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PyNWB Changelog

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)

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)
  • 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)