trigger-workflow-2 #24
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| name: pkgdown | |
| on: | |
| repository_dispatch: | |
| types: [trigger-workflow-2] | |
| jobs: | |
| build-and-deploy: | |
| runs-on: ubuntu-latest | |
| container: rformassspectrometry/metabonaut:latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Quarto | |
| run: | | |
| wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.5.57/quarto-1.5.57-linux-amd64.deb | |
| sudo dpkg -i quarto-1.5.57-linux-amd64.deb | |
| - name: Verify Quarto Installation | |
| run: quarto --version | |
| - name: Install rcmdcheck | |
| run: | | |
| install.packages('rcmdcheck') | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: | | |
| Rscript -e "rcmdcheck::rcmdcheck(args = c('--no-manual'), error_on = 'error', check_dir = 'check')" | |
| shell: bash {0} | |
| - name: Install deploy dependencies | |
| run: | | |
| apt-get update | |
| apt-get -y install rsync | |
| - name: Install pkgdown | |
| if: github.ref == 'refs/heads/main' | |
| run: | | |
| install.packages('pkgdown') | |
| shell: Rscript {0} | |
| - name: Install package | |
| if: github.ref == 'refs/heads/main' | |
| run: R CMD INSTALL . | |
| - name: Deploy package | |
| if: github.ref == 'refs/heads/main' | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "GitHub Action" | |
| git config --global --add safe.directory /__w/metabonaut/metabonaut | |
| Rscript -e "pkgdown::build_article('a-end-to-end-untargeted-metabolomics', new_process = FALSE, quiet = FALSE)" | |
| Rscript -e "pkgdown::deploy_to_branch(lazy = TRUE, new_process = FALSE, install = FALSE)" | |
| shell: bash {0} | |
| ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE) | |
| ## at least one locally before this will work. This creates the gh-pages | |
| ## branch (erasing anything you haven't version controlled!) and | |
| ## makes the git history recognizable by pkgdown. |