Updating for numpy 2 C API

.github/workflows/test_and_deploy.yml

@@ -22,8 +22,8 @@ jobs:
     runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-latest]  # windows-latest
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        platform: [ubuntu-latest, macos-latest] # , windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v2

setup.py

@@ -61,10 +61,10 @@ def setup_package():
                      use_scm_version={'write_to': 'src/pyift/_version.py'},
                      setup_requires=build_requires,
                      install_requires=[
-                         'numpy',
+                         'numpy>=2',
                          'scipy',
                      ],
-                     python_requires=">=3.8",
+                     python_requires=">=3.9",
                      package_dir={'': 'src'},
                      ext_modules=exts,
                      classifiers=[
@@ -76,9 +76,11 @@ def setup_package():
                          'Programming Language :: C',
                          'Programming Language :: Python :: 3',
                          'Programming Language :: Python :: 3 :: Only',
-                         'Programming Language :: Python :: 3.8',
                          'Programming Language :: Python :: 3.9',
                          'Programming Language :: Python :: 3.10',
+                         'Programming Language :: Python :: 3.11',
+                         'Programming Language :: Python :: 3.12',
+                         'Programming Language :: Python :: 3.13',
                          'Topic :: Scientific/Engineering',
                          'Topic :: Software Development :: Libraries :: Python Modules',
                      ],

src/pyift/shortestpath.py

@@ -4,8 +4,12 @@
 from typing import Optional, Tuple, Dict, Union
 
 
-def seed_competition(seeds: np.ndarray, image: Optional[np.ndarray] = None, graph: Optional[sparse.csr_matrix] = None,
-                     image_3d: bool = False) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
+def seed_competition(
+    seeds: np.ndarray,
+    image: Optional[np.ndarray] = None,
+    graph: Optional[Union[sparse.csr_matrix, sparse.csr_array]] = None,
+    image_3d: bool = False,
+) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
     """
     Performs the shortest path classification from the `seeds` nodes
     using the image foresting transform algorithm [1]_.
@@ -102,8 +106,8 @@ def seed_competition(seeds: np.ndarray, image: Optional[np.ndarray] = None, grap
         return _pyift.seed_competition_grid(image, seeds)
 
     # graph is provided
-    if not isinstance(graph, sparse.csr_matrix):
-        raise TypeError('`graph` must be a `csr_matrix`.')
+    if not isinstance(graph, (sparse.csr_matrix, sparse.csr_array)):
+        raise TypeError('`graph` must be a `csr_matrix` or `csr_array`.')
 
     if graph.shape[0] != graph.shape[1]:
         raise ValueError('`graph` must be a square adjacency matrix, current shape %r.' % graph.shape)

src/pyift_c_ext/_livewire.h

@@ -12,6 +12,7 @@ extern "C" {
 #define NO_IMPORT_ARRAY
 #define PY_ARRAY_UNIQUE_SYMBOL PYIFT_ARRAY_API
 #include "numpy/arrayobject.h"
+#include "numpy/npy_math.h"
 
 
 typedef enum {

src/pyift_c_ext/_shortestpath.h

@@ -13,6 +13,7 @@ extern "C" {
 #define NO_IMPORT_ARRAY
 #define PY_ARRAY_UNIQUE_SYMBOL PYIFT_ARRAY_API
 #include "numpy/arrayobject.h"
+#include "numpy/npy_math.h"
 
 
 PyObject *_seedCompetitionGrid(PyArrayObject *image, PyArrayObject *seeds);