Add Cython 3.1 support

.github/workflows/ci.yml

@@ -21,7 +21,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Python dependencies
-      run: python -m pip install --prefer-binary meson-python meson ninja setuptools "cython>=0.28,<3.0" "matplotlib>=3,<4" ${{ matrix.numpy-version }}
+      run: python -m pip install --prefer-binary meson-python meson ninja setuptools "cython>=3.1" "matplotlib>=3,<4" ${{ matrix.numpy-version }}
     - name: Build and install Raysect
       run: dev/install_editable.sh
     - name: Run tests

dev/root-meson.build

@@ -4,5 +4,6 @@ py = import('python').find_installation(pure: false)
 numpy = dependency('numpy', method: 'config-tool')
 fs = import('fs')
 
-cython_args = ['--annotate']
+# disabling explicit noexcept until pycharm fixes their cython 3 support (causes a large number of build warnings)
+cython_args = ['--annotate', '-X legacy_implicit_noexcept=True']
 cython_dependencies = [numpy]

meson.build

@@ -7,7 +7,8 @@ py = import('python').find_installation(pure: false)
 numpy = dependency('numpy', method: 'config-tool')
 fs = import('fs')
 
-cython_args = ['--annotate']
+# disabling explicit noexcept until pycharm fixes their cython 3 support
+cython_args = ['--annotate', '-Xlegacy_implicit_noexcept=True']
 cython_dependencies = [numpy]
 
 subdir('raysect')

pyproject.toml

@@ -27,5 +27,5 @@ Issues = "https://github.com/raysect/source/issues"
 Changelog = "https://github.com/raysect/source/blob/master/CHANGELOG.txt"
 
 [build-system]
-requires = ["meson-python", "setuptools", "wheel", "numpy", "cython<3.0"]
+requires = ["meson-python", "setuptools", "wheel", "numpy", "cython>=3.1"]
 build-backend = "mesonpy"

raysect/core/acceleration/accelerator.pxd

@@ -33,10 +33,9 @@ from raysect.core.ray cimport Ray
 from raysect.core.math cimport Point3D
 from raysect.core.intersection cimport Intersection
 
+
 cdef class Accelerator:
 
     cpdef build(self, list primitives)
-
     cpdef Intersection hit(self, Ray ray)
-
     cpdef list contains(self, Point3D point)

raysect/core/acceleration/accelerator.pyx

@@ -32,13 +32,10 @@
 cdef class Accelerator:
 
     cpdef build(self, list primitives):
-
         pass
 
     cpdef Intersection hit(self, Ray ray):
-
         raise NotImplementedError("Accelerator virtual method hit() has not been implemented.")
 
     cpdef list contains(self, Point3D point):
-
         raise NotImplementedError("Accelerator virtual method contains() has not been implemented.")

raysect/core/acceleration/boundprimitive.pxd

@@ -37,12 +37,11 @@ from raysect.core.intersection cimport Intersection
 
 cdef class BoundPrimitive:
 
-    cdef readonly Primitive primitive
-    cdef readonly BoundingBox3D box
-    cdef bint _primitive_tested
+    cdef:
+        readonly Primitive primitive
+        readonly BoundingBox3D box
+        bint _primitive_tested
 
     cdef Intersection hit(self, Ray ray)
-
     cdef Intersection next_intersection(self)
-
     cdef bint contains(self, Point3D point)

raysect/core/acceleration/kdtree.pxd

@@ -33,12 +33,15 @@ from raysect.core.acceleration.accelerator cimport Accelerator as _Accelerator
 from raysect.core.math.spatial.kdtree3d cimport KDTree3DCore as _KDTreeCore
 from raysect.core.intersection cimport Intersection
 
+
 cdef class _PrimitiveKDTree(_KDTreeCore):
+
     cdef:
         list primitives
         Intersection hit_intersection
 
 
 cdef class KDTree(_Accelerator):
+
     cdef _PrimitiveKDTree _kdtree
 

raysect/core/acceleration/kdtree.pyx

@@ -154,7 +154,6 @@ cdef class _PrimitiveKDTree(_KDTreeCore):
         # dereference the primitives and check if they contain the point
         enclosing_primitives = []
         for item in range(count):
-
             index = self._nodes[id].items[item]
             primitive = <BoundPrimitive> self.primitives[index]
             if primitive.contains(point):

raysect/core/acceleration/unaccelerated.pxd

@@ -35,5 +35,6 @@ from raysect.core.boundingbox cimport BoundingBox3D
 
 cdef class Unaccelerated(Accelerator):
 
-    cdef list primitives
-    cdef BoundingBox3D world_box
+    cdef:
+        list primitives
+        BoundingBox3D world_box

raysect/core/acceleration/unaccelerated.pyx

@@ -37,6 +37,7 @@ from raysect.core.math cimport Point3D
 from raysect.core.intersection cimport Intersection
 from raysect.core.acceleration.boundprimitive cimport BoundPrimitive
 
+
 cdef class Unaccelerated(Accelerator):
 
     def __init__(self):
@@ -54,7 +55,6 @@ cdef class Unaccelerated(Accelerator):
         self.world_box = BoundingBox3D()
 
         for primitive in primitives:
-
             accel_primitive = BoundPrimitive(primitive)
             self.primitives.append(accel_primitive)
             self.world_box.union(accel_primitive.box)
@@ -70,23 +70,17 @@ cdef class Unaccelerated(Accelerator):
 
         # does the ray intersect the space containing the primitives
         if not self.world_box.hit(ray):
-
             return None
 
         # find the closest primitive-ray intersection
         closest_intersection = None
 
-        # intial search distance is maximum possible ray extent
+        # initial search distance is maximum possible ray extent
         distance = ray.max_distance
-
         for primitive in self.primitives:
-
             intersection = primitive.hit(ray)
-
             if intersection is not None:
-
                 if intersection.ray_distance < distance:
-
                     distance = intersection.ray_distance
                     closest_intersection = intersection
 
@@ -101,15 +95,12 @@ cdef class Unaccelerated(Accelerator):
             BoundPrimitive primitive
 
         if not self.world_box.contains(point):
-
             return []
 
         enclosing_primitives = []
 
         for primitive in self.primitives:
-
             if primitive.contains(point):
-
                 enclosing_primitives.append(primitive.primitive)
 
         return enclosing_primitives

raysect/core/boundingbox.pxd

@@ -40,37 +40,21 @@ cdef class BoundingBox3D:
     cdef Point3D upper
 
     cdef Point3D get_centre(self)
-
     cpdef bint hit(self, Ray ray)
-
     cpdef tuple full_intersection(self, Ray ray)
-
     cdef bint intersect(self, Ray ray, double *front_intersection, double *back_intersection)
-
     cdef void _slab(self, double origin, double direction, double lower, double upper, double *front_intersection, double *back_intersection) nogil
-
     cpdef bint contains(self, Point3D point)
-
     cpdef object union(self, BoundingBox3D box)
-
     cpdef object extend(self, Point3D point, double padding=*)
-
     cpdef double surface_area(self)
-
     cpdef double volume(self)
-
     cpdef list vertices(self)
-
     cpdef double extent(self, int axis) except -1
-
     cpdef int largest_axis(self)
-
     cpdef double largest_extent(self)
-
     cpdef object pad(self, double padding)
-
     cpdef object pad_axis(self, int axis, double padding)
-
     cpdef BoundingSphere3D enclosing_sphere(self)
 
 
@@ -95,23 +79,14 @@ cdef class BoundingBox2D:
     cdef Point2D upper
 
     cpdef bint contains(self, Point2D point)
-
     cpdef object union(self, BoundingBox2D box)
-
     cpdef object extend(self, Point2D point, double padding=*)
-
     cpdef double surface_area(self)
-
     cpdef list vertices(self)
-
     cpdef double extent(self, int axis) except -1
-
     cpdef int largest_axis(self)
-
     cpdef double largest_extent(self)
-
     cpdef object pad(self, double padding)
-
     cpdef object pad_axis(self, int axis, double padding)
 
 

raysect/core/boundingbox.pyx

@@ -32,18 +32,19 @@
 # TODO: add docstrings
 
 cimport cython
+from libc.math cimport INFINITY
 from raysect.core.math cimport new_point3d, new_point2d
 
-# cython doesn't have a built-in infinity constant, this compiles to +infinity
-DEF INFINITY = 1e999
 
 # axis defines
-DEF X_AXIS = 0
-DEF Y_AXIS = 1
-DEF Z_AXIS = 2
+cdef enum:
+    X_AXIS = 0
+    Y_AXIS = 1
+    Z_AXIS = 2
+
 
 # defines the padding on the sphere which encloses the BoundingBox3D.
-DEF SPHERE_PADDING = 1.000001
+cdef const double SPHERE_PADDING = 1.000001
 
 
 @cython.freelist(256)
@@ -258,6 +259,7 @@ cdef class BoundingBox3D:
             return False
         if (point.z < self.lower.z) or (point.z > self.upper.z):
             return False
+
         return True
 
     cpdef object union(self, BoundingBox3D box):

raysect/core/boundingsphere.pxd

@@ -39,19 +39,11 @@ cdef class BoundingSphere3D:
         Point3D centre
 
     cpdef bint hit(self, Ray ray)
-
     cpdef tuple full_intersection(self, Ray ray)
-
     cdef bint intersect(self, Ray ray, double *front_intersection, double *back_intersection)
-
     cpdef bint contains(self, Point3D point)
-
     cpdef object union(self, BoundingSphere3D sphere)
-
     cpdef object extend(self, Point3D point, double padding=*)
-
     cpdef double surface_area(self)
-
     cpdef double volume(self)
-
     cpdef object pad(self, double padding)

raysect/core/containers.pxd

@@ -46,22 +46,16 @@ cdef class LinkedList:
         _Item last
 
     cpdef bint is_empty(self)
-
     cpdef add(self, object value)
-
     cpdef add_items(self, object iterable)
-
     cpdef object get_index(self, int index)
-
     cpdef insert(self, object value, int index)
-
     cpdef object remove(self, int index)
 
 
 cdef class Stack(LinkedList):
 
     cpdef push(self, object value)
-
     cpdef object pop(self)
 
 

raysect/core/intersection.pyx

@@ -31,6 +31,7 @@
 
 cimport cython
 
+
 @cython.freelist(256)
 cdef class Intersection:
     """

raysect/core/math/_mat4.pxd

@@ -34,10 +34,7 @@ cdef class _Mat4:
     cdef double m[4][4]
 
     cdef double get_element(self, int row, int column)
-
     cdef void set_element(self, int row, int column, double v)
-
     cpdef bint is_identity(self, double tolerance=*)
-
     cpdef bint is_close(self, _Mat4 other, double tolerance=*)
 

raysect/core/math/_mat4.pyx

@@ -54,7 +54,6 @@ cdef class _Mat4:
 
         # special handling for _Mat4
         if isinstance(v, _Mat4):
-
             m = <_Mat4>v
             for i in range(0, 4):
                 for j in range(0, 4):
@@ -95,7 +94,6 @@ cdef class _Mat4:
         Expects a tuple (row, column) as the index.
 
         e.g. v = matrix[1, 2]
-
         """
 
         cdef int row, column

raysect/core/math/_vec3.pxd

@@ -32,16 +32,10 @@
 cdef class _Vec3:
 
     cdef public double x, y, z
-
     cpdef double dot(self, _Vec3 v)
-
     cpdef double angle(self, _Vec3 v)
-
     cdef double get_length(self) nogil
-
     cdef object set_length(self, double v)
-
     cdef double get_index(self, int index) nogil
-
     cdef void set_index(self, int index, double value) nogil
 

raysect/core/math/_vec3.pyx

@@ -58,8 +58,8 @@ cdef class _Vec3:
             return self.y
         elif i == 2:
             return self.z
-        else:
-            raise IndexError("Index out of range [0, 2].")
+
+        raise IndexError("Index out of range [0, 2].")
 
     def __setitem__(self, int i, double value):
         """Sets the vector coordinates by index ([0,1,2] -> [x,y,z])."""
@@ -74,6 +74,7 @@ cdef class _Vec3:
             raise IndexError("Index out of range [0, 2].")
 
     def __iter__(self):
+
         yield self.x
         yield self.y
         yield self.z
@@ -189,8 +190,8 @@ cdef class _Vec3:
             return self.y
         elif index == 2:
             return self.z
-        else:
-            return NAN
+
+        return NAN
 
     cdef void set_index(self, int index, double value) nogil:
         """

raysect/core/math/affinematrix.pxd

@@ -35,7 +35,6 @@ from raysect.core.math._mat4 cimport _Mat4
 cdef class AffineMatrix3D(_Mat4):
 
     cpdef AffineMatrix3D inverse(self)
-
     cdef AffineMatrix3D mul(self, AffineMatrix3D m)