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| name: CI/CD | |
| on: | |
| pull_request: | |
| branches: [devel] | |
| push: | |
| branches: [devel] | |
| env: | |
| cache-version: v1 | |
| jobs: | |
| # Job to build and check PRs | |
| build: | |
| 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 | |
| # Install system dependencies | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev | |
| # Set up caching for R packages | |
| - name: Cache R packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.R | |
| key: ${{ env.cache-version }}-${{ runner.os }}-R | |
| restore-keys: | | |
| ${{ env.cache-version }}-${{ runner.os }}-R- | |
| # Add R environment setup step | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| # Install R dependencies | |
| - name: Install R dependencies | |
| run: Rscript -e 'install.packages(c("evaluate", "rmarkdown", "knitr", "readr", "tidyr", "reactable", "maps", "plotly", "ggplot2", "tidygeocoder", "countrycode"))' | |
| # Run Quarto render to check for PRs | |
| - name: Render Quarto Project | |
| run: quarto render | |
| # Job to deploy only when merging to devel | |
| deploy: | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/devel' | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| # Install system dependencies for deployment | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev | |
| # Add R environment setup step | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| # Install R dependencies | |
| - name: Install R dependencies | |
| run: Rscript -e 'install.packages(c("evaluate", "rmarkdown", "knitr", "readr", "tidyr", "reactable", "maps", "plotly", "ggplot2", "tidygeocoder", "countrycode"))' | |
| # Add the CNAME file for the custom domain | |
| - name: Add CNAME for custom domain | |
| run: echo "training.bioconductor.org" > CNAME | |
| # Deploy to GitHub Pages | |
| - name: Publish to GitHub Pages (and render) | |
| uses: quarto-dev/quarto-actions/publish@v2 | |
| with: | |
| target: gh-pages | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |