Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-10-30

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All times shown according to UTC.

Time Nick Message
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06:54 github [bioperl-live] fangly pushed 10 new commits to seqlength: https://github.com/bioperl/bioperl-liv​e/compare/95d1f9452110...142af3ad9bc6
06:54 github bioperl-live/seqlength c9a9de1 Florent Angly: Added tests for Bio::PrimarySeq::length()
06:54 github bioperl-live/seqlength f1f62fa Florent Angly: More tests for Bio::PrimarySeq::length()
06:54 github bioperl-live/seqlength 2aeb811 Florent Angly: POD updated and beautification
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13:50 virushunter hi...can I ask a question about bug # 3298?
14:02 deafferret virushunter: of course
14:02 deafferret virushunter: no one can help if you don't ask
14:03 virushunter i submitted a patch for the bug but haven't heard anything about it.
14:03 virushunter how can I move it along to be incorporated into Bioperl?
14:08 deafferret virushunter: URL to patch?
14:08 virushunter https://redmine.open-bio.org/attachme​nts/1743/0001-Fixed-Bug-3298-and-adde​d-3-tests.-This-fix-does-not-.patch
14:09 virushunter i don't know if I created the patch correctly or not since I'm still learning this stuff
14:10 deafferret virushunter: we're all still learning. :)  let me get my -live up to date and I'll apply if it seems to make things Better :)
14:10 deafferret someone was foolish enough to give me a commit bit at some point
14:11 deafferret virushunter: do you happen to be github aware?
14:11 virushunter i'm also asking all this since I fixed bug 3343 and want to know if I should upload a patch much like I did for bug3298
14:11 deafferret virushunter: If I were you I'd be submitting github pull requests nowadays
14:12 virushunter how do I do that?
14:12 deafferret virushunter: are you familiar with git at all?
14:12 virushunter yes
14:12 virushunter average user ... but not expert
14:12 deafferret oh good. then just fork bioperl-live and patch on a topic branch
14:13 deafferret then you push a "submit pull request" button somewhere
14:13 virushunter i use git on command line
14:13 deafferret then some committer just clicks a button and you're merged
14:13 deafferret virushunter: that's fine too -- you don't *need* to use the github website other than to fork the repo
14:14 deafferret once you've done a couple you'll get a commit bit, then you don't have to use the github website ever again if you don't want to
14:15 deafferret virushunter: https://github.com/bioperl/bioperl-live
14:15 virushunter i'm not quite sure i understand everything you've said but i'll start looking into it
14:16 virushunter is the idea to create a new topic branch, say topic-bugXXXX, then make changes and then.....
14:16 deafferret commit, push
14:16 virushunter commit the changes and then do a git format-patch -1?
14:16 virushunter i'm pushing the topic branch , correct?
14:16 deafferret virushunter: you don't have to submit a patch -- any committer can see the differences between your fork and the main
14:16 deafferret yessir
14:17 virushunter i c
14:17 deafferret yessir/mam
14:17 virushunter sir
14:17 deafferret :)
14:17 deafferret virushunter: here's the current branches https://github.com/bioperl/bioperl-live/branches
14:18 deafferret so if I were you i'd name mine topic/bug-XXXX
14:18 virushunter so, after pushing the topic branch, should I send an email to bioperl-l@lists.open-bio.org?
14:18 deafferret virushunter: sure, or ask here, or there's a button in github which says "pull request"
14:18 virushunter ok topic/bug-XXXX it is then
14:18 virushunter ok, i haven't used github much....i'll take a look
14:19 deafferret you'll probably like it. I do, 98% of the time :)
14:20 virushunter ok, so are you taking care of my fix for bug 3298 right now?
14:21 virushunter if so, I won't create a topic branch for that one but will for 3343
14:21 deafferret virushunter: i was going to ya. but feel free to do it via github instead if you want
14:21 deafferret trying to recover my redmine login
14:22 virushunter ok, then let me give it a shot for both bugs.
14:22 virushunter thank you muchly
14:24 deafferret thank YOU!
14:24 virushunter you gotta try lastpass for all those accounts... i love it
14:24 deafferret ok, I'm in now -- highlight me when I can help again
14:24 deafferret ya, I just added this one to my lastpass :)
14:25 deafferret highlighting me will make me notice this window faster. e.g.:
14:25 deafferret deafferret: yo!
14:25 virushunter deafferret: like this?
14:25 deafferret yup
14:25 virushunter deafferret: is this syntax a private message?
14:26 deafferret nope, it's just "hilight"
14:26 virushunter deafferret: ok
14:26 deafferret I sit in ~30 IRC channels, so hilight is important
14:26 deafferret (for me) :)
14:26 deafferret private message is /msg deafferret yo!  -- but don't bother
14:27 virushunter deafferret: ok ty
14:27 deafferret Its rare I talk to anyone privately. it's too closed-sourcy for my taste :)
14:27 deafferret and my bank doesn't support IRC. :)
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16:51 deafferret virushunter: all set?
17:53 virushunter deafferret: sorry not yet
17:54 virushunter deafferret: bioperl is a hobby on the side. I'm at work now working on a grant that is due soon
17:55 virushunter deafferret: if you want (and I prefer) that you apply the fix for bug 3298 and I'll work on getting the bug 3343 stuff done later
17:56 deafferret virushunter: i'm happy to apply 3298 for you if that helps you out
17:56 virushunter deafferret: yes it would...ty
17:56 * deafferret proceeds
18:05 deafferret virushunter: you are 'Paul Cantalupo', yes?
18:06 virushunter deafferret: yes
18:06 deafferret commit will be this, unless you want it changed:
18:06 deafferret From Paul Cantalupo (IRC: virushunter). Fixes bug #3289, adds 3 tests.
18:07 deafferret oops 3298
18:09 deafferret virushunter: ^ ?
18:28 virushunter deafferret: shoot!
18:29 virushunter deafferret: sorry about that
18:30 virushunter deafferret: it should be 3298....can you fix it?
18:31 deafferret virushunter: yes, I fixed that bit.
18:31 github [bioperl-live] jhannah pushed 1 new commit to master: https://github.com/bioperl/bioperl-live/comm​it/4e947ea831537a1212cbdb3e494ded9669b7c2a9
18:31 github bioperl-live/master 4e947ea Jay Hannah: From Paul Cantalupo (IRC: virushunter). Fixes bug #3298, adds 3 tests.
18:31 virushunter deafferret: cool
18:32 deafferret virushunter: want to update redmine?
18:33 virushunter deafferret: sure
18:33 virushunter deafferret: but with what exactly?
18:33 deafferret virushunter: excellent patch, thank you. hereafter I'll go ahead and apply yours so the process will take 30s not 4 hours
18:34 deafferret virushunter: oh, well, we can close 3298, yes?
18:34 virushunter deafferret: yes
18:34 deafferret excellent. I'm going to commute now. back on later
18:35 virushunter deafferret: thank you for your help....later
18:35 deafferret :)    &
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