Update deploy.yaml #350
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: | |
| 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 | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| deploy: | |
| defaults: | |
| run: | |
| shell: bash | |
| name: Publish 🗞 | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip deploy]') | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| directory: | |
| [ | |
| "RNA-seq", | |
| "basic-teal", | |
| "efficacy", | |
| "exploratory", | |
| "longitudinal", | |
| "early-dev", | |
| "patient-profile", | |
| "python", | |
| "safety", | |
| ] | |
| channel: ["stable", "dev"] | |
| steps: | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v3 | |
| - name: Set channel related constants | |
| run: | | |
| if [ "${{ matrix.channel }}" = "stable" ]; then | |
| echo "BRANCH_NAME=deploy-apps@main" >> $GITHUB_ENV # TODO: Change the branch name to main | |
| else | |
| echo "BRANCH_NAME=deploy-apps@dev" >> $GITHUB_ENV # TODO: Change the branch name to deval | |
| fi | |
| - name: Check if cypress test exists | |
| id: find-cypress | |
| run: | | |
| if [ -d ${{ 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 | |
| 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' | |
| working-directory: ${{ matrix.directory }}/js | |
| run: | | |
| npm i | |
| - name: Restore renv from cache | |
| uses: actions/cache@v3 | |
| env: | |
| CACHE_KEY: renv-${{ runner.arch }}-${{ runner.os }}-${{ matrix.directory }}-${{ matrix.channel }} | |
| with: | |
| path: ${{ matrix.directory }}/renv/library | |
| key: ${{ env.CACHE_KEY }}-${{ hashFiles(format('{0}/renv.lock', matrix.directory)) }} | |
| restore-keys: ${{ env.CACHE_KEY }}- | |
| - name: Update renv.lock file with updated GitHub packages | |
| shell: Rscript {0} | |
| run: | | |
| setwd("${{ matrix.directory }}") | |
| lockfile <- renv::lockfile_read() | |
| pkg_name_structure <- ifelse("${{ matrix.channel }}" == "stable", "%s/%s@*release", "%s/%s") | |
| for (package in lockfile$Packages) { | |
| if (package$Source == "GitHub") { | |
| renv::record(sprintf(pkg_name_structure, package$RemoteUsername, package$Package)) | |
| } | |
| } | |
| - name: Install R packages using renv and update the renv snapshot | |
| shell: Rscript {0} | |
| working-directory: ${{ matrix.directory }} | |
| run: | | |
| options(renv.config.cache.symlinks = FALSE) | |
| lockfile_pkgs <- renv::lockfile_read()$Package | |
| github_pkgs <- names(lockfile_pkgs)[sapply(lockfile_pkgs, function(x) x$Source == "GitHub")] | |
| renv::restore(clean = TRUE) | |
| renv::update(exclude = github_pkgs) | |
| renv::snapshot() | |
| - name: Print the new renv.lock file for ${{ matrix.directory }} | |
| working-directory: ${{ 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@v6 | |
| with: | |
| build: npm install cypress | |
| working-directory: ${{ 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: ${{ matrix.directory }} | |
| run: | | |
| install.packages(c("BiocManager", "rsconnect")) | |
| - name: Deploy 🖨 ${{ matrix.directory }} 🎨 | |
| shell: Rscript {0} | |
| continue-on-error: true | |
| working-directory: ${{ matrix.directory }} | |
| run: | | |
| rsconnect::setAccountInfo( | |
| name = "${{ env.SHINYAPPSIO_ACCOUNT }}", | |
| token = "${{ secrets.SHINYAPPSIO_TOKEN }}", | |
| secret = "${{ secrets.SHINYAPPSIO_SECRET }}", | |
| server = "shinyapps.io" | |
| ) | |
| rsconnect::deployApp( | |
| appFiles = c("app.R", list.files("www", full.names = TRUE)), | |
| appName = rsconnect::generateAppName("${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ matrix.channel }}"), | |
| appTitle = "${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ matrix.channel }}", | |
| account = "${{ env.SHINYAPPSIO_ACCOUNT }}", | |
| upload = TRUE, | |
| logLevel = "normal", | |
| lint = FALSE, | |
| forceUpdate = TRUE | |
| ) | |
| - name: Commit updated renv.lock file | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "GitHub Action" | |
| git config --global --add safe.directory /__w/teal.gallery/teal.gallery | |
| git fetch | |
| git stash | |
| git checkout ${{ env.BRANCH_NAME }} | |
| git stash apply | |
| git pull | |
| if [ -n "$(git diff --staged)" ]; then | |
| git add ${{ matrix.directory }}/renv.lock | |
| git commit -m "[skip deploy] Update renv.lock file for ${{ matrix.directory }} app" | |
| git push origin ${{ env.BRANCH_NAME }} | |
| else | |
| echo "renv.lock was not modified. Nothing to commit."; | |
| fi |