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HDMF-ZARR Changelog

1.0.0 (Upcoming)

Enhancements

  • 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

Bug Fixes

  • Fix reading of cached specs and caching of specs during export. @rly #232

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
  • Added NWBZarrIO.read_nwb convenience method to simplify reading an NWB file. @oruebel #226

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 (May 2, 2024)

Enhancements

  • Added support for python 3.12. @mavaylon1 #172
  • Added support for forcing read of files without consolidated metadata using mode=r- in ZarrIO. @oruebel #183
  • Updated testing to not install in editable mode and not run coverage by default. @rly #188

Docs

  • Removed linkable from the documentation to keep in line with hdmf-schema-language. @mavaylon1 #180

Bug Fixes

  • Fixed bug in ZarrIO.__open_file_consolidated that led to remote files being opened without consolidated metadata. @oruebel #184
  • Fixed minor bug where ZarrIO.__open_file_consolidated used properties of ZarrIO instead of the provided input parameters. @oruebel #183

0.6.0 (February 21, 2024)

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
  • Updated writing references in compound datasets to same-sized array, rather than iteratively as an array of lists. @sneakers-the-rat #146

Bug Fixes

  • Fixed bug when converting HDF5 datasets with unlimited dimensions @oruebel #155
  • Fixed bug resolving bytes dtype when exporting from Zarr to Zarr @oruebel #161
  • Adjusted gallery tests to not fail on deprecation warnings from pandas. @rly #157
  • Fixed bug in pyproject.toml where duplicate versions of numcodec where specified. @oruebel #163

Internal Fixes

  • Updated actions in deploy_release.yml workflow to avoid use of deprecated Node.js 16. @oruebel #165

0.5.0 (December 8, 2023)

Enhancements

  • Added a new default to consolidate metadata in order more efficeintly traverse storage contents. @mavaylon1 #142
  • Fix linking for FSSpec and support passing of storage_options required reading data from S3 #138. @alejoe91 #120
  • Updated versioning to hatch-vcs and deprecated setup.py in full transition to pyproject.toml. @mavaylon1 #143

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 (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 (January 6, 2023)

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 dependencies @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

0.1.0 (August 23, 2022)

New features

  • Created new optional Zarr-based I/O backend for writing files using Zarr's zarr.store.DirectoryStore backend, including support for iterative write, chunking, compression, simple and compound data types, links, object references, namespace and spec I/O.