[Bioperl-l] Moose [was Re:Other object oddities]

Sat May 9 01:33:58 UTC 2009

thanks Siddhartha- very informative [but he misquotes Eliot in his header!]
cheers MAJ
----- Original Message ----- 
From: "Siddhartha Basu" <sidd.basu at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Friday, May 08, 2009 2:30 PM
Subject: [Bioperl-l] Re: Moose [was Re:Other object oddities]


> On Wed, 06 May 2009, Chris Fields wrote:
>
>> As a final bit: if we go the Moose route, we should be very careful about
>> which MooseX modules we want.  I don't think we want to expand the
>> dependency tree.  For instance, I am attempting to install one possible
>> module (MooseX::Declare) and the dependency tree was ginormous and included
>> modules only needed for installation.
>>
>> chris
>
> Since we are on the topic of Moose dependencies,  here is a nice article
> about it.
> http://chris.prather.org/perl/moose-dependencies-a-lurid-tale/
>
> -siddhartha
>
>>
>> On May 6, 2009, at 12:56 PM, Mark A. Jensen wrote:
>>
>> > Great discussion-- I have redacted the moose portions to
>> > http://www.bioperl.org/wiki/Talk:BioMoose and encourage all interested
>> > folks to log comments there as well. cheers Mark
>> > ----- Original Message ----- From: "Chris Mungall" <cjm at berkeleybop.org>
>> > To: "Chris Fields" <cjfields at illinois.edu>
>> > Cc: "BioPerl List" <Bioperl-l at lists.open-bio.org>; "Mark A. Jensen"
>> > <maj at fortinbras.us>; "Kevin Brown" <Kevin.M.Brown at asu.edu>
>> > Sent: Tuesday, May 05, 2009 2:28 PM
>> > Subject: [Bioperl-l] Moose [was Re: Other object oddities]
>> >
>> >
>> >>
>> >> On May 5, 2009, at 7:31 AM, Chris Fields wrote:
>> >>
>> >>> On May 5, 2009, at 7:31 AM, Hilmar Lapp wrote:
>> >>>
>> >>>>
>> >>>> On May 4, 2009, at 3:01 PM, Mark A. Jensen wrote:
>> >>>>
>> >>>>> Maybe this should be an element of
>> >>>>> the "Align refactor" that perhaps should be an overall
>> >>>>> "Seq refactor".
>> >>>>
>> >>>> Possibly. Most importantly, it'd be great if someone would  volunteer
>> >>>> to summarize what's been said here so it won't get lost.
>> >>>
>> >>> Looks like mark's done it.
>> >>>
>> >>>>> Are you saying that the trunk is fair game for api additions
>> >>>>> for this issue?
>> >>>>
>> >>>> There's been talk some (a long, actually) time ago about BioPerl  2.0
>> >>>> that would start on a clean slate and not be bothered by  backwards
>> >>>> compatibility demands. That effort never really took off,  but maybe
>> >>>> this is also a good time to ask the question again  whether it's better
>> >>>> to introduce the API changes we desire in add/ deprecate/remove cycles,
>> >>>> or in a more radical fashion starting on a  clean slate.
>> >>>
>> >>> That's what I'm thinking.
>> >>>
>> >>>> The obvious advantage of the former is that we get API improvements
>> >>>> sooner, but making them is possibly more dreadful, discouraging, or
>> >>>> not even doable due to compatibility constraints. The disadvantage  of
>> >>>> the latter is that it really needs a committed crew of people to  see
>> >>>> it through or otherwise all the nice changes die in some grand  but
>> >>>> half-finished 2.0 construction site. I think Chris also had  plans to
>> >>>> branch off a Perl6 version of BioPerl - maybe those could  be the same
>> >>>> efforts?
>> >>>
>> >>> I have been toying around with perl6 for a bit now (Rakudo on Parrot
>> >>> implementation).  It's possible an alpha for perl6 will be available  by
>> >>> christmas this year; Rakudo is now passing over 11000 spec tests.
>> >>>
>> >>> Just to note, Perl6 is another beast altogether from Perl5.  Yes,  there
>> >>> is supposed to be a backwards compatibility mode, but no one  has
>> >>> implemented that yet, and it likely won't be implemented in the  near
>> >>> future.  Based on that I'm not sure we could really call a  bioperl in
>> >>> perl6 bioperl 2.0, more like bioperl6 1.0, as it would be  a complete
>> >>> refactor.
>> >>>
>> >>> As for perl5, it has a nice OO set of modules (Moose) that could be
>> >>> used for refactoring.  It implements roles and a few other perl6-ish
>> >>> bits (along with MooseX modules).  perl 5.10 also has a few things
>> >>> backported from p6, say(), given/when, state vars, etc.  We could
>> >>> require Modern::Perl (perl5.10 with strict/warnings pragmas on) and
>> >>> Moose.  I have played around with both and find them quite nice, so  I
>> >>> suggest if we were to start a 2.0 effort it should include Moose,  and
>> >>> we should push most of the interfaces into roles.
>> >>
>> >> We're playing around with a rewrite of go-perl using Moose:
>> >> http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-moose/OBO/
>> >>
>> >> This is early enough that parts could be scrapped or rewritten.
>> >> Compatibility with bioperl is important.
>> >>
>> >> Speed was an initial concern but apparently there are some moose  tricks
>> >> to speed things up
>> >>
>> >> DBIx::Class compatibility is also important. Not sure if there is
>> >> specific support for this yet
>> >>
>> >>
>> >>>
>> >>> Anyway, I grabbed the git repos for bioperl6 and biomoose (bioperl
>> >>> implemented in Moose) on github.  We can set up something there  using
>> >>> those namespaces if needed.
>> >>>
>> >>>> I'm not trying to advocate one over the other here; rather, I'd  like
>> >>>> to help push on that front that is best able to capture the  energy of
>> >>>> volunteers, as that's what it takes in the end.
>> >>>>
>> >>>> -hilmar
>> >>>
>> >>> Depends on where everyone wants to place their efforts.  May be less
>> >>> work to port the most important core classes over to Moose, and a
>> >>> simple test implementation will give us an idea on what works Role- wise
>> >>> and what doesn't.  From there we could work on p6 variants;  that would
>> >>> have to be a separate project altogether.  We could also  include a few
>> >>> other MooseX modules if it makes life easier.
>> >>>
>> >>> chris
>> >>> _______________________________________________
>> >>> Bioperl-l mailing list
>> >>> Bioperl-l at lists.open-bio.org
>> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >>>
>> >>
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