Hdmf

New features and minor improvements
- Updated `ExternalResources` to have EntityKeyTable with updated tests/documentation and minor bug fix to ObjectKeyTable. mavaylon1 [872](https://github.com/hdmf-dev/hdmf/pull/872)
- Added abstract static method `HDMFIO.can_read()` and concrete static method `HDF5IO.can_read()`. bendichter [875](https://github.com/hdmf-dev/hdmf/pull/875)
- Added warning for `DynamicTableRegion` links that are not added to the same parent as the original container object. mavaylon1 [891](https://github.com/hdmf-dev/hdmf/pull/891)
- Added the `TermSet` class along with integrated validation methods for any child of `AbstractContainer`, e.g., `VectorData`, `Data`, `DynamicTable`. mavaylon1 [880](https://github.com/hdmf-dev/hdmf/pull/880)
- Added `AbstractContainer.read_io` property to be able to retrieve the HDMFIO object used for reading from the container and to ensure the I/O object used for reading is not garbage collected before the container is being deleted. bendichter oruebel [882](https://github.com/hdmf-dev/hdmf/pull/882)
- Allow for `datetime.date` to be used instead of `datetime.datetime`. bendichter [874](https://github.com/hdmf-dev/hdmf/pull/874)
- Updated `HDMFIO` and `HDF5IO` to support `ExternalResources`. mavaylon1 [895](https://github.com/hdmf-dev/hdmf/pull/895)
- Dropped Python 3.7 support. rly [897](https://github.com/hdmf-dev/hdmf/pull/897)
- Added HTML repr to `Container` objects which displays an interactive tree of a container's values and children in a Jupyter notebook and other HTML representations. edeno [883](https://github.com/hdmf-dev/hdmf/pull/883)
- Update software_process.rst with the correct external links. mavaylon1 [900](https://github.com/hdmf-dev/hdmf/pull/900)

Documentation and tutorial enhancements:
- Added tutorial for the new `TermSet` class mavaylon1 [880](https://github.com/hdmf-dev/hdmf/pull/880)

Bug fixes
- Fixed CI testing of minimum installation requirements, and removed some gallery tests run on each PR. rly
[877](https://github.com/hdmf-dev/hdmf/pull/877)
- Fixed reporting of version when installed using conda. rly [890](https://github.com/hdmf-dev/hdmf/pull/890)


HMDF 3.6.1 (May 18, 2023)

Bug fixes
- Fixed compatibility with hdmf_zarr for converting string arrays from Zarr to HDF5 by adding logic to determine the dtype for object arrays. oruebel [866](https://github.com/hdmf-dev/hdmf/pull/866)

New features and minor improvements
- Updated `ExternalResources` to have `FileTable` and new methods to query data. the `ResourceTable` has been removed along with methods relating to `Resource`. mavaylon1 [850](https://github.com/hdmf-dev/hdmf/pull/850)
- Updated hdmf-common-schema version to 1.6.0. mavaylon1 [850](https://github.com/hdmf-dev/hdmf/pull/850)
- Added testing of HDMF-Zarr on PR and nightly. rly [859](https://github.com/hdmf-dev/hdmf/pull/859)
- Replaced `setup.py` with `pyproject.toml`. rly [844](https://github.com/hdmf-dev/hdmf/pull/844)
- Use `ruff` instead of `flake8`. rly [844](https://github.com/hdmf-dev/hdmf/pull/844)
- Replaced `versioneer` with `setuptools_scm` for versioning. rly [844](https://github.com/hdmf-dev/hdmf/pull/844)
- Now recommending developers use `pre-commit`. rly [844](https://github.com/hdmf-dev/hdmf/pull/844)

Bug fixes
- Export cached specs that are loaded in source IO manager but not in export IO manager. rly
[855](https://github.com/hdmf-dev/hdmf/pull/855)
- Fixed issue with passing an S3 URL for source in the constructor of ``HDMFIO`` rly
[853](https://github.com/hdmf-dev/hdmf/pull/853)

Documentation and tutorial enhancements:
- Updated `ExternalResources` how to tutorial to include the new features. mavaylon1 [850](https://github.com/hdmf-dev/hdmf/pull/850)

Bug fixes
- Removed references to discontinued `requires.io` service in documentation. rly
[854](https://github.com/hdmf-dev/hdmf/pull/854)

Bug fixes
- Fixed error during export where an external link to the same file was created in some situations.
rly [847](https://github.com/hdmf-dev/hdmf/pull/847)
- Removed unused, deprecated `codecov` package from dev installation requirements. rly
[849](https://github.com/hdmf-dev/hdmf/pull/849)
- Fixed export with `'link_data': False'` not copying datasets in some situations. rly
[848](https://github.com/hdmf-dev/hdmf/pull/848)

Bug fixes
- Fixed typo in deploy release workflow. rly [845](https://github.com/hdmf-dev/hdmf/pull/845)

Bug fixes
- Fixed search bar and missing jquery in ReadTheDocs documentation. rly
[840](https://github.com/hdmf-dev/hdmf/pull/840)
- Fixed issue with dynamic class generation for a multi-container interface where one or more are required. rly
[839](https://github.com/hdmf-dev/hdmf/pull/839)

Minor improvements
- Added support for Python 3.11. rly [803](https://github.com/hdmf-dev/hdmf/pull/803)
- No longer set upper bounds on dependencies. rly [803](https://github.com/hdmf-dev/hdmf/pull/803)
- `DynamicTable.to_dataframe()` now sets the index (id) column dtype to int64 rather than the OS default (int32 on Windows, int64 on Mac, Linux). rly [803](https://github.com/hdmf-dev/hdmf/pull/803)