Promote CellProfiler parity and accelerated backends

.gitignore

@@ -123,6 +123,10 @@ dmypy.json
 output/
 *.json
 !examples/*.json
+!docs/source/development/mcp_knowledge_base_manifest.json
+!benchmark/manifests/official23_plus_monolayer.json
+!benchmark/manifests/extra_provided_not_in_23_axis1.json
+!benchmark/manifests/official23_plus_extra6_axis1.json
 tests/integration/tests_data/
 
 # Embedded repositories
@@ -134,12 +138,14 @@ archive/
 audit/
 plans/*
 !plans/root-artifact-cleanup.md
+!plans/core_surface_reduction_plan_20260509.md
 semantic_matrix_analyzer/
 tools/
 bin/
 local/
 
 # Development artifacts and temporary files
+.nra-cache/
 *_PLAN.md
 *_REVIEW.md
 *_SUMMARY.md
@@ -151,10 +157,13 @@ PR_*.md
 duck_typing_*.md
 measure_peak_memory.py
 test_caching_*.py
+openhcs_zmq_probe_*.py
 *-fail.txt
 *_output.txt
 *_logs.txt
 win_logs.txt
+/.zgroup
+benchmark/results/napari_streaming_validator/
 
 # Guardrails for accidental root artifacts
 /*.pdf

.gitmodules

@@ -9,7 +9,7 @@
 [submodule "external/arraybridge"]
 	path = external/arraybridge
 	url = https://github.com/OpenHCSDev/arraybridge.git
-	branch = main
+	branch = benchmark-platform
 [submodule "external/metaclass-registry"]
 	path = external/metaclass-registry
 	url = https://github.com/OpenHCSDev/metaclass-registry.git
@@ -25,7 +25,7 @@
 [submodule "external/PolyStore"]
 	path = external/PolyStore
 	url = https://github.com/OpenHCSDev/PolyStore.git
-	branch = main
+	branch = cellprofiler-raster-image-formats
 [submodule "external/pyqt-reactive"]
 	path = external/pyqt-reactive
 	url = https://github.com/OpenHCSDev/PyQT-reactive.git

benchmark/__init__.py

@@ -0,0 +1,113 @@
+"""Public API for the benchmark platform."""
+
+from __future__ import annotations
+
+import openhcs as _openhcs_dependency_bootstrap  # noqa: F401
+
+__all__ = (
+    "DatasetSpec",
+    "AcquiredDataset",
+    "MetricCollector",
+    "BenchmarkResult",
+    "ToolAdapter",
+    "ToolAdapterError",
+    "ToolExecutionError",
+    "ToolNotInstalledError",
+    "ToolVersionError",
+    "DatasetAcquisitionError",
+    "acquire_dataset",
+    "BBBC021_SINGLE_PLATE",
+    "DATASET_REGISTRY",
+    "get_dataset_spec",
+    "PipelineSpec",
+    "NUCLEI_SEGMENTATION",
+    "PIPELINE_REGISTRY",
+    "get_pipeline_spec",
+    "TimeMetric",
+    "MemoryMetric",
+    "BenchmarkCaseProgress",
+    "BenchmarkProgressEvent",
+    "BenchmarkProgressEventKind",
+    "BenchmarkProgressSnapshot",
+    "iter_progress_events",
+    "summarize_progress",
+    "CellProfilerAdapter",
+    "OpenHCSAdapter",
+    "CellProfilerCompatibilityResult",
+    "run_benchmark",
+    "run_cellprofiler_compatibility_benchmark",
+)
+
+_EXPORT_NAMES = frozenset(__all__)
+_MISSING_EXPORT = object()
+
+
+def _benchmark_export_modules():
+    import benchmark.contracts.dataset as dataset_contracts
+
+    yield dataset_contracts
+
+    import benchmark.contracts.metric as metric_contracts
+
+    yield metric_contracts
+
+    import benchmark.contracts.pipeline as pipeline_contracts
+
+    yield pipeline_contracts
+
+    import benchmark.contracts.tool_adapter as tool_adapter_contracts
+
+    yield tool_adapter_contracts
+
+    import benchmark.datasets as dataset_exports
+
+    yield dataset_exports
+
+    import benchmark.pipelines as pipeline_exports
+
+    yield pipeline_exports
+
+    import benchmark.metrics as metric_exports
+
+    yield metric_exports
+
+    import benchmark.progress as progress_exports
+
+    yield progress_exports
+
+    import benchmark.adapters.openhcs as openhcs_adapter
+
+    yield openhcs_adapter
+
+    import benchmark.adapters.cellprofiler as cellprofiler_adapter
+
+    yield cellprofiler_adapter
+
+    import benchmark.runner as runner_exports
+
+    yield runner_exports
+
+
+def resolve_benchmark_export(name: str):
+    """Resolve one public benchmark export from its owning module."""
+    if name not in _EXPORT_NAMES:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+    existing = globals().get(name, _MISSING_EXPORT)
+    if existing is not _MISSING_EXPORT:
+        return existing
+    for module in _benchmark_export_modules():
+        namespace = vars(module)
+        if name in namespace:
+            value = namespace[name]
+            globals()[name] = value
+            return value
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+def __getattr__(name: str):
+    """Resolve public benchmark re-exports from their owning modules on demand."""
+    return resolve_benchmark_export(name)
+
+
+def __dir__() -> list[str]:
+    return sorted(set(globals()) | _EXPORT_NAMES)

benchmark/adapters/__init__.py

@@ -0,0 +1,43 @@
+"""Tool adapters."""
+
+from __future__ import annotations
+
+__all__ = ("CellProfilerAdapter", "OpenHCSAdapter")
+
+_EXPORT_NAMES = frozenset(__all__)
+_MISSING_EXPORT = object()
+
+
+def _adapter_export_modules():
+    import benchmark.adapters.openhcs as openhcs_adapter
+
+    yield openhcs_adapter
+
+    import benchmark.adapters.cellprofiler as cellprofiler_adapter
+
+    yield cellprofiler_adapter
+
+
+def resolve_adapter_export(name: str):
+    """Resolve one public adapter export from its owning module."""
+    if name not in _EXPORT_NAMES:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+    existing = globals().get(name, _MISSING_EXPORT)
+    if existing is not _MISSING_EXPORT:
+        return existing
+    for module in _adapter_export_modules():
+        namespace = vars(module)
+        if name in namespace:
+            value = namespace[name]
+            globals()[name] = value
+            return value
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+def __getattr__(name: str):
+    """Resolve public adapter re-exports from their owning modules on demand."""
+    return resolve_adapter_export(name)
+
+
+def __dir__() -> list[str]:
+    return sorted(set(globals()) | _EXPORT_NAMES)