basic_checks.yaml

on: [push, pull_request]

env:
  cache-version: v1
  repo-name: bhuvad/genesetanalysisworkflow
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

jobs:
  job1:
    runs-on: ubuntu-latest
    container: bioconductor/bioconductor_docker:devel
    steps:
      - uses: actions/checkout@v1

      - 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@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 = "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@releases/v3
        with:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          BRANCH: gh-pages # The branch the action should deploy to.
          FOLDER: docs # The folder the action should deploy.

      - uses: docker/build-push-action@v1
        with:
          # The two entries below need to be entered as
          # github secrets. The "secret" names are "DOCKER_USERNAME"
          # and "DOCKER_PASSWORD". See https://docs.github.com/en/actions/reference/encrypted-secrets#creating-encrypted-secrets-for-a-repository
          # for detailed instructions.
          #
          # DO NOT EDIT THESE ENTRIES HERE. Doing so will
          # expose your docker username and password on github.
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}
          # Use the environment variable on first few lines to set repo name--just centralizes changes
          repository: ${{ env.repo-name }}
          tag_with_ref: true
          tag_with_sha: true
          tags: latest