diff --git a/docs/validation/graytocolor-singleton-binding-432-20261002/composed-consumer-controls.log b/docs/validation/graytocolor-singleton-binding-432-20261002/composed-consumer-controls.log new file mode 100644 index 0000000000..d3ccb44bc3 --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/composed-consumer-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 +2 passed, 392 deselected, 2 warnings in 7.08s + 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-unary-repair-437-20261002/pytest tests/unit/test_cellprofiler_module_execution.py -k colocalization or area_occupied -q --tb=short" + User time (seconds): 7.50 + System time (seconds): 0.30 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.86 + 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): 374568 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 72616 + Voluntary context switches: 2 + Involuntary context switches: 41 + 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-singleton-binding-432-20261002/declaration-plane-controls.log b/docs/validation/graytocolor-singleton-binding-432-20261002/declaration-plane-controls.log new file mode 100644 index 0000000000..a433301bbf --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/declaration-plane-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 +50 passed, 2 warnings in 3.31s + 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-unary-repair-437-20261002/pytest tests/unit/test_declared_singleton_composition_437.py tests/unit/test_image_plane_contracts.py tests/unit/test_runtime_image_singleton_alignment.py -q --tb=short" + User time (seconds): 3.74 + System time (seconds): 0.19 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.97 + 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): 197292 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 38050 + Voluntary context switches: 3 + Involuntary context switches: 17 + Swaps: 0 + File system inputs: 16 + 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-singleton-binding-432-20261002/existing-module-controls.log b/docs/validation/graytocolor-singleton-binding-432-20261002/existing-module-controls.log new file mode 100644 index 0000000000..9667d629f8 --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/existing-module-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 +9 passed, 385 deselected, 2 warnings in 6.84s + 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-unary-repair-437-20261002/pytest tests/unit/test_cellprofiler_module_execution.py -k compose_image or gray_to_color or image_math or invert_for_printing -q --tb=short" + User time (seconds): 7.45 + System time (seconds): 0.28 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.79 + 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): 374316 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 72182 + Voluntary context switches: 21 + Involuntary context switches: 45 + Swaps: 0 + File system inputs: 1080 + 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-singleton-binding-432-20261002/main-integration-controls.log b/docs/validation/graytocolor-singleton-binding-432-20261002/main-integration-controls.log new file mode 100644 index 0000000000..d0297b69f7 --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/main-integration-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 +............... 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"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","3df650bf7faf84f67dbad9acf9ee62a095ab1ecf","--head","51637fe437b212fcf66d4c78743f4da09c1edc1b"];sys.exit(main())" + User time (seconds): 12.45 + System time (seconds): 3.05 + Percent of CPU this job got: 90% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:17.20 + 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): 87508 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 1 + Minor (reclaiming a frame) page faults: 610169 + Voluntary context switches: 13420 + Involuntary context switches: 10596 + Swaps: 0 + File system inputs: 0 + 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-singleton-binding-432-20261002/new-declaration-controls.log b/docs/validation/graytocolor-singleton-binding-432-20261002/new-declaration-controls.log new file mode 100644 index 0000000000..060f5d29d9 --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/new-declaration-controls.log @@ -0,0 +1,113 @@ +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 +FFFF.... [100%] +=================================== FAILURES =================================== +______ test_new_declaration_reuses_generic_binding_and_executor[False-1] _______ +tests/unit/test_declared_singleton_composition_437.py:139: in test_new_declaration_reuses_generic_binding_and_executor + np.testing.assert_array_equal(image_payload_data(result), original_pixels) +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/numpy/_utils/__init__.py:85: in wrapper + return fun(*args, **kwargs) +../../.pyenv/versions/3.12.3/lib/python3.12/contextlib.py:81: in inner + return func(*args, **kwds) +E AssertionError: +E Arrays are not equal +E +E Mismatched elements: 20 / 20 (100%) +E ACTUAL: array(RuntimeSliceAlignedValues(slices=(MaskedImagePayload(data=array([[0. , 0.01, 0.02, 0.03, 0.04], +E [0.05, 0.06, 0.07, 0.08, 0.09], +E [0.1 , 0.11, 0.12, 0.13, 0.14],... +E DESIRED: array([[[0. , 0.01, 0.02, 0.03, 0.04], +E [0.05, 0.06, 0.07, 0.08, 0.09], +E [0.1 , 0.11, 0.12, 0.13, 0.14], +E [0.15, 0.16, 0.17, 0.18, 0.19]]], dtype=float32) +______ test_new_declaration_reuses_generic_binding_and_executor[False-3] _______ +tests/unit/test_declared_singleton_composition_437.py:139: in test_new_declaration_reuses_generic_binding_and_executor + np.testing.assert_array_equal(image_payload_data(result), original_pixels) +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/numpy/_utils/__init__.py:85: in wrapper + return fun(*args, **kwargs) +../../.pyenv/versions/3.12.3/lib/python3.12/contextlib.py:81: in inner + return func(*args, **kwds) +E AssertionError: +E Arrays are not equal +E +E Mismatched elements: 60 / 60 (100%) +E ACTUAL: array(RuntimeSliceAlignedValues(slices=(MaskedImagePayload(data=array([[0. , 0.01, 0.02, 0.03, 0.04], +E [0.05, 0.06, 0.07, 0.08, 0.09], +E [0.1 , 0.11, 0.12, 0.13, 0.14],... +E DESIRED: array([[[0. , 0.01, 0.02, 0.03, 0.04], +E [0.05, 0.06, 0.07, 0.08, 0.09], +E [0.1 , 0.11, 0.12, 0.13, 0.14],... +_______ test_new_declaration_reuses_generic_binding_and_executor[True-1] _______ +tests/unit/test_declared_singleton_composition_437.py:119: in test_new_declaration_reuses_generic_binding_and_executor + request = CellProfilerModuleExecutor(independently_declared_source_echo, contract)._image_request( +openhcs/interop/cellprofiler/runtime/module_execution.py:1334: in _image_request + payloads.append(image_strategy.runtime_input_value(request)) +openhcs/interop/cellprofiler/runtime/artifact_binding.py:250: in runtime_input_value + self.raw_runtime_input_value(request) +openhcs/interop/cellprofiler/runtime/artifact_binding.py:241: in raw_runtime_input_value + return metadata.payload_with( +openhcs/core/runtime_image_values.py:733: in payload_with + return ImageMetadataPayload(data=data, metadata=self) +:5: in __init__ + ??? +openhcs/core/runtime_image_values.py:1144: in __post_init__ + raise TypeError( +E TypeError: ImageMetadataPayload.data requires array-like image data, got AlignedImageStack. +_______ test_new_declaration_reuses_generic_binding_and_executor[True-3] _______ +tests/unit/test_declared_singleton_composition_437.py:119: in test_new_declaration_reuses_generic_binding_and_executor + request = CellProfilerModuleExecutor(independently_declared_source_echo, contract)._image_request( +openhcs/interop/cellprofiler/runtime/module_execution.py:1334: in _image_request + payloads.append(image_strategy.runtime_input_value(request)) +openhcs/interop/cellprofiler/runtime/artifact_binding.py:250: in runtime_input_value + self.raw_runtime_input_value(request) +openhcs/interop/cellprofiler/runtime/artifact_binding.py:241: in raw_runtime_input_value + return metadata.payload_with( +openhcs/core/runtime_image_values.py:733: in payload_with + return ImageMetadataPayload(data=data, metadata=self) +:5: in __init__ + ??? +openhcs/core/runtime_image_values.py:1144: in __post_init__ + raise TypeError( +E TypeError: ImageMetadataPayload.data requires array-like image data, got AlignedImageStack. +=============================== 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_declared_singleton_composition_437.py::test_new_declaration_reuses_generic_binding_and_executor[False-1] +FAILED tests/unit/test_declared_singleton_composition_437.py::test_new_declaration_reuses_generic_binding_and_executor[False-3] +FAILED tests/unit/test_declared_singleton_composition_437.py::test_new_declaration_reuses_generic_binding_and_executor[True-1] +FAILED tests/unit/test_declared_singleton_composition_437.py::test_new_declaration_reuses_generic_binding_and_executor[True-3] +4 failed, 4 passed, 2 warnings in 2.90s +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-unary-repair-437-20261002/pytest tests/unit/test_declared_singleton_composition_437.py -q --tb=short" + User time (seconds): 3.22 + System time (seconds): 0.19 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.44 + 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): 207776 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 39727 + Voluntary context switches: 5 + Involuntary context switches: 22 + Swaps: 0 + File system inputs: 80 + File system outputs: 16 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/docs/validation/graytocolor-singleton-binding-432-20261002/new-declaration-first.log b/docs/validation/graytocolor-singleton-binding-432-20261002/new-declaration-first.log new file mode 100644 index 0000000000..5e643ab702 --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/new-declaration-first.log @@ -0,0 +1,110 @@ +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 +FFFFFF.F [100%] +=================================== FAILURES =================================== +______ test_new_declaration_reuses_generic_binding_and_executor[False-1] _______ +tests/unit/test_declared_singleton_composition_437.py:114: in test_new_declaration_reuses_generic_binding_and_executor + request = CellProfilerModuleExecutor(independently_declared_source_echo, contract)._image_request( +:5: in __init__ + ??? +openhcs/interop/cellprofiler/runtime/module_execution.py:174: in __post_init__ + raise TypeError( +E TypeError: CellProfilerModuleExecutor requires a RuntimeAdapterSpec that manages artifact inputs and outputs. +______ test_new_declaration_reuses_generic_binding_and_executor[False-3] _______ +tests/unit/test_declared_singleton_composition_437.py:114: in test_new_declaration_reuses_generic_binding_and_executor + request = CellProfilerModuleExecutor(independently_declared_source_echo, contract)._image_request( +:5: in __init__ + ??? +openhcs/interop/cellprofiler/runtime/module_execution.py:174: in __post_init__ + raise TypeError( +E TypeError: CellProfilerModuleExecutor requires a RuntimeAdapterSpec that manages artifact inputs and outputs. +_______ test_new_declaration_reuses_generic_binding_and_executor[True-1] _______ +tests/unit/test_declared_singleton_composition_437.py:114: in test_new_declaration_reuses_generic_binding_and_executor + request = CellProfilerModuleExecutor(independently_declared_source_echo, contract)._image_request( +:5: in __init__ + ??? +openhcs/interop/cellprofiler/runtime/module_execution.py:174: in __post_init__ + raise TypeError( +E TypeError: CellProfilerModuleExecutor requires a RuntimeAdapterSpec that manages artifact inputs and outputs. +_______ test_new_declaration_reuses_generic_binding_and_executor[True-3] _______ +tests/unit/test_declared_singleton_composition_437.py:114: in test_new_declaration_reuses_generic_binding_and_executor + request = CellProfilerModuleExecutor(independently_declared_source_echo, contract)._image_request( +:5: in __init__ + ??? +openhcs/interop/cellprofiler/runtime/module_execution.py:174: in __post_init__ + raise TypeError( +E TypeError: CellProfilerModuleExecutor requires a RuntimeAdapterSpec that manages artifact inputs and outputs. +___________ test_declared_composed_scalar_introduces_one_source_axis ___________ +tests/unit/test_declared_singleton_composition_437.py:158: in test_declared_composed_scalar_introduces_one_source_axis + result = CellProfilerFunctionContractExecutor().execute( +openhcs/interop/cellprofiler/runtime/function_contract_execution.py:101: in execute + raise ValueError( +E ValueError: CellProfilerFunctionContractExecutor.execute received a raw callable that does not match compiled contract 'test_declared_singleton_composition_437'/'independently_declared_source_echo'. +___________ test_natural_declaration_retains_exact_singleton[False] ____________ +tests/unit/test_declared_singleton_composition_437.py:182: in test_natural_declaration_retains_exact_singleton + np.testing.assert_array_equal(image_payload_data(result), image_payload_data(source)) +../../code/projects/openhcs/.venv/lib/python3.12/site-packages/numpy/_utils/__init__.py:85: in wrapper + return fun(*args, **kwargs) +../../.pyenv/versions/3.12.3/lib/python3.12/contextlib.py:81: in inner + return func(*args, **kwds) +E AssertionError: +E Arrays are not equal +E +E Mismatched elements: 2 / 60 (3.33%) +E Max absolute difference among violations: 0.4 +E Max relative difference among violations: 1. +E ACTUAL: array([[[0. , 0.01, 0.02, 0.03, 0.04], +E [0.05, 0.06, 0.07, 0.08, 0.09], +E [0.1 , 0.11, 0.12, 0.13, 0.14],... +E DESIRED: array([[[0. , 0.01, 0.02, 0.03, 0.04], +E [0.05, 0.06, 0.07, 0.08, 0.09], +E [0.1 , 0.11, 0.12, 0.13, 0.14],... +________ test_composed_admission_does_not_supply_missing_spatial_domain ________ +tests/unit/test_declared_singleton_composition_437.py:191: in test_composed_admission_does_not_supply_missing_spatial_domain + with pytest.raises(ValueError, match="source.*(domain|shape)|spatial",): +E Failed: DID NOT RAISE +=============================== 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_declared_singleton_composition_437.py::test_new_declaration_reuses_generic_binding_and_executor[False-1] +FAILED tests/unit/test_declared_singleton_composition_437.py::test_new_declaration_reuses_generic_binding_and_executor[False-3] +FAILED tests/unit/test_declared_singleton_composition_437.py::test_new_declaration_reuses_generic_binding_and_executor[True-1] +FAILED tests/unit/test_declared_singleton_composition_437.py::test_new_declaration_reuses_generic_binding_and_executor[True-3] +FAILED tests/unit/test_declared_singleton_composition_437.py::test_declared_composed_scalar_introduces_one_source_axis +FAILED tests/unit/test_declared_singleton_composition_437.py::test_natural_declaration_retains_exact_singleton[False] +FAILED tests/unit/test_declared_singleton_composition_437.py::test_composed_admission_does_not_supply_missing_spatial_domain +7 failed, 1 passed, 2 warnings in 2.69s +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-unary-repair-437-20261002/pytest tests/unit/test_declared_singleton_composition_437.py -q --tb=short" + User time (seconds): 2.98 + System time (seconds): 0.18 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.19 + 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): 190008 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 35203 + Voluntary context switches: 6 + Involuntary context switches: 18 + Swaps: 0 + File system inputs: 104 + File system outputs: 16 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/docs/validation/graytocolor-singleton-binding-432-20261002/original-unary-red.log b/docs/validation/graytocolor-singleton-binding-432-20261002/original-unary-red.log new file mode 100644 index 0000000000..e812aac7ed --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/original-unary-red.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:93: 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:1608: 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:93: 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:1608: 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, 5 deselected, 2 warnings in 5.46s +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-singleton-binding-432-20261002/pytest tests/unit/test_gray_to_color_binding_axis_432.py -k declared_fitc -q --tb=short" + User time (seconds): 5.86 + System time (seconds): 0.36 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.27 + 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): 356520 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 69434 + Voluntary context switches: 2 + Involuntary context switches: 38 + 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: 1 diff --git a/docs/validation/graytocolor-singleton-binding-432-20261002/pr-body.md b/docs/validation/graytocolor-singleton-binding-432-20261002/pr-body.md new file mode 100644 index 0000000000..91671e0799 --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/pr-body.md @@ -0,0 +1,15 @@ +## Working unary source-domain repair + +Refs #432; follows merged #434. Production **ffc3a4f345cc6460f8906b36a7af4582c67ffdad** unchanged; source-qualified ordinary merge **51637fe437b212fcf66d4c78743f4da09c1edc1b** incorporates current main **3df650bf7faf84f67dbad9acf9ee62a095ab1ecf** (442/443). Root explicitly released only these three hunks in [394 coordination](https://github.com/OpenHCSDev/openhcs/pull/394#issuecomment-5948196848). + +Original `ImagePayloadConsumption` member declarations own singleton admission. The existing executor consumes that behavior; original alignment/projection/bundle/mask/context algorithms handle one source as for multiple. NATURAL singleton behavior and strict GrayToColor SOURCE_BINDING guard are unchanged. No axis relabel, source-channel fabrication, metadata/publication edits, registry, copied mechanism or #435/#404/#440/#441 takeover. Seven production lines replaced/removed,37 added. + +**68 focused source cases PASS**, serial1CPU/512MiB/60s shards. Both original implicit/explicit FITC cases execute the registered STACK runner. Independent declaration tests exercise actual generic binding/invocation/executor for one/three runtime planes and composition/executor for aligned inputs, preserving physical C2 identity, exact float values, masks, contexts, calibration and immutability. NATURAL ImageMath NONE retains its mask behavior; direct wrong-axis kernel input still rejects. Original source/fixture failures remain retained. + +**Original pinned R0 PASS**, current-main8551→productionffc3a4f, three production paths, all5215 deltas zero,16.82s/87580KiB. **Original R1 incomplete**, not passed: unchanged policy4c6282f5 and pinned NRA673, all3roots/eight exact Git dependencies, native55s preparation deadline under60s outer bound,57.06s/134392KiB. No context pruning, detector copy, retry or budget increase. Two local-Git-address preflight failures are also preserved. + +**Current-main integration PASS:** affected original unary7 + independent declaration8 controls,15PASS/5.78s/355060KiB; original pinned R0 exact main3df650bf7→merge51637fe43, all5215 deltas zero/17.20s/87508KiB. No additional production edits; all three released blobs equal ffc3a4f. No repeated full68-case qualification or R1 replay. Existing closed consumption member owns behavior (BOUND-8/IMPL-2); no generic switch/copy/roster (IMPL-1/3/5/12/13). New declaration needs no consumer edits. **Issue432 remains open** until parent installed full-composition acceptance. + +Fresh installed critical-path qualification belongs to parent/Root. Already-aligned generic binder ingress failure is retained and outside the released seam. Unary STACK produces a one-channel YXC image, not a scalar alias; this does not qualify the original four-step grayscale-renaming recipe or raw integer-unit preservation. No install/environment/build/native/scientific action here. Runtime publication ledger preserved; exact owned disposable scratch removed. + +[Full current receipt and original evidence](docs/validation/graytocolor-singleton-binding-432-20261002/repair-receipt.rst). No persisted format changes. No hosted-CI wait/global NRA claim. diff --git a/docs/validation/graytocolor-singleton-binding-432-20261002/receipt.rst b/docs/validation/graytocolor-singleton-binding-432-20261002/receipt.rst new file mode 100644 index 0000000000..8ba80ee347 --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/receipt.rst @@ -0,0 +1,95 @@ +Unary GrayToColor #432: original owner follow-up +============================================== + +Latest: repair-receipt.rst supersedes the historical waiting state below. +Root explicitly released the three hunks; working productionffc3a4f is pushed +to existing437 with source controls/R0 and retained incomplete bounded R1. + +Owner: Schrodinger. Source base: merged434 main902913616e19f5b242928d4e835b8c2e10ab2fce. +Branch: fix/graytocolor-singleton-binding-432-20261002, normally fast-forwarded +from preserved4e745. Same existing owned worktree; no environment/submodule +updates. Untracked required-runtime-qt-publication-20261002 ledger preserved +and excluded. No changes to completed434,394/435 or404. + +Original reproducer +------------------- + +Original installedfa049 failures37f69b64-2331-4bcb-a4f1-99f78da3d316 and +c81af5db-f805-434a-a067-930d5201975c remain terminal and retained in the prior +graytocolor-binding-axis-432-20261002 evidence. No scientific call was replayed. +The existing two-case public-step/compiler -> original image request -> bound +invocation -> registered Stack kernel regression, implicit/explicit FITC, +still reproduces the exact SOURCE_BINDING guard failure on current source. +Physical C2 source/path/calibration identity is correct before that failure. + +original-unary-red.log: 2FAIL/5deselected, pytest5.46s, wall6.27s, +356520KiB RSS, exit1. Actual one CPU, MemoryMax512MiB/MemorySwapMax0, +CPUQuota100%, tasksetCPU0, timeout60s, numerical thread pools1, existing +read-only Python3.12.3 and original source/ABI driver. New owned disposable +scratch: /home/ts/.cache/agent-scratch/graytocolor-singleton-binding-432-20261002. +After the terminal test, lsof found no open handles; the scratch root contained +no files (du -sb reported0 bytes). Removed that exact empty directory with +rmdir; durable original-red log retained,0 payload bytes released. No source, +ledger or scientific output was removed. +Resource helper returned advisory warning (RAM15.7GiB/home8.8GiB/root7.8GiB, +swap15.1GiB), not a hard admission failure; source limits retained. + +Exact remaining shared seam +---------------------------- + +compose_aligned_image_payload returns a singleton unchanged, including a +retained RUNTIME_SLICE. GrayToColor already declares COMPOSED, but that owned +consumption fact does not reach composition. Its unchanged kernel correctly +rejects the runtime axis: acquisition alignment is not a named input axis. + +Proposed narrow owner repair: ImagePayloadConsumption's member declarations +own singleton retention versus composed-source admission. The original +composition owner reuses its existing runtime-slice projection, alignment, +source-domain validation, masks and ImagePayloadBundleContext algorithms for +one source as for multiple; only the two singleton-return shortcuts differ. +The existing executor delegates its composition call to the declaration. +No GrayToColor guard or metadata/provenance/materialization edits are needed. +NATURAL singleton behavior remains unchanged, including ImageMath NONE. + +Root's explicit narrow release/integration requested before shared edits: +https://github.com/OpenHCSDev/openhcs/pull/394#issuecomment-5947783008. +Requested ONLY ImagePayloadConsumption in core/callable_contract.py, two +singleton admission checks in core/aligned_image_payload.py, and the existing +composition call in interop/cellprofiler/runtime/module_execution.py. +At this receipt production is untouched and no release has been received. +This draft is an exact source blocker/proposal, not a shipped repair. +Visible follow-up: https://github.com/OpenHCSDev/openhcs/pull/437. +Original-owner follow-through with exact published reproducer: +https://github.com/OpenHCSDev/openhcs/pull/394#issuecomment-5947837365. + +Required controls and honest limits +----------------------------------- + +New independent callable declaration must consume a named singleton without +editing consumers; test retained runtime axes of one AND multiple planes, +scalar source, masks, physical C2 identity, exact float values, and original +strict missing-domain rejection. Existing natural/unaligned/aligned singleton +controls must remain unchanged. Existing integer ingress normalization and +STACK-YXC-not-gray negative controls remain mandatory. + +Even repaired unary STACK creates a YXC color image with one channel, not a +scalar gray identity alias. It does not establish the original four-step +grayscale-renaming recipe, raw-integer units or biological acceptance. Integer +ingress remains float32/65535 before rescale_intensity=False. Parent owns +separate installed acceptance; no native/MCP/viewer/package calls here. +No final91/R0 replay, wide NRA/R1, environment, downloads or science array reads. + +Ownership review +---------------- + +Personally read current nra-refactoring/refactor-audit skills, authoritative +refactor-audit.skill ZIP SKILL.md/catalogue/identity/boundaries/implementation/ +surface-receipt and project00-RULES. BOUND-8: consume the original declaration +fact rather than flattening it at singleton admission. IDEN-1: keep runtime +alignment and named-source axes distinct. IMPL-1/3/5: no consumer function, +enum or concrete-type exception. IMPL-12/13: do not copy the alignment/bundle +algorithm into a color-local hook or weaken the existing source-domain guard. +No second store/catalog, axis relabel/squeeze, facade or ornamental MI. The +closed consumption family owns behavior through its member declarations; +existing composition ancestor algorithms remain the only implementation. +This review does not claim a new-case/MRO pass before an authorized repair. diff --git a/docs/validation/graytocolor-singleton-binding-432-20261002/repair-receipt.rst b/docs/validation/graytocolor-singleton-binding-432-20261002/repair-receipt.rst new file mode 100644 index 0000000000..623e146684 --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/repair-receipt.rst @@ -0,0 +1,191 @@ +Unary432 working composition repair +================================== + +Source owner Schrodinger; existing ready PR https://github.com/OpenHCSDev/openhcs/pull/437. +Production ffc3a4f345cc6460f8906b36a7af4582c67ffdad. Normal main integration +8551a48644b5a9cd054ca1c738ffef2295c5266f, merge d78d6634497d1434fae6b912490a6a6013c6d0f8. +Existing isolated openhcs-knowledge-declaration-source-376-20261001 worktree and +437 branch retained. Untracked required-runtime-qt-publication ledger preserved +and excluded. Root's explicit release supersedes the earlier waiting receipt: +https://github.com/OpenHCSDev/openhcs/pull/394#issuecomment-5948196848. +Only its three production hunks were edited; no394/435/404/440/441 takeover. + +Owner and removed decisions +--------------------------- + +Seven production lines replaced/removed;37 added. Existing ImagePayloadConsumption +member declarations own singleton retention. NATURAL retains it; COMPOSED +admits the source to the original compose_aligned_image_payload algorithm. +The existing executor calls that owned behavior, deleting its direct composer +import/call. The existing composer's two singleton shortcuts now honor that +admission; alignment, runtime projection, contexts, spatial alignment, bundle, +mask and provenance algorithms are unchanged and remain the sole mechanism. +No new bootstrap, registry, metadata store, output publisher or guard fallback. +gray_to_color and its SOURCE_BINDING-only guard are unchanged. + +Required relation: a runtime/acquisition axis is not a named source-binding +axis. Each actual runtime plane is projected through the original owner before +introducing the one-source bundle, then original aligned execution preserves +runtime ordering. No axis relabel, filename provenance, fabricated channel, +arbitrary squeeze or changes to physical C2 identity/calibration/float units. + +New declaration and controls +---------------------------- + +test_declared_singleton_composition_437.py declares an independent source echo +callable using existing artifact/COMPOSED/processing declarations and a minimal +CellProfilerModule leaf. No generic consumer edits are needed for that case. +Its dense one-/three-runtime-plane inputs exercise original compiled input +edges, nominal adapter, generic image request AND invocation hooks and actual +contract executor. Ordered values, masks, original C2 paths, runtime cardinality, +calibration, domain and source immutability are checked through nominal slice +projection. Already-aligned one-/three-plane inputs exercise the original +composition and execution owners, preserving exact slice contexts. Scalar +composition creates exactly one binding plane. NATURAL identity/cardinality +and original ImageMath NONE mask behavior are unchanged. Direct unprojected +RUNTIME_SLICE still fails the original GrayToColor guard. + +No ornamental MI introduced: consumption is an existing closed enum family; +new module declarations inherit the existing behavioral ancestors. No new +independent implementation capability was needed or invented. This is a +declaration/new-case behavioral proof, not a claim of a new cooperative-MRO +mechanism. Existing434 MRO/proof evidence is untouched, not replayed. + +Finite source evidence +---------------------- + +All shards serial: tasksetCPU0, CPUQuota100%, MemoryMax512MiB/MemorySwapMax0, +timeout60s, numerical thread pools1, original read-only Python3.12.3/ABI driver, +no conftest/plugin-autoload/cache writes. No environment, install, build, +downloads, Fiji/provider, native/viewer/MCP or scientific image-array reads. +Initial resource admission RAM12.7GiB/home5.6GiB; later RAM14.4GiB/home4.8GiB. +Critical disk/swap advisory retained; lightweight source peak below366MiB +preserves the separate8GiB job headroom. No parallel tests or agents. + +* unary-repair-controls.log:7PASS,pytest4.94s/wall5.85s,345616KiB. Both implicit + and explicit FITC cases reach actual registered Stack execution. Existing + two-role identity, integer normalization and STACK-not-scalar controls pass. +* declaration-plane-controls.log:50PASS,pytest3.31s/wall3.97s,197292KiB; + eight new declaration controls plus42 original plane/singleton controls. +* existing-module-controls.log:9PASS/385deselected,pytest6.84s/wall7.79s, + 374316KiB; original selected composition/color/ImageMath controls. +* composed-consumer-controls.log:2PASS/392deselected,pytest7.08s/wall7.86s, + 374568KiB; original selected other composed-consumer controls. +Total68 distinct focused cases pass; source formatting/diff-check is clean. +Raw log warning whitespace is preserved, not a whole-evidence diff-check pass. + +Original failures are retained, not relabeled +------------------------------------------- + +original-unary-red.log remains the original2RED on merged434; no pre-fix rerun. +unary-repair-first.log:2FAIL/5PASS at the old diagnostic assertion that the +request must remain an unchanged runtime payload. The corrected test asserts +the stronger declared relation: outer nominal aligned owner plus inner +SOURCE_BINDING and exact FITC alias, before all original output assertions. +new-declaration-first.log:7FAIL/1PASS. Fixture omitted the required runtime +adapter, supplied a noncanonical wrapper, expected NONE to ignore masks and +assumed an absent spatial declaration must fail (the original bundle owner +can derive it). Those assumptions were corrected, not production guards. +new-declaration-controls.log:4FAIL/4PASS. The independent masked-output +contract returns a nominal aligned value set, not a dense ndarray; final tests +use existing RuntimeSliceProjection to check every value without reshaping. +Its already-aligned binder attempt separately fails ImageMetadataPayload.data +requires array-like data, got AlignedImageStack, artifact_binding.py241. This +is retained as a Root-owned pre-composition ingress limitation, not fixed or +hidden: final aligned coverage is explicitly composition/execution only. + +Original guards and remaining qualification +------------------------------------------ + +unary-repair-r0.log: original pinned agent-comms3b03785f45df2ef5dc62ba6aed99294192ecbb01, +actual Python3.14 and original read-only metaclass backing. Exact current-main +8551a486 -> productionffc3a4f, three changed production paths: exit0/16.82s/ +87580KiB. All5215 deltas zero (including foreign probes, chains, type/string +dispatch and class growth). Original stdout preserved; no copied detector. + +run_original_r1.py creates disposable LOCAL no-checkout Git metadata views, +then calls the UNCHANGED original scripts.check_refactor_r1.compare. Policy +SHA2564c6282f52e7c188068dd9d63399f5522a7cb1d222504d0c0b809be10303884ca; +pinned NRA673c062fc656e9c74f1eddcab30f036c9befbc1f. Policy retains all3roots, +all8exact dependency Git trees, original detectors/report scope/source identity. +No source/context pruning, cache spoof, schema roster or alternate detector. +Dependency-store corrections are explicit identity-verified local Git metadata: +ArrayBridge1e53d03 exists in retained arraybridge-release-035 WT, not the stale +parent submodule store; PyCodify792b034 exists in original modules/external/uneval +store with its actual PyCodify remote. No fetch/download/shared metadata edit. +unary-repair-r1.log and unary-repair-r1-verified.log retain both preflight +failures,0.14s/16864KiB and0.11s/16836KiB; neither reached a source scan. +unary-repair-r1-exact-context.log retains the one actual complete-context +attempt: native ScanDeadlineExceeded during parse_python_module/semantic +source hashing at55.000s,wall57.06s/134392KiB,exit1, before baseline scan_counts +completed.55s internal fits the required60s outer bound; no comparison result, +R1 pass, waiver or global FULL claim. No identical scan retry/budget increase. +Parent/Root own later completed qualification and fresh installed critical path. + +Architecture review +------------------- + +Personally reread installed NRA/refactor-audit skills, latest authoritative +ZIP SKILL.md/catalogue/identity/implementation/boundaries/surface receipt and +project00-RULES before code. BOUND-8: executor consumes the original declaration, +not a parallel composition-kind decision. IDEN-1: separate acquisition and +named-source axes. IMPL-2: closed member owns admission instead of consumers +switching on its value. IMPL-1/3/5: no function/enum/concrete-type consumer +switch or duplicate dispatch. IMPL-12/13: original alignment/bundle algorithms +are kept, not copied into a color-local hook or weakened. No compatibility +facade, mirrored catalog/store or replacement code left beside its predecessor. + +Installed scope remains parent-owned. Unary STACK creates YXC with one color +channel, NOT a scalar-gray naming alias; original integer ingress is float32/ +65535 before rescale_intensity=False. Passing source checks does not qualify +the original four-step grayscale-renaming recipe, persisted publication435, +biological/scientific results, cross-device behavior or fresh installed live. + +Exact disposable cleanup +------------------------ + +After every owned test/guard process reached terminal, lsof found no open +handles under /home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002. +Remaining418473 logical bytes were only owned pytest/Git metadata fixtures; +removed that exact root. The original policy had already reclaimed its peak +93MiB staged source/cache through TemporaryDirectory on deadline. All original +failed logs, reproducibility driver, exact source/dependency IDs, source and +publication ledger remain persistent. No other owner's cache/output was removed. + +Current-main source integration +------------------------------- + +Remote437 was independently verified at8669a1305229375c4db07c75940adab005ca4462, +already pushed and ready, before this continuation. Normally merged current +main3df650bf7faf84f67dbad9acf9ee62a095ab1ecf (442/443) into the same branch: +source-qualified merge51637fe437b212fcf66d4c78743f4da09c1edc1b. No conflict; +all three released production blobs equal originalffc3a4f. No additional +production edit, dependency gitlink change or Root394/435 hunk taken. The +merge hook's absent submodule-worktree warning was reviewed; all eight recorded +gitlinks remain unchanged and no backing/submodule checkout was modified. + +main-integration-controls.log: the original unary7 and independent declaration8 +controls all PASS on51637fe43, pytest5.03s/wall5.78s/355060KiB. Existing read-only +driver and environment, serial1CPU/512MiB/60s, numerical pools1. These15 repeat +only the affected integration path, not another full68-case qualification. +main-integration-r0.log: original pinned3b03785f45df2ef5dc62ba6aed99294192ecbb01 +guard, actual Python3.14/backing as above; exact3df650bf7 ->51637fe43 comparison +of the three changed production paths, exit0/wall17.20s/87508KiB. All5215 +deltas zero. The original complete-context R1 deadline remains incomplete; +no replay, waiver, source pruning or expanded budget. + +Reviewed current diff against BOUND-8 and IMPL-2/1/3/5/12/13: original member +owns admission, generic executor queries it, original composer remains the +only alignment/bundle algorithm. New source-echo declaration needs no consumer +edit; the same actual invocation controls remain green after integration. +No new independent capability or ornamental MI was introduced. No stored +format change. Source/test diff-check passes; original raw-log whitespace is +retained rather than claiming a whole-evidence whitespace pass. + +Admission RAM13.7GiB/home3.7GiB with disk/swap advisory retained; bounded serial +peak347MiB leaves over8GiB RAM headroom. No new env/build/install/download/native +or biological attempt. The newly named pytest scratch address +/home/ts/.cache/agent-scratch/graytocolor-unary-main-integration-437-20261002 +was never materialized by these tests; no cleanup or other-owner deletion. +The untracked required-runtime-qt-publication ledger remains untouched/excluded. +Issue432 stays OPEN pending parent-owned full installed composition acceptance. diff --git a/docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py b/docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py new file mode 100644 index 0000000000..aa9be27fd0 --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py @@ -0,0 +1,60 @@ +"""Run the unchanged R1 owner against exact Git trees, without source checkouts. + +Only small, disposable local Git metadata views are created. The original +policy owns source materialization, all three roots/eight recorded dependencies, +detector selection, source/dependency identity, deadlines and comparison. +""" + +import json +from pathlib import Path +import subprocess +import sys + + +def git_output(repo, *args): + return subprocess.check_output(("git", "-C", str(repo), *args), text=True).strip() + + +def main(): + source_root = Path(__file__).resolve().parents[3] + scratch = Path(sys.argv[1]) + base, head = sys.argv[2:4] + scratch.mkdir(parents=True, exist_ok=True) + view = scratch / "git-view" + common = Path(git_output(source_root, "rev-parse", "--git-common-dir")).resolve() + store_overrides = dict(argument.split("=", 1) for argument in sys.argv[4:]) + dependencies = {} + for revision in (base, head): + for entry in git_output(source_root, "ls-tree", "-r", revision).splitlines(): + metadata, path = entry.split("\t", 1) + mode, _kind, oid = metadata.split() + if mode == "160000": + dependencies.setdefault(path, set()).add(oid) + stores = {path: Path(store_overrides.get(path, common / "modules" / path)) + for path in dependencies} + for path, object_ids in sorted(dependencies.items()): + for oid in sorted(object_ids): + git_output(stores[path], "cat-file", "-e", f"{oid}^{{commit}}") + print("Read-only exact dependency stores:", + {path: str(store) for path, store in sorted(stores.items())}, flush=True) + subprocess.run(("git", "clone", "--shared", "--no-checkout", "--no-tags", + str(source_root), str(view)), check=True) + for path, object_ids in sorted(dependencies.items()): + store = stores[path] + # Read exact original object stores. No fetch, checkout or source writes. + subprocess.run(("git", "clone", "--shared", "--no-checkout", "--no-tags", + str(store), str(view / path)), check=True) + for oid in sorted(object_ids): + git_output(view / path, "cat-file", "-e", f"{oid}^{{commit}}") + print("Exact original R1 dependency context:", + {path: sorted(ids) for path, ids in sorted(dependencies.items())}, flush=True) + sys.path.insert(0, str(source_root)) + from scripts.check_refactor_r1 import compare + from nominal_refactor_advisor.json_reports import json_report_object + result = compare(view, base, head, scratch / "scan", budget_seconds=55) + print(json.dumps(json_report_object(result), indent=2), flush=True) + return int(bool(result.increased)) + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-controls.log b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-controls.log new file mode 100644 index 0000000000..7e4399444a --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-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 +7 passed, 2 warnings in 4.94s + 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-unary-repair-437-20261002/pytest tests/unit/test_gray_to_color_binding_axis_432.py -q --tb=short" + User time (seconds): 5.47 + System time (seconds): 0.33 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.85 + 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): 345616 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 68842 + Voluntary context switches: 2 + Involuntary context switches: 32 + 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-singleton-binding-432-20261002/unary-repair-first.log b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-first.log new file mode 100644 index 0000000000..1bade34380 --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-first.log @@ -0,0 +1,60 @@ +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:87: in test_declared_fitc_runtime_plane_retains_values_and_physical_identity + assert image_payload_metadata(request.payload).plane_axis is RuntimePlaneAxis.RUNTIME_SLICE +E AssertionError: assert None is +E + where None = ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(), unit=)),), slice_contexts=())) +E + where AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1000., 2000., 3000., 4000.],\n [ 5000.,...=None, source_channel_axis=None, plane_axis=)),), slice_contexts=()) = CellProfilerImageRequest(source_image_name='FITC', execution_mode=)),), slice_contexts=()), source_aliases=('FITC',)).payload +E + and = RuntimePlaneAxis.RUNTIME_SLICE +_ test_declared_fitc_runtime_plane_retains_values_and_physical_identity[True] __ +tests/unit/test_gray_to_color_binding_axis_432.py:87: in test_declared_fitc_runtime_plane_retains_values_and_physical_identity + assert image_payload_metadata(request.payload).plane_axis is RuntimePlaneAxis.RUNTIME_SLICE +E AssertionError: assert None is +E + where None = ImagePayloadMetadata(source_voxel_spacing=SourceVoxelSpacing(values_zyx=(), unit=)),), slice_contexts=())) +E + where AlignedImageStack(slices=(ImageMetadataPayload(data=array([[[ 0., 1000., 2000., 3000., 4000.],\n [ 5000.,...=None, source_channel_axis=None, plane_axis=)),), slice_contexts=()) = CellProfilerImageRequest(source_image_name='FITC', execution_mode=)),), slice_contexts=()), source_aliases=('FITC',)).payload +E + and = RuntimePlaneAxis.RUNTIME_SLICE +=============================== 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, 5 passed, 2 warnings in 4.92s +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-unary-repair-437-20261002/pytest tests/unit/test_gray_to_color_binding_axis_432.py -q --tb=short" + User time (seconds): 5.19 + System time (seconds): 0.32 + Percent of CPU this job got: 97% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.64 + 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): 351588 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 66716 + Voluntary context switches: 377 + Involuntary context switches: 42 + Swaps: 0 + File system inputs: 17928 + File system outputs: 16 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-r0.log b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-r0.log new file mode 100644 index 0000000000..74527ac75c --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-r0.log @@ -0,0 +1,15684 @@ +{ + "root": "openhcs/", + "base_revision": "8551a48644b5a9cd054ca1c738ffef2295c5266f", + "head_revision": "ffc3a4f345cc6460f8906b36a7af4582c67ffdad", + "paths": [ + "openhcs/core/aligned_image_payload.py", + "openhcs/core/callable_contract.py", + "openhcs/interop/cellprofiler/runtime/module_execution.py" + ], + "base": { + "StringDispatch:openhcs/core/aligned_image_payload.py": 0, + "StringDispatch:openhcs/core/callable_contract.py": 0, + "StringDispatch:openhcs/interop/cellprofiler/runtime/module_execution.py": 0, + 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"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","8551a48644b5a9cd054ca1c738ffef2295c5266f","--head","HEAD"];sys.exit(main())" + User time (seconds): 12.24 + System time (seconds): 2.86 + Percent of CPU this job got: 89% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:16.82 + 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): 87580 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 0 + Minor (reclaiming a frame) page faults: 528207 + Voluntary context switches: 13615 + Involuntary context switches: 10615 + Swaps: 0 + File system inputs: 3216 + 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-singleton-binding-432-20261002/unary-repair-r1-exact-context.log b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-r1-exact-context.log new file mode 100644 index 0000000000..3905f55b0b --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-r1-exact-context.log @@ -0,0 +1,86 @@ +Read-only exact dependency stores: {'external/ObjectState': '/home/ts/code/projects/openhcs/.git/modules/external/ObjectState', 'external/PolyStore': '/home/ts/code/projects/openhcs/.git/modules/external/PolyStore', 'external/arraybridge': '/home/ts/wt/arraybridge-release-035-20261001', 'external/metaclass-registry': '/home/ts/code/projects/openhcs/.git/modules/external/metaclass-registry', 'external/pycodify': '/home/ts/code/projects/openhcs/.git/modules/external/uneval', 'external/pyqt-reactive': '/home/ts/code/projects/openhcs/.git/modules/external/pyqt-reactive', 'external/python-introspect': '/home/ts/code/projects/openhcs/.git/modules/external/python-introspect', 'external/zmqruntime': '/home/ts/code/projects/openhcs/.git/modules/external/zmqruntime'} +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1-exact-context/git-view'... +done. +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1-exact-context/git-view/external/ObjectState'... +done. +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1-exact-context/git-view/external/PolyStore'... +done. +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1-exact-context/git-view/external/arraybridge'... +done. +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1-exact-context/git-view/external/metaclass-registry'... +done. +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1-exact-context/git-view/external/pycodify'... +done. +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1-exact-context/git-view/external/pyqt-reactive'... +done. +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1-exact-context/git-view/external/python-introspect'... +done. +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1-exact-context/git-view/external/zmqruntime'... +done. +Exact original R1 dependency context: {'external/ObjectState': ['b0004daf3223326ac78689ba7b2e68abc18ae298'], 'external/PolyStore': ['84f322e46871de5ed47e7fd20976ad03e533c1c4'], 'external/arraybridge': ['1e53d03d9f468322a1c085c8be29485fb139caf2'], 'external/metaclass-registry': ['393a7e03003cdc56df9013f932ed4f26e632d77a'], 'external/pycodify': ['792b03413331fdf107e369c924c257a2f0b16126'], 'external/pyqt-reactive': ['ad4948775ab81180a354d4b793d17ee5ddff3972'], 'external/python-introspect': ['4e8f8bde5f750d9a50eacac80acd3806123addd8'], 'external/zmqruntime': ['668edafcb5ee530a163377c936431ae1e8334e85']} +Traceback (most recent call last): + File "/home/ts/wt/openhcs-knowledge-declaration-source-376-20261001/docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py", line 60, in + raise SystemExit(main()) + ^^^^^^ + File "/home/ts/wt/openhcs-knowledge-declaration-source-376-20261001/docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py", line 54, in main + result = compare(view, base, head, scratch / "scan", budget_seconds=55) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/openhcs-knowledge-declaration-source-376-20261001/scripts/check_refactor_r1.py", line 310, in compare + scan_counts(snapshot, roots, changed, cache_root=work / "nra") + File "/home/ts/wt/openhcs-knowledge-declaration-source-376-20261001/scripts/check_refactor_r1.py", line 183, in scan_counts + result = analyze_compact_roots_with_cache( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/.pyenv/versions/3.12.3/lib/python3.12/contextlib.py", line 81, in inner + return func(*args, **kwds) + ^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/nra-bounded-full-audit-20260929/nominal_refactor_advisor/analysis.py", line 2292, in analyze_compact_roots_with_cache + build_results = worker_plan.map( + ^^^^^^^^^^^^^^^^ + File "/home/ts/wt/nra-bounded-full-audit-20260929/nominal_refactor_advisor/analysis.py", line 288, in map + return [function(item) for item in items] + ^^^^^^^^^^^^^^ + File "/home/ts/.pyenv/versions/3.12.3/lib/python3.12/contextlib.py", line 81, in inner + return func(*args, **kwds) + ^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/nra-bounded-full-audit-20260929/nominal_refactor_advisor/analysis.py", line 1237, in build_compact_projection_shard + modules = (source.parsed_module(),) + ^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/nra-bounded-full-audit-20260929/nominal_refactor_advisor/analysis.py", line 1013, in parsed_module + module = parser.parsed_source_path( + ^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/nra-bounded-full-audit-20260929/nominal_refactor_advisor/ast_tools.py", line 2686, in parsed_source_path + return _parse_source_module( + ^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/nra-bounded-full-audit-20260929/nominal_refactor_advisor/ast_tools.py", line 683, in _parse_source_module + semantic_hash = semantic_python_source_hash(source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/wt/nra-bounded-full-audit-20260929/nominal_refactor_advisor/ast_tools.py", line 485, in semantic_python_source_hash + f"{token.type}:{token.start[0]}:{token.start[1]}:" + ^^^^^^^^^^^^^^^^ + File "/home/ts/wt/nra-bounded-full-audit-20260929/nominal_refactor_advisor/deadline.py", line 91, in deadline_handler + raise error +nominal_refactor_advisor.deadline.ScanDeadlineExceeded: scan deadline exceeded during parse_python_module: 55.000s/55.000s +Command exited with non-zero status 1 + Command being timed: "/home/ts/wt/openhcs-generated-inputs-installed-parent-20261001/.venv/bin/python -B docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py /home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1-exact-context 8551a48644b5a9cd054ca1c738ffef2295c5266f ffc3a4f34 external/arraybridge=/home/ts/wt/arraybridge-release-035-20261001 external/pycodify=/home/ts/code/projects/openhcs/.git/modules/external/uneval" + User time (seconds): 55.14 + System time (seconds): 1.35 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:57.06 + 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): 134392 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 427 + Minor (reclaiming a frame) page faults: 63566 + Voluntary context switches: 25599 + Involuntary context switches: 24280 + Swaps: 0 + File system inputs: 166200 + File system outputs: 198664 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-r1-verified.log b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-r1-verified.log new file mode 100644 index 0000000000..42c3da804f --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-r1-verified.log @@ -0,0 +1,40 @@ +fatal: cannot change to '/home/ts/code/projects/openhcs/.git/modules/external/pycodify': No such file or directory +Traceback (most recent call last): + File "/home/ts/wt/openhcs-knowledge-declaration-source-376-20261001/docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py", line 60, in + raise SystemExit(main()) + ^^^^^^ + File "/home/ts/wt/openhcs-knowledge-declaration-source-376-20261001/docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py", line 37, in main + git_output(stores[path], "cat-file", "-e", f"{oid}^{{commit}}") + File "/home/ts/wt/openhcs-knowledge-declaration-source-376-20261001/docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py", line 15, in git_output + return subprocess.check_output(("git", "-C", str(repo), *args), text=True).strip() + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/.pyenv/versions/3.12.3/lib/python3.12/subprocess.py", line 466, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/.pyenv/versions/3.12.3/lib/python3.12/subprocess.py", line 571, in run + raise CalledProcessError(retcode, process.args, +subprocess.CalledProcessError: Command '('git', '-C', '/home/ts/code/projects/openhcs/.git/modules/external/pycodify', 'cat-file', '-e', '792b03413331fdf107e369c924c257a2f0b16126^{commit}')' returned non-zero exit status 128. +Command exited with non-zero status 1 + Command being timed: "/home/ts/wt/openhcs-generated-inputs-installed-parent-20261001/.venv/bin/python -B docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py /home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1-verified 8551a48644b5a9cd054ca1c738ffef2295c5266f ffc3a4f34 external/arraybridge=/home/ts/wt/arraybridge-release-035-20261001" + User time (seconds): 0.08 + System time (seconds): 0.02 + Percent of CPU this job got: 95% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.11 + 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): 16836 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 2 + Minor (reclaiming a frame) page faults: 5115 + Voluntary context switches: 369 + Involuntary context switches: 358 + Swaps: 0 + File system inputs: 848 + 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/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-r1.log b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-r1.log new file mode 100644 index 0000000000..c5d54a72c4 --- /dev/null +++ b/docs/validation/graytocolor-singleton-binding-432-20261002/unary-repair-r1.log @@ -0,0 +1,48 @@ +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1/git-view'... +done. +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1/git-view/external/ObjectState'... +done. +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1/git-view/external/PolyStore'... +done. +Cloning into '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1/git-view/external/arraybridge'... +done. +fatal: Not a valid object name 1e53d03d9f468322a1c085c8be29485fb139caf2^{commit} +Traceback (most recent call last): + File "/home/ts/wt/openhcs-knowledge-declaration-source-376-20261001/docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py", line 52, in + raise SystemExit(main()) + ^^^^^^ + File "/home/ts/wt/openhcs-knowledge-declaration-source-376-20261001/docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py", line 40, in main + git_output(view / path, "cat-file", "-e", f"{oid}^{{commit}}") + File "/home/ts/wt/openhcs-knowledge-declaration-source-376-20261001/docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py", line 15, in git_output + return subprocess.check_output(("git", "-C", str(repo), *args), text=True).strip() + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/.pyenv/versions/3.12.3/lib/python3.12/subprocess.py", line 466, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/ts/.pyenv/versions/3.12.3/lib/python3.12/subprocess.py", line 571, in run + raise CalledProcessError(retcode, process.args, +subprocess.CalledProcessError: Command '('git', '-C', '/home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1/git-view/external/arraybridge', 'cat-file', '-e', '1e53d03d9f468322a1c085c8be29485fb139caf2^{commit}')' returned non-zero exit status 128. +Command exited with non-zero status 1 + Command being timed: "/home/ts/wt/openhcs-generated-inputs-installed-parent-20261001/.venv/bin/python -B docs/validation/graytocolor-singleton-binding-432-20261002/run_original_r1.py /home/ts/.cache/agent-scratch/graytocolor-unary-repair-437-20261002/r1 8551a48644b5a9cd054ca1c738ffef2295c5266f ffc3a4f34" + User time (seconds): 0.06 + System time (seconds): 0.05 + Percent of CPU this job got: 82% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.14 + 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): 16864 + Average resident set size (kbytes): 0 + Major (requiring I/O) page faults: 23 + Minor (reclaiming a frame) page faults: 7925 + Voluntary context switches: 493 + Involuntary context switches: 429 + Swaps: 0 + File system inputs: 4104 + File system outputs: 1168 + Socket messages sent: 0 + Socket messages received: 0 + Signals delivered: 0 + Page size (bytes): 4096 + Exit status: 1 diff --git a/openhcs/core/aligned_image_payload.py b/openhcs/core/aligned_image_payload.py index 23e33482c5..7c6dfae012 100644 --- a/openhcs/core/aligned_image_payload.py +++ b/openhcs/core/aligned_image_payload.py @@ -1306,6 +1306,8 @@ def compose_aligned_image_payload( metadata_mode: ImagePayloadMetadataCompositionMode = ( ImagePayloadMetadataCompositionMode.BUNDLE ), + *, + retain_single_input: bool = True, ) -> ImagePayloadComposition: """Compose one or more image payloads into an executor-ready payload.""" if not image_payloads: @@ -1384,7 +1386,7 @@ def compose_aligned_image_payload( "unaligned inputs require an explicit aligned stack owner. " f"Unowned input indices: {unowned_inputs!r}." ) - if len(aligned_payloads) == 1: + if len(aligned_payloads) == 1 and retain_single_input: if len(image_payloads) == 1: return ImagePayloadComposition( payload=aligned_payloads[0], @@ -1424,7 +1426,7 @@ def compose_aligned_image_payload( ), execution_mode=ImagePayloadExecutionMode.ALIGNED_MULTI_IMAGE_STACK, ) - if len(image_payloads) == 1: + if len(image_payloads) == 1 and retain_single_input: return ImagePayloadComposition( payload=image_payloads[0], execution_mode=ImagePayloadExecutionMode.NATURAL, diff --git a/openhcs/core/callable_contract.py b/openhcs/core/callable_contract.py index 097a69a3aa..701a3dda0e 100644 --- a/openhcs/core/callable_contract.py +++ b/openhcs/core/callable_contract.py @@ -9,7 +9,7 @@ import dataclasses import inspect from abc import ABC, abstractmethod -from collections.abc import Callable, Iterable, MutableMapping +from collections.abc import Callable, Iterable, MutableMapping, Sequence from dataclasses import MISSING, asdict, dataclass, fields, is_dataclass from enum import Enum from functools import wraps @@ -58,6 +58,10 @@ ) if TYPE_CHECKING: + from openhcs.core.aligned_image_payload import ( + AlignedImageSliceContext, + ImagePayloadComposition, + ) from openhcs.core.function_reference import FunctionReference from openhcs.core.image_file_serialization import ImageFileSourceMetadata from openhcs.core.pipeline.compilation_session import CompilationPathResolver @@ -206,8 +210,33 @@ def require_uniform( class ImagePayloadConsumption(str, Enum): """How a callable consumes its primary image payload.""" - NATURAL = "natural" - COMPOSED = "composed" + def __new__(cls, value: str, retain_single_input: bool): + member = str.__new__(cls, value) + member._value_ = value + member._retain_single_input = retain_single_input + return member + + NATURAL = ("natural", True) + COMPOSED = ("composed", False) + + def compose_image_payload( + self, + owner_name: str, + image_payloads: tuple[Any, ...], + *, + slice_contexts: Sequence[AlignedImageSliceContext] = (), + stack_broadcast_source_indices: Sequence[int | None] = (), + ) -> ImagePayloadComposition: + """Admit primary sources to the original alignment/bundle algorithm.""" + from openhcs.core.aligned_image_payload import compose_aligned_image_payload + + return compose_aligned_image_payload( + owner_name, + image_payloads, + slice_contexts=slice_contexts, + stack_broadcast_source_indices=stack_broadcast_source_indices, + retain_single_input=self._retain_single_input, + ) class PrimaryImageCarrierRequirement(str, Enum): diff --git a/openhcs/interop/cellprofiler/runtime/module_execution.py b/openhcs/interop/cellprofiler/runtime/module_execution.py index 840624bfaf..9c458e2143 100644 --- a/openhcs/interop/cellprofiler/runtime/module_execution.py +++ b/openhcs/interop/cellprofiler/runtime/module_execution.py @@ -16,7 +16,6 @@ AlignedImageStack, ImageOutputBundle, ImagePayloadExecutionMode, - compose_aligned_image_payload, ) from openhcs.core.artifacts import ( ArtifactOutputPlan, @@ -1344,7 +1343,7 @@ def _image_request( align_primary_images = len(image_inputs) > 1 and broadcast_sources == tuple( spec.ref() for spec in image_inputs ) - composition = compose_aligned_image_payload( + composition = self.callable_contract.image_payload_consumption.compose_image_payload( f"{module_type.require_module_name()} image inputs " f"{tuple(spec.name for spec in image_inputs)!r}", tuple(payloads), diff --git a/tests/unit/test_declared_singleton_composition_437.py b/tests/unit/test_declared_singleton_composition_437.py new file mode 100644 index 0000000000..2256df6f97 --- /dev/null +++ b/tests/unit/test_declared_singleton_composition_437.py @@ -0,0 +1,317 @@ +"""Declaration-owned admission to the unchanged source-bundle algorithm.""" + +from dataclasses import replace + +import numpy as np +import pytest + +from openhcs.core.aligned_image_payload import ( + AlignedImageSliceContext, + AlignedImageStack, + ImagePayloadExecutionMode, +) +from openhcs.core.callable_contract import CallableContract, ImagePayloadConsumption +from openhcs.core.component_group_scope import RuntimeExecutionAxisScope +from openhcs.core.function_patterns import ( + FunctionInvocationKey, + InvocationArtifactInputEdgePlan, + InvocationArtifactInputProjectionKey, +) +from openhcs.core.memory.decorators import numpy as numpy_contract +from openhcs.core.pipeline.function_contracts import ( + artifact_inputs, + composed_image_payload, +) +from openhcs.core.artifacts import ArtifactSpec, ImageArtifactType +from openhcs.core.runtime_image_values import ( + ImagePayloadMetadata, + image_payload_data, + image_payload_mask, + image_payload_metadata, +) +from openhcs.core.runtime_plane_projection import ( + RuntimePlaneAxis, + RuntimePlaneAxisValueProjection, + RuntimePlaneProjection, +) +from openhcs.core.runtime_slice_projection import RuntimeSliceProjection +from openhcs.core.runtime_stores import RuntimeValueStore +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.interop.cellprofiler.module_declarations import CellProfilerModule +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.processing.backends.cellprofiler.image_math import ( + image_math, + MathOperation, +) +from openhcs.processing.backends.cellprofiler.color import ( + gray_to_color, + GrayToColorModule, +) +from openhcs.processing.backends.lib_registry.unified_registry import ProcessingContract +from tests.unit.cellprofiler_runtime_test_support import ( + cellprofiler_runtime_adapter_for_test, +) + + +@artifact_inputs(ArtifactSpec.input("FITC", ImageArtifactType)) +@composed_image_payload +@numpy_contract(contract=ProcessingContract.PURE_3D) +def independently_declared_source_echo(image): + """A new source consumer, not a GrayToColor alias or special-case branch.""" + assert image_payload_metadata(image).plane_axis is RuntimePlaneAxis.SOURCE_BINDING + return RuntimeSliceProjection.value_for_slice( + image, + RuntimePlaneAxisValueProjection.from_selected_plane( + axis=RuntimePlaneAxis.SOURCE_BINDING, + plane_index=0, + axis_size=1, + source_aliases=("FITC",), + ), + ) + + +class IndependentlyDeclaredSourceEchoModule(CellProfilerModule): + module_name = "IndependentlyDeclaredSourceEcho437" + function_name = "independently_declared_source_echo" + + +def _runtime_source(slice_count): + pixels = ( + np.arange(slice_count * 20, dtype=np.float32).reshape(slice_count, 4, 5) / 100 + ) + masks = np.ones_like(pixels, dtype=bool) + masks[:, 0, 0] = False + metadata = ImagePayloadMetadata( + plane_axis=RuntimePlaneAxis.RUNTIME_SLICE, + source_image_names=("FITC",), + source_image_provenance_planes=SourceImageProvenancePlanes.from_components( + paths=tuple( + f"/synthetic/A01_s{index + 1}_w2.tif" for index in range(slice_count) + ), + component_metadata=tuple( + {"well": "A01", "site": str(index + 1), "channel": "2"} + for index in range(slice_count) + ), + ), + source_voxel_spacing=SourceVoxelSpacing((1.25, 2.5)), + source_spatial_domain=SourceSpatialDomain( + origin_yx=(0, 0), source_shape_yx=(4, 5) + ), + ) + return metadata.payload_with(pixels, masks) + + +@pytest.mark.parametrize("slice_count", (1, 3)) +@pytest.mark.parametrize("aligned", (False, True)) +def test_new_declaration_reuses_composition_and_executor(slice_count, aligned): + source = _runtime_source(slice_count) + original_pixels = image_payload_data(source).copy() + original_masks = image_payload_mask(source).copy() + projection = RuntimePlaneAxisValueProjection.preserve( + axis=RuntimePlaneAxis.RUNTIME_SLICE, + axis_size=slice_count, + ) + planes = tuple( + RuntimeSliceProjection.value_for_slice(source, projection.selected_plane(index)) + for index in range(slice_count) + ) + contexts = tuple( + AlignedImageSliceContext.main_flow(f"site{index + 1}") + for index in range(slice_count) + ) + current = AlignedImageStack(planes, contexts) if aligned else source + declared = CallableContract.from_callable(independently_declared_source_echo) + contract = replace( + declared, + metadata=replace( + declared.metadata, + runtime_adapter=CellProfilerRuntimeAdapter.runtime_adapter_spec(), + ), + ) + spec = contract.artifact_inputs.specs[0] + key = InvocationArtifactInputProjectionKey( + invocation_key=FunctionInvocationKey("new-declaration437", "default", 0), + input_index=0, + ) + edge = InvocationArtifactInputEdgePlan.from_source_declarations( + key=key, + spec=spec, + main_flow_artifacts=contract.artifact_inputs, + invocation_sources=contract.artifact_inputs, + ) + runtime = cellprofiler_runtime_adapter_for_test( + runtime_value_store=RuntimeValueStore(), + callable_contract=contract, + axis_scope=RuntimeExecutionAxisScope.from_raw( + "synthetic", component=None, value=None + ), + artifact_inputs={key: edge}, + ) + if aligned: + # This case exercises the composition owner, not Root394's unresolved + # pre-composition adapter ingress for already-aligned main-flow values. + composition = contract.image_payload_consumption.compose_image_payload( + "independent aligned declaration", + (current,), + ) + payload = composition.payload + execution_mode = composition.execution_mode + plane_projection = composition.preserved_plane_projection( + RuntimePlaneProjection.stack(slice_count) + ) + else: + request = CellProfilerModuleExecutor( + independently_declared_source_echo, contract + )._image_request( + current, + runtime, + module_type=IndependentlyDeclaredSourceEchoModule, + active_input_specs=contract.artifact_inputs.specs, + ) + invocation = CellProfilerModuleExecutor( + independently_declared_source_echo, contract + )._invocation_request( + image_request=request, + adapter=runtime, + current_image=current, + kwargs={}, + module_type=IndependentlyDeclaredSourceEchoModule, + ) + payload = invocation.image + execution_mode = invocation.execution_mode + plane_projection = invocation.plane_projection + assert execution_mode is ImagePayloadExecutionMode.ALIGNED_MULTI_IMAGE_STACK + assert isinstance(payload, AlignedImageStack) + assert plane_projection == projection + assert payload.slice_contexts == (contexts if aligned else ()) + for index, plane in enumerate(payload.slices): + metadata = image_payload_metadata(plane) + assert metadata.plane_axis is RuntimePlaneAxis.SOURCE_BINDING + assert metadata.source_image_names == ("FITC",) + assert metadata.source_component_metadata["channel"] == "2" + assert metadata.source_image_paths == (f"/synthetic/A01_s{index + 1}_w2.tif",) + np.testing.assert_array_equal( + image_payload_data(plane)[0], original_pixels[index] + ) + np.testing.assert_array_equal(image_payload_mask(plane), original_masks[index]) + result = CellProfilerFunctionContractExecutor().execute( + contract, + contract.resolve_canonical_raw_callable(), + payload, + {}, + execution_mode=execution_mode, + plane_projection=plane_projection, + ) + assert RuntimeSliceProjection.slice_count_from_values((result,)) == slice_count + for index in range(slice_count): + result_plane = RuntimeSliceProjection.value_for_slice( + result, projection.selected_plane(index) + ) + np.testing.assert_array_equal( + image_payload_data(result_plane), original_pixels[index] + ) + np.testing.assert_array_equal( + image_payload_mask(result_plane), original_masks[index] + ) + metadata = image_payload_metadata(result_plane) + assert metadata.plane_axis is None + assert metadata.source_channel_axis is None + assert ( + metadata.source_voxel_spacing + == image_payload_metadata(source).source_voxel_spacing + ) + assert ( + metadata.source_spatial_domain + == image_payload_metadata(source).source_spatial_domain + ) + np.testing.assert_array_equal(image_payload_data(source), original_pixels) + np.testing.assert_array_equal(image_payload_mask(source), original_masks) + + +def test_declared_composed_scalar_introduces_one_source_axis(): + source = _runtime_source(1) + scalar = RuntimeSliceProjection.value_for_slice( + source, + RuntimePlaneAxisValueProjection.from_selected_plane( + axis=RuntimePlaneAxis.RUNTIME_SLICE, + plane_index=0, + axis_size=1, + ), + ) + composition = CallableContract.from_callable( + independently_declared_source_echo + ).image_payload_consumption.compose_image_payload( + "independent scalar", + (scalar,), + ) + assert composition.execution_mode is ImagePayloadExecutionMode.FULL_STACK + assert ( + image_payload_metadata(composition.payload).plane_axis + is RuntimePlaneAxis.SOURCE_BINDING + ) + contract = CallableContract.from_callable(independently_declared_source_echo) + result = CellProfilerFunctionContractExecutor().execute( + contract, + contract.resolve_canonical_raw_callable(), + composition.payload, + {}, + execution_mode=composition.execution_mode, + ) + np.testing.assert_array_equal( + image_payload_data(result), image_payload_data(source)[0] + ) + + +@pytest.mark.parametrize("aligned", (False, True)) +def test_natural_declaration_retains_exact_singleton(aligned): + source = _runtime_source(3) + current = AlignedImageStack((source,)) if aligned else source + contract = CallableContract.from_callable(image_math) + assert contract.image_payload_consumption is ImagePayloadConsumption.NATURAL + composition = contract.image_payload_consumption.compose_image_payload( + "natural identity", (current,) + ) + assert composition.payload is current + assert composition.execution_mode is ( + ImagePayloadExecutionMode.ALIGNED_MULTI_IMAGE_STACK + if aligned + else ImagePayloadExecutionMode.NATURAL + ) + if not aligned: + result = CellProfilerFunctionContractExecutor().execute( + contract, + contract.resolve_canonical_raw_callable(), + composition.payload, + {"operation": MathOperation.NONE}, + execution_mode=composition.execution_mode, + ) + # NONE still applies the original mask policy: masked pixels become zero. + np.testing.assert_array_equal( + image_payload_data(result), + image_payload_data(source) * image_payload_mask(source), + ) + np.testing.assert_array_equal( + image_payload_mask(result), image_payload_mask(source) + ) + assert ( + image_payload_metadata(result).plane_axis is RuntimePlaneAxis.RUNTIME_SLICE + ) + + +def test_kernel_still_rejects_unprojected_runtime_axis(): + source = _runtime_source(1) + contract = CallableContract.from_callable(gray_to_color) + with pytest.raises(ValueError, match="requires a source-binding plane axis"): + contract.resolve_canonical_raw_callable()( + source, + color_scheme=GrayToColorModule.Scheme.STACK, + rescale_intensity=False, + ) diff --git a/tests/unit/test_gray_to_color_binding_axis_432.py b/tests/unit/test_gray_to_color_binding_axis_432.py index 6d337d43ef..bcb3525b78 100644 --- a/tests/unit/test_gray_to_color_binding_axis_432.py +++ b/tests/unit/test_gray_to_color_binding_axis_432.py @@ -7,7 +7,7 @@ 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.aligned_image_payload import AlignedImageStack, ImagePayloadBundleContext, ImagePayloadExecutionMode from openhcs.core.callable_contract import CallableContract from openhcs.core.artifacts import ArtifactSpec, ImageArtifactType from openhcs.core.config import StepSourceBindingsConfig @@ -84,7 +84,14 @@ def test_declared_fitc_runtime_plane_retains_values_and_physical_identity(explic 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 + # The source's acquisition axis remains distinct from the named input axis. + assert isinstance(request.payload, AlignedImageStack) + assert request.execution_mode is ImagePayloadExecutionMode.ALIGNED_MULTI_IMAGE_STACK + assert request.plane_projection.axis is RuntimePlaneAxis.RUNTIME_SLICE + assert request.plane_projection.axis_size == 1 + assert request.plane_projection.plane_index is None + assert image_payload_metadata(request.payload.slices[0]).plane_axis is RuntimePlaneAxis.SOURCE_BINDING + assert image_payload_metadata(request.payload.slices[0]).source_image_names == ("FITC",) execution = executor._invocation_request( image_request=request, adapter=runtime, current_image=source, module_type=GrayToColorModule,