Support zarr v3

[alejoe91]

Fixes #4014 - UPDATED 16/10/2026

Implement bulk changes from zarr v2 to zarr v3

• create_dataset -> create_array
• Serialization of non JSON serializable objects (recording/sorting/extensions) not supported anymore
• Compressors use zarr.codecs, which wrap numcodecs compressor (e.g., Blosc -> BloscCodec)
• Codec Pipeline: improved generation of codec pipeline to automatically chain filters (ArrayArrayCodec), serializers (standard unless an ArrayBytesCodec is used - e.g. Wavpack), and compressors (BytesBytesCodec)
• Sharding: new sharding option in the zarr save functions (save(..., format="zarr")), with tests on chunks and shards
• Backward compatibility: loading objects written with zarr v2 (recordings, sortings, templates, SortingAnalyzer with extensions), including zarr_class_info, channel_ids dtype handling, and storage_options
• NWB / zarr:
  • zarr links are read from _LINKS for pynwb
  • zarr children iteration is wrapped to skip arrays whose metadata zarr v3 can't parse
  • streaming zarr (stream_mode="zarr") now works with zarr>=3 and its test is re-enabled
  • NWB-zarr tests only run the hdf5 backend when hdmf-zarr is not installed
• Python: requires-python >= 3.11. The hdmf-zarr>=0.14.0 extras are restricted to python_version>='3.12', since hdmf-zarr 0.14.0 requires Python >=3.12. NWB-zarr (pynwb) is therefore unavailable on 3.11, while plain zarr reading/writing and zarr streaming work everywhere.
• Removed the requires_zarr_write test marker (zarr writing is always available) and cleaned up tests
• CI:
  • cross-version serialization workflow checks v2 -> v3 compatibility (including dev) on all supported versions
  • numpy pinned <2.5 in the cross-serialization tests
  • deepinterpolation action disabled
• Docs: updated the compression section

Depends on:

• ProbeInterface: Support zarr v3 probeinterface#387
• NWB (hdmf-zarr) 0.14.0

[alejoe91]

@h-mayorquin not this is Python 3.11, with optional install of hdmf-zarr. Good to merge on my end!