[Bioperl-l] bioperl-dev or branch?

Mark A. Jensen maj at fortinbras.us
Fri May 22 00:31:35 EDT 2009

----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Hilmar Lapp" <hlapp at gmx.net>
Cc: "Robert Buels" <rmb32 at cornell.edu>; "BioPerl List" 
<bioperl-l at lists.open-bio.org>
Sent: Thursday, May 21, 2009 11:08 PM
Subject: Re: [Bioperl-l] bioperl-dev or branch?
> Mm, yes, see what you're saying, the Bio::Root modules in dev should  be 
> removed.  Was there a particular reason those were present, Mark?   Do they 
> contain anything new? I ran a diff on a few of them and  couldn't find 
> anything.

I think I had a vague idea that the Root modules should exist directly
in the repository, but that is making less and less sense to me now,
especially after these discussions. The gross distinction I'm making now
is that while bioperl-live and bioperl-dev possess parallel organization,
they are otherwise very different animals: bioperl-live is a unit wherein
the component modules are (or can be expected to be) completely
interdependent, while different experiments going on in different
regions of bioperl-dev don't necessarily have to play at all together.
(That sounds suspiciously like a bunch of legitimate branches.)
>From this angle, Root shouldn't be there at all, unless it's also on the
operating table.

There are Root modules involved in building/testing. I thought that
these at least should be there, but now not so sure. What sense
does a bioperl-dev build make, since one is probably not interested
in installing everyone's random experiments at once? Probably
incorporating the desired code as a layer onto the current install
is the way to go.

I get the impression from Rob's insights that more sophistication (on my part,
definitely) in the use of version control would obviate a lot of our
consternation. So the question is: what's bioperl-dev got that svn ain't got?
Maybe the solution here is what you cjf have been suggesting lately, that
the trunk is your friend, and that frequent and fearless branching+merging
needs to become part of the Modern BioPerl Way.

[Jason, fellow bioperl-dev user, are you there?]


> I think, for the sake of not confusing users module names should be  new and 
> not conflict with a core module's already-claimed namespace.   I think it's 
> okay to have something new with a base namespace like  Bio::Root::*, but the 
> module name should be unique (I have thought of  Bio::Root::Moose, for 
> instance, as a Moose-based Root metaclass, but  that may go elsewhere...).

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