model-run.yml

name : Sipnet Model Run
on :
  pull_request:

  # allow manual triggering
  workflow_dispatch:

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

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

    steps:
    - name: Free Disk Space (Ubuntu)
      uses: jlumbroso/free-disk-space@main
      with:
        # this might remove tools that are actually needed,
        # if set to "true" but frees about 6 GB
        tool-cache: false
        
        # all of these default to true, but feel free to set to
        # "false" if necessary for your workflow
        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

    - 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 -d postgres
        sleep 30
        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 -d sipnet executor

    - name: Check if containers are running # This will be updated soon to a loop
      run: |
        docker ps
        sleep 50

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