Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-08-02

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All times shown according to UTC.

Time Nick Message
05:34 bag_ joined #bioperl
08:14 vinnana joined #bioperl
10:34 mc_wu joined #bioperl
10:34 mc_wu hi, all
10:35 mc_wu have anybody here ever used  Bio::TreeIO?
10:45 vinnana mc_wu: a bit
10:46 mc_wu hi, vinnana. I want to know how to use Bio::TreeIO
10:46 mc_wu I have searched the Internet for the usage, but I can't find an example to tell me how to use it.
10:48 mc_wu Can you give me an example to tell me how to use Bio::TreeIO
10:52 vinnana something like this? use Bio::TreeIO; my $ifh = new Bio::TreeIO(-file => $filename, -format => "nhx"); my $ofh = new Bio::Tree(-fh => \*STDOUT, -format => "newick"); $ofh->write_tree($ifh->next_tree); $ifh->close; $ofh->close;
10:54 mc_wu yes, but i don't have the $filename file.  However, I just found an example. I'm having a try.
11:45 flu_ joined #bioperl
14:24 genehack joined #bioperl
15:07 pyrimidine joined #bioperl
16:23 rbuels pyrimidine: did you see my blastogram about the hackathon?
16:24 rbuels pyrimidine: i suspect it did not go through
16:24 genehack rbuels: i saw it
16:25 rbuels genehack: on bioperl-l?  or which list
16:25 pyrimidine rbuels: yes, saw it
16:25 * rbuels wonders why he has not gotten it himself
16:26 pyrimidine I saw it on all the lists (biolib, biosql, bioperl, biopython, open-bio).  You left out bioruby.
16:27 rbuels oh heck
16:27 rbuels did not!
16:27 rbuels maybe it just didn't get modded it
16:27 rbuels er, in
16:28 pyrimidine that's possible, didn't see it come through
16:28 pyrimidine hilmar also forwarded it to phyloinformatics
16:28 rbuels yeah, the org committee kind of divvied up the known lists among ourselves
16:29 pyrimidine hopefully will be a good turnout!
16:29 rbuels i wonder if i should send it to any of the general perl lists
16:35 rbuels well it promises to be a pretty cool event.  we've got confirmation from lincoln stein, jason stajich, and chris mungall that they will be there at least part of the time
16:36 pyrimidine I likely can't make it for that one, unfortunately
16:36 rbuels :-(
16:36 pyrimidine (wife's expecting, Sept 4)
16:36 rbuels :-o
16:36 pyrimidine :)
16:36 rbuels everybody around me is having babies!
16:37 rbuels babies babies babies!  everywhere!
16:37 * rbuels looks around, expecting a baby to drop from the ceiling
16:37 rbuels heh
16:37 rbuels pyrimidine: well congratulations
16:37 pyrimidine thanks!
16:38 pyrimidine one reason I want to get 1.6.2 out, though things keep popping up here to slow it down
16:58 genehack rbuels: i saw it on bioperl. you may also want to submit it for the news page on http://www.bioinformatics.org/
16:59 rbuels genehack: ah good idea
17:00 pyrimidine rbuels: has it been tweeted yet?
17:00 * pyrimidine cringes at that word
17:00 rbuels pyrimidine: not yet.  i'll post an OBF news item on it maybe?
17:00 * rbuels is not sure it belongs as an obf news item
17:01 genehack pyrimidine: i know someone who insists that the past tense of 'to tweet' is 'twatted'
17:01 rbuels genehack: i use it in that way as well
17:01 rbuels genehack: also, 'the twatterwebs'
17:01 * rbuels learned that lovely turn of phrase from dukeleto
17:04 pyrimidine yes, heard that as well, just being too PC myself
17:04 pyrimidine rbuels: yes, OBF news item is a good idea as well
17:06 * rbuels twat it on his personal twatstream
17:07 * genehack has retwatted it
17:08 pyrimidine now you just need a trendy hashtag and the apocalypse will be complete
17:08 pyrimidine mwahahaha
17:10 rbuels gmod....pocalypse?
17:10 rbuels ahem.
17:16 pyrimidine re-twatted
17:22 rbuels ok i submitted it to bioinformatics .org
17:22 * rbuels had to fake out their photo thing to get it to crop his off-center photo right
17:53 driley joined #bioperl
18:17 ende joined #bioperl
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19:34 brandi joined #bioperl
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20:16 CIA-93 bioperl-live: Chris Fields master * r0f34da1 / Bio/SeqIO/genbank.pm : remove debugging - http://bit.ly/9tvNCh
20:16 CIA-93 bioperl-live: Chris Fields master * re9b8b59 / (Bio/SeqIO/genbank.pm Changes): [bug 2599] add support for DBLINK output, by just allowing some space ;> - http://bit.ly/9cI59t
20:22 pyrimidine rbuels: around?
20:22 rbuels pyrimidine: is that french for ping?
20:22 pyrimidine yes
20:23 pyrimidine (or maybe Texan)
20:23 pyrimidine Think I should go ahead and add this module for 1.6.2?  http://bugzilla.open-bio.org/show_bug.cgi?id=2701
20:23 pyrimidine has tests, etc.
20:24 pyrimidine though it would need a bit more work
20:24 * rbuels looks at it
20:25 pyrimidine no additional deps either
20:25 pyrimidine so might be worth adding in
20:25 pyrimidine (just in time to be split out again :)
20:26 rbuels pyrimidine: it is in master right now?
20:26 pyrimidine nope
20:26 rbuels pyrimidine: where is it?
20:27 pyrimidine bugzilla, that's it
20:27 pyrimidine would be nice to get it into VC
20:28 rbuels is genehack done and merged with deafferret's seqfeature roundtripping business?
20:28 pyrimidine don't think so
20:28 rbuels i thought i saw a commit from him on that ...
20:28 * rbuels looks
20:28 pyrimidine it's in a branch, last I sa
20:28 pyrimidine *saw
20:29 rbuels umm, separate issue, i am not at all sure about bioperl-live c1abbd13a50eff41f9fc5d3780765e6a89ead83a
20:30 rbuels nathan liles / gff and gff3
20:31 * pyrimidine looking...
20:31 pyrimidine ick, snuck a dependency in
20:31 rbuels filling in missing Name also seems like something that should be in application code.
20:31 rbuels cause some people might not WANT a bloody Name
20:31 pyrimidine right
20:32 rbuels not everybody uses gbrowe
20:32 rbuels s/e$/se/
20:32 pyrimidine oh, come on, don't you want unexpected side effects
20:32 pyrimidine ?
20:32 rbuels maybe the french do.
20:32 CIA-93 bioperl-live: Nathan Liles master * r09e0105 / (Bio/Tools/GFF.pm scripts/Bio-DB-GFF/genbank2gff3.PLS):
20:32 CIA-93 bioperl-live: Didn't realize there was already a subroutine to give the name field.
20:32 CIA-93 bioperl-live: Uncommented convert_to_name() in the genbank2gff3 converter script and deleted
20:32 CIA-93 bioperl-live: duplicate functionality in Bio::Tools::GFF - http://bit.ly/aAWsBI
20:32 CIA-93 bioperl-live: Nathan Liles master * r855db54 / (Bio/SeqIO/genbank.pm Changes): Merge branch 'master' of https://github.com/bioperl/bioperl-live - http://bit.ly/cNWTys
20:32 pyrimidine um, that was strange
20:32 rbuels speak of the devil
20:33 pyrimidine heh
20:33 rbuels in Texas no less.
20:33 pyrimidine A&M, IIRC
20:33 rbuels yep.
20:33 pyrimidine someone is still using Bio::DB::GFF?
20:33 rbuels yeah, doing these things in master with no review, is .. no.
20:33 rbuels no no.
20:33 * rbuels looks up nate's phone number.
20:35 pyrimidine actually, he just ripped that bit of code we were talking about
20:35 pyrimidine *ripped out
20:36 pyrimidine didn't pull the YAML dep, doing that now...
20:38 rbuels well, its in genbank2gff3 now, which is probably OK
20:40 pyrimidine true
20:41 rbuels pyrimidine: i added a note to the offending commit saying he should have thought a bit more
20:41 rbuels http://github.com/bioperl/bioperl-li​ve/commit/c1abbd13a50eff41f9fc5d3780​765e6a89ead83a#commitcomment-121440
20:42 rbuels anyway, where were we
20:42 rbuels ah yes, genehack's branch
20:42 * rbuels pops his stack
20:42 pyrimidine re: YAML, pushing that into 'recommends'.  We can add it to 'requires' if needed.
20:43 pyrimidine (after the dynamite has gone off)
20:44 pyrimidine okay, it looks like it has been merged in
20:44 pyrimidine http://github.com/bioperl/bioperl-live/comm​it/f63c4dba999c88f9481be9f173cb7c3005236329
20:45 pyrimidine http://github.com/bioperl/bioperl-live/comm​it/a3ee8b9c7dfb10b3601cfc8f0d851287832efdb1
20:45 pyrimidine two pull requests
20:53 rbuels pyrimidine: is that going to put the mysql backend's behavior out of sync with the other backends?
20:53 pyrimidine rbuels: possibly
20:54 genehack rbuels: no, it doesn't, because the other two backends inherit from the mysql one and don't reimplement that method.
20:54 genehack i.e., that method is the only place that work is done.
20:54 genehack (re: that design: BLUCK.)
20:54 rbuels BLUCK?
20:55 genehack that's the sound of me throwing up just a little bit.
20:55 rbuels ENOINFOBOT
20:55 pyrimidine assuming thats a combination of BLECH and F*CK
20:55 rbuels hah
20:55 pyrimidine oh, I'm on IRC, so FUCK
20:55 rbuels genehack: bio is packed to the gills with bluck.
20:56 genehack rbuels: yeah, i'm learning.
20:56 pyrimidine the backend code could probably be cleaned up, just hasn't been top priority
20:56 rbuels genehack: most code is written by people who are learning how to code *right then*
20:56 genehack i was worried about the different backends getting out of sync, so i looked at those as well, which was when i discovered the interesting inheritance patters.
20:56 genehack s/patters/patterns/
20:56 pyrimidine the mysql adaptor was the original one
20:56 rbuels ah the famous bio inheritance.
20:57 pyrimidine I'm assuming the others just override as needed
20:57 genehack pyrimidine: yeah, that's what it looks like.
20:57 rbuels it's so bad in bioperl, they wrote a web tool to try to navigate it!
20:57 * rbuels points at the deobfuscator
20:57 pyrimidine heh
20:57 * rbuels slaps his knee
20:57 rbuels tip your waitress
20:59 rbuels genehack: got tuits for any more bugs?
20:59 genehack i have to get going, b/c it's fetch-kids-from-daycare time here, but AFAIK deafferret's bug is fixed and i'm looking for something else to do
20:59 genehack rbuels: JINX
20:59 rbuels lol
21:00 rbuels genehack: i'm going to give you commit on the bioperl repos now, so the next one can be in a regular topic branch
21:00 genehack i'll be back on 3-4 hours from now and will check the scrollback, so feel free to point me at stuff
21:00 genehack rbuels: thanks!
21:00 * pyrimidine points at bugzilla
21:00 pyrimidine :)
21:00 genehack i'm feeling particularly motivated towards the de-monolithing, if there's anything i can do there.
21:01 genehack pyrimidine: that was my fallback plan, start at the low numbers and start banging. 8^)
21:01 rbuels genehack: oh there certainly is, we should talk about that when you have time
21:01 genehack okay, i'll catch up with you later.
21:01 pyrimidine I think we just bite the bullet and release 1.6.2 as the final monolithic release
21:01 rbuels genehack: but for right now, if you have tuits, http://bugzilla.open-bio.org/show_bug.cgi?id=2701 needs to be shoved into a topic branch so it can be reviewed properly
21:02 rbuels might have missed him
21:02 pyrimidine just looked at the tests for that one, will need a lot more
21:02 pyrimidine they're minimal, as in 'I have a test script, but there aren't any tests in it'
21:02 rbuels lol
21:02 rbuels use_ok(...,'module compiles');
21:02 rbuels done_testing;
21:03 pyrimidine not even that
21:04 rbuels i need to go work on $pressing_thing = 'Catalyst::Controller::CGIBin'
21:04 pyrimidine ok
21:04 rbuels hopefully genehack will have some tuits
21:04 pyrimidine oh, speaking of Catalyst...
21:04 pyrimidine know anything about the latest book?
21:04 rbuels pyrimidine: it's good, buy it.
21:04 rbuels pyrimidine: the one from mst right
21:04 pyrimidine ok, will do
21:05 pyrimidine no, there's another one
21:05 rbuels eh?
21:05 rbuels which
21:05 pyrimidine http://www.amazon.com/Catalyst-5-8-Perl-MVC​-Framework/dp/1847199240/ref=sr_1_4?ie=UTF8​&s=books&qid=1280783116&sr=8-4
21:05 * pyrimidine hates long URLs
21:06 rbuels pyrimidine: i don't know anything about that one, ask in #catalyst on irc.perl.org
21:06 rbuels actually, i will
21:10 rbuels pyrimidine: hmm nobody is listening
21:10 * rbuels looks at the book himself
21:10 pyrimidine IRC warnocked
21:11 pyrimidine yeah, was really confused to see two new books on Catalyst (mst and this one)
21:12 rbuels pyrimidine: ah, this is the update of jrock's earlier book
21:12 rbuels pyrimidine: because jrock did not want to do it
21:12 rbuels i would go with mst's.
21:12 pyrimidine that's what I'm thinking as well
21:12 rbuels i have that book and it's good
21:12 rbuels and i have jrock's earlier book too and it's not so good
21:12 rbuels and i don't know who antonio solar john is.
21:13 pyrimidine getting that plus Effective Perl, v2
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22:20 bag_ joined #bioperl
22:24 genehack i'll look at that bug
22:25 genehack and i haven't seen the new cat book but it's a bad sign when a perl book author only has a single CPAN module to their name and it's failing automated tests on everything in existence. (IMO.)

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