Fields, Christopher J | 2 Apr 04:19 2013

Re: Google Summer of Code - BioPerl proposals

On Apr 1, 2013, at 8:54 PM, Carnë Draug <carandraug+dev <at>> wrote:

> On 1 April 2013 23:23, Fields, Christopher J <cjfields <at>> wrote:
>> On Apr 1, 2013, at 12:17 PM, Carnë Draug <carandraug+dev <at>> wrote:
>>> Can I merge any branching between these and bioperl-live and set them
>>> up so you only have to run dzil on their repos?
>> I wouldn't worry about the branches, they are probably too stale.  Have it so dzil works for the various
repos from that project (it should already).
> I tried but I don't have push permissions for Bio-Root like I have for
> the other BioPerl repos.

Should be fixed now, that one repo didn't have team set, just owners.

>> We will likely need to think about having a stub Build.PL that can be used for basic installation, but
would be auto-generated based on the needs for that repo (and so shouldn't be committed to).  This is mainly
to help git-savvy users, not devs; we don't necessarily want users to install dzil, which had somewhere
north of 40 or so dependencies IIRC.
> Bah! People using development versions should be prepared to act as
> developers. Otherwise they should be content with the stable released
> versions. Development versions are not meant to be stable. I see no
> reason to give users the chance to shoot themselves, specially when
> it's more work for developers and maintainers.

I agree (though the definition of when something is in 'development' vs 'stable/release' is very
subjective).  I wouldn't do this unless requested, though, and I think the current plugin bundle does have
some basic functionality that supports something if needed.

>> Re: versioning: I'm not particularly hung up on any particular versioning scheme, but the key point is
support.  It's easy for me to say "as of bioperl v2 the installation scheme will be something completely
different" as opposed to doing so with v1.7.  Will installation of v1.7 be the same is it was for v1.6 (or even
similar)?  Will it install the same modules by default?  We would be changing a key step in using BioPerl
(installation) w/o much warning.
> That is my idea yes. Exactly what happened with Bio-Biblio, it changed
> close to nothing. There were a few minor changes on the code to pass
> the tests already in place, bust mostly it was in POD to use the
> BioPerl's distzilla and podweaver configuration.
> Carnë

That works for Bio-Biblio, but my point is: would one be able to get an old-school all-inclusive (e.g.
install everything) bioperl?  Maybe the answer should be 'of course not', and we should create a bundle to
take care of this instead.

I wouldn't worry about it, frankly.  We should just forge ahead, damn the torpedoes.