Mule2025.10.1 release

.github/pull_request_template.md

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+# PR Summary
+
+Code Reviewer: <!-- CR id, filled by SSD -->
+
+<!-- To be completed by the developer -->
+
+<!-- Provide a brief description of the changes in this PR, including any notes
+     useful for reviewers -->
+
+<!-- List any linked PRs here
+- linked MetOffice/<REPO-NAME>#<pr-number>
+-->
+
+<!-- List any blocking PRs or issues to be closed here
+- is blocked-by #pr-number
+- blocks #pr-number
+- closes #issue-number
+- fixes #issue-number
+- is related to #issue-number
+-->
+
+## Code Quality Checklist
+
+(_Some checks are automatically carried out via the CI pipeline_)
+
+- [ ] I have performed a self-review of my own code
+- [ ] My code follows the project's style guidelines
+- [ ] Comments have been included that aid undertanding and enhance the
+      readability of the code
+- [ ] My changes generate no new warnings
+
+## Testing
+
+- [ ] I have tested this change locally, using the rose-stem suite
+- [ ] If any tests fail (rose-stem or CI) the reason is understood and
+      acceptable (eg. kgo changes)
+- [ ] I have added tests to cover new functionality as appropriate (eg. system
+      tests, unit tests, etc.)
+
+<!-- Describe other testing performed (if applicable) -->
+
+### trac.log
+
+<!-- Paste your trac.log from testing output here -->
+
+## Security Considerations
+
+- [ ] This change does not introduce security vulnerabilities
+- [ ] I have reviewed the code for potential security issues
+- [ ] Sensitive data is properly handled (if applicable)
+- [ ] Authentication and authorisation are properly implemented (if applicable)
+
+## Performance Impact
+
+- [ ] Performance of the code has been considered and, if applicable, suitable
+      performance measurements have been conducted
+
+## Contributor License Agreement (CLA)
+
+- [ ] **Required** - I confirm that I have read and agree to the project's
+      [Contributor License Agreement](todo-enter-link-to-cla)
+
+## AI Assistance and Attribution
+
+- [ ] Some of the content of this change has been produced with the assistance
+      of _Generative AI tool name_ (e.g., Met Office Github Copilot Enterprise,
+      Github Copilot Personal, ChatGPT GPT-4, etc) and I have followed the
+      [Simulation Systems AI policy](todo-enter-link-to-policy-page) (including
+      attribution labels)
+
+## Documentation
+
+- [ ] Where appropriate I have updated documentation related to this change and
+      confirmed that it builds correctly
+
+# Code Review
+
+<!-- To be completed by the Code Reviewer -->
+
+- [ ] All dependencies have been resolved
+- [ ] Related Issues are properly linked and addressed
+- [ ] CLA compliance is confirmed
+- [ ] Code quality standards are met
+- [ ] Tests are adequate and passing
+- [ ] Documentation is complete and accurate
+- [ ] Security considerations have been addressed
+- [ ] Performance impact is acceptable

.github/workflows/checks.yaml

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+---
+name: Quality
+
+on:  # yamllint disable-line rule:truthy
+  pull_request:
+    types: [opened, synchronize, reopened]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+permissions: read-all
+
+jobs:
+
+  mule-checks:
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install dependencies
+        run: uv sync
+      - name: Python Lint
+        run: uv run ruff check .
+      - name: Python Format Check
+        if: always()
+        run: uv run ruff format --check --diff -s --respect-gitignore .
+      - name: Shell Check
+        if: always()
+        run: |
+          find . -type f \( -name "*.*sh" -o ! -name "*.*" \) \
+            -not -path "*.git/*" -not -path "*.venv/*" -print0 \
+            | xargs -0 file | grep "shell script" | cut -d: -f1 \
+            | xargs -r uv run shellcheck -S warning \
+            && echo "All checks passed!"
+      - name: CPPLINT
+        # See: CPPLINT.cfg
+        if: always()
+        run: |
+          uv run cpplint --recursive --extensions=c,h \
+            --exclude=.git --exclude=.venv .
+      - name: Minimize uv cache
+        run: uv cache prune --ci

.github/workflows/ci.yaml

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+---
+name: CI
+on:  # yamllint disable-line rule:truthy
+  push:
+    branches:
+      - main
+      - 'releases/**'
+  pull_request:
+    types: [opened, synchronize, reopened]
+  workflow_dispatch:
+
+permissions: read-all
+
+jobs:
+  build-test-mule:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 5
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ['3.12', '3.13']
+        numpy-version: ['1.26.4', '2.2.6']
+        exclude:
+            - python-version: '3.13'
+              numpy-version: '1.26.4'
+
+    steps:
+      - name: Checkout Mule
+        uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+      - name: Install Python Dependencies ${{ matrix.numpy-version }}
+        run: |
+          pip install setuptools
+          pip install six
+          pip install numpy==${{ matrix.numpy-version }}
+      - name: Build python-${{ matrix.python-version }}_numpy-${{ matrix.numpy-version }}
+        run: |
+          ./admin/install_mule.sh ./_build/lib ./_build/bin
+      - name: Test python-${{ matrix.python-version }}_numpy-${{ matrix.numpy-version }}
+        run: |
+          cd _build/lib
+          for name in ./*; do
+            python -m unittest discover -v ${name##*/}.tests
+          done

.github/workflows/docs.yaml

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+---
+name: Docs
+
+on:  # yamllint disable-line rule:truthy
+  push:
+    branches:
+      - main
+      - 'releases/**'
+  pull_request:
+    types: [opened, synchronize, reopened]
+    paths:
+      - 'mule/docs/**'
+      - '.github/workflows/docs.yaml'
+  workflow_dispatch:
+
+permissions: read-all
+
+jobs:
+
+  build-docs:
+    runs-on: ubuntu-latest
+    timeout-minutes: 3
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install dependencies
+        run: uv sync && uv pip install ./mule ./um_utils
+      - name: Build mule docs
+        run: uv run make clean html --directory ./mule/docs
+        working-directory: ${{ github.workspace }}
+      - name: Build um_utils docs
+        run: uv run make clean html --directory ./um_utils/docs
+        working-directory: ${{ github.workspace }}
+    #   - id: permissions
+    #     name: Set permissions
+    #     run: |
+    #       chmod -c -R +rX "./doc/_build/html/"
+      - name: Upload artifacts
+        uses: actions/upload-pages-artifact@v4
+        with:
+          name: github-pages
+          path: ./mule/docs/build/html
+      - name: Minimize uv cache
+        if: always()
+        run: uv cache prune --ci
+
+  # Deploy job
+  deploy:
+    if: github.ref == 'refs/heads/main' && github.event_name != 'pull_request'
+    # Add a dependency to the build job
+    needs: build-docs
+    permissions:
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+    # Deploy to the github-pages environment
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    # Specify runner + deployment step
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4