deploy-website.yml

## Github Actions workflow to deploy pkgdown website to GitHub pages
## This workflow is triggered by pushes to the devel branch
## and is only run on Linux runners

on:
  push:
    branches: [main, devel]
  pull_request:
    branches: [main, devel]

name: Deploy pkgdown site

permissions: read-all

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

    permissions:
      contents: write

    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }

    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
        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
        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
        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: 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 pkgdown
        run: |
          remotes::install_cran("pkgdown")
        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: |
          ## 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 package
        run: R CMD INSTALL .

      - name: Build pkgdown site
        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
        run: |
          apt-get update && apt-get -y install rsync

      - name: Deploy pkgdown site to GitHub pages 🚀
        uses: JamesIves/github-pages-deploy-action@releases/v4
        with:
          clean: false
          branch: gh-pages
          folder: docs