The plugin adds functionality to py.test to recognise and collect IPython
notebooks. The intended purpose of the tests is to determine whether execution
of the stored inputs match the stored outputs of the .ipynb file.
The tests were designed to ensure that IPython notebooks (especially those for reference and documentation), are executing consistently.
Each cell is taken as a test, a cell that doesn't reproduce the expected output will fail.
See documentation.ipynb for the full documentation.
After cloning this repository, the plugin is installed doing
sudo pip install .
from the main directory. It can be easily removed with:
sudo pip uninstall pytest_validate_nb
The extension looks through every cell that contains code in an IPython notebook
and then the py.test system compares the outputs stored in the notebook
with the outputs of the cells when they are executed. Thus, the notebook itself is
used as a testing function.
The output lines when executing the notebook can be sanitized passing an
extra option and file, when calling the py.test command. This file
is a usual configuration file for the ConfigParser library.
Regarding the execution, roughly, the script initiates an
IPython Kernel with a shell and
an iopub sockets. The shell is needed to execute the cells in
the notebook (it sends requests to the Kernel) and the iopub provides
an interface to get the messages from the outputs. The contents
of the messages obtained from the Kernel are organised in dictionaries
with different information, such as time stamps of executions,
cell data types, cell types, the status of the Kernel, username, etc.
In general, the functionality of the IPython notebook system is quite complex, but a detailed explanation of the messages and how the system works, can be found here
http://ipython.org/ipython-doc/stable/development/messaging.html
To execute this plugin, you need to execute py.test with the ipynb flag
to differentiate the testing from the usual python files:
py.test --ipynb
This will execute all the .ipynb files in the current folder. Alternatively,
it can be executed:
py.test --ipynb my_notebook.ipynb
for an specific notebook.
If the output lines are going to be sanitized, an extra flag, --sanitize-with
together with the path to a confguration file with regex expressions, must be passed,
i.e.
py.test --ipynb my_notebook.ipynb --sanitize-with path/to/my_sanitize_file
where my_sanitize_file has the following structure.
[Section1]
regex: [a-z]*
replace: abcd
regex: [1-9]*
replace: 0000
[Section2]
regex: foo
replace: bar
The regex option contains the expression that is going to be matched in the outputs, and
replace is the string that will replace the regex match. Currently, the section
names do not have any meaning or influence in the testing system, it will take
all the sections and replace the corresponding options.
The py.test system help can be obtained with py.test -h, which will
show all the flags that can be passed to the command, such as the
verbose -v option. The IPython notebook plugin can be found under the
general section.
This plugin was inspired by Andrea Zonca's py.test plugin for collecting unit tests in the IPython notebooks ( https://github.com/zonca/pytest-ipynb ).
It is mostly based on the template in https://gist.github.com/timo/2621679
and the code of a testing system for notebooks https://gist.github.com/minrk/2620735
which we integrated and mixed with the py.test system.
David Cortes-Ortuno, Oliver Laslett, Maximilian Albert, Ondrej Hovorka, Hans Fangohr
University of Southampton, 2014 - 2015, http://www.southampton.ac.uk