Running Jupyter notebook in a virtualenv: installed sklearn module not available

Question

I have installed a created a virtualenv machinelearn and installed a few python modules (pandas, scipy and sklearn) in that environment.

When I run jupyter notebook, I can import pandas and scipy in my notebooks - however, when I try to import sklearn, I get the following error message:

import sklearn

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-8fd979e02004> in <module>()
----> 1 import sklearn

ImportError: No module named 'sklearn'

I am able to import all modules, at the command line - so I know they have been successfully installed:

(machinelearn) me@yourbox:~/path/to/machinelearn$ python -c "import pandas, scipy, sklearn"
(machinelearn) me@yourbox:~/path/to/machinelearn$

How can I import sklearn in my jupyter notebook running in a virtualenv?

I think you have not started your notebook with the correct python executable. Its written towards the right of the page and there should be a dropdown. Check if it is the conda installable with the virtualenv and not root. — joydeep bhattacharjee
– joydeep bhattacharjee, Commented Feb 24, 2017 at 23:51

ogrisel · Accepted Answer · 2021-11-16 09:16:52Z

104

You probably have not installed jupyter / IPython in your virtualenv. Try the following:

python -c "import IPython"

and check that the jupyter command found in your $PATH is the one from the bin folder of your venv:

which jupyter

For windows users in a powershell console, you can use the following to check that the jupyter command in your $env:Path is the one from the Scripts folder of you venv:

get-command jupyter

Edit: if this is the problem, just run python -m pip install jupyter in your venv.

Edit 2: actually you might also need:

python -m ipykernel install --user --name=my-virtualenv-name

and then switch the kernel named "my-virtualenv-name" in the jupyter user interface.

Edit 3: maybe the --user flag in the last command is a bad idea:

python -m ipykernel install --name=my-virtualenv-name

edited Nov 16, 2021 at 9:16

answered Feb 25, 2017 at 10:08

ogrisel

40.3k14 gold badges120 silver badges125 bronze badges

Sign up to request clarification or add additional context in comments.

12 Comments

Homunculus Reticulli Over a year ago

Nope, installing jupyter in my virtenv did not reolve the issue, I still get the error message: ImportError: No module named 'sklearn'

ogrisel Over a year ago

> ImportError: No module named 'sklearn' Then it actually did resolve the jupyter issue. You just need to pip install scikit-learn in your venv as well.

andilabs Over a year ago

the answer of @ClimbsRocks

Now run the kernel "self-install" script:  python -m ipykernel install --user --name=my-virtualenv-name Replacing the --name parameter as appropriate.

solved the problem for me

cglacet Over a year ago

Don't forget to switch kernel in jupyter.

Valentas Over a year ago

ipykernel install works, but unfortunately adds a new kernel globally, i.e. on sessions not run within this virtual env.

|

ClimbsRocks · Accepted Answer · 2017-09-20 01:59:20Z

61

Another approach to take is to have one global jupyter installation, but to point to different kernels to run as the backend.

That approach is outlined here in their docs: http://help.pythonanywhere.com/pages/IPythonNotebookVirtualenvs

Copying below in case the link breaks: You can use a virtualenv for your IPython notebook. Follow the following steps:

Install the ipython kernel module into your virtualenv

workon my-virtualenv-name  # activate your virtualenv, if you haven't already
pip install ipykernel

Now run the kernel "self-install" script:

python -m ipykernel install --user --name=my-virtualenv-name

Replacing the --name parameter as appropriate.

You should now be able to see your kernel in the IPython notebook menu: Kernel -> Change kernel and be able so switch to it (you may need to refresh the page before it appears in the list). IPython will remember which kernel to use for that notebook from then on.

answered Sep 20, 2017 at 1:59

ClimbsRocks

1,15415 silver badges16 bronze badges

3 Comments

Elliptica Over a year ago

I can see the kernel find and connect to it in jupyter, but it can't find my modules still. Ideas?

Jed Over a year ago

@climbsrocks yea, as Elliiptica has stated, I've done this and still not able import packages. Any ideas?

Mathew Paul Over a year ago

Running python -m ipykernel install --user --name=my-virtualenv-name solved it for me.. Thank You

C. Feng · Accepted Answer · 2018-03-15 21:18:35Z

40

To use Jupyter notebook with virtual environment (using virtualenvwrapper) plus packages installed in that environment, follow steps below:

create a virtual environment

mkvirtualenv --no-site-packages --python=/your/python/path your_env_name

Activate the virtual environment
```
workon your_env_name
```
Install Jupyter and other packages
```
pip install jupyter, numpy
```

Add a new kernel to your Jupyter config

ipython kernel install --user --name=your_env_name

Done. You may now use Jupyter notebook under the virtual environment.
```
jupyter-notebook
```

Disclaimer: the question has been answered but is hidden in one of the replies. I googled and took sometime to find the right answer. So I just summarize it so someone having the same issue can easily follow.

answered Mar 15, 2018 at 21:18

C. Feng

4915 silver badges7 bronze badges

4 Comments

Cornelius Roemer Over a year ago

Amazing, this worked directly for me. In step 1 the --python flag was unnecessary for me (didn't know what to put there so left it out), also step 2 was redundant for me.

Roger Steinberg Over a year ago

thats the real answer... the order is crucial to making this work.

Kriticoder Over a year ago

launching jupyter-notebook from the same terminal where my env was activated did the trick for me..thanks!!!

jtlz2 Over a year ago

Step 4 makes this a golden answer - thank you so so much!! Highly bookmarkable.

Pujan Mehta · Accepted Answer · 2019-03-08 14:28:33Z

20

Assuming that jupyter is installed on your machine, not on the virtual environtment.

Using a virtual environment with Jupyter notebook

VENV_NAME = "YOUR VIRTUAL ENV NAME"

1) virtualenv VENV_NAME

2) source venv/bin/activate

3) Add this package if not present: pip3 install ipykernel

4) Then execute this command: ipython kernel install --user --name=VENV_NAME

5) Now open up the Jupyter Notebook and in change kernel select VENV_NAME

6) To install a new package perform pip3 install <PACKAGE NAME> in your terminal and repeat step 4.

Hope it helps!

answered Mar 8, 2019 at 14:28

Pujan Mehta

5085 silver badges8 bronze badges

3 Comments

MrR Over a year ago

Where is 5 performed? In the activated VENV_NAME? why should I repeat step 4 every time I install a package??

carverd Over a year ago

I found this in the 'kernal' -> 'change kernal' drop down within the notebook that I was working in. I don't think you need to repeat step 4.

WHOATEMYNOODLES Over a year ago

That fixed it for me. Thanks!!

user_3pij · Accepted Answer · 2019-11-27 15:51:46Z

6

Solution without adding a new kernel globally!!

create a new virtual environment by

python3 -m virtualenv envname

Activate your enviroment and install jupyter in it by

pip install jupyter

One thing you have to make sure before installing jupyter is that you don't have following packages already installed in it.

ipykernel             
ipython               
ipython-genutils      
ipywidgets            
jupyter               
jupyter-client        
jupyter-console     
jupyter-core

If you've previously installed them then first uninstall them by pip uninstall.

Install your desired packages in activated virtualenv and launch jupyter in it and voila!

answered Nov 27, 2019 at 15:51

user_3pij

1,40214 silver badges23 bronze badges

Comments

Tiphaine Champetier · Accepted Answer · 2018-02-22 09:43:37Z

Creation of virtualenv with python3 -m venv command

I had the same problem as yours. In my case I had created the virtualenv with the command

python3 -m venv ./my_virtual_env --system-site-packages

The problem was I could not install jupyter inside the virtual environment as it was already in the system-site-package (when you try to install it, it tells you "Requirement already satisfied").

To install jupyter, (and in a first instance pip, that does not get installed neither in your virtual environment with this command) but still have access to system-site-package you can run :

python3 -m venv ./my_virtual_env

Activate you virtual environment, run pip3 install jupyter (and pip3 install pip) and then turn on the option include-system-site-packages in the file ./my_virtual_env/pyvenv.cfg.

After deactivation and reactivation of you environment, you will have access to system site-packages.

Creation of virtualenv with virtualenv command

Given this answer you can prevent the access to system site-packages by creating a file ./my_virtual_env/lib/python3.4/no-global-site-packages.txt, and get the access back by removing it.

NWMT · Accepted Answer · 2025-08-12 14:53:53Z

Here is a more self-contained solution. Step 5 is the what is different from all other answers.

Create the virtual environment

python -m venv envname
Activate virtual environment

source path_to_envname/bin/activate
Install packages (in the new virtual environment)

pip install scikit-learn jupyter
Locate the jupyter exectuable in path_to_envname/bin/
Run the version of jupyter that is inside your virtual environment

path_to_envname/bin/jupyter notebook

This way you don't muck up the "global" jupyter notebook

UPDATE: Here's how to achieve this using uv. This works great and it's my new workflow.

Initialize the virtual environment. This creates and populates a new directory (or folder) callet project

uv init project
Go into the new directory. Once in the directory uv commands will apply to the virtual environment of this project

cd project
Install packates (super fast with uv)

uv add scikit-learn jupyter
Run jupyter within the project's environment

uv run jupyter notebook

hack3rman · Accepted Answer · 2023-04-06 22:10:14Z

0

Assuming you've set up the environment properly as others have noted, make sure you have installed the proper scikit-learn package. You can check with:

pip list

If you see something like: sklearn 0.0.post1

You need to run:

pip install scikit-learn

The following is depreciated and will not work:

pip install sklearn

answered Apr 6, 2023 at 22:10

hack3rman

11 bronze badge

Comments

damdafayton · Accepted Answer · 2024-03-27 20:50:00Z

0

Those with VScode, can click Python version box on the right > "Select Another Kernel" > "Python environments" and select the one that has their venv path.

answered Mar 27, 2024 at 20:50

damdafayton

2,6674 gold badges14 silver badges24 bronze badges

Comments

Patrick · Accepted Answer · 2018-07-09 16:24:56Z

-1

You can still install jupyter inside your virtual-environment if you have created your virtual env using:

python -m venv --system-site-packages path/to/my-venv

Simply do this:

activate-your-env
pip install -I jupyter

And you are now ready to go

jupyter notebook

edited Jul 9, 2018 at 16:24

Patrick

1,7377 gold badges21 silver badges28 bronze badges

answered Jul 9, 2018 at 14:42

Vijay Kumar

11 silver badge4 bronze badges

Collectives™ on Stack Overflow

Running Jupyter notebook in a virtualenv: installed sklearn module not available

10 Answers 10

12 Comments

3 Comments

4 Comments

3 Comments

Comments

Comments

Comments

Comments

Comments

Comments

Your Answer

Linked

Hot Network Questions

Collectives™ on Stack Overflow

10 Answers 10

12 Comments

3 Comments

4 Comments

3 Comments

Comments

Comments

Comments

Comments

Comments

Comments

Your Answer

Sign up or log in

Post as a guest

Linked

Related