generate_data.yaml

on:
#  schedule:
#    - cron: "0 0 * * *" # daily
#  push:
#    branches:
#      - master  # Set a branch to deploy
#      - develop # Note has logic around deployment
#      - fix-pipeline

name: build

jobs:
  production:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GH_OPENPHARMA }}
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python 3.9 # Specify the right version of python
        uses: actions/setup-python@v3
        with:
          python-version: "3.9"
          
      - name: Snakemake # python3 -m pip install --upgrade networkx pygraphvis
        run: |
          python3 -m pip install --upgrade pip
          python3 -m pip install pulp==2.7.0
          python3 -m pip install snakemake==7.32.4
          python3 -m pip install numpy==1.26.4
          python3 -m pip install pandas==1.4.2
          python3 -m pip install boto3==1.24.9
          python3 -m pip install requests==2.28
          python3 -m pip install PyYAML
          python3 -m pip install scikit-learn==1.1.1
          python3 -m pip install pyarrow


      - name: Install system libs
        run: |
          sudo apt-get install libcurl4-openssl-dev
          sudo apt-get install libharfbuzz-dev libfribidi-dev
      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.1.0'
      - uses: r-lib/actions/setup-renv@v2
      - uses: r-lib/actions/setup-pandoc@v2


# IF develop
      - name: Build dev
        if: ${{ github.ref == 'refs/heads/develop' }}
        env:
          OPENPHARMA_AWS_ACCESS_KEY_ID: ${{ secrets.OPENPHARMA_AWS_ACCESS_KEY_ID }}
          OPENPHARMA_AWS_SECRET_ACCESS_KEY: ${{ secrets.OPENPHARMA_AWS_SECRET_ACCESS_KEY }}
          OPENPHARMA_AWS_DEFAULT_REGION: ${{ secrets.OPENPHARMA_AWS_DEFAULT_REGION }}
          OPENPHARMA_PAT: ${{ secrets.OPENPHARMA_PAT }}
        run: |
          snakemake -j2  -F python_icon_readme
          
          
        
# IF main
      - name: Build prod 
        if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/fix-pipeline' }}
        env:
          OPENPHARMA_AWS_ACCESS_KEY_ID: ${{ secrets.OPENPHARMA_AWS_ACCESS_KEY_ID }}
          OPENPHARMA_AWS_SECRET_ACCESS_KEY: ${{ secrets.OPENPHARMA_AWS_SECRET_ACCESS_KEY }}
          OPENPHARMA_AWS_DEFAULT_REGION: ${{ secrets.OPENPHARMA_AWS_DEFAULT_REGION }}
          OPENPHARMA_PAT: ${{ secrets.OPENPHARMA_PAT }}
        run: |
          snakemake -j4 -F all
          mkdir build
          cp index.html ./build
          cp os-health.html ./build
          
      - name: Deploy site 🚀
        uses: JamesIves/github-pages-deploy-action@4.1.4
        if: ${{ github.ref == 'refs/heads/master' }}
        with:
          branch: gh-pages # The branch the action should deploy to.
          folder: build # The folder the action should deploy.