated HDMF requirement to version 3.5.1. #1611
• Increased the stacklevel of the warning from _add_missing_timezone in pynwb.file to make identification of which datetime field is missing a timezone easier. @CodyCBakerPhD #1641

Documentation and tutorial enhancements:

• Adjusted ecephys tutorial to create fake data with proper dimensions @bendichter #1581
• Refactored testing documentation, including addition of section on pynwb.testing.mock submodule. @bendichter
  #1583
• Updated round trip tutorial to the newer NWBH5IOMixin and AcquisitionH5IOMixin classes. @bendichter
  #1586
• Added more informative error message for common installation error. @bendichter, @rly
  #1591
• Updated citation for PyNWB in docs and duecredit to use the eLife NWB paper. @oruebel #1604
• Fixed docs build warnings due to use of hardcoded links. @oruebel #1604
• Updated the iterative write tutorial to reference the new GenericDataChunkIterator functionality and use the new H5DataIO.dataset property to simplify the custom I/O section. @oruebel #1633
• Updated the parallel I/O tutorial to use the new H5DataIO.dataset feature to set up an empty dataset for parallel write. @oruebel #1633

Bug fixes

• Added shape constraint to PatchClampSeries.data. @bendichter
  #1596
• Updated the images tutorial to provide example usage of an IndexSeries
  with a reference to Images. @bendichter #1602
• Fixed an issue with the tox tool when upgrading to tox 4. @rly #1608
• Fixed an issue where Images were not allowed as stimulus templates. @rly #1638