CovidHub-ensemble #4
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| name: "CovidHub-ensemble" | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "00 15 * * 4" | |
| jobs: | |
| generate-covidhub-ensemble: | |
| runs-on: ubuntu-latest | |
| 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: ${{ secrets.GH_APP_KEY }} | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| install-r: false | |
| use-public-rspm: true | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("hubEnsembles", "dplyr", "lubridate", "purrr", "yaml", "argparser", "remotes")) | |
| remotes::install_github("hubverse-org/hubData") | |
| shell: Rscript {0} | |
| - name: generate ensemble | |
| run: | | |
| TODAY=$(date +'%Y-%m-%d') | |
| REF_DATE=$(date -d "$TODAY + 2 days" +'%Y-%m-%d') | |
| Rscript src/code/get_ensemble.r --reference-date "$REF_DATE" | |
| - 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 a quantile median ensemble forecast." | |
| env: | |
| GH_TOKEN: ${{ steps.get_workflow_token.outputs.token }} |