ModuleNotFoundError: No module named 'pydantic_core._pydantic_core' even though pydantic-core is installed

I'm using a Docker container based on node:20-alpine and running Python 3.13 inside it. I installed my Python packages using uv pip install mcp==1.6.0.

When I try to run this import:

from mcp.server import NotificationOptions, Server

I get this error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/app/standalone/.venv/lib/python3.11/site-packages/mcp/__init__.py", line 1, in <module>
    from .client.session import ClientSession
  ...
  File "/app/standalone/.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'

But I already have pydantic-core installed, as shown in uv pip freeze:

pydantic==2.11.3  
pydantic-core==2.33.1

Does anyone know why this is happening or how to fix it?

EDIT (Added debugging information)

This issue can be reproduced using the following 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

Then build and run the container:

docker build -t mcp-test .

docker run mcp-test`

This will result in the same 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'

Despite pydantic_core being installed as shown by:

uv pip freeze Output:

pydantic==2.11.3
pydantic-core==2.33.1

This error happens because Python versions < 3.13 don’t properly infer the extension suffix for compiled libraries like pydantic-core.

The fix is to use Python 3.13 or later (see python/cpython#95855).