fix(codespace): attempt to fix

Author: amyheather

.devcontainer/.devcontainer.json

@@ -3,6 +3,7 @@
 {
   "name": "RStudio with Quarto",
   "image": "ghcr.io/rocker-org/devcontainer/tidyverse:4.4",
+  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
   "waitFor": "onCreateCommand",
 
   "features": {
@@ -25,9 +26,7 @@
       "extensions": [
         "REditorSupport.r",
         "rdebugger.r-debugger",
-        "quarto.quarto",
-        "ms-toolsai.jupyter",
-        "ms-python.python"
+        "quarto.quarto"
       ]
     }
   },
@@ -37,12 +36,12 @@
     "8787": {
       "label": "RStudio",
       "requireLocalPort": true,
-      "onAutoForward": "openBrowser"
+      "onAutoForward": "ignore"
     }
   },
 
-  "onCreateCommand": "bash .devcontainer/setup.sh",
-  "postAttachCommand": "bash .devcontainer/welcome.sh",
-
+  // Use 'postCreateCommand' to run commands after the container is created.
+  "postCreateCommand": "bash .devcontainer/setup.sh",
+  "postAttachCommand": "sudo rstudio-server start &> /dev/null && bash .devcontainer/welcome.sh",
   "remoteUser": "rstudio"
 }

.devcontainer/setup.sh

@@ -1,20 +1,13 @@
-# Source: Adapted from https://github.com/boettiger-lab/nasa-topst-env-justice (MIT)
+# Source: https://github.com/boettiger-lab/nasa-topst-env-justice (MIT)
+# Comments from https://github.com/AnushaPB/codespacer
 
-#!/usr/bin/env bash
-set -euo pipefail
+# Copies a configuration file to disable authentication on RStudio Server,
+# making it accessible without needing to log in.
+sudo cp /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
 
-# Ensure RStudio runs without password inside Codespace
-if [ -f /etc/rstudio/disable_auth_rserver.conf ]; then
-  sudo cp /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
-fi
+# Adds "USER=rstudio" to the end of the /etc/environment file,
+# setting a system-wide environment variable to specify the default user for RStudio.
+sudo sudo bash -c 'echo "USER=rstudio" >>/etc/environment'
 
-# Make sure USER is rstudio so RStudio knows who to log in
-sudo bash -c 'echo "USER=rstudio" >> /etc/environment'
-
-# Start RStudio Server in the background if not running
-if ! pgrep -x "rserver" > /dev/null 2>&1; then
-  sudo rstudio-server start
-fi
-
-# Minimal R packages you might want – optional
-Rscript -e 'install.packages(c("quarto"), repos = "https://cloud.r-project.org")' || true
+# Start the RStudio Server in the background
+sudo /init &> /dev/null &

.devcontainer/welcome.sh

@@ -1,34 +1,13 @@
 # Source: Adapted from https://github.com/boettiger-lab/nasa-topst-env-justice (MIT)
 
-#!/usr/bin/env bash
-set -euo pipefail
-
-# Ensure RStudio is running (idempotent)
-if ! pgrep -x "rserver" > /dev/null 2>&1; then
-  sudo rstudio-server start
-fi
-
-cat <<'EOF'
-========================================
- Welcome to this R + Quarto Codespace
-========================================
-
-RStudio Server is available at:
-
-  http://127.0.0.1:8787
-
-In GitHub Codespaces:
-
-- Open the "Ports" panel.
-- Find the "RStudio (8787)" port.
-- If it is not already open, choose "Open in browser".
-
-Once RStudio is open, you can:
-- Open a .qmd file
-- Use the "Render" button or run:
-
-    quarto::quarto_preview()
-
-to preview your document.
-========================================
-EOF
+# Construct the message
+message="## [Open in RStudio](https://$CODESPACE_NAME-8787.app.github.dev)
+"
+# Echo the message to the terminal
+echo "
+👋 Welcome to Codespaces! You are on our custom image. 
+   - It includes runtimes and tools for R using RStudio 
+
+🌐 Open the RStudio editor here: https://$CODESPACE_NAME-8787.app.github.dev
+   - (This may take a few seconds to load, retry if necessary)
+"