Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-05-16

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All times shown according to UTC.

Time Nick Message
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18:47 rbuels pyrimidine: http://www.perl.com/pub/2011/05/new-fe​atures-of-perl-514-package-block.html
18:47 rbuels package block syntax is nice
18:58 scottcain rbuels: perhaps, but how long until BioPerl could require 5.14?  It seems like we just dropped 5.6.1 last month (exaggeration, but still).
18:59 rbuels oh, i know ....  wasn't suggesting bioperl require 5.14
18:59 rbuels though at some point, people are going to have to start using perlbrew
18:59 rbuels because the rate that perl is adding new features is *far* outstripping the rate at which packagers are upgrading it
19:00 scottcain Funny: "have to".  Good one.
19:00 rbuels at some point;.
19:00 rbuels heh, they will if bioperl starts requiring, say, 5.12 in 2013.
19:00 rbuels o_O
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19:34 pyrimidine Actually, did we ever drop 5.6.1?
19:36 pyrimidine anyway, the features added are, for the most part, influenced heavily by perl 6 (including 'package Foo {}', which isn't a far cry from 'class Foo does Bar {}')
19:41 rbuels pyrimidine: well, what we do depends on how backward-compatible the new FeatureIO is
19:41 pyrimidine it's not, or at least it's to be dramatically simplified
19:41 rbuels it should be mostly backcompat, since BSFA was mostly backcompat with BSFG
19:41 rbuels (Bio::SeqFeature::Annotated, Bio::SeqFeature::Generic)
19:42 pyrimidine BSFA was always broken to a large degree
19:42 pyrimidine and half-implemented
19:42 pyrimidine and half horribly implemented
19:43 rbuels pyrimidine: does the new FeatureIO have all of the functionality of the old one?
19:43 pyrimidine no, but it's not intended to
19:43 pyrimidine here's my problem with it:
19:44 pyrimidine <pause>
19:44 rbuels pyrimidine: erm, it's just parsing feature formats though
19:44 pyrimidine it does more than that
19:44 rbuels and writing i guess
19:44 pyrimidine yes
19:44 pyrimidine but it attempts to (forcibly) validate GO
19:44 pyrimidine sorry, SO
19:44 rbuels oh, that
19:44 pyrimidine yes
19:44 rbuels yeah, don't need to worry about that going away
19:45 rbuels those kinds of secondary behaviors, i don't think we need to worry about breaking backcompat with them
19:45 rbuels i doubt there is anybody relying on them
19:45 pyrimidine rightm but it is doing this by default
19:45 pyrimidine *right
19:46 rbuels yeah, i don't think we need to worry about it not validating as a side effect any more
19:46 rbuels i file that under "don't care"
19:47 rbuels the documentation should *mention* that it doesn't do that anymore though
19:47 rbuels of course
19:47 pyrimidine yeah, I basically think we just need to scrub BSFA out completely
19:48 pyrimidine maybe have Ontology checking and other things (unflattening, for instance) be pluggable
19:49 pyrimidine but mainly separate that stuff out (whole 'separation of concerns' thing)
19:49 rbuels eh, don't even need a plugin, probably should just have a Bio::Ontology::Validator or something
19:49 pyrimidine yeah, that would work, too
19:50 pyrimidine something that would accept either a single feature or a stream of features and validate them
19:50 pyrimidine same thing with unflattener
19:50 rbuels and if people want to check their terms,   my $so = Bio::Ontology->load_however('SO');  $so->find_term( $f->type ) or die "aiiee!"
19:51 rbuels something like that
19:51 pyrimidine right
20:04 pyrimidine that's probably a shitload easier to implement than
20:04 pyrimidine oh, I don't know, throwing all your code into one module
20:17 rbuels we should have a whole mailing list just for parsing blast reports.
20:17 * rbuels is mostly kidding
20:49 * jhannah rubs rbuels funny bone
20:49 jhannah '
20:49 * rbuels sneezes
20:59 pyrimidine seems like that is one of the primary things that pops up (BLAST report parsing).  Also happens to be one of the biggest PITA
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