[Biopython-dev] Jupyter notebook tutorial tests

[Vincent Davis]

Doing a little research on testing notebooks:

https://github.com/bollwyvl/nosebook
is not up-to-date, i.e. will not run with jupyter and maybe not with
python3.5.

I tested pytest-ipynb, it works but has 2 issues, 1, looks for files
starting with test_ 2, uses py.test.
https://pypi.python.org/pypi/pytest-ipynb

Both of the above projects could possibly be modified to work.


A very simple option to verify the notebooks run (without error) is to just
run this command (you can provide a list of notebooks)

$ jupyter nbconvert --to notebook --execute "02 - Quick Start.ipynb"

If there is an error it will stop and report the error.


I am also trying to extract the source and result from a notebook (this is
easy) and insert them into a doctest. I have parts of this working thanks
to the python mailing list.



Vincent Davis
720-301-3003
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