Hdmf

Bug fixes
- Fixed release deployment CI. rly (734, 735, 736)

New features
- Added utility functions and classes useful for implementation of I/O backend to ease maintainability and reuse of functionality across I/O backends. oruebel (697)
- Added `HDF5IODataChunkIteratorQueue` class in `hdmf.backends.hdf5.h5_utils` as a new helper class for managing the write of `DataChunkIterator`s to HDF5. oruebel (697)
- Added new `hdmf/io/utils.py` module with new I/O utility classes: 1) `WriteStatusTracker` as a simple data structure for tracking the write status of `Builders`, and 2) `NamespaceToBuilderHelper` to help with converting of a namespace to a `Builder` for I/O. oruebel (697)
- Added `get_min_bounds` function to `hdmf.data_utils.DataChunk`. This functionality was originally part of `HDF5IO.__write_chunk__()` and has been moved here to enable reuse of the code across data backends. oruebel (697)
- Added `ignore_string_to_byte` option for `TestCase.assertContainerEqual` to allow us to ignore conversion from string to bytes and just compare unicode values, as different backends may store strings differently. oruebel (697)
- Allow `zarr.Array` as array datatype in docval to support conversion data stored in Zarr to HDMF HDF5 data. oruebel (721)
- Allow `hdmf.common.table.DynamicTable.add_column` to accept nested lists as column data and automatically create the `VectorIndex` and `VectorData` objects required to represent the ragged array. oruebel (728)
- Added a warning when the ``__init__`` 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 (730)
- Added helper function `hdmf.utils.popargs_to_dict` for popping docval args into a dict. rly (732)

Bug fixes
- Fixed error with modifying files that contain external links to other files (e.g., shallow copies). rly (709)
- Fixed opening of files in append mode on Windows when the files contain links to other open files. rly (710)
- Updated `HDF5IO` to always set the `location` attribute of `GroupBuilders`, `DatasetBuilders`, and `LinkBuilders` on read. oruebel (697)
- Updated `HDF5IO.get_types` to correctly determine the data type for `bytes` data. oruebel (697)

Minor improvements
- Updated `HDF5IO` to use the new `WriteStatusTracker`, `NamespaceToBuilderHelper`, and `HDF5IODataChunkIteratorQueue` helper classes. oruebel (697)
- Updated `hdmf.common.sparse.CSRMatrix` to avoid direct dependency on h5py as a particular storage backend. oruebel (697)
- Improved readability of ``Container`` code. rly (707)
- Use GitHub Actions for all CI. rly (718)
- Allow `write_args=None` to be passed to `HDF5IO.export`. rly (733)
- Updated requirements and fixed minor documentation issues and warnings. rly (731)

Test enhancements
- Moved test functions to ease reuse and updated tests accordingly. oruebel (697)
- Moved `Baz`, `BazData`, `BazCpdData`, `BazBucket`, `get_baz_buildmanager` test data classes from `tests.unit.test_io_hdf5_h5tools` to `tests.unit.utils` to ease reuse and updated tests accordingly. Also `_get_baz_manager` was renamed to `get_baz_buildmanager` as part of this move. oruebel (697)
- Added numerous tests to `tests/unit/common/test_sparse.py` to enhance testing of the `CSRMatrix` type. oruebel (697)

Documentation and tutorial enhancements:
- Add copy button to code blocks. weiglszonja oruebel (726)

Bug fixes
- Fixed release CI that prevented distribution from being uploaded to PyPI. rly (699)

New features
- Added ``hdmf.container.Row.__str__`` to improve print of rows. oruebel (667)
- Added ``to_dataframe`` method for ``hdmf.common.resources.ExternalResource`` to improve visualization. oruebel (667)
- Added ``export_to_sqlite`` method for ``hdmf.common.resources.ExternalResource``. oruebel (667)
- Added ``reset_parent`` method for ``hdmf.container.Container``. rly (692)

Minor improvements
- Plotted results in external resources tutorial. oruebel (667)
- Added support for Python 3.10. rly (679)
- Updated requirements. rly TheChymera (681)
- Improved testing for `ExternalResources`. mavaylon1 (673)
- Improved docs for export. rly (674)
- Enhanced data chunk iteration speeds through new ``GenericDataChunkIterator`` class. CodyCBakerPhD (672)
- Enhanced issue template forms on GitHub. CodyCBakerPHD (700)

Bug fixes
- Fixed `setup.py` not being able to import `versioneer` when installing in an embedded Python environment. rly (662)
- Fixed broken tests in Python 3.10. rly (664)
- Fixed broken LaTeX PDF build of the docs. oruebel (669)
- Fixed adding containers as a child to a parent container sometimes not marking the parent container as modified. rly
(683)
- Fixed `to_hierarchcial_dataframe` failing when a table contains a `VectorIndex` column as a regular data column.
oruebel (666)
- Stop testing against base Python error messages because they may change in the future. rly (689)

Bug fixes
- Updated the new ``DynamicTableRegion.get_linked_tables`` function (added in 3.1.0) to return lists of ``typing.NamedTuple``
objects rather than lists of dicts. oruebel (660)

New features
- Added several features to simplify interaction with ``DynamicTable`` objects that link to other tables via
``DynamicTableRegion`` columns. oruebel (645)
- Added ``DynamicTable.get_foreign_columns`` to find all columns in a table that are a ``DynamicTableRegion``
- Added ``DynamicTable.has_foreign_columns`` to identify if a ``DynamicTable`` contains ``DynamicTableRegion`` columns
- Added ``DynamicTable.get_linked_tables`` to retrieve all tables linked to either directly or indirectly from
the current table via ``DynamicTableRegion``
- Implemented the new ``get_foreign_columns``, ``has_foreign_columns``, and ``get_linked_tables`` also for
``AlignedDynamicTable``
- Added new module ``hdmf.common.hierarchicaltable`` with helper functions to facilitate conversion of
hierarchically nested ``DynamicTable`` objects via the following new functions:
- ``to_hierarchical_dataframe`` to merge linked tables into a single consolidated pandas DataFrame.
- ``drop_id_columns`` to remove "id" columns from a DataFrame.
- ``flatten_column_index`` to replace a ``pandas.MultiIndex`` with a regular ``pandas.Index``

Bug fixes
- Do not build wheels compatible with Python 2 because HDMF requires Python 3.7. rly (642)
- ``AlignedDynamicTable`` did not overwrite its ``get`` function. When using ``DynamicTableRegion`` to reference ``AlignedDynamicTable`` this led to cases where the columns of the category subtables where omitted during data access (e.g., conversion to pandas.DataFrame). This fix adds the ``AlignedDynamicTable.get`` based on the existing ``AlignedDynamicTable.__getitem__``. oruebel (645)
- Fixed 651 to support selection of cells in an ``AlignedDynamicTable`` via slicing with ``[int, (str, str)]``(and ``[int, str, str]``) to select a single cell, and ``[int, str]`` to select a single row of a category table. oruebel (645)

Minor improvements
- Updated ``DynamicTable.to_dataframe()`` and ``DynamicTable.get`` functions to set the ``.name`` attribute
on generated pandas DataFrame objects. oruebel (645)
- Added ``AlignedDynamicTable.get_colnames(...)`` to support look-up of the full list of columns as the
``AlignedDynamicTable.colnames`` property only includes the columns of the main table for compliance with
``DynamicTable`` oruebel (645)
- Fix documentation for `DynamicTable.get` and `DynamicTableRegion.get`. rly (650)
- Allow passing string column name to `DynamicTableRegion`, i.e., `dtr['col_name']` is a shortcut to
`dtr.table['col_name']`. rly (657)