Fields, Christopher J | 1 Apr 05:28 2013

Re: Google Summer of Code - BioPerl proposals

On Mar 31, 2013, at 9:05 PM, Carnë Draug <carandraug+dev <at>> wrote:

> On 1 April 2013 01:34, Fields, Christopher J <cjfields <at>> wrote:
>> I agree.  Another approach might be to cleave off a section that you could mould into your own; this could be
done for bioperl-run, bioperl-live, etc.
> Why did the project ran out of time 2 years ago? The blog posts about
> it are very few and don't sound too bad. It mentions having prepared a
> couple of them, but none was actually ever released. Instead, the
> source was also kept in bioperl-live and seems to have already
> branched. Is there any reason for this? It was my understanding that
> splitting the project is still desirable, from a discussion back in
> February
> it just happens that no one has picked it up yet.

The project actually made a lot of headway; the particular pieces moved out (Bio::Root, Bio::Factory,
etc) worked fine, but we never followed up on exactly what to do next on master branch.  It's perfectly
feasible for someone to go ahead and finish the initial part of that (in fact, I believe there were some
branches that started along this path but never merged back in).

FWIW, Sheena also started the Dist::Zilla bundle you have been working on as well, with the same intent you
have.  So the fundamental groundwork is there.

> I think splitting bioperl-live into subdistributions and make a new
> 1.70 release of each of them is perfectly doable over a summer. And I
> say this after having split and release Bio-Biblio. This is one of my
> itches with BioPerl. I have been using it for almost 3 years, but have
> never seen a release. I would like to make new releases of everything,
> no changes at the start, but take them to the point that "dzil
> release" does everything. Make it really easy for anyone to come in
> and contribute and even easier for a maintainer to make a new release
> after receiving a contribution. Is this desirable for the project?
> Carnë

The last Bioperl release was in 2011 IIRC, so we're long overdue, but it's not quite 3 yrs :)  

Hilmar's point is pretty valid, namely that a case would have to be made as to why the initial run at it wasn't
completed, or why it would work better this time.  We're not suggesting that this can't be done, but the
above point would have to be answered.  Frankly, the project has been pretty reliant on me for releases, so
it's perfectly valid to point out the modules haven't made it out yet b/c I haven't made a release since
then.  From that point of view, this would be a continuation of that work, maybe with the intent/focus on
making code releases much easier.

Regarding updating Bioperl to use Dist::Zilla amongst other modern perl tools (Moose included), yes, it
is very much our wish/intent to have this, in any way possible.  But I don't think we can call it BioPerl v1.7,
simply based on past release cycles; we're somewhat bound by deprecations, etc.  We really need a clean

So, my general feeling is that while we are cleaving out code and releasing the independent dist and core, we
should re-christen core as 1.9 (e.g. pre-v2).  We move to v2 when we feel we're at the right point.  Each of the
individual distributions would have to start with their own versions, anything greater than the point
where they left the core/live distribution should work.  I agree with you in that I don't think it would take
a long time, but we also have bioperl-run in the mix (and in many cases it would make sense to combine
wrappers with the proper parsers), so simply cleaving out from one repo may not be the best approach.

With that in mind, my point was meant to indicate we can also start afresh with a section of the code that you
would like to focus on, using some of the same ideas (pulling out the relevant modules you want to work on). 
This might be an attainable goal in the minds of GSoC reviewers and might suit your particular needs (for
instance, if you had a research project reliant on such code).  I'm supportive either way, and I don't think
you'll have a problem finding a mentor if you need one.