Incorrect edge discovery when having two small loops

... And which side of the loop is chosen depends on whether the SciPy version used is 1.10 or earlier or 1.11 or later. 😕

Here's a reproducible example:

import napari
import numpy as np
from skimage.draw import random_shapes
from skimage.morphology import skeletonize
from skan import Skeleton, summarize

# Generate a random skeletons, first is a skeleton with a closed loop with side branches
kwargs = {"image_shape": (128, 128),
          "max_shapes": 20,
          "channel_axis": None,
          "shape": None,
          "rng": 1,
          "allow_overlap": True,
          "min_size": 20}

kwargs["rng"] = 13588686514
kwargs["min_size"] = 20
random_images, _ = random_shapes(**kwargs)
mask = np.where(random_images != 255, 1, 0)
skeleton_linear1 = skeletonize(mask)

viewer = napari.Viewer()
layer = viewer.add_labels(skeleton_linear1)

skeleton = Skeleton(skeleton_linear1)
all_paths = [skeleton.path_coordinates(i) for i in range(skeleton.n_paths)]
paths_table = summarize(skeleton, separator='_')
paths_table.reset_index(inplace=True, names='branch-id')

shp_layer = viewer.add_shapes(
        all_paths,
        shape_type='path',
        features=paths_table,
        metadata={'skeleton': skeleton},
        )

shp_layer.edge_color = 'branch-id'
shp_layer.edge_color_cycle = [
        'red', 'green', 'blue', 'cyan', 'magenta', 'yellow'
        ]

napari.run()

This is the output on SciPy 1.10:

The same code with SciPy 1.11 produces:

Both are wrong (both loops should be completely closed).

jni / skan

Incorrect edge discovery when having two small loops #225