example-workflow.yml

on:
  workflow_dispatch:
  
name: Workflow that tests the actions

env:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

jobs:
  pkg-at-root:
    name: Root Pkg - Bioc ${{ matrix.bioc-version }} (${{ matrix.os }})
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04, windows-2019, windows-2022, macos-12, macos-13, macos-14]
        ## Test using both Bioconductor devel and release
        bioc-version: [devel, release]

    runs-on: ${{ matrix.os }}
    
    steps:
    
      - uses: actions/checkout@v4
          
      - name: Setup R and Bioconductor
        uses: grimbough/bioc-actions/setup-bioc@v1
        with:
          bioc-version: ${{ matrix.bioc-version }}
          bioc-mirror: https://bioconductor.posit.co/
          use-public-rspm: false
          Ncpus: 1
          
      - name: Install pandoc
        uses: r-lib/actions/setup-pandoc@v2
          
      - name: Install dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 1
          
      - name: Build, Install, Check
        id: build-install-check
        uses: grimbough/bioc-actions/build-install-check@v1
        with:
          package-directory: '.'
      
      ## Turn off the checks that we know will fail
      ## Cause the workflow to error if any new errors appear
      - name: Run BiocCheck with arguments
        uses: grimbough/bioc-actions/run-BiocCheck@v1
        with:
          package-directory: '.'
          arguments: '--no-check-bioc-views --no-check-vignettes --no-check-bioc-help'
          error-on: 'error'
          
      ## upload the Rcheck folder regardless of success of failure
      - name: Upload output
        uses: actions/upload-artifact@v4
        if: always()
        with:
          name: ${{ matrix.os }}-bioc-${{ matrix.bioc-version}}-Rcheck
          path: |
            ${{ steps.build-install-check.outputs.check-dir }}

      ## upload source and binary packages
      - name: Upload check output
        uses: actions/upload-artifact@v4
        with:
          name: ${{ matrix.os }}-bioc-${{ matrix.bioc-version}}-pkgs
          path: |
            ${{ steps.build-install-check.outputs.source-tarball }}
            ${{ steps.build-install-check.outputs.package-binary }}

  pkg-in-subfolder:
    name: Subfolder Pkg - Bioc ${{ matrix.bioc-version }} (${{ matrix.os }}) 
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-22.04]
        bioc-version: [release]
        
    runs-on: ${{ matrix.os }}
    
    steps:
    
      - uses: actions/checkout@v4
      
      ## We only using Ubuntu and BioC-release here, 
      ## so lets use the Rstudio package manager
      ## to install binary linux packages
      - name: Setup R and Bioconductor
        uses: grimbough/bioc-actions/setup-bioc@v1
        with:
          bioc-version: ${{ matrix.bioc-version }}
          bioc-mirror: https://packagemanager.rstudio.com/bioconductor
          
      - name: Install dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 1
      
      ## Run the complete build, install, check process like the Bioc Build System
      - name: Build, Install, Check
        id: build-install-check
        uses: grimbough/bioc-actions/build-install-check@v1
        with:
          package-directory: 'inst/nestedPKG'
      
      ## Run all tests in BiocCheck, include those we know fail
      ## Use the 'error-on' to prevent this failing the workflow
      - name: Run BiocCheck without arguments
        uses: grimbough/bioc-actions/run-BiocCheck@v1
        with:
          package-directory: 'inst/nestedPKG'
          error-on: 'never'
          
      ## upload the Rcheck folder if the workflow fails
      - name: Upload output
        uses: actions/upload-artifact@v4
        if: failure()
        with:
          name: ${{ matrix.os }}-bioc-${{ matrix.bioc-version}}-sub_folder
          path: |
            ${{ steps.build-install-check.outputs.check-dir }}

  using-bioc-docker:
    name: Docker Devel
    strategy:
      fail-fast: false

    runs-on: ubuntu-22.04
    container: bioconductor/bioconductor_docker:devel
    
    steps:
    
      - uses: actions/checkout@v4
      
      ##################################################
      ## no need to install R, BiocManager, or Pandoc ##
      ##################################################
      
      ## cache installed packages
      - name: Cache install R packages
        uses: actions/cache@v4
        with:
          path: /usr/local/lib/R/site-library
          key: docker-1
          restore-keys: docker-
      
      ## we can use BiocManager will install binary packages in the Docker container
      - name: Install dependencies
        run: |
            BiocManager::install(c('AnnotationHub', 'rtracklayer', 'knitr', 'rmarkdown', 'BiocStyle'))
        shell: Rscript {0}
          
      - name: Build, Install, Check
        id: build-install-check
        uses: grimbough/bioc-actions/build-install-check@v1
        with:
          package-directory: '.'
      
      ## Turn off the checks that we know will fail
      ## Cause the workflow to error if any new errors appear
      - name: Run BiocCheck with arguments
        uses: grimbough/bioc-actions/run-BiocCheck@v1
        with:
          package-directory: '.'
          arguments: '--no-check-bioc-views --no-check-vignettes --no-check-bioc-help'
          error-on: 'error'

      - name: Upload built package binary
        uses: actions/upload-artifact@v4
        with:
          name: docker-binary
          path: |
            ${{ steps.build-install-check.outputs.package-binary }}