Failed to run server: No module named 'sqlalchemy'

[WaqarQureshii]

Unable to import any python modules that have to be uv pip installed.

Steps to reproduce the behavior:

1. Using uv to create a venv
2. activate venv
3. uv add sqlalchemy
4. from sqlalchemy import create_engine
5. run server using cli command: uv run mcp install main.py

Expected behavior
I expect the server on claude's desktop app to show me the tools I have in my main.py file after refreshing (ctrl + R)
I do see this when I remove the import polars as pl line, then my functions show up when they're not reliant on any external function. Below is showing that I have the relevant python modules installed in my venv.

Claude log:
2025-04-29T18:25:10.114Z [test2] [info] Initializing server...
2025-04-29T18:25:10.133Z [test2] [info] Server started and connected successfully
2025-04-29T18:25:10.134Z [test2] [info] Message from client: {"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"claude-ai","version":"0.1.0"}},"jsonrpc":"2.0","id":0}
Failed to run server: No module named 'sqlalchemy'
2025-04-29T18:25:12.426Z [test2] [info] Server transport closed
2025-04-29T18:25:12.426Z [test2] [info] Client transport closed
2025-04-29T18:25:12.427Z [test2] [info] Server transport closed unexpectedly, this is likely due to the process exiting early. If you are developing this MCP server you can add output to stderr (i.e. console.error('...') in JavaScript, print('...', file=sys.stderr) in python) and it will appear in this log.
2025-04-29T18:25:12.427Z [test2] [error] Server disconnected. For troubleshooting guidance, please visit our debugging documentation {"context":"connection"}
2025-04-29T18:25:12.427Z [test2] [info] Client transport closed

Claude Developer Screenshot:

claude_desktop_config.json config:
{
"mcpServers": {
"test2": {
"command": "uv",
"args": [
"run",
"--with",
"mcp[cli]",
"mcp",
"run",
"C:\Users\WaqarQ\OneDrive - Trez Capital\Documents\099. Personal Waqar\Python\mcp-trez\main.py"
]
}
}
}

uv pip list
Package Version

---

annotated-types 0.7.0
anyio 4.9.0
certifi 2025.1.31
click 8.1.8
colorama 0.4.6
greenlet 3.2.1
h11 0.14.0
httpcore 1.0.8
httpx 0.28.1
httpx-sse 0.4.0
idna 3.10
markdown-it-py 3.0.0
mcp 1.6.0
mdurl 0.1.2
numpy 2.2.5
pandas 2.2.3
polars 1.28.1
pydantic 2.11.3
pydantic-core 2.33.1
pydantic-settings 2.9.1
pygments 2.19.1
pyodbc 5.2.0
python-dateutil 2.9.0.post0
python-dotenv 1.1.0
pytz 2025.2
rich 14.0.0
shellingham 1.5.4
six 1.17.0
sniffio 1.3.1
sqlalchemy 2.0.40
sse-starlette 2.2.1
starlette 0.46.2
typer 0.15.2
typing-extensions 4.13.2
typing-inspection 0.4.0
tzdata 2025.2
uvicorn 0.34.2

OS
Windows 10 Enterprise

I also installed sqlalchemy globally to see if that would work and that did not.

[Dadiya-Harsh]

@WaqarQureshii
In windows, path require double slash in claude_desktop_config.json config try to set path like this:

{
    "mcpServers": {
        "weather": {
            "command": "uv",
            "args": [
                "--directory",
                "E:\\Projects\\MCP\\mcp-demo\\learning",
                "run",
                "weather.py"
            ]
        },
        "web-search":{
            "command": "uv",
            "args":[
                "--directory",
                "E:\\Projects\\MCP\\mcp-demo\\learning",
                "run",
                "web_search_using_tavily.py"
            ]
        }
    }
}
 

[Dadiya-Harsh]

@WaqarQureshii and keep in mind your server should be running

[WaqarQureshii]

## @Dadiya-Harsh Understood, I've implemented the format you suggested as follows in my config.json file:

{ "mcpServers": { "main": { "command": "uv", "args": [ "--directory", "C:\\Users\\WaqarQu\\Path\\To\\Server\\Folder\\server_folder\\main.py" ] } } }

This is the Error I am getting in the log:

2025-04-30T15:32:53.031Z [main] [info] Initializing server...
2025-04-30T15:32:53.049Z [main] [info] Server started and connected successfully
2025-04-30T15:32:53.131Z [main] [info] Message from client: {"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"claude-ai","version":"0.1.0"}},"jsonrpc":"2.0","id":0}
error: 'uv.exe' requires a subcommand but one was not provided
[subcommands: run, init, add, remove, sync, lock, export, tree, tool, python, pip, venv, virtualenv, v, build, publish, build-backend, cache, self, clean, version, generate-shell-completion, --generate-shell-completion, help]

Usage: uv.exe [OPTIONS]

so I tried adding "uv run" in the command as well but this is the error I get:

2025-04-30T15:44:19.293Z [main] [info] Initializing server...
2025-04-30T15:44:19.313Z [main] [error] spawn uv run ENOENT {"context":"connection","stack":"Error: spawn uv run ENOENT\n at ChildProcess._handle.onexit (node:internal/child_process:285:19)\n at onErrorNT (node:internal/child_process:483:16)\n at process.processTicksAndRejections (node:internal/process/task_queues:82:21)"}
2025-04-30T15:44:19.314Z [main] [error] spawn uv run ENOENT {"stack":"Error: spawn uv run ENOENT\n at ChildProcess._handle.onexit (node:internal/child_process:285:19)\n at onErrorNT (node:internal/child_process:483:16)\n at process.processTicksAndRejections (node:internal/process/task_queues:82:21)"}

So i added the absolute path to uv so I added the absolute path to the uv.exe in my command, but this is the error I get

error: 'uv.exe' requires a subcommand but one was not provided
[subcommands: run, init, add, remove, sync, lock, export, tree, tool, python, pip, venv, virtualenv, v, build, publish, build-backend, cache, self, clean, version, generate-shell-completion, --generate-shell-completion, help]

Usage: uv.exe [OPTIONS]

**So I tried added run in the args but I get this:

error: The directory name is invalid. (os error 267)

** I tried adding the run command after the uv.exe absolute path but get this error:

{"stack":"Error: spawn C:\Users\Waqar\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\Scripts\uv.exe run ENOENT\n at ChildProcess._handle.onexit (node:internal/child_process:285:19)\n at onErrorNT (node:internal/child_process:483:16)\n at process.processTicksAndRejections (node:internal/process/task_queues:82:21)"}

[Dadiya-Harsh]

@WaqarQureshii are you sure when you are using this tools in Claude desktop server is on?

[Dadiya-Harsh]

@WaqarQureshii is it possible you could share your source code then it would be easier to debug, if it is possible

[Dadiya-Harsh]

## @Dadiya-Harsh Understood, I've implemented the format you suggested as follows in my config.json file:

{ "mcpServers": { "main": { "command": "uv", "args": [ "--directory", "C:\\Users\\WaqarQu\\Path\\To\\Server\\Folder\\server_folder\\main.py" ] } } }

This is the Error I am getting in the log:

2025-04-30T15:32:53.031Z [main] [info] Initializing server... 2025-04-30T15:32:53.049Z [main] [info] Server started and connected successfully 2025-04-30T15:32:53.131Z [main] [info] Message from client: {"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"claude-ai","version":"0.1.0"}},"jsonrpc":"2.0","id":0} error: 'uv.exe' requires a subcommand but one was not provided [subcommands: run, init, add, remove, sync, lock, export, tree, tool, python, pip, venv, virtualenv, v, build, publish, build-backend, cache, self, clean, version, generate-shell-completion, --generate-shell-completion, help]

Usage: uv.exe [OPTIONS]

so I tried adding "uv run" in the command as well but this is the error I get:

2025-04-30T15:44:19.293Z [main] [info] Initializing server... 2025-04-30T15:44:19.313Z [main] [error] spawn uv run ENOENT {"context":"connection","stack":"Error: spawn uv run ENOENT\n at ChildProcess._handle.onexit (node:internal/child_process:285:19)\n at onErrorNT (node:internal/child_process:483:16)\n at process.processTicksAndRejections (node:internal/process/task_queues:82:21)"} 2025-04-30T15:44:19.314Z [main] [error] spawn uv run ENOENT {"stack":"Error: spawn uv run ENOENT\n at ChildProcess._handle.onexit (node:internal/child_process:285:19)\n at onErrorNT (node:internal/child_process:483:16)\n at process.processTicksAndRejections (node:internal/process/task_queues:82:21)"}

So i added the absolute path to uv so I added the absolute path to the uv.exe in my command, but this is the error I get

error: 'uv.exe' requires a subcommand but one was not provided [subcommands: run, init, add, remove, sync, lock, export, tree, tool, python, pip, venv, virtualenv, v, build, publish, build-backend, cache, self, clean, version, generate-shell-completion, --generate-shell-completion, help]

Usage: uv.exe [OPTIONS]

**So I tried added run in the args but I get this:

error: The directory name is invalid. (os error 267)

** I tried adding the run command after the uv.exe absolute path but get this error:

{"stack":"Error: spawn C:\Users\Waqar\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\Scripts\uv.exe run ENOENT\n at ChildProcess._handle.onexit (node:internal/child_process:285:19)\n at onErrorNT (node:internal/child_process:483:16)\n at process.processTicksAndRejections (node:internal/process/task_queues:82:21)"}

see this configuration file closely you have not added run command after the directory

{
    "mcpServers": {
        "weather": {
            "command": "uv",
            "args": [
                "--directory",
                "E:\\Projects\\MCP\\mcp-demo\\learning",
                "run",
                "weather.py"
            ]
        },
        "web-search":{
            "command": "uv",
            "args":[
                "--directory",
                "E:\\Projects\\MCP\\mcp-demo\\learning",
                "run",
                "web_search_using_tavily.py"
            ]
        }
    }
}
 

[Dadiya-Harsh]

    "mcpServers": {

        "enhanced_folder_server":{   
            "command": "uv" ,    
            "args":[
                "--directory",
                "E:\\Projects\\MCP\\mcp-demo\\learning\\Servers",
                "run",
                "enhanced_folder_server.py"
            ]
        }
    }
}

first the server name: enhanced_folder_server what you want to give it is up to you,
command : uv since i am using uv python manager,
then in args: --directory where your file is stored not the full path of your file,
the since i am using uv i have to specify run(because to run python file using uv command is uv run filename.py) ,
then at the end your file name in which the server is stored

[Dadiya-Harsh]

    "mcpServers": {

        "main:{
            "command": "uv",
            "args":[
                "--directory",
                "C:\\Users\\WaqarQu\\Path\\To\\Server\\Folder\\server_folder",
                "run",
                "main.py"
            ]
        }
    }
}

@WaqarQureshii
according to this conversation paste above code it should work now
and make sure server is running, that is main.py file is running in background then only will able to access the tools in your client or host application (i.e., Claude desktop)

[WaqarQureshii]

@Dadiya-Harsh Feels like you're heading in the right direction. I'll share the source code in a bit. Following the format above (which makes logical sense now, thank you for explaining it in that way), I get this in the log:
2025-04-30T18:48:35.531Z [mcp-demo] [info] Initializing server...
2025-04-30T18:48:35.551Z [mcp-demo] [info] Server started and connected successfully
2025-04-30T18:48:35.552Z [mcp-demo] [info] Message from client: {"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"claude-ai","version":"0.1.0"}},"jsonrpc":"2.0","id":0}
...
2025-04-30T18:48:36.849Z [mcp-demo] [info] Server transport closed
2025-04-30T18:48:36.850Z [mcp-demo] [info] Client transport closed
2025-04-30T18:48:36.850Z [mcp-demo] [info] Server transport closed unexpectedly, this is likely due to the process exiting early. If you are developing this MCP server you can add output to stderr (i.e. console.error('...') in JavaScript, print('...', file=sys.stderr) in python) and it will appear in this log.
2025-04-30T18:48:36.850Z [mcp-demo] [error] Server disconnected. For troubleshooting guidance, please visit our debugging documentation {"context":"connection"}
2025-04-30T18:48:36.851Z [mcp-demo] [info] Client transport closed

Wondering if it is how I am running my server?

I am using uv run mcp run main.py which changes my terminal suggesting it is running:

The 3 dots are my print('...', file=sys.stderr) statement in my main.py

Within my Claude desktop it says it cannot connect obviously.

Can this have anything to do with firewalls or how I installed uv?
I used the non-pip method of installing uv.

[WaqarQureshii]

@Dadiya-Harsh here is the source code:
https://github.com/WaqarQureshii/mcp_server_demo

[Dadiya-Harsh]

@Dadiya-Harsh Feels like you're heading in the right direction. I'll share the source code in a bit. Following the format above (which makes logical sense now, thank you for explaining it in that way), I get this in the log: 2025-04-30T18:48:35.531Z [mcp-demo] [info] Initializing server... 2025-04-30T18:48:35.551Z [mcp-demo] [info] Server started and connected successfully 2025-04-30T18:48:35.552Z [mcp-demo] [info] Message from client: {"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"claude-ai","version":"0.1.0"}},"jsonrpc":"2.0","id":0} ... 2025-04-30T18:48:36.849Z [mcp-demo] [info] Server transport closed 2025-04-30T18:48:36.850Z [mcp-demo] [info] Client transport closed 2025-04-30T18:48:36.850Z [mcp-demo] [info] Server transport closed unexpectedly, this is likely due to the process exiting early. If you are developing this MCP server you can add output to stderr (i.e. console.error('...') in JavaScript, print('...', file=sys.stderr) in python) and it will appear in this log. 2025-04-30T18:48:36.850Z [mcp-demo] [error] Server disconnected. For troubleshooting guidance, please visit our debugging documentation {"context":"connection"} 2025-04-30T18:48:36.851Z [mcp-demo] [info] Client transport closed

Wondering if it is how I am running my server?

I am using uv run mcp run main.py which changes my terminal suggesting it is running:

The 3 dots are my print('...', file=sys.stderr) statement in my main.py

Within my Claude desktop it says it cannot connect obviously.

Can this have anything to do with firewalls or how I installed uv? I used the non-pip method of installing uv.

@WaqarQureshii, I noticed you haven’t specified the transport method in your server code. You should add the following section:

if __name__ == "__main__":
    mcp.run(transport="stdio")

Also, check out this repo to follow my learning journey with MCP. It might give you a better idea of how to use it effectively:
👉 https://github.com/Dadiya-Harsh-wappnet/MCP-DEMO.git

Make sure to follow the MCP documentation carefully as well.
and you can just run the server with this command:

uv run main.py

you don't have to write mcp run

[kk6]

@WaqarQureshii The uv in my development environment and the uv bundled with Claude Desktop are different.
When you add dependencies in Claude’s settings.json, you have to install sqlalchemy explicitly, just as you already do with mcp[cli].

I ran into a “python-frontmatter not found” error in my own repository and fixed it like this:

"minerva": {
  "command": "uv",
  "args": [
    "run",
    "--with",
    "mcp[cli]",
    "--with",
    "python-frontmatter",
    "mcp",
    "run",
    "/path/to/project/server.py:mcp"
  ]
}

Here’s the command to install the above settings into Claude’s configuration file from within the repository:

uv run mcp install /path/to/project/server.py:mcp -f .env --with python-frontmatter

[Kludex]

This is not an MCP issue.