Merge pull request #1567 from emlys/task/556

update to Cython 3

HISTORY.rst

@@ -65,6 +65,7 @@ Unreleased Changes
     * Add support for latest GDAL versions; remove test-specific constraint on
       GDAL versions from invest requirements.
       https://github.com/natcap/invest/issues/916
+    * Updated to Cython 3 (https://github.com/natcap/invest/issues/556)
 * Annual Water Yield
     * Added the results_suffix to a few intermediate files where it was
       missing. https://github.com/natcap/invest/issues/1517

pyproject.toml

@@ -45,7 +45,7 @@ invest = "natcap.invest.cli:main"
 # that we can provide a much easier build experience so long as GDAL is
 # available at runtime.
 requires = [
-    'setuptools>=61', 'wheel', 'setuptools_scm>=8.0', 'cython', 'babel',
+    'setuptools>=61', 'wheel', 'setuptools_scm>=8.0', 'cython>=3.0.0', 'babel',
     'oldest-supported-numpy'
 ]
 build-backend = "setuptools.build_meta"

requirements-dev.txt

@@ -10,7 +10,6 @@
 # scripts/convert-requirements-to-conda-yml.py as though it can only be found
 # on pip.
 
-Cython<3.0.0
 virtualenv>=12.0.1
 pytest
 pytest-subtests

setup.py

@@ -2,7 +2,7 @@
 import platform
 import subprocess
 
-import Cython.Build
+from Cython.Build import cythonize
 import numpy
 from setuptools import setup
 from setuptools.command.build_py import build_py as _build_py
@@ -46,14 +46,14 @@ def run(self):
 
 setup(
     install_requires=_REQUIREMENTS,
-    ext_modules=[
+    ext_modules=cythonize([
         Extension(
             name=f'natcap.invest.{package}.{module}',
             sources=[f'src/natcap/invest/{package}/{module}.pyx'],
-            include_dirs=[numpy.get_include()],
             extra_compile_args=compiler_and_linker_args,
             extra_link_args=compiler_and_linker_args,
-            language='c++'
+            language='c++',
+            define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")]
         ) for package, module in [
             ('delineateit', 'delineateit_core'),
             ('recreation', 'out_of_core_quadtree'),
@@ -62,9 +62,9 @@ def run(self):
             ('sdr', 'sdr_core'),
             ('seasonal_water_yield', 'seasonal_water_yield_core')
         ]
-    ],
+    ], compiler_directives={'language_level': '3'}),
+    include_dirs=[numpy.get_include()],
     cmdclass={
-        'build_ext': Cython.Build.build_ext,
         'build_py': build_py
     }
 )

src/natcap/invest/delineateit/delineateit_core.pyx

@@ -1,4 +1,3 @@
-# cython: language_level=3
 import numpy
 import pygeoprocessing
 cimport numpy
@@ -105,5 +104,3 @@ cpdef cset[cpair[double, double]] calculate_pour_point_array(
     # return set of (x, y) coordinates referenced to the same coordinate system
     # as the original raster
     return pour_points
-
-

src/natcap/invest/ndr/ndr_core.pyx

@@ -1,5 +1,3 @@
-# cython: profile=False
-# cython: language_level=2
 import tempfile
 import logging
 import os
@@ -129,9 +127,9 @@ cdef class _ManagedRaster:
         self.block_xbits = numpy.log2(self.block_xsize)
         self.block_ybits = numpy.log2(self.block_ysize)
         self.block_nx = (
-            self.raster_x_size + (self.block_xsize) - 1) / self.block_xsize
+            self.raster_x_size + (self.block_xsize) - 1) // self.block_xsize
         self.block_ny = (
-            self.raster_y_size + (self.block_ysize) - 1) / self.block_ysize
+            self.raster_y_size + (self.block_ysize) - 1) // self.block_ysize
 
         self.lru_cache = new LRUCache[int, double*](MANAGED_RASTER_N_BLOCKS)
         self.raster_path = <bytes> raster_path
@@ -197,7 +195,7 @@ cdef class _ManagedRaster:
             if dirty_itr != self.dirty_blocks.end():
                 self.dirty_blocks.erase(dirty_itr)
                 block_xi = block_index % self.block_nx
-                block_yi = block_index / self.block_nx
+                block_yi = block_index // self.block_nx
 
                 # we need the offsets to subtract from global indexes for
                 # cached array
@@ -261,7 +259,7 @@ cdef class _ManagedRaster:
 
     cdef void _load_block(self, int block_index) except *:
         cdef int block_xi = block_index % self.block_nx
-        cdef int block_yi = block_index / self.block_nx
+        cdef int block_yi = block_index // self.block_nx
 
         # we need the offsets to subtract from global indexes for cached array
         cdef int xoff = block_xi << self.block_xbits
@@ -322,7 +320,7 @@ cdef class _ManagedRaster:
                     self.dirty_blocks.erase(dirty_itr)
 
                     block_xi = block_index % self.block_nx
-                    block_yi = block_index / self.block_nx
+                    block_yi = block_index // self.block_nx
 
                     xoff = block_xi << self.block_xbits
                     yoff = block_yi << self.block_ybits
@@ -488,7 +486,7 @@ def ndr_eff_calculation(
             # hasn't already been set for processing.
             flat_index = processing_stack.top()
             processing_stack.pop()
-            global_row = flat_index / n_cols
+            global_row = flat_index // n_cols
             global_col = flat_index % n_cols
 
             crit_len = <float>crit_len_raster.get(global_col, global_row)

src/natcap/invest/recreation/out_of_core_quadtree.pyx

@@ -1,5 +1,3 @@
-# cython: profile=True
-# cython: language_level=2
 """A hierarchical spatial index for fast culling of points in 2D space."""
 
 import os
@@ -22,7 +20,7 @@ from osgeo import osr
 cimport numpy
 
 MAX_BYTES_TO_BUFFER = 2**27  # buffer a little over 128 megabytes
-import buffered_numpy_disk_map
+from natcap.invest.recreation import buffered_numpy_disk_map
 _ARRAY_TUPLE_TYPE = (
     buffered_numpy_disk_map.BufferedNumpyDiskMap._ARRAY_TUPLE_TYPE)
 

src/natcap/invest/scenic_quality/viewshed.pyx

@@ -1,5 +1,3 @@
-# coding=UTF-8
-# cython: language_level=2
 """
 Implements the Wang et al (2000) viewshed based on reference planes.
 
@@ -307,9 +305,9 @@ cdef class _ManagedRaster:
         self.block_xbits = numpy.log2(self.block_xsize)
         self.block_ybits = numpy.log2(self.block_ysize)
         self.block_nx = (
-            self.raster_x_size + (self.block_xsize) - 1) / self.block_xsize
+            self.raster_x_size + (self.block_xsize) - 1) // self.block_xsize
         self.block_ny = (
-            self.raster_y_size + (self.block_ysize) - 1) / self.block_ysize
+            self.raster_y_size + (self.block_ysize) - 1) // self.block_ysize
 
         self.lru_cache = new LRUCache[int, double*](MANAGED_RASTER_N_BLOCKS)
         self.raster_path = <bytes> raster_path
@@ -375,7 +373,7 @@ cdef class _ManagedRaster:
             if dirty_itr != self.dirty_blocks.end():
                 self.dirty_blocks.erase(dirty_itr)
                 block_xi = block_index % self.block_nx
-                block_yi = block_index / self.block_nx
+                block_yi = block_index // self.block_nx
 
                 # we need the offsets to subtract from global indexes for
                 # cached array
@@ -439,7 +437,7 @@ cdef class _ManagedRaster:
 
     cdef void _load_block(self, int block_index) except *:
         cdef int block_xi = block_index % self.block_nx
-        cdef int block_yi = block_index / self.block_nx
+        cdef int block_yi = block_index // self.block_nx
 
         # we need the offsets to subtract from global indexes for cached array
         cdef int xoff = block_xi << self.block_xbits
@@ -500,7 +498,7 @@ cdef class _ManagedRaster:
                     self.dirty_blocks.erase(dirty_itr)
 
                     block_xi = block_index % self.block_nx
-                    block_yi = block_index / self.block_nx
+                    block_yi = block_index // self.block_nx
 
                     xoff = block_xi << self.block_xbits
                     yoff = block_yi << self.block_ybits

src/natcap/invest/sdr/sdr_core.pyx

@@ -1,5 +1,3 @@
-# cython: profile=False
-# cython: language_level=3
 import logging
 import os
 
@@ -196,7 +194,7 @@ cdef class _ManagedRaster:
             if dirty_itr != self.dirty_blocks.end():
                 self.dirty_blocks.erase(dirty_itr)
                 block_xi = block_index % self.block_nx
-                block_yi = block_index / self.block_nx
+                block_yi = block_index // self.block_nx
 
                 # we need the offsets to subtract from global indexes for
                 # cached array

src/natcap/invest/seasonal_water_yield/seasonal_water_yield_core.pyx

@@ -1,5 +1,3 @@
-# cython: profile=False
-# cython: language_level=2
 import logging
 import os
 import collections
@@ -146,9 +144,9 @@ cdef class _ManagedRaster:
         self.block_xbits = numpy.log2(self.block_xsize)
         self.block_ybits = numpy.log2(self.block_ysize)
         self.block_nx = (
-            self.raster_x_size + (self.block_xsize) - 1) / self.block_xsize
+            self.raster_x_size + (self.block_xsize) - 1) // self.block_xsize
         self.block_ny = (
-            self.raster_y_size + (self.block_ysize) - 1) / self.block_ysize
+            self.raster_y_size + (self.block_ysize) - 1) // self.block_ysize
 
         self.lru_cache = new LRUCache[int, double*](MANAGED_RASTER_N_BLOCKS)
         self.raster_path = <bytes> raster_path
@@ -214,7 +212,7 @@ cdef class _ManagedRaster:
             if dirty_itr != self.dirty_blocks.end():
                 self.dirty_blocks.erase(dirty_itr)
                 block_xi = block_index % self.block_nx
-                block_yi = block_index / self.block_nx
+                block_yi = block_index // self.block_nx
 
                 # we need the offsets to subtract from global indexes for
                 # cached array
@@ -278,7 +276,7 @@ cdef class _ManagedRaster:
 
     cdef void _load_block(self, int block_index) except *:
         cdef int block_xi = block_index % self.block_nx
-        cdef int block_yi = block_index / self.block_nx
+        cdef int block_yi = block_index // self.block_nx
 
         # we need the offsets to subtract from global indexes for cached array
         cdef int xoff = block_xi << self.block_xbits
@@ -339,7 +337,7 @@ cdef class _ManagedRaster:
                     self.dirty_blocks.erase(dirty_itr)
 
                     block_xi = block_index % self.block_nx
-                    block_yi = block_index / self.block_nx
+                    block_yi = block_index // self.block_nx
 
                     xoff = block_xi << self.block_xbits
                     yoff = block_yi << self.block_ybits