GenerateEnsemble #12
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| name: GenerateEnsemble | |
| on: | |
| workflow_dispatch: | |
| workflow_run: | |
| workflows: [GenerateBaseline] | |
| types: | |
| - completed | |
| jobs: | |
| ensemble: | |
| if: ${{ github.event.workflow_run.conclusion == 'success' && github.repository_owner == 'european-modelling-hubs' }} | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| # checkout repo | |
| - uses: actions/checkout@v3 | |
| with: | |
| path: './repo/' | |
| # Checkout the python tools repo | |
| # ------------------------------------------- | |
| - name: checkout python tools repo | |
| uses: actions/checkout@v3 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| repository: 'european-modelling-hubs/hub-tools' | |
| ref: 'main' | |
| path: './tools/' | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| install-r: false | |
| use-public-rspm: true | |
| - name: Installing dependencies | |
| run: | | |
| install.packages("remotes") | |
| remotes::install_github("Infectious-Disease-Modeling-Hubs/hubData") | |
| remotes::install_github("Infectious-Disease-Modeling-Hubs/hubEnsembles") | |
| install.packages("dplyr") | |
| install.packages("jsonlite") | |
| install.packages("optparse") | |
| install.packages("purrr") | |
| shell: Rscript {0} | |
| - name: Generate Ensemble | |
| id: generate_ensemble | |
| run: | | |
| # call R script from tools | |
| Rscript ./tools/R-code/generate-ensemble.R --hub_path "./repo" --agg_fun "median" --model_id "hubEnsemble" --team_id "respicast" | |
| - name: Commit changes | |
| uses: EndBug/add-and-commit@v7 | |
| with: | |
| cwd: './repo' | |
| message: "Update ensemble data" | |
| default_author: github_actions | |
| push: true | |
| # Save changes to artifact for later persisting | |
| - name: Save changes to artifact | |
| env: | |
| changed_files: ${{ steps.generate_ensemble.outputs.ensemble_file }} | |
| run: | | |
| echo "{ \"pr-changes\" : \"$changed_files\" }" > pr_changes.json | |
| - name: Upload changes | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: pr_changes | |
| path: ./pr_changes.json |