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Add/icephys meta #1349

Merged
merged 119 commits into from
Jul 30, 2021
Merged

Add/icephys meta #1349

merged 119 commits into from
Jul 30, 2021

Commits on Apr 5, 2021

  1. Ignore flake8 warning in test_io

    @oruebel
    oruebel committed Apr 5, 2021
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  2. Declare SweepTable as deprecated on init

    @oruebel
    oruebel committed Apr 5, 2021
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  3. Add TimeSeriesReferenceVectorData Container class

    @oruebel
    oruebel committed Apr 5, 2021
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  4. Add simple test for TimeSeriesReferenceVectorData

    @oruebel
    oruebel committed Apr 5, 2021
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Commits on Apr 6, 2021

  1. Update nwb-schema branch

    @oruebel
    oruebel committed Apr 6, 2021
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  2. Add icephys metadata container classes

    @oruebel
    oruebel committed Apr 6, 2021
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  3. Update NWBFile to support icephys metadata tables

    @oruebel
    oruebel committed Apr 6, 2021
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  4. Add unit tests for icephys metadata tables

    @oruebel
    oruebel committed Apr 6, 2021
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Commits on Apr 7, 2021

  1. Update imports and fix SweepTable integration tests

    @oruebel
    oruebel committed Apr 7, 2021
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  2. Fix test available namespaces testcase

    @oruebel
    oruebel committed Apr 7, 2021
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  3. Update SweepTable tutorial and declare as deprecated

    @oruebel
    oruebel committed Apr 7, 2021
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  4. Add new icephys tutorial using the new hierarchical metadata tables

    @oruebel
    oruebel committed Apr 7, 2021
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  5. Add IntracellularRecordingsTable illustration

    @oruebel
    oruebel committed Apr 7, 2021
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  6. Fix flake8 issues

    @oruebel
    oruebel committed Apr 7, 2021
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Commits on Apr 8, 2021

  1. Remove use of HierarchiclaDynamicTableMixin use for now

    @oruebel
    oruebel committed Apr 8, 2021
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Commits on Apr 14, 2021

  1. Add source PowerPoint file for icephys docs

    @oruebel
    oruebel committed Apr 14, 2021
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  2. Merge branch 'dev' into add/icephys_meta

    @oruebel
    oruebel committed Apr 14, 2021
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  3. Fix make clean command for docs to also clean sphinx-gallery files

    @oruebel
    oruebel committed Apr 14, 2021
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  4. Updated CHANGELOG to describe changes from this PR

    @oruebel
    oruebel committed Apr 14, 2021
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  5. Add thumbnails for domain-specfic tutorials

    @oruebel
    oruebel committed Apr 14, 2021
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  6. Add thumbnaisl for general tutorials

    @oruebel
    oruebel committed Apr 14, 2021
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  7. Update changelog

    @oruebel
    oruebel committed Apr 14, 2021
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Commits on Apr 17, 2021

  1. Remove ic_filtering/icephys_filtering duplicate and fix test

    @oruebel
    oruebel committed Apr 17, 2021
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Commits on Apr 28, 2021

  1. Fix description of ExperimentalConditionsTable

    @oruebel
    oruebel committed Apr 28, 2021
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Commits on May 28, 2021

  1. Merge branch 'dev' into add/icephys_meta

    @oruebel
    oruebel committed May 28, 2021
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Commits on Jun 14, 2021

  1. Use nwb schema branch for icephys meta

    @rly
    rly committed Jun 14, 2021
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Commits on Jun 17, 2021

  1. Ensure start_index and count are set to -1 if TimeSeries is None

    @oruebel
    oruebel authored Jun 17, 2021
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  2. Add test for conversion of start_index and index_count vals

    @oruebel
    oruebel committed Jun 17, 2021
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  3. Fix flake8 in __compute_index docstring

    @oruebel
    oruebel committed Jun 17, 2021
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Commits on Jun 18, 2021

  1. Update schema (updated version to 1.4.0-alpha)

    @rly
    rly committed Jun 18, 2021
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Commits on Jul 6, 2021

  1. Fix icephys metadata roundtrip NWBFile test base on update DynamicTab… 

    …leRegion behavior
    @oruebel
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  2. Merge branch 'add/icephys_meta' of https://github.com/NeurodataWithou… 

    …tBorders/pynwb into add/icephys_meta
    @oruebel
    oruebel committed Jul 6, 2021
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Commits on Jul 7, 2021

  1. Merge branch 'dev' into add/icephys_meta

    @rly
    rly committed Jul 7, 2021
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  2. Merge branch 'rc/2.0.0' into add/icephys_meta

    @rly
    rly committed Jul 7, 2021
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  3. Move SweepTable DeprectationWarning to the constructor of SweepTable … 

    …to clean up code
    @oruebel
    oruebel committed Jul 7, 2021
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  4. Suppress SweepTable Deprecation warning in icephys integration test

    @oruebel
    oruebel committed Jul 7, 2021
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  5. Ignore and assert deprecation warning for SweepTable during SweepTabl… 

    …e roundtrip tests
    @oruebel
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  6. Merge branch 'rc/2.0.0' into add/icephys_meta

    @rly
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  7. Merge branch 'rc/2.0.0' into add/icephys_meta

    @rly
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  8. Fix falke8 on icephys tutorial galleries

    @oruebel
    oruebel committed Jul 7, 2021
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  9. Merge branch 'add/icephys_meta' of https://github.com/NeurodataWithou… 

    …tBorders/pynwb into add/icephys_meta
    @oruebel
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  10. Use extension in docs to simplify linking to common targets

    @oruebel
    oruebel committed Jul 7, 2021
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  11. Move advanced data I/O tutorials to their own section and move parall… 

    …el I/O tutorial
    @oruebel
    oruebel committed Jul 7, 2021
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  12. Update Changelog for tutorials

    @oruebel
    oruebel committed Jul 7, 2021
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  13. Updated deprecation warning in SweepTable tutorial

    @oruebel
    oruebel committed Jul 7, 2021
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Commits on Jul 16, 2021

  1. Fix minor spelling error in make_test_files

    @oruebel
    oruebel committed Jul 16, 2021
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  2. Several corrections and enhancments for the icephys tutorial

    @oruebel
    oruebel committed Jul 16, 2021
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  3. Moved functions to create icephys test file from tests to pynwb

    @oruebel
    oruebel committed Jul 16, 2021
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  4. Moved functions to create icephys test file from tests to pynwb

    @oruebel
    oruebel committed Jul 16, 2021
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  5. Start for new tutorial to show conversion of icephys tables to pandas… 

    … dataframes
    @oruebel
    oruebel committed Jul 16, 2021
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  6. Test to_hierarchical_dataframe and to_denormalized_dataframe functions

    @oruebel
    oruebel committed Jul 16, 2021
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Commits on Jul 17, 2021

  1. Updated tutorial to convert icephys tabels to pandas

    @oruebel
    oruebel committed Jul 17, 2021
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  2. Fix minor spelling error in NWBFile docstring

    @oruebel
    oruebel committed Jul 17, 2021
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  3. Add TimeseriesReferenceVectorData.get method to mask missing values o… 

    …n load
    @oruebel
    oruebel committed Jul 17, 2021
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  4. Update IntracellularRecordingsTable. Update add_recording defaults fo… 

    …r startindex and count to None and update to_dataframe method to handle missing values in TimeSeriesReferenceVectorData
    @oruebel
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  5. Update create_icephys_testfile to create testdata with missing stimuli

    @oruebel
    oruebel committed Jul 17, 2021
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  6. Update existing tests to match the new behavior

    @oruebel
    oruebel committed Jul 17, 2021
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  7. Update icephys tutorial for match new behavior

    @oruebel
    oruebel committed Jul 17, 2021
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  8. Update icephys pandas tutorial to demonstrate new behavior

    @oruebel
    oruebel committed Jul 17, 2021
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  9. Remove debug print statements

    @oruebel
    oruebel committed Jul 17, 2021
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  10. Add table augmentation and queries to the icephys_pandas tutorial

    @oruebel
    oruebel committed Jul 17, 2021
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  11. Fix flake8

    @oruebel
    oruebel committed Jul 17, 2021
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Commits on Jul 18, 2021

  1. Update to use keyword args

    @oruebel
    oruebel committed Jul 18, 2021
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Commits on Jul 19, 2021

  1. Clarify text in icephys tutorial

    @oruebel
    oruebel committed Jul 19, 2021
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Commits on Jul 20, 2021

  1. Fix flake8 on tutorial

    @oruebel
    oruebel committed Jul 20, 2021
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  2. Fix flake8

    @oruebel
    oruebel committed Jul 20, 2021
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  3. Update to use dev branch of nwb-schema

    @oruebel
    oruebel committed Jul 20, 2021
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  4. Set default name and default description for TimeSeriesReferenceVecto… 

    …rData
    @oruebel
    oruebel committed Jul 20, 2021
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Commits on Jul 21, 2021

  1. added icephys_testutils to pynwb.testing.__init__

    @oruebel
    oruebel committed Jul 21, 2021
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  2. Added test for IntracellularRecordingsTable.to_dataframe with options

    @oruebel
    oruebel committed Jul 21, 2021
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  3. Always use MaskedArrya in TimeSeriesReferenceVectorData instead of Ma… 

    …skedConstant
    @oruebel
    oruebel committed Jul 21, 2021
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  4. Add tests for TimeSeriesReferenceVectorData.get

    @oruebel
    oruebel committed Jul 21, 2021
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  5. Updated change log

    @oruebel
    oruebel committed Jul 21, 2021
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Commits on Jul 22, 2021

  1. Merge pull request #1383 from NeurodataWithoutBorders/add/denormalize… 

    …_df_for_icephys

Add icephys functions to interact with pandas
    @oruebel
    oruebel authored Jul 22, 2021
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  2. Fix minor docstring issue in TimeSeriesReferenceData.get

    @oruebel
    oruebel committed Jul 22, 2021
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Commits on Jul 23, 2021

  1. Clarify docstring for TimeSeriesReferenceData.get

    @oruebel
    oruebel committed Jul 23, 2021
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  2. Merge branch 'rc/2.0.0' into add/icephys_meta

    @oruebel
    oruebel committed Jul 23, 2021
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Commits on Jul 27, 2021

  1. Update CHANGELOG.md

    @rly
    rly authored Jul 27, 2021
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  2. Update icephys.py

    @rly
    rly authored Jul 27, 2021
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  3. Update docs/gallery/domain/plot_icephys.py

    @rly
    rly authored Jul 27, 2021
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  4. Update plot_icephys.py 

    Minor text fixes
    @rly
    rly authored Jul 27, 2021
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  5. Update plot_icephys_pandas.py 

    Minor text edits
    @rly
    rly authored Jul 27, 2021
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  6. Update icephys_testutils.py 

    Minor docstring edits
    @rly
    rly authored Jul 27, 2021
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  7. Update file.py

    @rly
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  8. Fix typos

    @rly
    rly authored Jul 27, 2021
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  9. Update docs/gallery/domain/plot_icephys.py Replace master with main

    @oruebel
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  10. Mention use of create_icephys_testfile function 

    Co-authored-by: Ryan Ly <[email protected]>
    @oruebel @rly
    oruebel and rly authored Jul 27, 2021
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  11. Remove old comment in TimeSeriesReferenceVectorData 

    Co-authored-by: Ryan Ly <[email protected]>
    @oruebel @rly
    oruebel and rly authored Jul 27, 2021
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  12. Fix typo in changelog

    @oruebel
    oruebel committed Jul 27, 2021
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  13. Fix broken link target

    @oruebel
    oruebel committed Jul 27, 2021
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  14. Fix flake8 in docs/gallery

    @oruebel
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Commits on Jul 28, 2021

  1. Minor text fixes

    @rly
    rly authored Jul 28, 2021
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  2. Minor text and formatting fixes

    @rly
    rly authored Jul 28, 2021
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  3. Update tests/unit/test_icephys_metadata_tables.py 

    Co-authored-by: Ryan Ly <[email protected]>
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  4. Use namedtuple instead of numpy masked structed array to represent va… 

    …lues of TimeSeriesReferenceVectorData
    @oruebel
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  5. Update tests/unit/test_icephys_metadata_tables.py 

    Co-authored-by: Ryan Ly <[email protected]>
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  6. Update tests/unit/test_icephys_metadata_tables.py 

    Co-authored-by: Ryan Ly <[email protected]>
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  7. Update tests/unit/test_icephys_metadata_tables.py 

    Co-authored-by: Ryan Ly <[email protected]>
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  8. Update tests/unit/test_icephys_metadata_tables.py 

    Co-authored-by: Ryan Ly <[email protected]>
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    oruebel and rly authored Jul 28, 2021
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  9. Update tests/unit/test_icephys_metadata_tables.py 

    Co-authored-by: Ryan Ly <[email protected]>
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  10. Update tests/unit/test_icephys_metadata_tables.py 

    Co-authored-by: Ryan Ly <[email protected]>
    @oruebel @rly
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  11. Update tests/unit/test_icephys_metadata_tables.py 

    Co-authored-by: Ryan Ly <[email protected]>
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  12. Update tests/unit/test_icephys_metadata_tables.py 

    Co-authored-by: Ryan Ly <[email protected]>
    @oruebel @rly
    oruebel and rly authored Jul 28, 2021
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Commits on Jul 29, 2021

  1. Fix bad indent in test

    @oruebel
    oruebel committed Jul 29, 2021
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  2. Update base.py - minor text edits

    @rly
    rly authored Jul 29, 2021
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  3. Enhance introspection, slicing, and data addition for TimeSeriesRefer… 

    …ence and TimeSeriesReferenceVectorData
    @oruebel
    oruebel committed Jul 29, 2021
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  4. Updated icephys query tutorial to use latest get_linked_tables behavi… 

    …or and improve rendering
    @oruebel
    oruebel committed Jul 29, 2021
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  5. Fix flake8 in gallery

    @oruebel
    oruebel committed Jul 29, 2021
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  6. Fix spelling in error message

    @oruebel
    oruebel committed Jul 29, 2021
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  7. Update src/pynwb/base.py 

    Co-authored-by: Ryan Ly <[email protected]>
    @oruebel @rly
    oruebel and rly authored Jul 29, 2021
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  8. Update src/pynwb/base.py 

    Co-authored-by: Ryan Ly <[email protected]>
    @oruebel @rly
    oruebel and rly authored Jul 29, 2021
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  9. Update src/pynwb/base.py 

    Co-authored-by: Ryan Ly <[email protected]>
    @oruebel @rly
    oruebel and rly authored Jul 29, 2021
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  10. Update src/pynwb/base.py 

    Co-authored-by: Ryan Ly <[email protected]>
    @oruebel @rly
    oruebel and rly authored Jul 29, 2021
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  11. Update src/pynwb/base.py 

    Co-authored-by: Ryan Ly <[email protected]>
    @oruebel @rly
    oruebel and rly authored Jul 29, 2021
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  12. Update src/pynwb/base.py 

    Co-authored-by: Ryan Ly <[email protected]>
    @oruebel @rly
    oruebel and rly authored Jul 29, 2021
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  13. Fix bug in TimeSeriesReference.timestamps and add comments

    @oruebel
    oruebel committed Jul 29, 2021
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Commits on Jul 30, 2021

  1. Use hdmf 3.1.1

    @rly
    rly committed Jul 30, 2021
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  2. Merge branch 'add/icephys_meta' of https://github.com/NeurodataWithou… 

    …tBorders/pynwb into add/icephys_meta
    @rly
    rly committed Jul 30, 2021
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  3. Fix gallery tests to handle allensdk pinning pynwb/hdmf

    @rly
    rly committed Jul 30, 2021
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