Promote CellProfiler parity and accelerated backends

.gitignore

@@ -123,6 +123,9 @@ dmypy.json
 output/
 *.json
 !examples/*.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
@@ -134,6 +137,7 @@ archive/
 audit/
 plans/*
 !plans/root-artifact-cleanup.md
+!plans/core_surface_reduction_plan_20260509.md
 semantic_matrix_analyzer/
 tools/
 bin/

.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 +1,81 @@
+"""Public API for the benchmark platform."""
+
+from __future__ import annotations
+
+import importlib
+from typing import Any
+
+import openhcs as _openhcs_dependency_bootstrap  # noqa: F401
+
+
+_PUBLIC_EXPORTS: dict[str, tuple[str, str]] = {
+    "DatasetSpec": ("benchmark.contracts.dataset", "DatasetSpec"),
+    "AcquiredDataset": ("benchmark.contracts.dataset", "AcquiredDataset"),
+    "MetricCollector": ("benchmark.contracts.metric", "MetricCollector"),
+    "BenchmarkResult": ("benchmark.contracts.tool_adapter", "BenchmarkResult"),
+    "ToolAdapter": ("benchmark.contracts.tool_adapter", "ToolAdapter"),
+    "ToolAdapterError": ("benchmark.contracts.tool_adapter", "ToolAdapterError"),
+    "ToolExecutionError": ("benchmark.contracts.tool_adapter", "ToolExecutionError"),
+    "ToolNotInstalledError": ("benchmark.contracts.tool_adapter", "ToolNotInstalledError"),
+    "ToolVersionError": ("benchmark.contracts.tool_adapter", "ToolVersionError"),
+    "DatasetAcquisitionError": (
+        "benchmark.datasets.acquire",
+        "DatasetAcquisitionError",
+    ),
+    "acquire_dataset": ("benchmark.datasets.acquire", "acquire_dataset"),
+    "BBBC021_SINGLE_PLATE": (
+        "benchmark.datasets.registry",
+        "BBBC021_SINGLE_PLATE",
+    ),
+    "DATASET_REGISTRY": ("benchmark.datasets.registry", "DATASET_REGISTRY"),
+    "get_dataset_spec": ("benchmark.datasets.registry", "get_dataset_spec"),
+    "PipelineSpec": ("benchmark.pipelines.registry", "PipelineSpec"),
+    "NUCLEI_SEGMENTATION": (
+        "benchmark.pipelines.registry",
+        "NUCLEI_SEGMENTATION",
+    ),
+    "PIPELINE_REGISTRY": ("benchmark.pipelines.registry", "PIPELINE_REGISTRY"),
+    "get_pipeline_spec": ("benchmark.pipelines.registry", "get_pipeline_spec"),
+    "TimeMetric": ("benchmark.metrics.time", "TimeMetric"),
+    "MemoryMetric": ("benchmark.metrics.memory", "MemoryMetric"),
+    "OpenHCSAxisSelection": ("benchmark.adapters.openhcs", "OpenHCSAxisSelection"),
+    "BenchmarkCaseProgress": ("benchmark.progress", "BenchmarkCaseProgress"),
+    "BenchmarkProgressEvent": ("benchmark.progress", "BenchmarkProgressEvent"),
+    "BenchmarkProgressEventKind": (
+        "benchmark.progress",
+        "BenchmarkProgressEventKind",
+    ),
+    "BenchmarkProgressSnapshot": (
+        "benchmark.progress",
+        "BenchmarkProgressSnapshot",
+    ),
+    "iter_progress_events": ("benchmark.progress", "iter_progress_events"),
+    "summarize_progress": ("benchmark.progress", "summarize_progress"),
+    "CellProfilerAdapter": (
+        "benchmark.adapters.cellprofiler",
+        "CellProfilerAdapter",
+    ),
+    "OpenHCSAdapter": ("benchmark.adapters.openhcs", "OpenHCSAdapter"),
+    "CellProfilerCompatibilityResult": (
+        "benchmark.runner",
+        "CellProfilerCompatibilityResult",
+    ),
+    "run_benchmark": ("benchmark.runner", "run_benchmark"),
+    "run_cellprofiler_compatibility_benchmark": (
+        "benchmark.runner",
+        "run_cellprofiler_compatibility_benchmark",
+    ),
+}
+
+
+def __getattr__(name: str) -> Any:
+    """Load public benchmark symbols on demand."""
+    if name not in _PUBLIC_EXPORTS:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+    module_name, attribute_name = _PUBLIC_EXPORTS[name]
+    value = getattr(importlib.import_module(module_name), attribute_name)
+    globals()[name] = value
+    return value
+
+
+__all__ = tuple(_PUBLIC_EXPORTS)

benchmark/adapters/__init__.py

@@ -0,0 +1,28 @@
+"""Tool adapters."""
+
+from __future__ import annotations
+
+import importlib
+from typing import Any
+
+
+_PUBLIC_EXPORTS: dict[str, tuple[str, str]] = {
+    "CellProfilerAdapter": (
+        "benchmark.adapters.cellprofiler",
+        "CellProfilerAdapter",
+    ),
+    "OpenHCSAdapter": ("benchmark.adapters.openhcs", "OpenHCSAdapter"),
+}
+
+
+def __getattr__(name: str) -> Any:
+    """Load adapter classes on demand."""
+    if name not in _PUBLIC_EXPORTS:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+    module_name, attribute_name = _PUBLIC_EXPORTS[name]
+    value = getattr(importlib.import_module(module_name), attribute_name)
+    globals()[name] = value
+    return value
+
+
+__all__ = tuple(_PUBLIC_EXPORTS)