Clean up jupyter example app (#255)

* Create example app

* Add comments

* Test example with CI

* Replace jupyter

* Clean up unused apps

* Add back jupyter-template which is still in use by UI

Author: pantherman594

.github/workflows/test-pr.yaml

@@ -25,13 +25,10 @@ jobs:
             - 'startupscript/**'
             - 'test/**'
         config:
-          # BENCH-4080: Re-enable cirrocumulus test
           - jupyter-template:
               user: jupyter
             jupyter:
               user: jovyan
-            shiny:
-              user: shiny
             r-analysis:
               user: rstudio
               workbench_tools: true

README.md

@@ -18,3 +18,5 @@ The `.devcontainer.json` file in the custom app folder (e.g. r-analysis/) contai
 `post-startup.sh` contains workbench specific set up.
 
 Please visit https://support.workbench.verily.com/docs/guides/cloud_apps/create_custom_apps/ for details about using a dev container specification to create a custom app in Workbench.
+
+For an example app, see [src/jupyter](https://github.com/verily-src/workbench-app-devcontainer/tree/main/src/jupyter).

src/cirrocumulus/.devcontainer.json

@@ -1,17 +1,21 @@
 {
-  "name": "Jupyter app",
+  "name": "Workbench Example Jupyter App",
   "dockerComposeFile": "docker-compose.yaml",
   "service": "app",
   "shutdownAction": "none",
   "workspaceFolder": "/workspace",
+  // This post create command is required to set up the user environment with
+  // the Workbench CLI and mount workspace resources. To add additional setup
+  // commands, specify a string shell command instead.
+  // "postCreateCommand": "./startupscript/post-startup.sh 'jovyan' '/home/jovyan' '${templateOption:cloud}' '${templateOption:login}' && echo 'Additional setup commands can go here.'",
   "postCreateCommand": [
     "./startupscript/post-startup.sh",
-    "jovyan",
+    "jovyan", // This must be the user inside the container and their home directory.
     "/home/jovyan",
     "${templateOption:cloud}",
     "${templateOption:login}"
   ],
-  // re-mount bucket files on container start up
+  // Re-mount workspace resources on container start up
   "postStartCommand": [
     "./startupscript/remount-on-restart.sh",
     "jovyan",
@@ -20,12 +24,17 @@
     "${templateOption:login}"
   ],
   "features": {
-    "ghcr.io/devcontainers/features/java@sha256:df67d6ff6e9cdd858207ae9e92a99ddb88384b789f79eecd6f873216e951d286": {
+    // The below features are required for the Workbench CLI. If the image
+    // already comes with these features, they can be omitted. Feel free to add
+    // other devcontainer features as desired (see
+    // https://containers.dev/features).
+    "ghcr.io/devcontainers/features/java:1": {
       "version": "17"
     },
-    "ghcr.io/devcontainers/features/aws-cli@sha256:bbc9fd513c22e331953126c75ad7b2ed1f9044f1cd5890b7073b634810459b18": {},
-    "ghcr.io/dhoeric/features/google-cloud-cli@sha256:fa5d894718825c5ad8009ac8f2c9f0cea3d1661eb108a9d465cba9f3fc48965f": {}
+    "ghcr.io/devcontainers/features/aws-cli:1": {},
+    "ghcr.io/dhoeric/features/google-cloud-cli:1": {}
   },
+  // This is the user that will run the post create and post start commands.
   "remoteUser": "root",
   "customizations": {
     "workbench": {

src/cirrocumulus/Dockerfile

@@ -1,7 +1,7 @@
 
-# Jupyter (jupyter)
+# Workbench Example Jupyter App (jupyter)
 
-A Template to run jupyter on workbench
+An example app containing a JupyterLab image
 
 ## Options
 
@@ -14,4 +14,4 @@ A Template to run jupyter on workbench
 
 ---
 
-_Note: This file was auto-generated from the [devcontainer-template.json](https://github.com/verily-src/workbench-app-devcontainers/blob/main/src/jupyter/devcontainer-template.json).  Add additional notes to a `NOTES.md`._
+_Note: This file was auto-generated from the [devcontainer-template.json](devcontainer-template.json).  Add additional notes to a `NOTES.md`._