Comprehensive CI infrastructure modernization and enhancements

.github/ISSUE_TEMPLATE/ci_issue.yml

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+name: CI/Build Issue
+description: Report a problem with continuous integration or build processes
+title: "[CI]: "
+labels: ["ci", "infrastructure"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for reporting a CI/build issue. Please provide as much detail as possible.
+
+  - type: dropdown
+    id: workflow
+    attributes:
+      label: Which workflow is affected?
+      options:
+        - CI (ci.yml)
+        - Python PyTest (python-pytest.yml)
+        - Code Formatting (python-yapf.yml)
+        - Examples (python-example.yml)
+        - Tutorials (python-tutorials.yml)
+        - Code Coverage (coverage.yml)
+        - PR Comment (pr-comment.yml)
+        - Other
+    validations:
+      required: true
+
+  - type: input
+    id: workflow-run
+    attributes:
+      label: Workflow Run URL
+      description: Link to the failed workflow run
+      placeholder: https://github.com/SECQUOIA/PySA/actions/runs/...
+    validations:
+      required: false
+
+  - type: dropdown
+    id: python-version
+    attributes:
+      label: Python Version
+      options:
+        - "3.8"
+        - "3.9"
+        - "3.10"
+        - "3.11"
+        - "3.12"
+        - All versions
+        - Not applicable
+    validations:
+      required: false
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: What happened? What did you expect to happen?
+      placeholder: Describe the CI issue...
+    validations:
+      required: true
+
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant Log Output
+      description: Please copy and paste any relevant log output from the workflow
+      render: shell
+    validations:
+      required: false
+
+  - type: textarea
+    id: steps
+    attributes:
+      label: Steps to Reproduce
+      description: How can we reproduce this issue locally?
+      placeholder: |
+        1. Run command '...'
+        2. See error '...'
+    validations:
+      required: false
+
+  - type: checkboxes
+    id: checklist
+    attributes:
+      label: Checklist
+      options:
+        - label: I have checked the CI documentation (docs/CI_INFRASTRUCTURE.md)
+        - label: I have verified this issue exists on the latest commit
+        - label: I have checked existing issues for duplicates

.github/PULL_REQUEST_TEMPLATE.md

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+## Description
+<!-- Provide a brief description of the changes in this PR -->
+
+## Type of Change
+<!-- Mark the relevant option with an "x" -->
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Documentation update
+- [ ] CI/Infrastructure update
+- [ ] Performance improvement
+- [ ] Code refactoring
+
+## Related Issues
+<!-- Link to related issues using #issue_number -->
+Closes #
+
+## Changes Made
+<!-- Describe the changes in detail -->
+- 
+- 
+- 
+
+## Testing
+<!-- Describe how you tested these changes -->
+- [ ] Unit tests pass locally (`pytest tests/`)
+- [ ] Code follows style guidelines (`yapf --style=google -d -r .`)
+- [ ] Added tests for new functionality
+- [ ] All examples run successfully
+- [ ] Tutorials execute without errors (if applicable)
+- [ ] Documentation updated (if needed)
+
+## Checklist
+<!-- Mark completed items with an "x" -->
+- [ ] My code follows the project's style guidelines
+- [ ] I have performed a self-review of my code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have made corresponding changes to the documentation
+- [ ] My changes generate no new warnings
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes
+- [ ] Any dependent changes have been merged and published
+
+## Additional Notes
+<!-- Add any additional notes, context, or screenshots -->

.github/dependabot.yml

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+version: 2
+updates:
+  # GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    open-pull-requests-limit: 5
+    labels:
+      - "dependencies"
+      - "github-actions"
+    commit-message:
+      prefix: "ci"
+      include: "scope"
+
+  # Python dependencies
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    open-pull-requests-limit: 10
+    labels:
+      - "dependencies"
+      - "python"
+    commit-message:
+      prefix: "deps"
+      include: "scope"
+    ignore:
+      # Ignore major version updates for stable dependencies
+      - dependency-name: "numpy"
+        update-types: ["version-update:semver-major"]
+      - dependency-name: "scipy"
+        update-types: ["version-update:semver-major"]

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [ main, ci-testing ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Code Formatting Check
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+        cache: 'pip'
+
+    - name: Install yapf
+      run: |
+        python -m pip install --upgrade pip
+        pip install yapf==0.32.0
+        pip install toml
+
+    - name: Check format with YAPF
+      run: |
+        yapf --style=google -d -r .
+
+  test:
+    name: Test Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    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'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e . pytest pytest-cov pytest-xdist
+
+    - name: Run tests
+      run: |
+        pytest -rA -n auto --cov=pysa --cov-report=xml --cov-report=term tests/
+
+    - name: Upload coverage to artifact
+      if: matrix.python-version == '3.11'
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage-report
+        path: coverage.xml
+        retention-days: 7
+
+  coverage:
+    name: Upload Coverage
+    needs: test
+    runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request' || github.ref == 'refs/heads/main'
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Download coverage report
+      uses: actions/download-artifact@v4
+      with:
+        name: coverage-report
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        fail_ci_if_error: false
+      continue-on-error: true
+
+  examples:
+    name: Examples Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    needs: test
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.11"]
+
+    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'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e . termplotlib
+
+    - name: Run examples
+      run: |
+        python examples/example_ising.py
+        python examples/example_qubo.py
+        python examples/example_ais.py
+
+  tutorials:
+    name: Tutorials Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    needs: test
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e . papermill matplotlib plotly jupyter hyperopt torch torchvision
+
+    - name: Run tutorials
+      run: |
+        cd tutorials/
+        papermill example_ising.ipynb output_example_ising.ipynb || true
+        papermill hpo_demo.ipynb output_hpo_demo.ipynb || true
+        papermill ising_tutorial.ipynb output_ising_tutorial.ipynb || true
+        papermill RBM_tutorial.ipynb output_RBM_tutorial.ipynb || true
+
+    - name: Upload tutorial outputs
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: tutorial-outputs-py${{ matrix.python-version }}
+        path: tutorials/output_*.ipynb
+        retention-days: 7
+      continue-on-error: true
+
+  all-checks-passed:
+    name: All Checks Passed
+    needs: [lint, test, examples, tutorials]
+    runs-on: ubuntu-latest
+    if: always()
+    steps:
+    - name: Check if all jobs passed
+      run: |
+        if [[ "${{ needs.lint.result }}" != "success" ]] || \
+           [[ "${{ needs.test.result }}" != "success" ]] || \
+           [[ "${{ needs.examples.result }}" != "success" ]] || \
+           [[ "${{ needs.tutorials.result }}" != "success" ]]; then
+          echo "One or more jobs failed"
+          exit 1
+        fi
+        echo "All checks passed successfully!"