[Bioperl-l] bioperl-dev or branch?

Hilmar Lapp hlapp at gmx.net
Thu May 21 21:33:52 EDT 2009

On May 21, 2009, at 7:31 PM, Robert Buels wrote:

> Just to clarify, it doesn't look like bioperl-dev is actually in a  
> separate repo, it's just separated from bioperl-live as a different  
> distribution, but still in the 'bioperl' repository.

True, actually, my mistake. I guess I was assuming from the early days  
of cvs that these are actually different repositories. Sorry 'bout that.

So in essence bioperl-dev and bioperl-live are different directory  
trees within the same repository.

On May 21, 2009, at 5:52 PM, Chris Fields wrote:

> The key aspect that started this all is to have a lean (read: few  
> dependencies, relatively stable) core set of modules.  Other related  
> modules which add additional dependencies could be moved into a  
> bioperl-tools. And (finally) anything lacking the guarantee of API  
> stability would be bioperl-dev.  I think several other alternatives  
> came up but these seemed to be the final ones.
> So:
> core  = minimal functionality
> tools = complete functionality (requires core)
> dev   = experimental APIs, etc (requires core and possibly tools)

I do like this. Am I right that the way we should be looking at this  
is as disjoint subsets that as a total make up BioPerl. So a module  
would be found in one and only one subset, and if I wanted the entire  
BioPerl package I download each one. Bioperl-dev then isn't for  
holding different (e.g., more experimental) versions of the same  
modules that are also in bioperl-core (aka bioperl-live).

Likewise, each subset then has its tags and branches and main trunk,  
right? (Though hopefully the release tags would be present in all)

That sounds all good to me, except that bioperl-dev has Bio/Root/*  
replicated. It should not, right? If we want to introduce experimental  
changes to Bio/Root modules, they should go into a bioperl-live  
branch, right? (Otherwise I'm confused what a bioperl-live branch is  

So in this picture Chase's project would go into bioperl-dev, main  
trunk. Users would obtain it by downloading bioperl-dev from svn or as  
package and simply install on top of a Bioperl-core package, without  
fear of clobbering stable modules that came with Bioperl-core. Right?

If that's the idea it makes a lot of sense to me and seems sane.  
Conversely, using bioperl-dev as another way to branch bioperl-core  
modules doesn't, though I may be missing something.

(I hope I'm making sense. Please do say if I'm not ...)


: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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