Jupyter 3: Magics

Magics constitute a simple command language that significantly extends the power of Jupyter notebooks. There are two types of magics:

  • Line magics: Commands that are prepended by %, and whose arguments only extend to the end of the line.
  • Cell magics: Commands that start with %% and then apply to the whole cell. Must be written on the first line of a cell.

Now list all available magics with %lsmagic (which itself is a magic). You add a question mark to a magic to show the help (e.g. %lsmagic?). Some of them act as shortcuts for commonly used shell commands (%ls, %cp, %cat, ..). Others are useful for debugging and optimizing your code (%timeit, %debug, %prun, ..). For more information see the magics documentation Links to an external site..

A very useful magic, in particular when using shell commands a lot in your work, is %%capture. This will capture the stdout/stderr of any code cell and store them in a Python object. Run %%capture? to display the help and try to understand how it works. Try it out with either some Python code, other magics or shell commands. Here is an example of how you can make it work:

%%capture output
%%bash
echo "Print to stdout"
echo "Print to stderr" >&2

… And in another cell:

print("stdout:" + output.stdout)
print("stderr:" + output.stderr)

Tip
You can capture the output of some magics directly like this: my_dir = %pwd.

The %%script magic is used for specifying a program (Bash, Perl, Ruby, ..) with which to run the code (similar to a shebang). For some languages it’s possible to use these shortcuts:

  • %%ruby
  • %%perl
  • %%bash
  • %%html
  • %%latex
  • %%R

Note on R code
In order to use the %%R magic you need to install the rpy2 extension, for example with Conda. This package is already installed in the jupyter-env environment you’re using for this tutorial. However, you also have to load it by running %load_ext rpy2.ipython in a cell.

Try this out if you know any of the languages above. Otherwise you can always try to print the quadratic formula with LaTeX!

\begin{array}{*{20}c} {x = \frac{{ - b \pm \sqrt {b^2 - 4ac} }}{{2a}}} & {{\rm{when}}} & {ax^2 + bx + c = 0} \\ \end{array}

Another useful magic is %precision which sets the floating point precision in the notebook. As a quick example, add the following to a cell and run it:

float(100/3)

Next set the precision to 4 decimal points by running a cell with:

%precision 4

Now run the cell with float(100/3) again to see the difference.

Running %precision without additional arguments will restore the default.

Quick recap
In this section we’ve learned:

  • The basics of Jupyter magics and the difference between line magics and cell magics
  • How to capture and use output from notebook cells with %%capture
  • How to use magics to run non-Python code in notebooks