validate-submission.yaml

name: "Hub Submission Validation (R)"

on:
  workflow_dispatch:
  pull_request:
    branches: main

jobs:
  validate-submission:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - uses: actions/checkout@v6

      - uses: r-lib/actions/setup-r@v2
        with:
          install-r: true
          use-public-rspm: true
          extra-repositories: 'https://hubverse-org.r-universe.dev'

      - name: "Update R"
        run: |
          sudo apt-get update

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          pak-version: "devel"
          packages: |
            any::hubValidations
            any::sessioninfo

      - name: "Get model output changes"
        id: get_changed_files_in_model_output
        uses: step-security/changed-files@v47
        with:
          path: model-output
          dir_names: "true"

      - name: "check output dirs modified"
        run: |
          if [ "${{ steps.get_changed_files_in_model_output.outputs.all_modified_files }}" == "CovidHub-ensemble" ]; then
            { echo "model=ensemble" | tee -a $GITHUB_ENV; }
          else
            { echo "model=other" | tee -a $GITHUB_ENV; }
          fi

      - name: "Run validations"
        env:
          PR_NUMBER: ${{ github.event.number }}
        run: |
          library("hubValidations")
          v <- hubValidations::validate_pr(
              gh_repo = Sys.getenv("GITHUB_REPOSITORY"),
              pr_number = Sys.getenv("PR_NUMBER"),
              skip_submit_window_check = Sys.getenv("model") == "ensemble"
          )
          hubValidations::check_for_errors(v, verbose = TRUE)
        shell: Rscript {0}