jupyter

IPython Sphinx Directive

Attention

This is copied verbatim from the old IPython wiki and is currently under development. Much of the information in this part of the development guide is out of date.

The ipython directive is a stateful ipython shell for embedding in sphinx documents. It knows about standard ipython prompts, and extracts the input and output lines. These prompts will be renumbered starting at 1. The inputs will be fed to an embedded ipython interpreter and the outputs from that interpreter will be inserted as well. For example, code blocks like the following:

.. code:: python3

   In [136]: x = 2

   In [137]: x**3
   Out[137]: 8

will be rendered as

In [136]: x = 2

In [137]: x**3
Out[137]: 8

Note

This tutorial should be read side-by-side with the Sphinx source for this document because otherwise you will see only the rendered output and not the code that generated it. Excepting the example above, we will not in general be showing the literal ReST in this document that generates the rendered output.

The state from previous sessions is stored, and standard error is trapped. At doc build time, ipython’s output and std err will be inserted, and prompts will be renumbered. So the prompt below should be renumbered in the rendered docs, and pick up where the block above left off.

In [138]: z = x*3   # x is recalled from previous block

In [139]: z
Out[139]: 6

In [140]: print z
--------> print(z)
6

In [141]: q = z[)   # this is a syntax error -- we trap ipy exceptions
------------------------------------------------------------
   File "<ipython console>", line 1
     q = z[)   # this is a syntax error -- we trap ipy exceptions
     ^
SyntaxError: invalid syntax

The embedded interpreter supports some limited markup. For example, you can put comments in your ipython sessions, which are reported verbatim. There are some handy “pseudo-decorators” that let you doctest the output. The inputs are fed to an embedded ipython session and the outputs from the ipython session are inserted into your doc. If the output in your doc and in the ipython session don’t match on a doctest assertion, an error will be

In [1]: x = 'hello world'

# this will raise an error if the ipython output is different
@doctest
In [2]: x.upper()
Out[2]: 'HELLO WORLD'

# some readline features cannot be supported, so we allow
# "verbatim" blocks, which are dumped in verbatim except prompts
# are continuously numbered
@verbatim
In [3]: x.st<TAB>
x.startswith  x.strip

Multi-line input is supported.

In [130]: url = 'http://ichart.finance.yahoo.com/table.csv?s=CROX\
   .....: &d=9&e=22&f=2009&g=d&a=1&br=8&c=2006&ignore=.csv'

In [131]: print url.split('&')
--------> print(url.split('&'))
['http://ichart.finance.yahoo.com/table.csv?s=CROX', 'd=9', 'e=22',

You can do doctesting on multi-line output as well. Just be careful when using non-deterministic inputs like random numbers in the ipython directive, because your inputs are ruin through a live interpreter, so if you are doctesting random output you will get an error. Here we “seed” the random number generator for deterministic output, and we suppress the seed line so it doesn’t show up in the rendered output

In [133]: import numpy.random

@suppress
In [134]: numpy.random.seed(2358)

@doctest
In [135]: numpy.random.rand(10,2)
Out[135]:
array([[ 0.64524308,  0.59943846],
 [ 0.47102322,  0.8715456 ],
 [ 0.29370834,  0.74776844],
 [ 0.99539577,  0.1313423 ],
 [ 0.16250302,  0.21103583],
 [ 0.81626524,  0.1312433 ],
 [ 0.67338089,  0.72302393],
 [ 0.7566368 ,  0.07033696],
 [ 0.22591016,  0.77731835],
 [ 0.0072729 ,  0.34273127]])

Another demonstration of multi-line input and output

In [106]: print x
--------> print(x)
jdh

In [109]: for i in range(10):
   .....:     print i
   .....:
   .....:
0
1
2
3
4
5
6
7
8
9

Most of the “pseudo-decorators” can be used an options to ipython mode. For example, to setup matplotlib pylab but suppress the output, you can do. When using the matplotlib use directive, it should occur before any import of pylab. This will not show up in the rendered docs, but the commands will be executed in the embedded interpreter and subsequent line numbers will be incremented to reflect the inputs:

.. code:: python3

   In [144]: from pylab import *

   In [145]: ion()
In [144]: from pylab import *

In [145]: ion()

Likewise, you can set :doctest: or :verbatim: to apply these settings to the entire block. For example,

In [9]: cd mpl/examples/
/home/jdhunter/mpl/examples

In [10]: pwd
Out[10]: '/home/jdhunter/mpl/examples'


In [14]: cd mpl/examples/<TAB>
mpl/examples/animation/        mpl/examples/misc/
mpl/examples/api/              mpl/examples/mplot3d/
mpl/examples/axes_grid/        mpl/examples/pylab_examples/
mpl/examples/event_handling/   mpl/examples/widgets

In [14]: cd mpl/examples/widgets/
/home/msierig/mpl/examples/widgets

In [15]: !wc *
    2    12    77 README.txt
   40    97   884 buttons.py
   26    90   712 check_buttons.py
   19    52   416 cursor.py
  180   404  4882 menu.py
   16    45   337 multicursor.py
   36   106   916 radio_buttons.py
   48   226  2082 rectangle_selector.py
   43   118  1063 slider_demo.py
   40   124  1088 span_selector.py
  450  1274 12457 total

You can create one or more pyplot plots and insert them with the @savefig decorator.

@savefig plot_simple.png width=4in
In [151]: plot([1,2,3]);

# use a semicolon to suppress the output
@savefig hist_simple.png width=4in
In [151]: hist(np.random.randn(10000), 100);

In a subsequent session, we can update the current figure with some text, and then resave

In [151]: ylabel('number')

In [152]: title('normal distribution')

@savefig hist_with_text.png width=4in
In [153]: grid(True)

You can also have function definitions included in the source.

In [3]: def square(x):
   ...:     """
   ...:     An overcomplicated square function as an example.
   ...:     """
   ...:     if x < 0:
   ...:         x = abs(x)
   ...:     y = x * x
   ...:     return y
   ...:

Then call it from a subsequent section.

In [4]: square(3)
Out [4]: 9

In [5]: square(-2)
Out [5]: 4

Writing Pure Python Code

Pure python code is supported by the optional argument python. In this pure python syntax you do not include the output from the python interpreter. The following markup:

.. code:: python

   foo = 'bar'
   print foo
   foo = 2
   foo**2

Renders as

foo = 'bar'
print foo
foo = 2
foo**2

We can even plot from python, using the savefig decorator, as well as, suppress output with a semicolon

@savefig plot_simple_python.png width=4in
plot([1,2,3]);

Similarly, std err is inserted

foo = 'bar'
foo[)

Comments are handled and state is preserved

# comments are handled
print foo

If you don’t see the next code block then the options work.

ioff()
ion()

Multi-line input is handled.

line = 'Multi\
        line &\
        support &\
        works'
print line.split('&')

Functions definitions are correctly parsed

def square(x):
    """
    An overcomplicated square function as an example.
    """
    if x < 0:
        x = abs(x)
    y = x * x
    return y

And persist across sessions

print square(3)
print square(-2)

Pretty much anything you can do with the ipython code, you can do with a simple python script. Obviously, though it doesn’t make sense to use the doctest option.

Pseudo-Decorators

Here are the supported decorators, and any optional arguments they take. Some of the decorators can be used as options to the entire block (eg verbatim and suppress), and some only apply to the line just below them (eg savefig).

@suppress

execute the ipython input block, but suppress the input and output block from the rendered output. Also, can be applied to the entire ..ipython block as a directive option with :suppress:.

@verbatim

insert the input and output block in verbatim, but auto-increment the line numbers. Internally, the interpreter will be fed an empty string, so it is a no-op that keeps line numbering consistent. Also, can be applied to the entire ..ipython block as a directive option with :verbatim:.

@savefig OUTFILE [IMAGE_OPTIONS]

save the figure to the static directory and insert it into the document, possibly binding it into a minipage and/or putting code/figure label/references to associate the code and the figure. Takes args to pass to the image directive (scale, width, etc can be kwargs); see image options for details.

@doctest

Compare the pasted in output in the ipython block with the output generated at doc build time, and raise errors if they don’t match. Also, can be applied to the entire ..ipython block as a directive option with :doctest:.

Configuration Options

ipython_savefig_dir

The directory in which to save the figures. This is relative to the Sphinx source directory. The default is html_static_path.

ipython_rgxin

The compiled regular expression to denote the start of IPython input lines. The default is re.compile(‘In [(d+)]:s?(.*)s*’). You shouldn’t need to change this.

ipython_rgxout

The compiled regular expression to denote the start of IPython output lines. The default is re.compile(‘Out[(d+)]:s?(.*)s*’). You shouldn’t need to change this.

ipython_promptin

The string to represent the IPython input prompt in the generated ReST. The default is ‘In [%d]:’. This expects that the line numbers are used in the prompt.

ipython_promptout

The string to represent the IPython prompt in the generated ReST. The default is ‘Out [%d]:’. This expects that the line numbers are used in the prompt.