Zarr 3.0 compatibility #904
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #904 +/- ##
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- Coverage 99.90% 99.88% -0.03%
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Files 70 70
Lines 8735 8735
Branches 1149 1149
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- Hits 8727 8725 -2
- Misses 3 5 +2
Partials 5 5 ☔ View full report in Codecov by Sentry. |
Merged
shaneahmed
added
bug
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Zarr v3 is not compatible with tifffile cgohlke/tifffile#282 czbiohub-sf/iohub#292 |
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Zarr 3 is supported by tifffile. However, zarr 3 only supports Python 3.11+. |
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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