Hdmf

Enhancements
- Updated `TermSet` to be used with `TermSetWrapper`, allowing for general use of validation for datasets and attributes. This also brings updates to `HERD` integration and updates on `write` to easily add references for wrapped datasets/attributes. mavaylon1 [950](https://github.com/hdmf-dev/hdmf/pull/950)

Minor improvements
- Removed warning when namespaces are loaded and the attribute marking where the specs are cached is missing. bendichter [926](https://github.com/hdmf-dev/hdmf/pull/926)

Bug fixes
- Fixed bug allowing `DynamicTable` to be constructed with empty `id` column when initializing all columns via `AbstractDataChunkIterator` objects. oruebel [953](https://github.com/hdmf-dev/hdmf/pull/953)

New features and minor improvements
- Increased raw data chunk cache size for reading HDF5 files from 1 MiB to 32 MiB. bendichter, rly [925](https://github.com/hdmf-dev/hdmf/pull/925)
- Increased default chunk size for `GenericDataChunkIterator` from 1 MB to 10 MB. bendichter, rly [925](https://github.com/hdmf-dev/hdmf/pull/925)
- Added the magic `__reduce__` method as well as two private semi-abstract helper methods to enable pickling of the `GenericDataChunkIterator`. codycbakerphd [924](https://github.com/hdmf-dev/hdmf/pull/924)
- Updated `add_ref_termset` to add all instances of `TermSet` within a given root container. mavaylon1 [935](https://github.com/hdmf-dev/hdmf/pull/935)
- Added Dynamic Enumerations and Schemasheets support to `TermSet`. mavaylon1 [923](https://github.com/hdmf-dev/hdmf/pull/923)
- Updated `HERD` to support user defined file name for the `HERD` zip file. mavaylon1 [941](https://github.com/hdmf-dev/hdmf/pull/941)
- Added method `Container.set_data_io`, which wraps an existing data field in a `DataIO`. bendichter [938](https://github.com/hdmf-dev/hdmf/pull/938)

Bug fixes
- Fixed error when calling `HDF5IO.read` twice. rly [915](https://github.com/hdmf-dev/hdmf/pull/915)

New features and minor improvements
- Added the ability to write ExternalResources if the path is provided and the container has a linked instance of ExternalResources. mavaylon1 [910](https://github.com/hdmf-dev/hdmf/pull/910)

Bug fixes
- Fixed bug on `add_ref_term_set` in which attributes that were not subscribtable returned an error. mavaylon1 [909](https://github.com/hdmf-dev/hdmf/pull/909)

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`. mavaylon [850](https://github.com/hdmf-dev/hdmf/pull/850)
- Updated hdmf-common-schema version to 1.6.0. mavaylon [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. mavaylon [850](https://github.com/hdmf-dev/hdmf/pull/850)