Add numpy 2 compatibility

.github/workflows/test.yml

@@ -21,11 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
-        python: [3.8, 3.9, "3.10"]
-        include:
-          # test big sur on 3.9.0
-          - python: 3.9
-            platform: macos-11.0
+        python: ["3.9", "3.12"]
 
     steps:
       - uses: actions/checkout@v3

pyproject.toml

@@ -38,14 +38,14 @@ keywords = [
     'image processing',
     'skeletons'
 ]
-requires-python = '>=3.8'
+requires-python = '>=3.9'
 dependencies = [
     'imageio>=2.10.1',
     'magicgui>=0.7.3',
     'matplotlib>=3.4',
     'networkx>=2.7',
     'numba>=0.53',
-    'numpy>=1.21',
+    'numpy>=1.25',
     'pandas>=2.0.2',
     'openpyxl>=2.6',
     'scikit-image>=0.17.1',

src/skan/_testdata.py

@@ -25,8 +25,8 @@
 
 
 _zeros1 = np.zeros_like(skeleton1)
-skeleton2 = np.column_stack((skeleton1, _zeros1))
-skeleton2 = np.row_stack((skeleton2, skeleton2[:, ::-1]))
+skeleton2 = np.concatenate((skeleton1, _zeros1), axis=1)
+skeleton2 = np.concatenate((skeleton2, skeleton2[:, ::-1]), axis=0)
 
 skeleton3d = np.array([[[1, 0, 0, 0, 0],
                         [0, 0, 0, 0, 0],

src/skan/csr.py

@@ -760,7 +760,7 @@ def summarize(
                 "to silence this warning, use `separator='-'` to maintain "
                 "current behavior and use `separator='_'` to switch to the "
                 "new default behavior.",
-                np.VisibleDeprecationWarning,
+                np.exceptions.VisibleDeprecationWarning,
                 stacklevel=2,  # make sure warning points to calling line
                 )
         separator = '-'

src/skan/nputil.py

@@ -240,9 +240,9 @@ def _raveled_offsets_and_distances(
     ...         )
     >>> off  # doctest: +SKIP
     array([-5, -1,  1,  5, -6, -4,  4,  6, 10,  9, 11])
-    >>> d[0]
+    >>> float(d[0])  # avoid np.float64 repr
     1.0
-    >>> d[-1]  # distance from (1, 1) to (3, 2)
+    >>> float(d[-1])  # distance from (1, 1) to (3, 2)
     2.236...
     """
     ndim = len(image_shape)

src/skan/test/test_csr.py

@@ -358,7 +358,7 @@ def test_skeleton_integer_dtype(dtype):
 
 
 def test_default_summarize_separator():
-    with pytest.warns(np.VisibleDeprecationWarning,
+    with pytest.warns(np.exceptions.VisibleDeprecationWarning,
                       match='separator in column name'):
         stats = csr.summarize(csr.Skeleton(skeletonlabel))
     assert 'skeleton-id' in stats