Prepare1.2

.github/workflows/ci_PR.yml

@@ -1,33 +1,41 @@
-name: DeerLab PR tests
-on:
-  pull_request:
-    branches:
-    - "**"
-
-jobs:
-  tests:
-    name: python test
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.11','3.12']
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: setup.py
-      - run: |
-          python -m pip install --upgrade pip
-          pip install wheel
-          pip install .
-
-      - name: Test with pytest
-        run: |
-          pytest
+name: DeerLab PR tests
+
+on:
+  pull_request:
+    branches:
+      - "**"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  tests:
+    name: python test
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.12', '3.13', '3.14']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: setup.py
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+
+      - name: Test with pytest
+        run: pytest

.github/workflows/ci_scheduled.yml

@@ -1,70 +1,37 @@
-name: Scheduled DeerLab tests
-on:
-  workflow_dispatch:
-  schedule:
-    # Run once a week on Monday at 6:30 AM
-    - cron:  '30 6 * * 1'
-
-jobs:
-  matrix_test:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.9, "3.10", "3.11", "3.12"]
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: setup.py
-      - run: |
-          python -m pip install --upgrade pip
-          pip install wheel
-          pip install .
-
-#       - uses: actions/cache@v2
-#         if: startsWith(runner.os, 'Windows')
-#         with:
-#           path: |
-#             ~\AppData\Local\pip\Cache
-#           key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
-#           restore-keys: |
-#             {{ runner.os }}-pip-
-
-#       - uses: actions/cache@v2
-#         if: startsWith(runner.os, 'macOS')
-#         with:
-#           path: |
-#             ~/Library/Caches/pip
-#           key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
-#           restore-keys: |
-#             {{ runner.os }}-pip-
-
-#       - uses: actions/cache@v2
-#         if: startsWith(runner.os, 'Linux')
-#         with:
-#           path: |
-#             ~/.cache/pip
-#           key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
-#           restore-keys: |
-#             {{ runner.os }}-pip-
-
-#       - name: Install dependencies
-#         if: steps.cache.outputs.cache-hit != 'false'
-#         run: |
-#           python -m pip install --upgrade pip
-#           pip install wheel
-#           pip install .
-
-#       - name: Windows MKL linking 
-#         if: matrix.os == 'windows-latest'
-#         run: |
-#           python upgrade_mkl.py
-
-      - name: Test with pytest
-        run: pytest
+name: Scheduled DeerLab tests
+
+on:
+  workflow_dispatch:
+  schedule:
+    # Run once a week on Monday at 6:30 AM UTC
+    - cron: '30 6 * * 1'
+
+permissions:
+  contents: read
+
+jobs:
+  matrix_test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: setup.py
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+
+      - name: Test with pytest
+        run: pytest

.github/workflows/deploy_ghpages.yml

@@ -1,44 +1,53 @@
 name: Docs Build & Deployment
 
-on: 
+on:
   workflow_dispatch:
   release:
     types: [published]
 
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
 jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+          cache: 'pip'
+          cache-dependency-path: setup.py
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install furo numpydoc sphinx-gallery sphinxcontrib-httpdomain sphinxcontrib-ghcontributors sphinx-issues sphinx-copybutton sphinx sphinx-design .
+          sudo apt-get update -y
+          sudo apt-get install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
+
+      - name: Configure Pages
+        uses: actions/configure-pages@v5
+
+      - name: Build with Sphinx
+        run: sphinx-build -E -b html ./docsrc/source ./docs
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./docs
 
   deploy:
+    needs: build
     runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
     steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-        cache: 'pip'
-        cache-dependency-path: setup.py
-    - name: Install dependencies
-      run: |
-           python -m pip install --upgrade pip
-           python -m pip install furo
-           python -m pip install numpydoc
-           python -m pip install sphinx-gallery
-           python -m pip install sphinxcontrib-httpdomain
-           python -m pip install sphinxcontrib-ghcontributors
-           python -m pip install sphinx-issues
-           python -m pip install sphinx-copybutton  
-           python -m pip install sphinx
-           python -m pip install sphinx-design
-           python -m pip install .
-           sudo apt-get update -y
-           sudo apt-get install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
-    - name: Build with Sphinx
-      run: |
-           sphinx-build -E -b html ./docsrc/source ./docs
-    - name: Deploy to GH-Pages
-      if: always()
-      uses: peaceiris/actions-gh-pages@v3
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./docs
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/docs_PR.yml

@@ -1,44 +1,41 @@
-name: Test documentation build PR
-
-on: 
-  pull_request:
-    branches:
-    - "**"
-    paths:
-    - 'docsrc/**'
-    - '.github/workflows/deploy_ghpages.yml'
-    - '.github/workflows/docs_PR.yml'
-    - '.github/workflows/examples_PR.yml'
-jobs:
-
-  docsbuild:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-        cache: 'pip'
-        cache-dependency-path: setup.py   
-    - name: Install dependencies
-      run: |
-           python -m pip install --upgrade pip
-           pip install furo
-           pip install numpydoc
-           pip install sphinx-gallery
-           pip install sphinxcontrib-httpdomain
-           pip install sphinxcontrib-ghcontributors
-           pip install sphinx-issues
-           pip install sphinx-copybutton  
-           pip install sphinx
-           pip install sphinx-design
-           python -m pip install .
-           sudo apt-get update -y
-           sudo apt-get install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
-
-
-    - name: Build with Sphinx
-      run: |
-           sphinx-build -E -b html ./docsrc/source ./docs -D  plot_gallery=0
+name: Test documentation build PR
+
+on:
+  pull_request:
+    branches:
+      - "**"
+    paths:
+      - 'docsrc/**'
+      - '.github/workflows/deploy_ghpages.yml'
+      - '.github/workflows/docs_PR.yml'
+      - '.github/workflows/examples_PR.yml'
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  docsbuild:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+          cache: 'pip'
+          cache-dependency-path: setup.py
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install furo numpydoc sphinx-gallery sphinxcontrib-httpdomain sphinxcontrib-ghcontributors sphinx-issues sphinx-copybutton sphinx sphinx-design .
+          sudo apt-get update -y
+          sudo apt-get install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
+
+      - name: Build with Sphinx
+        run: sphinx-build -E -b html ./docsrc/source ./docs -D plot_gallery=0