Add workflow_dispatch trigger for manual deploys #32
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| name: Build and Deploy | |
| on: | |
| push: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| permissions: | |
| contents: read | |
| pages: write | |
| id-token: write | |
| env: | |
| FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true | |
| jobs: | |
| build-and-deploy: | |
| runs-on: ubuntu-latest | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.4' | |
| use-public-rspm: true | |
| - name: Install system dependencies for R packages | |
| run: sudo apt-get install -y libarchive-dev libcurl4-openssl-dev libssl-dev libxml2-dev | |
| - name: Cache R packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: r-pkgs-v2-${{ runner.os }}-r4.4-${{ hashFiles('shiny_apps/gwat_portfolio/app.R') }} | |
| restore-keys: r-pkgs-v2-${{ runner.os }}-r4.4- | |
| - name: Install R packages | |
| run: | | |
| Rscript -e " | |
| options(repos = c( | |
| RSPM = 'https://packagemanager.posit.co/cran/__linux__/noble/latest', | |
| CRAN = 'https://cloud.r-project.org' | |
| )) | |
| install.packages(c('shinylive', 'shiny', 'plotly', 'dplyr', 'stringr'), dependencies = TRUE) | |
| stopifnot(requireNamespace('shinylive', quietly = TRUE)) | |
| cat('shinylive', as.character(packageVersion('shinylive')), 'ready\n') | |
| " | |
| - name: Export Shiny app with shinylive | |
| run: | | |
| mkdir -p ai_studio/public/shiny/gwat_rnaseq | |
| Rscript -e "shinylive::export('shiny_apps/gwat_portfolio', 'ai_studio/public/shiny/gwat_rnaseq')" | |
| echo "=== shinylive output ===" | |
| ls -lh ai_studio/public/shiny/gwat_rnaseq/ | |
| - name: Setup Node | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: '20' | |
| - name: Install dependencies | |
| working-directory: ai_studio | |
| run: npm install | |
| - name: Stage public assets | |
| run: | | |
| mkdir -p ai_studio/public/assets/images | |
| cp assets/images/headshot.jpg ai_studio/public/assets/images/headshot.jpg | |
| cp Dearborn_CV_March_2026.pdf ai_studio/public/Dearborn_CV_March_2026.pdf | |
| - name: Stage LNP analysis assets | |
| run: | | |
| mkdir -p ai_studio/public/assets/images/lnp | |
| cp assets/images/lnp/*.png ai_studio/public/assets/images/lnp/ | |
| mkdir -p ai_studio/public/notebooks | |
| cp assets/notebooks/lnp_10x.html ai_studio/public/notebooks/lnp_10x.html | |
| - name: Stage TM01 analysis assets | |
| run: | | |
| mkdir -p ai_studio/public/assets/images/tm01 | |
| cp assets/images/tm01/*.png ai_studio/public/assets/images/tm01/ | |
| cp assets/notebooks/tm01.html ai_studio/public/notebooks/tm01.html | |
| - name: Stage SRA_to_BigWigs assets | |
| run: | | |
| mkdir -p ai_studio/public/assets/images/sra_to_bigwigs | |
| cp assets/images/sra_to_bigwigs/*.png ai_studio/public/assets/images/sra_to_bigwigs/ | |
| cp assets/notebooks/sra_to_bigwigs.html ai_studio/public/notebooks/sra_to_bigwigs.html | |
| - name: Build | |
| working-directory: ai_studio | |
| run: npm run build | |
| - name: Setup Pages | |
| uses: actions/configure-pages@v5 | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: ai_studio/dist | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 |