docs: update pkgdown.yaml #9
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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 | |
| # By Stefanie Peschel: Adapted to install Bioconductor packages in advance | |
| name: pkgdown.yaml | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| permissions: read-all | |
| jobs: | |
| pkgdown: | |
| runs-on: ubuntu-latest | |
| # Only restrict concurrency for non-PR jobs | |
| concurrency: | |
| group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| permissions: | |
| contents: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::pkgdown, any::BiocManager, local::. | |
| needs: website | |
| - name: Install Bioconductor dependencies | |
| run: | | |
| Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' | |
| Rscript -e 'BiocManager::install(c("metagenomeSeq", "Biobase", "phyloseq"))' | |
| - name: Build site | |
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | |
| shell: Rscript {0} | |
| - name: Deploy to GitHub pages 🚀 | |
| if: github.event_name != 'pull_request' | |
| uses: JamesIves/[email protected] | |
| with: | |
| clean: false | |
| branch: gh-pages | |
| folder: docs |