integration_checks.yaml

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
    - testing-ci
  pull_request:
    branches: 
    - main

jobs:
  check-package:
    runs-on: ubuntu-latest
    
    # Use the `satijalab/seurat-ci` Docker image as the container environment. 
    # This image is pre-configured with everything required for running
    # integration checks, for more details, see
    # https://hub.docker.com/repository/docker/satijalab/seurat-ci/general.
    container:
      image: satijalab/seurat-ci:latest

    steps:
      # Pull the latest changes from the repository down to the runner.
      - name: Checkout
        uses: actions/checkout@v4
      
      # Install the package and _all_ its dependencies.
      - name: Install Dependencies
        run: installAllDeps.r
      
      # Run CRAN checks, if any ERRORs or WARNINGs are raised the check fails
      # and the output of `rcmdcheck` will be uploaded as an artifact.
      - name: Run Checks
        run: |
          rcmdcheck::rcmdcheck(
            args = c("--no-manual", "--as-cran"), 
            build_args="--no-manual", 
            error_on="warning"
          )
        shell: Rscript {0}
        continue-on-error: true
      
      # Build the pkgdown site.
      - name: Build Website
        run: | 
          pkgdown::build_site_github_pages(
            new_process = FALSE, 
            install = FALSE
          )
        shell: Rscript {0}