[Biopython-dev] Tutorial problems

Peter Cock p.j.a.cock at googlemail.com
Mon Dec 7 14:02:19 UTC 2015

On Mon, Dec 7, 2015 at 12:51 PM, Tiago Rodrigues Antao <tra at popgen.net> wrote:
> On Mon, 7 Dec 2015 10:59:11 +0000
> Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> 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.
> There are quite a few things that are not being tested right now, and
> they are failing (see previous email).

Yes - which is why I think the effort thus far with test_Tutorial.py
has paid for itself, and we should strive for having more of the
documentation and examples automatically tested.

> I will have a look at making the notebooks testable.


> In any case, I think the tutorial format needs a revamp for modern
> times (interestingly I believe it is mostly adding code snippets and,
> above all, REMOVING text).

Dry/heavy text is probably best moved into the relevant module
docstrings (making that prettier with RST is another ongoing effort).

Do you have any particular bits in mind?


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