Add OpenAI API key config and environment setup guide

.devcontainer/devcontainer.json

@@ -9,6 +9,10 @@
     "jupyter.alwaysTrustNotebooks": true,
     "workbench.startupEditor": "none"
   },
+  "runArgs": ["--env-file", "${localWorkspaceFolder}/.env"],
+  "containerEnv": {
+    "OPENAI_API_KEY": "${localEnv:OPENAI_API_KEY}"
+  },
   "postCreateCommand": "pip install -r requirements.txt && chmod +x .devcontainer/jupyter-setup.sh && .devcontainer/jupyter-setup.sh && chmod +x .devcontainer/windsurf-auth-setup.sh",
   "postStartCommand": "bash .devcontainer/postStartCommand.sh && WINDSURF_AUTH_TOKEN='eyJhbGciOiJSUzI1NiIsImtpZCI6IjU5MWYxNWRlZTg0OTUzNjZjOTgyZTA1MTMzYmNhOGYyNDg5ZWFjNzIiLCJ0eXAiOiJKV1QifQ.eyJwaWN0dXJlIjoiaHR0cHM6Ly9hdmF0YXJzLmdpdGh1YnVzZXJjb250ZW50LmNvbS91LzE5NDMyOTQ4ND92PTQiLCJpc3MiOiJodHRwczovL3NlY3VyZXRva2VuLmdvb2dsZS5jb20vZXhhMi1mYjE3MCIsImF1ZCI6ImV4YTItZmIxNzAiLCJhdXRoX3RpbWUiOjE3NDY1NzA2ODAsInVzZXJfaWQiOiJNTVJZY3NVb3ZVaFNVc2RhMkhrd1J4UE5tTWQyIiwic3ViIjoiTU1SWWNzVW92VWhTVXNkYTJIa3dSeFBObU1kMiIsImlhdCI6MTc0NjU3MDY4MSwiZXhwIjoxNzQ2NTc0MjgxLCJlbWFpbCI6ImppbUBqb3JkYW5sYWIub3JnIiwiZW1haWxfdmVyaWZpZWQiOmZhbHNlLCJmaXJlYmFzZSI6eyJpZGVudGl0aWVzIjp7ImdpdGh1Yi5jb20iOlsiMTk0MzI5NDg0Il0sImVtYWlsIjpbImppbUBqb3JkYW5sYWIub3JnIl19LCJzaWduX2luX3Byb3ZpZGVyIjoiZ2l0aHViLmNvbSJ9fQ.kgY8pNERRK3d2weIc4eR0EI_JKfATIxE9b6ACKdQE1XVwU26_p07PGfvdWo4ty8oXjCdUdnUiprM1LKaT2yZPGnleOdeJtH31Ua1DNc7hNTEideMeTyZUAOXv6O1VJdXqpcRfjc5Q5JxEjJdj1cGdomFA1c_kn3VbGyL8BsAfH6Sg6q7fB4eRRQ5MlHPBDxQl7neHsdDVGhqGprRnWfJsOI0PJhsWC4jzSBM5HO3uFKOnl_9-BdGY_zN6j_uRcFXfHB3VxfSecinepjz3u5fdmEd71YpGJNRhGXYiM7pZBhETCvA9Ri-b1Jh74dsoAyPfmnDOdt0c0xBF2TmPEPgZA' .devcontainer/windsurf-auth-setup.sh && jupyter notebook --no-browser --ip=0.0.0.0 --port=8888 --NotebookApp.token='' --NotebookApp.password='' --allow-root &",
   "extensions": [

.devcontainer/postStartCommand.sh

@@ -8,12 +8,14 @@ echo "📦 Installing Python dependencies..."
 pip install -r requirements.txt
 
 # Set up GitHub CLI if available
+SETUP_NEEDED=false
 if command -v gh &> /dev/null; then
     echo "🔧 GitHub CLI found, checking authentication..."
     # This won't authenticate, but will show status and prompt user if needed
     gh auth status || echo "⚠️  GitHub CLI needs authentication. Run 'gh auth login' to set up."
 else
     echo "⚠️  GitHub CLI not found. Some features may not work properly."
+    SETUP_NEEDED=true
 fi
 
 # Ensure directories exist
@@ -23,6 +25,7 @@ mkdir -p Data/chroma_index
 if [ -z "$OPENAI_API_KEY" ]; then
     echo "⚠️  OPENAI_API_KEY environment variable not set. Smart-Fill will not work."
     echo "    Set it in your Codespace secrets or run 'export OPENAI_API_KEY=your-key'."
+    SETUP_NEEDED=true
 fi
 
 # Check Jupyter installation and dashboard dependencies
@@ -66,6 +69,13 @@ echo "🧪 LAB AGENT ENVIRONMENT READY 🧪"
 echo "Start using the lab agent by typing in the VS Code Chat window."
 echo "For a health check, run: python Agent/test_environment.py"
 echo "To view the Protocol Dashboard, open Analysis/protocol_dashboard.ipynb"
+
+# Point to setup guide if needed
+if [ "$SETUP_NEEDED" = true ]; then
+    echo ""
+    echo "⚠️ Environment issues detected. Please see ENVIRONMENT_SETUP.md for instructions"
+    echo "   on how to properly configure your environment."
+fi
 echo ""
 
 # Exit with success

ENVIRONMENT_SETUP.md

@@ -0,0 +1,62 @@
+# Environment Setup Guide
+
+This guide helps you set up your development environment correctly to avoid warnings about missing GitHub CLI and OpenAI API keys.
+
+## GitHub CLI
+
+GitHub CLI has been added to the Dockerfile and will be automatically installed when your container is built. If you're seeing warnings about GitHub CLI missing, you may need to:
+
+1. Rebuild your container by running the command in VS Code:
+   - Press `F1` and search for "Rebuild Container"
+   - Or select "Dev Containers: Rebuild Container" from the command palette
+
+2. After rebuilding, authenticate with GitHub:
+   ```bash
+   gh auth login
+   ```
+
+## OpenAI API Key
+
+To permanently set up your OpenAI API key (required for Smart-Fill functionality):
+
+### Option 1: GitHub Codespace Secrets (Recommended)
+
+1. Go to [GitHub Codespace Secrets](https://github.com/settings/codespaces)
+2. Click on "New secret"
+3. Name: `OPENAI_API_KEY`
+4. Value: Your OpenAI API key
+5. Select the repositories where this secret should be available
+6. Click "Add secret"
+7. Rebuild your codespace for the changes to take effect
+
+### Option 2: Environment Variable in .bashrc
+
+Add the following to your `.bashrc` file in the container:
+
+```bash
+export OPENAI_API_KEY="your-openai-api-key"
+```
+
+### Option 3: Local .env File
+
+1. Uncomment the `runArgs` section in the `.devcontainer/devcontainer.json` file
+2. Create a `.env` file in the root of your repository with:
+   ```
+   OPENAI_API_KEY=your-openai-api-key
+   ```
+3. Add `.env` to your `.gitignore` to prevent accidentally committing your API key
+4. Rebuild your container
+
+## Verifying Your Setup
+
+After completing these steps, you can verify your setup by running:
+
+```bash
+# Check GitHub CLI
+gh --version
+
+# Verify OpenAI API key is set
+echo $OPENAI_API_KEY | grep -o "sk-..."
+```
+
+If properly configured, you should no longer see warnings about missing GitHub CLI or OpenAI API key when starting your environment.