test: deploy efficacy

.github/workflows/deploy.yaml

@@ -0,0 +1,154 @@
+---
+name: Deploy Apps 🚀
+
+on:
+  push:
+    branches:
+      - 78_simplify_joinkeys@main # TODO: change this to `dev` in `deploy_dev.yaml` and `main` in `deploy_stable.yaml`
+  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
+  APP_SUFFIX: dev # TODO: change this to `dev` in `deploy_dev.yaml` and `stable` in `deploy_stable.yaml`
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+  BRANCH: 78_simplify_joinkeys@main # TODO: change this to `dev` in `deploy_dev.yaml` and `main` in `deploy_stable.yaml`
+
+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: ["efficacy"]
+    steps:
+      - name: Checkout repo 🛎
+        uses: actions/checkout@v3
+
+      - 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" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Setup system dependencies for cypress and python app
+        run: >
+          apt-get update && apt-get install --yes
+          libgtk2.0-0 libgbm-dev libnotify-dev libgconf-2-4 xvfb python3.10-venv
+
+      - name: Setup Node
+        uses: actions/setup-node@v3
+        if: steps.find-cypress.outputs.has-cypress-tests == 'true'
+        with:
+          node-version: 16
+
+      - name: Restore renv from cache
+        uses: actions/cache@v3
+        env:
+          CACHE_KEY: renv-${{ runner.arch }}-${{ runner.os }}-${{ matrix.directory }}-${{ env.APP_SUFFIX }}
+        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()
+          for (package in lockfile$Packages) {
+              if (package$Source == "GitHub") {
+                  renv::record(paste0(package$RemoteUsername, "/", package$Package)) # TODO: This installs packages form main branch, make necessary change for release version.
+              }
+          }
+
+      - 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 deploy 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 }}_${{ env.APP_SUFFIX }}"),
+            appTitle = "${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ env.APP_SUFFIX }}",
+            account = "${{ env.SHINYAPPSIO_ACCOUNT }}",
+            upload = TRUE,
+            logLevel = "normal",
+            lint = FALSE,
+            forceUpdate = TRUE
+          )
+
+      - name: Commit updated renv.lock file
+        continue-on-error: true
+        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 pull
+          git stash apply
+          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