[skip deploy] Update renv.lock file for efficacy app #972
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 | |
| - deploy | |
| paths: | |
| - RNA-seq/** | |
| - basic-teal/** | |
| - efficacy/** | |
| - exploratory/** | |
| - longitudinal/** | |
| - early-dev/** | |
| - patient-profile/** | |
| - python/** | |
| - safety/** | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "12 3 * * *" | |
| env: | |
| SHINYAPPSIO_ACCOUNT: genentech | |
| APP_PREFIX: NEST | |
| GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }} | |
| jobs: | |
| deploy: | |
| permissions: | |
| contents: write | |
| defaults: | |
| run: | |
| shell: bash | |
| name: Publish 🗞 | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio:2024.03.05 | |
| 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: Set channel related constants | |
| run: | | |
| echo "BRANCH_NAME=dev" >> $GITHUB_ENV | |
| if [ "${{ matrix.channel }}" == "stable" ]; then | |
| echo "BRANCH_NAME=main" >> $GITHUB_ENV | |
| fi | |
| - name: Setup job token 🔑 | |
| id: github-token | |
| run: | | |
| if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then | |
| echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN." | |
| echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | |
| else | |
| echo "Using REPO_GITHUB_TOKEN." | |
| echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | |
| fi | |
| shell: bash | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: "${{ env.BRANCH_NAME }}" | |
| token: "${{ steps.github-token.outputs.token }}" | |
| - name: Add safe directory in git config | |
| run: | | |
| git config --global --add safe.directory $(pwd) | |
| - name: Check if Cypress tests exist | |
| 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: Install additional system dependencies | |
| run: | | |
| apt-get update | |
| apt-get install --yes \ | |
| libgtk2.0-0 \ | |
| libgbm-dev \ | |
| libnotify-dev \ | |
| libgconf-2-4 \ | |
| xvfb | |
| if [ " ${{ matrix.directory }}" == "python" ] | |
| then { | |
| apt-get install --yes python3.10-venv | |
| } | |
| fi | |
| - name: Setup Node | |
| uses: actions/setup-node@v4 | |
| if: steps.find-cypress.outputs.has-cypress-tests == 'true' | |
| with: | |
| node-version: 20 | |
| - name: Restore renv from cache | |
| uses: actions/cache@v4 | |
| env: | |
| CACHE_KEY: renv-${{ 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("${{ matrix.channel }}" == "stable", "%s/%s@*release", "%s/%s") | |
| unreleased_packages <- c( | |
| "osprey", "hermes", "goshawk", "teal.osprey", | |
| "teal.modules.hermes", "teal.goshawk", "nestcolor" | |
| ) | |
| for (package in lockfile$Packages) { | |
| if (package$Source == "GitHub") { | |
| print(package$Package) | |
| if (package$Package %in% unreleased_packages) { | |
| print(paste0("Recording ", package$Package, " from main")) | |
| renv::record(sprintf("%s/%s", package$RemoteUsername, package$Package)) | |
| } else { | |
| print(paste0("Recording ", package$Package, " from stable")) | |
| renv::record(sprintf(pkg_name_structure, package$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' | |
| uses: cypress-io/github-action@v6 | |
| with: | |
| build: npm install cypress --save-dev | |
| working-directory: ${{ matrix.directory }}/tests | |
| start: npm run run-app | |
| wait-on: "http://localhost:3333" | |
| wait-on-timeout: 500 | |
| - name: Install deployment-related R package dependencies | |
| shell: Rscript {0} | |
| working-directory: ${{ matrix.directory }} | |
| run: | | |
| install.packages(c("BiocManager", "rsconnect")) | |
| - name: Deploy 🖨 ${{ matrix.directory }} 🎨 | |
| shell: Rscript {0} | |
| 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"), | |
| 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 and push changes 📌 | |
| run: | | |
| git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com" | |
| git config --global user.name "github-actions" | |
| git config --global --add safe.directory /__w/teal.gallery/teal.gallery | |
| git fetch | |
| git stash | |
| git checkout ${{ env.BRANCH_NAME }} | |
| git pull | |
| if [ -n "$(git stash list)" ]; then | |
| git stash apply | |
| else | |
| echo "No stash entries found." | |
| fi | |
| git add ${{ matrix.directory }}/renv.lock | |
| git add ${{ matrix.directory }}/renv/activate.R | |
| if [ -n "$(git diff --staged)" ]; then | |
| 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 |