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mavaylon1 authored Mar 11, 2024
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# HDMF Changelog

## HDMF 3.12.3
### Enhancements
- Update `TermSetWrapper` to support validating a single field within a compound array. @mavaylon1 [#1061](https://github.com/hdmf-dev/hdmf/pull/1061)

## HDMF 3.12.2 (February 9, 2024)

### Bug fixes
Expand Down Expand Up @@ -126,8 +130,8 @@ will increase the minor version number to 3.10.0. See the 3.9.1 release notes be
## HDMF 3.6.0 (May 12, 2023)

### 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)
- 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)
Expand All @@ -141,7 +145,7 @@ will increase the minor version number to 3.10.0. See the 3.9.1 release notes be
[#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)
- Updated `ExternalResources` how to tutorial to include the new features. @mavaylon1 [#850](https://github.com/hdmf-dev/hdmf/pull/850)

## HDMF 3.5.6 (April 28, 2023)

Expand Down Expand Up @@ -181,13 +185,13 @@ will increase the minor version number to 3.10.0. See the 3.9.1 release notes be

### Bug fixes
- Fixed issue with conda CI. @rly [#823](https://github.com/hdmf-dev/hdmf/pull/823)
- Fixed issue with deprecated `pkg_resources`. @mavaylon [#822](https://github.com/hdmf-dev/hdmf/pull/822)
- Fixed `hdmf.common` deprecation warning. @mavaylon [#826]((https://github.com/hdmf-dev/hdmf/pull/826)
- Fixed issue with deprecated `pkg_resources`. @mavaylon1 [#822](https://github.com/hdmf-dev/hdmf/pull/822)
- Fixed `hdmf.common` deprecation warning. @mavaylon1 [#826]((https://github.com/hdmf-dev/hdmf/pull/826)

### Internal improvements
- A number of typos fixed and Github action running codespell to ensure that no typo sneaks in [#825](https://github.com/hdmf-dev/hdmf/pull/825) was added.
- Added additional documentation for `__fields__` in `AbstactContainer`. @mavaylon [#827](https://github.com/hdmf-dev/hdmf/pull/827)
- Updated warning message for broken links. @mavaylon [#829](https://github.com/hdmf-dev/hdmf/pull/829)
- Added additional documentation for `__fields__` in `AbstactContainer`. @mavaylon1 [#827](https://github.com/hdmf-dev/hdmf/pull/827)
- Updated warning message for broken links. @mavaylon1 [#829](https://github.com/hdmf-dev/hdmf/pull/829)

## HDMF 3.5.1 (January 26, 2023)

Expand All @@ -206,9 +210,9 @@ will increase the minor version number to 3.10.0. See the 3.9.1 release notes be
- Added ``HDMFIO.__del__`` to ensure that I/O objects are being closed on delete. @oruebel[#811](https://github.com/hdmf-dev/hdmf/pull/811)

### Minor improvements
- Added support for reading and writing `ExternalResources` to and from denormalized TSV files. @mavaylon [#799](https://github.com/hdmf-dev/hdmf/pull/799)
- Changed the name of `ExternalResources.export_to_sqlite` to `ExternalResources.to_sqlite`. @mavaylon [#799](https://github.com/hdmf-dev/hdmf/pull/799)
- Updated the tutorial for `ExternalResources`. @mavaylon [#799](https://github.com/hdmf-dev/hdmf/pull/799)
- Added support for reading and writing `ExternalResources` to and from denormalized TSV files. @mavaylon1 [#799](https://github.com/hdmf-dev/hdmf/pull/799)
- Changed the name of `ExternalResources.export_to_sqlite` to `ExternalResources.to_sqlite`. @mavaylon1 [#799](https://github.com/hdmf-dev/hdmf/pull/799)
- Updated the tutorial for `ExternalResources`. @mavaylon1 [#799](https://github.com/hdmf-dev/hdmf/pull/799)
- Added `message` argument for assert methods defined by `hdmf.testing.TestCase` to allow developers to include custom error messages with asserts. @oruebel [#812](https://github.com/hdmf-dev/hdmf/pull/812)
- Clarify the expected chunk shape behavior for `DataChunkIterator`. @oruebel [#813](https://github.com/hdmf-dev/hdmf/pull/813)

Expand Down Expand Up @@ -349,7 +353,7 @@ the fields (i.e., when the constructor sets some fields to fixed values). @rly
- 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`. @mavaylon (#673)
- 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)
Expand Down Expand Up @@ -425,7 +429,7 @@ the fields (i.e., when the constructor sets some fields to fixed values). @rly
- Allow passing ``index=True`` to ``DynamicTable.to_dataframe()`` to support returning `DynamicTableRegion` columns
as indices or Pandas DataFrame. @rly (#579)
- Improve ``DynamicTable`` documentation. @rly (#639)
- Updated external resources tutorial. @mavaylon (#611)
- Updated external resources tutorial. @mavaylon1 (#611)

### Breaking changes and deprecations
- Previously, when using ``DynamicTable.__getitem__`` or ``DynamicTable.get`` to access a selection of a
Expand Down Expand Up @@ -510,7 +514,7 @@ the fields (i.e., when the constructor sets some fields to fixed values). @rly
- Add experimental namespace to HDMF common schema. New data types should go in the experimental namespace
(hdmf-experimental) prior to being added to the core (hdmf-common) namespace. The purpose of this is to provide
a place to test new data types that may break backward compatibility as they are refined. @ajtritt (#545)
- `ExternalResources` was changed to support storing both names and URIs for resources. @mavaylon (#517, #548)
- `ExternalResources` was changed to support storing both names and URIs for resources. @mavaylon1 (#517, #548)
- The `VocabData` data type was replaced by `EnumData` to provide more flexible support for data from a set of
fixed values.
- Added `AlignedDynamicTable`, which defines a `DynamicTable` that supports storing a collection of sub-tables.
Expand Down

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