feat: Migrate to raysect v0.9

.github/workflows/ci.yml

@@ -7,12 +7,11 @@ on:
 jobs:
   tests:
     name: Run tests
-    runs-on: ubuntu-22.04  # Needed for Python 3.7 compatibility
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        numpy-version: ["oldest-supported-numpy", "'numpy<2'"]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
     steps:
     - name: Checkout code
       uses: actions/checkout@v2
@@ -23,9 +22,9 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Python dependencies
-      run: python -m pip install --prefer-binary cython~=3.0 ${{ matrix.numpy-version }} scipy matplotlib "pyopencl[pocl]>=2022.2.4"
+      run: python -m pip install --prefer-binary setuptools cython~=3.1 numpy>=2 scipy matplotlib "pyopencl[pocl]>=2022.2.4"
     - name: Install Raysect from pypi
-      run: pip install raysect==0.8.1.*
+      run: pip install raysect==0.9.*
     - name: Build cherab
       run: dev/build.sh
     - name: Run tests

CHANGELOG.md

@@ -8,6 +8,8 @@ New:
 * Add Function6D framework. (#478)
 * Add e_field attribute to Plasma object for electric field vector. (#465)
 * Add Integrator2D base class for integration of two-dimensional functions. (#472)
+* Support Raysect 0.9. (#486)
+* Test against Python 3.9, 3.10, 3.11, 3.12, 3.13 and latest released Numpy. Drop Python 3.7, 3.8 and older Numpy from tests. (#486)
 
 Release 1.5.0 (27 Aug 2024)
 -------------------
@@ -134,7 +136,7 @@ API changes:
 
 New:
 * Merged cherab-openadas package into the core cherab package to simplify installation.
-* Beam object uses a cone primitive instead of a cylinder for the bounding volume of divergent beams. 
+* Beam object uses a cone primitive instead of a cylinder for the bounding volume of divergent beams.
 * Added Clamp functions.
 * Added ThermalCXRate.
 * Added optimised ray transfer grid calculation tools.
@@ -162,7 +164,7 @@ New:
 
 Bug fixes:
 * Improved handling on non c-order arrays in various methods.
-* Numerous minor bug fixes (see commit history) 
+* Numerous minor bug fixes (see commit history)
 
 
 Release 1.0.1 (1 Oct 2018)

cherab/core/VERSION

@@ -1 +1 @@
-1.6.0.dev1
+1.6.0.dev2

cherab/core/model/laser/profile.pyx

@@ -738,7 +738,7 @@ def generate_segmented_cylinder(radius, length):
     Generates a segmented cylindrical laser geometry
 
     Approximates a long cylinder with a cylindrical segments to optimize
-    targetted and importance sampling. The height of a cylinder segments is roughly
+    targeted and importance sampling. The height of a cylinder segments is roughly
     2 * cylinder radius.
 
     :return: List of cylinders

cherab/tools/observers/bolometry.py

@@ -18,16 +18,17 @@
 # under the Licence.
 
 from enum import Enum
+from warnings import warn
 import functools
 import numpy as np
 
 from raysect.core import Node, translate, rotate_basis, Point3D, Vector3D, Ray as CoreRay, Primitive, World
-from raysect.core.math.sampler import TargettedHemisphereSampler, RectangleSampler3D
+from raysect.core.math.sampler import TargetedHemisphereSampler, RectangleSampler3D
 from raysect.primitive import Box, Cylinder, Subtract, Union
 from raysect.optical.observer import PowerPipeline0D, RadiancePipeline0D, \
-    SpectralPowerPipeline0D, SpectralRadiancePipeline0D, SightLine, TargettedPixel
+    SpectralPowerPipeline0D, SpectralRadiancePipeline0D, SightLine, TargetedPixel
 from raysect.optical.observer import PowerPipeline2D, RadiancePipeline2D, \
-    SpectralPowerPipeline2D, SpectralRadiancePipeline2D, TargettedCCDArray
+    SpectralPowerPipeline2D, SpectralRadiancePipeline2D, TargetedCCDArray
 from raysect.optical.material.material import NullMaterial
 from raysect.optical.material import AbsorbingSurface
 
@@ -213,7 +214,7 @@ class BolometerSlit(Node):
        larger than the slit dx and dy, which can cause partial occlusion of
        nearby primitives. It also relies on no rays being launched with directions
        outside the solid angle of the aperture's bounding sphere: depending on the
-       foil-slit distance and slit size, and also the foil's targetted_path_prob,
+       foil-slit distance and slit size, and also the foil's targeted_path_prob,
        this may not be guaranteed. Supplying a proper mesh geometry for the camera
        is recommended instead of using a CSG aperture.
 
@@ -351,7 +352,7 @@ def curvature_radius(self):
         return self._curvature_radius
 
 
-class BolometerFoil(TargettedPixel):
+class BolometerFoil(TargetedPixel):
     """
     A rectangular foil bolometer detector.
 
@@ -447,7 +448,7 @@ def __init__(self, detector_id, centre_point, basis_x, dx, basis_y, dy, slit,
         translation = translate(centre_point.x, centre_point.y, centre_point.z)
         rotation = rotate_basis(normal_vec, basis_y)
 
-        super().__init__([slit.target], targetted_path_prob=1.0,
+        super().__init__([slit.target], targeted_path_prob=1.0,
                          pixel_samples=1000, x_width=dx, y_width=dy, spectral_bins=1, quiet=True,
                          parent=parent, transform=translation * rotation, name=detector_id)
 
@@ -516,6 +517,24 @@ def accumulate(self, value):
             # Discard any samples from previous accumulate behaviour
             pipeline.value.clear()
 
+    @property
+    def targetted_path_prob(self):
+        warn(
+            "The 'targetted_path_prob' property is deprecated, use 'targeted_path_prob' instead.",
+            DeprecationWarning,
+            stacklevel=2
+        )
+        return self._targeted_path_prob
+
+    @targetted_path_prob.setter
+    def targetted_path_prob(self, value):
+        warn(
+            "The 'targetted_path_prob' property is deprecated, use 'targeted_path_prob' instead.",
+            DeprecationWarning,
+            stacklevel=2
+        )
+        self.targeted_path_prob = value
+
     def as_sightline(self):
         """
         Constructs a SightLine observer for this bolometer.
@@ -661,8 +680,8 @@ def calculate_etendue(self, ray_count=10000, batches=10, max_distance=1e999):
         # generate bounding sphere and convert to local coordinate system
         sphere = target.bounding_sphere()
         spheres = [(sphere.centre.transform(self.to_local()), sphere.radius, 1.0)]
-        # instance targetted pixel sampler to sample directions
-        targetted_sampler = TargettedHemisphereSampler(spheres)
+        # instance targeted pixel sampler to sample directions
+        targeted_sampler = TargetedHemisphereSampler(spheres)
         # instance rectangle pixel sampler to sample origins
         point_sampler = RectangleSampler3D(width=self.x_width, height=self.y_width)
 
@@ -671,8 +690,8 @@ def etendue_single_run(_):
             origins = point_sampler(samples=ray_count)
             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
                 # Transform to world space
                 origin = origin.transform(detector_transform)
@@ -701,7 +720,7 @@ def etendue_single_run(_):
         return etendue, etendue_error
 
 
-class BolometerIRVB(TargettedCCDArray):
+class BolometerIRVB(TargetedCCDArray):
     """
     A rectangular infra red video bolometer (IRVB).
 
@@ -784,7 +803,7 @@ def __init__(self, name, width, pixels, slit, transform, parent=None,
         self._accumulate = None  # Will be set after pipeline is created.
 
         super().__init__([slit.target], pixels=pixels, width=width,
-                         targetted_path_prob=0.99, parent=parent, pipelines=[],
+                         targeted_path_prob=0.99, parent=parent, pipelines=[],
                          transform=transform, name=name)
         self.pixel_samples = 1000
         self.spectral_bins = 1
@@ -896,6 +915,24 @@ def accumulate(self, value):
             if pipeline.frame is not None:
                 pipeline.frame.clear()
 
+    @property
+    def targetted_path_prob(self):
+        warn(
+            "The 'targetted_path_prob' property is deprecated, use 'targeted_path_prob' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return self._targeted_path_prob
+
+    @targetted_path_prob.setter
+    def targetted_path_prob(self, value):
+        warn(
+            "The 'targetted_path_prob' property is deprecated, use 'targeted_path_prob' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        self.targeted_path_prob = value
+
     def as_sightlines(self):
         """
         Constructs a SightLine observer for each pixel in this bolometer.

cherab/tools/observers/group/targettedpixel.py

@@ -17,14 +17,14 @@
 # under the Licence.
 
 from numpy import ndarray
-from raysect.optical.observer import TargettedPixel
+from raysect.optical.observer import TargetedPixel
 
 from .base import Observer0DGroup
 
 
 class TargettedPixelGroup(Observer0DGroup):
     """
-    A group of targetted pixel under a single scene-graph node.
+    A group of targeted pixel under a single scene-graph node.
 
     A scene-graph object regrouping a series of 'TargettedPixel'
     observers as a scene-graph parent. Allows combined observation and display
@@ -35,7 +35,8 @@ class TargettedPixelGroup(Observer0DGroup):
     :ivar list targets: Targets for preferential sampling
     :ivar list targetted_path_prob: Probability of ray being casted at the target
     """
-    _OBSERVER_TYPE = TargettedPixel
+
+    _OBSERVER_TYPE = TargetedPixel
 
     @property
     def x_width(self):
@@ -76,7 +77,7 @@ def targets(self):
         """
         List of target lists used by pixels for preferential sampling
 
-        :param list value: List of primitives to be set to each pixel or 
+        :param list value: List of primitives to be set to each pixel or
                            list of lists containing targets specific for each pixel
                            in this case the number of lists must match number of pixels
 
@@ -100,17 +101,16 @@ def targets(self, value):
 
     @property
     def targetted_path_prob(self):
-        return [pixel.targetted_path_prob for pixel in self._observers]
-    
+        return [pixel.targeted_path_prob for pixel in self._observers]
+
     @targetted_path_prob.setter
     def targetted_path_prob(self, value):
         if isinstance(value, (list, tuple)):
             if len(value) == len(self._observers):
                 for pixel, v in zip(self._observers, value):
-                    pixel.targetted_path_prob = v
+                    pixel.targeted_path_prob = v
             else:
-                raise ValueError("The length of 'value' ({}) "
-                                 "mismatches the number of pixels ({}).".format(len(value), len(self._observers)))
+                raise ValueError("The length of 'value' ({}) mismatches the number of pixels ({}).".format(len(value), len(self._observers)))
         else:
             for pixel in self._observers:
-                pixel.targetted_path_prob = value
+                pixel.targeted_path_prob = value

cherab/tools/tests/test_observer_groups.py

@@ -1,7 +1,7 @@
 import unittest
 
 from raysect.core.workflow import RenderEngine
-from raysect.optical.observer import Observer0D, SightLine, FibreOptic, Pixel, TargettedPixel, PowerPipeline0D, SpectralPowerPipeline0D
+from raysect.optical.observer import Observer0D, SightLine, FibreOptic, Pixel, TargetedPixel, PowerPipeline0D, SpectralPowerPipeline0D
 from raysect.primitive import Sphere
 
 from cherab.tools.observers.group.base import Observer0DGroup
@@ -26,7 +26,7 @@ def test_get_item(self):
         idx = slice(1, 3, 1)
         for observer, input_observer in zip(group[idx], self.observers[idx]):
             self.assertIs(observer, input_observer)
-        
+
         for i, name in enumerate(names):
             self.assertIs(group[name], self.observers[i])
 
@@ -83,7 +83,7 @@ def test_assignments(self):
         with self.assertRaises(ValueError):
             group.pipelines = [ppln_0]
 
-        # render_engine        
+        # render_engine
         engine = RenderEngine()
         group.render_engine = engine
         for group_engine in group.render_engine:
@@ -102,7 +102,7 @@ def test_assignments(self):
         with self.assertRaises(ValueError):
             group.render_engine = [RenderEngine() for _ in range(len(group) - 1)]
 
-        # wavelengths        
+        # wavelengths
         wvl = 500
         group.min_wavelength = wvl - 100
         group.max_wavelength = wvl + 100
@@ -139,7 +139,7 @@ def test_assignments(self):
         with self.assertRaises(ValueError):
             group.spectral_bins = [1000] * (len(group) + 1)
 
-        # quiet        
+        # quiet
         quiet = [True] * len(group)
         group.quiet = quiet
         self.assertListEqual(group.quiet, quiet)
@@ -152,7 +152,7 @@ def test_assignments(self):
         with self.assertRaises(ValueError):
             group.quiet = [False] * (len(group) + 1)
 
-        # rays        
+        # rays
         probs = [0.2 + i*0.1 for i in range(len(group))]
         max_depths = [5 + i for i in range(len(group))]
         min_depths = [2 + i for i in range(len(group))]
@@ -196,7 +196,7 @@ def test_assignments(self):
             group.ray_importance_sampling = [False] * (len(group) + 1)
         with self.assertRaises(ValueError):
             group.ray_important_path_weight = [0.7] * (len(group) + 1)
-        
+
         # samples
         pixel_samples = [2000 + i*500 for i in range(len(group))]
         per_task = [5000 + i*100 for i in range(len(group))]
@@ -352,7 +352,7 @@ class TargettedPixelGroupTestCase(PixelGroupTestCase):
     _GROUP_CLASS = TargettedPixelGroup
 
     def setUp(self):
-        self.observers = [TargettedPixel(targets=[Sphere()], pipelines=[PowerPipeline0D()]) for _ in range(self._NUM)]
+        self.observers = [TargetedPixel(targets=[Sphere()], pipelines=[PowerPipeline0D()]) for _ in range(self._NUM)]
 
     def test_targets(self):
         group = self._GROUP_CLASS(observers=self.observers)
@@ -381,8 +381,8 @@ def test_targets(self):
 
         prob = 0.8
         group.targetted_path_prob = prob
-        for group_targetted_path_prob in group.targetted_path_prob:
-            self.assertEqual(group_targetted_path_prob, prob)
+        for group_targeted_path_prob in group.targetted_path_prob:
+            self.assertEqual(group_targeted_path_prob, prob)
 
         with self.assertRaises(ValueError):
             group.targetted_path_prob = [0.7] * (len(group) + 1)

cherab/tools/tests/test_voxels.py

@@ -280,8 +280,7 @@ def test_rectangle_area(self):
         for rectangle in RECTANGULAR_VOXEL_COORDS:
             coords = np.asarray(rectangle)
             voxel = AxisymmetricVoxel(coords)
-            dx = coords[:, 0].ptp()
-            dy = coords[:, 1].ptp()
+            dx, dy = np.ptp(coords, axis=0)
             expected_area = dx * dy
             self.assertEqual(voxel.cross_sectional_area, expected_area)
 

pyproject.toml

@@ -1,3 +1,3 @@
 [build-system]
-requires = ["setuptools>=62.3", "oldest-supported-numpy", "cython~=3.0", "raysect==0.8.1.*"]
+requires = ["setuptools>=62.3", "numpy", "cython~=3.1", "raysect==0.9.1.*"]
 build-backend="setuptools.build_meta"

requirements.txt

@@ -1,5 +1,5 @@
-cython~=3.0
-numpy>=1.14,<2.0
+cython~=3.1
+numpy>=2.0
 scipy
 matplotlib
-raysect==0.8.1.*
+raysect==0.9.1.*

setup.py

@@ -117,14 +117,14 @@
     long_description=long_description,
     long_description_content_type="text/markdown",
     install_requires=[
-        "numpy>=1.14,<2.0",
+        "numpy>=2.0",
         "scipy",
         "matplotlib",
-        "raysect==0.8.1.*",
+        "raysect==0.9.1.*",
     ],
     extras_require={
         # Running ./dev/build_docs.sh runs setup.py, which requires cython.
-        "docs": ["cython~=3.0", "sphinx", "sphinx-rtd-theme", "sphinx-tabs"],
+        "docs": ["cython~=3.1", "sphinx", "sphinx-rtd-theme", "sphinx-tabs"],
     },
     packages=find_packages(include=["cherab*"]),
     package_data={"": [