[skip deploy] Update renv.lock file for python app #195
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| --- | |
| name: Deploy Apps 🚀 | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| paths: | |
| - RNA-seq/** | |
| - basic-teal/** | |
| - efficacy/** | |
| - exploratory/** | |
| - longitudinal/** | |
| - early-dev/** | |
| - patient-profile/** | |
| - python/** | |
| - safety/** | |
| 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.REPO_GITHUB_TOKEN }} | |
| jobs: | |
| deploy: | |
| permissions: | |
| contents: write | |
| defaults: | |
| run: | |
| shell: bash | |
| name: Publish 🗞 | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio: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: 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 [ " ${{ matrix.directory }}" == "python" ] | |
| then { | |
| apt-get install --yes python3.10-venv | |
| } | |
| fi | |
| - name: Setup Node | |
| uses: actions/setup-node@v4 | |
| if: steps.find-cypress.outputs.has-cypress-tests == 'true' | |
| with: | |
| node-version: 20 | |
| - name: Restore renv from cache | |
| uses: actions/cache@v3 | |
| env: | |
| CACHE_KEY: renv-${{ 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$Source == "GitHub") { | |
| # TODO: After teal.slice is released we have to remove this change. | |
| # This workaround is because update to {bslib} breaks current release of teal.slice | |
| if (package$Package == "teal.slice" && "${{ matrix.channel }}" == "stable") { | |
| renv::record("insightsengineering/teal.slice@103491c67e26a9a85d636bd105a806904a0111ec") | |
| } else { | |
| renv::record(sprintf(pkg_name_structure, package$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 --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 📌 | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "[skip deploy] Update renv.lock file for ${{ matrix.directory }} app" | |
| file_pattern: "${{ matrix.directory }}/renv/activate.R ${{ matrix.directory }}/renv.lock" | |
| commit_user_name: github-actions | |
| commit_user_email: >- | |
| 41898282+github-actions[bot]@users.noreply.github.com | |
| continue-on-error: true |