Bug 2338926

Summary: Incompatible with Zarr 3
Product: [Fedora] Fedora Reporter: Elliott Sales de Andrade <quantum.analyst>
Component: python-hdmfAssignee: Luis Bazan <bazanluis20>
Status: CLOSED RAWHIDE QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: medium Docs Contact:
Priority: unspecified    
Version: 42CC: bazanluis20, code, neuro-sig
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OS: Linux   
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Last Closed: 2025-12-21 07:21:36 UTC Type: ---
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Bug Blocks: 2264279    

Description Elliott Sales de Andrade 2025-01-20 00:15:31 UTC 
I've prepared a test build of this package with Zarr 3 which shows it is not compatible yet: https://copr.fedorainfracloud.org/coprs/qulogic/zarr3/build/8547556/

I've reported a bug upstream already.

Reproducible: Always

Steps to Reproduce:
Build against the linked copr.
Actual Results:  
=========================== short test summary info ============================
FAILED tests/unit/test_io_hdf5_h5tools.py::TestWriteHDF5withZarrInput::test_roundtrip_basic
FAILED tests/unit/test_io_hdf5_h5tools.py::TestWriteHDF5withZarrInput::test_roundtrip_empty_dataset
FAILED tests/unit/test_io_hdf5_h5tools.py::TestWriteHDF5withZarrInput::test_write_zarr_dataset_compress_gzip
FAILED tests/unit/test_io_hdf5_h5tools.py::TestWriteHDF5withZarrInput::test_write_zarr_float32_dataset
FAILED tests/unit/test_io_hdf5_h5tools.py::TestWriteHDF5withZarrInput::test_write_zarr_int32_dataset
FAILED tests/unit/test_io_hdf5_h5tools.py::TestWriteHDF5withZarrInput::test_write_zarr_string_dataset
===== 6 failed, 1504 passed, 80 skipped, 1 xfailed, 96 warnings in 17.67s ======

Expected Results:  
Build should pass
Comment 1 Ben Beasley 2025-02-05 18:21:36 UTC 
As noted in the upstream issue https://github.com/hdmf-dev/hdmf/issues/1235, HDMF 4.0.0 (https://src.fedoraproject.org/rpms/python-hdmf/pull-request/24) still doesn’t support Zarr 3, at least initially.

However, hdmf 4.0.0 did restore the "zarr" extra that was removed in 3.14.2, so we do have more options now. If it gets to the point where hdmf is one of the last packages blocking a zarr update, and upstream support is still not available, we could drop and obsolete the python3-hdmf+zarr metapackage, on which nothing currently depends.
Comment 2 Aoife Moloney 2025-02-26 13:24:47 UTC 
This bug appears to have been reported against 'rawhide' during the Fedora Linux 42 development cycle.
Changing version to 42.
Comment 3 Ben Beasley 2025-12-21 07:21:36 UTC 
This is *not* fixed upstream or downstream, but it has become irrelevant for now. Since hdmf 4.1.1, preserving the metapackage for the zarr extra would have required packaging an additional dependency, https://pypi.org/project/hdmf-zarr/. I didn’t want to do that (nothing would have depended on the extra), so I dropped the zarr extra metapackage in Fedora starting with F44. As described in https://bugzilla.redhat.com/show_bug.cgi?id=2338926#c1 above, that means this package is no longer one of the blockers for upgrading zarr.