docker-stack-sipnet.yml

name : Docker Stack Model Test
on :
  pull_request:

  # allow manual triggering
  workflow_dispatch:

  schedule:
    # run Thursday 4:30 AM UTC
  - cron: '30 4 * * 4'    
jobs:
  sipnet:
    runs-on: ubuntu-latest

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
    - name: Free Disk Space (Ubuntu)
      uses: jlumbroso/free-disk-space@main
      with:
        tool-cache: false
        android: true
        dotnet: true
        haskell: true
        large-packages: true
        docker-images: false
        swap-storage: true

    - name: Checkout source code
      uses: actions/checkout@v4

    - name: Set up Docker Compose
      run: |
          sudo apt-get update
          sudo apt-get -y install docker-compose
          
    - name: Add Volumes to Executor
      run: |
          cp docker-compose.dev.yml docker-compose.override.yml
          sed -i'' '/R_library/d' docker-compose.override.yml

    - name: Build Containers
      run: |
        cp docker/env.example .env
        echo "COMPOSE_PROJECT_NAME=pecan" >> .env
        echo "PECAN_VERSION=develop" >> .env
        echo "UID=$(id -u)" >> .env
        echo "GID=$(id -g)" >> .env
        
        docker compose up --wait -d postgres
        docker run --rm --network pecan_pecan pecan/db:ci
        docker run --rm --network pecan_pecan --volume pecan_pecan:/data --env FQDN=docker pecan/data:develop
        docker image rm pecan/db:ci pecan/data:develop
    
    - name: Run required containers
      run: |
        docker compose up --wait -d sipnet executor monitor

    - name: List running containers
      run: |
        sleep 50
        docker ps

    # - name: Add models
    #   run: |
    #     docker compose cp scripts/add.util.sh postgres:/tmp/add.util.sh
    #     docker compose cp scripts/add.models.sh postgres:/tmp/add.models.sh
    #     docker compose exec postgres /tmp/add.models.sh

    - name: Run SIPNET
      run: |
        docker compose exec --workdir /pecan/tests executor R CMD ../web/workflow.R --settings docker-ghaction.sipnet.xml