[Bioperl-l] Bio::DB::Fasta changes

Fields, Christopher J cjfields at illinois.edu
Sun Oct 28 23:04:46 EDT 2012


On Oct 28, 2012, at 9:50 PM, Florent Angly <florent.angly at gmail.com> 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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