create_ensemble.yaml

name: "CovidHub-ensemble"
on:
  workflow_dispatch:
  schedule:
    - cron: "00 15 * * 4"

jobs:
  generate-covidhub-ensemble:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
    - uses: actions/checkout@v4
    - uses: r-lib/actions/setup-r@v2
      with:
        install-r: false
        use-public-rspm: true
      
    - name: Install dependencies
      run: |        
        install.packages(c("hubEnsembles", "dplyr", "lubridate", "purrr", "yaml", "remotes"))
        remotes::install_github("hubverse-org/hubData")
      shell: Rscript {0}
  
    - name: generate ensemble
      run:  Rscript src/code/get_ensemble.r

    - name: Commit changes
      uses: EndBug/add-and-commit@v9
      with: 
        message: "Add CovidHub ensemble forecasts"
        default_author: github_actions
        push: true
        new_branch: add-ensemble

    - name: Create pull request
      id: create_pr
      run: |
        gh pr create --base main --head add-ensemble --title "Add ensemble forecast" --body "This PR is generated automatically to add ensemble forecast."
      env:
        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}