basic_checks.yaml

on: [push]

env:
  cache-version: v1
  repo-name: tidytranscriptomics-workshops/iscb2022_tidytranscriptomics
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 

jobs:
  r-build-and-check:
    runs-on: ubuntu-latest
    container: bioconductor/bioconductor_docker:RELEASE_3_14
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
    steps:
      - uses: actions/checkout@v3

      - name: Query dependencies and update old packages
        run: |
          # We'll install the specific versions from the install instructions
          BiocManager::install("stemangiola/tidyseurat@v0.5.1")
          BiocManager::install("stemangiola/tidySingleCellExperiment@v1.3.2")
          
          # Then install the other dependencies in the usual way
          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@v1
        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-
          
       # This lets us augment with additional dependencies	
      - name: Install system dependencies	
        if: runner.os == 'Linux'	
        env:	
          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc	
        run: |	
          Rscript -e "remotes::install_github('r-hub/sysreqs')"	
          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")	
          sudo -s eval "$sysreqs"
          
      - name: Install dependencies
        run: |
          options(repos = c(CRAN = "https://cran.r-project.org"))
          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 = c("--no-manual"), error_on = "error", check_dir = "check")
        shell: Rscript {0}

      - name: Build pkgdown
        if: github.ref == 'refs/heads/master' 
        run: |
           PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")'

      # deploy needs rsync? Seems so.
      - name: Install deploy dependencies
        if: github.ref == 'refs/heads/master'
        run: |
          apt-get update
          apt-get -y install rsync

      - name: Deploy 🚀
        uses: JamesIves/github-pages-deploy-action@releases/v3
        if: github.ref == 'refs/heads/master'
        with:
          GITHUB_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@v3
        
      - 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@1e95c1de343b5b0c23352d6417ee3e48d5bcd422
        with:
          cosign-release: 'v1.4.0'


      # Workaround: https://github.com/docker/build-push-action/issues/461
      - name: Setup Docker buildx
        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf

      # 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@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
        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@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
        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@ad44023a93711e3deb337508980b4b5e9bcdc5dc
        with:
          context: .
          push: ${{ github.event_name != 'pull_request' }}
          tags: |
            ${{ env.IMAGE }}:latest
            ${{ env.IMAGE }}:${{ env.GIT_SHA }}

      # Sign the resulting Docker image digest except on PRs.
      # This will only write to the public Rekor transparency log when the Docker
      # repository is public to avoid leaking data.  If you would like to publish
      # transparency data even for private images, pass --force to cosign below.
      # https://github.com/sigstore/cosign
      - name: Sign the published Docker image
        if: ${{ github.event_name != 'pull_request' }}
        env:
          COSIGN_EXPERIMENTAL: "true"
        # This step uses the identity token to provision an ephemeral certificate
        # against the sigstore community Fulcio instance.
        run: cosign sign ${{ env.IMAGE }}@${{ steps.build-and-push.outputs.digest }}