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

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

2.2.0

PyNWB 2.2.0 (October 19, 2022)

Enhancements and minor changes

• Enhanced pynwb.validate API function to accept a list of file paths as well as the ability to operate on cached
  namespaces. Also adjusted the validate CLI to directly use the API function. @CodyCBakerPhD
  #1511

Internal enhancements

• Moved CI to GitHub Actions. @rly #1560,
  #1566

Bug fixes

• Fixed bug in pynwb.testing.mock.file.mock_NWBFile to identifier UUID to string. @oruebel
  #1557
• Minor fixes to test suite to prevent warnings. @rly
  #1571
• Made build wheel python 3 only. @mavaylon1
  #1572
• Updated README.rst. @mavaylon1
  #1573

2.1.1

PyNWB 2.1.1 (September 1, 2022)

Documentation and tutorial enhancements:

• Added support for explicit ordering of sphinx gallery tutorials in the docs. @oruebel
  #1504, @bdichter
  #1495
• Added developer guide on how to create a new tutorial. @oruebel
  #1504
• Added images tutorial. @weiglszonja
  #1470
• Added example code for fsspec in the streaming tutorial. @bdichter
  #1499
• Add voxel_mask tutorial. @CodyCBakerPhD (#1544)

Enhancements and minor changes

• Updated coverage workflow, report separate unit vs integration coverage. @rly
  #1509
• Deleted test files generated from running sphinx gallery examples. @rly
  #1517
• Enabled passing an S3File created through s3fs, which provides a method for reading an NWB file directly
  from s3 that is an alternative to ros3. This required relaxing of NWBHDF5IO input validation. The path
  arg is not needed if file is provided. mode now has a default value of "r".
  @bendichter
  #1499
• Added a method to NWBMixin that only raises an error when a check is violated on instance creation,
  otherwise throws a warning when reading from a file. The new checks in ImageSeries when external_file
  is provided is used with this method to ensure that that files with invalid data can be read, but prohibits
  the user from creating new instances when these checks are violated. @weiglszonja
  #1516
• Created a GitHub Actions workflow to generate test files for testing backward compatibility. @rly
  #1548
• Updated requirements, including allowing numpy 1.23. @rly
  #1550
• Enhanced docs for LabMetaData to clarify its usage. @oruebel
  #1546
• Add testing/mock, which provides mock neurodata objects for testing. @bendichter
  #1454