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fix: delegate v3 inference I/O through copick - #41

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fix: delegate v3 inference I/O through copick#41
uermel wants to merge 4 commits into
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@uermel

@uermel uermel commented Aug 19, 2026

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Tracks #35 and is the second PR in the copick-easymode OME-Zarr 0.5 / Zarr v3 migration stack.

This keeps volume ownership in copick and proves the handoff with real local copick entities:

  • equivalent numeric/nonnumeric OME-Zarr 0.4 / Zarr v2 and OME-Zarr 0.5 / Zarr v3 inputs;
  • canonical core-writer and noncanonical gzip/chunk layouts;
  • identical model inputs, exact threshold semantics, and uint8 output;
  • OME-Zarr 0.5 / Zarr v3 output validation through the public OME model;
  • consistent sanitized copick identities while preserving raw easymode model lookup;
  • exist_ok=True entity reuse for working overwrite behavior;
  • skip-before-read and v2/v3 failed-inference preservation contracts; and
  • model/run failure continuation, config-save timing, and unconditional runtime cleanup.

Validation: 31 tests pass against the published copick==2.0.0a1 environment.

No direct Zarr/OME storage code is added to the package runtime, and no release or publication work is included.

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