Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-29

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All times shown according to UTC.

Time Nick Message
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07:43 dbolser rbuels: cool, he actually said he was cranky ;-)
07:43 dbolser its my fault for logging anonymous bugs
07:44 dbolser I assumed I was logged in
08:05 * deafferret blames rbuels
08:05 * deafferret goes home
08:08 * dbolser shakes fists
08:49 kai yay, only 10 bioperl deps to go
11:10 CIA-94 bioperl-live: Lincoln Stein master * r6ded082 / Bio/DB/SeqFeature/Store/DBI/Pg.pm : Fixed sql syntax error in creation of interval_stats table - http://bit.ly/8Xfk0N
11:10 CIA-94 bioperl-live: Lincoln Stein master * r2faecfa / (6 files in 6 dirs): merge - http://bit.ly/dg8UEu
12:11 dbolser kai: and those deps...
12:48 brandi joined #bioperl
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15:18 pyrimidine joined #bioperl
15:25 pyrimidine woohoo!  no warnings on biome when I upgraded to Moose 1.09!
15:25 * pyrimidine must be doing something right...
15:26 CIA-94 bioperl-live: Scott Cain master * r34a9857 / Bio/DB/SeqFeature/Store/DBI/Pg.pm : fixed a problem where the loader tried to create the summary stats table twice - http://bit.ly/9i7UGa
15:32 Jun Hi, pyrimidine
15:32 Jun I got a question?
15:33 pyrimidine sure
15:33 pyrimidine Jun: go ahead
15:33 Jun As you know, I am implementing packages retrieving online alignment sequences.
15:34 pyrimidine yes
15:34 Jun The Pfam part is nearly finished. So I went through other databases this week.
15:34 Jun Unfortunately, I found Pfam seems to be the only database providing whole protein alignment
15:35 pyrimidine that's not too surprising
15:35 Jun SMART and PROSITE provide alignment, but only for protein domains
15:35 pyrimidine that might suffice for some users
15:35 Jun Uniprot does not include any alignment, but they have online submission form to run clustalw
15:36 pyrimidine wouldn't worry about that one
15:36 pyrimidine users can install and run alignments locally if needed
15:36 pyrimidine using clustalw, muscle, etc
15:36 pyrimidine might look at Rfam as well
15:36 Jun Ok, then maybe i will just implement another package on PROSITE, and/or SMART on domain alignment sequences
15:36 Jun ok, I will check Rfam
15:37 Jun Yep, Rfam looks good. I will implement that too.
15:38 Jun Another problem is SMART doesnot use a standard RESTful service...So it is hard for me to work on it. Do you have any suggestions?
15:38 pyrimidine Another one might be NCBI's various resources, but they're notoriously hard to get at sometimes
15:38 Jun You can see this page in SMART: http://smart.embl.de/smart/do​_annotation.pl?DOMAIN=SM00181
15:38 pyrimidine http://www.ncbi.nlm.nih.gov/proteinclusters being one
15:39 Jun I have no idea how to implement a method to work as the button on that page ...
15:39 pyrimidine you wouldn't (or, at least I wouldn't)
15:40 pyrimidine the code would likely be very brittle
15:40 Jun yep ,you are right
15:41 pyrimidine according to the FAQ, the models are available via InterPro
15:41 Jun So I will work on NCBI protein clusters && Rfam && PROSITE for the next week
15:41 pyrimidine http://www.ebi.ac.uk/interpro/
15:41 Jun Yep, but it seems InterPro doest have any alignment to download either
15:43 pyrimidine correct, see that now
15:44 Jun Ok, I get the directions now
15:45 Jun This part of work (retrieving online sequences) will probably be finished by the end of next week.
15:47 Jun After that we will have about two weeks left, I will try to work on the memory issue of alignment. If it works, we can include that in the code submitted to google. Otherwise, I think I will just submit the Bio::SimpleAlign and Bio::DB::Align to google
15:49 Jun Or, another option is, we stop after next week, and I start to run bug checks and online HOWTO, and really finish the work before the end of August. I will continue the plan on memory efficiency in Bio::Align and/or Bio::Assembly after August.
15:51 Jun What do you say?
16:05 pyrimidine sorry, stepped away for a second, back now
16:05 pyrimidine I think working on the memory issues would be good, even if we get to a point where it isn't quite complete
16:06 pyrimidine HOWTO and tests are critical, though
16:06 Jun Ok, then I will just run the tests.  I will write the HOWTO after August, that will be easier
16:07 Jun I will start the memory issue after next week
16:07 pyrimidine sounds like a plan!
16:07 Jun ok, then I will stick to that :D Talk to you later. I will keep you updated.
16:09 pyrimidine np
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17:44 * deafferret prefers interLayman
18:08 CIA-94 bioperl-live: John SJ Anderson master * ra3ee8b9 / scripts/Bio-SeqFeature-Sto​re/bp_seqfeature_gff3.PLS : (log message trimmed)
18:08 CIA-94 bioperl-live: Introspect feature objects and call apporpriate GFF output method
18:08 CIA-94 bioperl-live: Depending on how the database was built, next_seq() may return
18:08 CIA-94 bioperl-live: something that supports gff3_string() or someting that supports
18:08 CIA-94 bioperl-live: gff_string(). Introspect on the feature object to figure out which of
18:08 CIA-94 bioperl-live: these two methods are supported, and call the appropriate one:
18:08 CIA-94 bioperl-live: gff3_string() if it exists, gff_string() otherwise.
18:08 CIA-94 bioperl-live: John SJ Anderson master * rf63c4db / Bio/DB/SeqFeature/Store/DBI/mysql.pm : (log message trimmed)
18:08 CIA-94 bioperl-live: Expand how sequence features are rebuilt when objects are _NOT_ stored in the database
18:08 CIA-94 bioperl-live: When an object is being rebuilt by _rebuild_object(), if we don't have all of:
18:08 CIA-94 bioperl-live:  * start
18:08 CIA-94 bioperl-live:  * end
18:08 CIA-94 bioperl-live:  * typeid
18:08 CIA-94 bioperl-live:  * db_seqid
18:09 pyrimidine blammo~
18:26 rbuels where's the bitly link?
18:26 * rbuels grumbles
18:31 dukeleto what is the deal with these PLS files?
18:32 pyrimidine PLS files?
18:32 dbolser just delete them
18:35 deafferret the deal?
18:36 pyrimidine wots
18:36 * deafferret deleted dbolser
18:42 * dbolser recovers himself from the tape backup
18:42 deafferret oooo ... self bootstrappng dbolsers
18:43 pyrimidine dbolser == SkyNet
18:43 pyrimidine and has become self-aware
18:46 dbolser http://music.yellowgrey.com/Dan/DJ%2​0Special%20Needs/Wedding%20Music%20-​%20Raunch/owner_of_a_lovely_butt.mp3
18:46 dbolser the new global national anthem
20:35 pyrimidine git ready for a branch merge....
20:36 CIA-94 bioperl-live: Chris Fields branch-1-6 * r0c61488 / (371 files in 94 dirs): merge with master branch (+210 more commits...) - http://bit.ly/cbxvnt
20:36 pyrimidine heh
20:37 pyrimidine only 210 changes since 1.6.1, that's all
20:38 pyrimidine sorry, 210 *commits*
20:40 CIA-94 bioperl-live: Chris Fields branch-1-6 * r40eb18f / (4 files in 3 dirs): Merge branch 'master' into branch-1-6 - http://bit.ly/aqsI3S
20:40 rbuels wow. a merge.  just like that.
20:40 rbuels try *that* with svn, mr. cain!
20:41 rbuels ;-)
20:41 pyrimidine well, it had a LOT of conflicts
20:41 pyrimidine but they were easily merged
20:42 pyrimidine s/merged/dealt with/
20:44 pyrimidine I think, after the 1.6.2 release, we should move the network and database tests into a dev-specific test suite, and have them on all the time
20:44 pyrimidine (i.e. let us know if they fail)
20:45 pyrimidine right now they pass silently if db connects fail
20:45 rbuels pyrimidine: well, the other approach would be to tweak stuff to have some kind of 'dev mode' where they are on by default
20:45 rbuels 6 of one, half dozen of the other, really
20:46 deafferret and a third of 18
20:46 rbuels right.
20:46 * rbuels gives deafferret a gold star
20:46 pyrimidine yes, true
20:46 deafferret doesn't know why "a third of 18" isn't as popular
20:46 pyrimidine not as catchy
20:46 rbuels i think it's catchy.
20:47 pyrimidine doesn't have that je ne sais quoi
20:48 rbuels or, as the french say, "i don't know what"
20:48 deafferret "the options we are discussing appear to be identical to one another"
20:49 pyrimidine :)
20:49 deafferret oh, they know. they're just being French
20:50 rbuels gaullicly reticent.
20:51 CIA-94 bioperl-live: Chris Fields branch-1-6 * r4b125a5 / (Bio/Root/Build.pm Bio/Root/Version.pm): first alpha - http://bit.ly/91XpFT
20:51 * pyrimidine thinking we'll move to Dist::Zilla for future releases
20:52 pyrimidine at least pave the way for it...
20:58 bag_ joined #bioperl
20:59 pyrimidine if anyone has anything specific to add to the Changes file, feel free to do so (on master, not on 1.6 branch).
21:01 pyrimidine speaking of tests passing when they should fail, Scansite isn't working
21:01 pyrimidine t/Tools/Analysis/Protein/Scansite.t .......... 1/14
21:01 pyrimidine --------------------- WARNING ---------------------
21:01 pyrimidine MSG: There was an internal server error !- text below
21:01 pyrimidine --------------------------​-------------------------
21:01 pyrimidine ick
21:01 rbuels blech
21:02 pyrimidine yet it passes.  Not good.
21:02 deafferret echo 'jhannah picked up his replacement clutch lever today' >> Changes
21:03 rbuels deafferret: so you picked that clutch lever up in 1996?
21:03 rbuels good memory
21:04 deafferret my bash is patched for improved >>
21:04 deafferret bash6
21:05 rbuels bash star?
21:05 deafferret no u
21:17 pyrimidine anyone up from stripping the $Id$ tags out of a ton of bioperl code?
21:18 rbuels pyrimidine: yeah, i've got the one-liner foo for that
21:18 rbuels pyrimidine: in master?
21:19 pyrimidine rbuels: yes, or in a branch thereof
21:19 rbuels i'll branch for safety
21:20 pyrimidine probably wouldn't hurt to do it for the other repos (run, db, network, pedigree)
21:20 pyrimidine if you have time
21:20 pyrimidine (those don't have to be on a branch)
21:21 rbuels what are those frickin things called
21:21 * rbuels looks in the CVS and SVN manuals for a list of them
21:22 rbuels dukeleto: do you know?
21:22 rbuels dukeleto: those $Id$ and $Author$ things that CVS and SVN interpolated in checked out code
21:23 pyrimidine keyword substitution
21:23 * dukeleto forgets
21:23 pyrimidine http://stackoverflow.com/questions/3841​08/moving-from-cvs-to-git-id-equivalent
21:23 rbuels ah there it is
21:24 pyrimidine "The whole notion of keyword substitution is just totally idiotic." - L. Torvalds
21:24 rbuels yep.
21:24 dukeleto lulz
21:24 dukeleto that is what "git log" is for
21:26 CIA-94 bioperl-live: Chris Fields master * rf69a789 / Bio/Tools/Analysis/Protein/Scansite.pm : domain flag borking the request; fix courtesy John Obenauer - http://bit.ly/cdD5wg
21:26 * rbuels has it 90% of the way
21:26 pyrimidine And just as quickly, Scansite is fixed
21:28 CIA-94 bioperl-live: Robert Buels topic/strip_vc_interp_tags * ra6d9191 / (723 files in 109 dirs): strip keyword substitution from perl modules - http://bit.ly/bEanED
21:28 CIA-94 bioperl-live: Robert Buels topic/strip_vc_interp_tags * rebe37d5 / (74 files in 22 dirs): strip keyword substitution from perl scripts - http://bit.ly/d9EuG0
21:28 * deafferret misses $Head$ and $Id$ tags -- they were handy when using VC to publish
21:29 deafferret L. Torvalds is good at being opinionated
21:29 rbuels hahaha.  got too aggressive with that one and hosed my .git
21:30 pyrimidine ouch.  at least it was on a branch
21:30 deafferret umm... hosing .git probably not good for your local clone  :)
21:31 deafferret rm -rf to the rescue!
21:33 * rbuels reclones
21:33 rbuels pyrimidine: anyway, i think i got them in that branch i pushed
21:34 pyrimidine okay, will co and run tests
21:34 kblin what did $Head$ tags do?
21:34 kblin I think I remember $Id$ tags
21:34 pyrimidine dangerous question to ask here :)
21:36 kblin I've been using git since 2005, I've suppressed all my memory from using CVS
21:37 kblin I barely remember how to do git-cvsimport ;)
21:37 kblin on a more serious note, I think I almost have a bioperl rpm build on suse
21:39 kblin I still need to tackle GraphViz, and there's a weird issue packaging Graph, other than that, things look good
21:39 kblin https://build.opensuse.org/proje​ct/monitor?project=home%3Akblin
21:40 pyrimidine kblin: nice!
21:40 pyrimidine IIRC, GraphViz is only used in one module.  Graph is used in Bio::Ontology methinks...
21:41 kblin I'll try to get these into some more official repositories once it's working
21:42 kblin like devel:languages:perl and science
21:43 * pyrimidine is wondering how bioperl modularization will work with various packaging :P
21:44 kblin should be doable
21:44 pyrimidine at least it might be easier
21:45 kblin that'll just make different packages depend on different subsets of the deps you need to build now
21:51 CIA-94 bioperl-live: Robert Buels master * r1d4985c / (723 files in 109 dirs): strip keyword substitution from perl modules - http://bit.ly/d2IEEf
21:51 CIA-94 bioperl-live: Robert Buels master * r4017a48 / (74 files in 22 dirs): strip keyword substitution from perl scripts - http://bit.ly/9I70cj
21:52 pyrimidine rbuels: want me to delete the remote branch?
21:52 rbuels pyrimidine: sure, fire away
21:52 pyrimidine done
21:53 kblin anyway, bedtime for me. night folks
21:53 * pyrimidine always finds it a bit scary that 'git push origin :topic/strip_vc_interp_tags' deletes branchs
21:53 pyrimidine night kblin
21:54 kblin pyrimidine: but everybody else still has a copy, probably even your local branch :)
21:54 pyrimidine nope, deleted locally
21:55 kblin and not sure how this'd work on github, but for a repository on a server I have access to, I can recover the branch until I call git gc
21:55 pyrimidine that is true
21:55 pyrimidine I think changes are stashed until automatic gc is called
21:55 kblin which reminds me of another nifty feature that saved my patches after I accidently screwed up in a rebase
21:55 rbuels kblin: github might have the commits around for a while, but i'm sure they gc periodically
21:56 pyrimidine rbuels: they do
21:56 kblin it's called git reflog
21:56 rbuels kblin: if you have the commits locally though you can always push the branch back there and the commits will go back with it
21:56 kblin and it has all the commits you did since your last cleanup
21:56 CIA-94 bioperl-live: Chris Fields branch-1-6 * rf69a789 / Bio/Tools/Analysis/Protein/Scansite.pm : domain flag borking the request; fix courtesy John Obenauer - http://bit.ly/cdD5wg
21:56 CIA-94 bioperl-live: Robert Buels branch-1-6 * r1d4985c / (723 files in 109 dirs): strip keyword substitution from perl modules - http://bit.ly/d2IEEf
21:56 CIA-94 bioperl-live: Robert Buels branch-1-6 * r4017a48 / (74 files in 22 dirs): strip keyword substitution from perl scripts - http://bit.ly/9I70cj
21:57 CIA-94 bioperl-live: Chris Fields branch-1-6 * r81582e4 / (797 files in 131 dirs): Merge branch 'master' into branch-1-6 - http://bit.ly/d5P4RB
21:57 kblin so even if you do a git reset --hard HEAD^^^ and realize you only wanted to kill two commits, the reflog still has the third one and you can cherry-pick it
21:57 rbuels pyrimidine: cutting a release must be so much nicer with git
21:57 pyrimidine will work on a few small fixes on master and will make an initial alpha tonight/tomorrow
21:57 pyrimidine rbuels: yes, it is
21:57 pyrimidine will be nicer if we can automate some of it
21:58 rbuels yep.
22:00 rbuels i had a phone conf with scott this morning, sounds like he realizes that he will like git in a couple of months.
22:00 rbuels lol
22:01 pyrimidine Scott was pretty, um, skeptical of git at BOSC, but that's b/c he was expecting something like a souped-up svn
22:02 pyrimidine he emailed me after I added nathan to the devs on github, seemed okay
22:03 pyrimidine commuting. back tomorrow!
22:03 deafferret o7
22:04 rbuels night
22:07 deafferret he's not coming back, is he...?  -sniff-
22:07 * deafferret wimpers
22:07 * deafferret whimpers
22:07 * deafferret blutos
22:08 deafferret hmm. don't know how to type that sentence with the correct emphasis
22:09 deafferret damn you IRC

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