Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-09-09

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All times shown according to UTC.

Time Nick Message
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15:38 * deafferret shakes his fist at wobbling restriction enzymes
15:39 deafferret make up your mind already!!
15:39 deafferret :)
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18:47 Biome biome: Chris Fields master SHA1-280ddd6
18:47 Biome rename roles according to CONVENTIONS
18:47 Biome http://bit.ly/pDaRu
18:47 Biome biome: Chris Fields master SHA1-f1c7a9b
18:47 Biome switch over to Native types
18:47 Biome http://bit.ly/U44Gs
18:47 Biome left #bioperl
18:50 pyrimidine mwahahaha
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18:51 Biome biome: Chris Fields master SHA1-54a914b
18:51 Biome bump required Moose ver to 0.89_01 (for Native types) and MooseX::Aliases to 0.03 (for init_arg stuff)
18:51 Biome http://bit.ly/2g7Ey3
18:51 Biome left #bioperl
18:51 xp_prg hi all
18:51 pyrimidine o/
18:51 xp_prg what is the best free moleculvar vision software?
18:51 xp_prg visualization
18:52 pyrimidine Best?  Is there a 'best'?
18:52 pyrimidine 'Best' prob. depends on what you want to do
18:53 pyrimidine PyMOL is good (haven't used it in a while though).  VMD, though I'm biased (they're from here)
18:53 pyrimidine 'here' = Univ. of Illinois, NCSA
18:55 * deafferret can't remember the name of the commercial software our chem dept uses
18:55 xp_prg vmd, what is that?
18:55 * pyrimidine gasps
18:55 pyrimidine http://www.ks.uiuc.edu/Research/vmd/
18:56 pyrimidine ;)
18:57 xp_prg nice thanks!
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19:28 Biome biome: Chris Fields master SHA1-acbbdbf
19:28 Biome change Annotate->Annotatable (note: this is not the same as Bio::AnnotatableI!) per CONVENTIONS
19:28 Biome http://bit.ly/miRmN
19:28 Biome biome: Chris Fields master SHA1-86faf4f
19:28 Biome changes per CONVENTIONS
19:28 Biome http://bit.ly/11iZ1K
19:28 Biome biome: Chris Fields master SHA1-f6a1eba
19:28 Biome changes towards Native types, come in line with CONVENTIONS
19:28 Biome http://bit.ly/bbVnx
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19:33 Biome biome: Chris Fields master SHA1-3cf7950
19:33 Biome final batch of commits; may revisit Annotatable vs Annotate later but it's semantics (and we might get rid of heavy-weight Annotations in Biome anyway)
19:33 Biome http://bit.ly/ynl0J
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21:15 jonathan__ hello
21:15 * deafferret waves
21:16 jonathan__ i have uploaded a working beta of my robotics module to CPAN, it should be listed in a few days
21:17 jonathan__ but I am not sure if I should register each module, or having multiple modules in one tar is OK for CPAN
21:17 pyrimidine register each
21:17 jonathan__ I have Robotics:: which is Robotics.pm and Robotics::Tecan and Robotics::Gemini all under Robotics::
21:18 jonathan__ register each and upload each separately?
21:18 pyrimidine no
21:19 pyrimidine basically, if you have already uploaded them and have entered everything in PAUSE correctly you should be fine
21:19 deafferret wow. search.cpan.org is very quiet when searching for 'robotics'  :)
21:19 jonathan__ I got the approval email but it said it would take a couple days ot be listed in the DB
21:20 jonathan__ took maybe 2.5 wks to get approved, quite lengthy
21:20 deafferret should this be under Device:: ?
21:20 pyrimidine jonathan__: you should be okay, then.
21:20 jonathan__ Robotics is an abstraction layer for multiple devices, not a device itself
21:20 deafferret ah, approved already by cpan-authors? cool.  :)
21:21 jonathan__ perhaps Device::Tecan would be the proper destination only for the h/w layer
21:21 pyrimidine see any problems here: http://search.cpan.org/~lds/CGI.pm-3.46/
21:21 pyrimidine ?
21:21 jonathan__ I may get access to a tecan EVO so the next one would be Tecan::EVO
21:22 jonathan__ the picture?
21:22 pyrimidine well, the complete lack of modules, for one
21:22 pyrimidine just a META.yml
21:22 * deafferret downloads the tarball
21:23 deafferret jonathan__: if the codebase isn't huge, I'd just push up a single Robotics-0.01.tgz for now
21:23 jonathan__ go to the previous version then CGI stuff shows up
21:23 deafferret jonathan__: and split the dists once development patterns start to break up a bit
21:23 deafferret pyrimidine: oh, crap.  :(
21:24 pyrimidine deafferret: just emailed Lincoln JIC
21:24 deafferret eek! ...  /me checks pause co-maint
21:25 deafferret Mark Stosberg  co-maint
21:25 pyrimidine but it's showing up under LDS
21:26 pyrimidine that's Lincoln's boo-boo
21:27 deafferret https://pause.perl.org/pause/authenque​ry?pause99_tail_logfile_1=40000&pa​use99_tail_logfile_sub=Tail+characters
21:27 deafferret I'm surprised PAUSE thought that was OK
21:28 pyrimidine me too
21:29 pyrimidine here's a link for you (I attended this one): http://www.youtube.com/watch?v=OFkgSjRnay4
21:29 deafferret lstein: you broke the intertubes!
21:30 pyrimidine just checked the PAUSE upload, CGI-3.47 is waiting there (it looks correct)
21:31 deafferret laugh... http://icanhascheezburger.files.wo​rdpress.com/2008/05/funny-pictures​-pony-mechanic.jpg?w=393&h=260
21:31 pyrimidine ftp://pause.cpan.org/incoming
21:33 deafferret ah, yep. in the pause log too
21:33 deafferret I didn't search for 2 today
21:36 pyrimidine that git/github web seminar (webinar?) was pretty good.  It's not apparent from the video, but someone asked Scott whether they would open-source github (he remained noticeably silent)
21:36 deafferret right after search.cpan.org goes open source  :)
21:37 pyrimidine there's talk of that (actually, of os-ing a lot of perl-related sites)
21:38 pyrimidine though pudge probably won't give up use.perl.org stuff (would prob. have to rip it from his cold dead hands)
21:40 deafferret -shrug- it's their code. they can do as they please. I'd have loved to have the pod2html of search.cpan.org for the last few years  :)
21:40 deafferret intranets
21:41 pyrimidine agreed.  activestate's got a good one as well, just don't want to install activeperl to get it ;)
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21:41 pyrimidine bah, closed window
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21:42 jonathan__ what is this for,  my %hardware = Robotics::query();
21:42 jonathan__ oops wrong paste
21:43 pyrimidine happens
21:43 jonathan__ what is this for,  META.yml
21:43 Lynx_ hey all! can anyone here help with the popgen modules?
21:43 pyrimidine Lynx_: that one might be one for the mail list.
21:44 jonathan__ uh, nevermind I'll read about meta.yml on the wiki
21:44 Lynx_ pyrimidine: ok, thanks
21:44 pyrimidine np
21:44 Lynx_ i also have a more genreal question, what was it with the moduleI vs. module names?
21:45 deafferret jonathan__: Module::Starter uses MANIFEST instead, so that's what I use
21:45 pyrimidine Lynx_: interface (abstract) classes vs. actual implementations
21:46 Lynx_ pyrimidine: ah, ok
21:46 pyrimidine gotta go.  commuting &
21:48 pyrimidine before I go
21:48 pyrimidine jonathan__: http://module-build.sourcefor​ge.net/META-spec-current.html
21:48 deafferret Lynx_: http://www.bioperl.org/wiki/Advance​d_BioPerl#Bioperl_Interface_design
21:48 pyrimidine (and I'm glad to see they're migrating to more JSON-y stuff)
21:50 Lynx_ deafferret: Thanks, I knew I read about it some month back
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