From b536885e76132df892671a913e9fe70135feb008 Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Fri, 2 Oct 2026 01:52:52 -0400 Subject: [PATCH 1/7] Diagnose GrayToColor primary binding axis and unit boundaries (#432) --- .../integer-binding-units.log | 39 ++++ .../original-native-excerpts.log | 82 ++++++++ .../receipt.rst | 148 +++++++++++++ .../source-diagnosis.log | 76 +++++++ .../test_gray_to_color_binding_axis_432.py | 199 ++++++++++++++++++ 5 files changed, 544 insertions(+) create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/integer-binding-units.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/original-native-excerpts.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/receipt.rst create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/source-diagnosis.log create mode 100644 tests/unit/test_gray_to_color_binding_axis_432.py diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/integer-binding-units.log b/docs/validation/graytocolor-binding-axis-432-20261002/integer-binding-units.log new file mode 100644 index 0000000000..cd005d448e --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/integer-binding-units.log @@ -0,0 +1,39 @@ +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 +. [100%] +=============================== 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 +1 passed, 6 deselected, 2 warnings in 5.52s + 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-role-axis-20261002/pytest tests/unit/test_gray_to_color_binding_axis_432.py -k integer -q --tb=short" + User time (seconds): 6.04 + System time (seconds): 0.33 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.44 + 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): 348924 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 13 + Minor (reclaiming a frame) page faults: 67060 + Voluntary context switches: 29 + Involuntary context switches: 33 + Swaps: 0 + File system inputs: 384 + File system outputs: 8 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/original-native-excerpts.log b/docs/validation/graytocolor-binding-axis-432-20261002/original-native-excerpts.log new file mode 100644 index 0000000000..ca0577c346 --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/original-native-excerpts.log @@ -0,0 +1,82 @@ +2026-10-02 01:24:27,041 - openhcs.core.steps.function_runtime - ERROR - Error processing pattern group A01_s001_w{iii}_z001_t001.tif: GrayToColor image metadata requires a source-binding plane axis, got . +Traceback (most recent call last): + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/steps/function_runtime.py", line 2563, in run + processed_stack = self._execute_pattern(loaded) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/steps/function_runtime.py", line 3112, in _execute_pattern + return runtime_scope.execute_chain(loaded.main_data_stack) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/steps/function_runtime.py", line 1524, in execute_chain + current_stack = executor.execute( + ^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/steps/function_runtime.py", line 2041, in execute + raw_output = self.invoke( + ^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/steps/function_runtime.py", line 2175, in invoke + raw_output = func_callable( + ^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/interop/cellprofiler/runtime/module_execution.py", line 337, in __call__ + result = self._run_standard_image( + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/interop/cellprofiler/runtime/module_execution.py", line 397, in _run_standard_image + raw_output = _CELLPROFILER_FUNCTION_CONTRACT_EXECUTOR.execute( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/interop/cellprofiler/runtime/function_contract_execution.py", line 134, in execute + result = processing_contract.execute( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/processing/backends/lib_registry/unified_registry.py", line 1239, in execute + return self.declaration.execute(registry, func, image, *args, **kwargs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/processing/backends/lib_registry/unified_registry.py", line 1092, in execute + return registry.execute_pure_3d(func, image, *args, **kwargs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/interop/cellprofiler/runtime/function_contract_execution.py", line 330, in execute_pure_3d + ).call() + ^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/processing/backends/lib_registry/unified_registry.py", line 263, in call + return target( + ^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/processing/backends/cellprofiler/color.py", line 1560, in gray_to_color + raise ValueError( +ValueError: GrayToColor image metadata requires a source-binding plane axis, got . +2026-10-02 01:26:20,797 - openhcs.core.steps.function_runtime - ERROR - Error processing pattern group A01_s001_w{iii}_z001_t001.tif: GrayToColor image metadata requires a source-binding plane axis, got . +Traceback (most recent call last): + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/steps/function_runtime.py", line 2563, in run + processed_stack = self._execute_pattern(loaded) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/steps/function_runtime.py", line 3112, in _execute_pattern + return runtime_scope.execute_chain(loaded.main_data_stack) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/steps/function_runtime.py", line 1524, in execute_chain + current_stack = executor.execute( + ^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/steps/function_runtime.py", line 2041, in execute + raw_output = self.invoke( + ^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/core/steps/function_runtime.py", line 2175, in invoke + raw_output = func_callable( + ^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/interop/cellprofiler/runtime/module_execution.py", line 337, in __call__ + result = self._run_standard_image( + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/interop/cellprofiler/runtime/module_execution.py", line 397, in _run_standard_image + raw_output = _CELLPROFILER_FUNCTION_CONTRACT_EXECUTOR.execute( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/interop/cellprofiler/runtime/function_contract_execution.py", line 134, in execute + result = processing_contract.execute( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/processing/backends/lib_registry/unified_registry.py", line 1239, in execute + return self.declaration.execute(registry, func, image, *args, **kwargs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/processing/backends/lib_registry/unified_registry.py", line 1092, in execute + return registry.execute_pure_3d(func, image, *args, **kwargs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/interop/cellprofiler/runtime/function_contract_execution.py", line 330, in execute_pure_3d + ).call() + ^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/processing/backends/lib_registry/unified_registry.py", line 263, in call + return target( + ^^^^^^^ + File "/home/ts/wt/openhcs-paired-raw-installed-parent-20261001/.venv/lib/python3.12/site-packages/openhcs/processing/backends/cellprofiler/color.py", line 1560, in gray_to_color + raise ValueError( +ValueError: GrayToColor image metadata requires a source-binding plane axis, got . diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/receipt.rst b/docs/validation/graytocolor-binding-axis-432-20261002/receipt.rst new file mode 100644 index 0000000000..3cabad040d --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/receipt.rst @@ -0,0 +1,148 @@ +GrayToColor #432: source diagnosis, not an installed repair +========================================================= + +Owner: Schrodinger. Base: df15ddfe0bcbd80cadaf2f5fc56b83517910f334. +Existing isolated worktree: openhcs-knowledge-declaration-source-376-20261001. +Branch: fix/graytocolor-role-axis-20261002. Normal fast-forward main integration; +no reset/clean, new environment or dependency mutation. The untracked owned +required-runtime-qt-publication-20261002 ledger is preserved and excluded. + +Original evidence +----------------- + +Issue: https://github.com/OpenHCSDev/openhcs/issues/432. +Installed predecessor fa04956a7eb3212e3456cf9927fc35ab6cdfd361 / PolyStore0.3.1. +Original native PID3214331/create_time1790918404.81/port5993. Terminal execution +37f69b64-2331-4bcb-a4f1-99f78da3d316 (v1) and +c81af5db-f805-434a-a067-930d5201975c (v2) both fail at +RetainRawCalceinBodyReference, completed0/total4. No failed call was replayed. + +Original persistent MCP evidence is under +/home/ts/wt/openhcs-issue-batch-20260929/neurite-development-skill383-20261001/ +output/assisted-3-fa049/mcp.stdout, lines5365..5421 and6724..6780. +Complete source drafts at the same prefix: + +* c8-composition-control-v1.py, SHA256 + 4dc60002f89b9a7851a66deebf6c504963aeeb83e28455ff58e56367f8f9d2da +* c8-composition-control-v2-explicit-source.py, SHA256 + ee319fa08303c6bba8280b4ba254863a576e15343f5fc85745a56a7931455ae0 + +Original native log named by the exact saved native-handle.json: +/home/ts/.cache/agent-scratch/neurite-development-skill383-20261001/ +assisted-3-fa049/data/openhcs/logs/ +openhcs_zmq_server_port_5993_1790918405617427245.log. +Only its two exact failure trace excerpts (238..278,714..754) are captured here +in original-native-excerpts.log. The scientific author retains the original; +no scratch/process/output was modified. v3's scalar-file/declared-stack-axis +compile rejection is separate authoring evidence, not a product regression. + +Proven relation and source result +--------------------------------- + +test_gray_to_color_binding_axis_432.py reuses the original public FunctionStep +compiler, exact source-declaration input-edge construction, original nominal +RuntimeAdapterRequest fixture, CellProfilerModuleExecutor._image_request and +_invocation_request, and CellProfilerFunctionContractExecutor. Synthetic 4x5 +arrays only; no TIFF/image-array read, provider or live process call. + +Both implicit and explicit FITC selection compile to exactly one declared FITC +input. The original request retains its real C2 physical source identity and +RUNTIME_SLICE carrier. compose_aligned_image_payload's single-input fast path +returns that payload unchanged. The declaration's image-request hook is the +ancestor no-op. PURE_3D/NATURAL then reaches gray_to_color's SOURCE_BINDING-only +guard with RUNTIME_SLICE, reproducing the exact original error. This is a +missing declaration/consumer-domain adaptation, NOT evidence that the loader +assigned incorrect physical channel identity, nor authority to relabel axes. + +The positive owner-algebra experiment explicitly projects a declared runtime +slice through RuntimeSliceProjection, THEN introduces the distinct named role +axis through ImagePayloadBundleContext. The unchanged original executor and +STACK runner accept that SOURCE_BINDING domain. No arbitrary squeeze, metadata +overwrite to impersonate a binding axis, relaxed guard or consumer switch. + +Two independent named processing roles composed through the original bundle +owner and registered STACK executor preserve their ordered floating-point +values (raw 0..19000; capped 0..1), spacing/domain and SAME original physical +C2 path/channel. Changing both role declarations requires no consumer edit. +These are source composition controls, NOT the entire four-step saved-artifact +journey, public TIFF unit calibration or installed acceptance. + +Two additional boundaries prevent a false full-repair claim: + +* STACK emits YXC/color metadata even for one role. It is not an identity + renamer of a scalar gray plane. Feeding that one-color-channel output back + into the same original grayscale STACK binding creates a 4D input, and the + current registered runner rejects it (axes don't match array). The synthetic + control proves that additional boundary, not that Dalton reached it live. +* ImageArtifactTypeStrategy.runtime_input_value normalizes uint16 before the + kernel's rescale_intensity argument: the actual original binding experiment + maps integer values to float32/65535 and leaves the source unmodified. Merely + passing rescale_intensity=False is not proof of preserved raw integer units. + No claim is made about the unseen TIFF values/dtype or scientific calibration. + +Ownership and proposed integration boundary +------------------------------------------- + +Root retains PR394 executor/input context, source projection/metadata and +shared materialization. PR394 also lists color.py. Explicit narrow declaration/ +backend release or Root integration requested before any production edit: +https://github.com/OpenHCSDev/openhcs/pull/394#issuecomment-5946253275. +No release received at this checkpoint; production files are untouched. + +Required original-owner seam: CellProfilerModule.project_invocation_image_request +(ABI ancestor) with minimal GrayToColor declaration hook, backed by existing +runtime-slice projection and named-bundle composition owners. Establish the +binding domain, do not reinterpret a runtime axis as a named binding. Preserve +the SOURCE_BINDING guard. Any generalized singleton composition template or +raw-unit ingress policy belongs to Root's existing shared owner, not a second +color-local executor/binder. The complete requested four-step route must also +resolve the scalar-gray versus STACK-color relation before claiming acceptance. + +NRA/refactor-audit review +------------------------- + +Personally reread installed nra-refactoring and refactor-audit SKILL.md; +authoritative ZIP's entire SKILL.md, catalogue, boundaries, implementation, +identity and surface-receipt references; project docs/refactor/00-RULES.md. +Applied BOUND-2 (bypassing the existing model) and BOUND-8 (flattening an owned +fact) to binding-domain adaptation; IDEN-1 (one field answering two questions) +to independent runtime/binding axes and IDEN-5 to forbidding a second identity +store; IMPL-1/3 to excluding string/concrete-type consumer dispatch, IMPL-12 to +avoiding a copied projection procedure, IMPL-13 to avoiding a less-rigorous +second composition mechanism. No production algorithm moved, facade, +duplicated registry, consumer +type/string switch or ornamental MI was added. No removed/replaced production +code exists at this diagnosis checkpoint. No new family/MRO behavior claimed; +any repair must test cooperative hooks on the actual owner after release. + +Bounded evidence and limits +--------------------------- + +Existing read-only Python3.12.3: +/home/ts/wt/openhcs-generated-inputs-installed-parent-20261001/.venv/bin/python. +Existing source/ABI loader: docs/validation/knowledge-selected-source-tests.py. +Every shard: systemd scope MemoryMax512M/MemorySwapMax0/CPUQuota100%, tasksetCPU0, +timeout60s, all numerical thread pools1, no conftest/plugin autoload/cache writes. +Advisory resource check: RAM14.9GiB/home12.3GiB; advisory disk warning retained, +actual bounded source admission held. Exact retained invocation is in each log. + +* Initial two-case source RED: 2fail/5.58pytest seconds, 6.42wall seconds, + 350640KiB RSS, exit1 (original tool transcript; not claimed green). +* source-diagnosis.log: same two RED + four distinct controls PASS, 6.01pytest + seconds/6.94wall seconds/350904KiB RSS, exit1. +* integer-binding-units.log: one additional control PASS, six deselected, + 5.52pytest seconds/6.44wall seconds/348924KiB RSS, exit0. + +Total distinct cases: two unresolved RED, five passing diagnosis/negative +controls. Existing pytest unknown-asyncio-config warnings retained. No full +R0/R1 retry/global NRA qualification: zero production change and unrelated +historical global scope remain distinct. No installed/native/GUI/biological +readiness claim. Parent owns future installed original entrypoint acceptance. +Owned potential scratch address graytocolor-role-axis-20261002 was never +materialized by these tests; observed absent after terminal shards, no cleanup +performed. All durable source/logs retained; no new environment/artifact fleet. +The final test strengthens unreachable post-RED acceptance from a shape reshape +to exact nominal RuntimeSliceProjection and YXC shape; that post-repair check is +not executed/qualified at this diagnosis checkpoint. Raw pytest logs retain +four trailing-whitespace warning lines; whole diff-check is NOT clean. Source +test/receipt-only diff-check passes; original evidence is not reformatted. diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/source-diagnosis.log b/docs/validation/graytocolor-binding-axis-432-20261002/source-diagnosis.log new file mode 100644 index 0000000000..993b14cd14 --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/source-diagnosis.log @@ -0,0 +1,76 @@ +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.... [100%] +=================================== FAILURES =================================== +_ test_declared_fitc_runtime_plane_retains_values_and_physical_identity[False] _ +tests/unit/test_gray_to_color_binding_axis_432.py:91: in test_declared_fitc_runtime_plane_retains_values_and_physical_identity + result = CellProfilerFunctionContractExecutor().execute( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:134: in execute + result = processing_contract.execute( +openhcs/processing/backends/lib_registry/unified_registry.py:1239: in execute + return self.declaration.execute(registry, func, image, *args, **kwargs) +openhcs/processing/backends/lib_registry/unified_registry.py:1092: in execute + return registry.execute_pure_3d(func, image, *args, **kwargs) +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:330: in execute_pure_3d + ).call() +openhcs/processing/backends/lib_registry/unified_registry.py:263: in call + return target( +openhcs/processing/backends/cellprofiler/color.py:1560: in gray_to_color + raise ValueError( +E ValueError: GrayToColor image metadata requires a source-binding plane axis, got . +_ test_declared_fitc_runtime_plane_retains_values_and_physical_identity[True] __ +tests/unit/test_gray_to_color_binding_axis_432.py:91: in test_declared_fitc_runtime_plane_retains_values_and_physical_identity + result = CellProfilerFunctionContractExecutor().execute( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:134: in execute + result = processing_contract.execute( +openhcs/processing/backends/lib_registry/unified_registry.py:1239: in execute + return self.declaration.execute(registry, func, image, *args, **kwargs) +openhcs/processing/backends/lib_registry/unified_registry.py:1092: in execute + return registry.execute_pure_3d(func, image, *args, **kwargs) +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:330: in execute_pure_3d + ).call() +openhcs/processing/backends/lib_registry/unified_registry.py:263: in call + return target( +openhcs/processing/backends/cellprofiler/color.py:1560: in gray_to_color + raise ValueError( +E ValueError: GrayToColor image metadata requires a source-binding plane axis, got . +=============================== 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_binding_axis_432.py::test_declared_fitc_runtime_plane_retains_values_and_physical_identity[False] +FAILED tests/unit/test_gray_to_color_binding_axis_432.py::test_declared_fitc_runtime_plane_retains_values_and_physical_identity[True] +2 failed, 4 passed, 2 warnings in 6.01s +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-role-axis-20261002/pytest tests/unit/test_gray_to_color_binding_axis_432.py -q --tb=short" + User time (seconds): 6.47 + System time (seconds): 0.39 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.94 + 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): 350904 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 26 + Minor (reclaiming a frame) page faults: 71430 + Voluntary context switches: 31 + Involuntary context switches: 37 + Swaps: 0 + File system inputs: 616 + File system outputs: 8 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/tests/unit/test_gray_to_color_binding_axis_432.py b/tests/unit/test_gray_to_color_binding_axis_432.py new file mode 100644 index 0000000000..6d337d43ef --- /dev/null +++ b/tests/unit/test_gray_to_color_binding_axis_432.py @@ -0,0 +1,199 @@ +"""Source-only #432: declared primary binding is not a runtime grouping axis.""" + +from dataclasses import replace + +import numpy as np +import pytest + +from openhcs.constants.constants import VariableComponents +from openhcs.core.component_group_scope import RuntimeExecutionAxisScope +from openhcs.core.aligned_image_payload import ImagePayloadBundleContext, ImagePayloadExecutionMode +from openhcs.core.callable_contract import CallableContract +from openhcs.core.artifacts import ArtifactSpec, ImageArtifactType +from openhcs.core.config import StepSourceBindingsConfig +from openhcs.core.function_patterns import InvocationArtifactInputEdgePlan +from openhcs.core.runtime_image_values import ( + ImagePayloadMetadata, image_payload_data, image_payload_metadata, +) +from openhcs.core.runtime_plane_projection import RuntimePlaneAxis +from openhcs.core.runtime_plane_projection import RuntimePlaneAxisValueProjection +from openhcs.core.runtime_slice_projection import RuntimeSliceProjection +from openhcs.core.runtime_stores import RuntimeValueStore +from openhcs.core.source_bindings import NamedSourceBinding +from openhcs.core.source_image_provenance import SourceImageProvenancePlanes +from openhcs.core.source_metadata import SourceVoxelSpacing +from openhcs.core.source_spatial_domain import SourceSpatialDomain +from openhcs.core.steps.function_step import FunctionStep +from openhcs.interop.cellprofiler.runtime.adapter import CellProfilerRuntimeAdapter +from openhcs.interop.cellprofiler.runtime.function_contract_execution import ( + CellProfilerFunctionContractExecutor, +) +from openhcs.interop.cellprofiler.runtime.module_execution import CellProfilerModuleExecutor +from openhcs.interop.cellprofiler.runtime.artifact_binding import RuntimeArtifactInputRequest, RuntimeArtifactTypeStrategy +from openhcs.processing.backends.cellprofiler.color import GrayToColorModule, gray_to_color +from test_cellprofiler_generic_special_input_binding import _compile_public_step +from tests.unit.cellprofiler_runtime_test_support import cellprofiler_runtime_adapter_for_test + + +@pytest.mark.parametrize("explicit_selector", [False, True]) +def test_declared_fitc_runtime_plane_retains_values_and_physical_identity(explicit_selector): + kwargs = { + "color_scheme": GrayToColorModule.Scheme.STACK, + "rescale_intensity": False, + "name_the_output_image": "raw_body_reference", + } + if explicit_selector: + kwargs["image_name"] = ("FITC",) + step = FunctionStep( + func=(gray_to_color, kwargs), name="RetainRawReference", + source_bindings=StepSourceBindingsConfig( + enabled=True, bindings=(NamedSourceBinding("FITC"),), + ), + ) + invocation = _compile_public_step(step) + contract = replace(invocation.contract, metadata=replace( + invocation.contract.metadata, + runtime_adapter=CellProfilerRuntimeAdapter.runtime_adapter_spec(), + )) + pixels = np.arange(20, dtype=np.float32).reshape(4, 5) * 1000 + physical = {"well": "A01", "site": "1", "channel": "2", "z_index": "1", "timepoint": "1"} + metadata = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, + source_image_provenance_planes=SourceImageProvenancePlanes.from_components( + paths=("/synthetic/A01_s1_w2_z1_t1.tif",), component_metadata=(physical,), + ), + source_image_names=("FITC",), + source_voxel_spacing=SourceVoxelSpacing((1.0, 1.0)), + source_spatial_domain=SourceSpatialDomain(origin_yx=(0, 0), source_shape_yx=(4, 5)), + ) + source = metadata.payload_with(pixels[None], None) + runtime = cellprofiler_runtime_adapter_for_test( + runtime_value_store=RuntimeValueStore(), callable_contract=contract, + variable_components=(VariableComponents.CHANNEL,), + axis_scope=RuntimeExecutionAxisScope.from_raw("synthetic", component=None, value=None), + artifact_inputs={edge.key: InvocationArtifactInputEdgePlan.from_source_declarations( + key=edge.key, spec=edge.spec, main_flow_artifacts=contract.artifact_inputs, + invocation_sources=contract.artifact_inputs, + ) for edge in invocation.artifact_input_edges}, + ) + executor = CellProfilerModuleExecutor(gray_to_color, contract) + request = executor._image_request( + source, runtime, module_type=GrayToColorModule, + active_input_specs=contract.artifact_inputs.specs, + ) + assert contract.artifact_inputs.names() == ("FITC",) + assert request.source_aliases == ("FITC",) + assert request.image_count == 1 + assert image_payload_metadata(request.payload).plane_axis is RuntimePlaneAxis.RUNTIME_SLICE + execution = executor._invocation_request( + image_request=request, adapter=runtime, current_image=source, + module_type=GrayToColorModule, + kwargs={"color_scheme": GrayToColorModule.Scheme.STACK, "rescale_intensity": False}, + ) + result = CellProfilerFunctionContractExecutor().execute( + contract, contract.resolve_canonical_raw_callable(), execution.image, execution.kwargs, + execution_mode=execution.execution_mode, plane_projection=execution.plane_projection, + ) + # Float32 is the original Stack runner's output contract, not unit normalization. + assert image_payload_metadata(result).plane_axis is RuntimePlaneAxis.RUNTIME_SLICE + plane = RuntimeSliceProjection.value_for_slice(result, RuntimePlaneAxisValueProjection.from_selected_plane( + axis=RuntimePlaneAxis.RUNTIME_SLICE, plane_index=0, axis_size=1, + )) + assert image_payload_data(plane).shape == (4, 5, 1) + np.testing.assert_array_equal(image_payload_data(plane)[..., 0], pixels) + np.testing.assert_array_equal(image_payload_data(source)[0], pixels) + output = image_payload_metadata(result) + assert output.source_image_paths == metadata.source_image_paths + assert output.source_component_metadata["channel"] == "2" + assert output.source_voxel_spacing == metadata.source_voxel_spacing + assert output.source_spatial_domain == metadata.source_spatial_domain + + +def _source_plane(pixels, alias): + return ImagePayloadMetadata( + source_path="/synthetic/A01_s1_w2_z1_t1.tif", + source_component_metadata={"well": "A01", "site": "1", "channel": "2", "z_index": "1", "timepoint": "1"}, + source_image_names=(alias,), + source_voxel_spacing=SourceVoxelSpacing((1.0, 1.0)), + source_spatial_domain=SourceSpatialDomain(origin_yx=(0, 0), source_shape_yx=pixels.shape[:2]), + ).payload_with(pixels, None) + + +def _execute_bound_stack(bundle): + contract = CallableContract.from_callable(gray_to_color) + return CellProfilerFunctionContractExecutor().execute( + contract, contract.resolve_canonical_raw_callable(), bundle, + {"color_scheme": GrayToColorModule.Scheme.STACK, "rescale_intensity": False}, + execution_mode=ImagePayloadExecutionMode.FULL_STACK, + plane_projection=RuntimePlaneAxisValueProjection.preserve( + axis=RuntimePlaneAxis.SOURCE_BINDING, + axis_size=image_payload_data(bundle).shape[0], + source_aliases=image_payload_metadata(bundle).source_image_names, + ), + ) + + +@pytest.mark.parametrize("aliases", [("RawBody", "CappedOutgrowth"), ("IndependentRoleA", "IndependentRoleB")]) +def test_two_processing_roles_share_physical_channel_without_fabrication(aliases): + raw = np.arange(20, dtype=np.float32).reshape(4, 5) * 1000 + capped = np.clip(raw / 6000, 0, 1) + inputs = tuple(_source_plane(pixels, alias) for pixels, alias in zip((raw, capped), aliases, strict=True)) + bundle = ImagePayloadBundleContext.from_payloads(inputs).compose() + assert image_payload_metadata(bundle).plane_axis is RuntimePlaneAxis.SOURCE_BINDING + result = _execute_bound_stack(bundle) + np.testing.assert_array_equal(image_payload_data(result)[..., 0], raw) + np.testing.assert_array_equal(image_payload_data(result)[..., 1], capped) + np.testing.assert_array_equal(image_payload_data(inputs[0]), raw) + metadata = image_payload_metadata(result) + assert metadata.plane_axis is None + assert metadata.source_channel_axis == -1 + assert metadata.source_component_metadata["channel"] == "2" + assert set(metadata.source_image_paths) == {"/synthetic/A01_s1_w2_z1_t1.tif"} + assert metadata.source_voxel_spacing == image_payload_metadata(inputs[0]).source_voxel_spacing + assert metadata.source_spatial_domain == image_payload_metadata(inputs[0]).source_spatial_domain + + +def test_projected_runtime_plane_needs_a_separate_named_binding_axis(): + pixels = np.arange(20, dtype=np.float32).reshape(4, 5) * 1000 + scalar = _source_plane(pixels, "FITC") + metadata = image_payload_metadata(scalar) + retained = replace(metadata, plane_axis=RuntimePlaneAxis.RUNTIME_SLICE).payload_with(pixels[None], None) + projected = RuntimeSliceProjection.value_for_slice(retained, RuntimePlaneAxisValueProjection.from_selected_plane( + axis=RuntimePlaneAxis.RUNTIME_SLICE, plane_index=0, axis_size=1, + )) + assert image_payload_metadata(projected).plane_axis is None + bundle = ImagePayloadBundleContext.from_payloads((projected,)).compose() + assert image_payload_metadata(bundle).plane_axis is RuntimePlaneAxis.SOURCE_BINDING + result = _execute_bound_stack(bundle) + assert image_payload_data(result).shape == (4, 5, 1) + np.testing.assert_array_equal(image_payload_data(result)[..., 0], pixels) + assert image_payload_metadata(result).source_channel_axis == -1 + + +def test_stack_color_output_is_not_a_second_scalar_gray_binding(): + pixels = np.arange(20, dtype=np.float32).reshape(4, 5) + named = ImagePayloadBundleContext.from_payloads((_source_plane(pixels, "FITC"),)).compose() + color = _execute_bound_stack(named) + # The existing STACK contract emits YXC even for one role. A second grayscale + # binding introduces C,Y,X,source-color rather than the required C,Y,X. + assert image_payload_metadata(color).source_channel_axis == -1 + second_named = ImagePayloadBundleContext.from_payloads((color,)).compose() + with pytest.raises(ValueError, match="axes don't match array"): + _execute_bound_stack(second_named) + + +def test_integer_primary_binding_units_are_owned_before_stack_rescale_flag(): + pixels = np.arange(20, dtype=np.uint16).reshape(4, 5) * 1000 + source = _source_plane(pixels, "FITC") + request = RuntimeArtifactInputRequest( + spec=ArtifactSpec.input("FITC", ImageArtifactType), value=source, + ) + binding_owner = RuntimeArtifactTypeStrategy.for_artifact_type(ImageArtifactType) + bound = binding_owner.runtime_input_value(request) + # This conversion happens in the original input owner, before GrayToColor's + # rescale_intensity argument. Do not claim a raw-unit-preserving four-step fix + # from a passing floating-point Stack kernel test. + np.testing.assert_array_equal(image_payload_data(bound), pixels.astype(np.float32) / 65535) + np.testing.assert_array_equal(image_payload_data(source), pixels) + assert image_payload_metadata(bound).source_image_paths == image_payload_metadata(source).source_image_paths + assert image_payload_metadata(bound).source_component_metadata["channel"] == "2" From b16e96fc33fb0dbb3387102a951bccee8d8bf963 Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Fri, 2 Oct 2026 02:31:06 -0400 Subject: [PATCH 2/7] Capture actual GrayToColor created-carrier compile failure (#432) --- .../carrier-compile-diagnosis.log | 65 ++++++++ .../carrier-compile-parent-admission.log | 65 ++++++++ .../carrier-creation-receipt.rst | 143 ++++++++++++++++++ .../carrier-runtime-lanes.log | 49 ++++++ .../original-assisted4-status-excerpts.log | 58 +++++++ .../receipt.rst | 5 + .../test_gray_to_color_carrier_compile_432.py | 114 ++++++++++++++ 7 files changed, 499 insertions(+) create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-compile-diagnosis.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-compile-parent-admission.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-creation-receipt.rst create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-runtime-lanes.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/original-assisted4-status-excerpts.log create mode 100644 tests/unit/test_gray_to_color_carrier_compile_432.py diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-compile-diagnosis.log b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-compile-diagnosis.log new file mode 100644 index 0000000000..d900bf3ed9 --- /dev/null +++ b/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= 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. diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-runtime-lanes.log b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-runtime-lanes.log new file mode 100644 index 0000000000..d768f43281 --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-runtime-lanes.log @@ -0,0 +1,49 @@ +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 +.F [100%] +=================================== FAILURES =================================== +______________ test_scalar_role_outputs_consume_the_color_carrier ______________ +tests/unit/test_gray_to_color_carrier_compile_432.py:114: in test_scalar_role_outputs_consume_the_color_carrier + 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= Date: Fri, 2 Oct 2026 02:54:24 -0400 Subject: [PATCH 3/7] Prove created color carriers and project scalar outputs (#432) --- .../carrier-creation-receipt.rst | 3 + .../carrier-repair-controls.log | 40 ++++++ .../carrier-repair-initial.log | 39 ++++++ .../carrier-repair-newcase.log | 39 ++++++ .../carrier-repair-receipt.rst | 98 +++++++++++++++ openhcs/core/callable_contract.py | 45 ++++++- openhcs/core/function_patterns.py | 60 +++++++-- openhcs/core/pipeline/compiler.py | 61 ++++++--- .../processing/backends/cellprofiler/color.py | 73 ++++++++--- .../test_gray_to_color_carrier_compile_432.py | 119 +++++++++++++++++- 10 files changed, 521 insertions(+), 56 deletions(-) create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-controls.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-initial.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-newcase.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-creation-receipt.rst b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-creation-receipt.rst index e807a57883..f7b766779a 100644 --- a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-creation-receipt.rst +++ b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-creation-receipt.rst @@ -1,6 +1,9 @@ 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 -------------------------------- diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-controls.log b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-controls.log new file mode 100644 index 0000000000..b1ec3adc77 --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-controls.log @@ -0,0 +1,40 @@ +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 +........................................................................ [ 93%] +..... [100%] +=============================== 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 +77 passed, 2 warnings in 5.97s + 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-repair-432-20261002/pytest tests/unit/test_gray_to_color_carrier_compile_432.py tests/unit/test_primary_image_carrier_compile_gate.py tests/unit/test_callable_contract.py tests/unit/test_cellprofiler_output_cardinality_declarations.py tests/unit/test_cellprofiler_artifact_activation_identity.py -q --tb=short" + User time (seconds): 6.32 + System time (seconds): 0.40 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.77 + 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): 372764 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 80201 + Voluntary context switches: 4 + Involuntary context switches: 48 + Swaps: 0 + File system inputs: 24 + File system outputs: 200 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-initial.log b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-initial.log new file mode 100644 index 0000000000..761452635f --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-initial.log @@ -0,0 +1,39 @@ +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 +..................... [100%] +=============================== 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 +21 passed, 2 warnings in 5.30s + 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-repair-432-20261002/pytest tests/unit/test_gray_to_color_carrier_compile_432.py tests/unit/test_primary_image_carrier_compile_gate.py -q --tb=short" + User time (seconds): 5.62 + System time (seconds): 0.40 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.09 + 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): 373380 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 4 + Minor (reclaiming a frame) page faults: 79928 + Voluntary context switches: 28 + Involuntary context switches: 44 + Swaps: 0 + File system inputs: 56 + File system outputs: 176 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-newcase.log b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-newcase.log new file mode 100644 index 0000000000..08658dee1f --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-newcase.log @@ -0,0 +1,39 @@ +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 +.......................... [100%] +=============================== 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 +26 passed, 2 warnings in 5.43s + 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-repair-432-20261002/pytest tests/unit/test_gray_to_color_carrier_compile_432.py tests/unit/test_primary_image_carrier_compile_gate.py -q --tb=short" + User time (seconds): 5.72 + System time (seconds): 0.41 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.19 + 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): 369632 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 79712 + Voluntary context switches: 3 + Involuntary context switches: 41 + Swaps: 0 + File system inputs: 8 + File system outputs: 200 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst new file mode 100644 index 0000000000..5e8bd53156 --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst @@ -0,0 +1,98 @@ +#432/#434 working created-carrier and scalar-output repair +======================================================== + +Ownership and predecessor +------------------------- + +Tristan explicitly assigned this narrow production repair to parent/Schrodinger. +Latest split: Root owns394; parent/Singer own404; Schrodinger owns432/434. Shared +hunks were named to Root before editing: +https://github.com/OpenHCSDev/openhcs/pull/394#issuecomment-5946842034. +Only callable_contract.py, function_patterns.py, pipeline/compiler.py and +cellprofiler/color.py are production changes. Root's prepared signatures, +executor, metadata/materialization implementations and runtime annotations +are untouched. No foreign worktree edits or competing394/404 integration. + +Base df15ddfe0bcbd80cadaf2f5fc56b83517910f334. Historical diagnosis and failures +at b16e96fc33fb0dbb3387102a951bccee8d8bf963 remain intact; their pending-release +wording describes that predecessor, not this subsequently authorized repair. +Original installed ASSISTED4 five-step compile failure and complete four-step +execution5e3474f4 are retained in carrier-creation-receipt.rst/raw excerpts. +No installed five-step or biological pass is claimed here. + +Actual owner, hooks and removed mechanisms +----------------------------------------- + +PrimaryImageCarrierTransition remains the existing effect authority. Its +members now declare creation independently of preservation. Shared proves() +and creates() derive behavior from those declarations, replacing the old +PRESERVE identity switch. GrayToColor supplies only the truthful +CREATE_SOURCE_CHANNEL_AXIS annotation through the original metadata boundary. +No source header is rewritten and ColorToGray's strict requirement is unchanged. + +CompiledFunctionGroup.primary_image_carrier_proof owns the one backwards +invocation traversal. Inherited/created/unproved nominal proof results expose +the source-validation obligation and exact failed invocation; they are local +proof results, not another registry, metadata mirror or persisted state store. +The compiler's original ancestry owner uses that result, stopping only at a +creator of the required carrier. The preservation-only first_unproved method +and _carrier_source_plan tuple/sentinel path are deleted, not left as facades. + +ImageChannelType declarations own selected-versus-derived scalar projection. +RGB and CHANNELS select through original ImagePayloadMetadata.project_channel_payload; +HSV derives from all inputs through original metadata/payload owners while +consuming the channel axis. The RGB-only consumer branch and stale non-RGB +payload path are deleted. Mask projection, physical provenance and strict +domain validation remain with the existing metadata owner, not copied here. + +Independent new-case behavior and strict negatives +------------------------------------------------- + +A new test-local creator and preserver require only their own declarations. +Actual lane construction/copy executes, then unchanged consumer validation +passes both same-group and cross-step paths without reading scalar source +headers. A source-read trap proves ancestry terminates at creation. False +PRESERVE still fails exact grayscale source validation. Unknown operations +before a creator do not invalidate its output, but unknown operations after +creation fail closed. A second ColorToGray cannot inherit the consumed carrier. +Existing missing/unknown-source, dependency and source-transformation cases pass. + +Original registered Stack -> CHANNELS split preserves both raw/capped arrays, +order, physical C2 identity/path and yields actual YX outputs without a channel +carrier. RGB/HSV/CHANNELS tests retain masks, source names, calibration/domain +and unchanged input data. No new independent production capability requires +MI in this boundary; no ornamental inheritance or untested MRO claim is made. + +Current NRA review +------------------ + +Personally read current nra-refactoring/refactor-audit instructions and the +authoritative ZIP SKILL.md, catalogue, boundaries/identity/implementation and +surface-receipt references, plus project00-RULES before decisions. BOUND-8: +carry actual producer evidence across its original contract. IDEN-1: creation +is distinct from preservation. IMPL-1/2/3/5: no new consumer leaf/name/type +switch or doubled dispatch. IMPL-12/13: reuse original metadata algorithms and +strictness; delete replaced traversal/branches. New catalogs/rosters/importers, +compatibility aliases, squeeze/axis-acceptance heuristics and source mirrors: +none. Existing unrelated numeric HSV dispatch is not expanded or relocated. + +Source-only evidence and bounds +------------------------------- + +Existing read-only Python3.12.3/ABI source driver; no new environment, downloads +or installed changes. Each shard CPU0/CPUQuota100%, thread pools1, +MemoryMax512M/MemorySwapMax0, timeout60s. Actual admission RAM12.6GiB/home11.2GiB; +resource-helper advisory warning was not represented as a hard-limit pass. + +* carrier-repair-initial.log: 21PASS,6.09s,373380KiB,exit0. +* carrier-repair-newcase.log: 26PASS,6.19s,369632KiB,exit0. +* carrier-repair-controls.log: 77PASS,6.77s,372764KiB,exit0. + +Two original unary GrayToColor naming REDs remain separate and unchanged; +ordinary scalar ImageMath naming is the retained installed successful route. +Raw logs preserve warning whitespace; no whole-log diff-check-clean claim. +No full/global NRA/R1 retry or qualification, provider/science/native/UI/MCP +launch, installation or frozen-author edit. Parent owns later installed +acceptance. Untracked required-runtime-qt-publication ledger remains excluded. +Original pinned R0 and disposable fixture cleanup will be appended after their +finite terminal checks, without modifying predecessor failures. diff --git a/openhcs/core/callable_contract.py b/openhcs/core/callable_contract.py index d6de5863a5..097a69a3aa 100644 --- a/openhcs/core/callable_contract.py +++ b/openhcs/core/callable_contract.py @@ -241,14 +241,34 @@ def validate_source_metadata( class PrimaryImageCarrierTransition(str, Enum): """Declared effect of a callable on its primary-image carrier semantics.""" - PRESERVE = "preserve" + def __new__( + cls, + value: str, + preserves: bool, + creates: tuple[PrimaryImageCarrierRequirement, ...], + ): + member = str.__new__(cls, value) + member._value_ = value + member._preserves = preserves + member._creates = creates + return member + + PRESERVE = ("preserve", True, ()) + CREATE_SOURCE_CHANNEL_AXIS = ( + "create_source_channel_axis", + False, + (PrimaryImageCarrierRequirement.SOURCE_CHANNEL_AXIS,), + ) + + def creates(self, requirement: PrimaryImageCarrierRequirement) -> bool: + """Return whether this member supplies evidence without source inheritance.""" + + return requirement in self._creates def proves(self, requirement: PrimaryImageCarrierRequirement) -> bool: - """Return whether this transition preserves the requested evidence.""" + """Return whether this member preserves or creates the requested evidence.""" - if self is PrimaryImageCarrierTransition.PRESERVE: - return True - raise AssertionError(f"Unhandled primary image carrier transition {self!r}.") + return self._preserves or self.creates(requirement) def _validate_optional_enum( @@ -1705,6 +1725,21 @@ def preserves_primary_image_carrier(func: Any) -> Any: return func +def declares_primary_image_carrier_transition( + transition: PrimaryImageCarrierTransition, +) -> Any: + """Attach a member-owned carrier effect through the original metadata boundary.""" + + def decorator(func: Any) -> Any: + attach_callable_contract_metadata( + func, + primary_image_carrier_transition=transition, + ) + return func + + return decorator + + def prepare_processing_callable(func: Any) -> None: """Prepare declarations through their shared process-local operation contract.""" from openhcs.core.processing_preparation import CallablePreparation diff --git a/openhcs/core/function_patterns.py b/openhcs/core/function_patterns.py index b79b4fc695..b96bf70048 100644 --- a/openhcs/core/function_patterns.py +++ b/openhcs/core/function_patterns.py @@ -8,6 +8,7 @@ from __future__ import annotations +from abc import ABC, abstractmethod from collections.abc import Callable, Hashable, Iterator, Mapping, Sequence from dataclasses import dataclass, field, replace from enum import Enum @@ -818,25 +819,62 @@ def preserves_input_main_flow(self) -> bool: for invocation in self.invocations ) - def first_unproved_primary_image_carrier_invocation( + def primary_image_carrier_proof( self, requirement: PrimaryImageCarrierRequirement, *, stop_before: int | None = None, - ) -> CompiledFunctionInvocation | None: - """Return the first invocation without a typed carrier proof.""" + ) -> PrimaryImageCarrierProof: + """Resolve a consumer's evidence backwards to its creation or source.""" invocations = ( self.invocations if stop_before is None else self.invocations[:stop_before] ) - return next( - ( - invocation - for invocation in invocations - if not invocation.proves_primary_image_carrier(requirement) - ), - None, - ) + for invocation in reversed(invocations): + if not invocation.proves_primary_image_carrier(requirement): + return UnprovedPrimaryImageCarrierProof(invocation) + transition = invocation.contract.primary_image_carrier_transition + if transition.creates(requirement): + return CreatedPrimaryImageCarrierProof() + return InheritedPrimaryImageCarrierProof() + + +class PrimaryImageCarrierProof(ABC): + """One group-owned proof result, not another carrier metadata authority.""" + + @property + def unproved_invocation(self) -> CompiledFunctionInvocation | None: + return None + + @property + @abstractmethod + def requires_source_validation(self) -> bool: + """Return whether proof still needs the exact original source carrier.""" + + +class InheritedPrimaryImageCarrierProof(PrimaryImageCarrierProof): + @property + def requires_source_validation(self) -> bool: + return True + + +class CreatedPrimaryImageCarrierProof(PrimaryImageCarrierProof): + @property + def requires_source_validation(self) -> bool: + return False + + +@dataclass(frozen=True, slots=True) +class UnprovedPrimaryImageCarrierProof(PrimaryImageCarrierProof): + invocation: CompiledFunctionInvocation + + @property + def unproved_invocation(self) -> CompiledFunctionInvocation: + return self.invocation + + @property + def requires_source_validation(self) -> bool: + return False @dataclass(frozen=True, slots=True) diff --git a/openhcs/core/pipeline/compiler.py b/openhcs/core/pipeline/compiler.py index 154cdd48b6..1adcb097ef 100644 --- a/openhcs/core/pipeline/compiler.py +++ b/openhcs/core/pipeline/compiler.py @@ -1427,12 +1427,13 @@ def validate_primary_image_carrier_requirements( f"{group.group_key!r}, invocation " f"{invocation.contract.function_name!r}" ) - unproved_prefix = ( - group.first_unproved_primary_image_carrier_invocation( + prefix_proof = ( + group.primary_image_carrier_proof( requirement, stop_before=invocation_index, ) ) + unproved_prefix = prefix_proof.unproved_invocation if unproved_prefix is not None: failures.append( f"{owner}: carrier requirement {requirement.value!r} " @@ -1441,6 +1442,8 @@ def validate_primary_image_carrier_requirements( "same group." ) continue + if not prefix_proof.requires_source_validation: + continue source_binding_plan = PipelineCompiler._source_anchor_binding_plan( plan, group, @@ -1457,7 +1460,7 @@ def validate_primary_image_carrier_requirements( "projection represents this callable's main flow." ) continue - source_proof = PipelineCompiler._carrier_source_plan( + PipelineCompiler._validate_inherited_primary_image_carrier_requirement( session=session, plan=plan, group_key=group.group_key, @@ -1466,9 +1469,7 @@ def validate_primary_image_carrier_requirements( requirement=requirement, failures=failures, ) - if source_proof is None: - continue - _source_plan, source_binding_plan = source_proof + continue PipelineCompiler._validate_pipeline_start_carrier_requirement( session=session, source_binding_plan=( @@ -1536,7 +1537,7 @@ def _source_anchor_binding_plan( ) from error @staticmethod - def _carrier_source_plan( + def _validate_inherited_primary_image_carrier_requirement( *, session: CompilationSession, plan: CompiledStepPlan, @@ -1545,8 +1546,8 @@ def _carrier_source_plan( owner: str, requirement: PrimaryImageCarrierRequirement, failures: list[str], - ) -> tuple[CompiledStepPlan, CompiledSourceBindingPlan | None] | None: - """Trace a carrier-preserving main-flow chain to its source-owning plan.""" + ) -> None: + """Validate inheritance until a declaration creates the required carrier.""" try: ancestry = session.main_flow_plan_ancestry(plan.step_index) @@ -1555,7 +1556,7 @@ def _carrier_source_plan( f"{owner}: carrier requirement {requirement.value!r} has an " f"invalid compiled step dependency: {error}" ) - return None + return current_source_binding_plan = initial_source_binding_plan for ancestry_index, producer in enumerate(ancestry): @@ -1566,7 +1567,7 @@ def _carrier_source_plan( f"{owner}: carrier requirement {requirement.value!r} has no " f"compiled producer proof for step {producer.step_index}." ) - return None + return try: producer_group = producer.compiled_function_pattern.group_for_component( group_key @@ -1577,29 +1578,32 @@ def _carrier_source_plan( f"select a carrier-producing group from step " f"{producer.step_index}: {error}" ) - return None + return if producer_group is None: failures.append( f"{owner}: carrier requirement {requirement.value!r} has no " f"producer group {group_key!r} at step {producer.step_index}." ) - return None + return if not producer_group.invocations: failures.append( f"{owner}: carrier requirement {requirement.value!r} has an " f"empty producer group at step {producer.step_index}." ) - return None - unproved = producer_group.first_unproved_primary_image_carrier_invocation( + return + proof = producer_group.primary_image_carrier_proof( requirement ) + unproved = proof.unproved_invocation if unproved is not None: failures.append( f"{owner}: carrier requirement {requirement.value!r} is not " f"preserved by producer step {producer.step_index} callable " f"{unproved.contract.function_name!r}." ) - return None + return + if not proof.requires_source_validation: + return current_source_binding_plan = PipelineCompiler._source_anchor_binding_plan( producer, producer_group, @@ -1610,14 +1614,21 @@ def _carrier_source_plan( current_source_binding_plan is not None and current_source_binding_plan.primary_plane_bindings ): - return producer, current_source_binding_plan + PipelineCompiler._validate_pipeline_start_carrier_requirement( + session=session, + source_binding_plan=current_source_binding_plan, + owner=owner, + requirement=requirement, + failures=failures, + ) + return if producer.requires_terminal_source_projection: failures.append( f"{owner}: carrier requirement {requirement.value!r} has no " f"exact primary source-binding projection at producer step " f"{producer.step_index}." ) - return None + return current = ancestry[-1] try: @@ -1627,8 +1638,18 @@ def _carrier_source_plan( f"{owner}: carrier requirement {requirement.value!r} cannot be " f"traced to an exact pipeline-start source: {error}" ) - return None - return current, current_source_binding_plan + return + PipelineCompiler._validate_pipeline_start_carrier_requirement( + session=session, + source_binding_plan=( + CompiledSourceBindingPlan.empty() + if current_source_binding_plan is None + else current_source_binding_plan + ), + owner=owner, + requirement=requirement, + failures=failures, + ) @staticmethod def _validate_pipeline_start_carrier_requirement( diff --git a/openhcs/processing/backends/cellprofiler/color.py b/openhcs/processing/backends/cellprofiler/color.py index b7e5ad86ca..a762c62592 100644 --- a/openhcs/processing/backends/cellprofiler/color.py +++ b/openhcs/processing/backends/cellprofiler/color.py @@ -27,7 +27,9 @@ ImageArtifactType, ) from openhcs.core.callable_contract import ( + PrimaryImageCarrierTransition, PrimaryImageCarrierRequirement, + declares_primary_image_carrier_transition, requires_primary_image_carrier, ) from openhcs.core.memory.decorators import numpy @@ -80,10 +82,53 @@ from openhcs.interop.cellprofiler.settings_binder import SettingsBinder +class ColorToGrayScalarOutputProjection(ABC): + """Own whether a scalar output selects a source channel or derives from all.""" + + @abstractmethod + def project( + self, image: RuntimeArrayData, *, channel_index: int, output: RuntimeArrayData + ) -> RuntimeArrayData: ... + + +class SelectedColorChannelProjection(ColorToGrayScalarOutputProjection): + def project( + self, image: RuntimeArrayData, *, channel_index: int, output: RuntimeArrayData + ) -> RuntimeArrayData: + return image_payload_metadata(image).project_channel_payload( + source_payload=image, + source_data=image_payload_data(image), + channel_index=channel_index, + channel_data=output, + channel_axis=-1, + ) + + +class DerivedColorChannelProjection(ColorToGrayScalarOutputProjection): + def project( + self, image: RuntimeArrayData, *, channel_index: int, output: RuntimeArrayData + ) -> RuntimeArrayData: + del channel_index + return with_image_payload_data( + image, output, + metadata=image_payload_metadata(image).without_source_channel_axis(), + ) + + class ImageChannelType(Enum): - RGB = "rgb" - HSV = "hsv" - CHANNELS = "channels" + def __new__(cls, value: str, projection: type[ColorToGrayScalarOutputProjection]): + member = object.__new__(cls) + member._value_ = value + member._scalar_output_projection = projection() + return member + + RGB = ("rgb", SelectedColorChannelProjection) + HSV = ("hsv", DerivedColorChannelProjection) + CHANNELS = ("channels", SelectedColorChannelProjection) + + @property + def scalar_output_projection(self) -> ColorToGrayScalarOutputProjection: + return self._scalar_output_projection class ColorToGrayMode(Enum): @@ -1490,6 +1535,9 @@ def run(self, request: GrayToColorRequest) -> np.ndarray: return self.final_rgb(rgb_image, request) +@declares_primary_image_carrier_transition( + PrimaryImageCarrierTransition.CREATE_SOURCE_CHANNEL_AXIS, +) @required_variable_components(VariableComponents.CHANNEL) @composed_image_payload @numpy(contract=ProcessingContract.PURE_3D) @@ -1613,23 +1661,14 @@ def color_to_gray( output, metadata=color_to_gray_combine_output_metadata(image), ) - image_data = image_payload_data(image) outputs = split_color_to_gray(image, image_type, channel_indices) - if image_type is ImageChannelType.RGB: - return pack_aligned_image_outputs( - tuple( - image_payload_metadata(image).project_channel_payload( - source_payload=image, - source_data=image_data, - channel_index=channel_index, - channel_data=output, - channel_axis=-1, - ) - for channel_index, output in zip(channel_indices, outputs, strict=True) + return pack_aligned_image_outputs( + tuple( + image_type.scalar_output_projection.project( + image, channel_index=channel_index, output=output, ) + for channel_index, output in zip(channel_indices, outputs, strict=True) ) - return pack_aligned_image_outputs( - tuple(with_image_payload_data(image, output) for output in outputs) ) diff --git a/tests/unit/test_gray_to_color_carrier_compile_432.py b/tests/unit/test_gray_to_color_carrier_compile_432.py index bad8f59583..942c6b498d 100644 --- a/tests/unit/test_gray_to_color_carrier_compile_432.py +++ b/tests/unit/test_gray_to_color_carrier_compile_432.py @@ -6,16 +6,20 @@ import pytest import tifffile -from openhcs.core.callable_contract import CallableContract, PrimaryImageCarrierTransition +from openhcs.core.callable_contract import ( + CallableContract, PrimaryImageCarrierRequirement, PrimaryImageCarrierTransition, + declares_primary_image_carrier_transition, preserves_primary_image_carrier, +) from openhcs.core.compiled_step_plan import CompiledStepPlan from openhcs.core.function_patterns import CompiledFunctionGroup, CompiledFunctionPattern from openhcs.core.pipeline.compiler import PipelineCompiler -from openhcs.core.runtime_image_values import image_payload_data, image_payload_metadata +from openhcs.core.runtime_image_values import image_payload_data, image_payload_mask, image_payload_metadata from openhcs.core.aligned_image_payload import ImagePayloadBundleContext, ImagePayloadExecutionMode from openhcs.core.step_dependencies import StepInputDependency from openhcs.interop.cellprofiler.runtime.function_contract_execution import CellProfilerFunctionContractExecutor from openhcs.processing.backends.cellprofiler.color import ( ColorToGrayMode, ImageChannelType, color_to_gray, gray_to_color, + split_color_to_gray, ) from test_gray_to_color_binding_axis_432 import _execute_bound_stack, _source_plane from test_primary_image_carrier_compile_gate import _compiled_pattern, _session @@ -43,7 +47,7 @@ def _gray_creator_session(tmp_path): def test_declared_gray_creator_proves_color_consumer_before_execution(tmp_path): # Intended acceptance: unchanged strict consumer accepts a declared creator. - # Current RED matches the installed producer-step error, not a live replay. + # Original RED matched the installed producer-step error, not a live replay. PipelineCompiler.validate_primary_image_carrier_requirements(_gray_creator_session(tmp_path)) @@ -112,3 +116,112 @@ def test_scalar_role_outputs_consume_the_color_carrier(): for output in result.slices: assert image_payload_data(output).shape == (4, 5) assert image_payload_metadata(output).source_channel_axis is None + + +@pytest.mark.parametrize("same_group", [False, True]) +def test_independent_creator_declaration_needs_no_consumer_edits(tmp_path, monkeypatch, same_group): + @declares_primary_image_carrier_transition( + PrimaryImageCarrierTransition.CREATE_SOURCE_CHANNEL_AXIS, + ) + def independent_lane_creator(image): + return np.stack((image, image * 2), axis=-1) + + @preserves_primary_image_carrier + def independent_lane_preserver(image): + return image.copy() + + # Behavior, not an inheritance assertion or a fake source-color header. + gray = np.arange(20, dtype=np.float32).reshape(4, 5) + created = independent_lane_preserver(independent_lane_creator(gray)) + np.testing.assert_array_equal(created[..., 0], gray) + np.testing.assert_array_equal(created[..., 1], gray * 2) + session = _gray_creator_session(tmp_path) + producer_invocations = tuple( + invocation + for callable_ in (independent_lane_creator, independent_lane_preserver) + for invocation in _compiled_pattern(callable_).iter_invocations() + ) + if same_group: + consumer_invocations = tuple(session.plans[1].compiled_function_pattern.iter_invocations()) + session.plans = {0: replace(session.plans[0], compiled_function_pattern=CompiledFunctionPattern( + groups=(CompiledFunctionGroup("default", producer_invocations + consumer_invocations),), + is_grouped=False, + ))} + else: + session.plans[0] = replace(session.plans[0], compiled_function_pattern=CompiledFunctionPattern( + groups=(CompiledFunctionGroup("default", producer_invocations),), is_grouped=False, + )) + session.context.step_plans = session.plans + + def reject_source_backtracking(*args, **kwargs): + pytest.fail("A declared creator must stop source-carrier backtracking") + + monkeypatch.setattr( + "openhcs.core.pipeline.compiler.require_image_file_source_metadata", + reject_source_backtracking, + ) + PipelineCompiler.validate_primary_image_carrier_requirements(session) + + +@pytest.mark.parametrize("unknown_after_creator", [False, True]) +def test_group_proof_stops_at_creator_but_rejects_later_unknown(unknown_after_creator): + def unknown(image): + return image + + functions = (gray_to_color, unknown) if unknown_after_creator else (unknown, gray_to_color) + invocations = tuple( + invocation for callable_ in functions + for invocation in _compiled_pattern(callable_).iter_invocations() + ) + proof = CompiledFunctionGroup("default", invocations).primary_image_carrier_proof( + PrimaryImageCarrierRequirement.SOURCE_CHANNEL_AXIS, + ) + assert not proof.requires_source_validation + if unknown_after_creator: + assert proof.unproved_invocation is invocations[-1] + else: + assert proof.unproved_invocation is None + + +def test_color_to_gray_does_not_preserve_consumed_carrier_for_later_consumer(tmp_path): + session = _gray_creator_session(tmp_path) + consumer = session.plans[1] + session.plans[2] = replace( + consumer, step_index=2, step_name="RejectSecondScalarSplit", + main_input_dependency=StepInputDependency.step_output( + source_step_index=1, source_step_scope_id="step-1", + ), + ) + session.plans[1] = replace(consumer, step_scope_id="step-1") + session.context.step_plans = session.plans + with pytest.raises(ValueError, match="not preserved by producer step 1 callable 'color_to_gray'"): + PipelineCompiler.validate_primary_image_carrier_requirements(session) + + +@pytest.mark.parametrize("image_type", tuple(ImageChannelType)) +def test_scalar_projection_modes_keep_pixels_mask_and_original_source(image_type): + pixels = np.arange(60, dtype=np.float32).reshape(4, 5, 3) / 60 + mask = np.arange(20).reshape(4, 5) % 3 != 0 + source = _source_plane(pixels, "OriginalColor") + metadata = image_payload_metadata(source).replace_fields(source_channel_axis=-1) + source = metadata.payload_with(pixels, mask) + expected = split_color_to_gray(source, image_type, (0, 1)) + contract = CallableContract.from_callable(color_to_gray) + result = CellProfilerFunctionContractExecutor().execute( + contract, contract.resolve_canonical_raw_callable(), source, + {"mode": ColorToGrayMode.SPLIT, "image_type": image_type, + "channel_indices": (0, 1), "contributions": (1.0, 1.0)}, + execution_mode=ImagePayloadExecutionMode.NATURAL, + ) + for output, expected_pixels in zip(result.slices, expected, strict=True): + np.testing.assert_array_equal(image_payload_data(output), expected_pixels) + np.testing.assert_array_equal(image_payload_mask(output), mask) + output_metadata = image_payload_metadata(output) + assert output_metadata.source_channel_axis is None + assert output_metadata.source_path == metadata.source_path + assert output_metadata.source_component_metadata == metadata.source_component_metadata + assert output_metadata.source_image_names == metadata.source_image_names + assert output_metadata.source_voxel_spacing == metadata.source_voxel_spacing + assert output_metadata.source_spatial_domain == metadata.source_spatial_domain + np.testing.assert_array_equal(image_payload_data(source), pixels) + assert image_payload_metadata(source).source_channel_axis == -1 From 6370ac5f609bd98544eacdddedc6b9c013d76f09 Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Fri, 2 Oct 2026 02:59:38 -0400 Subject: [PATCH 4/7] Let carrier proof owners reject invalid invocation chains --- openhcs/core/function_patterns.py | 16 ++++++---- openhcs/core/pipeline/compiler.py | 32 +++++++++++-------- .../test_gray_to_color_carrier_compile_432.py | 5 +-- 3 files changed, 32 insertions(+), 21 deletions(-) diff --git a/openhcs/core/function_patterns.py b/openhcs/core/function_patterns.py index b96bf70048..5c31858ad6 100644 --- a/openhcs/core/function_patterns.py +++ b/openhcs/core/function_patterns.py @@ -842,9 +842,11 @@ def primary_image_carrier_proof( class PrimaryImageCarrierProof(ABC): """One group-owned proof result, not another carrier metadata authority.""" - @property - def unproved_invocation(self) -> CompiledFunctionInvocation | None: - return None + def require_proven_invocations( + self, + failure_message: Callable[[CompiledFunctionInvocation], str], + ) -> None: + """Accept proven transitions; a failed proof owns its rejection.""" @property @abstractmethod @@ -868,9 +870,11 @@ def requires_source_validation(self) -> bool: class UnprovedPrimaryImageCarrierProof(PrimaryImageCarrierProof): invocation: CompiledFunctionInvocation - @property - def unproved_invocation(self) -> CompiledFunctionInvocation: - return self.invocation + def require_proven_invocations( + self, + failure_message: Callable[[CompiledFunctionInvocation], str], + ) -> None: + raise ValueError(failure_message(self.invocation)) @property def requires_source_validation(self) -> bool: diff --git a/openhcs/core/pipeline/compiler.py b/openhcs/core/pipeline/compiler.py index 1adcb097ef..ce7449d392 100644 --- a/openhcs/core/pipeline/compiler.py +++ b/openhcs/core/pipeline/compiler.py @@ -1433,14 +1433,17 @@ def validate_primary_image_carrier_requirements( stop_before=invocation_index, ) ) - unproved_prefix = prefix_proof.unproved_invocation - if unproved_prefix is not None: - failures.append( - f"{owner}: carrier requirement {requirement.value!r} " - "is not preserved by earlier callable " - f"{unproved_prefix.contract.function_name!r} in the " - "same group." + try: + prefix_proof.require_proven_invocations( + lambda unproved: ( + f"{owner}: carrier requirement {requirement.value!r} " + "is not preserved by earlier callable " + f"{unproved.contract.function_name!r} in the " + "same group." + ) ) + except ValueError as error: + failures.append(str(error)) continue if not prefix_proof.requires_source_validation: continue @@ -1594,13 +1597,16 @@ def _validate_inherited_primary_image_carrier_requirement( proof = producer_group.primary_image_carrier_proof( requirement ) - unproved = proof.unproved_invocation - if unproved is not None: - failures.append( - f"{owner}: carrier requirement {requirement.value!r} is not " - f"preserved by producer step {producer.step_index} callable " - f"{unproved.contract.function_name!r}." + try: + proof.require_proven_invocations( + lambda unproved: ( + f"{owner}: carrier requirement {requirement.value!r} is not " + f"preserved by producer step {producer.step_index} callable " + f"{unproved.contract.function_name!r}." + ) ) + except ValueError as error: + failures.append(str(error)) return if not proof.requires_source_validation: return diff --git a/tests/unit/test_gray_to_color_carrier_compile_432.py b/tests/unit/test_gray_to_color_carrier_compile_432.py index 942c6b498d..9e9c2aae65 100644 --- a/tests/unit/test_gray_to_color_carrier_compile_432.py +++ b/tests/unit/test_gray_to_color_carrier_compile_432.py @@ -178,9 +178,10 @@ def unknown(image): ) assert not proof.requires_source_validation if unknown_after_creator: - assert proof.unproved_invocation is invocations[-1] + with pytest.raises(ValueError, match="unknown"): + proof.require_proven_invocations(lambda invocation: invocation.contract.function_name) else: - assert proof.unproved_invocation is None + proof.require_proven_invocations(lambda invocation: pytest.fail("Unexpected failed proof")) def test_color_to_gray_does_not_preserve_consumed_carrier_for_later_consumer(tmp_path): From e2d72f9233e950277fc0d5970bd9447482e789f7 Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Fri, 2 Oct 2026 03:08:27 -0400 Subject: [PATCH 5/7] Retain focused carrier controls and exact unresolved R0 findings --- .../carrier-repair-binding-controls.log | 39 + .../carrier-repair-owned-proof-controls.log | 40 + .../carrier-repair-owned-proof-r0.log | 15698 ++++++++++++++++ .../carrier-repair-r0.log | 15698 ++++++++++++++++ .../carrier-repair-receipt.rst | 48 +- .../working-pr-body.md | 28 + 6 files changed, 31547 insertions(+), 4 deletions(-) create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-binding-controls.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-owned-proof-controls.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-owned-proof-r0.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-r0.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/working-pr-body.md diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-binding-controls.log b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-binding-controls.log new file mode 100644 index 0000000000..0b313f79dd --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-binding-controls.log @@ -0,0 +1,39 @@ +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 +..... [100%] +=============================== 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 +5 passed, 2 deselected, 2 warnings in 4.43s + 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-repair-432-20261002/pytest tests/unit/test_gray_to_color_binding_axis_432.py -k not declared_fitc_runtime_plane -q --tb=short" + User time (seconds): 4.86 + System time (seconds): 0.29 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.20 + 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): 345556 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 69287 + Voluntary context switches: 46 + Involuntary context switches: 43 + Swaps: 0 + File system inputs: 0 + File system outputs: 8 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-owned-proof-controls.log b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-owned-proof-controls.log new file mode 100644 index 0000000000..35b16abec2 --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-owned-proof-controls.log @@ -0,0 +1,40 @@ +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 +........................................................................ [ 87%] +.......... [100%] +=============================== 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 +82 passed, 2 deselected, 2 warnings in 6.29s + 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-repair-432-20261002/pytest tests/unit/test_gray_to_color_carrier_compile_432.py tests/unit/test_primary_image_carrier_compile_gate.py tests/unit/test_callable_contract.py tests/unit/test_cellprofiler_output_cardinality_declarations.py tests/unit/test_cellprofiler_artifact_activation_identity.py tests/unit/test_gray_to_color_binding_axis_432.py -k not declared_fitc_runtime_plane -q --tb=short" + User time (seconds): 6.67 + System time (seconds): 0.41 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.15 + 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): 372756 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 80948 + Voluntary context 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+ "CodecSubclass:openhcs/core/pipeline/compiler.py": 0, + "CodecSubclass:openhcs/processing/backends/cellprofiler/color.py": 0, + "StringSubscript": 0 + } +} +Command exited with non-zero status 1 + Command being timed: "/home/ts/.local/share/uv/python/cpython-3.14-linux-x86_64-gnu/bin/python3.14 -I -B -c import sys;sys.path[:0]=["/home/ts/wt/openhcs-namespace-guard-tool-20261001/src","/home/ts/wt/basicpy-live-candidate-20260930/.venv/lib/python3.12/site-packages"];from agent_comms.debt_ratchet import main;sys.argv=["agent-comms-ratchet","--root","openhcs","--base","df15ddfe0bcbd80cadaf2f5fc56b83517910f334","--head","0513c8e4c"];sys.exit(main())" + User time (seconds): 13.67 + System time (seconds): 2.65 + Percent of CPU this job got: 90% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:18.09 + 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): 87504 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 3 + Minor (reclaiming a frame) page faults: 499677 + Voluntary context switches: 13896 + Involuntary context switches: 10886 + Swaps: 0 + File system inputs: 3152 + File system outputs: 3008 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst index 5e8bd53156..0ef8eec802 100644 --- a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst +++ b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst @@ -31,8 +31,8 @@ CREATE_SOURCE_CHANNEL_AXIS annotation through the original metadata boundary. No source header is rewritten and ColorToGray's strict requirement is unchanged. CompiledFunctionGroup.primary_image_carrier_proof owns the one backwards -invocation traversal. Inherited/created/unproved nominal proof results expose -the source-validation obligation and exact failed invocation; they are local +invocation traversal. Inherited/created/unproved nominal proof results own +the source-validation obligation and failed-invocation rejection; they are local proof results, not another registry, metadata mirror or persisted state store. The compiler's original ancestry owner uses that result, stopping only at a creator of the required carrier. The preservation-only first_unproved method @@ -87,6 +87,9 @@ resource-helper advisory warning was not represented as a hard-limit pass. * carrier-repair-initial.log: 21PASS,6.09s,373380KiB,exit0. * carrier-repair-newcase.log: 26PASS,6.19s,369632KiB,exit0. * carrier-repair-controls.log: 77PASS,6.77s,372764KiB,exit0. +* carrier-repair-binding-controls.log: 5PASS/2deselected,5.20s,345556KiB,exit0. +* carrier-repair-owned-proof-controls.log: current82PASS/2deselected, + 7.15s,372756KiB,exit0 after the proof-owner correction below. Two original unary GrayToColor naming REDs remain separate and unchanged; ordinary scalar ImageMath naming is the retained installed successful route. @@ -94,5 +97,42 @@ Raw logs preserve warning whitespace; no whole-log diff-check-clean claim. No full/global NRA/R1 retry or qualification, provider/science/native/UI/MCP launch, installation or frozen-author edit. Parent owns later installed acceptance. Untracked required-runtime-qt-publication ledger remains excluded. -Original pinned R0 and disposable fixture cleanup will be appended after their -finite terminal checks, without modifying predecessor failures. +Original pinned R0 remains RED as detailed below. No waiver or zero-positive +claim. Parent is independently qualifying the working installed behavior; +source tests, architecture guard and actual installed acceptance stay distinct. + +Original guard follow-through (not a waiver) +------------------------------------------- + +Production0513c8e4c6800c2822660bb3a3503b05c3fb840b passed77+5 focused controls. +Original pinned guard tool3b03785f45df2ef5dc62ba6aed99294192ecbb01, Python3.14 +with read-only original metaclass backing, rejected +21 +GodClassExcess:PipelineCompiler and +2 ForeignAbsenceProbe:compiler.py. +carrier-repair-r0.log retains that18.09s/87504KiB exit1 result. No detector +copy, scope removal, suppression or proof waiver. Initial attribution to the +optional unproved_invocation consumer checks was incorrect: the original +detector counts the new negated requires_source_validation property queries. + +Corrected at6370ac5f6: PrimaryImageCarrierProof.require_proven_invocations +owns the transition guard, and the Unproved leaf raises for its exact failed +invocation. Compiler only supplies existing contextual error wording and +collects validation errors. Removed the optional projection/property, but not +the two negated source-obligation queries. Behavior unchanged, current82 +controls PASS. Final carrier-repair-owned-proof-r0.log is terminal RED: ++27 GodClassExcess:PipelineCompiler and +2 ForeignAbsenceProbe:compiler.py, +19.34s/87516KiB/exit1. Exact production6370ac5f609bd98544eacdddedc6b9c013d76f09 +versusdf15ddfe0bcbd80cadaf2f5fc56b83517910f334; all other deltas nonpositive. +This is a specific unresolved architecture guard violation, not a runtime +failure, global NRA result, source-clean claim or installed acceptance. +No wider architecture/audit expansion while parent runs installed qualification. + +Exact disposable cleanup +------------------------ + +All source shards and both guard processes terminal. Verified own fixture root +/home/ts/.cache/agent-scratch/graytocolor-carrier-repair-432-20261002, +10602 logical bytes, containing only generated tiny synthetic test headers and +pytest links; lsof +D reports no open handles. Delete only this exact disposable +root. Source, publication ledger and durable original/current raw logs remain. +No scientific data/output or uncertain external input is removed. Fixtures are +reproducible from retained test source; no unrelated cleanup or environment edit. diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/working-pr-body.md b/docs/validation/graytocolor-binding-axis-432-20261002/working-pr-body.md new file mode 100644 index 0000000000..89a93a5750 --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/working-pr-body.md @@ -0,0 +1,28 @@ +## Working narrow repair for #432 + +Production source checkpoint: `6370ac5f609bd98544eacdddedc6b9c013d76f09` (supersedes `0513c8e4c` for proof-result ownership only), based on main `df15ddfe0bcbd80cadaf2f5fc56b83517910f334`. + +Dalton's retained installed ASSISTED4 four-step ImageMath scalar aliases -> named raw/cap GrayToColor STACK completed (`5e3474f4-f736-4e61-a27f-1d7eb6ec7abd`). The fifth ColorToGray step failed the actual compiler at `mcp.stdout18793`. The source repair now distinguishes **created** channel carriers from inherited preservation; it does not manufacture RGB source metadata or relax the strict consumer. + +### Original owners, not another protocol + +- Existing `PrimaryImageCarrierTransition` members declare preservation/creation. GrayToColor adds only its truthful creation annotation through the original metadata boundary. +- Existing compiled-group owner resolves evidence backwards once. Compiler ancestry stops at the creator of the exact required carrier; unknown later operations, missing-source and false-preservation controls still reject. Replaced preservation-only walk/tuple-sentinel path is deleted. +- `ImageChannelType` declarations select original metadata projection behavior. RGB/CHANNELS use original channel provenance/mask projection; HSV retains its derived-source context and clears the consumed axis. Removed RGB-only consumer branch and stale non-RGB output path. +- No consumer function/type/name exceptions, mirrored registry/store, fake channel, arbitrary squeeze, timeout change or new importer. Current NRA catalogue review covers BOUND-8, IDEN-1, IMPL-1/2/3/5/12/13 in the receipt. + +### Behavioral evidence / bounds + +Current 82 focused declaration/compiler/runtime/binding controls PASS, 7.15s, 372756KiB. Prior 77+5 receipts remain retained; two separate original unary naming REDs are explicitly deselected, retained and **not fixed or passed** here. Each source shard uses existing read-only Python3.12.3/ABI, CPU0/pools1, MemoryMax512M, timeout60s. + +Independent creator/preserver declarations construct real lanes and pass unchanged consumers in same-group and cross-step paths; a source-read trap confirms creation stops backtracking. False PRESERVE, later unknown and second scalar split fail closed. RGB/HSV/CHANNELS preserve pixels, masks, physical identity/calibration and original input while clearing the consumed channel axis. No ornamental MI or untested MRO claim. + +Original RED/setup/control/native receipts remain unchanged. Original pinned R0 on0513 rejected +21 PipelineCompiler class-growth and +2 foreign-absence probes (18.09s, 87504KiB, exit1), retained without waiver.6370 moves failed-chain rejection onto the proof owner via `require_proven_invocations`, deleting the optional failure field and consumer checks; runtime repair is unchanged. **Final R0 remains RED: +27 PipelineCompiler class-growth and +2 negated source-obligation queries**, 19.34s, 87516KiB, exit1; other deltas nonpositive. Initial optional-field attribution was incorrect. Both exact guard failures are published; no zero-positive/full/global NRA/R1 claim or suppression. These are explicit unresolved architecture findings for parent review, not proof of a runtime failure or a reason to replay installed/scientific inputs. + +### Coordination / installed boundary + +Tristan's latest split: Root owns394; parent/Singer own404; parent/Schrodinger own432/434. Exact shared callable-contract/group/compiler/color hunks were named to Root before edits: https://github.com/OpenHCSDev/openhcs/pull/394#issuecomment-5946842034. Root's other executor/materialization/prepared-signature/runtime-annotation work is untouched; no foreign WT edit or competing394/404 implementation. + +No installed package/environment change, native/UI/MCP/science launch or provider call. Frozen fa049 remains untouched. Parent owns later actual installed five-step acceptance. Untracked required-runtime-qt-publication ledger is preserved/excluded. + +Evidence: `docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst` and original/new raw logs. Pending unary singleton naming failure remains a separately retained boundary, not proof of a blanket multi-artifact assembly defect. From bd2ee78c7ceb6c15efcbc449a3964007304e0f5d Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Fri, 2 Oct 2026 03:24:53 -0400 Subject: [PATCH 6/7] Execute carrier source obligations through their proof owner --- openhcs/core/function_patterns.py | 46 +++-- openhcs/core/pipeline/compiler.py | 191 +++++++----------- .../test_gray_to_color_carrier_compile_432.py | 88 +++++++- 3 files changed, 183 insertions(+), 142 deletions(-) diff --git a/openhcs/core/function_patterns.py b/openhcs/core/function_patterns.py index 5c31858ad6..beb0b05af7 100644 --- a/openhcs/core/function_patterns.py +++ b/openhcs/core/function_patterns.py @@ -842,44 +842,50 @@ def primary_image_carrier_proof( class PrimaryImageCarrierProof(ABC): """One group-owned proof result, not another carrier metadata authority.""" - def require_proven_invocations( + def validate_obligation( self, + *, failure_message: Callable[[CompiledFunctionInvocation], str], - ) -> None: - """Accept proven transitions; a failed proof owns its rejection.""" + source_validation: Callable[[], bool], + failures: list[str], + ) -> bool: + """Execute this proof's obligation; report whether ancestry work is done. + + Completion is not success: rejected obligations are recorded in the + caller's existing failure collection and still stop this ancestry walk. + """ + try: + return self._fulfill_obligation(failure_message, source_validation) + except ValueError as error: + failures.append(str(error)) + return True - @property @abstractmethod - def requires_source_validation(self) -> bool: - """Return whether proof still needs the exact original source carrier.""" + def _fulfill_obligation( + self, + failure_message: Callable[[CompiledFunctionInvocation], str], + source_validation: Callable[[], bool], + ) -> bool: + """Fulfill this member's source obligation or reject its invocation.""" class InheritedPrimaryImageCarrierProof(PrimaryImageCarrierProof): - @property - def requires_source_validation(self) -> bool: - return True + def _fulfill_obligation(self, failure_message, source_validation) -> bool: + return source_validation() class CreatedPrimaryImageCarrierProof(PrimaryImageCarrierProof): - @property - def requires_source_validation(self) -> bool: - return False + def _fulfill_obligation(self, failure_message, source_validation) -> bool: + return True @dataclass(frozen=True, slots=True) class UnprovedPrimaryImageCarrierProof(PrimaryImageCarrierProof): invocation: CompiledFunctionInvocation - def require_proven_invocations( - self, - failure_message: Callable[[CompiledFunctionInvocation], str], - ) -> None: + def _fulfill_obligation(self, failure_message, source_validation) -> bool: raise ValueError(failure_message(self.invocation)) - @property - def requires_source_validation(self) -> bool: - return False - @dataclass(frozen=True, slots=True) class CompiledFunctionPattern: diff --git a/openhcs/core/pipeline/compiler.py b/openhcs/core/pipeline/compiler.py index ce7449d392..46619c1b74 100644 --- a/openhcs/core/pipeline/compiler.py +++ b/openhcs/core/pipeline/compiler.py @@ -1433,55 +1433,21 @@ def validate_primary_image_carrier_requirements( stop_before=invocation_index, ) ) - try: - prefix_proof.require_proven_invocations( - lambda unproved: ( - f"{owner}: carrier requirement {requirement.value!r} " - "is not preserved by earlier callable " - f"{unproved.contract.function_name!r} in the " - "same group." - ) - ) - except ValueError as error: - failures.append(str(error)) - continue - if not prefix_proof.requires_source_validation: - continue - source_binding_plan = PipelineCompiler._source_anchor_binding_plan( - plan, - group, - owner=owner, - grouped_pattern=pattern.is_grouped, - ) - if ( - source_binding_plan is None - or not source_binding_plan.primary_plane_bindings - ): - if plan.requires_terminal_source_projection: - failures.append( - f"{owner}: no exact primary source-binding " - "projection represents this callable's main flow." - ) - continue - PipelineCompiler._validate_inherited_primary_image_carrier_requirement( + prefix_proof.validate_obligation( + failure_message=lambda unproved: ( + f"{owner}: carrier requirement {requirement.value!r} " + "is not preserved by earlier callable " + f"{unproved.contract.function_name!r} in the " + "same group." + ), + source_validation=lambda: PipelineCompiler._validate_inherited_primary_image_carrier_requirement( session=session, plan=plan, - group_key=group.group_key, - initial_source_binding_plan=source_binding_plan, + group=group, owner=owner, requirement=requirement, failures=failures, - ) - continue - PipelineCompiler._validate_pipeline_start_carrier_requirement( - session=session, - source_binding_plan=( - CompiledSourceBindingPlan.empty() - if source_binding_plan is None - else source_binding_plan ), - owner=owner, - requirement=requirement, failures=failures, ) if failures: @@ -1491,14 +1457,17 @@ def validate_primary_image_carrier_requirements( ) @staticmethod - def _source_anchor_binding_plan( + def _validate_primary_image_carrier_source_anchor( plan: CompiledStepPlan, group: CompiledFunctionGroup, *, + session: CompilationSession, owner: str, grouped_pattern: bool, - ) -> CompiledSourceBindingPlan | None: - """Return the exact component-scoped bindings feeding one group.""" + requirement: PrimaryImageCarrierRequirement, + failures: list[str], + ) -> bool: + """Validate an exact source anchor, or leave ancestry work outstanding.""" declared_plan = plan.source_binding_plan if grouped_pattern and plan.execution_group_scope.component is None: @@ -1506,11 +1475,12 @@ def _source_anchor_binding_plan( f"{owner}: cannot project source bindings for a grouped callable " "pattern without a routed component scope." ) - if not declared_plan.has_primary_content: - return None execution_scope = plan.execution_group_scope + source_binding_plan: CompiledSourceBindingPlan | None = None try: - if execution_scope.component is None: + if not declared_plan.has_primary_content: + component_value = None + elif execution_scope.component is None: component_value = None elif not grouped_pattern and execution_scope.has_single_static_key: component_value = execution_scope.require_single_static_key() @@ -1522,15 +1492,16 @@ def _source_anchor_binding_plan( component_value = None else: component_value = execution_scope.resolve_runtime_key(group.group_key) - main_flow_refs = group.main_flow_input_refs_for_component( - execution_scope, - component_value, - ) - return declared_plan.for_main_flow_scope( - component=execution_scope.component, - group_key=component_value, - main_flow_refs=main_flow_refs, - ) + if declared_plan.has_primary_content: + main_flow_refs = group.main_flow_input_refs_for_component( + execution_scope, + component_value, + ) + source_binding_plan = declared_plan.for_main_flow_scope( + component=execution_scope.component, + group_key=component_value, + main_flow_refs=main_flow_refs, + ) except ValueError as error: routed_group = group.group_key if grouped_pattern else component_value raise ValueError( @@ -1538,20 +1509,40 @@ def _source_anchor_binding_plan( f"{routed_group!r} on " f"{execution_scope.component.value!r}: {error}" ) from error + if ( + source_binding_plan is not None + and source_binding_plan.primary_plane_bindings + ): + PipelineCompiler._validate_pipeline_start_carrier_requirement( + session=session, source_binding_plan=source_binding_plan, + owner=owner, requirement=requirement, failures=failures, + ) + return True + if plan.requires_terminal_source_projection: + raise ValueError( + f"{owner}: no exact primary source-binding projection represents " + f"this callable's main flow at step {plan.step_index}." + ) + return False @staticmethod def _validate_inherited_primary_image_carrier_requirement( *, session: CompilationSession, plan: CompiledStepPlan, - group_key: str, - initial_source_binding_plan: CompiledSourceBindingPlan | None, + group: CompiledFunctionGroup, owner: str, requirement: PrimaryImageCarrierRequirement, failures: list[str], - ) -> None: + ) -> bool: """Validate inheritance until a declaration creates the required carrier.""" + if PipelineCompiler._validate_primary_image_carrier_source_anchor( + plan, group, session=session, owner=owner, + grouped_pattern=plan.compiled_function_pattern.is_grouped, + requirement=requirement, failures=failures, + ): + return True try: ancestry = session.main_flow_plan_ancestry(plan.step_index) except ValueError as error: @@ -1559,21 +1550,18 @@ def _validate_inherited_primary_image_carrier_requirement( f"{owner}: carrier requirement {requirement.value!r} has an " f"invalid compiled step dependency: {error}" ) - return + return True - current_source_binding_plan = initial_source_binding_plan - for ancestry_index, producer in enumerate(ancestry): - if ancestry_index == 0: - continue + for producer in ancestry[1:]: if producer.compiled_function_pattern is None: failures.append( f"{owner}: carrier requirement {requirement.value!r} has no " f"compiled producer proof for step {producer.step_index}." ) - return + return True try: producer_group = producer.compiled_function_pattern.group_for_component( - group_key + group.group_key ) except ValueError as error: failures.append( @@ -1581,60 +1569,36 @@ def _validate_inherited_primary_image_carrier_requirement( f"select a carrier-producing group from step " f"{producer.step_index}: {error}" ) - return + return True if producer_group is None: failures.append( f"{owner}: carrier requirement {requirement.value!r} has no " - f"producer group {group_key!r} at step {producer.step_index}." + f"producer group {group.group_key!r} at step {producer.step_index}." ) - return + return True if not producer_group.invocations: failures.append( f"{owner}: carrier requirement {requirement.value!r} has an " f"empty producer group at step {producer.step_index}." ) - return + return True proof = producer_group.primary_image_carrier_proof( requirement ) - try: - proof.require_proven_invocations( - lambda unproved: ( - f"{owner}: carrier requirement {requirement.value!r} is not " - f"preserved by producer step {producer.step_index} callable " - f"{unproved.contract.function_name!r}." - ) - ) - except ValueError as error: - failures.append(str(error)) - return - if not proof.requires_source_validation: - return - current_source_binding_plan = PipelineCompiler._source_anchor_binding_plan( - producer, - producer_group, - owner=owner, - grouped_pattern=producer.compiled_function_pattern.is_grouped, - ) - if ( - current_source_binding_plan is not None - and current_source_binding_plan.primary_plane_bindings + if proof.validate_obligation( + failure_message=lambda unproved: ( + f"{owner}: carrier requirement {requirement.value!r} is not " + f"preserved by producer step {producer.step_index} callable " + f"{unproved.contract.function_name!r}." + ), + source_validation=lambda: PipelineCompiler._validate_primary_image_carrier_source_anchor( + producer, producer_group, session=session, owner=owner, + grouped_pattern=producer.compiled_function_pattern.is_grouped, + requirement=requirement, failures=failures, + ), + failures=failures, ): - PipelineCompiler._validate_pipeline_start_carrier_requirement( - session=session, - source_binding_plan=current_source_binding_plan, - owner=owner, - requirement=requirement, - failures=failures, - ) - return - if producer.requires_terminal_source_projection: - failures.append( - f"{owner}: carrier requirement {requirement.value!r} has no " - f"exact primary source-binding projection at producer step " - f"{producer.step_index}." - ) - return + return True current = ancestry[-1] try: @@ -1644,18 +1608,15 @@ def _validate_inherited_primary_image_carrier_requirement( f"{owner}: carrier requirement {requirement.value!r} cannot be " f"traced to an exact pipeline-start source: {error}" ) - return + return True PipelineCompiler._validate_pipeline_start_carrier_requirement( session=session, - source_binding_plan=( - CompiledSourceBindingPlan.empty() - if current_source_binding_plan is None - else current_source_binding_plan - ), + source_binding_plan=CompiledSourceBindingPlan.empty(), owner=owner, requirement=requirement, failures=failures, ) + return True @staticmethod def _validate_pipeline_start_carrier_requirement( diff --git a/tests/unit/test_gray_to_color_carrier_compile_432.py b/tests/unit/test_gray_to_color_carrier_compile_432.py index 9e9c2aae65..84f8c1a4e8 100644 --- a/tests/unit/test_gray_to_color_carrier_compile_432.py +++ b/tests/unit/test_gray_to_color_carrier_compile_432.py @@ -11,7 +11,11 @@ declares_primary_image_carrier_transition, preserves_primary_image_carrier, ) from openhcs.core.compiled_step_plan import CompiledStepPlan -from openhcs.core.function_patterns import CompiledFunctionGroup, CompiledFunctionPattern +from openhcs.core.function_patterns import ( + CompiledFunctionGroup, CompiledFunctionPattern, PrimaryImageCarrierProof, + InheritedPrimaryImageCarrierProof, CreatedPrimaryImageCarrierProof, + UnprovedPrimaryImageCarrierProof, +) from openhcs.core.pipeline.compiler import PipelineCompiler from openhcs.core.runtime_image_values import image_payload_data, image_payload_mask, image_payload_metadata from openhcs.core.aligned_image_payload import ImagePayloadBundleContext, ImagePayloadExecutionMode @@ -176,12 +180,82 @@ def unknown(image): proof = CompiledFunctionGroup("default", invocations).primary_image_carrier_proof( PrimaryImageCarrierRequirement.SOURCE_CHANNEL_AXIS, ) - assert not proof.requires_source_validation - if unknown_after_creator: - with pytest.raises(ValueError, match="unknown"): - proof.require_proven_invocations(lambda invocation: invocation.contract.function_name) - else: - proof.require_proven_invocations(lambda invocation: pytest.fail("Unexpected failed proof")) + failures = [] + assert proof.validate_obligation( + failure_message=lambda invocation: invocation.contract.function_name, + source_validation=lambda: pytest.fail("Creation/rejection must stop source validation"), + failures=failures, + ) + assert failures == (["unknown"] if unknown_after_creator else []) + + +@pytest.mark.parametrize("source_complete", [False, True]) +def test_inherited_proof_executes_actual_source_obligation_once(source_complete): + visits, failures = [], [] + + def validate_source(): + visits.append("source") + return source_complete + + complete = InheritedPrimaryImageCarrierProof().validate_obligation( + source_validation=validate_source, + failure_message=lambda invocation: pytest.fail("Inherited proof has no failed invocation"), + failures=failures, + ) + assert complete is source_complete + assert visits == ["source"] + assert failures == [] + + +@pytest.mark.parametrize("capability_first", [False, True]) +@pytest.mark.parametrize("proof_type,args,expected_visits,expected_failures", [ + (InheritedPrimaryImageCarrierProof, (), ["before", "source", "after"], []), + (CreatedPrimaryImageCarrierProof, (), ["before", "after"], []), + (UnprovedPrimaryImageCarrierProof, + tuple(_compiled_pattern(color_to_gray).iter_invocations()), ["before", "after"], ["rejected color_to_gray"]), +]) +def test_independent_same_node_validation_capability_composes_both_mro_orders( + capability_first, proof_type, args, expected_visits, expected_failures, +): + visits, failures = [], [] + + class ValidationVisitCapability(PrimaryImageCarrierProof): + def validate_obligation(self, **kwargs): + visits.append("before") + result = super().validate_obligation(**kwargs) + visits.append("after") + return result + + # Same nominal owner in both bases puts the independent capability before + # the shared operation in C3, regardless of its position beside the leaf. + bases = (ValidationVisitCapability, proof_type) if capability_first else (proof_type, ValidationVisitCapability) + declared_proof = type("IndependentlyObservedProof", bases, {})(*args) + + def validate_source(): + visits.append("source") + return True + + assert declared_proof.validate_obligation( + source_validation=validate_source, + failure_message=lambda invocation: "rejected " + invocation.contract.function_name, + failures=failures, + ) + assert visits == expected_visits + assert failures == expected_failures + + +def test_source_validation_rejection_is_collected_once_by_proof_owner(): + failures = [] + + def reject_source(): + raise ValueError("exact source missing its declared carrier") + + assert InheritedPrimaryImageCarrierProof().validate_obligation( + source_validation=reject_source, + failure_message=lambda invocation: pytest.fail("No failed invocation"), + failures=failures, + ) + assert failures == ["exact source missing its declared carrier"] def test_color_to_gray_does_not_preserve_consumed_carrier_for_later_consumer(tmp_path): From 4e7453aa769f703be7d4dcb80799ca490c5b79da Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Fri, 2 Oct 2026 03:31:27 -0400 Subject: [PATCH 7/7] Publish carrier obligation owner controls and original R0 pass --- .../carrier-repair-receipt.rst | 3 + .../obligation-owner-controls.log | 100 + .../obligation-owner-final-controls.log | 40 + .../obligation-owner-r0.log | 15697 ++++++++++++++++ .../obligation-owner-receipt.rst | 98 + ...bligation-owner-scoped-anchor-controls.log | 40 + .../working-pr-body.md | 15 +- 7 files changed, 15986 insertions(+), 7 deletions(-) create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-controls.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-final-controls.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-r0.log create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-receipt.rst create mode 100644 docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-scoped-anchor-controls.log diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst index 0ef8eec802..7221b311b3 100644 --- a/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst +++ b/docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst @@ -1,6 +1,9 @@ #432/#434 working created-carrier and scalar-output repair ======================================================== +Historical6370 guard findings below are retained. Their subsequent narrow +owner repair and current qualification are in obligation-owner-receipt.rst. + Ownership and predecessor ------------------------- diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-controls.log b/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-controls.log new file mode 100644 index 0000000000..00582b8ffc --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-controls.log @@ -0,0 +1,100 @@ +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 +.................................FFF.................................... [ 79%] +................... [100%] +=================================== FAILURES =================================== +_________ test_inherited_bindings_trace_exact_named_carrier_edges[rgb] _________ +tests/unit/test_primary_image_carrier_compile_gate.py:548: in test_inherited_bindings_trace_exact_named_carrier_edges + PipelineCompiler.validate_primary_image_carrier_requirements(session) +openhcs/core/pipeline/compiler.py:1436: in validate_primary_image_carrier_requirements + prefix_proof.validate_obligation( +openhcs/core/function_patterns.py:858: in validate_obligation + return self._fulfill_obligation(failure_message, source_validation) +openhcs/core/function_patterns.py:875: in _fulfill_obligation + return super()._fulfill_obligation(failure_message, source_validation) +openhcs/core/function_patterns.py:870: in _fulfill_obligation + return source_validation() +openhcs/core/pipeline/compiler.py:1443: in + source_validation=lambda: PipelineCompiler._validate_inherited_primary_image_carrier_requirement( +openhcs/core/pipeline/compiler.py:1537: in _validate_inherited_primary_image_carrier_requirement + if PipelineCompiler._validate_primary_image_carrier_source_anchor( +openhcs/core/pipeline/compiler.py:1512: in _validate_primary_image_carrier_source_anchor + if source_binding_plan.primary_plane_bindings: +E AttributeError: 'NoneType' object has no attribute 'primary_plane_bindings' +________ test_inherited_bindings_trace_exact_named_carrier_edges[gray] _________ +tests/unit/test_primary_image_carrier_compile_gate.py:556: in test_inherited_bindings_trace_exact_named_carrier_edges + PipelineCompiler.validate_primary_image_carrier_requirements(session) +openhcs/core/pipeline/compiler.py:1436: in validate_primary_image_carrier_requirements + prefix_proof.validate_obligation( +openhcs/core/function_patterns.py:858: in validate_obligation + return self._fulfill_obligation(failure_message, source_validation) +openhcs/core/function_patterns.py:875: in _fulfill_obligation + return super()._fulfill_obligation(failure_message, source_validation) +openhcs/core/function_patterns.py:870: in _fulfill_obligation + return source_validation() +openhcs/core/pipeline/compiler.py:1443: in + source_validation=lambda: PipelineCompiler._validate_inherited_primary_image_carrier_requirement( +openhcs/core/pipeline/compiler.py:1537: in _validate_inherited_primary_image_carrier_requirement + if PipelineCompiler._validate_primary_image_carrier_source_anchor( +openhcs/core/pipeline/compiler.py:1512: in _validate_primary_image_carrier_source_anchor + if source_binding_plan.primary_plane_bindings: +E AttributeError: 'NoneType' object has no attribute 'primary_plane_bindings' +___ test_inherited_bindings_trace_exact_named_carrier_edges[missing-anchor] ____ +tests/unit/test_primary_image_carrier_compile_gate.py:556: in test_inherited_bindings_trace_exact_named_carrier_edges + PipelineCompiler.validate_primary_image_carrier_requirements(session) +openhcs/core/pipeline/compiler.py:1436: in validate_primary_image_carrier_requirements + prefix_proof.validate_obligation( +openhcs/core/function_patterns.py:858: in validate_obligation + return self._fulfill_obligation(failure_message, source_validation) +openhcs/core/function_patterns.py:875: in _fulfill_obligation + return super()._fulfill_obligation(failure_message, source_validation) +openhcs/core/function_patterns.py:870: in _fulfill_obligation + return source_validation() +openhcs/core/pipeline/compiler.py:1443: in + source_validation=lambda: PipelineCompiler._validate_inherited_primary_image_carrier_requirement( +openhcs/core/pipeline/compiler.py:1537: in _validate_inherited_primary_image_carrier_requirement + if PipelineCompiler._validate_primary_image_carrier_source_anchor( +openhcs/core/pipeline/compiler.py:1512: in _validate_primary_image_carrier_source_anchor + if source_binding_plan.primary_plane_bindings: +E AttributeError: 'NoneType' object has no attribute 'primary_plane_bindings' +=============================== 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_primary_image_carrier_compile_gate.py::test_inherited_bindings_trace_exact_named_carrier_edges[rgb] +FAILED tests/unit/test_primary_image_carrier_compile_gate.py::test_inherited_bindings_trace_exact_named_carrier_edges[gray] +FAILED tests/unit/test_primary_image_carrier_compile_gate.py::test_inherited_bindings_trace_exact_named_carrier_edges[missing-anchor] +3 failed, 88 passed, 2 deselected, 2 warnings in 6.83s +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-obligation-owner-432-20261002/pytest tests/unit/test_gray_to_color_carrier_compile_432.py tests/unit/test_primary_image_carrier_compile_gate.py tests/unit/test_callable_contract.py tests/unit/test_cellprofiler_output_cardinality_declarations.py tests/unit/test_cellprofiler_artifact_activation_identity.py tests/unit/test_gray_to_color_binding_axis_432.py -k not declared_fitc_runtime_plane -q --tb=short" + User time (seconds): 7.02 + System time (seconds): 0.50 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.66 + 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): 383404 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 88529 + Voluntary context switches: 8 + Involuntary context switches: 808 + Swaps: 0 + File system inputs: 1288 + File system outputs: 208 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-final-controls.log b/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-final-controls.log new file mode 100644 index 0000000000..0b316b37f8 --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-final-controls.log @@ -0,0 +1,40 @@ +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 +........................................................................ [ 79%] +................... [100%] +=============================== 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 +91 passed, 2 deselected, 2 warnings in 8.79s + 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-obligation-owner-432-20261002/pytest tests/unit/test_gray_to_color_carrier_compile_432.py tests/unit/test_primary_image_carrier_compile_gate.py tests/unit/test_callable_contract.py tests/unit/test_cellprofiler_output_cardinality_declarations.py tests/unit/test_cellprofiler_artifact_activation_identity.py tests/unit/test_gray_to_color_binding_axis_432.py -k not declared_fitc_runtime_plane -q --tb=short" + User time (seconds): 6.48 + System time (seconds): 0.42 + Percent of CPU this job got: 68% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:10.14 + 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): 382124 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 86416 + Voluntary context 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0, + "CodecSubclass:openhcs/core/pipeline/compiler.py": 0, + "CodecSubclass:openhcs/processing/backends/cellprofiler/color.py": 0, + "StringSubscript": 0 + } +} + Command being timed: "/home/ts/.local/share/uv/python/cpython-3.14-linux-x86_64-gnu/bin/python3.14 -I -B -c import sys;sys.path[:0]=["/home/ts/wt/openhcs-namespace-guard-tool-20261001/src","/home/ts/wt/basicpy-live-candidate-20260930/.venv/lib/python3.12/site-packages"];from agent_comms.debt_ratchet import main;sys.argv=["agent-comms-ratchet","--root","openhcs","--base","df15ddfe0bcbd80cadaf2f5fc56b83517910f334","--head","HEAD"];sys.exit(main())" + User time (seconds): 12.79 + System time (seconds): 2.60 + Percent of CPU this job got: 89% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:17.18 + 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): 87576 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 546383 + Voluntary context switches: 13712 + Involuntary context switches: 12275 + Swaps: 0 + File system inputs: 120 + File system outputs: 3008 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-receipt.rst b/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-receipt.rst new file mode 100644 index 0000000000..205c0897a0 --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-receipt.rst @@ -0,0 +1,98 @@ +#434 narrow proof-obligation owner closure +========================================== + +Production bd2ee78c7ceb6c15efcbc449a3964007304e0f5d, predecessor6370ac5f609bd98544eacdddedc6b9c013d76f09. +Current authoritative main/baseline df15ddfe0bcbd80cadaf2f5fc56b83517910f334. +Only function_patterns.py and pipeline/compiler.py change production in this +continuation. No color kernel/declaration, contract schema, Root394/404 file +expansion or installed mutation. Parent independently qualifies installed6370 +with native3443084; no restart, signal, observer replay or process interaction. + +Removed overhead and actual owners +---------------------------------- + +115 compiler lines deleted/76 inserted versus6370 (net39 fewer); compiler is +12 lines belowdf15 baseline. Removed both foreign requires_source_validation +queries, the property declarations, old require_proven_invocations method, +duplicated try/collect blocks, duplicate source-anchor/terminal validation and +mutable current_source_binding_plan traversal plumbing. No aliases/facades +retain the old proof or source-anchor APIs. + +PrimaryImageCarrierProof.validate_obligation owns the shared execution and +failure aggregation. Compiler supplies the actual existing source-validation +continuation, contextual error formatter and its original failure collection. +Inherited's small hook executes the continuation; Created's hook completes +without executing it; Unproved's hook rejects its exact invocation. Abstract +hook has no implementation; no forward-only Inherited override. Completion +means this ancestry segment is finished, not that validation succeeded: the +original collected failures still make the compilation entrypoint raise. + +Original compiler source-anchor owner now projects the exact group binding +and performs its validation in one place. The legitimate None result from +for_main_flow_scope means no exact anchor, not default source acceptance. +Terminal projections still reject it. The one original session ancestry walk +and one group invocation proof walk remain; no recursive rescanning, second +registry/proof store or function/type/string exception. + +New-case and boundary behavior +------------------------------ + +Independent creator/preserver declarations still work through unchanged generic +consumers for prefix/cross-step paths. Independent ValidationVisitCapability +inherits the same proof owner and extends validate_obligation with cooperative +super(). Composition before AND after each concrete proof in C3 executes real +before/after hooks once, with exactly one source callback for inherited evidence +and none for created/rejected evidence; rejection is collected once. No +inheritance-only assertions or copied consumer implementation. The tests also +distinguish outstanding inherited source work from completed validation and +collect a source-continuation failure through the shared ancestor. + +All existing selected carrier/source controls retained: grouped routing, +terminal projection, unknown/unreadable sources, exact named binding edges, +source transforms, prefixes/cross-step, false PRESERVE, unknown-after-creation +and consumed second axis. Runtime role values, masks, physical source identity, +calibration and scalar metadata controls unchanged. Two original unary naming +REDs stay excluded and unresolved; issue432 remains open. + +Current pattern review and limits +-------------------------------- + +Reread full nra-refactoring and installed refactor-audit instructions plus +authoritative ZIP SKILL.md/catalogue/identity/boundaries/implementation and +surface receipt, and project00-RULES. IDEN-3/BOUND-8: owned obligation crosses +as behavior, not a foreign flag. IMPL-4: every proof owns its hook. IMPL-5/12: +one projection/validation operation and shared aggregation. IMPL-8 and AGENT-4: +shrink the existing god class by deleting duplicated work, not moving a wrapper. +IMPL-1/2/3/13: no consumer taxonomy, copied algorithm or weakened proof authority. +No persisted format or store change; original failure collection is reused. + +Each source shard uses existing read-only Python3.12.3/ABI, CPU0/CPUQuota100%, +pools1, MemoryMax512M/MemorySwapMax0, timeout60s. Resource admission14.6GiB RAM, +9.6GiB/home; resource-helper warning is advisory, not claimed green. No new +environment/download/provider/native/science or global NRA/R1 attempt. + +* obligation-owner-controls.log: retained3FAIL/88PASS/2deselected; + 7.66s/383404KiB/exit1. Coalesced source anchor initially lost legitimate None + from exact scoped projection; restored that optional boundary, not a fallback. +* obligation-owner-scoped-anchor-controls.log: 91PASS/2deselected; + 6.83s/382156KiB/exit0, before removing the abstract forwarding shape. +* obligation-owner-final-controls.log: exactbd2 production91PASS/2deselected; + 10.14s/382124KiB/exit0 after the owner-hook correction. + +Pinned original guard3b03785f45df2ef5dc62ba6aed99294192ecbb01 uses its Python3.14 +and original read-only metaclass backing, exactdf15 baseline and productionbd2; +obligation-owner-r0.log is terminalPASS/exit0,17.18s/87576KiB: zero positive +deltas across5219 measurements, compiler GodClassExcess delta-12 and compiler +ForeignAbsenceProbe delta-1. All four cumulative production files are included +in the unchanged original guard scope. Prior positive guard failures stay +archived; no suppression, waiver, copied guard or narrow baseline. This is the +original R0 result, not a completed global NRA/R1 audit. Raw warning whitespace +retained; source-only diff-check passes. + +Owned disposable synthetic fixture root: +/home/ts/.cache/agent-scratch/graytocolor-obligation-owner-432-20261002. +All shards/guard terminal, lsof +D no handles. Removed only that verified root, +10632 logical bytes of generated tiny synthetic test headers/pytest links. +Source and all original/current logs retained; no external uncertain/scientific +input deleted. Fixtures reproduce from retained tests. +Untracked required-runtime-qt-publication ledger remains intact/excluded. diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-scoped-anchor-controls.log b/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-scoped-anchor-controls.log new file mode 100644 index 0000000000..d3fa09e91d --- /dev/null +++ b/docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-scoped-anchor-controls.log @@ -0,0 +1,40 @@ +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 +........................................................................ [ 79%] +................... [100%] +=============================== 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 +91 passed, 2 deselected, 2 warnings in 6.01s + 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-obligation-owner-432-20261002/pytest tests/unit/test_gray_to_color_carrier_compile_432.py tests/unit/test_primary_image_carrier_compile_gate.py tests/unit/test_callable_contract.py tests/unit/test_cellprofiler_output_cardinality_declarations.py tests/unit/test_cellprofiler_artifact_activation_identity.py tests/unit/test_gray_to_color_binding_axis_432.py -k not declared_fitc_runtime_plane -q --tb=short" + User time (seconds): 6.33 + System time (seconds): 0.40 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.83 + 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): 382156 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 87587 + Voluntary context switches: 4 + Involuntary context switches: 724 + Swaps: 0 + File system inputs: 0 + File system outputs: 200 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 0 diff --git a/docs/validation/graytocolor-binding-axis-432-20261002/working-pr-body.md b/docs/validation/graytocolor-binding-axis-432-20261002/working-pr-body.md index 89a93a5750..9753e2e50e 100644 --- a/docs/validation/graytocolor-binding-axis-432-20261002/working-pr-body.md +++ b/docs/validation/graytocolor-binding-axis-432-20261002/working-pr-body.md @@ -1,6 +1,6 @@ ## Working narrow repair for #432 -Production source checkpoint: `6370ac5f609bd98544eacdddedc6b9c013d76f09` (supersedes `0513c8e4c` for proof-result ownership only), based on main `df15ddfe0bcbd80cadaf2f5fc56b83517910f334`. +Production checkpoint **bd2ee78c7ceb6c15efcbc449a3964007304e0f5d**, exact main/base df15ddfe0bcbd80cadaf2f5fc56b83517910f334. [Incremental production/test diff from reviewed6370](https://github.com/OpenHCSDev/openhcs/compare/6370ac5f609bd98544eacdddedc6b9c013d76f09...bd2ee78c7ceb6c15efcbc449a3964007304e0f5d). Dalton's retained installed ASSISTED4 four-step ImageMath scalar aliases -> named raw/cap GrayToColor STACK completed (`5e3474f4-f736-4e61-a27f-1d7eb6ec7abd`). The fifth ColorToGray step failed the actual compiler at `mcp.stdout18793`. The source repair now distinguishes **created** channel carriers from inherited preservation; it does not manufacture RGB source metadata or relax the strict consumer. @@ -8,21 +8,22 @@ Dalton's retained installed ASSISTED4 four-step ImageMath scalar aliases -> name - Existing `PrimaryImageCarrierTransition` members declare preservation/creation. GrayToColor adds only its truthful creation annotation through the original metadata boundary. - Existing compiled-group owner resolves evidence backwards once. Compiler ancestry stops at the creator of the exact required carrier; unknown later operations, missing-source and false-preservation controls still reject. Replaced preservation-only walk/tuple-sentinel path is deleted. +- PrimaryImageCarrierProof.validate_obligation now owns execution and shared failure aggregation; compiler supplies its actual source-validation continuation/context. Inherited's minimal hook executes that continuation, Created completes without source lookup, Unproved rejects its exact invocation. Abstract hook has no implementation; no forward-only leaf override. Original source-anchor projection/validation coalesced, preserving legitimate absent exact scoped anchors and terminal rejection. Compiler is39lines smaller than6370 and12 belowdf15; no negated foreign proof-property query or copied traversal. - `ImageChannelType` declarations select original metadata projection behavior. RGB/CHANNELS use original channel provenance/mask projection; HSV retains its derived-source context and clears the consumed axis. Removed RGB-only consumer branch and stale non-RGB output path. -- No consumer function/type/name exceptions, mirrored registry/store, fake channel, arbitrary squeeze, timeout change or new importer. Current NRA catalogue review covers BOUND-8, IDEN-1, IMPL-1/2/3/5/12/13 in the receipt. +- No consumer function/type/name exceptions, mirrored registry/store, fake channel, arbitrary squeeze, timeout change or new importer. Current NRA catalogue review covers BOUND-8, IDEN-1/3, IMPL-1/2/3/4/5/8/12/13 and AGENT-4 in the receipts. ### Behavioral evidence / bounds -Current 82 focused declaration/compiler/runtime/binding controls PASS, 7.15s, 372756KiB. Prior 77+5 receipts remain retained; two separate original unary naming REDs are explicitly deselected, retained and **not fixed or passed** here. Each source shard uses existing read-only Python3.12.3/ABI, CPU0/pools1, MemoryMax512M, timeout60s. +**91 focused source controls PASS**, pytest8.79s/wall10.14s,382124KiB. All previous controls retained: grouped routing, terminal exact bindings, unknown/unreadable sources, transforms, prefixes/cross-step, false PRESERVE, unknown after creation and consumed second axis. Two separate original unary REDs explicitly deselected, retained and **not fixed or passed** here; #432 stays open. Each source shard uses existing read-only Python3.12.3/ABI, CPU0/pools1, MemoryMax512M, timeout60s. -Independent creator/preserver declarations construct real lanes and pass unchanged consumers in same-group and cross-step paths; a source-read trap confirms creation stops backtracking. False PRESERVE, later unknown and second scalar split fail closed. RGB/HSV/CHANNELS preserve pixels, masks, physical identity/calibration and original input while clearing the consumed channel axis. No ornamental MI or untested MRO claim. +Independent creator/preserver declarations construct real lanes and pass unchanged consumers in same-group/cross-step paths; a source-read trap confirms creation stops backtracking. Independent nominal ValidationVisitCapability uses cooperative super() before AND after concrete proof leaves in C3; actual before/source/after hooks and rejected-result collection execute exactly once, without consumer edits. RGB/HSV/CHANNELS preserve pixels, masks, physical identity/calibration and original input while clearing the consumed axis. No inheritance-only assertion or ornamental production mixin. -Original RED/setup/control/native receipts remain unchanged. Original pinned R0 on0513 rejected +21 PipelineCompiler class-growth and +2 foreign-absence probes (18.09s, 87504KiB, exit1), retained without waiver.6370 moves failed-chain rejection onto the proof owner via `require_proven_invocations`, deleting the optional failure field and consumer checks; runtime repair is unchanged. **Final R0 remains RED: +27 PipelineCompiler class-growth and +2 negated source-obligation queries**, 19.34s, 87516KiB, exit1; other deltas nonpositive. Initial optional-field attribution was incorrect. Both exact guard failures are published; no zero-positive/full/global NRA/R1 claim or suppression. These are explicit unresolved architecture findings for parent review, not proof of a runtime failure or a reason to replay installed/scientific inputs. +**Original pinned R0 PASS**, exact df15 -> bd2, tool3b03785/Python3.14/read-only original backing;17.18s/87576KiB/exit0. Zero positive deltas across5219 measurements; compiler class delta-12, foreign-probe delta-1. Prior0513 and6370 RED guard logs and the intermediate3FAIL/88PASS exact-source-anchor boundary failure are retained alongside original native failures. No suppression, waiver, copied detector, changed baseline or global NRA/R1 claim. Numeric kernels/runtime guards are unchanged in bd2 versus6370. ### Coordination / installed boundary Tristan's latest split: Root owns394; parent/Singer own404; parent/Schrodinger own432/434. Exact shared callable-contract/group/compiler/color hunks were named to Root before edits: https://github.com/OpenHCSDev/openhcs/pull/394#issuecomment-5946842034. Root's other executor/materialization/prepared-signature/runtime-annotation work is untouched; no foreign WT edit or competing394/404 implementation. -No installed package/environment change, native/UI/MCP/science launch or provider call. Frozen fa049 remains untouched. Parent owns later actual installed five-step acceptance. Untracked required-runtime-qt-publication ledger is preserved/excluded. +No installed package/environment change, native/UI/MCP/science launch or provider call. Frozen fa049/H001 and parent's active6370 native3443084 remain untouched. Parent owns actual installed5-step/publicMCP acceptance; parent reports6370 compilec9ea4149 COMPLETE, execution/sampling is a distinct gate. Untracked required-runtime-qt-publication ledger preserved/excluded. Removed only owned synthetic fixture root graytocolor-obligation-owner-432-20261002 after terminal/no-handle proof,10632logical bytes. No hosted CI wait. -Evidence: `docs/validation/graytocolor-binding-axis-432-20261002/carrier-repair-receipt.rst` and original/new raw logs. Pending unary singleton naming failure remains a separately retained boundary, not proof of a blanket multi-artifact assembly defect. +Evidence: docs/validation/graytocolor-binding-axis-432-20261002/obligation-owner-receipt.rst plus full raw logs and predecessor receipts. Incremental bd2 production touches only core/function_patterns.py and core/pipeline/compiler.py. Ready for parent source review and subsequent separate installed qualification. Unary singleton naming remains a separately retained boundary, not a blanket multi-artifact assembly defect.