Error with zarr v3, pin zarr<3

[sommerc]

Many thanks for this great and useful tool!

I noticed an issue with N5 writing using zarr v3.

  File "C:\Users\mdallave\AppData\Local\uv\cache\archive-v0\9_mtizE_WueqUcKm_uJTw\Lib\site-packages\pybdv\converter.py", line 593, in make_scales_dask
    store = zarr.N5FSStore(data_path, overwrite=overwrite)
            ^^^^^^^^^^^^^^
AttributeError: module 'zarr' has no attribute 'N5FSStore'

Using the latest zarr==2.8.17 resolved the issue.

Let me know if I should create a PR.

Cheers,
Chris

[constantinpape]

Hi @sommerc ,
n5 support was indeed removed from zarr v3. I am not sure about the best way to resolve this though. I don't really want to pin to zarr < 3 due to other important features in there (especially sharding). Maybe you could add a PR with a meaningful error message that indicates downgrading zarr when trying to use the dask converter with n5?

[sommerc]

True, yes I can do that.

In addition, what about an "extras_require" field for n5? Then zarr v2. could be installed with pybdv[n5]?

[sommerc]

I had a look at the pybdv source code, and it seems it relies on zarr v2 (e.g. using the old zarr.DirectoryStore).

Updating it to zarr v3, while keeping zarr v2 for the N5 realated parts seems not trivial to me....