Hdmf-zarr

Enhancements
* Added support for python 3.12. mavaylon1 [172](https://github.com/hdmf-dev/hdmf-zarr/pull/172)
* Added support for forcing read of files without consolidated metadata using `mode=r-` in `ZarrIO`. oruebel [183](https://github.com/hdmf-dev/hdmf-zarr/pull/183)
- Updated testing to not install in editable mode and not run `coverage` by default. rly [188](https://github.com/hdmf-dev/hdmf-zarr/pull/188)

Docs
* Removed `linkable` from the documentation to keep in line with `hdmf-schema-language`. mavaylon1 [180](https://github.com/hdmf-dev/hdmf-zarr/pull/180)

Bug Fixes
* Fixed bug in `ZarrIO.__open_file_consolidated` that led to remote files being opened without consolidated metadata. oruebel [184](https://github.com/hdmf-dev/hdmf-zarr/pull/184)
* Fixed minor bug where `ZarrIO.__open_file_consolidated` used properties of `ZarrIO` instead of the provided input parameters. oruebel [183](https://github.com/hdmf-dev/hdmf-zarr/pull/183)

Enhancements
* Enhanced `ZarrIO` and `ZarrDataIO` to infer io settings (e.g., chunking and compression) from HDF5 datasets to preserve storage settings on export if possible oruebel [153](https://github.com/hdmf-dev/hdmf-zarr/pull/153)
* Updated writing references in compound datasets to same-sized array, rather than iteratively as an array of lists. sneakers-the-rat [146](https://github.com/hdmf-dev/hdmf-zarr/pull/146)

Bug Fixes
* Fixed bug when converting HDF5 datasets with unlimited dimensions oruebel [155](https://github.com/hdmf-dev/hdmf-zarr/pull/155)
* Fixed bug resolving bytes dtype when exporting from Zarr to Zarr oruebel [161](https://github.com/hdmf-dev/hdmf-zarr/pull/161)
* Adjusted gallery tests to not fail on deprecation warnings from pandas. rly [157](https://github.com/hdmf-dev/hdmf-zarr/pull/157)
* Fixed bug in `pyproject.toml` where duplicate versions of `numcodec` where specified. oruebel [163](https://github.com/hdmf-dev/hdmf-zarr/pull/163)

Internal Fixes
* Updated actions in `deploy_release.yml` workflow to avoid use of deprecated Node.js 16. oruebel [165](https://github.com/hdmf-dev/hdmf-zarr/pull/165)

Enhancements
* Added a new default to consolidate metadata in order more efficeintly traverse storage contents. mavaylon1 [142](https://github.com/hdmf-dev/hdmf-zarr/pull/142)
* Fix linking for FSSpec and support passing of `storage_options` required reading data from S3 138. alejoe91 [120](https://github.com/hdmf-dev/hdmf-zarr/pull/138)
* Updated versioning to hatch-vcs and deprecated setup.py in full transition to `pyproject.toml`. mavaylon1 [143](https://github.com/hdmf-dev/hdmf-zarr/pull/143)

Enhancements
* Enhanced ZarrIO to resolve object references lazily on read similar to HDMF's `HDF5IO` backend. mavaylon1 [120](https://github.com/hdmf-dev/hdmf-zarr/pull/120)
* Updated storage of references to also save the ``object_id`` and ``source_object_id``. While not strictly necessary this information is useful for validation and rigor of references. oruebel [57](https://github.com/hdmf-dev/hdmf-zarr/pull/57)

New Features
* Added parallel write support for the ``ZarrIO`` for datasets wrapped with ``GenericDataChunkIterator``. CodyCBakerPhD [118](https://github.com/hdmf-dev/hdmf-zarr/pull/118) oruebel [#128](https://github.com/hdmf-dev/hdmf-zarr/pull/128)

Dependencies
* Updated HDMF and PyNWB version to the most recent release mavaylon1 [120](https://github.com/hdmf-dev/hdmf-zarr/pull/120)
* Updated minimum Python version from 3.7 to 3.8 mavaylon1 [120](https://github.com/hdmf-dev/hdmf-zarr/pull/120)
* Added ``threadpoolctl`` dependency for parallel write. CodyCBakerPhD [118](https://github.com/hdmf-dev/hdmf-zarr/pull/118)
* Added support for specifying optional dependencies and add optional dependency for ``tqdm`` used in parallel write. CodyCBakerPhD [118](https://github.com/hdmf-dev/hdmf-zarr/pull/118)

Bug fixes
* Fixed error in deploy workflow. mavaylon1 [109](https://github.com/hdmf-dev/hdmf-zarr/pull/109)
* Fixed build error for ReadtheDocs by degrading numpy for python 3.7 support. mavaylon1 [115](https://github.com/hdmf-dev/hdmf-zarr/pull/115)
* Fixed bug in the resolution of references to Containers. Previously references were only resolved to Builders. mavaylon1 [120](https://github.com/hdmf-dev/hdmf-zarr/pull/120)

New Features
* Added support, tests, and docs for using ``DirectoryStore``, ``TempStore``, and
``NestedDirectoryStore`` Zarr storage backends with ``ZarrIO`` and ``NWBZarrIO``.
oruebel [62](https://github.com/hdmf-dev/hdmf-zarr/pull/62)

Minor enhancements
* Updated handling of references on read to simplify future integration of file-based Zarr
stores (e.g., ZipStore or database stores). oruebel [62](https://github.com/hdmf-dev/hdmf-zarr/pull/62)
* Added ``can_read`` classmethod to ``ZarrIO``. bendichter [97](https://github.com/hdmf-dev/hdmf-zarr/pull/97)

Test suite enhancements
* Modularized unit tests to simplify running tests for multiple Zarr storage backends.
oruebel [62](https://github.com/hdmf-dev/hdmf-zarr/pull/62)
* Fixed CI testing of minimum and optional installation requirement. rly
[99](https://github.com/hdmf-dev/hdmf-zarr/pull/99)
* Updated tests to handle upcoming changes to ``HDMFIO``. rly
[102](https://github.com/hdmf-dev/hdmf-zarr/pull/102)


Docs
* Added developer documentation on how to integrate new storage backends with ZarrIO. oruebel
[62](https://github.com/hdmf-dev/hdmf-zarr/pull/62)

API Changes
* Removed unused ``filepath`` argument from ``ZarrIO.get_builder_exists_on_disk`` [62](https://github.com/hdmf-dev/hdmf-zarr/pull/62)

Bug fixes
* Fixed error in nightly CI. rly [93](https://github.com/hdmf-dev/hdmf-zarr/pull/93)

Bugs
* Updated the storage of links/references to use paths relative to the current Zarr file to avoid breaking
links/reference when moving Zarr files oruebel [46](https://github.com/hdmf-dev/hdmf-zarr/pull/46)
* Fixed bugs in requirements defined in setup.py oruebel [46](https://github.com/hdmf-dev/hdmf-zarr/pull/46)
* Fixed bug regarding Sphinx external links mavaylon1 [53](https://github.com/hdmf-dev/hdmf-zarr/pull/53)
* Updated gallery tests to use test_gallery.py and necessary package dependencies
mavaylon1 [53](https://github.com/hdmf-dev/hdmf-zarr/pull/53)
* Updated dateset used in conversion tutorial, which caused warnings
oruebel [56](https://github.com/hdmf-dev/hdmf-zarr/pull/56)

Docs
* Added tutorial illustrating how to create a new NWB file with NWBZarrIO
oruebel [46](https://github.com/hdmf-dev/hdmf-zarr/pull/46)
* Added docs for describing the mapping of HDMF schema to Zarr storage
oruebel [48](https://github.com/hdmf-dev/hdmf-zarr/pull/48)
* Added ``docs/gallery/resources`` for storing local files used by the tutorial galleries
oruebel [61](https://github.com/hdmf-dev/hdmf-zarr/pull/61)
* Removed dependency on ``dandi`` library for data download in the conversion tutorial by storing the NWB files as
local resources oruebel [61](https://github.com/hdmf-dev/hdmf-zarr/pull/61)