GitHub Pages pkgdown site build #134
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples and adapted | |
| on: | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| - cron: '0 4 * * *' | |
| name: 'GitHub Pages pkgdown site build' | |
| jobs: | |
| build-deploy: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: bioconductor/bioconductor_docker:latest | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} #to push results to gh-pages branch! | |
| if: | | |
| (github.event_name == 'push' && github.ref == 'refs/heads/main') || | |
| (github.event_name == 'schedule' && github.ref == 'refs/heads/devel') | |
| steps: #Series of steps that is executed sequencially: https://github.com/r-lib/actions/ | |
| - name: Install system dependencies | |
| run: | | |
| apt-get update | |
| apt-get install -y libglpk40 git libxml2-dev libcurl4-openssl-dev libssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev cmake rsync | |
| echo "R_VERSION=`R --version | head -n 1 | awk '{print $3}' | cut -b 1-3`" >> $GITHUB_ENV | |
| echo "R_LIBS_USER=`Rscript -e 'cat(.libPaths()[1L])'`" >> $GITHUB_ENV | |
| - uses: actions/checkout@v4 # goes to gh-pages branch to work there | |
| - uses: r-lib/actions/setup-pandoc@v2 #installs pandoc | |
| - name: Set up R dependency cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ env.R_VERSION }} | |
| restore-keys: | | |
| ${{ runner.os }}-r-${{ env.R_VERSION }} | |
| - name: Install pkgdown & OmnipathR | |
| run: | | |
| Rscript -e 'install.packages("remotes")' | |
| Rscript -e 'install.packages("pkgdown")' | |
| Rscript -e "remotes::install_github('saezlab/OmnipathR@devel')" | |
| - name: Install EnhancedVolcano (not yet in Bioc 3.22) | |
| run: | | |
| Rscript -e 'remotes::install_github("kevinblighe/EnhancedVolcano")' | |
| # Set Bioconductor back to release and install other Bioconductor dependencies | |
| - name: Install other Bioconductor dependencies from release | |
| run: | | |
| Rscript -e 'remotes::install_deps(dependencies = TRUE)' | |
| # ComplexUpset should be installed after ggplot2 to ensure compatibility, especially on Linux/Ubuntu. | |
| - name: Install latest ggplot2 | |
| run: Rscript -e 'install.packages("ggplot2", type="source")' | |
| - name: Install ComplexUpset from source | |
| run: Rscript -e 'install.packages("ComplexUpset", type="source")' | |
| - name: Install MetaProViz from GitHub by remotes | |
| run: Rscript -e 'remotes::install_github("saezlab/MetaProViz", dependencies = TRUE)' #we install from GitHub as if we are a random user | |
| - name: Build pkgdown 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 |