Issue 275: Prototype VARIMA (Analysis - do not merge) #220
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| name: Pipeline Run Check | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| jobs: | |
| run-pipeline: | |
| runs-on: ubuntu-latest | |
| 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: "Install poetry" | |
| run: pip install poetry | |
| - name: "Install pyrenew-hew" | |
| run: poetry install | |
| - name: "Set up Quarto" | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| - 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 |