pipeline-run-check.yaml

name: Pipeline Run Check

on:
  pull_request:
  push:
    branches: [main]

concurrency:
  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
  cancel-in-progress: true

jobs:
  run-pipeline:
    strategy:
      matrix:
        os: [ubuntu-22.04, macos-latest]
    runs-on:  ${{matrix.os}}

    env:
      NHSN_API_KEY_ID: ${{ secrets.NHSN_API_KEY_ID }}
      NHSN_API_KEY_SECRET: ${{ secrets.NHSN_API_KEY_SECRET }}
    steps:
      - uses: actions/checkout@v4
      - name: Set up python
        uses: actions/setup-python@v5
        with:
          python-version: "3.12"
      - name: "Set up R"
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: "release"
          use-public-rspm: true
      - name: "Set up Quarto"
        uses: quarto-dev/quarto-actions/setup@v2
      - name: "Install poetry"
        run: pip install poetry
      - name: "Install pyrenew-hew"
        run: poetry install
      - name: "Set up dependencies for hewr"
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          working-directory: hewr
      - name: "Install extra pkgs"
        run: |
            pak::local_install("hewr", ask = FALSE)
            pak::pkg_install("cmu-delphi/epipredict@main", ask = FALSE)
            pak::pkg_install("cmu-delphi/epiprocess@main", ask = FALSE)
        shell: Rscript {0}
      - name: "Run pipeline"
        run: poetry run bash pipelines/tests/test_end_to_end.sh pipelines/tests