Hdmf

Enhancements
- Added docs page that lists limitations of support for the HDMF specification language. rly [1069](https://github.com/hdmf-dev/hdmf/pull/1069)
- Added warning when using `add_row` or `add_column` to add a ragged array to `DynamicTable` without an index parameter. stephprince [1066](https://github.com/hdmf-dev/hdmf/pull/1066)

Bug fixes
- Fixed recursion error in html representation generation in jupyter notebooks. stephprince [1038](https://github.com/hdmf-dev/hdmf/pull/1038)

Bug fixes
- Fixed retrieving the correct path for a `HERD` zip file on read. [1046](https://github.com/hdmf-dev/hdmf/pull/1046)
- Fixed internal links in docstrings and tutorials. stephprince [1031](https://github.com/hdmf-dev/hdmf/pull/1031)
- Fixed issue with creating documentation links to classes in docval arguments. rly [1036](https://github.com/hdmf-dev/hdmf/pull/1036)
- Fixed issue with validator not validating against the spec that defines the data type of the builder. rly [1050](https://github.com/hdmf-dev/hdmf/pull/1050)

Enhancements
- Add Data.set_data_io(), which allows for setting a `DataIO` to a data object after-the-fact. bendichter and CodyCBakerPhD [1013](https://github.com/hdmf-dev/hdmf/pull/1013)
- Added `add_ref_termset`, updated helper methods for `HERD`, revised `add_ref` to support validations prior to populating the tables
and added `add_ref_container`. mavaylon1 [968](https://github.com/hdmf-dev/hdmf/pull/968)
- Use `stacklevel` in most warnings. rly [1027](https://github.com/hdmf-dev/hdmf/pull/1027)
- Fixed broken links in documentation and added internal link checking to workflows. stephprince [1031](https://github.com/hdmf-dev/hdmf/pull/1031)

Minor Improvements
- Updated `__gather_columns` to ignore the order of bases when generating columns from the super class. mavaylon1 [991](https://github.com/hdmf-dev/hdmf/pull/991)
- Update `get_key` to return all the keys if there are multiple within a `HERD` instance. mavaylon1 [999](https://github.com/hdmf-dev/hdmf/pull/999)
- Improve HTML rendering of tables. bendichter [998](https://github.com/hdmf-dev/hdmf/pull/998)
- Improved issue and PR templates. rly [1004](https://github.com/hdmf-dev/hdmf/pull/1004)
- Added check during validation for if a variable length dataset is empty. bendichter, oruebel [789](https://github.com/hdmf-dev/hdmf/pull/789)

Bug fixes
- Fixed issue with custom class generation when a spec has a `name`. rly [1006](https://github.com/hdmf-dev/hdmf/pull/1006)
- Fixed issue with usage of deprecated `ruamel.yaml.safe_load` in `src/hdmf/testing/validate_spec.py`. rly [1008](https://github.com/hdmf-dev/hdmf/pull/1008)
- Fixed issue where `ElementIdentifiers` data could be set to non-integer values. rly [1009](https://github.com/hdmf-dev/hdmf/pull/1009)
- Fixed issue where string datasets/attributes with isodatetime-formatted values failed validation against a text spec. rly [1026](https://github.com/hdmf-dev/hdmf/pull/1026)

Enhancements
- Added `target_tables` attribute to `DynamicTable` to allow users to specify the target table of any predefined
`DynamicTableRegion` columns of a `DynamicTable` subclass. rly [971](https://github.com/hdmf-dev/hdmf/pull/971)
- Updated `TermSet` to include `_repr_html_` for easy to read notebook representation. mavaylon1 [967](https://github.com/hdmf-dev/hdmf/pull/967)

Minor improvements
- Set up GitHub dependabot to check for updates to GitHub Actions. rly [977](https://github.com/hdmf-dev/hdmf/pull/977)
- Simplify tox configuration. rly [988](https://github.com/hdmf-dev/hdmf/pull/988)
- Add testing for Python 3.12. rly [988](https://github.com/hdmf-dev/hdmf/pull/988)

Bug fixes
- Updated custom class generation to handle specs with fixed values and required names. rly [800](https://github.com/hdmf-dev/hdmf/pull/800)
- Fixed custom class generation of `DynamicTable` subtypes to set attributes corresponding to column names for correct write. rly [800](https://github.com/hdmf-dev/hdmf/pull/800)
- Added a `.mailmap` file to correct mapping of names/emails in git logs. oruebel [976](https://github.com/hdmf-dev/hdmf/pull/976)

Since version 3.9.1 should have been released as 3.10.0 but failed to release on PyPI and conda-forge, this release
will increase the minor version number to 3.10.0. See the 3.9.1 release notes below for new features.

Bug fixes
- Fixed issue with testing and deployment of releases. rly [957](https://github.com/hdmf-dev/hdmf/pull/957)