Merge pull request #68 from pmneila/numpy2

Add support for NumPy 2.0

.github/workflows/maxflow-ci.yml

@@ -1,14 +1,17 @@
-name: PyMaxflow CI
+name: PyMaxflow tests
 
-on: [push]
+on:
+  push:
+    branches: [master]
+  pull_request:
 
 jobs:
   test:
     name: Build and test
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v3
@@ -18,76 +21,20 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip setuptools cython oldest-supported-numpy
-      - name: Build the package
+          python -m pip install --upgrade pip
+      - name: Install the package
         run: |
-          python setup.py build_ext --inplace
-      - name: Test and coverage
+          python -m pip install -e .
+      - name: Install dependencies for test
         run: |
-          python -m pip install imageio networkx
           python -m pip install pytest>=7.2.0 pytest-cov>=4.0 codecov
+          python -m pip install imageio networkx
+      - name: Test and coverage
+        run: |
+          mkdir output
           python -m pytest --cov=maxflow --cov-report=xml
           codecov
       - name: Flake8
         run: |
           python -m pip install flake8
           flake8 .
-
-  deploy-sdist:
-    name: Deploy source distribution
-    runs-on: ubuntu-latest
-    needs: test
-    env:
-      TWINE_USERNAME: __token__
-      TWINE_PASSWORD: ${{ secrets.PYPI }}
-    if: github.ref == 'refs/heads/master'
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.9'
-      - name: Install cibuildwheel
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install build
-      - name: Build sdist
-        run: python -m build --sdist
-      - name: Deploy sdist
-        run: |
-          python3 -m pip install twine
-          python3 -m twine upload --skip-existing dist/*
-
-  deploy-wheels:
-    name: Deploy wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    needs: test
-    env:
-      CIBW_ARCHS: "auto64"
-      CIBW_BUILD: "cp37-* cp38-* cp39-* cp310-* cp311-* pp*"
-      CIBW_SKIP: "*musllinux* pp*-win* pp*-macosx*"
-      TWINE_USERNAME: __token__
-      TWINE_PASSWORD: ${{ secrets.PYPI }}
-    if: github.ref == 'refs/heads/master'
-
-    strategy:
-      matrix:
-        os: [ubuntu-20.04, windows-2019, macOS-11]
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.9'
-      - name: Install cibuildwheel
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install cibuildwheel==2.11.4
-      - name: Build wheels
-        run: python3 -m cibuildwheel --output-dir wheelhouse
-      - name: Deploy
-        run: |
-          python3 -m pip install twine
-          python3 -m twine upload --skip-existing wheelhouse/*.whl

.github/workflows/maxflow-deployment.yml

@@ -0,0 +1,61 @@
+name: PyMaxflow deployment
+
+on:
+  push:
+    tags: 'v[0-9]+*'
+
+jobs:
+  deploy-sdist:
+    name: Deploy source distribution
+    runs-on: ubuntu-latest
+    env:
+      TWINE_USERNAME: __token__
+      TWINE_PASSWORD: ${{ secrets.PYPI }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build
+      - name: Build sdist
+        run: python -m build --sdist
+      - name: Deploy sdist
+        run: |
+          python3 -m pip install twine
+          python3 -m twine upload --skip-existing dist/*
+
+  deploy-wheels:
+    name: Deploy wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    env:
+      CIBW_ARCHS: "auto64"
+      CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
+      CIBW_SKIP: "*musllinux* pp*-win* pp*-macosx* pp*"
+      TWINE_USERNAME: __token__
+      TWINE_PASSWORD: ${{ secrets.PYPI }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest, macos-13]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install cibuildwheel
+      - name: Build wheels
+        run: python3 -m cibuildwheel --output-dir wheelhouse
+      - name: Deploy
+        run: |
+          python3 -m pip install twine
+          python3 -m twine upload --skip-existing wheelhouse/*.whl

doc/source/tutorial.rst

@@ -194,7 +194,7 @@ belongs to the sink segment (i.e., the corresponding pixel has the label 0). We
 now get the labels for each pixel::
 
   # The labels should be 1 where sgm is False and 0 otherwise.
-  img2 = np.int_(np.logical_not(sgm))
+  img2 = np.int64(np.logical_not(sgm))
   # Show the result.
   from matplotlib import pyplot as ppl
   ppl.imshow(img2)

examples/binary_restoration.py

@@ -22,7 +22,7 @@
 sgm = g.get_grid_segments(nodeids)
 
 # The labels should be 1 where sgm is False and 0 otherwise.
-img2 = np.int_(np.logical_not(sgm))
+img2 = np.int64(np.logical_not(sgm))
 # Show the result.
 ppl.imshow(img2, cmap=ppl.cm.gray, interpolation='nearest')
 ppl.show()

examples/layout_examples.py

@@ -60,7 +60,7 @@
 central_node = nodeids[12]
 rest_of_nodes = np.hstack([nodeids[:12], nodeids[13:]])
 
-nodeids = np.empty((2, 24), dtype=np.int_)
+nodeids = np.empty((2, 24), dtype=np.int64)
 nodeids[0] = central_node
 nodeids[1] = rest_of_nodes
 

maxflow/__init__.py

@@ -35,7 +35,7 @@
 import numpy as np
 from . import _maxflow
 from ._maxflow import GraphInt, GraphFloat, moore_structure, vonNeumann_structure
-from .version import __version__, __version_str__, __version_core__
+from .version import __version__, __version_core__
 from .fastmin import aexpansion_grid, abswap_grid
 
 Graph = {int: GraphInt, float: GraphFloat}

maxflow/fastmin.py

@@ -95,7 +95,7 @@ def abswap_grid(unary, binary, max_cycles=None, labels=None):
         if num_labels <= 127:
             labels = np.int8(unary.argmin(axis=-1))
         else:
-            labels = np.int_(unary.argmin(axis=-1))
+            labels = np.int64(unary.argmin(axis=-1))
     else:
         if labels.min() < 0:
             raise ValueError("Values of labels must be non-negative")
@@ -182,7 +182,7 @@ def aexpansion_grid(unary, binary, max_cycles=None, labels=None):
         if num_labels <= 127:
             labels = np.int8(unary.argmin(axis=-1))
         else:
-            labels = np.int_(unary.argmin(axis=-1))
+            labels = np.int64(unary.argmin(axis=-1))
     else:
         if labels.min() < 0:
             raise ValueError("Values of labels must be non-negative")

maxflow/src/_maxflow.pyx

@@ -161,7 +161,7 @@ cdef public class GraphInt [object PyObject_GraphInt, type GraphInt]:
         """
         num_nodes = np.prod(shape)
         first = self.thisptr.add_node(int(num_nodes))
-        nodes = np.arange(first, first+num_nodes, dtype=np.int_)
+        nodes = np.arange(first, first+num_nodes, dtype=np.int64)
         return np.reshape(nodes, shape)
     def add_edge(self, int i, int j, long capacity, long rcapacity):
         """
@@ -639,7 +639,7 @@ cdef public class GraphFloat [object PyObject_GraphFloat, type GraphFloat]:
         """
         num_nodes = np.prod(shape)
         first = self.thisptr.add_node(int(num_nodes))
-        nodes = np.arange(first, first+num_nodes, dtype=np.int_)
+        nodes = np.arange(first, first+num_nodes, dtype=np.int64)
         return np.reshape(nodes, shape)
     def add_edge(self, int i, int j, double capacity, double rcapacity):
         """

maxflow/src/grid.h

@@ -88,7 +88,7 @@ std::vector<T> getVector(PyArrayObject* arr, int length)
         return std::vector<T>(length, value);
     }
 
-    // add_ndim == 1
+    // arr_ndim == 1
     if(arr_shape[0] < length)
         throw std::runtime_error("the length of `periodic` must be equal to the number of dimensions of `nodeids`");
 
@@ -149,11 +149,11 @@ void Graph<captype,tcaptype,flowtype>::add_grid_edges(PyArrayObject* _nodeids,
     }
     catch(std::exception& e)
     {
-            Py_DECREF(periodicArr);
-            Py_DECREF(structureArr);
-            Py_DECREF(weights);
-            Py_DECREF(nodeids);
-            throw e;
+        Py_DECREF(periodicArr);
+        Py_DECREF(structureArr);
+        Py_DECREF(weights);
+        Py_DECREF(nodeids);
+        throw e;
     }
 
     // Create the edges
@@ -168,6 +168,7 @@ void Graph<captype,tcaptype,flowtype>::add_grid_edges(PyArrayObject* _nodeids,
 
     if(iter == NULL)
     {
+        Py_DECREF(periodicArr);
         Py_DECREF(structureArr);
         Py_DECREF(weights);
         Py_DECREF(nodeids);

maxflow/version.py

@@ -1,5 +1,4 @@
 # -*- encoding:utf-8 -*-
 
-__version__ = (1, 3, 0)
-__version_str__ = ".".join(map(str, __version__))
+__version__ = "1.3.2"
 __version_core__ = (3, 0, 4)

pyproject.toml

@@ -1,3 +1,3 @@
 [build-system]
-requires = ["setuptools", "wheel", "Cython", "oldest-supported-numpy"]
+requires = ["setuptools", "wheel", "Cython", "numpy~=2.0"]
 build-backend = "setuptools.build_meta"

setup.py

@@ -9,7 +9,7 @@
 from Cython.Build import cythonize
 
 # Get the version number.
-__version_str__ = runpy.run_path("maxflow/version.py")["__version_str__"]
+__version__ = runpy.run_path("maxflow/version.py")["__version__"]
 
 
 def extensions():
@@ -44,7 +44,7 @@ def extensions():
 
 setup(
     name="PyMaxflow",
-    version=__version_str__,
+    version=__version__,
     description="A mincut/maxflow package for Python",
     author="Pablo Márquez Neila",
     author_email="[email protected]",
@@ -82,5 +82,5 @@ def extensions():
     ],
     packages=["maxflow"],
     ext_modules=extensions(),
-    install_requires=['numpy']
+    install_requires=['numpy>=1.26']
 )

test_maxflow.py

@@ -172,7 +172,7 @@ def test_fastmin_edge_cases():
 
     # Array with 0 spatial dimensions
     unary = np.zeros((0, 0, 3))
-    binary = np.ones((3, 3), dtype=np.float_) - np.eye(3, dtype=np.float_)
+    binary = np.ones((3, 3), dtype=np.float64) - np.eye(3, dtype=np.float64)
     labels = maxflow.aexpansion_grid(unary, binary)
     assert labels.shape == (0, 0)
 
@@ -203,7 +203,7 @@ def test_fastmin_edge_cases():
     # Shape of initial labels do not match the shape of the unary array
     unary = np.zeros((3, 3, 3))
     binary = np.zeros((3, 3))
-    labels = np.ones((4, 4), dtype=np.int_)
+    labels = np.ones((4, 4), dtype=np.int64)
     with pytest.raises(Exception):
         maxflow.aexpansion_grid(unary, binary, labels=labels)
     with pytest.raises(Exception):
@@ -212,7 +212,7 @@ def test_fastmin_edge_cases():
     # Initial labels contain values larger than num_labels
     unary = np.zeros((3, 3, 3))
     binary = np.zeros((3, 3))
-    labels = np.full((3, 3), 5, dtype=np.int_)
+    labels = np.full((3, 3), 5, dtype=np.int64)
     with pytest.raises(ValueError):
         maxflow.aexpansion_grid(unary, binary, labels=labels)
     with pytest.raises(ValueError):
@@ -221,7 +221,7 @@ def test_fastmin_edge_cases():
     # Initial labels contain negative values
     unary = np.zeros((3, 3, 3))
     binary = np.zeros((3, 3))
-    labels = np.full((3, 3), -1, dtype=np.int_)
+    labels = np.full((3, 3), -1, dtype=np.int64)
     with pytest.raises(ValueError):
         maxflow.aexpansion_grid(unary, binary, labels=labels)
     with pytest.raises(ValueError):