The `insert_execute_code_cell` tool stuck when `PYTHONDEVMODE=1` environment variable is set

[Atry]

Description

The insert_execute_code_cell tool stuck when PYTHONDEVMODE=1 environment variable is set

Reproduce

1. Create the following .mcp.json

   {
     "mcpServers": {
       "jupyter": {
         "command": "uvx",
         "args": [ "jupyter-mcp-server" ],
         "env": {
           "JUPYTER_URL": "http://localhost:8888",
           "JUPYTER_TOKEN": "my token",
           "ALLOW_IMG_OUTPUT": "true",
           "PYTHONDEVMODE": "1"
         }
       }
     }
   }
   

2. Run claude cli
3. Ask the agent to use insert_execute_code_cell

Then claude cli stuck.

Expected behavior

claude cli should not get stuck.

Context

Workaround: unset PYTHONDEVMODE

[echarles]

Thx for opening the issue. Are there other tools that get stuck? (like execute_code, or insert_cell...)?

[Atry]

execute_code, insert_cell and use_notebook work

execute_cell also gets stuck

[echarles]

will try to reproduce. which python version? Any logs appearing?

[Atry]

$ python --version
Python 3.13.8

[Atry]

Any logs appearing?

I did not see any abnormal logs from claude cli. I guess jupyter-mcp-server accedentally prints some logs to stdout when PYTHONDEVMODE=1 but I cannot directly see jupyter-mcp-server's logs from claude cli.

However, I do see the following logs from jupyter lab when claude cli get stuck.

[E 2025-11-04 02:06:09.192 ServerApp] Failed to write message
    Traceback (most recent call last):
      File "/nix/store/j8p98639hb4xm9g63hgl6f5pwmsq07al-agentic-sql-dev-env/lib/python3.13/site-packages/jupyter_server_ydoc/handlers.py", line 282, in send
        self.write_message(message, binary=True)
        ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
      File "/nix/store/j8p98639hb4xm9g63hgl6f5pwmsq07al-agentic-sql-dev-env/lib/python3.13/site-packages/tornado/websocket.py", line 332, in write_message
        raise WebSocketClosedError()
    tornado.websocket.WebSocketClosedError

If I remove PYTHONDEVMODE from .mcp.json, I would not see the above error logs from jupyter lab

[ChengJiale150]

@Atry Thank for your reporting, I am curious why do you set PYTHONDEVMODE=1 in Jupyter-MCP-Server, debug or dev for MCP Server?

[Atry]

I set PYTHONDEVMODE globally for debugging. I set PYTHONDEVMODE in .mcp.json in order to reproduce this issue only.

[ChengJiale150]

If I remove PYTHONDEVMODE from .mcp.json, I would not see the above error logs from jupyter lab

Maybe, A temporary solution is remove PYTHONDEVMODE=1 in .mcp.json. Jupyter MCP Server run in separate Python enviroment using uvx and may not affect PYTHONDEVMODE for global Python Env.