[Bioperl-l] [gsoc-2014] Presentation

Fields, Christopher J cjfields at illinois.edu
Thu Feb 27 13:44:14 UTC 2014

On Feb 27, 2014, at 4:29 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, Feb 27, 2014 at 6:09 AM, Israel Leiva <israel.leiva at usach.cl> wrote:
>> Hello!
>> My name is Israel Leiva, I'm a computer science student at University of
>> Santiago, Chile (more personal info on [1]). I got here by the Google
>> Summer of Code. I have a good knowledge of Perl (+5 years) and databases,
>> and I think OBF (and in particular BioPerl) is a very interesting project,
>> quite enough to spent the summer coding! You can check some of my codes on
>> [2] or in my CPAN profile [3] (two modules, one mine, one "adopted"). Some
>> of the project ideas that captured my attention were "Convert BioPerl-DB to
>> DBIx::Class", eventhough I have no experience with DBIx::Class but I'm
>> willing to learn :). The other one was the "Major BioPerl Reorganization,
>> Part 2". Both of them seem to involve lot of work, so I'll apreciate any
>> guidelines and/or feedback concerning these ideas, how to get started with
>> BioPerl and see if I'm suitable for this year's gsoc.
> I'll let someone from BioPerl answer that…

Yes, they are particularly broad in scope (in particular the second, splitting out code).  DBIx::Class might be a little easier to tackle but it does require reading up.  Hilmar might have some thoughts on this.

>> One last thing, the links for browsing the "bioperl-live" code and
>> subprojects are broken in the "open-bio" wiki.
> Where are these broken links please?
>> After some searching I found links to a github repo
>> and a redmine, which one should I consider official?
> BioPerl development is now on GitHub, using a git repository.
> For reporting bugs, BioPerl is still using Redmine, (and the GitHub
> issue tracker has not been enabled), see also:
> http://bioperl.org/wiki/Bugs
> (At some point a migration from Redmine to GitHub seems possible,
> we're doing this slowly for Biopython - while BioRuby already moved.)
> Peter

We have a general plan on migration; the one significant impediment is we need to do it a little more piecemeal, since we’re splitting the main repo up to make it more modular (so we’ll need to split the Redmine issues to the right repos).  We’ll also have the fun of wiki conversion to Github md.  

I tested out a script that can do the migration using the Redmine and Github REST APIs, seemed to work fine but I ended up spamming everyone :) 


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