Fix the app deployments

.github/workflows/deploy.yaml

@@ -3,20 +3,18 @@ name: Deploy Apps 🚀
 
 on:
   push:
-    branches:
-      - main
-    tags:
-      - "*"
   workflow_dispatch:
-  #schedule:
-  #  - cron: '12 3 * * *'
+  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:
@@ -29,45 +27,143 @@ jobs:
       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=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: |
+          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:
-          path: ${{ github.event.repository.name }}
+          node-version: 16
 
-      - name: Overwrite the global Rprofile ✍️
+      - 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: ${{ env.CACHE_KEY }}-
+
+      - name: Update renv.lock file with updated GitHub packages
+        shell: Rscript {0}
         run: |
-          cat > /usr/local/lib/R/etc/Rprofile.site <<RPROFILE
-           options(
-            repos = c(
-              Pharmaverse = "https://pharmaverse.r-universe.dev",
-              CRAN = "https://cloud.r-project.org",
-              BioC = BiocManager::repositories()
-            ),
-            download.file.method = 'libcurl',
-            HTTPUserAgent = sprintf(
-              "R/%s R (%s)",
-              getRversion(),
-              paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"])
-            )
-          )
-          RPROFILE
+          setwd("${{ 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: Deploy apps 🖨 ${{ github.event.repository.name }} 🎨
+      - name: Install R packages using renv and update the renv snapshot
+        shell: Rscript {0}
+        working-directory: ${{ matrix.directory }}
         run: |
-          Sys.setenv(GITHUB_PAT="${{ secrets.GITHUB_TOKEN }}")
-          devtools::install_local(
-            ".",
-            upgrade = "never",
-            dependencies = TRUE
+          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"
           )
-          teal.gallery::deploy_all_apps(
-            api_key = "${{ secrets.SHINYAPPSIO_TOKEN }}",
-            api_secret = "${{ secrets.SHINYAPPSIO_SECRET }}",
-            title_prefix = "NEST",
-            title_suffix = "${{ github.ref_name }}",
-            server = "https://${{ env.SHINYAPPSIO_ACCOUNT }}.shinyapps.io",
-            create_manifest = TRUE
+          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
           )
-        working-directory: ${{ github.event.repository.name }}
-        shell: Rscript {0}
+
+      - 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

README.md

@@ -15,27 +15,34 @@ A gallery of sample apps based on the [`teal`](https://github.com/insightsengine
 
 ### Development version
 
-- [basic-teal](https://genentech.shinyapps.io/NEST_basic-teal_main/)
-- [exploratory](https://genentech.shinyapps.io/NEST_exploratory_main/)
-- [safety](https://genentech.shinyapps.io/NEST_safety_main/)
-- [efficacy](https://genentech.shinyapps.io/NEST_efficacy_main/)
-- [patient-profile](https://genentech.shinyapps.io/NEST_patient-profile_main/)
-- [early-dev](https://genentech.shinyapps.io/NEST_early-dev_main/)
-- [longitudinal](https://genentech.shinyapps.io/NEST_longitudinal_main/)
-- [RNA-seq](https://genentech.shinyapps.io/NEST_RNA-seq_main/)
-- [python](https://genentech.shinyapps.io/NEST_python_main/)
+- [basic-teal](https://genentech.shinyapps.io/NEST_basic-teal_stable/)
+- [exploratory](https://genentech.shinyapps.io/NEST_exploratory_stable/)
+- [safety](https://genentech.shinyapps.io/NEST_safety_stable/)
+- [efficacy](https://genentech.shinyapps.io/NEST_efficacy_stable/)
+- [patient-profile](https://genentech.shinyapps.io/NEST_patient-profile_stable/)
+- [early-dev](https://genentech.shinyapps.io/NEST_early-dev_stable/)
+- [longitudinal](https://genentech.shinyapps.io/NEST_longitudinal_stable/)
+- [RNA-seq](https://genentech.shinyapps.io/NEST_RNA-seq_stable/)
+- [python](https://genentech.shinyapps.io/NEST_python_stable/)
 
 ## Running the apps
 
 You can run any of these apps by just executing these two lines of code in your R console.
 
 By sourcing the [sourceme.R](https://github.com/insightsengineering/teal.gallery/blob/main/utils/sourceme.R) file you make sure that you have access to the `restore_and_run()`
 
+Note: Make sure to install [renv](https://rstudio.github.io/renv/index.html) before you do this. Also, it is recommended that you create and use a Github PAT. Once you have the PAT, run the following:
+
+```R
+Sys.setenv(GITHUB_PAT = "your_access_token_here")
+```
+
 Running the `restore_and_run("APP_NAME")` will run the `APP_NAME` by restoring the packages using [renv](https://rstudio.github.io/renv/)
 
 ```R
 source("https://raw.github.com/insightsengineering/teal.gallery/main/_internal/utils/sourceme.R")
-# Assuming you want to run the "basic-teal" app. Refer to the list above to know which apps are possible
+
+# Run the basic-teal app
 restore_and_run("basic-teal")
 ```
 
@@ -47,8 +54,14 @@ All `teal` sample apps are wrapped into this package for the sake of portability
 
 Adding a sample app involves the following steps:
 
-1. Copy each sample app into a file named `app.R` into a sensible folder name inside it's own directory. The directory is also the `APP_NAME`.
-2. Make sure that `{renv}` is used for the teal app.
-3. Create a GIF recording ([KAP](https://getkap.co/) is a good tool for this). Make sure that the dimensions of the GIF is 970x555 px and the size is about 1 MB. (It can be done by recording using KAP in 1470x840 px and rendering 5fps and downsizing 33%). Place the GIF inside the `_internal/quarto/assets/img` directory. Also, make sure that the name of the GIF is `APP_NAME.gif`. Also, make sure to place a static image with the name dimention called `APP_NAME.png` that will be displayed in the demo page when the card is not hovered.
-4. Update the `_internal/quarto/demo-apps.yml` with a new `app/title`. This should be the `APP_NAME`.
-5. Run the `_internal/utils/generate_app_readme.R` to generate the readme for the app inside it's own directory.
+#### Hard requirements
+
+1. Copy each sample app into a file named `app.R` into a sensible folder name inside it's own directory. The directory has to be named with the `APP_NAME`.
+2. Update the `_internal/quarto/demo-apps.yml` with a new `app/title`. This should be the `APP_NAME`.
+3. Run the `_internal/utils/generate_app_readme.R` to generate the readme for the app inside it's own directory.
+
+#### Optional/Soft requirements
+
+1. You can snapshot the teal app dependencies using `{renv}` but make sure to snapshot using GitHub references to the teal packages.
+2. Create a GIF recording ([KAP](https://getkap.co/) is a good tool for this). Make sure that the dimensions of the GIF is 970x555 px and the size is about 1 MB. (It can be done by recording using KAP in 1470x840 px and rendering 5fps and downsizing 33%). Place the GIF inside the `_internal/quarto/assets/img` directory. Also, make sure that the name of the GIF is `APP_NAME.gif`. Also, make sure to place a static image with the name dimention called `APP_NAME.png` that will be displayed in the demo page when the card is not hovered.
+3. Add front-end tests with the help of cypress. Copy the contents of the `js` directory within some other app's directory inside your app directory to get the node dependencies. Place the cypress tests inside the `tests/cypress` inside your app's directory. Please refer to an existing app's tests so that the `.github/deploy.yaml` will automaticall run the cypress tests.

RNA-seq/README.md

@@ -6,11 +6,13 @@
 ### Run the app yourself
 
     source("https://raw.github.com/insightsengineering/teal.gallery/main/_internal/utils/sourceme.R")
-    restore_and_run("RNA-seq")
+
+    # Run the app
+    restore_and_run("RNA-seq", package_repo = "https://insightsengineering.r-universe.dev")
 
 ### View the deployed app
 
-Deployed app: <https://genentech.shinyapps.io/NEST_RNA-seq_main>
+Deployed app: <https://genentech.shinyapps.io/NEST_RNA-seq_stable>
 
 ### Preview the app