Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-04-12

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All times shown according to UTC.

Time Nick Message
01:25 delinquentme joined #bioperl
01:28 delinquentme # of people in here running unix as their primary OS?
01:29 delinquentme or some form of it .. that would be distinctly * not * linux
01:59 deafferret all linux
02:03 delinquentme deafferret, any reason not unix?
02:07 deafferret cause linux rocks  :)
02:10 delinquentme haha well i do run linux and it is pretty legit
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04:08 CIA-119 bioperl-live: Scott Cain master * r5ff758a / Bio/DB/GFF/Adaptor/dbi/mysql.pm : simple "real number maker" to silence compaints about mysql versions (like 5.5.9) not being a number. - http://bit.ly/gois7w
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09:24 Topic for #bioperl is now Be patient!  Sometimes it takes a few minutes for people to notice your question! | http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | nopaste to gist.github.com
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13:13 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * r212498a / (Bio/Root/Build.pm Bio/Root/Test.pm Build.PL):
13:13 CIA-119 bioperl-live: * Get basic tests and other Build.PL features working
13:13 CIA-119 bioperl-live: * Disable optional CPAN installs entirely (doesn't work with perlbrew and other tools
13:13 CIA-119 bioperl-live: * Script installation and cleanup NYI - http://bit.ly/ftABOt
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14:57 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * r2fa2c0a / (Bio/Root/Build.pm Build.PL): set up some specific cleanup steps for us - http://bit.ly/fKoOi9
15:04 CIA-119 bioperl-live: Chris Fields master * r1e4d2ee / t/LocalDB/BioDBGFF.t : default to memory if the adaptor is SQLite - http://bit.ly/hu3fAh
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16:09 CIA-119 bioperl-live: Chris Fields master * rf49c7d5 / t/LocalDB/DBFasta.t : squash local warnings - http://bit.ly/hgzCgs
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17:51 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * rd2c80ff / (2 files in 2 dirs): mv netinstall to utilities folder - http://bit.ly/euZm9M
17:57 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * r8ce558a / (2 files): mv netinstaller to bp_* and change docs accordingly - http://bit.ly/g1f55e
18:03 scottcain joined #bioperl
18:03 pyrimidine scottcain: :)
18:04 scottcain Hi pyrimidine
18:04 pyrimidine o/
18:04 pyrimidine scottcain: still working on the $!%& Module::Build stuff
18:04 scottcain A cyclops smirking?
18:04 scottcain I'm not here to put pressure on you :-)
18:05 pyrimidine look at it normally (instead of tilted).  hand wave
18:05 pyrimidine happy: \o/
18:05 pyrimidine happy, but partial amputee: \o.
18:05 scottcain Nice
18:05 rbuels Dogs grinding alone on the head of a pin, shouting, "Who is John Galt and would he want to dance with me?" ?
18:06 pyrimidine O_o
18:06 * rbuels nods
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18:15 deafferret ..o.o... Oo...___..     .
18:16 pyrimidine scottcain: is there any reason we need to symlink 'bp_bulk_load_gff.pl' => 'bp_pg_bulk_load_gff.pl'
18:16 pyrimidine ?
18:17 pyrimidine scottcain: e.g. is this script name required in some toolchain?
18:17 pyrimidine (there's some crufty shit going on in the bioperl build/install process I'm working on removing)
18:17 scottcain There used to be two bulk loading scripts: one for mysql, one for Pg.  Then somebody (Ben F? probably
18:18 scottcain did the work to unify them.
18:18 scottcain So, the decision was made to make the name of the pg bulk loader just be a symlink
18:19 scottcain The number of people who would notice if that went away would probably be pretty miniscule.
18:19 pyrimidine I think it would be easier to remove it and (if it pops up redirect them to use the main bulk loader
18:20 pyrimidine *(if it pops)
18:20 scottcain I'm fine with that.
18:20 pyrimidine ok
18:26 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * r356fec5 / (4 files in 3 dirs):
18:26 CIA-119 bioperl-live: * git rid of post-install step (see what I did there?)
18:26 CIA-119 bioperl-live: * will refer anyone looking for the one symlinked bp_pg_bulk_load_gff to look at the regular bulk loader (per Scott Cain) - http://bit.ly/gwDNr7
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19:31 rbuels scottcain should enjoy this: http://www.youtube.com/watch?v=CDeG4S-mJts
19:32 rbuels god that scene has so many uses
19:33 rbuels we should do a bioperl one
19:46 deafferret ROFL
19:47 deafferret "Linux uses CVS at home"
19:47 deafferret Linus
19:47 scottcain rbuels: Very funny, though I had to stop watching it in the middle because my daughter is now watching over my shoulder--can't be sure it's kid friendly. :-)
19:47 rbuels we should do a live-action bioperl one.  i volunteer to be hitler
19:48 scottcain you'd make an excellent hitler
19:48 deafferret its all german so its just a crazy looking angry guy yelling
19:48 rbuels scottcain: it's not quite kid-friendly though
19:49 rbuels "Rob ...  we have to release the whole thing for a bugfix in one part...."
19:49 rbuels "What?!?!  ..."
19:49 * rbuels chuckles
19:54 scottcain "later I took a dump that had a better look and feel than git" :-D
19:56 * pyrimidine realizes that googling 'Hitler uses Subversion' doesn't get the answer he expects :P
20:14 rbuels bio::gff3::lowlevel enables correctly-quoting gff3-munging one-liners
20:15 rbuels sometimes, i just want to kiss myself on the lips.
20:15 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * r131283a / Bio/Root/Build.pm : some comments on the general state of things re: Bio::Root::Build - http://bit.ly/eFPLWo
20:16 pyrimidine rbuels: is that like one hand clapping?
20:16 rbuels pyrimidine: yeah, except totally hot
20:17 scottcain rbuels: Does it handle Target values correctly?  I only found out last month that Bio::FeatureIO::gff didn't.
20:18 rbuels scottcain: it doesn't do anything special with them
20:18 rbuels i thought about being smart about them ... but then i didn't.
20:18 scottcain that is, if Target values are uri encoded, it's supposed to stay that way (not unencode them).
20:18 rbuels orly?
20:18 * rbuels looks at the spec
20:19 rbuels oh, i see "if the target_id contains spaces, they must be escaped"
20:19 rbuels hmmm
20:19 rbuels scottcain: is that the part you're talking about, or is it more than that?
20:22 scottcain rbuels: no, but now I can't find the section that talks about.
20:25 rbuels also, keeping your gff3 in git as you massage it is indescribably great
20:26 * rbuels effuses all over the place
20:35 * pyrimidine ducks to avoid effusion
20:36 pyrimidine scottcain: do you mean, if Target is uri-encoded, it is not to be uri-decoded?
20:36 * scottcain thinks I imagined the whole thing.
20:37 scottcain pyrimidine: yes.
20:37 rbuels scottcain: well, that thing about encoding spaces is a little bit of a gotcha
20:37 scottcain The problem is that if you decode spaces, then subsequent parsing of the target value based on spaces won't work.
20:37 pyrimidine scottcain: I recall you adding a test for this for featureIO at some point (featureIO in bioperl-live, not the split-off one)
20:38 rbuels probably would be useful to have gff3_parse_target and gff3_format_target in Bio::GFF3::LowLevel
20:38 scottcain pyrimidine: right, though now I'm wondering if I over did it, and I should only have left spaces uri encoded
20:38 scottcain (it is easier just to leave the whole thing uri encoded though)
20:38 rbuels that would parse a target to and from { id => 'X', start => 34, end => 54, strand => '+/-' }
20:40 pyrimidine scottcain: I think you're talking about (from the spec)  'If the target_id contains spaces, they must be escaped as hex escape %20'
20:40 pyrimidine so basically leave Target alone
20:40 * rbuels just said that
20:40 * pyrimidine thumbs nose at rbuels
20:41 rbuels well no, it's "don't escape the spaces that are semantically significant in Target
20:41 pyrimidine :)
20:41 scottcain Right, rbuels did just say that, and I thought it wasn't enough.
20:41 * rbuels thumbs his nose at both scottcain and pyrimidine
20:41 * rbuels uses both thumbs
20:41 rbuels heh
20:41 scottcain Better than both noses
20:41 * pyrimidine uses a certain other digit
20:42 rbuels Dogs exerting their powers of mesmerism to make a slave somnambulist of financial mogul J.P. Morgan (1837-1913).
20:42 pyrimidine um... interesting
20:43 * pyrimidine wants what rbuels is smoking/imbibing
20:43 scottcain I'm sure Portland is a fun place to be.
20:43 scottcain All kinds of good stuff to be had.
20:44 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * r88b19d8 / Bio/Root/Build.pm :
20:44 CIA-119 bioperl-live: continue the subtle dismantling of Bio::Root::Build to follow the
20:44 CIA-119 bioperl-live: Module::Build API as close as possible - http://bit.ly/fV83IF
20:45 pyrimidine rbuels: unrelated, but know of any real reason we should keep MANIFEST/MANIFEST.SKIP in the bioperl-live repo?
20:46 rbuels nope.
20:46 rbuels pyrimidine: off with its head
20:46 rbuels that can and should be autogenerated upon release
20:46 deafferret ya, i get yelled at when I add those
20:46 pyrimidine kinda what I thought as well
20:47 rbuels ya, i yell at people when they add those
20:47 scottcain I can understand not having manifest, but doesn't having manifest.skip make sense?
20:48 rbuels oh, you're right.
20:48 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * re3e94b1 / (MANIFEST MANIFEST.SKIP): remove MANIFEST/MANIFEST.SKIP (only need for dist release) - http://bit.ly/hxxHRa
20:48 pyrimidine well, now you tell me :)
20:48 * rbuels chuckles
20:49 pyrimidine most dists seem to autogenerate the MANIFEST.SKIP as well
20:49 scottcain OK, but most dists are simple.  BioPerl is not.
20:49 rbuels there's a default manifest.skip that is generated ....
20:49 rbuels i guess we should only commit it if it's significantly different from the default
20:50 rbuels er, well different at all, really
20:50 scottcain unless there isn't anything that should be skipped that isn't caught by the autogenerated one.  I know that's not true for GBrowse for instance.
20:50 pyrimidine the problem is, the old Build.PL clobbers both MANIFEST and MANIFEST.SKIP, sort of defeating the purpose
20:50 rbuels sorry, i'm distracted.  bon jovi's "livin' on a prayer" was just on pandora, it made me kind of delirious
20:50 deafferret scottcain: I find bioperl is very simple when you're totally comfortable not understanding 99% of it  :)
20:51 rbuels it clobbers them?
20:51 * rbuels is skeptical
20:51 rbuels oh, the *old* one
20:51 pyrimidine yes
20:52 pyrimidine I kind of understand why Sendu set Bio::Root::Build up this way, but there are much saner things that could be done....
20:52 rbuels perhaps at the time, M::B was less mature
20:53 pyrimidine still is (less mature)
20:53 rbuels most of the faffing about is because of having too much stuff in the distro
20:54 rbuels and google's 5K says that the ball is going to start rolling on that this summer
20:54 pyrimidine re: Module::Build, it's a fight between doing too much and not doing enough.  Not easy to deal with unless one is pluggable (which it really isn't)
20:55 pyrimidine re: Google, good to hear!
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21:00 pyrimidine looking at the current MANIFEST.SKIP in master, seems like it's avoiding lots of stuff that wouldn't be generated in a *clean* clone (or one that has been 'git clean'-ed)
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21:03 * pyrimidine -> home
21:08 CIA-119 bioperl-live: hyphaltip master * rb6540ba / Bio/SeqIO.pm : revert throw statment that was preventing default STDOUT as default - http://bit.ly/fHL2bd
21:08 CIA-119 bioperl-live: hyphaltip master * r1574aed / (3 files in 2 dirs): Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/heVnez
21:09 CIA-119 bioperl-live: hyphaltip master * rb6d9b6b / Bio/SeqIO.pm : small doc change - https://github.com/bioperl/bioperl-live/comm​it/b6d9b6bff7de239980760cbde4a1acc63facd355
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