shinyapps_deploy.yml

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help

name: shiny-deploy

on:
  push:
    branches:
      - develop
      - release*

jobs:
  shiny-deploy:
    runs-on: ubuntu-latest
 
    steps:
 
      - name: Install System Dependencies
        run: |
          sudo apt-get update
          # The rsconnect R package needs cUrl.  This app needs the Java JDK (runtime AND compiler).
          sudo apt-get install -y libcurl4-openssl-dev default-jdk
 
      - uses: actions/checkout@v2
        
      - name: Install R packages
        run: |
          options(repos = 'http://cran.fhcrc.org')
          # This list of packages came from global.R.  Also we need rsconnect to deploy the app'
          install.packages(c("DT", "png", "rJava", "rcdk", "fingerprint", "enrichR", 
          "webchem", "plyr", "dplyr", "tidyr", "purrr", "tibble", "plotly", "shinyBS", "shinythemes", 
          "visNetwork", "igraph", "shinyjs", "shinycssloaders", "XML", "rsconnect", "renv", "conflicted",'rjson', 'callr'))
          # running this step as 'sudo' is necessary to be able to install packages in default library
        shell: sudo Rscript {0}

      - name: Deploy app
        run: |
          branch<-Sys.getenv("GITHUB_REF_NAME")
          repo<-Sys.getenv("GITHUB_REPOSITORY")
          appName<-strsplit(repo, "/")[[1]][2]
          if (!startsWith(branch, "release")) {
             appName = paste(appName, "staging", sep="-")
          }
          rsConnectUser <-"${{ secrets.RSCONNECT_USER }}"
          rsConnectToken <- "${{ secrets.RSCONNECT_TOKEN }}"
          rsConnectSecret <- "${{ secrets.RSCONNECT_SECRET }}" 
          rsconnect::setAccountInfo(rsConnectUser, rsConnectToken, rsConnectSecret)
          # omit renv/ folder from the collection to be deployed
          appFiles<-dir(all.files=T,no..=T)[which(dir(all.files=T,no..=T)!="renv")]
          rsconnect::deployApp(appName = appName, appFiles=appFiles)
          # important NOT to run this step as sudo, otherwise env var's will be missing
        shell: Rscript {0}