Release 1.6.0

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/build.yml

@@ -0,0 +1,115 @@
+name: Build wheels
+
+# We don't want to spend CI compute cycles on every commit, so restrict building
+# of wheels to published releases. This includes stable and beta/RC releases.
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  # Build a wheel for each Python version in a separate parallel job.
+  build_wheels:
+    name: Build wheels for ${{ matrix.python }} on ${{ matrix.target.name }}
+    runs-on: ${{ matrix.target.runner }}
+    strategy:
+      matrix:
+        python: [cp39, cp310, cp311, cp312, cp313, cp314]
+        target:
+          - name: Linux (x86-64)
+            runner: ubuntu-latest
+            platform: manylinux_x86_64
+            arch: x86_64
+
+          # TODO: add other platforms once Raysect provides wheels on them.
+          # - name: Linux (ARM)
+          #   runner: ubuntu-24.04-arm
+          #   platform: manylinux_aarch64
+          #   arch: aarch64
+
+          # - name: macOS (Apple Silicon)
+          #   runner: macos-latest
+          #   platform: macosx_arm64
+          #   arch: arm64
+
+          # - name: macOS (Intel)
+          #   runner: macos-15-intel
+          #   platform: macosx_x86_64
+          #   arch: x86_64
+
+          # - name: Windows
+          #   runner: windows-2022
+          #   platform: win_amd64
+          #   arch: AMD64
+
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+
+      - name: Determine manylinux image
+        if: ${{ contains(matrix.target.name, 'Linux') }}
+        # Build on manylinux2014 where possible for greatest compatibility,
+        # but need newer manylinux_2_28 for Python >=3.14.
+        # TODO: use cp314|cp315 if we provide Python 3.15 wheels before dropping
+        # manylinux2014 (RHEL7) support.
+        # TODO: remove this step entirely once we drop manylinux2014 support.
+        run: |
+          case ${{ matrix.python }} in
+          cp314)
+              echo "CIBW_MANYLINUX_X86_64_IMAGE=manylinux_2_28" >> "$GITHUB_ENV"
+              ;;
+          *)
+              echo "CIBW_MANYLINUX_X86_64_IMAGE=manylinux2014" >> "$GITHUB_ENV"
+              ;;
+          esac
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v4.2.0
+        env:
+          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.target.platform }}
+          CIBW_ARCH: ${{ matrix.target.arch }}
+          # Avoid trying to compile e.g. Pillow (raysect->matplotlib dependency) from
+          # source on older manylinux with newer Python. An old version is fine.
+          CIBW_ENVIRONMENT: 'PIP_PREFER_BINARY=1'
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist-wheel-${{ matrix.target.platform }}-${{ matrix.python }}
+          path: ./wheelhouse/*.whl
+
+  make_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist-sdist
+          path: dist/*.tar.gz
+
+  # Wheels are built in parallel jobs: gather the outputs into a single artifact
+  # for more convenient retrieval. At some stage we may consider automatic
+  # upload to PyPI from this job (since its `needs` entry ensures the SDist and
+  # wheels all built successfully).
+  gather_artifacts:
+    name: Gather SDist and wheel outputs into a single artifact
+    runs-on: ubuntu-latest
+    needs: [build_wheels, make_sdist]
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          pattern: dist-*
+          path: dist
+          merge-multiple: true
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: artifacts
+          path: dist/*

.github/workflows/ci.yml

@@ -3,16 +3,21 @@ name: CI
 on:
   push:
   pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
 
 jobs:
   tests:
+    if: ${{ github.event_name == 'push' || !github.event.pull_request.draft }}
     name: Run tests
     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 +28,9 @@ 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

.gitignore

@@ -21,4 +21,11 @@ build/
 .nfs*
 .coverage
 htmlcov*
-cherab.egg-info/
+cherab.egg-info/
+
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+
+# Ignore lock files until we start using them
+pixi.lock

CHANGELOG.md

@@ -1,6 +1,36 @@
 Project Changelog
 =================
 
+Release 1.6.0 (Sep 2026)
+-------------------
+
+API changes:
+* Rename `GaussianQuadrature` to `GaussianQuadrature1D` to conform to Cherab's naming convention. Original name kept as an alias for backwards compatibility until the next minor release. (#475)
+* Rename `TargettedPixelGroup` to `TargetedPixelGroup` for correct spelling. Still keep `TargettedPixelGroup` as an alias for backwards compatibility until the next major release. (#487)
+* Add emission model attribute access to line and lineshape . (#294)
+* The `generate_derivative_operators` function in `admt_utils` can now return sparse matrices rather than dense if requested. (#427)
+* Only 1 of the 1D-to-2D or 2D-to-1D voxel mappings is now required for `admt_utils.generate_derivative_operators`: if the other is missing it is computed automatically. (#427)
+* The `calculate_admt` function in `admt_utils` will return a sparse matrix if the input derivative operators are themselves sparse. (#427)
+
+Bug fixes:
+* Fix the import statement for `netcdf_file` in `calcam.py` for compatibility with the upcoming `scipy` v2.0.0. (#510)
+
+New:
+* Add an optional Pixi workspace for package builds and isolated development environments, with tasks for testing, documentation, formatting, and static analysis, and include the corresponding developer guide in the Sphinx documentation. (#489)
+* Add GaussianQuadrature2D integrator. (#475)
+* 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)
+* Add generic distribution function. (#481)
+* 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)
+* Make values in `cherab.core.utility.constants` accessible to Python. (#509)
+* Generomak now contains an example bolometer diagnostic. (#427)
+* The regularisation utilities in `admt_utils` are now in the HTML documention. (#427)
+* A new non-negative least squares inversion using sparse matrices, to complement the existing dense version. (#427)
+* A demo performing bolometry inversions using both isotropic and anisotropic regularisation. (#427)
+
 Release 1.5.0 (27 Aug 2024)
 -------------------
 
@@ -126,7 +156,7 @@ 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.
@@ -154,7 +184,7 @@ 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)

README.md

@@ -85,12 +85,19 @@ of code / physics algorithm quality standards.
 TMC Members
 -----------
 
+- Jack Lovell (Oak Ridge National Laboratory, USA)
+- Matej Tomes (Institute of Plasma Physics of the Czech Academy of Sciences, Czechia)
+- Koyo Munechika (ITER Organisation)
+- Jakub Svoboda (Institute of Plasma Physics of the Czech Academy of Sciences, Czechia)
+
+
+Former TMC Members
+-----------
+
 - Alys Brett (chairwoman, master account holder, responsible for delegation, UKAEA, UK)
 - Matt Carr (External consultant, diagnostic physics models)
-- Jack Lovell (Oak Ridge, USA)
 - Alex Meakins (External consultant, Architecture, software integrity)
 - Vlad Neverov (NRC Kurchatov Institute, Moscow)
-- Matej Tomes (Compass, IPP, Prague)
 
 
 Citing The Code

cherab/core/VERSION

@@ -1 +1 @@
-1.5.0
+1.6.0rc1

cherab/core/atomic/gaunt.pxd

@@ -21,7 +21,7 @@ from cherab.core.math cimport Function2D
 
 cdef class FreeFreeGauntFactor():
 
-    cpdef double evaluate(self, double z, double temperature, double wavelength) except? -1e999
+    cdef double evaluate(self, double z, double temperature, double wavelength) except? -1e999
 
 
 cdef class InterpolatedFreeFreeGauntFactor(FreeFreeGauntFactor):

cherab/core/atomic/gaunt.pyx

@@ -37,9 +37,9 @@ cdef class FreeFreeGauntFactor():
     The base class for temperature-averaged free-free Gaunt factors.
     """
 
-    cpdef double evaluate(self, double z, double temperature, double wavelength) except? -1e999:
+    cdef double evaluate(self, double z, double temperature, double wavelength) except? -1e999:
         """
-        Returns the temperature-averaged free-free Gaunt factor for the supplied parameters.
+        Return the temperature-averaged free-free Gaunt factor for the supplied parameters.
 
         :param double z: Species charge or effective plasma charge.
         :param double temperature: Electron temperature in eV.
@@ -51,7 +51,7 @@ cdef class FreeFreeGauntFactor():
 
     def __call__(self, double z, double temperature, double wavelength):
         """
-        Returns the temperature-averaged free-free Gaunt factor for the supplied parameters.
+        Return the temperature-averaged free-free Gaunt factor for the supplied parameters.
 
         :param double z: Species charge or effective plasma charge.
         :param double temperature: Electron temperature in eV.
@@ -106,9 +106,9 @@ cdef class InterpolatedFreeFreeGauntFactor(FreeFreeGauntFactor):
         self._gaunt_factor = Interpolator2DArray(np.log10(u), np.log10(gamma2), gaunt_factor, 'cubic', 'none', 0, 0)
 
     @cython.cdivision(True)
-    cpdef double evaluate(self, double z, double temperature, double wavelength) except? -1e999:
+    cdef double evaluate(self, double z, double temperature, double wavelength) except? -1e999:
         """
-        Returns the temperature-averaged free-free Gaunt factor for the supplied parameters.
+        Return the temperature-averaged free-free Gaunt factor for the supplied parameters.
 
         :param double z: Species charge or effective plasma charge.
         :param double temperature: Electron temperature in eV.

cherab/core/atomic/line.pyx

@@ -33,6 +33,10 @@ cdef class Line:
       specify the n-levels with integers (e.g. (3,2)). For all other ions the full spectroscopic
       configuration string should be specified for both states. It is up to the atomic data
       provider package to define the exact notation.
+
+    :ivar Element element: See parameter 'element'.
+    :ivar int charge: See parameter 'charge'.
+    :ivar tuple transition: See parameter 'transition'.
 
     .. code-block:: pycon
 

cherab/core/atomic/tests/test_line.py

@@ -0,0 +1,27 @@
+import unittest
+
+from cherab.core.atomic import Line, deuterium
+
+
+class TestLine(unittest.TestCase):
+
+    def test_initialisation(self):
+        line = Line(deuterium, 0, (3, 2))
+        self.assertEqual(line.element, deuterium)
+        self.assertEqual(line.charge, 0)
+        self.assertEqual(line.transition, (3, 2))
+
+        # test invalid charge
+        with self.assertRaises(ValueError):
+            Line(deuterium, 2, (3, 2))
+        with self.assertRaises(ValueError):
+            Line(deuterium, -1, (3, 2))
+
+    def test_properties(self):
+        element = deuterium
+        charge = 0
+        transition = (3, 2)
+        line = Line(element, charge, transition)
+        self.assertEqual(line.element, element)
+        self.assertEqual(line.charge, charge)
+        self.assertEqual(line.transition, transition)