[Biopython-dev] Ipython notebook biopython tutorials

[Peter Cock]

On Thu, Mar 20, 2014 at 2:48 PM, Tiago Antao <tra at popgen.net> wrote:
> On Thu, 20 Mar 2014 14:19:51 +0000
> Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
>> +1 for any *.ipynb files being under source code control.
>>
>> There are perhaps advantages to using a separate repository,
>> but still under Biopython on GitHub? This might also help if we
>> wanted to build on existing external tutorials which are under
>> a CC licence etc...
>
>
> My original plan was to draw "heavy inspiration" (credited, of course)
> from the existing Tutorial and maybe your workshop work.
>
> This all started when I noticed the need to change the tutorial due to
> simcoal changes... As I had to re-visit this, the idea followed...
>
> If people are fine with something under the biopython organization, I
> am fine with that.
>
> I have two proposals, though:
>
> 1. Base it on recent infrastructure (python 3.4 or maybe 3.3, and above
> all ipython 2.0)
>
> 2. Go on and "do stuff", see where it goes and then maybe re-organize
> in the future (as opposed to do lots of planning first). This is, in
> some sense, a new line of direction and I would suggest that being
> exploratory would be better than being cautious...
>
> Tiago

So make a new repository and explore away :)

Regarding https://github.com/peterjc/biopython_workshop - my
workshop stuff I did wonder at the time about using iPython
notebook but it adds another step to the workshop setup - and
another barrier for people to repeat what they did at home.

I was/am hoping to improve the TravisCI coverage of that
work to check all the examples work under Python 2.6, 2.7
3.3 etc.

I wonder if iPython notebooks make automated testing any
easier or not?

Peter