Add Physalia microbiome workshop #158
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| 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 job for pull requests | |
| 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 | |
| - 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') }} | |
| restore-keys: | | |
| ${{ env.cache-version }}-${{ runner.os }}- | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Install R dependencies | |
| run: Rscript -e 'install.packages("remotes"); remotes::install_deps(dependencies = TRUE)' | |
| - name: Render Quarto Project | |
| run: quarto render | |
| # Deploy job for pushes to devel and scheduled builds | |
| deploy: | |
| if: github.ref == 'refs/heads/devel' && (github.event_name == 'push' || github.event_name == 'schedule') | |
| 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 | |
| - 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') }} | |
| restore-keys: | | |
| ${{ env.cache-version }}-${{ runner.os }}- | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Install R dependencies | |
| run: Rscript -e 'install.packages("remotes"); remotes::install_deps(dependencies = TRUE)' | |
| - name: Add CNAME for custom domain | |
| run: echo "training.bioconductor.org" > CNAME | |
| - name: Publish to GitHub Pages (and render) | |
| uses: quarto-dev/quarto-actions/publish@v2 | |
| with: | |
| target: gh-pages | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |