python-test.yml

name: Reproducibility CI

on:
  push:
    branches: [ main, develop ]
  pull_request:
    branches: [ main, develop ]
  release:
    types: [published]

jobs:
  check-artifacts:
    name: Check Critical Artifacts
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    
    - name: Verify critical files presence
      run: |
        MISSING=0
        for file in \
          Data_Package_FAIR2/Compound_Properties_Database.csv \
          Data_Package_FAIR2/API_Calculations_Full.xlsx \
          Data_Package_FAIR2/Python_Code_API_Monte_Carlo.py \
          Data_Package_FAIR2/R_Code_Figures_S2.R; do
          if [ ! -f "$file" ]; then
            echo "❌ MISSING: $file"
            MISSING=$((MISSING + 1))
          else
            echo "✅ OK: $file"
          fi
        done
        if [ $MISSING -gt 0 ]; then
          echo "::error::$MISSING critical files missing"
          exit 1
        fi

  test-reproducibility:
    name: Test 1-Click Reproducibility
    runs-on: ubuntu-latest
    needs: check-artifacts
    
    steps:
    - uses: actions/checkout@v4
    
    - name: Set up Python 3.11
      uses: actions/setup-python@v4
      with:
        python-version: '3.11'
    
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install -r Data_Package_FAIR2/requirements.txt
        pip install pytest pytest-cov
    
    - name: Validate data integrity
      run: |
        cd Data_Package_FAIR2
        python data_validation.py
    
    - name: Quick Check API values
      timeout-minutes: 2
      run: |
        cd Data_Package_FAIR2
        python quickcheck_api.py
    
    - name: Run full API calculation (< 60s)
      timeout-minutes: 2
      run: |
        cd Data_Package_FAIR2
        mkdir -p output
        python Python_Code_API_Monte_Carlo.py --all
    
    - name: Run unit tests
      run: |
        cd Data_Package_FAIR2
        python -m pytest test_api_calculations.py -v --tb=short --cov=. --cov-report=term
    
    - name: Upload test outputs
      uses: actions/upload-artifact@v3
      if: always()
      with:
        name: test-outputs
        path: |
          Data_Package_FAIR2/output/
          Data_Package_FAIR2/*.png
        retention-days: 30