Prove created GrayToColor carriers and project scalar outputs (#432)

docs/validation/graytocolor-binding-axis-432-20261002/carrier-compile-diagnosis.log

@@ -0,0 +1,65 @@
+Interpreter: /home/ts/wt/openhcs-generated-inputs-installed-parent-20261001/.venv/bin/python 3.12.3 (main, May 22 2025, 14:39:13) [GCC 14.2.1 20250207]
+Discovery owner: /home/ts/wt/metaclass-registry-selected-discovery-376-20261001/src/metaclass_registry/__init__.py
+EEEF                                                                     [100%]
+==================================== ERRORS ====================================
+_ ERROR at setup of test_declared_gray_creator_proves_color_consumer_before_execution _
+../../.pyenv/versions/3.12.3/lib/python3.12/pathlib.py:1311: in mkdir
+    os.mkdir(self, mode)
+E   FileNotFoundError: [Errno 2] No such file or directory: '/home/ts/.cache/agent-scratch/graytocolor-carrier-432-20261002/pytest'
+_ ERROR at setup of test_declared_gray_creator_proves_same_group_color_consumer _
+../../.pyenv/versions/3.12.3/lib/python3.12/pathlib.py:1311: in mkdir
+    os.mkdir(self, mode)
+E   FileNotFoundError: [Errno 2] No such file or directory: '/home/ts/.cache/agent-scratch/graytocolor-carrier-432-20261002/pytest'
+_ ERROR at setup of test_preservation_annotation_cannot_create_missing_source_carrier _
+../../.pyenv/versions/3.12.3/lib/python3.12/pathlib.py:1311: in mkdir
+    os.mkdir(self, mode)
+E   FileNotFoundError: [Errno 2] No such file or directory: '/home/ts/.cache/agent-scratch/graytocolor-carrier-432-20261002/pytest'
+=================================== FAILURES ===================================
+____ test_original_stack_runtime_carrier_splits_into_unchanged_scalar_roles ____
+tests/unit/test_gray_to_color_carrier_compile_432.py:101: in test_original_stack_runtime_carrier_splits_into_unchanged_scalar_roles
+    assert image_payload_metadata(output).source_channel_axis is None
+E   assert -1 is None
+E    +  where -1 = ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(1.0, 1.0), unit=<SourceVoxelSpacingUnit.MICRO...urce_plane_dtypes=(), physical_border_edges_yx=None, mask_defines_border=None, source_channel_axis=-1, plane_axis=None).source_channel_axis
+E    +    where ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(1.0, 1.0), unit=<SourceVoxelSpacingUnit.MICRO...urce_plane_dtypes=(), physical_border_edges_yx=None, mask_defines_border=None, source_channel_axis=-1, plane_axis=None) = image_payload_metadata(ImageMetadataPayload(data=array([[0.        , 0.01525902, 0.03051804, 0.04577707, 0.06103609],\n       [0.07629511, 0.0...rce_plane_dtypes=(), physical_border_edges_yx=None, mask_defines_border=None, source_channel_axis=-1, plane_axis=None)))
+=============================== warnings summary ===============================
+../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441
+  /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope
+
+    self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
+
+../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441
+  /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode
+
+    self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
+
+-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
+=========================== short test summary info ============================
+FAILED tests/unit/test_gray_to_color_carrier_compile_432.py::test_original_stack_runtime_carrier_splits_into_unchanged_scalar_roles
+ERROR tests/unit/test_gray_to_color_carrier_compile_432.py::test_declared_gray_creator_proves_color_consumer_before_execution
+ERROR tests/unit/test_gray_to_color_carrier_compile_432.py::test_declared_gray_creator_proves_same_group_color_consumer
+ERROR tests/unit/test_gray_to_color_carrier_compile_432.py::test_preservation_annotation_cannot_create_missing_source_carrier
+1 failed, 2 warnings, 3 errors in 4.75s
+Command exited with non-zero status 1
+	Command being timed: "/home/ts/wt/openhcs-generated-inputs-installed-parent-20261001/.venv/bin/python docs/validation/knowledge-selected-source-tests.py --basetemp=/home/ts/.cache/agent-scratch/graytocolor-carrier-432-20261002/pytest tests/unit/test_gray_to_color_carrier_compile_432.py -q --tb=short"
+	User time (seconds): 4.97
+	System time (seconds): 0.34
+	Percent of CPU this job got: 97%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.44
+	Average shared text size (kbytes): 0
+	Average unshared data size (kbytes): 0
+	Average stack size (kbytes): 0
+	Average total size (kbytes): 0
+	Maximum resident set size (kbytes): 347856
+	Average resident set size (kbytes): 0
+	Major (requiring I/O) page faults: 0
+	Minor (reclaiming a frame) page faults: 74931
+	Voluntary context switches: 6
+	Involuntary context switches: 879
+	Swaps: 0
+	File system inputs: 376
+	File system outputs: 8
+	Socket messages sent: 0
+	Socket messages received: 0
+	Signals delivered: 0
+	Page size (bytes): 4096
+	Exit status: 1

docs/validation/graytocolor-binding-axis-432-20261002/carrier-compile-parent-admission.log

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+Interpreter: /home/ts/wt/openhcs-generated-inputs-installed-parent-20261001/.venv/bin/python 3.12.3 (main, May 22 2025, 14:39:13) [GCC 14.2.1 20250207]
+Discovery owner: /home/ts/wt/metaclass-registry-selected-discovery-376-20261001/src/metaclass_registry/__init__.py
+FF.F                                                                     [100%]
+=================================== FAILURES ===================================
+______ test_declared_gray_creator_proves_color_consumer_before_execution _______
+tests/unit/test_gray_to_color_carrier_compile_432.py:47: in test_declared_gray_creator_proves_color_consumer_before_execution
+    PipelineCompiler.validate_primary_image_carrier_requirements(_gray_creator_session(tmp_path))
+openhcs/core/pipeline/compiler.py:1484: in validate_primary_image_carrier_requirements
+    raise ValueError(
+E   ValueError: Primary image carrier requirements failed before execution:
+E   - step 1 ('SplitComposedRoles'), group 'default', invocation 'color_to_gray': carrier requirement 'source_channel_axis' is not preserved by producer step 0 callable 'gray_to_color'.
+_________ test_declared_gray_creator_proves_same_group_color_consumer __________
+tests/unit/test_gray_to_color_carrier_compile_432.py:61: in test_declared_gray_creator_proves_same_group_color_consumer
+    PipelineCompiler.validate_primary_image_carrier_requirements(session)
+openhcs/core/pipeline/compiler.py:1484: in validate_primary_image_carrier_requirements
+    raise ValueError(
+E   ValueError: Primary image carrier requirements failed before execution:
+E   - step 0 ('ComposeScalarRoles'), group 'default', invocation 'color_to_gray': carrier requirement 'source_channel_axis' is not preserved by earlier callable 'gray_to_color' in the same group.
+____ test_original_stack_runtime_carrier_splits_into_unchanged_scalar_roles ____
+tests/unit/test_gray_to_color_carrier_compile_432.py:101: in test_original_stack_runtime_carrier_splits_into_unchanged_scalar_roles
+    assert image_payload_metadata(output).source_channel_axis is None
+E   assert -1 is None
+E    +  where -1 = ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(1.0, 1.0), unit=<SourceVoxelSpacingUnit.MICRO...urce_plane_dtypes=(), physical_border_edges_yx=None, mask_defines_border=None, source_channel_axis=-1, plane_axis=None).source_channel_axis
+E    +    where ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(1.0, 1.0), unit=<SourceVoxelSpacingUnit.MICRO...urce_plane_dtypes=(), physical_border_edges_yx=None, mask_defines_border=None, source_channel_axis=-1, plane_axis=None) = image_payload_metadata(ImageMetadataPayload(data=array([[0.        , 0.01525902, 0.03051804, 0.04577707, 0.06103609],\n       [0.07629511, 0.0...rce_plane_dtypes=(), physical_border_edges_yx=None, mask_defines_border=None, source_channel_axis=-1, plane_axis=None)))
+=============================== warnings summary ===============================
+../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441
+  /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_default_fixture_loop_scope
+
+    self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
+
+../../code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441
+  /home/ts/code/projects/openhcs/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: asyncio_mode
+
+    self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
+
+-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
+=========================== short test summary info ============================
+FAILED tests/unit/test_gray_to_color_carrier_compile_432.py::test_declared_gray_creator_proves_color_consumer_before_execution
+FAILED tests/unit/test_gray_to_color_carrier_compile_432.py::test_declared_gray_creator_proves_same_group_color_consumer
+FAILED tests/unit/test_gray_to_color_carrier_compile_432.py::test_original_stack_runtime_carrier_splits_into_unchanged_scalar_roles
+3 failed, 1 passed, 2 warnings in 6.49s
+Command exited with non-zero status 1
+	Command being timed: "/home/ts/wt/openhcs-generated-inputs-installed-parent-20261001/.venv/bin/python docs/validation/knowledge-selected-source-tests.py --basetemp=/home/ts/.cache/agent-scratch/graytocolor-carrier-432-20261002/pytest tests/unit/test_gray_to_color_carrier_compile_432.py -q --tb=short"
+	User time (seconds): 6.72
+	System time (seconds): 0.53
+	Percent of CPU this job got: 97%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.41
+	Average shared text size (kbytes): 0
+	Average unshared data size (kbytes): 0
+	Average stack size (kbytes): 0
+	Average total size (kbytes): 0
+	Maximum resident set size (kbytes): 423264
+	Average resident set size (kbytes): 0
+	Major (requiring I/O) page faults: 0
+	Minor (reclaiming a frame) page faults: 103459
+	Voluntary context switches: 21
+	Involuntary context switches: 1203
+	Swaps: 0
+	File system inputs: 856
+	File system outputs: 56
+	Socket messages sent: 0
+	Socket messages received: 0
+	Signals delivered: 0
+	Page size (bytes): 4096
+	Exit status: 1

docs/validation/graytocolor-binding-axis-432-20261002/carrier-creation-receipt.rst

@@ -0,0 +1,146 @@
+GrayToColor #432: creation is not preservation
+============================================
+
+Historical diagnosis retained verbatim below. The subsequently authorized
+working repair and current ownership are in carrier-repair-receipt.rst.
+
+Latest original installed witness
+--------------------------------
+
+Dalton's ASSISTED4 on frozen fa049/native3309214 completed execution
+5e3474f4-f736-4e61-a27f-1d7eb6ec7abd using ordinary scalar ImageMath NONE aliases
+then two named scalar processing-role inputs to registered GrayToColor STACK.
+Original mcp.stdout execution status is COMPLETE, error null. This supersedes
+any hypothesis of a general native multi-artifact assembly failure.
+
+The parent reports installed output1024x1024x2 float32, lane0=raw/65535 and
+lane1=(clip(raw,39,6000)-39)/5961, error<=1.2e-7 at11bounded coordinates. These
+are retained parent/author MCP findings, not a new scientific run or an
+independent image decoding/biological qualification by Schrodinger.
+
+The five-step v1 adds registered color_to_gray CHANNELS split and fails actual
+compile before execution at original mcp.stdout18793: source_channel_axis is
+not preserved by producer step3 gray_to_color. No native attempt of that
+five-step document is inferred. Original source/status location:
+/home/ts/wt/openhcs-issue-batch-20260929/neurite-development-skill383-20261001/
+output/assisted-4-fa049/. Exact bounded status excerpts captured in
+original-assisted4-status-excerpts.log. Complete original drafts:
+
+* named-role-composition-control-v1.py SHA256
+  d2d160144d12196dcccc63645e4ba3a78f07c07fcacdf509550a137a7ec7a70c
+* named-role-assembly-control-v2.py SHA256
+  81e6128ce150a8994ee5292ec51e44faa9c28492252f150eb9e3c8d7f7754aac
+
+Required relation and original owners
+------------------------------------
+
+Runtime GrayToColor establishes source_channel_axis=-1 on YXC output from
+scalar gray planes. It does not preserve a source color carrier: those gray
+source files have none. The consumer requires SOURCE_CHANNEL_AXIS truthfully.
+The current callable metadata transition owner can declare only PRESERVE.
+CompiledFunctionInvocation.proves_primary_image_carrier delegates to it;
+CompiledFunctionGroup.first_unproved_primary_image_carrier_invocation and
+PipelineCompiler._carrier_source_plan only prove preservation back to exact
+source files. GrayToColor has no transition, so the actual failure follows.
+Adding preserves_primary_image_carrier would remain false/inadequate: the
+unchanged strict source proof rejects the original scalar source.
+
+Own source b536885e76132df892671a913e9fe70135feb008; actual Root394 head
+7241ca99b4f00e48f2a742c8a1fdf57c2bd896db fetched/read-only inspected. Root's
+transition owner and invocation proof have the same limitation; no stale949
+qualification is applied to his current work. Root's color.py changes include
+runtime argument annotations, not a creation declaration.
+
+Working integration target, not a second authority:
+
+1. Extend PrimaryImageCarrierTransition's original nominal effect owner to
+   express a supplied requirement separately from inherited preservation.
+2. Let original compiled group/plan owners resolve proof origin: traverse from
+   consumer backwards; a truthful creator establishes evidence, a preserving
+   operation carries it, a later unknown/destroying operation rejects it.
+   Stop source-file backtracking only at a creator of the exact requirement.
+   Both same-group and cross-step paths must use that original owner algorithm.
+3. GrayToColor supplies its small truthful creation declaration through the
+   original metadata attachment mechanism. Keep ColorToGray's requirement,
+   SOURCE_BINDING guard, missing-source and unknown-transition failures.
+
+No function-name/string/type exception, synthetic source-file RGB declaration,
+alternate registry, consumer bypass or mirrored metadata store is acceptable.
+New legitimate creators/preservers must need only declarations/hooks; generic
+consumers must not be edited per leaf. This is a required behavioral test for
+the eventual effect-owner repair, not a claim about an unimplemented MRO.
+
+Ownership and concrete shared-file boundary
+------------------------------------------
+
+Schrodinger retains #434 diagnosis and independent color declaration/backend
+work. Root owns shared callable_contract.py / function_patterns.py / generic
+compiler ancestry and metadata/projector integration; color.py is also touched
+in394. No shared production file has been edited in434. Integration/release
+request, naming the exact owner operations above:
+https://github.com/OpenHCSDev/openhcs/pull/394#issuecomment-5946649033.
+The production repair needs that owner integration or explicit narrow release;
+there is no license to implement a competing contract locally.
+
+Minimal original-owner source reproducer and findings
+---------------------------------------------------
+
+test_gray_to_color_carrier_compile_432.py reuses the original compile-gate
+fixtures/session ancestry and PipelineCompiler.validate_primary_image_carrier_requirements.
+Only new tiny synthetic grayscale TIFF headers in owned scratch are used.
+
+* Cross-step GrayToColor -> ColorToGray: RED with the exact producer failure.
+* Same-group GrayToColor -> ColorToGray: RED at the corresponding prefix proof.
+* False-PRESERVE counterexample: PASS, strict grayscale source rejection stays.
+  Test-local dataclass replacement does not mutate the real function/registry.
+* Original registered Stack -> ColorToGray CHANNELS runtime executor: PASS for
+  both scalar pixel arrays, order and same physical C2 source path/identity.
+* Scalar-output carrier consumption: RED. Current CHANNELS split emits actual
+  YX arrays but keeps source_channel_axis=-1. Its non-RGB branch uses
+  with_image_payload_data without channel projection. The RGB branch already
+  uses original ImagePayloadMetadata.project_channel_payload, which owns
+  channel mask/provenance projection and removes the consumed channel axis.
+  This is source kernel/executor evidence after the compiler boundary, NOT a
+  claim of an executed installed five-step failure. Retain this assertion; do
+  not weaken it to turn the needed scalar-role acceptance green. Coordinate
+  the existing color declaration/projection hook with Root, not a second axis
+  dispatch or blanket metadata clearing policy.
+
+Five distinct cases: three RED, two passing controls. Pixel preservation and
+carrier consumption are separated so correct numeric output cannot hide stale
+metadata. The previous unary naming RED cases remain unchanged and separate.
+
+Bounded receipts, failures and cleanup
+------------------------------------
+
+Read current installed NRA/refactor-audit skills and authoritative ZIP's full
+SKILL.md, catalogue, relevant boundaries/identity/implementation references and
+surface-receipt instructions; project refactor rules before this continuation.
+Applicable BOUND-8: carry the producer's actual semantic effect across its
+contract boundary. IDEN-1: creation and preservation answer different questions.
+IMPL-1/2/3/5: no consumer leaf/name/enum dispatch or second implementation;
+IMPL-12/13: reuse original proof/projection algorithm and strictness. No
+production code moved/duplicated/deleted and no new registry/state store.
+Full/global NRA/R1 remains separate, not a gate for this bounded diagnosis.
+
+All shards use existing read-only Python3.12.3/ABI driver, CPU0/CPUQuota100%,
+all numerical pools1, MemoryMax512M/MemorySwapMax0 and timeout60s. Resource
+admission RAM12.6GiB/home11.2GiB; helper's advisory warning retained in tool
+transcript, no large source scan/fleet. No downloads/env/install/native/UI/MCP
+process launch, provider call or scientific replay; fa049 remains untouched.
+
+* carrier-compile-diagnosis.log: initial parent-directory fixture error retained
+  (three setup errors), plus scalar-output metadata RED; 5.44s/347856KiB/exit1.
+* carrier-compile-parent-admission.log: parent directory admitted, actual two
+  compiler RED, false-PRESERVE PASS and metadata RED; 7.41s/423264KiB/exit1.
+* carrier-runtime-lanes.log: split numeric and metadata acceptance; one PASS,
+  one RED/three deselected; 5.37s/351380KiB/exit1.
+
+Raw pytest/status logs preserve warning whitespace/CRLF; no whole diff-check
+clean claim. Source/receipt-only check passes. All original failures remain
+published, not overwritten. Owned disposable source-fixture scratch root:
+/home/ts/.cache/agent-scratch/graytocolor-carrier-432-20261002,
+1090 logical bytes/three synthetic-gray.tif files, no open handles after all
+shards were terminal. Removed only that verified root; fixtures are reproducible
+from retained source and raw logs persist. Publication ledger remains untracked
+and excluded. Parent controls future stopped-slot installation/live acceptance.