merge dev into main

Author: lguerard

README.md

@@ -53,6 +53,8 @@ pip install "patchworks[all]"       # Everything, incl. the napari viewer
 > `[imaris]` adds native `.ims` support (HDF5, no JVM). Physical pixel
 > calibration is read from the input and written into the OME-ZARR.
 
+<!-- -->
+
 > **`cupy` is never installed automatically**, unlike Cellpose's GPU support
 > (which comes for free via PyTorch's self-contained CUDA wheels). Any
 > `use_gpu=True`/`dilate_gpu: true` option (the `dog` plugin, `dilate_labels`)

tests/test_ome_zarr.py

@@ -104,7 +104,10 @@ def test_tiff_sequence_conversion(tmp_path):
     result = np.asarray(load_ome_zarr(out, channel=None))
     assert result.shape == (n_z, n_c, size, size)
     # each plane's constant value encodes its (z, c) position.
-    assert (result[:, :, 0, 0] == [[z * 10 + c for c in range(n_c)] for z in range(n_z)]).all()
+    assert (
+        result[:, :, 0, 0]
+        == [[z * 10 + c for c in range(n_c)] for z in range(n_z)]
+    ).all()
     assert _level_scale(out, 0) == pytest.approx([1.0, 1.0, 0.5, 0.5])
 
 

workflow/scripts/_pw.py

@@ -152,7 +152,9 @@ def build_fn(cfg):
     if dilate:
         from patchworks import dilate_labels
 
-        fn = dilate_labels(fn, iterations=dilate, use_gpu=cfg.get("dilate_gpu", False))
+        fn = dilate_labels(
+            fn, iterations=dilate, use_gpu=cfg.get("dilate_gpu", False)
+        )
 
     return fn