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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?

Homunculus Reticulli
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  • 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 Feb 24 '17 at 23:51

8 Answers8

80

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
ogrisel
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  • Interesting, I don't have IPython installed in the virtenv, but running `which jupyter` shows its in `/usr/bin/jupyter`, Ill try pip installing Jupyter in the virtenv and see if that resolves the issue. – Homunculus Reticulli Feb 25 '17 at 10:57
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    Nope, installing jupyter in my virtenv did not reolve the issue, I still get the error message: `ImportError: No module named 'sklearn'` – Homunculus Reticulli Feb 25 '17 at 11:02
  • Actually, I created a new virtenv (--no-site-packages) and pip installed the modules I wanted - now it works. Thanks – Homunculus Reticulli Feb 25 '17 at 11:18
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    > 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. – ogrisel Feb 26 '17 at 21:37
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    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 – andilabs Aug 31 '18 at 15:25
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    Don't forget to switch kernel in jupyter. – cglacet Mar 03 '19 at 14:59
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    `ipykernel install` works, but unfortunately adds a new kernel globally, i.e. on sessions not run within this virtual env. – Valentas Apr 23 '19 at 13:05
  • Yep, that's a problem for sure. – cglacet May 21 '19 at 23:19
  • Installing jupyter in virtualenv is not working here: it fails to connect to the kernel – xtof54 Aug 06 '19 at 14:26
  • If it's not working for you, try running `python -m ipykernel install --name=my-virtualenv-name` from within your activated virtual environment. Note: I removed the `--user` flag. This will install the kernelspec to the system directory. I'm not an expert on the topic, but I it seems to source the correct path when you launch jupyter-lab. Worked for me! – chiceman Nov 09 '21 at 19:53
  • The last command returns `Installed kernelspec env in /usr/local/share/jupyter/kernels/env` and does not solve the issue. `where python` gives the correct path. – Rick Dec 22 '22 at 23:42
45

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.

ClimbsRocks
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    I can see the kernel find and connect to it in jupyter, but it can't find my modules still. Ideas? – Elliptica Aug 02 '18 at 22:59
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    @climbsrocks yea, as Elliiptica has stated, I've done this and still not able import packages. Any ideas? – Jed Aug 06 '19 at 16:57
30

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

  1. create a virtual environment

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

  2. Activate the virtual environment

    workon your_env_name

  3. Install Jupyter and other packages

    pip install jupyter, numpy

  4. Add a new kernel to your Jupyter config

    ipython kernel install --user --name=your_env_name

  5. 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.

C. Feng
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12

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!

Pujan Mehta
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    Where is 5 performed? In the activated VENV_NAME? why should I repeat step 4 every time I install a package?? – MrR Jun 12 '20 at 21:50
5

Solution without adding a new kernel globally!!

  1. create a new virtual environment by 
python3 -m virtualenv envname
  1. 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.

  1. Install your desired packages in activated virtualenv and launch jupyter in it and voila!
user_3pij
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2

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.

Tiphaine Champetier
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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
hack3rman
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-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
Patrick
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Vijay Kumar
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