check-bioc.yml

## Read more about GitHub actions the features of this GitHub Actions workflow
## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
##
## For more details, check the biocthis developer notes vignette at
## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
##
## You can add this workflow to other packages using:
## > biocthis::use_bioc_github_action()
##
## Using GitHub Actions exposes you to many details about how R packages are
## compiled and installed in several operating system.s
### If you need help, please follow the steps listed at
## https://github.com/r-lib/actions#where-to-find-help
##
## If you found an issue specific to biocthis's GHA workflow, please report it
## with the information that will make it easier for others to help you.
## Thank you!

## Acronyms:
## * GHA: GitHub Action
## * OS: operating system

on:
  push:
  pull_request:

name: R-CMD-check-bioc

## These environment variables control whether to run GHA code later on that is
## specific to testthat, covr, and pkgdown.
##
## If you need to clear the cache of packages, update the number inside
## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
## Note that you can always run a GHA test without the cache by using the word
## "/nocache" in the commit message.
env:
  has_testthat: 'true'
  run_covr: 'false'
  run_pkgdown: 'true'
  has_RUnit: 'false'
  cache-version: 'cache-v1'

jobs:
  build-check:
    runs-on: ${{ matrix.config.os }}
    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
    container: ${{ matrix.config.cont }}
    ## Environment variables unique to this job.

    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
          # - { os: windows-latest, r: '4.3', bioc: '3.18'}
          ## Check https://github.com/r-lib/actions/tree/master/examples
          ## for examples using the http-user-agent
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      NOT_CRAN: true
      TZ: UTC
      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:

      ## Set the R library to the directory matching the
      ## R packages cache step further below when running on Docker (Linux).
      - name: Set R Library home on Linux
        if: runner.os == 'Linux'
        run: |
          mkdir /__w/_temp/Library
          echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile

      ## Most of these steps are the same as the ones in
      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
      ## If they update their steps, we will also need to update ours.
      - name: Checkout Repository
        uses: actions/checkout@v3

      ## R is already included in the Bioconductor docker images
      - name: Setup R from r-lib
        if: runner.os != 'Linux'
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}

      ## pandoc is already included in the Bioconductor docker images
      - name: Setup pandoc from r-lib
        if: runner.os != 'Linux'
        uses: r-lib/actions/setup-pandoc@v2

      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
        shell: Rscript {0}

      - name: Restore R package cache
        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
        uses: actions/cache@v3
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-

      - name: Cache R packages on Linux
        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
        uses: actions/cache@v3
        with:
          path: /home/runner/work/_temp/Library
          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-

      - name: Install Linux system dependencies
        if: runner.os == 'Linux'
        run: |
          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
          echo $sysreqs
          sudo -s eval "$sysreqs"

      - name: Install macOS system dependencies
        if: matrix.config.os == 'macOS-latest'
        run: |
          ## Enable installing XML from source if needed
          brew install libxml2
          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV

          ## Required to install magick as noted at
          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
          brew install imagemagick@6

          ## For textshaping, required by ragg, and required by pkgdown
          brew install harfbuzz fribidi

          ## For installing usethis's dependency gert
          brew install libgit2

          ## Required for tcltk
          brew install xquartz --cask

          brew install minimap2
          brew install samtools 

      - name: Install Windows system dependencies
        if: runner.os == 'Windows'
        run: |
          ## Edit below if you have any Windows system dependencies
          remotes::install_cran("igraph", build = FALSE)
        shell: Rscript {0}

      - name: Install BiocManager
        run: |
          message(paste('****', Sys.time(), 'installing BiocManager ****'))
          remotes::install_cran("BiocManager")
        shell: Rscript {0}

      - name: Set BiocVersion
        run: |
          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
        shell: Rscript {0}

      - name: Install dependencies pass 1
        run: |
          ## Try installing the package dependencies in steps. First the local
          ## dependencies, then any remaining dependencies to avoid the
          ## issues described at
          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
          ## https://github.com/r-lib/remotes/issues/296
          ## Ideally, all dependencies should get installed in the first pass.

          ## For running the checks
          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
          install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())

          ## Pass #1 at installing dependencies
          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
        continue-on-error: true
        shell: Rscript {0}

      - name: Install dependencies pass 2
        run: |
          ## Pass #2 at installing dependencies
          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
        shell: Rscript {0}

      - name: Install BiocGenerics
        if:  env.has_RUnit == 'true'
        run: |
          ## Install BiocGenerics
          BiocManager::install("BiocGenerics")
        shell: Rscript {0}

      - name: Install covr
        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
        run: |
          remotes::install_cran("covr")
        shell: Rscript {0}

      - name: Install pkgdown
        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
        run: |
          remotes::install_github("r-lib/pkgdown")
        shell: Rscript {0}

      - name: Session info
        run: |
          options(width = 100)
          pkgs <- installed.packages()[, "Package"]
          sessioninfo::session_info(pkgs, include_base = TRUE)
        shell: Rscript {0}

      - name: Run CMD check
        env:
          _R_CHECK_CRAN_INCOMING_: false
          DISPLAY: 99.0
        run: |
          options(crayon.enabled = TRUE)

          rcmdcheck::rcmdcheck(
              args = c("--no-manual", "--no-vignettes", "--timings"),
              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
              error_on = "warning",
              check_dir = "check"
          )
        shell: Rscript {0}

      ## Might need an to add this to the if:  && runner.os == 'Linux'
      - name: Reveal testthat details
        if:  env.has_testthat == 'true'
        run: find . -name testthat.Rout -exec cat '{}' ';'

      - name: Run RUnit tests
        if:  env.has_RUnit == 'true'
        run: |
          BiocGenerics:::testPackage()
        shell: Rscript {0}

      - name: Run BiocCheck
        env:
          DISPLAY: 99.0
        run: |
          BiocCheck::BiocCheck(
              dir('check', 'tar.gz$', full.names = TRUE),
              `quit-with-status` = TRUE,
              `no-check-R-ver` = TRUE,
              `no-check-bioc-help` = TRUE
          )
        shell: Rscript {0}

      - name: Test coverage
        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
        run: |
          covr::codecov()
        shell: Rscript {0}

      - name: Install package
        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
        run: R CMD INSTALL .

      - name: Build pkgdown site
        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
        shell: Rscript {0}
        ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
        ## at least one locally before this will work. This creates the gh-pages
        ## branch (erasing anything you haven't version controlled!) and
        ## makes the git history recognizable by pkgdown.

      - name: Install deploy dependencies
        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
        run: |
          apt-get update && apt-get -y install rsync

      - name: Deploy pkgdown site to GitHub pages 🚀
        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
        uses: JamesIves/github-pages-deploy-action@releases/v4
        with:
          clean: false
          branch: gh-pages
          folder: docs

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@master
        with:
          name: ${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-results
          path: check

  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 }}