build_deploy.yaml

name: pkgdown

on:
  push:
    branches:
    - main

jobs:
  build-and-deploy:
    runs-on: ubuntu-latest
    container: bioconductor/bioconductor_docker:RELEASE_3_19
    steps:
      ## Most of these steps are the same as the ones in
      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
      ## If they update their steps, we will also need to update ours.
      - uses: actions/checkout@v2

      - name: Install rcmdcheck
        run: |
          install.packages('rcmdcheck')
          install.packages("BiocManager")
          BiocManager::install("RforMassSpectrometry/MsBackendMetaboLights")
          BiocManager::install("RforMassSpectrometry/MsIO")
        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 "action@github.com"
          git config --global user.name "GitHub Action"
          git config --global --add safe.directory /__w/metabonaut/metabonaut
          Rscript -e "pkgdown::deploy_to_branch(new_process = 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.