microimpute/.github/workflows/pr_code_changes.yaml at main · PolicyEngine/microimpute · GitHub

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name: Pull request
on:
  pull_request:
    branches: [ main ]

jobs:
  Lint:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.13"
      - name: Install uv
        uses: astral-sh/setup-uv@v5
      - name: Install relevant dependencies
        run: |
          uv pip install black isort linecheck --system
      - name: Check code formatting
        run: make check-format

  Check-MDN-Changes:
    runs-on: ubuntu-latest
    outputs:
      mdn_changed: ${{ steps.check.outputs.mdn_changed }}
    steps:
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0
      - name: Check for MDN-related file changes
        id: check
        run: |
          # Get list of changed files in this PR
          CHANGED_FILES=$(git diff --name-only origin/${{ github.base_ref }}...HEAD)
          echo "Changed files:"
          echo "$CHANGED_FILES"

          # Check if any MDN-related files were changed
          if echo "$CHANGED_FILES" | grep -qE "(mdn|MDN)"; then
            echo "mdn_changed=true" >> $GITHUB_OUTPUT
            echo "MDN-related files were changed"
          else
            echo "mdn_changed=false" >> $GITHUB_OUTPUT
            echo "No MDN-related files were changed"
          fi

  Test:
    needs: Check-MDN-Changes
    strategy:
      matrix:
        os: [ ubuntu-latest ]
        python-version: ["3.12", "3.13"]
      fail-fast: false
    runs-on: ${{ matrix.os }}
    steps:
      - name: Checkout repo
        uses: actions/checkout@v3
      - name: Install uv
        uses: astral-sh/setup-uv@v5
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install slim version
        run: |
          uv pip install -e "." --system
      - name: Install R and dependencies (Python 3.13 only)
        if: matrix.python-version == '3.13'
        run: |
          sudo apt-get update
          sudo apt-get install -y r-base r-base-dev libtirpc-dev
      - name: Install R packages (Python 3.13 only)
        if: matrix.python-version == '3.13'
        run: |
          sudo Rscript -e 'install.packages("StatMatch", repos="https://cloud.r-project.org")'
          sudo Rscript -e 'install.packages("clue", repos="https://cloud.r-project.org")'
      - name: Install full test dependencies without MDN (Python 3.13)
        if: matrix.python-version == '3.13' && needs.Check-MDN-Changes.outputs.mdn_changed != 'true'
        run: |
          uv pip install -e ".[dev,matching]" --system
      - name: Install full test dependencies with MDN (Python 3.13)
        if: matrix.python-version == '3.13' && needs.Check-MDN-Changes.outputs.mdn_changed == 'true'
        run: |
          uv pip install -e ".[dev,matching,mdn]" --system
      - name: Install minimal test dependencies (Python 3.12)
        if: matrix.python-version == '3.12'
        run: |
          uv pip install -e ".[dev]" --system
      - name: Run full tests with coverage (Python 3.13)
        if: matrix.python-version == '3.13'
        run: make test
      - name: Run smoke test only (Python 3.12)
        if: matrix.python-version == '3.12'
        run: |
          python -m pytest tests/test_smoke_qrf.py -v
          python -m pytest tests/test_basic.py -v
      - name: Run pipeline example
        if: matrix.python-version == '3.13'
        run: |
          python examples/pipeline.py
      - name: Upload microimputation results
        if: always() && matrix.python-version == '3.13'
        uses: actions/upload-artifact@v4
        with:
          name: microimputation-results-${{ github.sha }}
          path: microimputation-dashboard/public/microimputation_results.csv
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v3
        with:
          file: ./coverage.xml
          fail_ci_if_error: false
          verbose: true