use safe negative binomial rng #1939
Workflow file for this run
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| name: "Synthetic validation check" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.head_ref }} | |
| cancel-in-progress: true | |
| on: | |
| pull_request: | |
| paths: | |
| # Directories with stan code and benchmarking code | |
| - "inst/stan/**" | |
| - "inst/dev/recover-synthetic/*" | |
| # Benchmarking config file | |
| - ".github/workflows/synthetic-validation.yaml" | |
| # Manual trigger | |
| - ".synthetic" | |
| workflow_dispatch: | |
| jobs: | |
| synthetic-validation: | |
| runs-on: macos-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Setup pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: NA | |
| install-pandoc: false | |
| extra-packages: | | |
| here | |
| scoringutils | |
| loo | |
| data.table | |
| rstan | |
| any::rmarkdown | |
| matrixStats | |
| local::. | |
| - name: Run synthetic validation | |
| run: | | |
| Rscript -e ' | |
| source("inst/dev/recover-synthetic/rt.R") | |
| source("inst/dev/recover-synthetic/eval_rt.R") | |
| ' | |
| - name: Upload validation figures | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: figures | |
| retention-days: 5 | |
| path: inst/dev/figs | |
| - name: Upload validation fits | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: fits | |
| retention-days: 5 | |
| path: synthetic.rds | |
| - name: Render synthetic recovery md | |
| run: | | |
| rmarkdown::render("inst/dev/synthetic_recovery.md") | |
| shell: Rscript {0} | |
| - name: Upload markdown | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: synthetic_recovery | |
| retention-days: 5 | |
| path: inst/dev/synthetic_recovery.html | |
| - name: Post the artifact | |
| uses: CDCgov/cfa-actions/post-artifact@main | |
| if: ${{ github.event_name == 'pull_request' }} | |
| with: | |
| artifact-name: synthetic_recovery | |
| gh-token: ${{ secrets.GITHUB_TOKEN }} | |
| message: 'Thank you for your contribution ${{ github.actor }} :rocket:! Your { artifact-name } markdown is ready for download :point_right: [here]({ artifact-url }) :point_left:!' | |