style: apply ruff format to 6 files

https://claude.ai/code/session_015Y9zQk4A8uKJAorKuvBoCk

Author: jameslehoux

braggtrack/cli/embed_dataset.py

@@ -39,8 +39,6 @@ def build_parser() -> argparse.ArgumentParser:
     return p
 
 
-
-
 def main() -> int:
     args = build_parser().parse_args()
     root = resolve_dataset_root(args.root)

braggtrack/cli/segment_dataset.py

@@ -53,7 +53,6 @@ def build_parser() -> argparse.ArgumentParser:
     return parser
 
 
-
 def _write_notebook(path: Path) -> None:
     nb = {
         "cells": [

braggtrack/cli/track_dataset.py

@@ -51,7 +51,6 @@ def build_parser() -> argparse.ArgumentParser:
     return parser
 
 
-
 def _load_embeddings_npz(path: Path) -> dict[int, np.ndarray]:
     with np.load(path) as z:
         labels = z["labels"]
@@ -69,7 +68,6 @@ def _merge_embeddings(rows: list[dict[str, Any]], emb: dict[int, np.ndarray]) ->
             row["embedding"] = emb[lid]
 
 
-
 def _write_notebook(path: Path) -> None:
     nb = {
         "cells": [

tests/test_error_paths.py

@@ -84,9 +84,15 @@ def test_parse_scan_index_extracts_digits(self) -> None:
 class BuildTracksEdgeTests(unittest.TestCase):
     def _make_spot(self, mu: float = 0.0, chi: float = 0.0, d: float = 0.0) -> dict:
         return {
-            "label": 1, "voxel_count": 10, "integrated_intensity": 100.0,
-            "centroid_mu": mu, "centroid_chi": chi, "centroid_d": d,
-            "eig_1": 0.5, "eig_2": 0.5, "eig_3": 0.5,
+            "label": 1,
+            "voxel_count": 10,
+            "integrated_intensity": 100.0,
+            "centroid_mu": mu,
+            "centroid_chi": chi,
+            "centroid_d": d,
+            "eig_1": 0.5,
+            "eig_2": 0.5,
+            "eig_3": 0.5,
         }
 
     def test_empty_scan_tables(self) -> None:

tests/test_integration.py

@@ -69,9 +69,7 @@ def setUpClass(cls) -> None:
         raw_thresholds = [otsu_threshold(v.ravel()) for v in cls.volumes]
         cls.smoothed = smooth_thresholds(raw_thresholds, window=5)
         cls.all_labels = [_segment(v, float(t)) for v, t in zip(cls.volumes, cls.smoothed)]
-        cls.all_features = [
-            extract_instance_table(lab, v) for lab, v in zip(cls.all_labels, cls.volumes)
-        ]
+        cls.all_features = [extract_instance_table(lab, v) for lab, v in zip(cls.all_labels, cls.volumes)]
 
     def test_discovers_three_scans(self) -> None:
         self.assertEqual(len(self.scans), 3)
@@ -91,11 +89,21 @@ def test_spot_counts_are_stable(self) -> None:
 
     def test_feature_tables_have_required_columns(self) -> None:
         required = {
-            "label", "voxel_count", "integrated_intensity",
-            "centroid_mu", "centroid_chi", "centroid_d",
-            "eig_1", "eig_2", "eig_3",
-            "bbox_min_z", "bbox_max_z", "bbox_min_y", "bbox_max_y",
-            "bbox_min_x", "bbox_max_x",
+            "label",
+            "voxel_count",
+            "integrated_intensity",
+            "centroid_mu",
+            "centroid_chi",
+            "centroid_d",
+            "eig_1",
+            "eig_2",
+            "eig_3",
+            "bbox_min_z",
+            "bbox_max_z",
+            "bbox_min_y",
+            "bbox_max_y",
+            "bbox_min_x",
+            "bbox_max_x",
         }
         for feats in self.all_features:
             for row in feats:

tests/test_semantic_week4.py

@@ -42,9 +42,12 @@ def test_crop_masked(self) -> None:
         lab = np.zeros((10, 10, 10), dtype=np.int32)
         lab[2:5, 3:6, 4:7] = 7
         bbox = {
-            "bbox_min_z": 2, "bbox_max_z": 4,
-            "bbox_min_y": 3, "bbox_max_y": 5,
-            "bbox_min_x": 4, "bbox_max_x": 6,
+            "bbox_min_z": 2,
+            "bbox_max_z": 4,
+            "bbox_min_y": 3,
+            "bbox_max_y": 5,
+            "bbox_min_x": 4,
+            "bbox_max_x": 6,
         }
         masked, mask = crop_spot_cube(vol, lab, 7, bbox, margin=0)
         self.assertTrue(np.all(masked[mask > 0] == 3.0))
@@ -55,9 +58,12 @@ def test_margin_clamps_to_boundary(self) -> None:
         labels = np.zeros((10, 10, 10), dtype=int)
         labels[0:2, 0:2, 0:2] = 1
         bbox = {
-            "bbox_min_z": 0, "bbox_max_z": 1,
-            "bbox_min_y": 0, "bbox_max_y": 1,
-            "bbox_min_x": 0, "bbox_max_x": 1,
+            "bbox_min_z": 0,
+            "bbox_max_z": 1,
+            "bbox_min_y": 0,
+            "bbox_max_y": 1,
+            "bbox_min_x": 0,
+            "bbox_max_x": 1,
         }
         masked, mask = crop_spot_cube(volume, labels, label_id=1, bbox=bbox, margin=5)
         self.assertGreater(mask.sum(), 0)
@@ -68,9 +74,12 @@ def test_other_labels_masked_out(self) -> None:
         labels[3, 3, 3] = 1
         labels[4, 4, 4] = 2
         bbox = {
-            "bbox_min_z": 3, "bbox_max_z": 4,
-            "bbox_min_y": 3, "bbox_max_y": 4,
-            "bbox_min_x": 3, "bbox_max_x": 4,
+            "bbox_min_z": 3,
+            "bbox_max_z": 4,
+            "bbox_min_y": 3,
+            "bbox_max_y": 4,
+            "bbox_min_x": 3,
+            "bbox_max_x": 4,
         }
         masked, mask = crop_spot_cube(volume, labels, label_id=1, bbox=bbox, margin=1)
         self.assertEqual(float(mask[mask.shape[0] // 2, mask.shape[1] // 2, mask.shape[2] // 2]), 0.0)