0.11.0

hdmf-zarr 0.11.0

0.10.0

0.10.0 (December 18, 2024)

Enhancements

• Added initial refactor of export, supporting references and internal/external links from Zarr to Zarr. This will introduce breaking changes that could lead to existing exported files to be invalid. This update removes '.' as the object default file source. @mavaylon1 #194
• Added support for Pathlib paths. @mavaylon1 #212
• Updated packages used for testing and readthedocs configuration. @mavaylon1, @rly #214
• Add force_overwite parameter for ZarrIO.__init__ to allow overwriting an existing file or directory. @oruebel #229
• Remove allowance of hdmf.Array in __init__ of AbstractZarrTableDataset and ZarrDataset to be compatible with HDMF 4.0. @rly #236
• Remove support for python 3.8 and added testing for Python 3.13. @mavaylon1 #240
• Added NWBZarrIO.read_nwb convenience method to simplify reading an NWB file. @oruebel #226
• Updated optional dependency groups in pyproject.toml and GitHub Actions workflows. @rly, @mavaylon1 #239
• Applied black code formatter. @rly #247

Bug Fixes

• Fix reading of cached specs and caching of specs during export. @rly #232
• Fix hiding of pynwb compatibility errors. @rly 242

0.9.0

0.9.0 (September 16, 2024)

Enhancements

• Added support for appending a dataset of references. @mavaylon1 #203
• NWBZarrIO load_namespaces=True by default. @mavaylon1 #204
• Added test for opening file with consolidated metadata from DANDI. @mavaylon1 #206
• Add dimension labels compatible with xarray. @mavaylon1 #207
• Added link_data --> clear_cache relationship to support repacking zarr nwbfiles: #215

0.8.0

0.8.0 (June 4, 2024)

Bug Fixes

• Fixed bug when opening a file in with mode=r+. The file will open without using the consolidated metadata. @mavaylon1 #182
• Fixed bug on how we access scalar arrays. Added warning filter for Zarr deprecation of NestedDirectoryStore. Fixed bug on how we write a dataset of references. @mavaylon1 #195

0.7.0

hdmf-zarr 0.7.0

0.6.0

hdmf-zarr 0.6.0

0.5.0

hdmf-zarr 0.5.0

0.4.0

0.4.0 (October 3, 2023)

Enhancements

• Enhanced ZarrIO to resolve object references lazily on read similar to HDMF's HDF5IO backend. @mavaylon1 #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

New Features

• Added parallel write support for the ZarrIO for datasets wrapped with GenericDataChunkIterator. @CodyCBakerPhD #118 @oruebel #128

Dependencies

• Updated HDMF and PyNWB version to the most recent release @mavaylon1 #120
• Updated minimum Python version from 3.7 to 3.8 @mavaylon1 #120
• Added threadpoolctl dependency for parallel write. @CodyCBakerPhD #118
• Added support for specifying optional dependencies and add optional dependency for tqdm used in parallel write. @CodyCBakerPhD #118

Bug fixes

• Fixed error in deploy workflow. @mavaylon1 #109
• Fixed build error for ReadtheDocs by degrading numpy for python 3.7 support. @mavaylon1 #115
• Fixed bug in the resolution of references to Containers. Previously references were only resolved to Builders. @mavaylon1 #120

0.3.0

0.3.0 (July 21, 2023)

New Features

• Added support, tests, and docs for using DirectoryStore, TempStore, and
  NestedDirectoryStore Zarr storage backends with ZarrIO and NWBZarrIO.
  @oruebel #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
• Added can_read classmethod to ZarrIO. @bendichter #97

Test suite enhancements

• Modularized unit tests to simplify running tests for multiple Zarr storage backends.
  @oruebel #62
• Fixed CI testing of minimum and optional installation requirement. @rly
  #99
• Updated tests to handle upcoming changes to HDMFIO. @rly
  #102

Docs

• Added developer documentation on how to integrate new storage backends with ZarrIO. @oruebel
  #62

API Changes

• Removed unused filepath argument from ZarrIO.get_builder_exists_on_disk #62

Bug fixes

• Fixed error in nightly CI. @rly #93

0.2.0

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
• Fixed bugs in requirements defined in setup.py @oruebel #46
• Fixed bug regarding Sphinx external links @mavaylon1 #53
• Updated gallery tests to use test_gallery.py and necessary package dependcies
  @mavaylon1 #53
• Updated dateset used in conversion tutorial, which caused warnings
  @oruebel #56

Docs

• Added tutorial illustrating how to create a new NWB file with NWBZarrIO
  @oruebel #46
• Added docs for describing the mapping of HDMF schema to Zarr storage
  @oruebel #48
• Added docs/gallery/resources for storing local files used by the tutorial galleries
  @oruebel #61
• Removed dependency on dandi library for data download in the conversion tutorial by storing the NWB files as
  local resources @oruebel #61