Maintain separate workflows for deployments (#96)

Maintain separate workflows for the `stable` and `dev` deployments. This brings the ability to trigger just one of them when needed.
insightsengineering · Nov 20, 2023 · 864e938 · 864e938
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diff --git a/.github/workflows/deploy_dev.yaml b/.github/workflows/deploy_dev.yaml
@@ -0,0 +1,165 @@
+---
+name: Deploy Dev Apps 🚀
+
+on:
+  push:
+    branches:
+      - dev
+  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
+  GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }}
+  BRANCH: dev
+
+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",
+          ]
+    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))
+              }
+          }
+
+      - 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
diff --git a/.github/workflows/deploy.yaml → .github/workflows/deploy_stable.yaml b/.github/workflows/deploy.yaml → .github/workflows/deploy_stable.yaml
@@ -1,5 +1,5 @@
 ---
-name: Deploy Apps 🚀
+name: Deploy Stable Apps 🚀
 
 on:
   push:
@@ -16,7 +16,9 @@ concurrency:
 env:
   SHINYAPPSIO_ACCOUNT: genentech
   APP_PREFIX: NEST
-  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+  APP_SUFFIX: stable
+  GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }}
+  BRANCH: main
 
 jobs:
   deploy:
@@ -44,19 +46,10 @@ jobs:
             "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=main" >> $GITHUB_ENV # TODO: Change the branch name to main
-          else
-            echo "BRANCH_NAME=dev" >> $GITHUB_ENV # TODO: Change the branch name to deval
-          fi
-
       - name: Check if cypress test exists
         id: find-cypress
         run: |
@@ -81,7 +74,7 @@ jobs:
       - name: Restore renv from cache
         uses: actions/cache@v3
         env:
-          CACHE_KEY: renv-${{ runner.arch }}-${{ runner.os }}-${{ matrix.directory }}-${{ matrix.channel }}
+          CACHE_KEY: renv-${{ 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)) }}
@@ -92,10 +85,9 @@ jobs:
         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))
+                  renv::record(paste0(package$RemoteUsername, "/", package$Package, "@*release"))
               }
           }
 
@@ -143,8 +135,8 @@ jobs:
           )
           rsconnect::deployApp(
             appFiles = c("app.R"),
-            appName = rsconnect::generateAppName("${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ matrix.channel }}"),
-            appTitle = "${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ matrix.channel }}",
+            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",
@@ -153,17 +145,19 @@ jobs:
           )
 
       - 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 stash apply
           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 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

diff --git a/README.md b/README.md
@@ -7,8 +7,6 @@
   <img align="right" width=auto height="100" src="https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/teal.gallery.png">
 </a>
 
-
-
 A gallery of sample apps based on the [`teal`](https://github.com/insightsengineering/teal) framework.
 
 ## Links to apps on `shinyapps.io`
@@ -48,7 +46,16 @@ restore_and_run("basic-teal")
 
 ## Development
 
-All `teal` sample apps are wrapped into this package for the sake of portability. All development standards and practices that we currently use for teal app development also apply to this repository.
+All `teal` sample apps are wrapped into this repository into it's own sub-directory. All development standards and practices that we currently use for teal app development also apply to this repository.
+
+### Auto-deployment
+
+All the sample apps are automatically deployed every day using the CI in two channels:
+
+- `stable` channel: The code for the Teal apps is taken from the `main` branch of `teal.gallery`, and the NEST packages are installed from the `main` branch of GitHub. This is done using the `deploy_stable.yaml`.
+- `dev` channel: The code for the Teal apps is taken from the `dev` branch of `teal.gallery` and the NEST packages are installed from the last `release tag` of GitHub. This is done using the `deploy_dev.yaml`.
+
+_IMPORTANT_: Although we can now test the unreleased features of the NEST packages in deployments, currently, the divergent `dev` and `main` branches must be managed and merged manually as needed to ensure that the apps work fine in both deployment channels, i.e., making sure to merge the app changes from `dev` to `main` by creating a PR.
 
 ### Adding a sample app to `teal.gallery`