Update GitHub actions (#861)

* updated versions
* documentation
* documentation
* Sphinx 8.1

Author: lfarv

.github/workflows/build-python-wheels.yml

@@ -22,8 +22,13 @@ jobs:
           # see: https://github.com/pypa/setuptools_scm/issues/480
           fetch-depth: 0
 
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.19.1
+        uses: pypa/cibuildwheel@v2.22
 
       - name: Upload wheels
         uses: actions/upload-artifact@v4

.github/workflows/docs.yml

@@ -0,0 +1,58 @@
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["master"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          # Necessary to fetch tags and allow setuptools_scm
+          # see: https://github.com/pypa/setuptools_scm/issues/480
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+          cache: pip
+
+      - name: Build and install at
+        run: python -m pip install ".[plot, doc]"
+
+      - name: Compile documentation
+        run: make html
+        working-directory: docs
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'docs/_build/html'
+          
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/documentation.yml

@@ -29,13 +29,13 @@ jobs:
     - name: Set up python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
         cache: pip
 
     - name: Set up MATLAB
       uses: matlab-actions/setup-matlab@v2
       with:
-        release: R2023a
+        release: R2024a
 
     - name: Atmexall
       uses: matlab-actions/run-command@v2

.github/workflows/matlab-tests.yml

@@ -6,7 +6,6 @@ name: Build Python extension and run tests
 
 on:
   push:
-  pull_request:
 
 jobs:
   build_and_run_tests:
@@ -16,7 +15,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
         os: [macos-latest, ubuntu-latest, windows-latest]
         exclude:
           - os: windows-latest

.github/workflows/python-tests.yml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.9"
+    python: "3.10"
     # You can also specify other tool versions:
     # nodejs: "16"
     # rust: "1.55"

.readthedocs.yaml

@@ -28,6 +28,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: Apache Software License",
     "Operating System :: MacOS",
@@ -52,7 +53,7 @@ ChangeLog = "https://github.com/atcollab/at/releases"
 mpi = ["mpi4py"]
 plot = ["matplotlib"]
 dev = ["pytest >= 2.9", "pytest-cov", "flake8"]
-doc = ["Sphinx ~= 7.2", "myst-parser", "myst-nb", "pydata-sphinx-theme ~= 0.14",
+doc = ["Sphinx ~= 8.1", "myst-parser", "myst-nb", "pydata-sphinx-theme",
     "sphinx_design", "sphinx-copybutton"]
 
 [tool.setuptools]
@@ -68,9 +69,10 @@ machine_data = ["*.m", "*.mat"]
 
 [tool.cibuildwheel]
 # Pypy does not have Scipy so we cannot support it.
-build = ["cp3{7,8,9,10,11,12}*"]
-# Skip 32-bit builds starting with python 3.12
-skip = ["cp312-win32", "cp312-*_i686"]
+build = ["cp3{7,8,9,10,11,12,13}*"]
+# build = ["cp312-*"]  # Only cp312 for test
+# Skip 32-bit builds
+skip = ["*-win32", "*_i686"]
 build-verbosity = "1"
 # "build" frontend fails on windows
 # build-frontend = "build"