Add Cython 3.1 support

.github/workflows/ci.yml

@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         numpy-version: ["numpy"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
@@ -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

CHANGELOG.txt

@@ -13,6 +13,9 @@ Build changes:
   - Meson-python performs the build out of the project folder, so the project source folders will no longer be polluted with build artefacts.
   - Cython build annotations are now always enabled, the annotation files can be found in the build folder under the build artefacts folder associated with each so file (*.so.p folder).
 
+API changes:
+* Corrected spelling of all classes, methods and functions where "targeted" was incorrectly spelt "targetted".
+
 
 Release 0.8.1 (12 Feb 2023)
 ---------------------------

demos/maths/plot_targetted_sampler.py → demos/maths/plot_targeted_sampler.py

@@ -2,7 +2,7 @@
 import matplotlib.pyplot as plt
 from math import atan2, sqrt, degrees
 
-from raysect.core.math import Point3D, TargettedHemisphereSampler, TargettedSphereSampler
+from raysect.core.math import Point3D, TargetedHemisphereSampler, TargetedSphereSampler
 
 
 def display_samples(samples, title):
@@ -34,8 +34,8 @@ def display_samples(samples, title):
 observation_point = Point3D(0, 0, 0)
 
 # generate samplers
-hemisphere = TargettedHemisphereSampler(targets)
-sphere = TargettedSphereSampler(targets)
+hemisphere = TargetedHemisphereSampler(targets)
+sphere = TargetedSphereSampler(targets)
 
 # sample for origin point and point at (0, 0, -10)
 h_samples = hemisphere(observation_point, samples=samples)

demos/observers/cornell_box_cooke_triplet.py

@@ -4,7 +4,7 @@
 from raysect.optical import World, Node, translate, rotate, Point3D
 from raysect.optical.material import Lambert, UniformSurfaceEmitter, AbsorbingSurface, Checkerboard
 from raysect.optical.library import *
-from raysect.optical.observer import TargettedCCDArray
+from raysect.optical.observer import TargetedCCDArray
 from raysect.optical.observer import RGBPipeline2D, BayerPipeline2D, PowerPipeline2D
 from raysect.optical.observer import RGBAdaptiveSampler2D
 from raysect.core.math import mm
@@ -184,9 +184,9 @@
 rgb = RGBPipeline2D(display_unsaturated_fraction=0.96, name="sRGB")
 sampler = RGBAdaptiveSampler2D(rgb, ratio=10, fraction=0.2, min_samples=1000, cutoff=0.01)
 
-# CCD targetting all rays at last lens element for speed
-ccd = TargettedCCDArray(
-    targetted_path_prob=1.0, targets=[l3],
+# CCD targeting all rays at last lens element for speed
+ccd = TargetedCCDArray(
+    targeted_path_prob=1.0, targets=[l3],
     width=mm(35), pixels=(512, 512),
     parent=image_plane, transform=translate(0, 0, 0)*rotate(0, 0, 180),
     pipelines=[rgb]

demos/observers/cornell_box_real_pinhole.py

@@ -5,7 +5,7 @@
 from raysect.optical import World, Node, translate, rotate, Point3D
 from raysect.optical.material import Lambert, UniformSurfaceEmitter, NullMaterial
 from raysect.optical.library import *
-from raysect.optical.observer import RGBPipeline2D, BayerPipeline2D, PowerPipeline2D, TargettedCCDArray
+from raysect.optical.observer import RGBPipeline2D, BayerPipeline2D, PowerPipeline2D, TargetedCCDArray
 from raysect.optical.observer import RGBAdaptiveSampler2D
 
 
@@ -144,7 +144,7 @@
 
 camera = Node(parent=world, transform=translate(0, 0, -3.3))
 pinhole = Sphere(0.0005, camera, transform=translate(0, 0, 0), material=NullMaterial())
-film = TargettedCCDArray(targetted_path_prob=1.0, targets=[pinhole], width=0.1, pixels=(512, 512), parent=camera,
+film = TargetedCCDArray(targeted_path_prob=1.0, targets=[pinhole], width=0.1, pixels=(512, 512), parent=camera,
                          transform=translate(0, 0, -0.1207), pipelines=pipelines)
 film.frame_sampler = sampler
 film.pixel_samples = 250

demos/observers/metal_with_lens.py

@@ -7,7 +7,7 @@
 from raysect.optical.library.metal import Gold, Silver, Copper, Titanium, Aluminium, Beryllium
 from raysect.optical.material import Lambert, UniformSurfaceEmitter, AbsorbingSurface, NullMaterial
 from raysect.optical.library import schott
-from raysect.optical.observer import RGBPipeline2D, BayerPipeline2D, TargettedCCDArray, CCDArray, RGBAdaptiveSampler2D
+from raysect.optical.observer import RGBPipeline2D, BayerPipeline2D, TargetedCCDArray, CCDArray, RGBAdaptiveSampler2D
 from raysect.optical.colour import ciexyz_x, ciexyz_y, ciexyz_z
 
 
@@ -49,7 +49,7 @@
 pipelines = [rgb, bayer]
 
 # ccd = CCDArray(parent=camera, pipelines=pipelines)
-ccd = TargettedCCDArray(targets=[aperture], parent=camera, pipelines=pipelines)
+ccd = TargetedCCDArray(targets=[aperture], parent=camera, pipelines=pipelines)
 ccd.frame_sampler = sampler
 ccd.pixels = (180*2, 120*2)  # (360, 240)
 ccd.pixel_samples = 250

demos/observers/targetted_pixel.py → demos/observers/targeted_pixel.py

@@ -3,7 +3,7 @@
 
 from raysect.primitive import Box
 from raysect.optical import World, translate, Point3D, Node
-from raysect.optical.observer import Pixel, TargettedPixel, PowerPipeline0D
+from raysect.optical.observer import Pixel, TargetedPixel, PowerPipeline0D
 from raysect.optical.material import UnitySurfaceEmitter
 
 
@@ -28,16 +28,16 @@
 basic_pipeline = PowerPipeline0D(name="Basic Pixel Observer")
 basic_pixel = Pixel(parent=world, pixel_samples=SAMPLES, pipelines=[basic_pipeline])
 
-# setup targetted pixel
-targetted_pipeline = PowerPipeline0D(name="Targeted Pixel Observer")
-targetted_pixel = TargettedPixel(parent=world, targets=targets, pixel_samples=SAMPLES, pipelines=[targetted_pipeline])
-targetted_pixel.targetted_path_prob = 1
+# setup targeted pixel
+targeted_pipeline = PowerPipeline0D(name="Targeted Pixel Observer")
+targeted_pixel = TargetedPixel(parent=world, targets=targets, pixel_samples=SAMPLES, pipelines=[targeted_pipeline])
+targeted_pixel.targeted_path_prob = 1
 
 # render
 ion()
 basic_pixel.observe()
 print()
-targetted_pixel.observe()
+targeted_pixel.observe()
 
 ioff()
 show()

demos/optics/etendue_of_pinhole.py

@@ -3,7 +3,7 @@
 import matplotlib.pyplot as plt
 
 from raysect.core import Point3D, Vector3D, rotate_basis, translate, Ray as CoreRay
-from raysect.core.math.sampler import DiskSampler3D, RectangleSampler3D, TargettedHemisphereSampler
+from raysect.core.math.sampler import DiskSampler3D, RectangleSampler3D, TargetedHemisphereSampler
 from raysect.optical import World
 from raysect.primitive import Box, Cylinder, Subtract
 from raysect.optical.material import AbsorbingSurface, NullMaterial
@@ -35,8 +35,8 @@ def raytraced_etendue(distance, detector_radius=0.001, ray_count=100000, batches
     sphere = target.bounding_sphere()
     spheres = [(sphere.centre.transform(detector_transform), sphere.radius, 1.0)]
 
-    # instance targetted pixel sampler
-    targetted_sampler = TargettedHemisphereSampler(spheres)
+    # instance targeted pixel sampler
+    targeted_sampler = TargetedHemisphereSampler(spheres)
 
     point_sampler = DiskSampler3D(detector_radius)
 
@@ -53,8 +53,8 @@ def raytraced_etendue(distance, detector_radius=0.001, ray_count=100000, batches
         passed = 0.0
         for origin in origins:
 
-            # obtain targetted vector sample
-            direction, pdf = targetted_sampler(origin, pdf=True)
+            # obtain targeted vector sample
+            direction, pdf = targeted_sampler(origin, pdf=True)
             path_weight = R_2_PI * direction.z/pdf
 
             origin = origin.transform(detector_transform)

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 (causes a large number of build warnings)
+cython_args = ['--annotate', '-X legacy_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)