⬆️ Zarr V3 compatibility

[measty]

Fixes the error related to zarr.errors.FSPathExistNotDir

It doesnt exist anymore since zarr v3.0.0, which instead just raises a standard FileNotFoundError

rather than checking for different error types in different versions of zarr, i've just removed the check for specific error type in favour of any errors

There are some other changes which we need to deal with from 3.0 also, as it has removed or changed zarr.LRUStoreCache, zarr.DirectoryStore, and zarr.SQLiteStore all of which tiatoolbox uses

We would also need to wait for tifffile to update to be compatible with zarr 3.0

See: https://zarr.readthedocs.io/en/latest/user-guide/v3_migration.html for more details

• 🆙 Upgrade Zarr >=3.08, tifffile>=2025.5.21
• Remove Python 3.10 as Zarr v3 has no support
• Remove object_codec in dask.to_zarr
• Refactor zarr.core.Array to zarr.Array
• Refactor canvas_zarr.store.path to canvas_zarr.store.root
• Refactor zarr.DirectoryStore to zarr.storage.LocalStore
• tuple input for zarr.resize
• Replace output.items() with output.members()
• Remove ngff.sqlitestore as zarr.SQLiteStore is no longer supported.
• Zarr path explicitly uses str key / i is replaced by key / str(i)

[codecov]

Codecov Report

❌ Patch coverage is 94.32624% with 8 lines in your changes missing coverage. Please review.
✅ Project coverage is 99.69%. Comparing base (36ecfa6) to head (58762df).

Files with missing lines	Patch %	Lines
tiatoolbox/utils/misc.py	87.50%	1 Missing and 2 partials ⚠️
tiatoolbox/wsicore/wsireader.py	94.73%	2 Missing and 1 partial ⚠️
tiatoolbox/models/engine/multi_task_segmentor.py	94.28%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #904      +/-   ##
===========================================
- Coverage    99.88%   99.69%   -0.19%     
===========================================
  Files           85       85              
  Lines        11576    11627      +51     
  Branches      1513     1523      +10     
===========================================
+ Hits         11563    11592      +29     
- Misses           6       20      +14     
- Partials         7       15       +8     

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[shaneahmed]

Zarr v3 is not compatible with tifffile cgohlke/tifffile#282 czbiohub-sf/iohub#292

[shaneahmed]

Zarr 3 is supported by tifffile. However, zarr 3 only supports Python 3.11+.

[shaneahmed]

All the errors have been fixed except FsspecJsonWSIReader.

[shaneahmed]

All the errors have been fixed except FsspecJsonWSIReader.

The updates to engines output breaks, test_hovernet_on_box which also needs to be fixed.

[aacic]

All the errors have been fixed except FsspecJsonWSIReader.

@shaneahmed I was able to make it work locally. I need some more time to verify the solution, and I'll try to submit a PR sometime next week. I'll keep you posted.

[shaneahmed]

All the errors have been fixed except FsspecJsonWSIReader.

@shaneahmed I was able to make it work locally. I need some more time to verify the solution, and I'll try to submit a PR sometime next week. I'll keep you posted.

Thank you @aacic That would be wonderful.

[shaneahmed]

All the errors have been fixed except FsspecJsonWSIReader.

The updates to engines output breaks, test_hovernet_on_box which also needs to be fixed.

@measty Please would you be able to check the error with test_hovernet_on_box? This is probably due to updates in the way new zarr output is saved.