basic_checks.yaml

name: Check, build, and push image

on: [push, pull_request]

env:
  cache-version: v1

jobs:
  r-build-and-check:
    runs-on: ubuntu-latest
    container: bioconductor/bioconductor_docker:devel

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: TRUE
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest

    steps:
      - name: Checkout Repository
        uses: actions/checkout@v4

      - name: Query dependencies and update old packages
        run: |
          BiocManager::install(ask=FALSE)
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
        shell: Rscript {0}
        
      - name: Cache R packages
        if: runner.os != 'Windows'
        uses: actions/cache@v4
        with:
          path: /usr/local/lib/R/site-library
          key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r-

      - name: Install dependencies
        run: |
          BiocManager::repositories()
          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
          remotes::install_cran("rcmdcheck")
        shell: Rscript {0}

      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
        shell: Rscript {0}

      - name: Build pkgdown
        run: |
           PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")'

      # deploy needs rsync? Seems so.
      - name: Install deploy dependencies
        run: |
          apt-get update
          apt-get -y install rsync

      - name: Deploy 🚀
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          TOKEN: ${{ secrets.GITHUB_TOKEN }}
          BRANCH: gh-pages # The branch the action should deploy to.
          FOLDER: docs # The folder the action should deploy.

  docker-build-and-push:
    #needs: r-build-and-check
    runs-on: ubuntu-latest
    permissions:
      contents: read
      packages: write
      # This is used to complete the identity challenge
      # with sigstore/fulcio when running outside of PRs.
      id-token: write

    steps:
      - name: Checkout Repository
        uses: actions/checkout@v4

      - name: Set Environment Variables
        run: |
          REPO_LOWER="$(echo "${{ github.repository }}" | tr '[:upper:]' '[:lower:]')"
          REGISTRY=ghcr.io
          echo "BUILD_DATE=$(date +'%Y-%m-%d %H:%M:%S')" >> $GITHUB_ENV
          echo "GIT_SHA=$(echo ${{ github.sha }} | cut -c1-7)" >> $GITHUB_ENV
          echo "REGISTRY=${REGISTRY}" >> $GITHUB_ENV
          echo "IMAGE=${REGISTRY}/${REPO_LOWER}" >> $GITHUB_ENV

      - name: Show environment
        run: |
          env

      # Install the cosign tool except on PR
      # https://github.com/sigstore/cosign-installer
      - name: Install cosign
        if: github.event_name != 'pull_request'
        uses: sigstore/cosign-installer@v3

      - name: Setup Docker buildx
        uses: docker/setup-buildx-action@v3

      # Login against a Docker registry except on PR
      # https://github.com/docker/login-action
      - name: Log into registry ${{ env.REGISTRY }}
        if: github.event_name != 'pull_request'
        uses: docker/login-action@v3
        with:
          registry: ${{ env.REGISTRY }}
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}

      # Extract metadata (tags, labels) for Docker
      # https://github.com/docker/metadata-action
      - name: Extract Docker metadata
        id: meta
        uses: docker/metadata-action@v5
        with:
          images: ${{ env.IMAGE }}

      # Build and push Docker image with Buildx (don't push on PR)
      # https://github.com/docker/build-push-action
      - name: Build and push Docker image
        id: build-and-push
        uses: docker/build-push-action@v5
        with:
          context: .
          push: ${{ github.event_name != 'pull_request' }}
          tags: |
            ${{ env.IMAGE }}:latest
            ${{ env.IMAGE }}:${{ env.GIT_SHA }}