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Gmane
From: Fields, Christopher J <cjfields <at> illinois.edu>
Subject: Re: Bio::DB::Fasta changes
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Monday 29th October 2012 03:04:46 UTC (over 4 years ago)
On Oct 28, 2012, at 9:50 PM, Florent Angly  wrote:

> Hi Chris,
> 
> I have done a bunch of work on Bio::DB::Fasta and associated modules
lately, with the goal of making them more useful and less redundant. There
was no intentional change of interface that would make it backward
incompatible and all bioperl tests passed fine. In fact, if I recall
correctly, I even added more tests because I noticed some holes in test
coverage.

More tests never hurt (well, unless we're adding a ton of files to the
repository).

> I suspect that this bug report you cited unveiled a corner case that was
not covered by the tests. I'll assign the bug to myself and investigate.

Okay.  I just want to ensure that everything for this particular module is
covered for the GMOD folks.

chris

> Florent
> 
> 
> 
> On 29/10/12 08:24, Fields, Christopher J wrote:
>> There have been a number of significant changes to Bio::DB::Fasta
recently that haven't been discussed on the bioperl list.  In particular,
much of the code has been moved to Bio::DB::IndexedBase.  At the moment
some of these changes are breaking compatibility with other tools (namely
MAKER, see: https://redmine.open-bio.org/issues/3389).
 In the latter case I would consider this a significant API change that
needs to be addressed.
>> 
>> Generally, whenever we make significant changes to modules these should
always be run on a branch first (see recent changes to Bio::Tree), and we
should at least discuss this on-list prior to merging with master.  I do
think we should start that discussion now and decide what to do, e.g. roll
back changes and push these to a branch, allow these to stay in master with
revisions, etc.
>> 
>> chris
>
 
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