rebuild.yaml

on:
  push

name: rebuild

jobs:
  rebuild:
    name: "Rebuilding dependency list."
    runs-on: ubuntu-latest
    container: bioconductor/bioconductor_docker:devel
    steps:
      - name: Get site library path
        run: |
          location=$(R --slave -e "cat(.libPaths()[1])")
          echo "R_PKG_DIR=${location}" >> $GITHUB_ENV

      - name: Cache packages
        uses: actions/cache@v3
        with:
          path: ${{ env.R_PKG_DIR }}
          key: installed-packages

      - name: Install packages
        run: |
          BiocManager::install('rebook')
        shell: Rscript {0}

      - name: Check out repo
        run: |
          git clone "https://oauth2:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}" ./book
          cd ./book && git checkout "${{ github.ref_name }}"

      - name: Update DESCRIPTION and Makefile
        working-directory: ./book
        run: |
          rebook::updateDependencies("inst/book", path='DESCRIPTION') 
          rebook::configureBook(prefix="SingleR")
        shell: Rscript {0}

      - name: Committing 
        working-directory: ./book
        run: | 
          git config --local user.email "action@github.com"
          git config --local user.name "GitHub Action"
          git add .
          git commit -m "Rebuilding sundries." || true
          git push