integration_checks.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
name: Integration Checks

# because `main` is a protected branch this workflow is triggered when a PR 
# is opened/updated and again when it is merged
on:
  push:
    branches: 
    - main
  pull_request:
    branches: 
    - main

jobs:
  check-package:
    # system dependencies for cannot be automatically resolved by 
    # `r-lib/actions/setup-r@v2` for macos or windows - to avoid having to 
    # maintain separate logic to infer and install system of those operating 
    # systems we'll only run integration checks with the ubuntu
    runs-on: ubuntu-latest

    # run integration checks with R-release, R-devel, and R-oldrelease
    strategy:
      matrix:
        r-version: ['release', 'devel', 'oldrel']

    steps:
      # pull the latest changes from the repository down to the runner
      - name: Checkout
        uses: actions/checkout@v4

      # install R and any system dependencies
      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          # install the R version specified by the current strategy
          r-version: ${{ matrix.r-version }}
          # specify additional repositories to pull dependencies not
          # available on CRAN (i.e. `BPCells`)
          extra-repositories: ${{ 'https://bnprks.r-universe.dev' }}
      
      # install R dependencies
      - name: Install Dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: 
            any::rcmdcheck
            any::pkgdown
          # installed packages are cached by default - force an upgrade to the 
          # latest version of all dependencies
          upgrade: 'TRUE'
      
      # run CRAN checks - fails if any ERRORs or WARNINGs are raised in which 
      # case the `rcmdcheck` output will be uploaded as an artifact
      - name: Run Checks
        uses: r-lib/actions/check-r-package@v2
        env:
            # suppress NOTEs that are accepted by CRAN
            # see: https://www.rdocumentation.org/packages/rcmdcheck/versions/1.4.0/topics/rcmdcheck
            _R_CHECK_PKG_SIZES_: false
            _R_CHECK_RD_XREFS_: false
            _R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_: false
            _R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_: true
        continue-on-error: true
      
      # build pkgdown site
      - name: Build Website
        run: | 
          pkgdown::build_site_github_pages(
            new_process = FALSE, 
            install = FALSE
          )
        shell: Rscript {0}