[codex] fix circular import in mussel.utils

mussel/utils/__init__.py

@@ -1,19 +1,5 @@
 from .artifact_removal import GrandQCArtifactRemover
 from .converter import AnyToTiffConverter
-from .feature_extract import (DatasetProcessor, FeatureExtractionResult,
-                              H5DatasetProcessor, ImageFolderProcessor,
-                              TileCoordProcessor, aggregate_sample_features,
-                              aggregate_slide_features,
-                              aggregate_slide_features_batch,
-                              extract_patch_features,
-                              extract_patch_features_batch, filter_features,
-                              get_batch_size_for_model,
-                              get_classifier_pkl_from_model_dir,
-                              get_dataset_processor, get_features,
-                              get_model_path_from_dir, process_dataset,
-                              resolve_aggregation_method,
-                              resolve_patch_encoder, save_features,
-                              subsample_tiles)
 from .file import (WSI_EXTENSIONS, collect_wsi_paths, download_model_path,
                    ensure_directory_exists, get_slide_id_from_path,
                    get_slide_ids_from_paths, is_remote_path, load_classifier,
@@ -27,3 +13,68 @@
 from .timer import timed
 from .visualization import visualize_heatmap
 from .wsi_backend import open_slide
+
+_FEATURE_EXTRACT_EXPORTS = {
+    "DatasetProcessor",
+    "FeatureExtractionResult",
+    "H5DatasetProcessor",
+    "ImageFolderProcessor",
+    "TileCoordProcessor",
+    "aggregate_sample_features",
+    "aggregate_slide_features",
+    "aggregate_slide_features_batch",
+    "extract_patch_features",
+    "extract_patch_features_batch",
+    "filter_features",
+    "get_batch_size_for_model",
+    "get_classifier_pkl_from_model_dir",
+    "get_dataset_processor",
+    "get_features",
+    "get_model_path_from_dir",
+    "process_dataset",
+    "resolve_aggregation_method",
+    "resolve_patch_encoder",
+    "save_features",
+    "subsample_tiles",
+}
+
+
+def __getattr__(name):
+    if name in _FEATURE_EXTRACT_EXPORTS:
+        from . import feature_extract
+
+        value = getattr(feature_extract, name)
+        globals()[name] = value
+        return value
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+__all__ = [
+    "GrandQCArtifactRemover",
+    "AnyToTiffConverter",
+    "WSI_EXTENSIONS",
+    "collect_wsi_paths",
+    "download_model_path",
+    "ensure_directory_exists",
+    "get_slide_id_from_path",
+    "get_slide_ids_from_paths",
+    "is_remote_path",
+    "load_classifier",
+    "load_features_from_h5",
+    "resolve_remote_paths",
+    "safe_path_join",
+    "save_hdf5",
+    "save_torch_tensor",
+    "collate_features",
+    "contours_to_polygon",
+    "draw_slide_mask",
+    "get_level_for_magnification",
+    "get_slide_mpp",
+    "save_patches_png",
+    "segment_tissue",
+    "export_tiles",
+    "timed",
+    "visualize_heatmap",
+    "open_slide",
+    *_FEATURE_EXTRACT_EXPORTS,
+]

tests/mussel/test_import_order.py

@@ -0,0 +1,32 @@
+import subprocess
+import sys
+
+
+def run_clean_import(script: str) -> None:
+    result = subprocess.run(
+        [sys.executable, "-c", script],
+        check=False,
+        capture_output=True,
+        text=True,
+    )
+    assert result.returncode == 0, result.stderr
+
+
+def test_extract_features_cli_imports_in_clean_interpreter():
+    run_clean_import("import mussel.cli.extract_features")
+
+
+def test_extract_features_cli_imports_after_datasets():
+    run_clean_import(
+        "import mussel.datasets; "
+        "import mussel.cli.extract_features; "
+        "from mussel.utils import aggregate_slide_features_batch"
+    )
+
+
+def test_feature_extract_exports_are_lazy_importable():
+    run_clean_import(
+        "from mussel.utils import ("
+        "DatasetProcessor, FeatureExtractionResult, aggregate_slide_features_batch"
+        ")"
+    )