Camelia, the Perl 6 bug

IRC log for #bioperl, 2013-03-14

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All times shown according to UTC.

Time Nick Message
15:40 scottcain joined #bioperl
17:12 * rbuels emails ian about it
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17:57 rbuels deafferret: just so you know, Google Play recently suggested that i try listening to Young Jeezy, since he is apparently popular with Ace Hood fans
18:27 deafferret rbuels: memorized!
18:28 deafferret his earlier works are stronger. some people like his "blue phase," but I prefer the raw edge of the formative years
18:35 rbuels deafferret: indeed. i find the apotheosis of his early period to be "I Luv It", http://www.youtube.com/watch?v=wUjfWwqFcFI
18:37 deafferret needs more mysogyny
18:37 deafferret oh, nm. there it is
18:38 deafferret i was 25s in
18:38 deafferret so assumed it was lacking
18:38 rbuels come now.
18:38 deafferret did you track the tail number of that car to the rental company?
18:38 rbuels hehehe
18:40 deafferret "closer to God" indeed
18:40 deafferret WWYJD?
18:41 rbuels deafferret: for masterful use of misogyny, look no further than his seminal collaboration with 2 Chainz, "SupaFreak". a visual and auditory tour de force.
18:41 rbuels deafferret: http://www.youtube.com/watch?v=9chJZcHU6_o
18:42 deafferret oh well, it does have an "after party" warning right in the first verse. #fairwarning
18:42 deafferret is this English?
18:42 deafferret i recognize some words, but...
18:43 deafferret oh, lol. typo in "super" -- where do I submit erratta?
18:43 rbuels deafferret: you presume, sir.
18:44 * deafferret submits 'erratta' errata to deafferret
18:44 rbuels deafferret: this piece uses an experimental patois of his own invention, meant to more precisely convey some shadings of street meaning that one struggles to express in standard english
18:45 * deafferret nods sagely
18:46 deafferret huh. that's the least sexy editing of sexy lady footage i've seen in a long time
18:46 deafferret #subtle
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22:33 carandraug hey! Is there any sort of Bio::Gene class?
23:17 deafferret carandraug: uh, I assume you searched metacpan.org or equivalent?
23:18 deafferret carandraug: my recollection is that "gene" is an ambiguous term
23:18 carandraug deafferret, uhhh! I think that should have made more sense.. I was was just looking through the bioperl-live repository looking at the source :p
23:19 carandraug deafferret, yes. Just today I read a paper about the undefinition of the term gene :)
23:19 deafferret https://metacpan.org/search?q=bio+gene
23:19 carandraug helen something, nature 2004
23:19 deafferret ya, it... seemed to depend on who you were talking to, when :)
23:19 carandraug deafferret, if it doesn't exist I'll start writing it
23:19 deafferret looks like it might ^^^^
23:20 carandraug deafferret, they had a link for a "quiz" full of wacky cases and asking you, is that a gene or not? My degree is is molecular biology, I was surprised when I couldn't answer half the cases
23:20 deafferret haha :)
23:21 deafferret life's a bitch :)   (life as in 'biology' :)
23:22 carandraug deafferret, ohh! They already exist. It's good, less work for me though I was looking forward to write it
23:22 carandraug deafferret, since you're here, do you mind two more questions?
23:23 deafferret carandraug: well, you could always write it using Moose (the biome project) or perl6 (the bioperl6 project) :)
23:23 deafferret .... or Scala
23:23 carandraug deafferret, with that reply, then I'll have 3 questions
23:23 carandraug deafferret, 1) do you know of a tool to make this sort of displays? http://picpaste.com/1fqB4e8h.png I don't want to believe they made it by hand
23:24 deafferret 1) nope, that looked "hand" drawn to me
23:24 deafferret ping the author?
23:25 deafferret there's lots of annotation software packages, but i haven't seen one that looks like that out of the box
23:25 carandraug deafferret, so anything similar? Otherwise I'll have to finallly learn PStricks
23:28 carandraug deafferret, 2) I took Bio-biblio out of bioperl-live and would like to make a release on CPAN. How does that work since cjfields already released something on that namespace? I never released anything on CPAN and don't want to break anything
23:28 deafferret not off the top of my head, sorry. I'd just start googling. and/or images.google.com
23:29 deafferret 2) If I post Bio and Bio::Foo to CPAN you can still post Bio::Bar. PAUSE / CPAN only stop exact dupes -- they don't protect trees of namespaces
23:30 carandraug deafferret, yes. But that's what I mean. He released Bio::Biblio and I'd release a split of Bio::Biblio
23:30 deafferret ah. is Bio::Biblio in bioperl-live ?
23:30 deafferret so ask Chris to grant you CO-MAINT in PAUSE
23:30 carandraug deafferret, it was. I made the split on the weekend
23:32 deafferret looks like 4 people have co-maint, you can be the 5th :)
23:32 carandraug deafferret, I already got a PAUSE account and I'm seeting up the distro with Dist::Zilla. But shouldn't the upload happen through bioperl "project", rather than bioperl "dev"? PAUSE doesn't seem to be project oriented like github
23:32 deafferret probably a dev release until a bioperl release removes that file from itself
23:33 carandraug deafferret, I already removed the files from bioperl-live
23:33 deafferret carandraug: right, but THAT version of BioPerl has not been uploaded to CPAN
23:33 deafferret (none has in ... 2 years?)
23:33 carandraug deafferret, not from the v1 branch though
23:33 carandraug deafferret, yeah, projects seems quite stale
23:34 deafferret ... I'm unfamiliar with the bioperl-live branches
23:34 deafferret ya, pushing to CPAN is a pain so most people just use github
23:34 deafferret the people who volunteer to do all the CPAN work get burned out
23:35 carandraug deafferret, there's the master branch where everything happens which is the future, and v1 branch, which is just for bug fixes of the one big monolithic release. Then there are 2000 branches with bug fixes that never got merged because need testing
23:35 deafferret uh-huh. umm, i'd need to spend some time learning the official release strategy
23:35 carandraug deafferret, installing from github is a pain because means all simpler users will not use it
23:36 deafferret yup. further, things don't get into OS packages until they're CPAN releases
23:36 deafferret apt-get install bioperl  :)
23:36 deafferret it's all just a matter of who has how much free time to donate
23:37 carandraug deafferret, and the code base... when I was looking through a Bio::Gene class on the source, noticed that many of the modules are actually empty. They have a bunch of methods that only throw unimplemented
23:37 deafferret ick. ya, cleanup of that would be great
23:37 carandraug deafferret, that's what I do. But then needed to replace some because of bug fixes
23:38 deafferret http://content.screencast.com/users/dea​fferret/folders/Jing/media/316439a8-664​4-47e3-a1a9-405c667c5d8e/00000154.png
23:39 carandraug deafferret, but what to do with such empty files? Remove them? They still have a couple of lines of dopcumentation on what they could have been. Could give ideas to otehrs but I think the extra stuff just makes things more difficult to maintain, more difficult to navigate, more scary, attracting less new devs, and overall just slow down even more
23:40 carandraug deafferret, some of the files in the bio-biblio distro also take up some space on bio::DB::. Anyway, I'll set up things first and then ask for the co-maintenance
23:41 carandraug deafferret, 3) what's the future of bioperl? moose or perl 6? There's some changes I want to do with bio-biblio but what direction should I take?
23:42 deafferret carandraug: um, link me to concrete example URLs in github so I can give concrete feedback?
23:42 deafferret I'd ask for co-maint NOW -- it might take a couple weeks for somebody to do it
23:42 deafferret I know I'm 1800 emails behind :)
23:43 deafferret carandraug: If I was going to throw 1000 hours into it, I'd probably go Biome (perl 5), or Scala. I'm supposed to be learning Scala anyway ;)
23:43 deafferret but 99.9% of your users are bioperl-live  :)
23:44 carandraug https://github.com/bioperl/bioperl-l​ive/blob/master/Bio/IdentifiableI.pm for example
23:45 carandraug https://github.com/bioperl/bioperl-li​ve/blob/master/Bio/Cluster/FamilyI.pm
23:45 deafferret carandraug: ya, so my brain rejects that as completely unnecessary, unuseful Interface scaffolding that I would throw away... Once you split it into your own release you have more leeway to implement as you see fit (is how I see it)
23:46 carandraug https://github.com/bioperl/bioperl-l​ive/blob/master/Bio/AnnotatableI.pm
23:46 deafferret if you were dev'ing inside bioperl-live then I would argue for consistency. But you're not, so...
23:46 carandraug there are others. I might compile a list of these cases and ask on the mailing list.
23:46 deafferret Ya, any *I.pm will look like that if they've only been stubbed (not actually written)
23:46 deafferret sure.
23:47 deafferret the mailing list is always a good idea. many folks there have more experience than I do.
23:47 carandraug deafferret, I don't wanna spend 1000 hours on it. I just wanna be able to do this kind of stuuf easily http://larsjuhljensen.wordpress.com/2013/0​1/05/analysis-science-used-to-be-simpler/
23:50 carandraug deafferret, one more thing, what would you suggest as a project for bioperl. I'm thinking of applying for GSoC
23:58 deafferret Bio::Biblio sounds like a great problem! If that's your itch, scratch it! If you can get some GSoC money / recognition at the same time, the more the better! :)
23:58 deafferret Once you split it out you can implement it however you want! Well, you can use MOose if you want to :)
23:58 deafferret (I would)
23:59 deafferret the rules of consistency and "no Moose" don't apply to your own package, I assume
23:59 deafferret Biome is "rewrite bioperl core using Moose"

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