CHANGELOG.md

PyNWB Changelog

PyNWB 2.8.3 (Upcoming)

Enhancements and minor changes

• 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

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

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

PyNWB 2.8.2 (September 9, 2024)

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

PyNWB 2.8.1 (July 3, 2024)

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

PyNWB 2.8.0 (May 28, 2024)

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

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

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

PyNWB 2.5.0 (August 18, 2023)

Enhancements and minor changes

• Added TimeSeries.get_timestamps(). @bendichter #1741
• Added TimeSeries.get_data_in_units(). @bendichter #1745
• Updated ExternalResources name change to HERD, along with HDMF 3.9.0 being the new minimum. @mavaylon1 #1754

Documentation and tutorial enhancements

• Updated streaming tutorial to ensure code is run on tests and clarify text. @bendichter #1760 @oruebel #1762
• Fixed minor documentation build warnings and broken links to basic_trials tutorial @oruebel #1762

PyNWB 2.4.1 (July 26, 2023)

• Stop running validation tests as part of integration tests. They cause issues in CI and can be run separately. @rly #1740

PyNWB 2.4.0 (July 23, 2023)

Enhancements and minor changes

• Added support for ExternalResources. @mavaylon1 #1684
• Updated 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
• Updated and fixed errors in tutorials. @bendichter @oruebel

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

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

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

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

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

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

PyNWB 2.1.0 (July 6, 2022)

Breaking changes:

• Updated TimeIntervals to use the new TimeSeriesReferenceVectorData type. This does not alter the overall structure of TimeIntervals in a major way aside from changing the value of the neurodata_type attribute of the TimeIntervals.timeseries column from VectorData to TimeSeriesReferenceVectorData. This change facilitates creating common functionality around TimeSeriesReferenceVectorData. For NWB files with version 2.4.0 and earlier, the TimeIntervals.timeseries column is automatically migrated on read in the TimeIntervalsMap object mapper class to use the TimeSeriesReferenceVectorData container class, so that users are presented a consistent API for existing and new files. This change affects all existing TimeIntervals tables e.g., NBWFile.epochs, NWBFile.trials, and NWBFile.invalid_times. While this is technically a breaking change, the impact user codes should be minimal as this change primarily adds functionality while the overall behavior of the API is largely consistent with existing behavior. @oruebel, @rly (#1390)

Enhancements and minor changes

• A warning is now raised if SpatialSeries.data has more than 3 columns. @bendichter, @rly (#1455, #1480)
• The arguments x, y, z, imp, location, filtering are no longer required in the electrodes table. @h-mayorquin, @rly (#1448)
• Added cell_id attribute to IntracellularElectrode. @bendichter (#1459)
• Added offset field to TimeSeries and its subtypes. @codycbakerphd (#1424)
• Added support for NWB 2.5.0.
  • Added support for updated IndexSeries type, new order_of_images field in Images, and new neurodata_type ImageReferences. @rly (#1483)
• Added support for HDMF 3.3.1. This is now the minimum version of HDMF supported. Importantly, HDMF 3.3 introduces warnings when the constructor of a class mapped to an HDMF-common data type or an autogenerated data type class is passed positional arguments instead of all keyword arguments. @rly (#1484)
• Moved logic that checks the 0th dimension of TimeSeries data equals the length of timestamps to a private method in the TimeSeries class. This is to avoid raising a warning when an ImageSeries is used with external file. @weiglszonja (#1486)
• Improved warning text when dimensions are not matched in TimeSeries, ElectricalSeries, and RoiResponseSeries. @rly (#1491)

Documentation and tutorial enhancements:

• Added tutorial on annotating data via TimeIntervals. @oruebel (#1390)
• Added copy button to code blocks. @weiglszonja (#1460)
• Created behavioral tutorial. @weiglszonja (#1464)
• Enhanced display of icephys pandas tutorial by using dataframe_image to render and display large tables as images. @oruebel (#1469)
• Created tutorial about reading and exploring an existing NWBFile. @weiglszonja (#1453)
• Added new logo for PyNWB. @oruebel (#1461)
• Minor text fixes. @oruebel @bendichter (#1443, #1462, #1463, #1466, #1472, #1473)

Bug fixes:

• Fixed input data types to allow only float for fields conversion and offset in definition of TimeSeries. @codycbakerphd (#1424)
• Fixed incorrect warning in RoiResponseSeries.__init__ about mismatch between the second dimension of data and the length of rois. @rly (#1491)

PyNWB 2.0.1 (March 16, 2022)

Bug fixes:

• Added environment-ros3.yml to MANIFEST.in for inclusion in source distributions. @rly (#1398)
• Fixed bad error check in IntracellularRecordingsTable.add_recording when adding IZeroClampSeries. @oruebel (#1410)
• Skipped ros3 tests if internet access or the ros3 driver are not available. @oruebel (#1414)
• Fixed CI issues. @rly (#1427)

Documentation and tutorial enhancements:

• Enhanced ordering of sphinx gallery tutorials to use alphabetic ordering based on tutorial headings. @oruebel (#1399)
• Updated the general tutorial to add documentation about the Images type. @bendichter (#1353)
• Updated the main index of the documentation to make the documentation easier to navigate. @oruebel (#1402)
• Merged the "NWB File" overview section with the "NWB File Basics" tutorial. @oruebel (#1402)
• Updated and created separated installation instructions for users and developers . @oruebel (#1402)
• Updated the Extracellular electrophysiology tutorial. @bendichter, @weiglszonja (#1391)
• Extended the general tutorial with more data types (e.g., Subject, SpatialSeries, Position). @weiglszonja (#1403)
• Improved constructor docstrings for Image types. @weiglszonja (#1418)
• Added documentation for exporting NWB files. @rly (#1417)
• Improved documentation formatting. @bendichter (#1438)
• Minor text fixes. @bendichter (#1437, #1400)

Minor improvements:

• Improved constructor docstrings for Image types. @weiglszonja (#1418)
• Added checks for data orientation in TimeSeries, ElectricalSeries, and RoiResponseSeries @bendichter (#1428)
• Added checks for data orientation in TimeSeries, ElectricalSeries, and RoiResponseSeries. @bendichter (#1426)
• Enhanced issue template forms on GitHub. @CodyCBakerPHD (#1434)

PyNWB 2.0.0 (August 13, 2021)

Breaking changes:

• SweepTable has been deprecated in favor of the new icephys metadata tables. Use of SweepTable is still possible but no longer recommended. @oruebel (#1349)
• TimeSeries.__init__ now requires the data argument because the 'data' dataset is required by the schema. If a TimeSeries is read without a value for data, it will be set to a default value. For most TimeSeries, this is a 1-dimensional empty array with dtype uint8. For ImageSeries and DecompositionSeries, this is a 3-dimensional empty array with dtype uint8. @rly (#1274)
• TimeSeries.__init__ now requires the unit argument because the 'unit' attribute is required by the schema. If a TimeSeries is read without a value for unit, it will be set to a default value. For most TimeSeries, this is "unknown". For IndexSeries, this is "N/A" according to the NWB 2.4.0 schema. @rly (#1274)

New features:

• Added new intracellular electrophysiology hierarchical table structure from ndx-icephys-meta to NWB core. This includes the new types TimeSeriesReferenceVectorData, IntracellularRecordingsTable, SimultaneousRecordingsTable, SequentialRecordingsTable, RepetitionsTable and ExperimentalConditionsTable as well as corresponding updates to NWBFile to support interaction with the new tables. @oruebel (#1349)
• Added support for NWB 2.4.0. See Release Notes for more details. @oruebel, @rly (#1349)
• Dropped Python 3.6 support, added Python 3.9 support. @rly (#1377)
• Updated requirements to allow compatibility with HDMF 3 and h5py 3. @rly (#1377)
  • When using HDMF 3 and h5py 3, users can now stream NWB files from an S3 bucket.

Tutorial enhancements:

• Added new tutorial for intracellular electrophysiology to describe the use of the new metadata tables and declared the previous tutorial using SweepTable as deprecated. @oruebel (#1349)
• Added new tutorial for querying intracellular electrophysiology metadata (docs/gallery/domain/plot_icephys_pandas.py). @oruebel (#1349, #1383)
• Added thumbnails for tutorials to improve presentation of online docs. @oruebel (#1349)
• Used sphinx.ext.extlinks extension in docs to simplify linking to common targets. @oruebel (#1349)
• Created new section for advanced I/O tutorials and moved parallel I/O tutorial to its own file. @oruebel (#1349)
• Overhauled documentation on extensions. @bendichter, @rly, @oruebel (#1350)
• Updated the optical physiology / Calcium imaging tutorial. @bendichter, @weiglszonja (#1375)
• Added a tutorial on streaming using the ROS3 driver. @rly (#1393)

Minor new features:

• Added RRID for citing PyNWB to the docs. @oruebel (#1372)
• Updated CI and tests to handle deprecations in libraries. @rly (#1377)
• Added test utilities for icephys (pynwb.testing.icephys_testutils) to ease creation of test data for tests and tutorials. @oruebel (#1349, #1383)
• Added on-push and nightly tests of streaming using the ROS3 driver. @rly (#1393)
  • These tests make use of a new dandiset for testing the API: https://gui.dandiarchive.org/#/dandiset/000126
• Improve documentation and test for CorrectedImageStack, MotionCorrection. @rly, @bendichter (#1306, #1374)

Bug fixes:

• Updated behavior of make clean command for docs to ensure tutorial files are cleaned up. @oruebel (#1349)
• Enforced electrode ID uniqueness during insertion into table. @CodyCBakerPhD (#1344)
• Fixed integration tests with invalid test data that will be caught by future hdmf validator version. @dsleiter, @rly (#1366, #1376)
• Fixed build warnings in docs. @oruebel (#1380)
• Fix intersphinx links in docs for numpy. @oruebel (#1386)
• Previously, the data argument was required in OpticalSeries.__init__ even though external_file could be provided in place of data. OpticalSeries.__init__ now makes data optional. However, this has the side effect of moving the position of data to later in the argument list, which may break code that relies on positional arguments for OpticalSeries.__init__. @rly (#1274)
• Fixed setup.py not being able to import versioneer when installing in an embedded Python environment. @ikhramts (#1395)
• Removed broken option to validate against a given namespace file and updated associated documentation. @rly (#1397)

PyNWB 1.5.1 (May 24, 2021)

Bug fixes:

• Raise minimum version of pandas from 0.23 to 1.0.5 to be compatible with numpy 1.20, and raise minimum version of HDMF to use the corresponding change in HDMF. @rly (#1363)
• Update documentation and update structure of requirements files. @rly (#1363)

PyNWB 1.5.0 (May 17, 2021)

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.

PyNWB 1.4.0 (August 12, 2020)

Users can now add/remove containers from a written NWB file and export the modified NWBFile to a new file path. @rly (#1280)

• See https://pynwb.readthedocs.io/en/stable/tutorials/general/add-remove-containers.html for examples and more information.

Compatibility warnings:

• PyNWB no longer works with HDMF version < 2.1.0. If you have pinned HDMF version < 2 in your package but allow PyNWB version 1.4.0, please beware that pip may install PyNWB version 1.4.0 with an incompatible version of HDMF (version < 2).
• Use of HDMF 2.1.0 fixes __getitem__-based access of MultiContainerInterface types, e.g,, fluorescence['roi_response_series_name'], where previously if the MultiContainerInterface contained only one item, then any key could be used within the square brackets to access the contained Container, even if the key did not match the name of the contained Container. This update patches this bug such that the key used within the square brackets must match the name of the contained Container or else an error will be raised.

Internal improvements:

• Update requirements to use HDMF 2.1.0. @rly (#1256)
• Start FAQ section in documentation. @rly (#1249)
• Improve deprecation warnings. @rly (#1261)
• Update CI to test Python 3.8, update requirements. @rly (#1267, #1275)
• Make use of MultiContainerInterface and LabelledDict that have been moved to HDMF. @bendichter @rly (#1260)

Bug fixes:

• For ImageSeries, add check if external_file is provided without starting_frame in __init__. @rly (#1264)
• Improve docstrings for TimeSeries.data and for the electrode table. @rly (#1271, #1272)
• Fix Azure Pipelines configuration. @rly (#1281)

PyNWB 1.3.3 (June 26, 2020)

Internal improvements:

• Update requirements to use HDMF 1.6.4. @rly (#1256)

Bug fixes:

• Fix writing optional args to electrodes table. @rly (#1246)
• Fix missing method UnitsMap.get_nwb_file. @rly (#1227)

PyNWB 1.3.2 (June 1, 2020)

Bug fixes:

• Add support for nwb-schema 2.2.5. @rly (#1243)
  • This schema version fixes incorrect dims and shape for ImagingPlane.origin_coords and ImagingPlane.grid_spacing, and fixes incorrect dims for TwoPhotonSeries.field_of_view.

PyNWB 1.3.1 (May 28, 2020)

Bug fixes:

• Fix bugged Device constructor. @rly (#1209)
• Fix link to code of conduct page in docs. @rly (#1229)
• Fix docs for get_type_map. @oruebel (#1233)
• Pass file object to parent when loading namespaces. @NileGraddis (#1242)

Internal improvements:

• Update CI to use supported MacOS version. @rly (#1211)
• Clean up tests to remove conversion warnings and use keyword args. @rly (#1202)
• Fix flake8 errors. @rly (#1235)
• Add changelog. @rly (#1215)
• Update release process with notes about coordinating with nwb-schema. @rly (#1214)
• Inform which unit value is actually overwritten. @yarikoptic (#1219)
• Do not print out logging.DEBUG statements to stdout for test.py. @rly (#1240)
• Add support for nwb-schema 2.2.4. @rly (#1213)
  • Make ImagingPlane.imaging_rate optional. This moves the imaging_rate argument down the list of constructor arguments for ImagingPlane.__init__. This will break existing code that calls the constructor of ImagingPlane with at least 6 positional arguments, such that one positional argument matches imaging_rate.

PyNWB 1.3.0 (Mar. 4, 2020)

New features:

• Add support for nwb-schema 2.2.2. @rly (#1146)
  • This is a large change. See the PR and schema release notes for more information.
• Validate against most specific namespace. @t-b, @rly (#1094)
• Replace 'ic_electrode' with 'icephys_electrode' in NWBFile. @oruebel (#1200)
• Integrate minor enhancements and bug fixes introduced in HDMF 1.6.0 and 1.6.1, including improved handling of namespaces that lack a version key,

Internal improvements:

• Add nightly testing of validation CLI. @t-b, @rly (#1164, #1195, #1197)
• Treat ipython notebooks as binary in git. @t-b (#1168)
• Use proper file removal in tests. @t-b (#1165)
• Use hdmf-docutils instead of nwb-docutils for documentation. @jcfr (#1176)
• Run minimum requirements testing n Python 3.6. @rly (#1194)

Bug fixes:

• Fix API documentation. @bendichter (#1159)
• Fix unit testing output. @rly (#1158)
• Fix copying files with Subject. @rly (#1171)
• Add "unit" attribute back as an optional attribute in icephys classes. @rly (#1188)
• Fix reported development status in setup.py. @rly (#1201)

PyNWB 1.2.1 (Jan. 22, 2020)

Bug fixes:

• Fix ReadTheDocs build. @rly (#1155)
• Update manifest to fix conda build. @rly (#1156)

PyNWB 1.2.0 (Jan. 21, 2020)

Minor enhancements:

• Add new logo to docs. @rly (#1096)
• Add warning when referencing electrode table before it exists. @ajtritt (#1098)
• Refactor internal calls to docval. @rly (#1104)
• Enhance icephys example and documentation. @t-b (#1081)
• Add multi index and time bounds to get_unit_spikes. @bendichter (#1001)
• Improve ophys docstrings. @bendichter (#1126)
• Improve icephys docstrings for gain. @bendichter (#1129)
• Update legal information. @rly (#1131)
• Add support for device description and manufacturer. @rly (#1135)
• Update dependencies and remove explicit six, unittest2 dependency. @rly (#1136, #1138, #1142, #1137, #1154)
• Add object ID tutorial. @rly (#1140)
• Update CI. @rly (#1141)
• Catch critical warnings and throw errors in unit tests. @rly (#1112)
• Create and use testing module, remove builder tests, clean up test code. @rly (#1117)
• Add and test minimum requirements for PyNWB. @rly (#1148)
• Improve docs for get_class. @bendichter (#1149)

Bug fixes:

• Fix versioneer reporting version. @rly (#1100)
• Fix DynamicTable import after move to hdmf.common. @bendichter (#1103)
• Fix handling of unmapped attributes. @rly (#1105)
• Update tests and documentation to reflect new selection behavior of DynamicTable. @oruebel (#1106)
• Fix reference images not being mapped in PlaneSegmentation. @rly (#1109)
• Fix legacy import of ObjectMapper. @rly (#1124)
• Fix extensions documentation typo: 'str' -> 'text'. @bendichter (#1132)
• Revert "PatchClampSeries: Force sweep_number to uint64". @t-b (#1123)
• Fix sphinx code to use latest sphinx. @rly (#1139)

PyNWB 1.1.2 (Oct. 15, 2019)

Minor features:

• Use latest HDMF 1.3.3. #1093 (@rly)
• Expose HDMF export_spec utility function for use by extensions. #1092 (@rly)

Bug fixes:

• Fix bug in writing SpikeEventSeries data or timestamps datasets with a DataChunkIterator. #1089 (@bendichter)

PyNWB 1.1.1 (Oct. 7, 2019)

PyNWB 1.1.0 does not work with HDMF>=1.3. This release will work with HDMF>=1.3.2.

Minor improvements:

• Support newly added channel-specific conversion factor for ElectricalSeries #1072 (@bendichter)
• Move generic types out of PyNWB into hdmf-common. #1061 (@ajtritt)
• Update documentation to reflect the above changes. #1078 (@rly)
• Add new case to the iterative write tutorial. #1029 (@oruebel)
• Improve CI. #1079 (@rly)
• Pin the current latest version of HDMF to requirements for setup.py. #1083 (@rly)

PyNWB 1.1.0 (Sep. 17, 2019)

New features:

• Add object ID to all neurodata types #991 (@ajtritt, @rly)
• Add NWBFile shallow copy method #994 (@ajtritt, @rly)
• Drop official Python 2.7 support #1028 (@rly)
• Add scratch space #1027 #1038 (@ajtritt, @rly)
• Support multiple experimenters #988 #1035 (@ajtritt, @rly)
• Support multiple related publications #1047 (@rly)
• Update schema to 2.1.0 (see release notes in https://nwb-schema.readthedocs.io/en/latest/format_release_notes.html) (@rly, @bendichter, @ajtritt, @oruebel, @t-b)

Minor enhancements:

• Add iterative write check for TimeSeries timestamps #1012 (@bendichter, @oruebel)
• Add functions to convert between pixel mask and image mask for ophys data #766 (@mamelara)
• Add cortical surface extension example #1040 (@bendichter)
• Match API with schema defaults #1033 (@rly)
• Core schema is now a git submodule #1045 (@ajtritt)
• Implement better support for floating point data for Python 3.5 on Windows #1043 (@rly)
• Enhance iterative write tutorial #1029 (@oruebel)
• Allow empty data in DynamicTable with non-empty VectorIndex #887 (@ajtritt)
• Allow OpticalSeries constructor argument 'field_of_view' to be H5Dataset #1063 (@bendichter)
• Clarify documentation for deprecated ImageSeries constructor arg 'bits_per_pixel' #1065 (@rly)
• Adjust code to explicitly map properties after changes made in HDMF 1.2 #1048 #1069 (@rly)
• Improvements to CI, documentation, and GitHub repo structure #1055 (@rly)

PyNWB 1.0.3 (Jul. 18, 2019)

New/modified functionality:

• Add MPI functionality to NWBHDF5IO (@bendichter)
• Add option to exclude columns from DynamicTable.to_dataframe() (@NileGraddis)
• Remove ability to add DecompositionSeries to LFP (@bendichter)
• Remove num_samples from TimeSeries (@NileGraddis)
• Automatically detect ragged arrays in from_dataframe (@bendichter)
• Cache the spec by default on write (@rly)
• Improve printing of NWB objects (@rly)
• Change ProcessingModule.add_data_interface() to .add(), ProcessingModule.get_data_interface() to .get(), NWBFile.modules to NWBFile.processing (@bendichter)
• Remove unused SpecFile type (@oruebel)
• Add ability to validate files against the cached spec (@t-b)
• Make CurrentClampSeries/VoltageClampSeries parameters optional (@t-b)
• Update documentation (@t-b, @rly)
• Update copyright/license
• Improve tests and CI
• Update requirements
• See also HDMF changes https://github.com/hdmf-dev/hdmf/releases/tag/1.0.4

Bug fixes:

• Fix dynamictableregion iteration failure after roundtrip (@NileGraddis)
• Fix from_dataframe for children of DynamicTable (@bendichter)
• Fix for modular (cross-file) storage of timeseries timestamps (@NileGraddis)
• Fix bug on loading lists of strings from hdmf 1.0.4 (@rly)
• Fix IO for intervals (@bendichter)
• Fix round trip for Subject.date_of_birth (@bendichter)

Schema changes:

• DecompositionSeries "source_timeseries" link is no longer required (@bendichter)
• Reorder keys (@rly)
• Remove NWBFile "specifications" group (@oruebel)
• CorrectedImageStack and ImagingRetinotopy inherits from NWBDataInterface instead of NWBContainer (@rly)
• Fix typo in unit of resistance_comp_prediction/correction (@t-b)
• Add option for third dimension for Units "waveforms" dataset to represent different electrodes (@bendichter)
• Update NWBFile.nwb_version to 2.0.2

PyNWB 1.0.2 (Apr. 19, 2019)