Update resources-table.tsv - add scRNA-seq #186
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| # NOTE: We render the site in GitHub Actions because some pages (e.g., instructors.qmd) | |
| # require R execution to pull dynamic data from CSV files. Netlify's build environment | |
| # does not include R, so we cannot rely on the Quarto Netlify plugin for rendering. | |
| # Instead, CI installs R + Quarto, renders the site, and deploys the pre-rendered HTML | |
| # to Netlify for both PR previews and production. | |
| name: CI/CD | |
| on: | |
| pull_request: | |
| branches: [devel] | |
| push: | |
| branches: [devel] | |
| schedule: | |
| - cron: '0 1 * * 0' # every Sunday at 01:00 UTC | |
| env: | |
| cache-version: v1 | |
| jobs: | |
| # Build & preview deploy for PRs | |
| build-preview: | |
| if: github.event_name == 'pull_request' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev | |
| - name: Cache R packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.R | |
| key: ${{ env.cache-version }}-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION', '**/renv.lock') }} | |
| restore-keys: | | |
| ${{ env.cache-version }}-${{ runner.os }}- | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Install R dependencies | |
| run: | | |
| Rscript -e 'install.packages("remotes", repos = "https://cloud.r-project.org")' | |
| Rscript -e 'remotes::install_deps(dependencies = TRUE)' | |
| - name: Render Quarto Project | |
| run: quarto render | |
| - name: Deploy Preview to Netlify | |
| run: | | |
| npm install -g netlify-cli | |
| netlify deploy \ | |
| --auth "$NETLIFY_AUTH_TOKEN" \ | |
| --site "$NETLIFY_SITE_ID" \ | |
| --dir docs \ | |
| --message "PR #${{ github.event.number }} - ${{ github.sha }}" \ | |
| --alias "pr-${{ github.event.number }}" | |
| env: | |
| NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }} | |
| NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }} | |
| # Production deploy on push/schedule to devel | |
| deploy-prod: | |
| if: github.ref == 'refs/heads/devel' && (github.event_name == 'push' || github.event_name == 'schedule') | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev | |
| - name: Cache R packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.R | |
| key: ${{ env.cache-version }}-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION', '**/renv.lock') }} | |
| restore-keys: | | |
| ${{ env.cache-version }}-${{ runner.os }}- | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Install R dependencies | |
| run: | | |
| Rscript -e 'install.packages("remotes", repos = "https://cloud.r-project.org")' | |
| Rscript -e 'remotes::install_deps(dependencies = TRUE)' | |
| - name: Render Quarto Project | |
| run: quarto render | |
| # If you still want GitHub Pages in addition to Netlify, keep this step. | |
| # Otherwise you can remove it and use Netlify as your sole host. | |
| - name: Add CNAME for GitHub Pages custom domain | |
| run: echo "training.bioconductor.org" > docs/CNAME | |
| - name: Publish to GitHub Pages (optional) | |
| uses: quarto-dev/quarto-actions/publish@v2 | |
| with: | |
| target: gh-pages | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Deploy Production to Netlify | |
| run: | | |
| npm install -g netlify-cli | |
| netlify deploy \ | |
| --auth "$NETLIFY_AUTH_TOKEN" \ | |
| --site "$NETLIFY_SITE_ID" \ | |
| --dir docs \ | |
| --prod \ | |
| --message "devel @ ${{ github.sha }}" | |
| env: | |
| NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }} | |
| NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }} |