Latest (updated on 2024-12-19 18:12 UTC)

update extracellular electrophysiology tutorial (#2012)

* update filteredephys, decomp, spikeevent examples

* update CHANGELOG

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

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