Comments (2)
Attempting to fix this proved to be more than a few minutes of import changes. The Zarr Python API changes quite a bit from v2 to v3, and it seems like some things that we use like ProcessSynchronizer and ThreadSynchronizer have been removed/replaced. I haven't looked deeply into it yet. But for now, I think we should limit zarr<3
until we can provide proper zarr-python v3 support
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some things that we use like ProcessSynchronizer and ThreadSynchronizer have been removed/replaced.
The main part where the synchronizers come in is in how we open the file:
hdmf-zarr/src/hdmf_zarr/backend.py
Line 158 in 58e2d45
and then that is being configured in the __init__
is here:
hdmf-zarr/src/hdmf_zarr/backend.py
Lines 109 to 116 in 58e2d45
We are really not doing anything special with the synchronizers and in most common cases, I think the synchronizer is not being used (I think this mainly comes in for parallel I/O). So if we need to update this for Zarr 3, I think we should be able doable to keep the changes centered around file open logic.
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Related Issues (20)
- [Bug]: Deploy and release workflow fails due to unsupported actions
- [Feature]: support Python 3.12 HOT 4
- [Feature]: Refactor tox.ini to match HDMF
- [Feature]: Write zarr without using pickle HOT 5
- kerchunk considerations HOT 23
- [Feature]: write `xarray`-compatible Zarr files HOT 9
- [Documentation]: `linkable` key has been deprecated HOT 2
- [Bug]: `export` fails to correctly save units after adding columns HOT 7
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- [Feature]: Use `copy_store` for copying existing zarr data HOT 5
- [Bug]: Zarr 2.18.0 with Blosc HOT 5
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- [Bug]: Writing NWB with `experimenter` (or any `ArrayLike[str]`) fails HOT 4
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