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

diagnostics/.gitignore

@@ -0,0 +1,5 @@
+# Raw receipts are preserved in the reviewed tar.gz, byte-for-byte.
+*.log
+*.xml
+*.json
+*.stderr

diagnostics/ACQUISITION_SHA256SUMS

@@ -0,0 +1,15 @@
+3514ad8f2346e5b5e82aaf4410610afc2fc8616eaf4596d5af1eaa387a85efe5  openhcs/core/aligned_image_payload.py
+cd6c7553efba0838205f153e96b15570c285894e304827d8c3f3d0c38de664bd  openhcs/core/runtime_slice_projection.py
+51fa66703e1d789c199ba485f80ec71152bb1f64a3864ed2414d167660ffc2f8  openhcs/interop/cellprofiler/runtime/function_contract_execution.py
+939b5cfa8c32eb2db38cee2606ffa755be3eaf96fbe3640674f038ced125f5fc  diagnostics/README.rst
+2dd04e5005b9cde8b1b9b86f0d17e3b9c45120795e9be0ed9b556787b33ffdf2  diagnostics/run_source_tests.py
+9599cb9152d642e834b4056d820856c3dba9593647ea7554c36f0589c72b3798  diagnostics/test_344_engineering_document.py
+f398b5db2435208a1317f0e97bf347e7e837e4b64f91ac0887e2e571d6da913c  diagnostics/test_344_source_binding_ingress.py
+0df290b3cb92862b5aba67a27f45558d0d6f10cd53504f9fffab6f6378a9c296  docs/refactor/344-engineering-acceptance.rst
+323ab83b8462a9a8f4e8cc873e446eab1de15a114a3f3a07740ea8b682b7666f  docs/refactor/examples/344-aligned-rescale-engineering.py
+4679d9be9612f31adb1dd42dad7efae887484466edf7fad6afe7e7937bccf095  diagnostics/engineering-source-bindings-ingress.log
+54f76ba7e2240dacadaaf95dedee73620a46dcd5650b79a9bedfec1b6c6a0391  diagnostics/engineering-source-bindings-ingress.xml
+0f9b93720ac0fe0c7c3b9ebc78c2dfeb6fa710173b071659e0d1f9072606c459  diagnostics/engineering-source-bindings-identity-controls.log
+79b7422ea0f90d73a7de03e2042e20c47af77cdbd9c51f643a76688dc1b57173  diagnostics/engineering-source-bindings-identity-controls.xml
+ef0531fa77aa73b5a47cbf40210d516cca94b8dc72330b1de0ab6d9c7ff4397a  diagnostics/engineering-acquisition-final-source.log
+5381057c14505fa925ff9e070ff3c2ed7ab839d85e7d98b74fb4979503a52994  diagnostics/engineering-acquisition-final-source.xml

diagnostics/NOMINAL_REVIEW_SHA256SUMS

@@ -0,0 +1,25 @@
+3514ad8f2346e5b5e82aaf4410610afc2fc8616eaf4596d5af1eaa387a85efe5  openhcs/core/aligned_image_payload.py
+cd6c7553efba0838205f153e96b15570c285894e304827d8c3f3d0c38de664bd  openhcs/core/runtime_slice_projection.py
+51fa66703e1d789c199ba485f80ec71152bb1f64a3864ed2414d167660ffc2f8  openhcs/interop/cellprofiler/runtime/function_contract_execution.py
+ffc6bfe96a431e72611da4e287d496065af9d4bed71984881a29c3f7a902a1ec  tests/unit/test_cellprofiler_full_stack_materialization.py
+ae1313ed11505caf35ef1d3e183b811a0d8968a187ff45f73cba1e30a572a63b  diagnostics/README.rst
+2dd04e5005b9cde8b1b9b86f0d17e3b9c45120795e9be0ed9b556787b33ffdf2  diagnostics/run_source_tests.py
+9599cb9152d642e834b4056d820856c3dba9593647ea7554c36f0589c72b3798  diagnostics/test_344_engineering_document.py
+b7493d7e12dafec853e02498f6f65979859c5c041010716bd4cf9f4669318fd4  docs/refactor/cp-aligned-full-stack-342.rst
+7183385aa0e0a5b79ec9fb343f596c79de29668d608154fdb48c7c0560e26d0b  docs/refactor/344-engineering-acceptance.rst
+5e0e39229fcfeb34548565dafeb6b04a4dbaa4b40c03603ef65d4f924d6608e2  docs/refactor/examples/344-aligned-rescale-engineering.py
+d9a74653eda0f076d505bd42471d09b24c66057ac91d8e5678fe74720bc06526  diagnostics/nominal-review-family-controls.log
+6611a228f092fc75374580b61f710f454bf24f6ac61617815d3bc34cc500fe28  diagnostics/nominal-review-family-controls.xml
+93bdd1a80cdd48b9ff3ff5c28a0d8ea449f934d9ec212a5c0ddf3f5796225ec0  diagnostics/nominal-review-opaque-controls.log
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+e79acaefe8b1e66a5b0f95b20c21e5c8040116d7939e178713582396962da39d  diagnostics/a14-consumer-controls.xml
+c9ac3b4f586accb4d7993b7b20c70f9035a53d195195b7532f61941091609ca9  diagnostics/a14-r0-openhcs.log
+96331d5fe50a4bd165a433b503caedbef0c2b4a2cf10689aeb5314f343c7e3ad  diagnostics/a14-r0-scripts.log
+c1d63a1befd427c68ecb3f5ea30f7e60ce72a361dbb979e36aef74cb46f74307  diagnostics/a14-r0-benchmark.log
+5938b383ffbd7bd3899cf642f956e0c12019b9549b4f0f68acaa675beb41ee8e  diagnostics/engineering-document-source.log
+b9213321e2975c2ec76550c6cfd02592a4b63ad63592061e13021468efe7a1c0  diagnostics/engineering-document-source.xml
+0621f1642170818f6c73edf6477a9052f71a1d61163296d2dbb7c3612796892c  diagnostics/engineering-document-source-corrected.log
+e88365a2b02946daebd1952f360047f6a5de4e76aaa0adaff3ab1d98262b9947  diagnostics/engineering-document-source-corrected.xml
+3f823fd0246416a730e68aed4eb63ef1cd4113d2d1d3319b1db74091a7f9e444  diagnostics/engineering-document-separate-planes.log
+2a0fd5014902bd62a8ba5638a0de37111d185db93ae27b40d315d6516e66a3ed  diagnostics/engineering-document-separate-planes.xml

diagnostics/README.rst

@@ -0,0 +1,156 @@
+Runtime repair #342 source receipts
+==================================
+
+Latest engineering authoring disposition
+---------------------------------------
+
+The public example is corrected to the parent's admitted acquisition contracts:
+IS_TIF filter; exact FILE_NAME acquisition metadata; METADATA pairing on
+well/site/z_index/timepoint; per-alias CHANNEL component_identity. The failed
+minimal example at 327cec9f6 remains in Git and the original a14 archive.
+No production code changes after a14d471e3. The existing native handler does
+not promise named source projection; do not infer ingestion owner from a
+requested microscope enum or input occurrences from storage-plan rendering.
+
+engineering-acquisition-final-source: 6 PASS, 2.78s pytest / 3.50s wall /
+334736 KiB RSS. Document parsing and synthetic path/declaration checks only;
+no pixel load, initialization, compile, scientific execution or native startup.
+engineering-source-bindings-ingress: initial 3 PASS / 1 FAIL, incorrect expected
+exception class for an existing metadata conflict; original receipt retained.
+engineering-source-bindings-identity-controls: 5 PASS, before final adoption
+of the parent's precise complete authoring recipe. Source receipts remain
+separate from the parent's installed21 and continuous installed MCP/native gate.
+Parent reports compile/run complete, 8192 comparisons with maximum error
+1.23e-7, exact declared calibration/first-source scope; no direct carrier/mask
+inspection and no biology or R1 acceptance. See 344-engineering-acceptance.rst.
+
+New authoring receipts: docs/refactor/receipts/cp-aligned-full-stack-342-acquisition.tar.gz
+and diagnostics/ACQUISITION_SHA256SUMS. Prior archives/manifests are unchanged;
+their source hashes authenticate their recorded snapshots, not this revised example.
+
+Owner: H003g runtime repair worker under parent integration; draft PR #344.
+H003g is permanently FAILED. These are synthetic source checks, not a trial
+retry, installed acceptance, result QA or biological success evidence.
+
+Runner: run_source_tests.py. It prepends this worktree's Python source and
+uses only the unchanged installed _tabular_native.abi3.so from
+/home/ts/wt/openhcs-s1-installed-parent-20261001. Existing dependency packages
+are reused without any download, build, install or configuration change.
+All execution shards use CPU affinity 0, one CPU quota, 512 MiB MemoryMax,
+zero swap, 60-second timeout, OPENHCS_CPU_ONLY=true, numerical threads 1,
+and PYTEST_DISABLE_PLUGIN_AUTOLOAD=1. Two unknown asyncio configuration
+warnings are expected because optional pytest plugins are disabled.
+
+Predecessor receipt interpretation (public 34203beb1)
+---------------------------------------------------
+
+merged-main-final-family-controls: 111 PASS, including 15 added full-stack
+tests plus 96 existing executor/projection/alignment/device/registry controls.
+merged-main-consumer-regressions: 45 PASS, including the unchanged-main ABI
+fixture corrected using the real diagnostic declaration owner.
+r0-merged-main-openhcs/scripts/benchmark: all PASS. Base main 7b0ec3f5,
+head b7702664, exact three changed production paths. Subsequent edits affect
+only tests/documentation/receipt packaging until the subsequent a14 correction.
+
+r1-original: import failure BEFORE scanning. The existing current NRA
+environment does not export RedundantTypeCheckDetector at the original
+guard's import site. Worktree external gitlinks are uninitialized as well.
+No passing R1 certificate or complete dependency-context audit is claimed.
+nra-before-corrected: deadline_incomplete structured report with null counts,
+20-second CLI deadline, parsing unfinished. Its admitted candidate external
+directory is uninitialized. This is NOT a successful no-findings report.
+
+Current source correction (a14d471e3)
+------------------------------------
+
+nominal-review-opaque-controls: 117 PASS (21 full-stack cases plus 96 existing
+family controls), 3.36 seconds pytest, 322644 KiB RSS. New calibrated subtype,
+real runtime-plane named bundle and opaque kwargs across all four contracts.
+a14-consumer-controls: 45 PASS, 3.96 seconds pytest, 372732 KiB RSS.
+a14-r0-openhcs/scripts/benchmark: exact original CI-pinned packaged ratchet,
+base main 7b0ec3f5, head a14d471e3, all PASS. Root wall times 16.93/1.88/2.45
+seconds, RSS 88124/59020/57732 KiB. Optional-neutral nominal resolution is
+the only additional production change after 34203beb1; opaque values keep
+identity at FULL_STACK while slice-mode registration remains strict.
+
+engineering-document-separate-planes: 1 PASS, source authoring only, 1.95
+seconds pytest / 2.55 seconds wall / 277676 KiB RSS. The initial
+decorator-wrapper object-identity failure and corrected
+nominal/raw-callable identity receipt remain in the supplemental archive.
+No compile, fixture pixels, MCP/native/viewer or installed check was run here.
+The complete document and identity/path/metadata acceptance gates are under
+docs/refactor/344-engineering-acceptance.rst and examples/.
+
+Parent independently retains the original installed opaque-kwargs failure;
+those predecessor receipts are not relabelled. Parent owns the normal main
+integration, paired rebuilt wheel and fresh installed/native numeric gate.
+Original R1 remains unqualified for the previously recorded environment and
+dependency-context limits; no new R1 completeness claim is made.
+
+Supplement: docs/refactor/receipts/cp-aligned-full-stack-342-a14-supplement.tar.gz.
+NOMINAL_REVIEW_SHA256SUMS authenticates the current three production files,
+test/document sources and new byte-preserved raw receipts. The original
+cp-aligned-full-stack-342-20261001.tar.gz and SHA256SUMS are unchanged.
+
+Unsuccessful receipts remain in the archive: first-repair slotted-dataclass
+super error; family-controls fixture argument and named bundle failure;
+family-controls-corrected mask-domain failure; complete-owned-families
+temporary metadata deletion error; frozen-executor-reproducer expected exact
+float(AlignedImageStack) failure using original executor 20ca4f825 with empty
+kwargs; provenance-contract-regressions stale diagnostic ABI fixture;
+unchanged-main-abi-fixture confirms that failure on full unchanged main
+0c0563e65; final-consumer-regressions nonexistent test paths/zero tests;
+r0-original interpreter/dependency import failures; and nra-before incorrectly
+admitted root. Earlier passing checkpoints are retained, not substituted for
+the merged-main receipts. Logs contain exact original argv and time/RSS/exit
+status, and JUnit files contain test identities and timestamps.
+
+Materialization scope
+---------------------
+
+The actual shared ABC algorithm owns pixels, masks and typed provenance.
+Dense stacks, same-slice bundles, aligned runtime stacks and named output
+bundles inherit it, with small axis/domain hooks. Existing nominal registry
+dispatch adds full-stack projection for primary images and image kwargs;
+other declared runtime families keep their own domains. No name switch,
+np.asarray fix, mirrored registry/store or copied executor is shipped.
+
+The MRO cases use two independent test-only capabilities over the actual
+composition owner: pixel offset and validity-mask creation. Both cooperative
+super orders verify exact pixel and mask effects. They are not a claim of
+production MI implementation or whole-package semantic equivalence.
+
+Artifact authority / bounded source replay
+------------------------------------------
+
+SHA256SUMS in this receipt archive covers all raw receipt files, the runner,
+the five final changed Python files and the architectural source receipt.
+Verify it after extracting into the reviewed source worktree. No science
+input or trial output is included. Archived original stdout is byte-preserved;
+whitespace within tracebacks is not normalized.
+
+Use the original runner and final log argv under the bounds above. To obtain
+the expected pre-repair executor failure, set BASELINE_EXECUTOR_REF=20ca4f825
+and select only test_real_rescale_full_stack_materializes_composed_runtime_sources.
+For a full unchanged-main baseline, git archive the recorded production and
+fixture paths and set SOURCE_BASELINE_ROOT to the owned extracted directory.
+No MCP/native/viewer startup is part of either source replay.
+
+R0 package: existing cached agent-comms package corresponding to original
+CI pin 3b03785f45df2ef5dc62ba6aed99294192ecbb01. debt_ratchet.py SHA256
+e323c94d49c2b72d9524a5169f123e64b4a6e46a41035ca9fb4497e49b6ca562;
+direct DeclaredFamily/FieldCodec/MroDispatch sources compare byte-identical.
+The successful entrypoint uses /usr/bin/python3.14 and existing local
+metaclass-registry source, matching the workflow interpreter, without install.
+Original R1 source/script is unchanged; its environment failure is retained.
+
+Disposable scratch ownership
+----------------------------
+
+Only owned scratch h003g-runtime-repair-baseline-20261001 under
+/home/ts/.cache/agent-scratch was used: 31 MiB unchanged-main source archive,
+recoverable from Git. Its process completed and its failure logs are preserved
+before cleanup. The attempted r1 scratch path was never created (import failed).
+No native/viewer/MCP process, lifecycle lock or shared slot was acquired.
+Parent owns installation/integration and actual synthetic installed acceptance
+after #338. Held-out/reference data and frozen H003g remain sealed/unmodified.

diagnostics/SHA256SUMS

@@ -0,0 +1,51 @@
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+2dd04e5005b9cde8b1b9b86f0d17e3b9c45120795e9be0ed9b556787b33ffdf2  diagnostics/run_source_tests.py
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+3514ad8f2346e5b5e82aaf4410610afc2fc8616eaf4596d5af1eaa387a85efe5  openhcs/core/aligned_image_payload.py
+504be26040871a58c127488bb9a1536ff30a6e538b5234a69a6c216c0030371f  openhcs/core/runtime_slice_projection.py
+51fa66703e1d789c199ba485f80ec71152bb1f64a3864ed2414d167660ffc2f8  openhcs/interop/cellprofiler/runtime/function_contract_execution.py
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+72918563a6e410956e41ba902ef2affb4fae35f60169c924dcabb233715c6e0a  tests/unit/test_cellprofiler_runtime_input_binding_contract.py
+489111c6b9dcb022ae452a072d3fa74dc287866387ea101578a81a36cdafc023  docs/refactor/cp-aligned-full-stack-342.rst