Merge pull request #111 from MarcSkovMadsen/enhancement/uv-tool-update

Enhancement/uv tool update

Author: MarcSkovMadsen

docs/explanation/architecture.md

@@ -112,9 +112,10 @@ MCP Server → MCP Client → AI Assistant (with app URL)
 
 ### Documentation Index
 
-Location: `~/.holoviz-mcp/chroma/`
+Location: `~/.holoviz-mcp/vector_db/`
 
 The documentation index uses ChromaDB to store:
+
 - Document embeddings (vector representations)
 - Document metadata (source, project, path)
 - Original document text

docs/explanation/security.md

@@ -26,12 +26,12 @@ HoloViz MCP is designed with security in mind, but like any tool that provides A
 
 **Localhost Only** (Secure):
 ```bash
-HOLOVIZ_MCP_HOST=127.0.0.1 HOLOVIZ_MCP_TRANSPORT=http uvx holoviz-mcp
+HOLOVIZ_MCP_HOST=127.0.0.1 HOLOVIZ_MCP_TRANSPORT=http holoviz-mcp
 ```
 
 **All Interfaces** (Requires firewall):
 ```bash
-HOLOVIZ_MCP_HOST=0.0.0.0 HOLOVIZ_MCP_TRANSPORT=http uvx holoviz-mcp
+HOLOVIZ_MCP_HOST=0.0.0.0 HOLOVIZ_MCP_TRANSPORT=http holoviz-mcp
 ```
 
 ### Docker Deployments
@@ -48,7 +48,7 @@ Docker images default to `0.0.0.0` for accessibility. Secure with:
 ### Documentation Indexing
 
 - **Data Flow**: GitHub → Local Machine → ChromaDB
-- **Storage**: `~/.holoviz-mcp/chroma/`
+- **Storage**: `~/.holoviz-mcp/vector_db/`
 - **External Services**: None (except GitHub for cloning)
 - **Privacy**: All processing is local
 
@@ -64,7 +64,7 @@ Docker images default to `0.0.0.0` for accessibility. Secure with:
 By default, ChromaDB telemetry is disabled. If you enable it:
 
 ```bash
-ANONYMIZED_TELEMETRY=true uvx holoviz-mcp
+ANONYMIZED_TELEMETRY=true holoviz-mcp
 ```
 
 Only anonymized usage statistics are sent to ChromaDB.
@@ -83,7 +83,7 @@ HoloViz MCP can read:
 
 HoloViz MCP writes to:
 - Configuration directory (`~/.holoviz-mcp/`)
-- Documentation index (`~/.holoviz-mcp/chroma/`)
+- Documentation index (`~/.holoviz-mcp/vector_db/`)
 - Log files (if configured)
 - Server processes (if code execution enabled)
 
@@ -217,7 +217,7 @@ Logs may contain:
 Set appropriately for your environment:
 
 ```bash
-HOLOVIZ_MCP_LOG_LEVEL=WARNING uvx holoviz-mcp
+HOLOVIZ_MCP_LOG_LEVEL=WARNING holoviz-mcp
 ```
 
 ## Security Checklist

docs/how-to/configuration.md

@@ -6,7 +6,7 @@ This guide explains how to customize HoloViz MCP behavior through configuration
 
 HoloViz MCP uses a YAML configuration file located at:
 
-```
+```bash
 ~/.holoviz-mcp/config.yaml
 ```
 
@@ -40,23 +40,23 @@ Values: `stdio`, `http`
 Default: `stdio`
 
 ```bash
-HOLOVIZ_MCP_TRANSPORT=http uvx holoviz-mcp
+HOLOVIZ_MCP_TRANSPORT=http holoviz-mcp
 ```
 
 **HOLOVIZ_MCP_HOST**
 Host address to bind to (HTTP transport only).
 Default: `127.0.0.1`
 
 ```bash
-HOLOVIZ_MCP_HOST=0.0.0.0 HOLOVIZ_MCP_TRANSPORT=http uvx holoviz-mcp
+HOLOVIZ_MCP_HOST=0.0.0.0 HOLOVIZ_MCP_TRANSPORT=http holoviz-mcp
 ```
 
 **HOLOVIZ_MCP_PORT**
 Port to bind to (HTTP transport only).
 Default: `8000`
 
 ```bash
-HOLOVIZ_MCP_PORT=9000 HOLOVIZ_MCP_TRANSPORT=http uvx holoviz-mcp
+HOLOVIZ_MCP_PORT=9000 HOLOVIZ_MCP_TRANSPORT=http holoviz-mcp
 ```
 
 **HOLOVIZ_MCP_LOG_LEVEL**
@@ -65,7 +65,7 @@ Values: `DEBUG`, `INFO`, `WARNING`, `ERROR`
 Default: `INFO`
 
 ```bash
-HOLOVIZ_MCP_LOG_LEVEL=DEBUG uvx holoviz-mcp
+HOLOVIZ_MCP_LOG_LEVEL=DEBUG holoviz-mcp
 ```
 
 **HOLOVIZ_MCP_SERVER_NAME**
@@ -78,7 +78,7 @@ Default: `holoviz-mcp`
 URL prefix for Panel apps when running remotely.
 
 ```bash
-JUPYTER_SERVER_PROXY_URL=/proxy/5007/ uvx holoviz-mcp
+JUPYTER_SERVER_PROXY_URL=/proxy/5007/ holoviz-mcp
 ```
 
 This is useful when running in JupyterHub or similar environments.
@@ -91,7 +91,7 @@ Values: `true`, `false`
 Default: `false`
 
 ```bash
-ANONYMIZED_TELEMETRY=true uvx holoviz-mcp
+ANONYMIZED_TELEMETRY=true holoviz-mcp
 ```
 
 ### Display Server Configuration
@@ -192,7 +192,7 @@ docs:
 After adding repositories, update the index:
 
 ```bash
-uvx holoviz-mcp update index
+holoviz-mcp update index
 ```
 
 ## IDE-Specific Configuration
@@ -206,10 +206,9 @@ Set environment variables in `mcp.json`:
   "servers": {
     "holoviz": {
       "type": "stdio",
-      "command": "uvx",
-      "args": ["holoviz-mcp"],
+      "command": "holoviz-mcp",
       "env": {
-        "HOLOVIZ_MCP_LOG_LEVEL": "DEBUG",
+        "HOLOVIZ_MCP_LOG_LEVEL": "DEBUG"
       }
     }
   }
@@ -222,8 +221,7 @@ Set environment variables in `mcp.json`:
 {
   "mcpServers": {
     "holoviz": {
-      "command": "uvx",
-      "args": ["holoviz-mcp"],
+      "command": "holoviz-mcp",
       "env": {
         "HOLOVIZ_MCP_LOG_LEVEL": "INFO"
       }
@@ -241,7 +239,7 @@ See the [Docker Guide](docker.md) for Docker-specific configuration options.
 HoloViz MCP includes a built-in configuration viewer. Run:
 
 ```bash
-uvx holoviz-mcp serve
+holoviz-mcp serve
 ```
 
 Navigate to the Configuration Viewer tool to see your current configuration.

docs/how-to/ide-configuration.md

@@ -4,31 +4,22 @@ This guide covers configuring HoloViz MCP with different IDEs and AI assistants.
 
 ## VS Code + GitHub Copilot
 
-### Quick Install
-
-Click to install automatically:
-
-[![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=flat-square)](https://vscode.dev/redirect?url=vscode%3Amcp%2Finstall%3F%257B%2522name%2522%253A%2522holoviz%2522%252C%2522command%2522%253A%2522uvx%2522%252C%2522args%2522%253A%255B%2522holoviz-mcp%255Bpanel-extensions%255D%2522%255D%257D)
-
-### Manual Configuration
-
 1. Open VS Code
 2. Press `Ctrl+Shift+P` (or `Cmd+Shift+P` on macOS)
 3. Type "MCP: Edit Settings" and press Enter
 4. Add this configuration to your `mcp.json`:
 
-```json
-{
-  "servers": {
-    "holoviz": {
-      "type": "stdio",
-      "command": "uvx",
-      "args": ["holoviz-mcp"]
-    }
-  },
-  "inputs": []
-}
-```
+  ```json
+  {
+    "servers": {
+      "holoviz": {
+        "type": "stdio",
+        "command": "holoviz-mcp"
+      }
+    },
+    "inputs": []
+  }
+  ```
 
 5. Save and restart VS Code
 
@@ -61,8 +52,7 @@ Click to install automatically:
 {
   "mcpServers": {
     "holoviz": {
-      "command": "uvx",
-      "args": ["holoviz-mcp"]
+      "command": "holoviz-mcp"
     }
   }
 }
@@ -90,8 +80,7 @@ After restarting Claude Desktop, look for the MCP indicator (🔌) in the interf
 ```json
 {
   "name": "holoviz",
-  "command": "uvx",
-  "args": ["holoviz-mcp"]
+  "command": "holoviz-mcp"
 }
 ```
 
@@ -105,8 +94,7 @@ Add to your Windsurf MCP configuration:
 {
   "mcpServers": {
     "holoviz": {
-      "command": "uvx",
-      "args": ["holoviz-mcp"]
+      "command": "holoviz-mcp"
     }
   }
 }
@@ -119,8 +107,7 @@ For other MCP-compatible clients, use the standard configuration:
 ```json
 {
   "name": "holoviz",
-  "command": "uvx",
-  "args": ["holoviz-mcp"]
+  "command": "holoviz-mcp"
 }
 ```
 
@@ -135,8 +122,7 @@ You can customize server behavior using environment variables:
   "servers": {
     "holoviz": {
       "type": "stdio",
-      "command": "uvx",
-      "args": ["holoviz-mcp"],
+      "command": "holoviz-mcp",
       "env": {
         "HOLOVIZ_MCP_LOG_LEVEL": "DEBUG"
       }
@@ -154,8 +140,7 @@ Use a custom directory for configuration and data:
   "servers": {
     "holoviz": {
       "type": "stdio",
-      "command": "uvx",
-      "args": ["holoviz-mcp"],
+      "command": "holoviz-mcp",
       "env": {
         "HOLOVIZ_MCP_USER_DIR": "/path/to/custom/dir"
       }
@@ -169,16 +154,19 @@ Use a custom directory for configuration and data:
 After configuration, test with your AI assistant:
 
 1. **Simple Query**:
+
    ```
    List available Panel input components
    ```
 
 2. **Detailed Query**:
+
    ```
    What parameters does the Panel TextInput component have?
    ```
 
 3. **Code Generation**:
+
    ```
    Create a simple Panel dashboard with a slider
    ```
@@ -190,31 +178,36 @@ If you get detailed, accurate responses, your configuration is working! 🎉
 ### Server Not Starting
 
 **Check the command**:
+
 ```bash
 # Test the server directly
-uvx holoviz-mcp
+holoviz-mcp
 ```
 
 **Verify uv installation**:
+
 ```bash
 uv --version
 ```
 
 **Check Python version**:
+
 ```bash
 python --version  # Should be 3.11 or higher
 ```
 
 ### AI Assistant Not Recognizing Components
 
 1. **Verify documentation index exists**:
+
    ```bash
    ls ~/.holoviz-mcp
    ```
 
 2. **Recreate the index**:
+
    ```bash
-   uvx holoviz-mcp update index
+   holoviz-mcp update index
    ```
 
 3. **Restart your IDE**
@@ -228,6 +221,7 @@ python --version  # Should be 3.11 or higher
 ### Permission Errors
 
 **Linux/macOS**: Ensure the configuration file is readable:
+
 ```bash
 chmod 644 ~/.config/Code/User/globalStorage/github.copilot/mcp.json
 ```