CovidHub-baseline #20
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| name: "CovidHub-baseline" | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "30 20 * * 3" | |
| jobs: | |
| generate-baseline-forecasts: | |
| if: ${{ github.repository_owner == 'CDCgov' }} | |
| runs-on: ubuntu-22.04 | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Get Token | |
| id: get_workflow_token | |
| uses: peter-murray/workflow-application-token-action@v4 | |
| with: | |
| application_id: ${{ vars.GH_APP_ID }} | |
| application_private_key: ${{ secrets.GH_APP_KEY }} | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| install-r: false | |
| use-public-rspm: true | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("readr", "dplyr", "tidyr", "purrr", "checkmate", "cli", "lubridate", "argparser", "remotes", "genlasso")) | |
| remotes::install_github("cmu-delphi/epiprocess") | |
| remotes::install_github("cmu-delphi/epipredict") | |
| shell: Rscript {0} | |
| - name: generate baseline | |
| run: | | |
| REF_DATE=$(Rscript -e "cat(strftime(lubridate::ceiling_date(lubridate::today(), 'week', week_start = 6, change_on_boundary = FALSE)))") | |
| Rscript src/get_baseline.R --reference-date "$REF_DATE" | |
| - name: Commit changes | |
| uses: EndBug/add-and-commit@v9 | |
| with: | |
| message: "Add baseline forecasts" | |
| default_author: github_actions | |
| push: true | |
| new_branch: add-baseline | |
| - name: Create pull request | |
| id: create_pr | |
| run: | | |
| gh pr create --base main --head add-baseline --title "Add baseline forecast" --body "This PR is generated automatically." | |
| env: | |
| GH_TOKEN: ${{ steps.get_workflow_token.outputs.token }} |