[Bioperl-l] module for description of sequence variants (where to place code)

[Fields, Christopher J]

On Mar 9, 2013, at 8:03 AM, Carnë Draug <carandraug+dev at gmail.com> wrote:

> On 4 March 2013 04:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> On Mar 3, 2013, at 10:15 PM, Carnë Draug <carandraug+dev at gmail.com>
>> wrote:
>> 
>>> On 4 March 2013 03:45, Fields, Christopher J <cjfields at illinois.edu> wrote:
>>>> [...] at some point it might be worth thinking about whether we need to
>>>> organize the various *Utils modules a bit better.  As most of these export
>>>> methods, they would be good targets for reorganization at some point
>>>> (maybe into a general Bio::Utils namespace).
>>> 
>>> Do you mean placing all of them into a separate Util distribution? I
>>> think it makes more sense to keep them close to what they deal with.
>> 
>> No, I agree we keep them in core.  I meant we should think about what specific domain the various methods contained within those modules deal with, and whether it would be best.  For instance, we also have an AlignUtils, TreeUtils, etc; at some point it might be easier to collect any of the *exportable* methods together in one common space.  At the moment they're a bit scattered, some are exportable, some not…
> 
> How would you define exportable? I usually don't like the idea of
> having functions exported by default. Specially since it's so easy for
> the user to load them themselves.
> 
> Carnë

Yes, I agree (no export by default).

chris