1.5.0

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.

1.4.0

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.

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)

1.3.3

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)

1.3.2

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.

1.3.1

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 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.

1.3.0

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: https://nwb-schema.readthedocs.io/en/latest/format_release_notes.html#march-2-2020
• 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)

1.2.1

Bug fixes:

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

1.2.0

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)

1.1.2

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)

1.1.1

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)