Modify priors on eta_sd and inf_feedback
#1073
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, prod] | |
| pull_request: | |
| branches: [main, prod] | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| name: pkgdown | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| version: | |
| - 'release' | |
| - 'devel' | |
| name: pkgdown site build (${{ matrix.version }}) | |
| runs-on: ubuntu-latest | |
| # Only restrict concurrency for non-PR jobs | |
| concurrency: | |
| group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}-${{ matrix.version }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| permissions: | |
| contents: write | |
| id-token: write | |
| pages: write | |
| steps: | |
| ########################################################################## | |
| # Identifying the latest and corresponding tag/sha to download | |
| ######################################################################### | |
| - name: Check the repo to download | |
| id: commit | |
| run: | | |
| gh api \ | |
| -H "Accept: application/vnd.github+json" \ | |
| -H "X-GitHub-Api-Version: 2022-11-28" \ | |
| /repos/CDCgov/ww-inference-model/releases/latest > \ | |
| latest_release | |
| echo -n "This job is running on tag/sha: " | |
| if [ "${{ matrix.version }}" = "release" ]; then | |
| echo $(jq -r '.tag_name' latest_release) | |
| echo "tag=$(jq -r '.tag_name' latest_release)" >> $GITHUB_OUTPUT | |
| else | |
| echo "tag=${{ github.sha }}" >> $GITHUB_OUTPUT | |
| echo ${{ github.sha }} | |
| fi | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ steps.commit.outputs.tag }} | |
| - name: Checkout the sha-associated repo | |
| if: ${{ matrix.version == 'release' }} | |
| uses: actions/checkout@v4 | |
| with: | |
| sparse-checkout: './_pkgdown.yml' | |
| path: pkgdown-${{ github.sha}} | |
| - name: Overwriting the _pkgdown.yml | |
| if: ${{ matrix.version == 'release' }} | |
| run: | | |
| cp pkgdown-${{ github.sha }}/_pkgdown.yml ./ | |
| rm -rf pkgdown-${{ github.sha }} | |
| - name: Checking if the release is cached | |
| if: ${{ matrix.version == 'release' }} | |
| id: cache-hit | |
| uses: actions/cache@v3 | |
| with: | |
| key: pkgdown_site-${{ matrix.version }}-${{ steps.commit.outputs.tag }}-${{ hashFiles( './_pkgdown.yml' ) }} | |
| path: './docs/' | |
| # These steps only happen if the cache is not hit | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| if: ${{ matrix.version != 'release' || steps.cache-hit.outputs.cache-hit != 'true' }} | |
| with: | |
| pandoc-version: "2.19.2" | |
| - uses: r-lib/actions/setup-r@v2 | |
| if: ${{ matrix.version != 'release' || steps.cache-hit.outputs.cache-hit != 'true' }} | |
| with: | |
| r-version: "release" | |
| use-public-rspm: true | |
| install-r: false | |
| extra-repositories: "https://mc-stan.org/r-packages/" | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| if: ${{ matrix.version != 'release' || steps.cache-hit.outputs.cache-hit != 'true' }} | |
| with: | |
| pak-version: rc | |
| extra-packages: any::pkgdown local::. | |
| needs: website | |
| - name: "Install cmdstan via cmdstanr" | |
| uses: epinowcast/actions/install-cmdstan@v1 | |
| if: ${{ matrix.version != 'release' || steps.cache-hit.outputs.cache-hit != 'true' }} | |
| with: | |
| cmdstan-version: "latest" | |
| - name: Build site | |
| if: ${{ matrix.version != 'release' || steps.cache-hit.outputs.cache-hit != 'true' }} | |
| run: | | |
| # Changing the URL if it is a development build | |
| if [ "${{ matrix.version }}" = "devel" ]; then | |
| # Forcing the development mode | |
| export PKGDOWN_DEV_MODE="devel" | |
| else | |
| # Setting the url | |
| sed -i'' 's|url: https://cdcgov.github.io/ww-inference-model/|url: https://cdcgov.github.io/ww-inference-model/release/|' _pkgdown.yml | |
| # Changing the navbar | |
| sed -i'' 's|href: https://cdcgov.github.io/ww-inference-model/release|href: https://cdcgov.github.io/ww-inference-model/|' _pkgdown.yml | |
| sed -i'' 's|text: (switch to release)|text: (switch to dev)|' _pkgdown.yml | |
| sed -i'' 's|icon: fa-toggle-on|icon: fa-toggle-off|' _pkgdown.yml | |
| # Forcing the release mode | |
| export PKGDOWN_DEV_MODE="release" | |
| fi | |
| Rscript --vanilla -e \ | |
| "pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)" | |
| if [ "${{ matrix.version }}" = "devel" ]; then | |
| mv docs docs-tmp | |
| mkdir docs | |
| mv docs-tmp/dev/* docs | |
| fi | |
| - name: Upload artifact for GH pages deployment | |
| id: upload-artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| path: "./docs/" | |
| name: pkgdown-site-${{ matrix.version }} | |
| combine: | |
| outputs: | |
| page_artifact_id: ${{ steps.upload-artifact.outputs.artifact_id }} | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download dev artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: pkgdown-site-devel | |
| path: ./docs/ | |
| - name: Download release artifacts | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: pkgdown-site-release | |
| path: ./docs/release | |
| - name: Upload pages artifact | |
| id: upload-artifact | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: ./docs/ | |
| name: github-pages | |
| retention-days: 7 | |
| deploy: | |
| # check builds on PRs but only deploy when main changes | |
| if: ${{ github.event_name != 'pull_request' }} | |
| needs: combine | |
| runs-on: ubuntu-latest | |
| permissions: | |
| pages: write | |
| id-token: write | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| steps: | |
| - name: Deploy to GitHub pages | |
| uses: actions/deploy-pages@v4 | |
| post-page-artifact: | |
| runs-on: ubuntu-latest | |
| if: ${{ github.event_name == 'pull_request' }} | |
| # This job depends on the `build` job | |
| needs: combine | |
| # Required permissions | |
| permissions: | |
| contents: read | |
| pull-requests: write | |
| steps: | |
| # Post the artifact pulling the id from the `readme` step. | |
| # The msg will refer to the arfitact as 'README file'. | |
| - name: Post the artifact | |
| uses: CDCgov/cfa-actions/[email protected] | |
| with: | |
| artifact-name: github-pages | |
| gh-token: ${{ secrets.GITHUB_TOKEN }} |