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Add functionality for linked DynamicTables #645

Merged
merged 63 commits into from
Jul 21, 2021
Merged

Add functionality for linked DynamicTables #645

merged 63 commits into from
Jul 21, 2021

Commits on Jul 16, 2021

  1. Updated DynamicTable to set the name of DataFrames and allow introspe… 

    …ction of nested tables containing DynamicTableRegion columns
    @oruebel
    oruebel committed Jul 16, 2021
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  2. Added module to convert nested DataFrames to a flat DataFrame

    @oruebel
    oruebel committed Jul 16, 2021
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  3. Added tests for the new functionality for nested DataFrames and Dynam… 

    …icTables
    @oruebel
    oruebel committed Jul 16, 2021
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  4. Updated Changelog

    @oruebel
    oruebel committed Jul 16, 2021
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  5. Fix flake8 on tests

    @oruebel
    oruebel committed Jul 16, 2021
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  6. Added PR info in Changelog

    @oruebel
    oruebel committed Jul 16, 2021
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  7. Added first draft of to_hierarchical_datafram and to_denormalized_dat… 

    …aframe functions
    @oruebel
    oruebel committed Jul 16, 2021
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  8. Added AlignedDynamicTable.get function to Fix #646

    @oruebel
    oruebel committed Jul 16, 2021
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  9. Add functions to drop id columns and flatten the columns of a hierarc… 

    …hical dataframe
    @oruebel
    oruebel committed Jul 16, 2021
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Commits on Jul 17, 2021

  1. Remove to_denormalized_dataframe and drop flatten_index parameter fro… 

    …m to_hierarchical_dataframe
    @oruebel
    oruebel committed Jul 17, 2021
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  2. Fix Flake8 and Changelog

    @oruebel
    oruebel committed Jul 17, 2021
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  3. Added TODO item

    @oruebel
    oruebel committed Jul 17, 2021
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  4. Add missing docstrings for extend and get methods for Data and Vector… 

    …Data
    @oruebel
    oruebel committed Jul 17, 2021
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  5. Remove unit test for removed function

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

  1. Use docval to document hierarchicaltable.py functions

    @oruebel
    oruebel committed Jul 18, 2021
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  2. Fix docstring formatting

    @oruebel
    oruebel committed Jul 18, 2021
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  3. Document allow_extra and allow_positional in docval

    @oruebel
    oruebel committed Jul 18, 2021
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  4. Minor spelling error in docstring

    @oruebel
    oruebel committed Jul 18, 2021
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  5. Added AlignedDynamicTable.has_foreign_columns and corresponding test

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

  1. Added AlignedDynamicTable.get_foreign_columns

    @oruebel
    oruebel committed Jul 19, 2021
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  2. Implemented AlignedDynamicTable.get_linked_tables and added tests

    @oruebel
    oruebel committed Jul 19, 2021
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  3. Add test to make sure DynamicTableRegion to AlignedDynamicTable is wo… 

    …rking
    @oruebel
    oruebel committed Jul 19, 2021
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  4. Fix case where DynamicTableRegion is a regular VectorData not a Vecto… 

    …rIndex in to_hierarchical_dataframe
    @oruebel
    oruebel committed Jul 19, 2021
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  5. Add a test for to_hierarchical_dataframe

    @oruebel
    oruebel committed Jul 19, 2021
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  6. Merge branch 'dev' into add/hierarchical_table_funcs

    @oruebel
    oruebel authored Jul 19, 2021
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  7. Add unit test for drop id columns

    @oruebel
    oruebel committed Jul 19, 2021
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  8. Fix bugs in drop_id_columns and flatten_column_index

    @oruebel
    oruebel committed Jul 19, 2021
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  9. Add tests for drop_id_columns and flatten_column_index

    @oruebel
    oruebel committed Jul 19, 2021
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  10. Add no-level to_hierarchical_dataframe test to imporve coverage

    @oruebel
    oruebel committed Jul 19, 2021
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  11. Add test for to_hierarchical_dataframe with multiple levels and using… 

    … VectorIndex to improve test coverage
    @oruebel
    oruebel committed Jul 19, 2021
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  12. Remove unnecceary error check

    @oruebel
    oruebel committed Jul 19, 2021
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  13. Fix bug in flatten_column_index where column names got shortened when… 

    … applied to an already flat columns index
    @oruebel
    oruebel committed Jul 19, 2021
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  14. Testing the corner case of to_hierarchical_dataframe on empty tables

    @oruebel
    oruebel committed Jul 19, 2021
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  15. Fix spelling error in test

    @oruebel
    oruebel committed Jul 19, 2021
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  16. Test to_hierarchical_dataframe without vectorindex on the top dtr

    @oruebel
    oruebel committed Jul 19, 2021
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  17. Cover the case where index dtr is at the last level in convert to_hie… 

    …rarchical_dataframe
    @oruebel
    oruebel committed Jul 19, 2021
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  18. Fix name of test cases for to_hierarchical_dataframe

    @oruebel
    oruebel committed Jul 19, 2021
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  19. Remove unused logic in to_hierarchcial_dataframe

    @oruebel
    oruebel committed Jul 19, 2021
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  20. Fix flake8

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

  1. Update docstring of get_foreign_columns 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 20, 2021
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  2. Update docstring of to_hierarchical_dataframe 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 20, 2021
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  3. Fix spelling in src/hdmf/common/hierarchicaltable.py 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 20, 2021
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  4. Update spelling in src/hdmf/common/hierarchicaltable.py 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 20, 2021
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  5. Update spelling in src/hdmf/common/hierarchicaltable.py 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 20, 2021
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  6. Removed old comment src/hdmf/common/hierarchicaltable.py

    @oruebel
    oruebel authored Jul 20, 2021
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  7. Update docstring src/hdmf/common/table.py 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 20, 2021
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  8. Update docstring src/hdmf/data_utils.py 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 20, 2021
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  9. Clean up comments and duplicate logic to simplify to_hierarchical_dat… 

    …aframe
    @oruebel
    oruebel committed Jul 20, 2021
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  10. Merge branch 'dev' into add/hierarchical_table_funcs

    @oruebel
    oruebel authored Jul 20, 2021
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  11. Added AlignedDynamicTable.get_colnames function and corresponding tests

    @oruebel
    oruebel committed Jul 20, 2021
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  12. Updated to_hierarchical_dataframe to use new AlignedDynamicTabel.get_… 

    …colnames and fix columns logic
    @oruebel
    oruebel committed Jul 20, 2021
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  13. Update src/hdmf/common/hierarchicaltable.py 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 20, 2021
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  14. Update src/hdmf/common/hierarchicaltable.py 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 20, 2021
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  15. Update src/hdmf/common/hierarchicaltable.py 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 20, 2021
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  16. Remove comments from old tests

    @oruebel
    oruebel committed Jul 20, 2021
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  17. Fix #651 Support [int, str], [int, (str, str)] type slicing for Align… 

    …edDynamicTable
    @oruebel
    oruebel committed Jul 20, 2021
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  18. Fix bug in to_hierarchical_dataframe when converting AlignedDynamicTa… 

    …ble with DynamicTableRegion
    @oruebel
    oruebel committed Jul 20, 2021
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Commits on Jul 21, 2021

  1. Fix spelling in src/hdmf/common/alignedtable.py 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 21, 2021
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  2. Clarify return value for AlignedDynamicTable.get_colnames 

    Co-authored-by: Ryan Ly <rly@lbl.gov>
    @oruebel @rly
    oruebel and rly authored Jul 21, 2021
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  3. Added documentation for the various cases for AlignedDynamicTable.get

    @oruebel
    oruebel committed Jul 21, 2021
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  4. Update failing test

    @oruebel
    oruebel committed Jul 21, 2021
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  5. Update src/hdmf/common/alignedtable.py

    @rly
    rly authored Jul 21, 2021
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  6. Update src/hdmf/common/alignedtable.py

    @rly
    rly authored Jul 21, 2021
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