WIP

Author: neelay-aign

pyproject.toml

@@ -138,7 +138,7 @@ dependencies = [
     "lxml>=6.0.2",                      # For python 3.14 pre-built wheels
     "filelock>=3.20.1",                 # CVE-2025-68146
     "marshmallow>=3.26.2",              # CVE-2025-68480
-    "fastmcp>=2.0.0,<3",                # MCP server - Major version 3 is in beta as of 26/01/2026 and has not been released on PyPI. Upgraded once a stable release is out.
+    "fastmcp>=2.0.0,<3",                # MCP server - Major version 3 is in beta as of 26/01/2026 and has not been released on PyPI. Upgrade once a stable release is out.
 ]
 
 [project.optional-dependencies]

src/aignostics/CLAUDE.md

@@ -11,7 +11,7 @@ This file provides a comprehensive overview of all modules in the Aignostics SDK
 | **wsi** | Whole slide image processing | ✅ | ✅ | ✅ |
 | **dataset** | IDC dataset downloads | ✅ | ✅ | ✅ |
 | **bucket** | Cloud storage operations | ✅ | ✅ | ✅ |
-| **utils** | Core utilities, DI & MCP | ✅ | ❌ | ✅ |
+| **utils** | Core utilities & DI | ✅ | ❌ | ✅ |
 | **gui** | Desktop launchpad | ❌ | ✅ | ✅ |
 | **notebook** | Marimo notebook server | ❌ | ✅ | ✅ |
 | **qupath** | QuPath integration | ✅ | ✅ | ✅ |
@@ -76,7 +76,7 @@ This file provides a comprehensive overview of all modules in the Aignostics SDK
 
 ### 🛠️ utils
 
-**Core infrastructure, shared utilities, and MCP server**
+**Core infrastructure and shared utilities**
 
 - **Core Features**:
   - Dependency injection, logging, settings, health checks
@@ -270,7 +270,7 @@ For detailed information about each module, see:
 - [wsi/CLAUDE.md](wsi/CLAUDE.md) - Image processing
 - [dataset/CLAUDE.md](dataset/CLAUDE.md) - Dataset operations
 - [bucket/CLAUDE.md](bucket/CLAUDE.md) - Storage management
-- [utils/CLAUDE.md](utils/CLAUDE.md) - Infrastructure details and MCP server
+- [utils/CLAUDE.md](utils/CLAUDE.md) - Infrastructure details
 - [gui/CLAUDE.md](gui/CLAUDE.md) - Desktop interface
 - [notebook/CLAUDE.md](notebook/CLAUDE.md) - Marimo notebook integration
 - [qupath/CLAUDE.md](qupath/CLAUDE.md) - QuPath integration

src/aignostics/cli.py

@@ -72,12 +72,12 @@ def notebook(
 def mcp_run() -> None:
     """Run the MCP server.
 
-    Starts an MCP server using stdio transport that exposes SDK functionality
+    Starts an MCP server using `stdio` transport that exposes SDK functionality
     to AI agents. The server automatically discovers and mounts tools from
     the SDK and any installed plugins.
 
     Examples:
-        aignostics mcp run
+        uv run aignostics mcp run
     """
     from aignostics.utils import mcp_run  # noqa: PLC0415
 
@@ -93,7 +93,7 @@ def mcp_list_tools() -> None:
     name and description.
 
     Examples:
-        aignostics mcp list-tools
+        uv run aignostics mcp list-tools
     """
     import operator  # noqa: PLC0415
 

src/aignostics/utils/_mcp.py

@@ -1,15 +1,16 @@
 """MCP (Model Context Protocol) server utilities.
 
-This module provides utilities for creating and running MCP servers that expose
-SDK functionality to AI agents. It follows the same simple pattern as _gui.py -
-functions and constants rather than classes.
+This module provides utilities for creating and running a central MCP server
+that exposes tools from the Aignostics SDK and any installed plugins. It
+includes functions to discover MCP servers, create a combined server, run
+the server, and list available tools.
 
 Example:
     # Start MCP server via CLI
-    aignostics mcp run
+    uv run aignostics mcp run
 
     # List available tools
-    aignostics mcp list-tools
+    uv run aignostics mcp list-tools
 
     # Use programmatically
     from aignostics.utils import mcp_create_server, mcp_run, mcp_list_tools