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

Answer 1

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!

Answer 2

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.

Answer 3

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.

Answer 4

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.

Answer 5

Solution without adding a new kernel globally!!

1. create a new virtual environment by

python3 -m virtualenv envname

2. 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.

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

Answer 6

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.