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Materialize aligned images at the CellProfiler full-stack contract boundary (#342) - #344

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trissim merged 13 commits into
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fix/cp-aligned-materialization-20261001
Oct 1, 2026
Merged

trissim merged 13 commits into
mainfrom
fix/cp-aligned-materialization-20261001

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@trissim trissim commented Oct 1, 2026 •

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Fixes #342. Parent-installed engineering acceptance completed; source owner Darwin, integration owner parent.

The existing ImagePayloadStackComposition ancestor owns shared pixel, mask and provenance composition. Dense contexts, same-slice bundles, aligned runtime stacks and named bundles use small domain hooks. Existing registered nominal projection strategies materialize aligned primary/auxiliary images before the real full-stack callable. Opaque whole-stack kwargs retain identity; slice-mode resolution remains strict. No callable-name switch, parallel registry, wrapper executor or duplicated numeric algorithm.

Evidence:

  • 117 source family cases and 45 source consumer cases pass. Independent pixel/mask test capabilities exercise cooperative super in both MRO orders. Original R0 passes unchanged; no global equivalence certificate is claimed.
  • Reviewed private wheel: 21 installed numeric cases pass, including opaque kwargs, calibrated subtype, source identity, masks and named-bundle/MRO behavior. Original installed opaque failure remains retained separately.
  • Actual installed MCP/native journey: fresh synthetic fixture, exact four selected channel/Z planes, complete PipelineDocument, artifact-plan inspection, headless compile and execution through ordinary registered RescaleIntensity, persisted inventory and full-resolution MCP sampling. Compile completes in 1.823s; execution in 0.745s. All 8192 pixel comparisons across ordinary and named output destinations match the expected global stretch within 1.23e-7. Output follows its declared first-source lineage and calibration.
  • Three initial engineering ingress failures are retained. The example now declares TIFF filtering, filename metadata, metadata pairing and explicit semantic channel identity through existing source-binding authorities. No guard bypass or source-selection library patch.
  • Exact owned native handle closed successfully with process_exited=true; MCP/client/native PIDs and listeners are gone. No frozen H003g retry, user-desktop interaction, new viewer, download or global package install.

Parent receipt: docs/refactor/344-installed-native-acceptance.rst. Reproducible transcript, inputs, outputs, runtime observation, verifier, JUnit/build/failure logs: docs/refactor/receipts/cp-stack-installed-native-344-20261001.tar.gz, SHA256 d6d53528b2a8508f4004a6d1d6b7adfc411a7dea9a1ed1844bb19736731faad5. Fresh-extraction recorded-payload verifier passes. Source/nominal/acquisition evidence is separately indexed in diagnostics/README.rst and docs/refactor/cp-aligned-full-stack-342.rst.

Limits: full NRA/R1 remains unqualified (original import/dependency-context failures and retained full-context parsing deadline). MCP does not directly expose the pre-materialization carrier or a nontrivial validity mask in this journey; those witnesses remain source/installed controls. Missing output grid_dimensions warning and shell exit1 are retained. This is installed dense-ABI continuity, not biological QA, blind generalization, all-backend/GPU coverage or complete S1/ZIP closure. H003g remains FAILED. Hosted CI is deferred under the owner's instruction; actual installed acceptance, not source tests alone, supports this checkpoint.

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trissim commented Oct 1, 2026

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Parent installed gate on source34203be integrated with merged main05c3cf288:

The isolated wheel's changed production files match source, and all15 numeric family tests pass through the installed package (2.70s,269MiB). A separate installed boundary check found an additional regression: full_stack_kwargs({'options': object()}) raises RuntimeSliceProjectionDeclarationError instead of preserving the opaque argument by identity. Exact failure retained; this is not a passing live gate.

Darwin already owns the repair in this PR: use the existing nominal strategy family for declared alignment while preserving opaque whole-stack arguments, with new-case/calibration and actual callable controls. Parent will consume the published coherent fix and repeat the affected installed/native synthetic path before merging. No competing implementation, native process, science retry or held-out/reference access was started. H003g remains frozen FAILED; NRA/R1 remains incomplete.

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trissim marked this pull request as ready for review October 1, 2026 08:14
Copilot AI balanced review requested due to automatic review settings October 1, 2026 08:14

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@trissim
trissim merged commit e7f7c05 into main Oct 1, 2026
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CellProfiler full-stack contract passes AlignedImageStack into dense scalar callable

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