In virtual environment wrong version of python is used

[eudaiman]

Description

In my virtual environment I installed jupyter notebook. But when I tried running it, I discovered that it's using the wrong python.

Reproduce

Create venv. Then install venv jupyter:
python -m pip install jupyter
python -m ipykernel install --name=my-kernel-name --prefix=$VIRTUAL_ENV
Then in jupyter notebook import sys and print sys.version. I warrant you it will not be the one in venv.

Expected behavior

Should be the same version as python -V in terminal.

Context

Using Ubuntu 20.04, everything else is latest version (python, jupyter etc.)

[minrk]

This suggests to me that perhaps there may be a different kernelspec installed somewhere unexpected. can you share jupyter kernelspec list? And cat $VIRTUAL_ENV/share/jupyter/kernels/my-kernel-name/kernel.json?

Here's what I get following your steps:

> python3 -m venv /tmp/my-env
minrk@heavy-3 [11:18:49] ~
> source /tmp/my-env/bin/activate
(my-env) minrk@heavy-3 [11:18:56] ~
> which python3
/tmp/my-env/bin/python3
(my-env) minrk@heavy-3 [11:19:05] ~
> python3 -m pip install ipykernel notebook
...
Successfully installed MarkupSafe-3.0.2 anyio-4.8.0 appnope-0.1.4 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-3.0.0 async-lru-2.0.4 attrs-25.1.0 babel-2.17.0 beautifulsoup4-4.13.3 bleach-6.2.0 certifi-2025.1.31 cffi-1.17.1 charset-normalizer-3.4.1 comm-0.2.2 debugpy-1.8.12 decorator-5.1.1 defusedxml-0.7.1 executing-2.2.0 fastjsonschema-2.21.1 fqdn-1.5.1 h11-0.14.0 httpcore-1.0.7 httpx-0.28.1 idna-3.10 ipykernel-6.29.5 ipython-8.32.0 isoduration-20.11.0 jedi-0.19.2 jinja2-3.1.5 json5-0.10.0 jsonpointer-3.0.0 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 jupyter-client-8.6.3 jupyter-core-5.7.2 jupyter-events-0.12.0 jupyter-lsp-2.2.5 jupyter-server-2.15.0 jupyter-server-terminals-0.5.3 jupyterlab-4.3.5 jupyterlab-pygments-0.3.0 jupyterlab-server-2.27.3 matplotlib-inline-0.1.7 mistune-3.1.1 nbclient-0.10.2 nbconvert-7.16.6 nbformat-5.10.4 nest-asyncio-1.6.0 notebook-7.3.2 notebook-shim-0.2.4 overrides-7.7.0 packaging-24.2 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 platformdirs-4.3.6 prometheus-client-0.21.1 prompt_toolkit-3.0.50 psutil-6.1.1 ptyprocess-0.7.0 pure-eval-0.2.3 pycparser-2.22 pygments-2.19.1 python-dateutil-2.9.0.post0 python-json-logger-3.2.1 pyyaml-6.0.2 pyzmq-26.2.1 referencing-0.36.2 requests-2.32.3 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.22.3 send2trash-1.8.3 six-1.17.0 sniffio-1.3.1 soupsieve-2.6 stack_data-0.6.3 terminado-0.18.1 tinycss2-1.4.0 tornado-6.4.2 traitlets-5.14.3 types-python-dateutil-2.9.0.20241206 typing_extensions-4.12.2 uri-template-1.3.0 urllib3-2.3.0 wcwidth-0.2.13 webcolors-24.11.1 webencodings-0.5.1 websocket-client-1.8.0
(my-env) minrk@heavy-3 [11:19:34] ~
> python3 -m ipykernel install --name=my-kernel-name --prefix=$VIRTUAL_ENV
Installed kernelspec my-kernel-name in /tmp/my-env/share/jupyter/kernels/my-kernel-name
(my-env) minrk@heavy-3 [11:20:28] ~
> jupyter kernelspec list
Available kernels:
  my-kernel-name    /tmp/my-env/share/jupyter/kernels/my-kernel-name
  python3           /tmp/my-env/share/jupyter/kernels/python3
(my-env) minrk@heavy-3 [11:21:00] ~
> cat /tmp/my-env/share/jupyter/kernels/my-kernel-name/kernel.json
{
 "argv": [
  "/tmp/my-env/bin/python3",
  "-Xfrozen_modules=off",
  "-m",
  "ipykernel_launcher",
  "-f",
  "{connection_file}"
 ],
 "display_name": "my-kernel-name",
 "language": "python",
 "metadata": {
  "debugger": true
 }
}%

and after launching jupyter-notebook, create a notebook with my-kernel-name:

In [1]: sys.executable
Out[1]: '/tmp/my-env/bin/python3'

so everything appears to be going as expected.

[prajwal-38]

The issue arises because the --prefix=$VIRTUAL_ENV flag for ipykernel install is incorrect. It installs the kernel in the wrong location, not properly linking it to the virtual environment's Python.

create your venv and then activate it, and while in venv you need to install jupyter and ipykernel using pip

pip install jupyter ipykernel

and then install kernel properly

python -m ipykernel install --user --name=my-kernel-name --display-name "Python(venv)"

Hope this helps

[RRosio]

Hi @eudaiman are you still experiencing this issue? Have you been able to take a look at the suggestions above?

[RRosio]

Hi @eudaiman, I hope the suggestions above were helpful and that you were able to resolve your issue! Since this doesn’t appear to be an error within the Notebook codebase, I’ll go ahead and close this. However, please feel free to open a new issue if you run into any other problems that should be addressed in this repository.