Validate element-type selection when reading Zarr stores - #1253
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kayoderaheem wants to merge 2 commits into
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kayoderaheem wants to merge 2 commits into
kayoderaheem wants to merge 2 commits into
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1253 +/- ##
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+ Coverage 91.40% 91.66% +0.25%
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Files 53 53
Lines 8381 8384 +3
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+ Hits 7661 7685 +24
+ Misses 720 699 -21
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Fixes #1172.
Invalid selection names currently pass through silently, which can return an empty SpatialData object or load only part of the requested data.
This change validates selection names before opening the Zarr store and raises a descriptive ValueError for invalid names or a bare string. It also narrows the type annotations for both reader entry points and corrects the SpatialData.read() documentation to use "tables".
Existing behavior is preserved for None, empty tuples, duplicate valid names, and valid element types absent from the store.
Testing: the new regression tests produced 8 failures and 14 passes before the fix, and all 22 passed afterward. Together with the existing read/write and partial-read suites, 177 tests passed, with 545 warnings. Ruff lint, formatting, and whitespace checks also passed. The full project suite and Python-version matrix were not run.
The issue discussion suggests narrower typing and optionally an assertion. This implementation uses ValueError so validation remains active under optimized Python. Feedback on that choice is welcome.