Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-06-26

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All times shown according to UTC.

Time Nick Message
00:17 deafferret git pull.   now in repo:  t/bugzilla/2537
00:18 brunov deafferret, there are some tests failing with the cloned repo that do not fail with the updated svn repo, should I care about those?
00:19 brunov I appiled the patch locally and it passes the affected tests, but don't know if I should pull this
00:19 brunov s/pull/push/
00:19 deafferret rbuels is FindBin 'ing it
00:20 deafferret gimme a sec
00:20 brunov ok, just let me know how should I proceed
00:20 brunov dinner &
00:25 deafferret git pull
00:25 deafferret looks good now
00:25 deafferret in a tests-failing sort of way
00:25 deafferret at least we have 1 example of bugzilla wars now
00:42 brunov deafferret, so before I mess up. You say I should create a folder with the bug number under t/bugzilla, or should I just mention the bug number in the commit message?
00:43 deafferret um, perhaps both...
00:44 deafferret so if you're scanning the change log you'll see the bug number, even without the list of files that changed
00:44 deafferret git pull and see 2537 for a n example
00:44 deafferret http://bugzilla.open-bio.org/show_bug.cgi?id=2537
00:45 deafferret rbuels thinks that's ok. I think it's freaking awesome  :)
00:45 rbuels brunov: you gonna apply your patch or what
00:45 brunov yes, I already have
00:45 brunov was making sure I was doing things properly
00:46 brunov before pushing
00:46 rbuels ok
00:46 * rbuels approves of doing things properly
00:51 rbuels deafferret says i'm not actually a dick
00:51 rbuels didn't mean to sound like one up there
00:51 brunov applied
00:51 rbuels 'you gonna apply your patch or what' is a bit brusque, so please do excuse me
00:51 * rbuels is actually quite courtly
00:52 brunov don't worry -- have to admit that it startled me a bit, but I know what irc is like
00:52 * brunov has been yelled at by mst
00:53 brunov rbuels, deafferret done -- this is fun, I'll see if I can fix another one
00:57 deafferret "brusque" is a pretty douchey word to use
00:58 * deafferret waits patiently for rbuels to cycle back to IRC
00:59 * rbuels paddles deafferret.  He is snorting.
00:59 rbuels literally
00:59 rbuels but not cocaine
00:59 rbuels air.
00:59 deafferret :D   staring at 2842 now
01:01 brunov deafferret, if you see some .svn thingies, don't worry, just removed them
01:02 deafferret no worries  :)
01:08 pyrimidine joined #bioperl
01:08 pyrimidine just dropping in
01:08 deafferret HI!  :D
01:08 rbuels oh helloooo
01:08 pyrimidine o/
01:08 deafferret we r in yur bio purlz
01:09 pyrimidine I see!
01:09 rbuels hackin yur codez
01:09 pyrimidine ONOZE
01:10 deafferret rbuels and I are laughing our heads off here in Pitt  !  :)
01:10 pyrimidine I suppose we have a way to merge these back to svn?
01:10 deafferret he fell off his chair earlier  :)
01:10 deafferret twice
01:10 rbuels pyrimidine: you do.  or you could give us commit bits and undo the damage later
01:10 pyrimidine little too much drinky drinky?
01:10 deafferret high on perl, man  :)
01:11 rbuels deafferret says it's just zest for bioperl
01:11 pyrimidine not a bad thing
01:11 pyrimidine I'm actually working a bit on Bio::Moose
01:11 rbuels no, the drinking has not started yet
01:11 rbuels we want to hit a few more bugs
01:12 pyrimidine (a break from some bioperl hacking)
01:12 pyrimidine but I'll be wrapping up Infernal fixes
01:12 pyrimidine bug fixes are good
01:12 deafferret Infernal? or internal?
01:12 pyrimidine Infernal (RNA motifs)
01:13 pyrimidine http://infernal.janelia.org/
01:13 pyrimidine (think of RNA-like HMMER)
01:13 deafferret ah. thanks
01:13 pyrimidine s/RNA-like/RNA-structure-like/
01:15 pyrimidine gah, my wireless sux
01:22 deafferret I pushed again
01:22 deafferret apparently rbuels can push git back to your svn if he has a commit bit?
01:22 deafferret I'm a git newb
01:24 deafferret pyrimidine: ^^^
01:24 pyrimidine we can probably set that up, rbuels, send me the following:
01:24 * deafferret is staring at 2069 now
01:24 * pyrimidine looking up the specifics
01:25 rbuels probably just ssh pubkey right
01:25 pyrimidine deafferret: don't burn your eyes out
01:25 rbuels and my desired username?
01:25 rbuels (that's the usual)
01:26 pyrimidine nah, first born and a few drops of blood for the signature
01:26 rbuels ENOFIRSTBORN
01:26 rbuels maybe an iou?
01:28 pyrimidine rbuels: http://www.bioperl.org/wiki/SVN_Account_Request
01:29 pyrimidine just pass it on to me, I'll forward it to the bp gods (with proper tithings of course)
01:29 pyrimidine and then it should come through
01:29 pyrimidine v
01:29 pyrimidine e
01:29 pyrimidine r
01:29 pyrimidine y
01:29 pyrimidine q
01:29 pyrimidine u
01:29 pyrimidine i
01:29 pyrimidine c
01:29 pyrimidine k
01:29 pyrimidine l
01:29 pyrimidine y
01:30 pyrimidine ;)
01:30 rbuels ok it's in your email
01:30 rbuels why the bureucracy?
01:31 * rbuels got a Moose commit bit even though he did not really want one
01:32 * brunov has a Moose commit bit too, those guys hand them out like flyers ;)
01:32 pyrimidine just the way it is, but we're fairly free about giving them out actually as long as we have someone to vouch for the commits
01:32 pyrimidine yes they do
01:33 pyrimidine that's a new mindset (not a bad one to have either)
01:33 rbuels where do ssh pubkeys go?
01:34 pyrimidine_ joined #bioperl
01:34 * rbuels seems to remember it's some other transport
01:34 * brunov looks at 2847
01:34 pyrimidine_ damn vpn
01:35 rbuels word.
01:35 rbuels dircproxy is nice for poopy connections
01:35 rbuels run a little thing on a server somewhere
01:35 rbuels connect to it on some weird port
01:35 rbuels and it connects to irc for you
01:35 rbuels and stays there
01:35 rbuels so you get backscroll too
01:36 rbuels it's like running irssi in screen, but without having to use irssi
01:36 pyrimidine_ Yeah, thought about setting that up but I mainly run off my laptop
01:37 pyrimidine_ when I have the server going in the next few months I'll set that up
01:37 * pyrimidine_ going for double-underscore
01:37 pyrimidine__ joined #bioperl
01:37 rbuels wooooo
01:37 rbuels he did it!
01:38 pyrimidine__ yeah!
01:44 ___pyrimidine___ okay, gotta go
01:44 ___pyrimidine___ rbuels: I'll keep an eye out for your email (didn't come to my illinois.edu one)
01:50 brunov WOHOO!
01:50 * brunov just fixed 2842
01:54 deafferret sorry, back now. $wife called
01:54 deafferret errr   use constant 'wife';
01:54 brunov LOL
01:55 deafferret you fixed 2842? I added the code, rbuels is adding tests? what are you doing?
01:55 deafferret i pushed the code out 20m or something
01:55 deafferret sorry if I failed to communicate
01:56 brunov whoa?
01:56 * deafferret stares at 2069
01:56 deafferret you meant 2847
01:56 rbuels oh, it was 2847.
01:56 * rbuels wipes his sweating brow
01:56 deafferret rbuels: it was 2847
01:57 deafferret brunov: you meant 2847
01:57 deafferret 2847
01:57 * deafferret stares at 2069
01:57 brunov sorry, mistyped the number
01:58 deafferret :)
01:59 * deafferret backs away slowly from 2069, runs
01:59 brunov some of those are freaky, uh?
01:59 brunov I actually found a solvable one, but it's bioperl-run, so no
01:59 brunov maybe for later and mail-patching
02:00 deafferret ya
02:00 * deafferret runs from 2213 too
02:00 brunov we should mark them as closed in bugzilla,right? Like, we *assume* these changes are happening?
02:01 deafferret um, no. I would think you should just comment it as "fixed in github" and leave it open until it hits the official repo
02:01 brunov OK!
02:01 deafferret GLOBAL DISCLAIMER:   Take or ignore all my Bio* suggestions on a whim. I know squat.
02:02 deafferret I'd put the github path in the ticket so there's no ambiguity about which github it's sitting in
02:02 deafferret even the first 6 chars of the commit ID would be cool... or URL thereof
02:02 deafferret or whatever
02:03 * deafferret walks away from 2513
02:05 * deafferret aproximates 2857 at 1 month of labor
02:07 * brunov looks at 2850
02:10 deafferret 2142 is smoking crack
02:14 brunov o_O
02:18 majensen joined #bioperl
02:18 deafferret majensen: HI!
02:18 majensen deafferret: you guys are ON FIRE!
02:18 deafferret we didn't start the fire
02:18 deafferret it was always burnin' since the world's ben turnin'
02:19 deafferret or since github freed our imaginations
02:19 brunov github++
02:19 * majensen making gagging noises.
02:19 * rbuels is drunk on power
02:19 deafferret and booze
02:19 majensen well, now I know...
02:19 rbuels not now, but i will be in about an house
02:19 rbuels er.
02:19 rbuels hour
02:20 majensen hehehehe.
02:20 rbuels i have words in my muscle memory
02:20 majensen I have muscle in my word memory.
02:20 rbuels sometimes i delegate to them a bit too much
02:20 majensen The BioPerl Y
02:20 majensen oops
02:20 majensen The BioPerl YPAC Coup of 2009
02:20 deafferret lol
02:20 majensen history as it happens.
02:21 deafferret THUS, ALWAYS TO TYRANTS!
02:21 deafferret oops
02:21 majensen hoist the github, me hearties, arrgh...
02:21 deafferret lol
02:21 rbuels um.
02:21 majensen hic semper hackers
02:21 majensen um.
02:21 * majensen rofl.
02:21 deafferret rbuels is just playing it safe since he wants a commit bit
02:21 rbuels is ewan birney going to be the next one to join this channel?
02:21 majensen you boys are always the same.
02:22 deafferret I, on the other hand, am just HACKSING YUR CODEZ
02:22 majensen Is Ewen Birney a myth? Details at 10.
02:22 rbuels ebirney: ZOMG WTF ARE YOU DOING
02:22 rbuels er.
02:22 deafferret majensen: did you know there are several tickets in bugzilla that are, in fact, a lot of work?  ;)
02:22 rbuels <ebirney> ZOMG WTF ARE YOU DOING
02:23 majensen deafferret: All bugs are shallow.
02:23 majensen or is that, all users? All devs? anyways...
02:24 deafferret sorry, what? was distracted by coeds
02:24 deafferret shallow? what?
02:24 majensen Yes, I am enjoying the YPAC squirmathon over bp-guts.
02:24 deafferret :)
02:24 majensen Let not the coeds distract from the codes.
02:25 majensen And other inscrutable wisdom.
02:25 majensen also, Able I was, ere I saw Elba.
02:25 majensen (are you getting all this, ilbot2?)
02:25 * deafferret attempts to tackle 2346 before booze-o'clock
02:26 * majensen descending again into the pit of $job.
02:26 majensen Have fun, and beer, all-- byebye
02:26 deafferret :)   OKBYE
02:27 majensen left #bioperl
02:50 deafferret I pushed 2346 FAIL up
02:50 deafferret researching
02:52 rbuels anybody besides my and deafferret still here?
02:52 brunov me
02:52 rbuels ah good
02:52 brunov just fixed 2850
02:52 brunov reproducing it was a b*tch
02:53 deafferret brunov++
02:53 deafferret YOU GUYS ROCK!
02:53 rbuels brunov++
02:53 deafferret except rbuels
02:53 brunov to you kids at home, don't forget to fail your bugs with a failing script
02:53 rbuels brunov: look at http://bugzilla.open-bio.org/show_bug.cgi?id=2842
02:53 rbuels i need a second opinion
02:53 rbuels in his example at the bottom
02:53 rbuels comment 4
02:54 rbuels you see how his masking thingy puts '?' on every column, even the gaps
02:54 * brunov looks
02:54 rbuels does it really make sense to do that?
02:54 rbuels i don't know, I'm not a multiple-sequence-alignment type guy
02:54 rbuels you know, those guys.
02:56 brunov well, I'm not either, but I guess it *does* make sense
02:56 brunov there'll never be a zone with gaps in *all* sequences
02:56 deafferret ya. (1) write the failing test (2) fix (3) test passes now
02:56 brunov so I guess that depending on the downstream use of the aln, you might want to mask low-quality zones like those too
02:57 brunov my take on that would be to apply the guys patch if it is easy enough, and let the bioperl gods decide afterwards
02:57 deafferret First fail the test cases. The idea is to ensure that the test really works and can catch an error. Once this is shown, the underlying functionality can be implemented. This has been coined the "Test-Driven Development Mantra", known as red/green/refactor where red means fail and green is pass.
02:57 deafferret http://en.wikipedia.org/wi​ki/Test-driven_development
02:57 brunov if it's too much trouble, I wouldn't sweat it.
02:57 brunov TDD++
03:00 rbuels brunov: ok, then masking-in-gaps it is.
03:01 rbuels henceforth, Tristan Lefebure shall be known among our people as Masks-in-the-Gaps
03:02 brunov Tristan++ # flashy name
03:02 deafferret like Dances-With-Wolves, only gappier
03:05 rbuels bioperl-bot: what do you do again?
03:05 rbuels hrm.
03:05 rbuels bioperl-bot-- #not funny
03:05 rbuels ok, i think i'm going to send tatertot in here
03:06 brunov bioperl-bot: translate GATTC
03:06 brunov bioperl-bot translate GATTC
03:06 bioperl-bot DS
03:06 brunov that's his thing
03:06 rbuels hrm.  still not funny,
03:06 rbuels but better.
03:09 brunov next bio-hackathon we should do something fun, like revamping bioperl-bot's tricks or doing some crazy stuff like autobox::bio
03:09 brunov "GATTC"->translate
03:09 rbuels hey that's a good idea
03:09 brunov "MAEELKKVIKP"->blast
03:10 brunov it shouldn't bee too hard, just wrapping Bio::Seq with autobox
03:16 rbuels well do it now
03:16 rbuels Bio::Seq::autobox
03:16 rbuels or something
03:16 deafferret faster, Trumpy. Kill. Kill.
03:17 brunov o_O but... but.. it's almost 1 am here
03:17 brunov I'm almost crawling to bed
03:19 deafferret you can sleep when you're dead. hacking time now
03:19 deafferret HACK!!  this is a death march!
03:19 deafferret or maybe we should drink now
03:22 deafferret http://www.youtube.com/watch?v=qW3GUdEkesw
03:24 rbuels brunov: ok you can go to bed when all your tests run correctly when you do prove -I. -r t/bugzilla in the distro root
03:24 rbuels there are unhappy things there now
03:26 rbuels brunov: test 2847, not up to coding standards
03:26 rbuels no 'use lib' at the top.
03:26 brunov rbuels, yes, I'm removing it now
03:27 brunov (silly me)
03:33 rbuels brunov: also, instead of Test::Exception, use Bio::Root::Test, and test_begin(...)
03:33 brunov hrm
03:33 brunov roight
03:33 rbuels see t/bugzilla/2842/mask.t for example
03:33 rbuels (might need to pull)
03:36 brunov pulling now
03:40 brunov weird, I just pulled but can't find 2842/mask.t
03:49 rbuels oh i think i need to push it
03:49 rbuels hold on
03:49 rbuels ok now pull
03:49 rbuels sorry
03:49 brunov no prob
03:50 rbuels oh it still didn't get in there
03:50 rbuels i screwed my git
03:51 rbuels ok there it is pull
03:53 rbuels be sure that you run the tests as prove -I. -r t/bugzilla
03:53 rbuels with current dir bioperl-live
03:54 rbuels test 2346 is supposed to fail
03:54 rbuels the others, not.
03:59 brunov ok, I just fixed my mistakes, and running your command from root dir tests 2850 and 2847 pass
03:59 rbuels to find your file paths, you can use Bio::Root::Test::test_input_file
03:59 rbuels or FindBin
03:59 rbuels if you use test_input_file, you put your test datafile in t/data
04:00 rbuels if you use FindBin, you can use the current dir
04:00 brunov rbuels, ok, FindBin seems nicer, I'll try that
04:00 rbuels but be sure to use File::Spec->catfile or File::Spec::Functions qw/catfile/ if you use FindBin
04:00 rbuels cause these tests need to pass on windows
04:06 brunov rbuels, done
04:06 brunov *phew*
04:06 * rbuels pulls
04:07 rbuels ah, lovely
04:08 * rbuels awards a score of 98%
04:08 rbuels (you could have alphabetized your 'use' statements)
04:08 rbuels lol
04:08 rbuels j/k
04:08 rbuels thanks a ton brunov
04:08 brunov O-O
04:08 rbuels have a good nigth
04:08 brunov ;_;
04:08 brunov thanks both of you
04:09 brunov hope we can do this again some time
04:09 brunov was fun
04:09 rbuels yeah quite fun
04:09 rbuels got 6 bugs done too
04:09 deafferret :D    toodles!
04:09 deafferret thanks for everything!
04:09 * rbuels hi-fives brunov
04:09 brunov cool!
04:09 deafferret updating 2346 now
04:09 brunov o/\o
04:09 deafferret group hug!
04:09 deafferret pile-on!
04:09 rbuels owwwww
04:09 deafferret CWS style
04:10 brunov rbuels++
04:10 deafferret dummy, why you on bottom?
04:10 brunov deafferret++
04:10 deafferret g'night
04:10 rbuels night
04:10 brunov night
04:10 rbuels beer &
04:10 brunov pillow &
07:02 viklund joined #bioperl
07:53 faceface what did I miss? ;-D
07:53 faceface looks awesome
08:31 faceface_ joined #bioperl
10:27 ptl_ joined #bioperl
12:42 deafferret ya, that was a blast!  :)
13:38 deafferret anyone up for round 2? I've got all day!  :)
13:39 deafferret HACKZ HACKZ HACKZ!
13:39 * deafferret takes strange vacations
13:39 deafferret they're just like $work, only I don't get paid
14:04 faceface and people tell you your an idiot for doing it
14:04 faceface ;-)
14:04 faceface gl deafferret
14:04 faceface may all your projects be completed on time!
14:04 deafferret time is an illusion. all is code
14:41 alper joined #bioperl
14:46 ptl So... Michael Jackson is dead. Now what is the impact of THAT on bioperl?
14:51 * faceface don't care
14:51 faceface however, the folloing mashup is awesome
14:52 faceface http://music.yellowgrey.com/Dan/ChenardChen​ard/080_fsz010_08-chenard_walcker-back.mp3
14:52 faceface prolly should download rather than stream
14:55 ptl what is that?
14:56 faceface a mashup by chenard walker
14:56 faceface walker
14:56 faceface http://www.chenardwalcker.com/freesamplezone.htm
14:57 faceface he made about 100 albums, and I made a best of, which that MJ song is a part of
14:58 faceface meh... I'm just depressed because I got feedback on the wiki... did you reaise there is a history feature? ZOMG! people could see earlier versions! KEEP EMAILING WORD DOCUMENTS EVERYONE
14:58 faceface because thats better
15:02 * deafferret laughs
15:37 faceface ;-)
15:37 faceface thinking about it though - it may just be a case of ignorance
15:37 faceface I think they may have got it into their heads that the history feature is like 'track changes' in word. I.e. every single character stroke is logged and can be reviewed.
15:38 faceface I need to somehow educate them on the different possible strategies, including preparing a polished revision and submitting it all in one fell swoop.
15:38 perl_splut it is the problem of the binary file that is Word. Want to clear that out, finish the document, then copy and paste to a new one
15:38 perl_splut history gone
15:39 faceface I may be setting a worrying example by saving garbage
15:39 faceface perl_splut: yeah but word != wiki
15:39 faceface but you have to have used wiki to know that
15:40 perl_splut That's the whole point of a wiki, heheh
15:40 faceface perl_splut: IMAGINE THE CHAOS!!!!oneoneoen
15:41 * perl_splut zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz *
15:41 deafferret people make mistakes? then fix them? holy crap! my world view is shattered!
15:41 faceface perl_splut: I saw you make a spelling mistake there! yoru out of my science club!
15:41 deafferret ideas evolve? GET OUT!
15:42 * faceface politely dies to make way for a new idea
15:42 perl_splut don't use evolve... ideas don't evolve. They are created and designed... evolution is a crock...
15:42 deafferret not yet, you
15:42 faceface I forget who said that - ideas never change, the old scientists just die
15:43 faceface perl_splut: I disagree ;-)
15:43 faceface evolution is the best idea ever I recon
15:44 perl_splut HOW DARE YOU DISAGREE WITH THE WORD OF THE ONE AND TRUE LORD... Sauron...
15:44 faceface don't necessarily confuse 'Darwinian evolution' with evolution
15:45 perl_splut )
15:45 perl_splut :)
15:46 faceface I wonder if the track changes feature has survived docx -> doc -> ooffice -> doc ... oh well...
15:47 perl_splut not sure it is the track changes feature that causes that
15:48 faceface causes what sorry?
15:49 perl_splut the ability to find the old text in the word document
15:52 faceface anyone ever posted a comment on PLoS One?
15:53 faceface I was trying to persuade myself to revew one full PLoS One article a month and submit it to the comments.
16:07 dean joined #bioperl
16:27 dean Hi.  I'm a little confused by the 1400 modules contained in bioperl-- selecting out the relevant ones seems tricky.  Is there a means of motif discovery within genetic sequences that incorporates sequences from multiple genomes?  I understand the WISE package will make tfbs prediction based on conservation within pairs of sequences-- are there other packages in bioperl that will do the same for multiple sequences (>2)?
16:37 perl_splut maybe - http://www.bioperl.org/wiki/Teiresias
16:38 deannew thank you splut-- I'll take a look
16:40 perl_splut http://cbcsrv.watson.ibm.c​om/Tutorial/aboutTspd.htm
16:40 deannew thanks!
17:37 viklund joined #bioperl
17:48 ende joined #bioperl
17:49 ende hullo
17:50 alper joined #bioperl
17:53 * deafferret waves
17:59 perl_splut hola, ende
18:00 ende what's the term again for channels with only a single # preceding the name?
18:02 deafferret isn't that all channels?
18:05 ende well there are some like ##channel
18:06 ende and there's different rules on freenode as far as ownership goes
18:06 ende there's two channels I really want to chwon
18:06 ende *chown
18:20 deafferret no clue sorry   :)
18:23 ende Unfortunately I can't just invade it ;)
18:34 rbuels i heard that single-# channels are for 'official organizations'
18:34 rbuels (ende)
18:34 rbuels and double-# channels are for everything else
18:34 ende ah
18:35 rbuels there is apparently some kind of freenode form you're supposed to fill out for a single-# channel
18:35 ende rbuels I see you're on #gmod too
18:35 rbuels they were talking about this on #bioinformatics a while ago
18:35 * ende nods
21:56 brunov joined #bioperl
22:28 brunov deafferret, you still in Pit?
22:55 deafferret brunov: ya  :)
23:21 nErVe joined #bioperl

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