python-science-skeleton

A handy project skeleton for data analysis projects using IPython notebook. Includes boilerplate for writing external modules and testing.

Austin G. Davis-Richardson

Motivation

I like IPython Jupyter notebook for interactive computing/data analysis but I find it difficult to write maintainable code.

This is an effort to promote writing better, re-usable code as seperate Python modules, with continuous integration using Travis, and also verify that notebooks build without error (I guess this is a form of integration testing). It is importanant that you never commit your notebooks to the master branch while they're in a failing state.

Get Started

Install dependencies

# create and activate a new virtual environment
pyenv virtualenv 2.7.9 $PWD
pyenv activate $PWD

# install dependencies
pip install -r requirements.txt

# start notebook
ipython notebook

Write functions common to all notebooks in lib/common.py to start. Use doctests for testing.

Testing

To run unit tests:

nosetests --with-doctests

To build notebooks:

# builds HTML by default
make 

# or, build notebooks in parallel
make -j 

(Travis will do both of these things and fail if you commit a notebook in a non-functioning state)

Building Notebooks

make will build any and all notebooks in $PWD.

Contributing

Plz do! I ❤️ pull requests.

TODO

• Experiment with sending output from notebooks built by Travis (ideally on GitHub or IPyNbViewer).