build-deploy-rmd.yaml

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master

name: build-deploy-rmd

jobs:
  build-deploy-rmd:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest, r: 'release'}

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      CRAN: ${{ matrix.config.cran }}
      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Check out repo
        uses: actions/checkout@v2
        with:
          submodules: true

      - name: Set up R
        uses: r-lib/actions/setup-r@master
        with:
          r-version: ${{ matrix.config.r }}

      - name: Set up pandoc
        uses: r-lib/actions/setup-pandoc@master

      - name: Install dependencies
        run: |
          install.packages(c('remotes', 'dplyr', 'ggplot2', 'rmarkdown',
                             'knitr', 'ggrepel', 'tibble', 'ggcorrplot'), 
                             Ncpu = 2L)
        shell: Rscript {0}

      - name: Session info
        run: |
          install.packages('sessioninfo', Ncpus = 2L)
          options(width = 100)
          pkgs <- installed.packages()[, "Package"]
          sessioninfo::session_info(pkgs, include_base = TRUE)
        shell: Rscript {0}
        
      - name: Render site
        run: |
          rmarkdown::render(input = "pca-intro.Rmd", clean = FALSE)
        shell: Rscript {0}

      - name: Prepare files to deploy
        run: |
          mkdir _site
          cp -r pca-intro_files pca-intro.html _site/

      - name: Deploy 🚀
        uses: JamesIves/github-pages-deploy-action@releases/v3
        with:
          ACCESS_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          BRANCH: gh-pages
          FOLDER: _site

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