update to cython 3

.github/workflows/build-py-dists.yml

@@ -8,8 +8,7 @@ jobs:
             fail-fast: false
             matrix:
                 os: [windows-latest, macos-latest]
-                python-version: [3.7, 3.8, 3.9, "3.10", "3.11", "3.12"]
-                python-arch: [x64]
+                python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
 
         steps:
             - uses: actions/checkout@v4
@@ -20,11 +19,10 @@ jobs:
             - name: Fetch git tags
               run: git fetch origin +refs/tags/*:refs/tags/*
 
-            - name: Set up python ${{ matrix.python-version }} ${{ matrix.python-arch }}
+            - name: Set up python ${{ matrix.python-version }}
               uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python-version }}
-                  architecture: ${{ matrix.python-arch }}
 
             - name: Install dependencies
               run: python -m pip install build
@@ -34,7 +32,7 @@ jobs:
 
             - uses: actions/upload-artifact@v1
               with:
-                  name: Wheel for ${{ matrix.os }} ${{ matrix.python-version }} ${{ matrix.python-arch }}
+                  name: Wheel for ${{ matrix.os }} ${{ matrix.python-version }}
                   path: dist
 
     build-sdist:
@@ -52,7 +50,7 @@ jobs:
             - name: Set up python
               uses: actions/setup-python@v5
               with:
-                  python-version: 3.7
+                  python-version: 3.12
 
             - name: Install dependencies
               run: python -m pip install build

HISTORY.rst

@@ -10,6 +10,7 @@ Unreleased Changes
   called with an invalid resampling algorithm. We now fall back to the
   underlying GDAL functions' error messages.
   https://github.com/natcap/pygeoprocessing/issues/387
+* Updated to Cython 3.
 
 2.4.3 (2024-03-06)
 ------------------

pyproject.toml

@@ -6,7 +6,7 @@
 # that we can provide a much easier build experience so long as GDAL is
 # available at runtime.
 requires = [
-    'setuptools', 'wheel', 'setuptools_scm', 'cython<3.0.0', 'oldest-supported-numpy'
+    'setuptools', 'wheel', 'setuptools_scm', 'cython>=3.0.0', 'oldest-supported-numpy'
 ]
 build-backend = "setuptools.build_meta"
 

requirements.txt

@@ -2,7 +2,6 @@
 # --------------------
 # This file records the packages and requirements needed in order for
 # pygeoprocessing to work as expected.
-Cython<3.0.0
 GDAL>=3.0.4
 numpy>=1.10.1
 Rtree>=0.8.3

setup.py

@@ -1,6 +1,7 @@
 """setup.py module for PyGeoprocessing."""
 import platform
 
+from Cython.Build import cythonize
 import numpy
 from setuptools import setup
 from setuptools.extension import Extension
@@ -62,7 +63,7 @@
         'Topic :: Scientific/Engineering :: GIS',
         'License :: OSI Approved :: BSD License'
     ],
-    ext_modules=[
+    ext_modules=cythonize([
         Extension(
             name="pygeoprocessing.routing.routing",
             sources=["src/pygeoprocessing/routing/routing.pyx"],
@@ -92,5 +93,5 @@
             extra_link_args=compiler_and_linker_args,
             language="c++"
         ),
-    ]
+    ])
 )

src/pygeoprocessing/geoprocessing_core.pyx

@@ -1,6 +1,3 @@
-# coding=UTF-8
-# distutils: language=c++
-# cython: language_level=3
 import logging
 import multiprocessing
 import os

src/pygeoprocessing/routing/watershed.pyx

@@ -1,5 +1,3 @@
-# coding=UTF-8
-# cython: language_level=3
 import logging
 import os
 import shutil