ModuleNotFoundError: No module named 'pydantic_core._pydantic_core' when importing from mcp.server even though pydantic-core is installed

[ABHIJITH-EA]

Describe the bug
I'm using the mcp package (version 1.6.0) in a Docker container based on node:20-alpine, running Python 3.11.12. When I try to import NotificationOptions and Server from mcp.server, I get the following error:

ModuleNotFoundError: No module named 'pydantic_core._pydantic_core'

Even though pydantic-core==2.33.1 and pydantic==2.11.3 are already installed.

To Reproduce
Steps to reproduce the behavior:

1. Use a Docker image based on node:20-alpine
2. Install Python 3.11.12
3. Install mcp==1.6.0 using uv pip install
4. Try this import in Python:

   from mcp.server import NotificationOptions, Server

5. See the ModuleNotFoundError for pydantic_core._pydantic_core

Expected behavior
The import should work as expected since pydantic-core is installed. There should be no missing module error if dependencies are properly installed.

Screenshots

Desktop (please complete the following information):

• OS: Alpine (via Docker node:20-alpine)
• Python version: 3.13
• MCP version: 1.6.0
• Install method: uv pip install mcp==1.6.0

Smartphone (please complete the following information):
Not applicable.

Additional context
Here is the relevant part of uv pip freeze:

pydantic==2.11.3  
pydantic-core==2.33.1  
mcp==1.6.0  

[SlagYouKnowZM]

Have same issue

[Viicos]

Could you provide your Dockerfile, as a MRE so that I can reproduce? More importantly, what is your host platform?

[marcoimme]

same issue, using python alpine as baseimage.

sample Dockefile

FROM python:3.12.3  AS py-build

COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/

WORKDIR /app

# Python files and uv.lock
COPY pyproject.toml ./
COPY uv.lock ./
COPY *.py ./
RUN uv sync --locked

# Sources
COPY *.py ./
COPY tools/ ./tools
COPY resources/ ./resources
COPY prompts/ ./prompts



# Create final layer
FROM python:3.12.3-alpine

COPY --from=py-build /app /app

WORKDIR /app

ENV PATH="/app/.venv/bin:$PATH"

CMD ["python" ,"server.py", "--transport", "sse", "--port", "8000"]

on run, I have

Traceback (most recent call last):
  File "/app/server.py", line 5, in <module>
    from pydantic import Field
  File "/app/.venv/lib/python3.12/site-packages/pydantic/__init__.py", line 5, in <module>
    from ._migration import getattr_migration
  File "/app/.venv/lib/python3.12/site-packages/pydantic/_migration.py", line 4, in <module>
    from .version import version_short
  File "/app/.venv/lib/python3.12/site-packages/pydantic/version.py", line 5, in <module>
    from pydantic_core import __version__ as __pydantic_core_version__
  File "/app/.venv/lib/python3.12/site-packages/pydantic_core/__init__.py", line 6, in <module>
    from ._pydantic_core import (
ModuleNotFoundError: No module named 'pydantic_core._pydantic_core'

[Viicos]

@marcoimme you are installing your dependencies on a different image than the one used to run the application. Alpine uses musl, which requires musl wheels to be used when installing pydantic-core.

Does it used to work? Or did you just encounter the issue when trying to setup your Dockerfile?

[marcoimme]

the error occurred during docker run, the build worked properly.
Now I switched the intermediate build layer using alpine as well

I workarounded the issue installing pydantic-core from alpine repo

now my Dockerfile looks like that

FROM ${default_image_registry}python:3.12.3-alpine  AS py-build

COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/

WORKDIR /app

RUN apk add py3-pydantic-core

# Python files and uv.lock
COPY pyproject.toml ./
COPY uv.lock ./
COPY *.py ./
RUN uv sync --locked

# Sources
COPY *.py ./
COPY tools/ ./tools
COPY resources/ ./resources
COPY prompts/ ./prompts



# Create final layer
FROM ${default_image_registry}python:3.12.3-alpine

COPY --from=py-build /app /app

WORKDIR /app

ENV PATH="/app/.venv/bin:$PATH"

CMD ["python" ,"server.py", "--transport", "sse", "--port", "8000"]

and it runs

[ABHIJITH-EA]

@Viicos Here’s a minimal Dockerfile that can be used to reproduce the issue. It's based on the LibreChat Dockerfile, which I was originally using: https://github.com/danny-avila/LibreChat/blob/main/Dockerfile

FROM node:20-alpine

# Install basic deps
RUN apk add --no-cache curl

# Install uv
RUN curl -LsSf https://astral.sh/uv/install.sh | sh

ENV PATH="/root/.local/bin:${PATH}"

WORKDIR /app

# Create a Python 3.11 virtual environment
RUN uv venv --python=3.11 && \
    uv pip install mcp

# Install the MCP server

# Add test file
COPY test_mcp.py .

# Run the test
CMD ["uv", "run", "test_mcp.py"]

test_mcp.py

from mcp.server import NotificationOptions, Server

Build and run Dockerfile

docker build -t mcp-test .

docker run mcp-test`

Error:

Traceback (most recent call last):
  File "/app/test_mcp.py", line 1, in <module>
    from mcp.server import NotificationOptions, Server
  File "/app/.venv/lib/python3.11/site-packages/mcp/__init__.py", line 1, in <module>
    from .client.session import ClientSession
  File "/app/.venv/lib/python3.11/site-packages/mcp/client/session.py", line 6, in <module>
    from pydantic import AnyUrl, TypeAdapter
  File "/app/.venv/lib/python3.11/site-packages/pydantic/__init__.py", line 5, in <module>
    from ._migration import getattr_migration
  File "/app/.venv/lib/python3.11/site-packages/pydantic/_migration.py", line 4, in <module>
    from .version import version_short
  File "/app/.venv/lib/python3.11/site-packages/pydantic/version.py", line 5, in <module>
    from pydantic_core import __version__ as __pydantic_core_version__
  File "/app/.venv/lib/python3.11/site-packages/pydantic_core/__init__.py", line 6, in <module>
    from ._pydantic_core import (
ModuleNotFoundError: No module named 'pydantic_core._pydantic_core'

In my case, I was trying to run this MCP server inside the Docker container: https://github.com/vivekVells/mcp-pandoc

The .python-version in that repo is set to 3.11, I got this error when starting the server:

ModuleNotFoundError: No module named 'pydantic_core._pydantic_core'

[Viicos]

Up until 3.13, Python wasn't properly inferring the extension suffix for shared libraries. This was fixed in python/cpython#95855, so you need to use Python 3.13 or latter.