ci.yml

name: R Shiny Tests

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

jobs:
  test:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: 'release'

      - name: Set up Pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Set up Chrome
        uses: browser-actions/setup-chrome@v1

      - name: System dependencies
        run: |
          sudo apt-get update
          # Install base libraries
          sudo apt-get install -y \
            libssl-dev libxml2-dev libcurl4-openssl-dev \
            libfontconfig1 libharfbuzz-dev libfribidi-dev \
            libfreetype6-dev libpng-dev libjpeg-dev \
            libgit2-dev libudunits2-dev libgdal-dev libv8-dev libmagick++-dev
          # TIFF library name changed on Ubuntu 24.04 (libtiff6). Try both.
          sudo apt-get install -y libtiff5 || \
          sudo apt-get install -y libtiff6 || \
          sudo apt-get install -y libtiff-dev

      - name: Install R dependencies (CRAN + Bioc)
        run: |
          R -q -e 'install.packages(c("remotes","BiocManager"), repos="https://cloud.r-project.org")'
          R -q -e 'cran <- c("shiny","shinytest2","chromote","DT","shinyBS","shinyWidgets","shinycssloaders","shinythemes","shinyjs","data.table","readxl","openxlsx","stringdist","limma","matrixStats","jsonlite","gridExtra","ggplot2","gplots","viridis","ggrepel","ggiraph"); install.packages(cran, repos="https://cloud.r-project.org")'
          R -q -e 'BiocManager::install(c("MsCoreUtils","BEclear","sva","UniProt.ws"), ask=FALSE, update=FALSE)'

      - name: Run shinytest2 tests
        env:
          NOT_CRAN: true
        run: |
          R -q -e 'options(chromote.startup_timeout=30, chromote.chrome_args=c("--headless=new","--no-first-run","--no-default-browser-check")); shinytest2::test_app()'