Deploy Apps 🚀 #251
Workflow file for this run
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| --- | |
| name: Deploy Apps 🚀 | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| tags: | |
| - "*" | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "12 3 * * *" | |
| concurrency: | |
| group: publish-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| SHINYAPPSIO_ACCOUNT: genentech | |
| APP_PREFIX: NEST | |
| jobs: | |
| deploy: | |
| defaults: | |
| run: | |
| shell: bash | |
| name: Publish 🗞 | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip deploy]') | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| directory: ["RNA-seq", "basic-teal"] | |
| repository: | |
| [ | |
| "https://insightsengineering.r-universe.dev", | |
| "https://pharmaverse.r-universe.dev", | |
| ] | |
| steps: | |
| - name: Set CHANNEL | |
| run: | | |
| if [ "${{ matrix.repository }}" = "https://insightsengineering.r-universe.dev" ]; then | |
| echo "CHANNEL=stable" >> $GITHUB_ENV | |
| else | |
| echo "CHANNEL=release" >> $GITHUB_ENV | |
| fi | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v3 | |
| with: | |
| path: ${{ github.event.repository.name }} | |
| - name: Overwrite the global Rprofile ✍️ | |
| run: | | |
| cat > /usr/local/lib/R/etc/Rprofile.site <<RPROFILE | |
| options( | |
| repos = c( | |
| Pharmaverse = "${{ matrix.repository }}", | |
| CRAN = "https://cloud.r-project.org", | |
| BioC = BiocManager::repositories() | |
| ), | |
| download.file.method = 'libcurl', | |
| HTTPUserAgent = sprintf( | |
| "R/%s R (%s)", | |
| getRversion(), | |
| paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"]) | |
| ) | |
| ) | |
| RPROFILE | |
| - name: Install jq | |
| run: sudo apt-get update && sudo apt-get install -y jq | |
| - name: Extract R version from lockfile | |
| run: printf 'R_VERSION=%s\n' "$(jq --raw-output .R.Version ${{ github.event.repository.name }}/${{ matrix.directory }}/renv.lock)" >> $GITHUB_ENV | |
| - name: Check if cypress test exists | |
| id: find-cypress | |
| run: | | |
| if [ -d ${{ github.event.repository.name }}/${{ matrix.directory }}/tests/cypress ]; then | |
| echo "has-cypress-tests=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "Skipping frontend tests because cypress directory does not exist." | |
| echo "has-cypress-tests=false" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Setup system dependencies for cypress and python app | |
| if: steps.find-cypress.outputs.has-cypress-tests == 'true' | |
| run: > | |
| apt-get update && apt-get install --yes | |
| libgtk2.0-0 libgbm-dev libnotify-dev libgconf-2-4 xvfb python3.10-venv | |
| - name: Setup Node | |
| uses: actions/setup-node@v3 | |
| if: steps.find-cypress.outputs.has-cypress-tests == 'true' | |
| with: | |
| node-version: 16 | |
| - name: Setup npm packages | |
| if: steps.find-cypress.outputs.has-cypress-tests == 'true' | |
| shell: bash | |
| working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }}/js | |
| run: | | |
| npm i | |
| - name: Restore renv from cache | |
| uses: actions/cache@v2 | |
| env: | |
| CACHE_KEY: renv-${{ runner.arch }}-${{ runner.os }}-${{ env.R_VERSION }}-${{ matrix.directory }}-${{ env.CHANNEL }} | |
| with: | |
| path: ${{ github.event.repository.name }}/${{ matrix.directory }}/renv/library | |
| key: ${{ env.CACHE_KEY }}-${{ hashFiles(format('{0}/{1}/renv.lock', github.event.repository.name, matrix.directory)) }} | |
| restore-keys: ${{ env.CACHE_KEY }}- | |
| - name: Install app dependencies using renv.lock | |
| shell: Rscript {0} | |
| working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }} | |
| run: | | |
| options(renv.config.cache.symlinks = FALSE) | |
| renv::update() | |
| renv::restore(clean = TRUE) | |
| renv::snapshot(update = TRUE) | |
| - name: Print the new renv.lock file for ${{ matrix.directory }} | |
| working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }} | |
| run: cat renv.lock | |
| - name: Front end test to check if the app works fine | |
| if: steps.find-cypress.outputs.has-cypress-tests == 'true' | |
| uses: cypress-io/github-action@v2 | |
| with: | |
| working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }}/js | |
| start: npm run run-app | |
| wait-on: "http://localhost:3333" | |
| wait-on-timeout: 500 | |
| project: ../tests | |
| - name: Deploy 🖨 ${{ matrix.directory }} 🎨 | |
| shell: Rscript {0} | |
| working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }} | |
| run: | | |
| install.packages('remotes') | |
| remotes::install_version("rsconnect", "0.8.29") | |
| rsconnect::setAccountInfo( | |
| name = "${{ env.SHINYAPPSIO_ACCOUNT }}", | |
| token = "${{ secrets.SHINYAPPSIO_TOKEN }}", | |
| secret = "${{ secrets.SHINYAPPSIO_SECRET }}", | |
| server = "shinyapps.io" | |
| ) | |
| rsconnect::deployApp( | |
| appFiles = "app.R", | |
| appName = rsconnect::generateAppName("${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ env.CHANNEL }}"), | |
| appTitle = "${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ env.CHANNEL }}", | |
| account = "${{ env.SHINYAPPSIO_ACCOUNT }}", | |
| upload = TRUE, | |
| logLevel = "normal", | |
| lint = FALSE, | |
| forceUpdate = TRUE | |
| ) | |
| - name: Commit updated renv.lock file | |
| if: ${{ env.CHANNEL == 'stable' }} #TODO: Will change this to release before merging | |
| uses: stefanzweifel/git-auto-commit-action@v4 | |
| continue-on-error: true | |
| with: | |
| repository: ${{ github.event.repository.name }} | |
| branch: deploy-apps@main # TODO: switch to the release branch before merging. | |
| commit_message: "[skip deploy] Update renv.lock file for ${{ matrix.directory }} app" | |
| file_pattern: "${{ matrix.directory }}/renv.lock" | |
| commit_user_name: insights-engineering-bot |