fix: address code review and Copilot feedback on PR #33

Code review fixes:
- Fix regionprops() missing spacing tuple conversion for cucim compat
- Remove unnecessary asnumpy(distance).shape — .shape works on both devices

Copilot feedback fixes:
- Make downscale_xy_only/filter_mode keyword-only in downscale_and_filter
  to preserve positional arg compatibility
- Make mask/dilate_seeds keyword-only in segment_watershed, keep ball_size
  as 3rd positional arg for backward compat
- Replace assert with ValueError for filter_shape validation
- Fix numpy scalar formatting in feature_extraction_3d notebook
  (np.issubdtype check instead of isinstance(x, float))
- Use uv sync + uv run in notebooks CI workflow (matches lint-format.yml)
- Remove dangling [tool.uv.sources] iohub entry from pyproject.toml

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: alxndrkalinin

.github/workflows/notebooks.yml

@@ -21,13 +21,13 @@ jobs:
       - name: set up python
         run: uv python install 3.11
 
-      - name: install jupyter
-        run: uv pip install jupyter
+      - name: install dependencies
+        run: uv sync --extra examples
 
       - name: convert notebooks to scripts
         run: |
           for nb in examples/notebooks/*.ipynb; do
-            jupyter nbconvert --to script "$nb" --output-dir examples/scripts
+            uv run jupyter nbconvert --to script "$nb" --output-dir examples/scripts
           done
 
       - name: commit generated scripts

cubic/feature/voxel.py

@@ -16,6 +16,9 @@ def regionprops(
     spacing: list[float] | None = None,
 ) -> list:
     """Extract region-based morphological features."""
+    # cucim requires spacing as tuple for kernel memoization
+    if spacing is not None:
+        spacing = tuple(spacing)
     return measure.regionprops(label_image, intensity_image, spacing=spacing)
 
 

cubic/segmentation/segment_utils.py

@@ -18,9 +18,10 @@ def downscale_and_filter(
     downscale_factor: float = 0.5,
     downscale_order: int = 3,
     downscale_anti_aliasing: bool = True,
-    downscale_xy_only: bool = True,
     filter_size: int = 3,
     filter_shape: str = "square",
+    *,
+    downscale_xy_only: bool = True,
     filter_mode: str = "nearest",
 ) -> npt.ArrayLike:
     """Subsample and filter image prior to segmentation.
@@ -58,10 +59,8 @@ def downscale_and_filter(
     """
     from ..scipy import ndimage as _ndimage
 
-    assert filter_shape in [
-        "square",
-        "circular",
-    ], "Filter shape must be 'square' or 'circular'."
+    if filter_shape not in ("square", "circular"):
+        raise ValueError("filter_shape must be 'square' or 'circular'.")
 
     if downscale_factor < 1.0:
         if downscale_xy_only:
@@ -283,8 +282,9 @@ def remove_thin_objects(label_image, min_z=2):
 def segment_watershed(
     image: npt.ArrayLike,
     markers: npt.ArrayLike | None = None,
-    mask: npt.ArrayLike | None = None,
     ball_size: int = 15,
+    *,
+    mask: npt.ArrayLike | None = None,
     dilate_seeds: bool = False,
 ) -> npt.ArrayLike:
     """Segment image using watershed algorithm.
@@ -335,7 +335,7 @@ def segment_watershed(
         footprint = to_same_device(footprint, distance)
         coords = feature.peak_local_max(distance, footprint=footprint, labels=image)
 
-        seed_mask = np.zeros(asnumpy(distance).shape, dtype=bool)
+        seed_mask = np.zeros(distance.shape, dtype=bool)
         seed_mask[tuple(asnumpy(coords).T)] = True
         seed_mask = to_device(seed_mask, device)
         if dilate_seeds:

examples/notebooks/feature_extraction_3d.ipynb

@@ -158,8 +158,8 @@
     "print(\"-\" * len(header))\n",
     "for i in range(n_objects):\n",
     "    row = \" \".join(\n",
-    "        f\"{props_np[c][i]:>16.2f}\"\n",
-    "        if isinstance(props_np[c][i], float)\n",
+    "        f\"{float(props_np[c][i]):>16.2f}\"\n",
+    "        if np.issubdtype(type(props_np[c][i]), np.floating)\n",
     "        else f\"{int(props_np[c][i]):>16d}\"\n",
     "        for c in key_cols\n",
     "    )\n",

pyproject.toml

@@ -82,6 +82,3 @@ convention = "numpy"
 
 [tool.ruff.lint.isort]
 length-sort = true
-
-[tool.uv.sources]
-iohub = { git = "https://github.com/czbiohub-sf/iohub" }