[Biopython-dev] Google Summer of Code Proposal

[Maximiliano David Bustos]

Peter,

Thanks for your feedback. I will consider this compatibility issues when
implementing.

Maxi.

On Wed, Apr 13, 2011 at 6:16 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Wed, Apr 13, 2011 at 3:55 AM, Maximiliano David Bustos
> <md.bustos90 at gmail.com> wrote:
> > Hello everybody,
> >
> > My name is Maximiliano David Bustos, I am a Computer Science student from
> La
> > Rioja, Argentina. I joined the list some days ago to start collaborating
> > with BioPython project and to get feedback in Google Summer of Code
> (GSoC).
> > The proposal I submitted to GSoC is titled *"Variant representation,
> parser,
> > generator, and coordinate
> > converter"*<
> https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B1Q10jdy75U_YzE4ZmUzMGEtNjA5Ni00Mjc4LTgwYTQtZTI1MTdkNTJiODc4&hl=en&authkey=CN_Dm8ML
> >.
> > This idea was taken from BioPython wiki.
> > The project mentor is Reece Hart, who had been helping me a lot in the
> > elaboration of my proposal. Brad Chapman made great contributions too.
> >
> > Reece recommended me to send my proposal to the mailing list. I would
> really
> > appreciate any feedback from you.
> >
> > Thanks in advance,
> >
> > Maxi.
>
> Hi Maxi,
>
> Just a couple of quick initial thoughts on the implementation section,
>
> >> Implementation
> >>
> >> I will implement the library in Python 2.7, using PLY (Python Lex-Yacc)
> >> or Pyparsing. I will follow BioPython coding conventions and
> abstractions
> >> so the project can be integrated from the beginning.
>
> Currently Biopython supports Python 2.5 to 2.7 (and we're working on Python
> 3).
> If you target Python 2.7 specific features it would be a problem for
> integrating
> your work into Biopython. You would ideally also run and test your code on
> Python 2.5, and on Python 3.
>
> On the bright side, PLY (Python Lex-Yacc) and Pyparsing are pure python
> and *should* work cross platform (we do want to support Windows). On
> the other hand, if we can do without them and use the standard Python
> library only, I'd be happier as it will keep our dependencies down. This is
> important for making Biopython easy to install and use. In this case they
> are run time dependencies so it isn't critical.
>
> Peter
>