Jupyter

The following webpage lists several Jupyter tricks (in particular, it illustrates many Ipython magic commands) that should improve your efficiency (note that this blog post is about two years old so some of the tricks may have been integrated in the default behavior of jupyter now).

The best solution to this is to install rpy2. On my machine, I have installed the python3-rpy2 debian package with apt-get install. An other alternative consists in going through the python package manager with

pip install rpy2

Then you'll be able to use both languages in the same notebook by:

1. Loading rpy2:

   %load_ext rpy2.ipython
   

2. Using the %R Ipython magic:

   %R 
   summary(cars)
   

   Python objects can then even be passed to R as follows (assuming df is a pandas dataframe):

   %%R -i df
   plot(df)
   

Obviously, you can convert to html or pdf using the using the File > Download as > HTML (or PDF) menu option. This can also be done from the command line with the following command:

ipython3 nbconvert --to pdf Untitled.ipynb

If you want to use a specific style, then the nbconvert exporter should be customised. This is discussed and demoed here. We encourage you to simply read the doc of nbconvert.

Instead of going directly through LaTeX and playing too much with the nbconvert exporter, an other option consists in exporting to Markdown and playing with pandoc. Both approaches work, it's rather a matter of taste.

Here is what you should install:

sudo apt-get install jupyter-notebook python3-pip python3-matplotlib python3-numpy

On my machine, I got the version 5.4.1:

jupyter-notebook --version

5.4.1

The ipython notebook can then be run with the following command:

jupyter-notebook

If you want to use the R kernel in jupyter, follow these instructions.

Alternatively, you can install rpy2 (see the Running R and Python in the same notebook section).

sudo apt-get python3-rpy2

Here is what I had to install on my recent debian machine to make sure the notebook export via latex works:

sudo apt-get install wkhtmltopdf
sudo apt-get install texlive-xetex

Here is our jupyter extension that allows to git push/pull from the notebooks:

jupyter nbextension install https://raw.githubusercontent.com/brospars/nb-git/master/nb-git.js
jupyter nbextension enable nb-git

Here are two interesting extensions that can improve readability:

• Code folding

  pip3 install jupyter_contrib_nbextensions
  # jupyter contrib nbextension install --user # not done yet
  

• Hiding code

  sudo pip3 install hide_code
  sudo jupyter-nbextension  install --py hide_code
  jupyter-nbextension  enable --py hide_code
  jupyter-serverextension enable --py hide_code