Deploy Apps 🚀 #259
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | |
| name: Deploy Apps 🚀 | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| tags: | |
| - "*" | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "12 3 * * *" | |
| concurrency: | |
| group: publish-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| SHINYAPPSIO_ACCOUNT: genentech | |
| APP_PREFIX: NEST | |
| jobs: | |
| deploy: | |
| defaults: | |
| run: | |
| shell: bash | |
| name: Publish 🗞 | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip deploy]') | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| directory: ["basic-teal"] | |
| repository: ["https://insightsengineering.r-universe.dev"] | |
| steps: | |
| - name: Set CHANNEL | |
| run: | | |
| if [ "${{ 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: ${{ github.event.repository.name }} | |
| - name: Install jq | |
| run: sudo apt-get update && sudo apt-get install -y jq | |
| - name: Extract R version from lockfile | |
| run: printf 'R_VERSION=%s\n' "$(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-cache-${{ runner.arch }}-${{ 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 R packages using renv and update the renv snapshot | |
| shell: Rscript {0} | |
| working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }} | |
| run: | | |
| options(renv.config.cache.symlinks = FALSE) | |
| lockfile_packages <- renv::lockfile_read()$Packages |> names() | |
| repos <- renv::lockfile_read()$R$Repositories | |
| repos$Pharmaverse <- "${{ matrix.repository }}" | |
| renv::lockfile_modify(repos = repos) |> renv::lockfile_write() | |
| renv::update(lockfile_packages) | |
| renv::snapshot(packages = lockfile_packages, 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' | |
| continue-on-error: 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: Install deploy R package dependencies | |
| shell: Rscript {0} | |
| working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }} | |
| run: | | |
| install.packages(c("BiocManager", "remotes")) | |
| remotes::install_version("rsconnect", "0.8.29") | |
| - name: Deploy 🖨 ${{ matrix.directory }} 🎨 | |
| shell: Rscript {0} | |
| continue-on-error: true | |
| working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }} | |
| run: | | |
| options( | |
| repos = c( | |
| Pharmaverse = "${{ matrix.repository }}", | |
| CRAN = "https://cloud.r-project.org", | |
| BioC = BiocManager::repositories() | |
| ) | |
| ) | |
| rsconnect::setAccountInfo( | |
| name = "${{ 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 | |
| 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 |