[Biopython-dev] Tutorial problems

Peter Cock p.j.a.cock at googlemail.com
Mon Dec 7 10:59:11 UTC 2015

On Sat, Dec 5, 2015 at 6:48 PM, Vincent Davis <vincent at vincentdavis.net> wrote:
> On Sat, Dec 5, 2015 at 9:31 AM, Tiago Antao <tra at popgen.net> wrote:
>> This all being said, I believe that the current PDF tutorial reeks of
>> 20th century lack of interactivity. It is difficult to see any advantage
>> of the current format against an interactive jupyter version... My real
>> suggestion would be to convert it (well, adapt it) and then make it the
>> official version.
> I agree, I think it would be great if the current tutorial was all
> notebooks.  As well as notebooks rendering in github they can
> also easily be exported as .py that will run as well as to html
> and pdfs.

We've had interest in turning the LaTeX tutorial into RST,
which can also be turned into HTML and PDF nicely. Also
internationalisation would be of interest - people have
translated snapshots but these are hard to keep up to date.

I don't have enough first hand experience of Ipython/Jupyter
to give an informed view, but this would still have a plain text
version control friendly back end with HTML and PDF output.
So that's positive.

For any change, preserving the automated testing of the Tutorial
examples would be vital. However, dealing with dependencies
here is a big pain (external libraries, external binaries, internet
connectivity), and the main reason we don't currently test all of
the tutorial examples.

Separately, extending test_Tutorial.py to handle online tests
should be fairly straightforward - even if it is only a short term
gain. Likewise checking for binary dependencies.


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