fix(omezarr): keep remote roots working under ngff-zarr 0.44 and later - #175
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Limit details: You’ve used all 4 included reviews currently available. Your 68 included PR review attempts over the past 7 days set your current allowance at 4 reviews per hour. 📝 WalkthroughWalkthroughThe OME-Zarr utilities now support URI-aware local and remote loading, remote metadata skeleton creation, and fallback handling for unsupported stepped lazy reads. Image, displacement, pyramid-level, pyramid, and metadata queries use the shared loader. ChangesOME-Zarr URI support
Estimated code review effort: 3 (Moderate) | ~20 minutes Merge Risk: ⚪ Minimal · up to This localized compatibility change is merge-ready after normal checks and review; no actionable merge-blocking risk remains. Sequence Diagram(s)sequenceDiagram
participant OMEZarrQuery
participant _from_ngff_zarr
participant fsspec
participant ngff_zarr
OMEZarrQuery->>_from_ngff_zarr: load remote URI
_from_ngff_zarr->>fsspec: create filesystem mapper
_from_ngff_zarr->>ngff_zarr: open mapped store
ngff_zarr-->>OMEZarrQuery: return OME-Zarr data or metadata
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Full details: Description checkExplanation The description clearly explains the compatibility problem, the implemented changes, related pull requests, and verification across supported zarr and ngff-zarr versions. It omits the template headings, explicit change-type selection, checklist status, and a direct statement about breaking changes, but the core required information is present. ✨ Finishing Touches📝 Generate docstrings
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Inline comments:
In `@konfai/utils/ome_zarr.py`:
- Line 1131: Update write_ome_zarr and the surrounding pyramid-level setup to
preserve the original remote URI string instead of converting it with
Path(store_path). Ensure _from_ngff_zarr receives the intact URI for loading the
base image, while using a temporary local path for metadata scratch-store
operations that currently rely on Path.with_name.
- Line 652: Update the span construction around the index comprehension so
negative-step slices preserve their source range: create an ascending unit-step
span covering the requested bounds before applying the original negative step.
Ensure a slice such as slice(8, 1, -2) yields indices 8, 6, 4, and 2 rather than
an empty result, while leaving non-negative-step handling unchanged.
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ngff-zarr >= 0.44 (the zarrista backend) reads a remote URL string as a local path, refuses stepped slices, and writes nothing a remote filesystem can see. The NGFF skeleton of a remote store is now written locally and uploaded through the root's own filesystem; a remote root is opened as a key-to-bytes mapping first, the URL second for older releases; and a lazy array that refuses a stepped slice is read over the unit-step span and stepped in numpy. Verified under zarr 3.1.6 and 3.3.0 with ngff-zarr 0.40, 0.44 and 0.45.
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CI went red on every PR without a code change: pip now resolves ngff-zarr >= 0.44, whose zarrista backend reads a remote URL string as a local path, refuses stepped slices, and writes nothing a remote filesystem can see. Reproduced identically on main with the same versions.
This carries the compatibility change alone, so every open PR can rebase on it: the NGFF skeleton of a remote store is written locally and uploaded through the root's own filesystem; a remote root is opened as a key-to-bytes mapping first, the URL second for older releases; a lazy array that refuses a stepped slice is read over the unit-step span and stepped in numpy.
Verified under zarr 3.1.6 and 3.3.0 with ngff-zarr 0.40, 0.44 and 0.45. #169 contains the same change and merges cleanly on top; merging this first turns #170-#174 green after a rebase.
Summary by CodeRabbit
New Features
Bug Fixes