Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-06-08

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All times shown according to UTC.

Time Nick Message
00:00 russellsmithies much quieter in here than on the mailing list!!!
00:10 deafferret :)
00:19 razi joined #bioperl
01:35 razi Hey all
01:35 razi i finished writing some code and tests
01:36 razi I commited them to my forked github repository
01:36 razi and now want to get them incorporated into the main repository
01:37 razi can anyone help me with doing a pull/push request?
01:40 deafferret razi: sure. where's your repo?
01:40 razi hmm ... im real new to git/github so bare with me
01:41 deafferret no rush. I'm here for a couple more hours  :)
01:41 deafferret what's your github.com username?
01:41 razi it is rkhaja
01:41 deafferret k. your repo is   http://github.com/rkhaja/bioperl-live    :)
01:41 razi http://github.com/rkhaja
01:42 razi ok
01:42 deafferret ya  :)
01:42 razi ok so it looks like my master is not up to date?
01:43 deafferret no worries. let me stare at your diff
01:43 razi sure
01:43 razi how do i let you do that?
01:43 deafferret (I only mostly know what I'm doing, so you'll have to bear with ME too.)
01:43 deafferret razi: anyone can do that
01:43 razi ok
01:46 razi let me know what differences you see and also, how can i see my own diffs?
01:46 deafferret hmm...
01:46 deafferret git remote -v    shows all your remotes
01:47 deafferret which for you is just github.com/rkhaja/bioperl-live
01:47 deafferret so you'd git remote add bioperl git://github.com/bioperl/bioperl-live.git
01:48 deafferret then git pull   then git diff  bioperl/master
01:48 deafferret I think
01:48 deafferret I'm doing the opposite -- adding your repo as another remote
01:48 deafferret and diffing bioperl vs. yours
01:48 razi ok
01:49 deafferret the only difference between me and you is that I can push to bioperl
01:49 deafferret which you'll be able to do soon too  :)
01:49 deafferret give it a try and see if you can see your diff
01:49 deafferret I'll race you   :)
01:51 deafferret hmm... git fetch   not git pull
01:53 deafferret (pull is fetch + merge)
01:54 razi2 joined #bioperl
01:55 deafferret razi2: what date did you make changes on?
01:55 deafferret and/or are you in a branch?
01:55 razi2 something happend to my irc
01:55 razi2 i had to log in again
01:55 razi2 do i have to push to my master?
01:56 deafferret (also, there's a "send pull request" button in github
01:56 deafferret razi2: ya. if your changes are only on your workstation then only you can see them
01:56 deafferret I'm not currently seeing any changes by you in http://github.com/rkhaja/bioperl-live
01:57 razi2 ok
01:57 razi2 i just finished executing: git push my.bioperl-live master
01:58 deafferret ah, there we go. 3 commits
01:58 razi2 yep
01:58 razi2 the first should be a new blast input file
01:58 razi2 the 2nd should be 106 test cases for blast.t
01:59 razi2 the 3rd should be fixes to Bio/SearchIO/blast.pm
01:59 razi2 so what do i do next?
02:00 deafferret well, you can click "send pull request" in github, and/or you can wait for me to stare at them
02:00 razi2 when you say "send pull request" in github ... do you mean from the web interface?
02:00 razi2 is there a way to do this on the command line?
02:01 deafferret 1 yes 2 no
02:01 razi2 ok
02:01 razi2 which is the recommended way?
02:01 deafferret "send pull request" is just a github thingy which sends an email saying "hey, please pull 7bbfa0df2670e91cc41e"
02:01 deafferret razi2: dunno  :)
02:02 razi2 ok ... so do yo want me to press the "pull request" button?
02:02 deafferret sure. so you know where it is
02:02 razi2 i dont want to make anything explode :)
02:02 razi2 yep i found it
02:02 deafferret nah  :)
02:02 razi2 ok
02:03 deafferret I'm attempting to follow my procedure from my notes here    http://jays.net/wiki/Git
02:03 deafferret worst case, someone beats me to it  :)
02:03 razi2 when i click it ... i get a dialogbox
02:03 deafferret ya, just describe your patch, like you did above
02:04 razi2 ok
02:05 razi2 alrighty
02:05 razi2 i sent the pull request
02:06 razi2 so should we see it in a couple of minutes on bioperl-guts?
02:07 deafferret real fast, yes
02:07 deafferret its there already
02:07 razi2 ok  ... im on gmail .. i didnt get it yet
02:07 deafferret err... no, it's in my personal email hmm
02:07 razi2 ok cool
02:08 razi2 .. so if your going to apply the patch
02:08 deafferret should hit guts in a few seconds?
02:08 razi2 i would recommend adding the test input file first, then the tests
02:08 razi2 then run the tests to see that 5 of the new tests fail
02:08 razi2 then patch blast.pm
02:09 deafferret there it is in guts
02:09 razi2 then run tests again to see that the 5 tests work
02:09 razi2 awesome
02:09 CIA-94 bioperl-live: Florent Angly master * r6789d5f / (17 files in 11 dirs): Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/bR1md6
02:09 razi2 i  see it in guts now too
02:11 deafferret hmm... wish I understood what fangley just did
02:11 * deafferret summons someone with git-fu
02:11 razi2 deaferret: im real anxious ... how soon do you think before my patch gets accepted? ... i wont be able to sleep otherwise :)
02:12 razi2 yep wish i understood what fangley did too
02:12 deafferret razi2: I'll do nothing else until yours is committed
02:12 deafferret sorry, I'm slow
02:12 deafferret I need the practice so I get faster
02:12 razi2 very cool
02:12 deafferret :)
02:13 deafferret well, I'll breathe, but that's it
02:13 razi2 thanks for helping me out with this github stuff
02:13 deafferret heh... you might want to wait until I accomplish something
02:13 deafferret ya never know what I might blow up  :)
02:13 razi2 ill be on IRC
02:14 razi2 its been like 10 or 11 years since I used IRC
02:14 razi2 Dave Messina suggested that I use IRC to figure out github
02:15 deafferret little did he know only I would be here   :)
02:16 razi2 dude
02:17 razi2 i seen your message on bioperl about joining in IRC for peace and quiet
02:17 razi2 glad i dropped by
02:18 deafferret yes. very calming in here  :)
02:19 deafferret wow. this is a big blast result file... can it be smaller and still prove all the tests?
02:19 razi2 sure
02:19 razi2 i would have to modify it by hand
02:20 deafferret ya. most of the t/data files are tweaked by hand so they're not so big
02:20 razi2 the blast statistics at the end would not be accurate ... but it would still get parsed
02:20 razi2 ok
02:20 razi2 so how bout i modify it
02:20 razi2 git add it
02:20 razi2 git commit it
02:20 razi2 then push to my master
02:20 razi2 and submit another pull request?
02:20 razi2 is that right?
02:21 deafferret you don't need another pull request. everything before that, yes
02:21 razi2 ok
02:21 deafferret modify it    git add; git commit; git push
02:21 razi2 ill do that right now
02:21 razi2 be back in a few minutes
02:23 * deafferret wonders how to stop that 6MB file from entering git history...
02:27 deafferret 6MB maybe not a big deal (?) but a 6PB file would be, so I wonder how to not end up with it while retaining your commit history...
02:27 razi2 k
02:27 razi2 i modified it
02:27 deafferret this is one place where I like Subversion   :)
02:27 deafferret did you push?
02:27 razi2 not yet
02:29 deafferret let me know when you have
02:30 razi2 ok
02:30 razi2 i just pushed master
02:31 razi2 i mean i just pushed to my master
02:31 razi2 is the pull still working?
02:33 deafferret i fetched your new commit, yes. creating and reviewing another merge branch
02:34 razi2 ok cool
02:34 deafferret oo! cool!   git said it was reducing that file from 6MB to less that 1MB
02:34 deafferret I wonder if it saves that space from everyone having to download it somehow
02:34 deafferret ... weird
02:35 razi2 ok ... i wrote that in my comment too
02:35 razi2 in my commit comment
02:35 deafferret i don't think it can --- since it's full history that 6MB will be added to the git repo forever I think
02:35 * deafferret shrugs
02:36 razi2 maybe chris feilds will figure out a way to get rid of it forever
02:38 deafferret ya. he and rbuels are the git expert types
02:39 deafferret they're both in here most days
02:39 razi2 k
02:40 CIA-94 bioperl-live: Razi Khaja master * r6c30046 / t/data/ZABJ4EA7014.CH878695.1.blast.txt : Added new blast output file ZABJ4EA7014.CH878695.1.blast.txt to test SearchIO blast parsing of 'Features in/flanking this part of a subject sequence' - http://bit.ly/cCKCFs
02:40 CIA-94 bioperl-live: Razi Khaja master * r6619982 / t/SearchIO/blast.t :
02:40 CIA-94 bioperl-live: Modified t/SearchIO/blast.t to include 106 new tests that test parsing of details from new blast output file ZABJ4EA7014.CH878695.1.blast.txt.
02:40 CIA-94 bioperl-live: In particular, test parsing of 5 "Features in/flanking this part of subject sequence:".
02:40 CIA-94 bioperl-live: Demonstrated that existing code in Bio/SearchIO/blast.pm fails 5 tests in parsing "Features in/flanking this part of subject sequence:". - http://bit.ly/9d1pZP
02:40 CIA-94 bioperl-live: Razi Khaja master * r09f33f9 / Bio/SearchIO/blast.pm :
02:40 CIA-94 bioperl-live: Modified Bio/SearchIO/blast.pm to fix 5 failed test in parsing "Features in/flanking this part of subject sequence:" for ZABJ4EA7014.CH878695.1.blast.txt
02:40 CIA-94 bioperl-live: Did not break old tests for parsing "Features in/flanking this part of subject sequence:" for old input file t/data/new_blastn.txt - http://bit.ly/9u826Z
02:40 CIA-94 bioperl-live: Razi Khaja master * rfccda77 / t/data/ZABJ4EA7014.CH878695.1.blast.txt : Reduced size of test data file ZABJ4EA7014.CH878695.1.blast.txt from 6MB to less than 1MB - http://bit.ly/9DtnE5
02:41 deafferret ooo... cool   author and committer credits http://github.com/bioperl/bioperl-live
02:41 deafferret razi2 needs a gravatar  :)
02:42 razi2 i have a gravatar
02:42 razi2 i just need to upload a picture
02:43 deafferret lol
02:43 deafferret "i have a website. i just need HTML."   :)
02:43 deafferret razi2++ # THANK YOU for your contribution!
02:43 razi2 your very welcome
02:44 razi2 i really apreciate the code getting committed so fast
02:44 deafferret you can email bioperl-l pointing out your commit and asking chris fields to add you as a co-maintainer of bioperl/bioperl-live if you're so inclined
02:44 razi2 is irc the way to get sttuff done faster?
02:44 deafferret then you can push straight there without me
02:44 razi2 ok
02:45 deafferret dunno if we have a policy on that. I think I did ~5 or so rounds of patching before I got my commit bit
02:45 razi2 well ... my last 4 or 5 commits were accepted ... all having to do with enhancements to blast.pm
02:45 razi2 well
02:45 deafferret :)   you the man
02:45 razi2 ... im a 9 year vetran of bioperl
02:45 razi2 just not a 9 year contributor
02:46 deafferret wow. I'm only at 4 years, so you've got me beat   :)
02:47 razi2 yeah ... but youve probably done alot more bioperl commiting
02:47 razi2 ive only used bioperl without paying back yet
02:47 razi2 until recently
02:47 razi2 but im mostly a BLAST monkey
02:47 razi2 what is CIA-94
02:48 razi2 is that a special IRC account?
02:48 deafferret not sure who runs that IRC bot. It watches github and spams us here in IRC on every commit   :)
02:48 deafferret http://bioperl.org/wiki/Bots
02:48 deafferret http://bioperl.org/wiki/IRC
02:49 deafferret ick. looks like CIA-94 isn't documented on the wiki
02:51 razi2 im going to put up a gravitar
02:51 razi2 ill also ask chris to become a co-maintainer
02:52 razi2 Jay where are you situated by the way?
02:52 deafferret http://bioperl.org/wiki/User:Jhannah
02:54 razi2 very awesome
02:55 razi2 i am at the moment working at hhmi http://www.hhmi.org/grants/sea/leadership.html but not really happy with my job
02:56 razi2 hence doing bioperl work ... cuz coding bioperl make me happy.
02:56 razi2 ^makes
02:56 razi2 anyway dude
02:56 razi2 i gotta go
02:56 razi2 again thanks for doing the commits
02:57 razi2 and teaching me about git/github
02:57 razi2 ttyl
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10:50 CIA-94 bioperl-live: Florent Angly master * rb7b20e4 / (Bio/SeqIO/phd.pm t/SeqIO/phd.t t/data/multiseq_tags.phd):
10:50 CIA-94 bioperl-live: Reworked Bio::SeqIO::phd->next_seq so that it is more robust,
10:50 CIA-94 bioperl-live: especially when parsing phd files that have WR tags - http://bit.ly/aWO7VV
10:50 CIA-94 bioperl-live: Florent Angly master * r0e70e88 / (3 files in 3 dirs): Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/ahkbf2
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12:47 kai hm, let's see if that works :)
13:16 kai hm, not quite
13:19 deafferret :)
13:58 kai I'm beginning to really like BioPerl :)
14:10 deafferret yes. breathe deeply the sweet sweet jasmine that is bioperl
14:11 * deafferret issues kai his black Nike shoess
14:16 pyrimidine joined #bioperl
14:33 pyrimidine deafferret: re: large files in git, hoping that doesn't come up often, but this article gives an answer: http://help.github.com/removing-sensitive-data/
14:40 deafferret pyrimidine: thanks
14:43 deafferret LOL  "There are a few simple tricks to avoid committing things you don’t want committed. The first, and simplest, is to use a visual tool like git-gui or gitx to make your commits. This lets you see exactly what you’re committing, and ensure that only the files you want are added to the repo."
14:43 deafferret pro tip: if you want, you can actually look at what you're committing before you commit it!
14:44 * deafferret sighs
14:46 pyrimidine joined #bioperl
14:47 kai deafferret: personally I like "git add --interactive" for that
14:47 kai best text adventure since the hitchhiker's guide to the galaxy
14:49 kai but as they say, I think most of the accidents are due to "git add ." and the like
14:53 deafferret :)   Top 10 git Accidents
14:54 pyrimidine Thing is, this could happen just as easily with any VCS.
14:55 pyrimidine sure, you may not have to deal with the file locally, but it's still on the remote repo
14:55 kai true
14:56 kai I just like the opportunity to pimp git add --interactive
14:57 pyrimidine well, the other thing is: don't push until you are sure everything is in good order.  And I agree, using git add --interactive is a good practice
14:57 kai it's perfect if you easily get side-tracked and need to pull apart changes in a single file that belong to two different commits
14:57 pyrimidine one can always revert a local commit with git reset HEAD^
14:58 pyrimidine or follow this: http://stackoverflow.com/questions/2327​050/git-push-after-removing-large-file
15:00 pyrimidine but those apply to commits not pushed
15:02 pyrimidine appears github runs 'git gc' on a regular basis, so removed files are likely purged at some point.
15:03 kai if you do the filter-branch trick
15:04 deafferret I always find it curious that people lose track of things. I always "run clean" -- meaning that my latest commit and my work area are identical many times a day, and I never leave anything uncommitted overnight.
15:05 deafferret my coworker at $work[0] runs for days -- up to 2 weeks without committing, then has tons of problems keeping crap organized
15:05 deafferret at $work[1] students don't update/commit for months then have even worse problems
15:05 * deafferret opens a free slapping booth
15:06 pyrimidine deafferret: be glad they even use s VCS
15:06 deafferret pyrimidine: required for course credit now
15:06 deafferret so you get rushed ugly commits at the end  :(
15:06 pyrimidine at least they use it
15:07 deafferret ya. usually.
15:07 pyrimidine we have a very good CS school here, but no one uses VCS of any kind
15:07 pyrimidine I know of many instances where they just pass code around in tarballs
15:07 pyrimidine also seen this in some industry settings
15:07 deafferret i continue to fail to understand that mentality
15:08 pyrimidine they don't want to learn anything above and beyond their specific needs
15:08 deafferret i'm not a zealot about *which* VCS anyone uses, but I just can't fathom not using one in the 21st century
15:08 pyrimidine agreed
15:09 pyrimidine It should be routine, something learned early on
15:09 deafferret it's like saying "we don't require students to learn email, because their job will teach them that"
15:09 deafferret it's fun-duh-mental
15:09 pyrimidine yep
15:10 * deafferret opens a school where use of a "keyboard" is mentioned but not required since that would clutter up the learning process
15:10 pyrimidine lol
15:11 pyrimidine pretty much the same thing
15:12 pyrimidine we have a project where code is released in 'versions'.  The version is essentially a specific tarball of whatever code a particular student hacked upon.  No commit history at all.
15:13 pyrimidine next student gets it, the code disappears for a year, voila, new version that doesn't resemble the old one, complete with new bugs, etc.
15:13 pyrimidine fun!
15:13 kai fun
15:14 kai though if every student getting in rewrites the whole project, commit history won't help much
15:15 pyrimidine we can at least say, early on, "Don't rewrite the entire project!"
15:15 pyrimidine code review some
15:16 kai true
15:16 kai speaking of code review...
15:16 pyrimidine yes?
15:16 * kai goes to hunt for his gsoc student's weekly report
15:16 perl_splut joined #bioperl
15:17 * pyrimidine already did a bit of that myself yesterday
15:18 kai that said, I still have no clue how ti fix that hmmer3 parser for files not containing alignments :/
15:19 pyrimidine maybe see how blast.pm handles this?
15:19 kai the control flow in that parser is a bit obscure
15:19 pyrimidine putting it mildly  ;)
15:19 kai it looks the same as in the hmmer.pm parser, but there's a subtle difference that I seem to be missing
15:20 kai of course the files differ enough that a "diff" doesn't help either
15:20 pyrimidine it's battle tested (or battle-fatigued, dep. on your view)
15:20 kai hm? the blast.pm? or the hmmer.pm?
15:21 pyrimidine blast.pm
15:21 pyrimidine in blast.pm, very top of the readline loop:
15:21 pyrimidine next if (/\Q***** No hits found ******\E/);
15:22 pyrimidine In your case, you may have to flag it somehow if there isn't an explicit message
15:22 pyrimidine (count num hits, for instance)
15:22 pyrimidine not sure
15:24 pyrimidine deafferret: see my post to moose-l?
15:25 deafferret pyrimidine: i'm not on any moose mailing lists. email--
15:25 pyrimidine ah
15:25 deafferret #moose, #moose-dev only   :)
15:25 pyrimidine I'm an old fogey, then
15:26 * pyrimidine grabs walker, swears at kids to get off his lawn
15:26 deafferret i'm just clausterphobic under a daily mountain of emails
15:26 deafferret hell, I still get ~100 a day that I delete without reading
15:26 pyrimidine yes, agreed, I tend to get too many myself, prob 200-300/day
15:26 kai pyrimidine: well, the trick here seems to be that the place in the code where the hits are parsed is not the place where the hit elements are created
15:26 * deafferret has too many computery interests
15:27 pyrimidine same here
15:27 pyrimidine kai: That seems...odd
15:27 kai and for some reason the "actually create the hit elements" only triggers in the path where the code parses alignments
15:28 kai I said the control flow was obscure :)
15:28 kai the hmmer.pm parser does it the same way, but has another "create the hit elements" loop on parsing the last line of the file
15:32 pyrimidine that last one is probably a fenceposting issue, has a dangling hit element
15:33 deafferret kai: are you kblin_ too?
15:34 kai deafferret: kblin, usually, seems like the last netsplit added a tail
15:34 kai this is my work box, the other is my box at home
15:34 deafferret k. just checking that you knew about that other guy working on hmmer right now  :D
15:34 kai yeah, I occasionally see him in mirrors
15:37 pyrimidine what does a 'no-hit' report look like?  Is there one in the bioperl-hmmer3 repo (or are you merging the hmmer parsers in a bioperl-live fork?)
15:37 pyrimidine Maybe no-paste or gist it?
15:40 * pyrimidine just looked at the bioperl-live network graph, it's pretty: http://github.com/bioperl/bioperl-live/network
15:41 kai well, I'm developing in a git live fork, as it's easiest to run the tests
15:41 kai but I've just pushed the code to http://github.com/kblin/biope​rl-hmmer3/tree/hmmsearch_fix
15:42 kai there's a t/data/hmmscan_noalign.out, where I deleted the alignment from the working hmmscan.out file, and a hmmsearch3.out
15:42 kai if you load the hmmscan_noalign.out in the hmmer3.t instead of the one with the alignment, you see the error triggering
15:43 pyrimidine Ok, so it has minimal hit data from the table, but no alignment (HSP) data
15:43 kai yeah
15:43 kai but I'd expect to be able to enumerate the hits, at least
15:43 kai and I don't get any
15:45 pyrimidine Right.  blast.pm does something like this, in that it stores the hit table data, but defers making the hit instances until we know there are no matching HSPs for those hits
15:45 kai on the hmmsearch output, the parser seemed getting stuck in the "below inclusion threshold" parsing, but adding a couple of regexes that also dropped back to the next higher level
15:45 kai didn't help in creating the hits
15:47 kai hm, how big is a tab in BioPerl, usually? 4 spaces or 8 spaces?
15:48 pyrimidine no real common setting.  I use 4.  I've seen variations from 2-8, or (gasp) even using real tabs
15:48 kai well, that's what (parts) of the hmmer3.pm seems to be using
15:49 pyrimidine oh, in a regex?  that seems very brittle
15:49 kai and I've used a 4-space indent to match up with a (seemingly) 8-space-wide \t, but github seems to like 4-space-wide \t, which makes the diffs a bit ugly
15:49 kai no, just looking at diffs via github
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15:50 pyrimidine what editor are you using
15:50 brandi left #bioperl
15:50 kai vim, with tabstop=8; expandtab; soft tabstop=4; shiftwidth=4
15:51 pyrimidine I would say, you could perltidy the code for modules for consistency.  I've done that in the past.
15:51 pyrimidine bug fixes preclude coding style, in my book
15:52 deafferret tabs? eww
15:54 kai I was mostly wondering if there was a consistent coding style that I should follow :)
15:54 kai I've worked with enough different styles that I don't care about details, as long as the code for that project stays consistent
15:55 kai though I hate working on projects with < 4 space indent
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16:01 pyrimidine_ Stay with what you feel is comfortable for you.  I think PBP is 4 spaces per tab, but it isn't enforced.
16:02 kai ok
16:02 * pyrimidine_ going for the double underscore
16:03 pyrimidine_ joined #bioperl
16:03 pyrimidine_ bah, still just one
16:04 pyrimi[tab] better
16:04 deafferret p[tab] works nicely
16:05 deafferret perl_splut: hi
16:05 deafferret py[tab] to be safe
16:05 deafferret perl_splut: you're blocking p[tab] uniqueness
16:06 * p[tab] blocking perl_splut
16:06 brandi joined #bioperl
16:06 deafferret p[[tab] works nicely
16:06 deafferret [[tab] ftw
16:07 ^I me++
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16:08 [tab][hunter] hi rbuels
16:08 ^I hi rbuels
16:08 ^I welcome to #bioperl-silly
16:08 rbuels ?
16:09 * pyrimidine rips mask off, Mission-Impossible style
16:09 pyrimidine_ pyrimidine: hey, give me my nick
16:09 * rbuels looks around in alarm
16:09 rbuels what the hell happened while i was asleep
16:09 kai rbuels: I'm currently hoping it'll go away if I don't look
16:09 pyrimidine_ rbuels: failure to be silly in a bannable offense
16:09 rbuels aah!  woopwoopwoop!
16:10 * rbuels jumps around
16:10 * rbuels grumbles, goes back to his coffee
16:10 pyrimidine_ :)
16:10 pyrimidine :)
16:12 * kai goes back to adding lots of $self->debug() statements to his parser
16:12 kai printf-debugging ftw!
16:13 * deafferret vows to understand Root verbose() (or wherever that is) someday
16:26 * kai sneakily uses the few rain-less moments to head home
16:27 pyrimidine I'm playing hooky today, but not completely (working from home)
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17:44 deafferret sneaky snakes
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17:48 _tristan__ hello and sorry for the basic question: say i installed bioperl with 'git clone git://github.com/bioperl/bioperl-live.git' (and also bioperl-run)
17:48 _tristan__ ', now say i want to update the code, how do i do?
17:48 _tristan__ I tried: git pull
17:49 _tristan__ git pull git://github.com/bioperl/bioperl-live.git
17:49 _tristan__ or git pull bioperl-live
17:49 _tristan__ and I always get the following: ''fatal: Not a git repository (or any of the parent directories): .git"
17:50 _tristan__ thanks guys
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17:53 _tristan__ got it, you have to be inside the bioperl-live directoty
17:53 _tristan__ funny, how by writting the question, the answer becomes obvious
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18:25 deafferret :)
18:26 deafferret _tristan__: ya, often by breaking the problem down to try to explain it to someone to help me I find the answer
18:26 deafferret just 'git pull' is sufficient
18:27 deafferret or 'git pull origin master' if you like being verbose
18:27 deafferret make sure your git client is current, that makes things a lot easier
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18:52 dukeleto_ deafferret: just typing "git pull" requires push.default = current in your ~/.gitconfig
18:54 deafferret dukeleto_: if so then by default that's in there nowadays
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19:12 CIA-94 biome: Chris Fields master * r06b947a / (t/Segment/SegmentContainer.t lib/Biome/Role/Range.pm): small changes - http://bit.ly/clRMJp
19:24 dukeleto_ deafferret: actually, that is for "git push" with no arguments.
19:26 deafferret dukeleto_: by default you can    git clone; git pull; git push;  and everything Just Works
19:32 pyrimidine I think, if you clone from a remote repo, the default branch is master (or whatever github sets it to in our case), and the initial origin is set to the remote.And then everything just works.
19:32 pyrimidine dukeleto_: you more interested in parrot or rakudo these days
19:38 pyrimidine (actually, that was a question)
19:38 dukeleto_ pyrimidine: i work more in parrot these days, but I got interested in parrot from working on the Perl 6 spec test suite and Rakudo
19:39 dukeleto pyrimidine: i am currently trying to make PL/Perl6 (Stored Procedures in Perl 6 for Postgres) work
19:39 pyrimidine dukeleto: I think I've seen posts on the parrot list re: that
19:39 pyrimidine nice!
19:40 pyrimidine I'm in on the #phasers meeting now (previously #rakduosketch) to catch the latest goings-on re: R*
19:40 deafferret rakduo?
19:40 pyrimidine dakrudo, yes
19:41 pyrimidine ;)
19:41 deafferret frak! druko!
19:41 deafferret BSG++
19:41 pyrimidine yes, should have been rakudosketch, but the #phasers one is correct
19:44 pyrimidine dukeleto: if you need a backlog, http://irclog.perlgeek.de/phasers/today
20:26 CIA-94 biome: Chris Fields master * ra93042b / (4 files in 4 dirs): simplify the exception handling, was mangling the implementation a bit - http://bit.ly/cctovX
20:26 CIA-94 biome: Chris Fields master * r7e13acc / (3 files in 3 dirs): Range, not Rangeable - http://bit.ly/9cIsEg
20:26 CIA-94 biome: Chris Fields master * r4f57cc4 / (lib/Biome.pm lib/Biome/Meta/Error.pm t/Error.t): move Error to Meta, clean up, stringify - http://bit.ly/ahUAt0
20:28 CIA-94 biome: Chris Fields master * r6bdbb00 / (6 files in 4 dirs): clean up remaining Range bits - http://bit.ly/b0sDKz
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20:42 CIA-94 biome: Chris Fields master * rfe0f116 / (t/Biome.t t/Meta/Error.t t/Moose.t t/Error.t): Root->Meta, changed error check (double failed was removed) - http://bit.ly/d7N59O
20:52 CIA-94 biome: Chris Fields master * rc2dfedf / lib/Biome/Meta/Error.pm : remove inline constructor - http://bit.ly/dtEBcZ
20:52 CIA-94 biome: Chris Fields master * rca7819f / t/SeqFeature/Generic.t : Rangeable->Range - http://bit.ly/cWvS0s
20:52 CIA-94 biome: Chris Fields master * rc476dca / lib/Biome/Tools/IUPAC.pm : Moose->Biome - http://bit.ly/d5Q0UB
20:52 CIA-94 biome: Chris Fields master * r42e3aaf / lib/Biome/Role/SeqFeature.pm : add type attribute - http://bit.ly/aSkA5n
20:52 CIA-94 biome: Chris Fields master * r349de29 / lib/Biome/Role/Segment/SegmentContainer.pm : a container type (distinguish from a segment type) - http://bit.ly/cpQODT
20:54 CIA-94 biome: Chris Fields cleanup_seqfeature * reec43ef / .gitignore : add MYMETA.yml (+12 more commits...) - http://bit.ly/9BKcOr
20:54 CIA-94 biome: Chris Fields master * reec43ef / .gitignore : add MYMETA.yml -
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