join-data.yml

name: Join Data

# Runs join_data.ipynb to combine application data with events and generate
# Pharmac applications.xlsx with Outcome__c and Summary__c fields extracted
# from application JSON files.

on:
  workflow_dispatch: # Allow manual triggering
  schedule:
    # Run weekly on Mondays at 01:00 UTC
    - cron: '0 1 * * 1'

concurrency:
  group: join-data
  cancel-in-progress: false

jobs:
  join-data:
    name: Run join_data.ipynb
    runs-on: ubuntu-latest
    # Normal runs take ~5 min (occasionally ~100); without a timeout a hung
    # run holds the runner for the full 6h job limit.
    timeout-minutes: 120

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          ref: ${{ github.ref }}

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.x'
          cache: 'pip'

      - name: Install Python dependencies
        run: pip install -r requirements.txt

      - name: Install Jupyter
        run: pip install jupyter nbconvert

      - name: Run join_data.ipynb
        run: jupyter nbconvert --to notebook --execute join_data.ipynb --inplace
        env:
          PYTHONUNBUFFERED: '1'

      - name: Render notebook as HTML
        run: jupyter nbconvert --to html join_data.ipynb --output index.html

      - name: Commit updated files
        run: |
          git config user.email "github-actions[bot]@users.noreply.github.com"
          git config user.name "github-actions[bot]"
          git add "Pharmac applications.xlsx" index.html join_data.ipynb
          git diff --staged --quiet && echo "No changes to commit" && exit 0

          # Count rows in the Excel file
          ROWS=$(python3 -c "import pandas as pd; df = pd.read_excel('Pharmac applications.xlsx'); print(len(df))")

          git commit -m "Update Pharmac applications.xlsx: ${ROWS} applications [skip ci]"
          git pull --rebase
          git push