Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-08-09

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All times shown according to UTC.

Time Nick Message
05:41 CIA-93 Bio-FeatureIO: Chris Fields master * r8df5303 / lib/Bio/FeatureIO/gff.pm : given/when - http://bit.ly/codb56
05:41 CIA-93 Bio-FeatureIO: Chris Fields master * r2b3e481 / Build.PL : min. perl 5.10 for FeatureIO - http://bit.ly/awZtZg
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08:31 dbolser genehack: ty
08:31 dbolser now I'm not clear either...
08:34 dbolser deafferret: what are you freebasing?
08:36 dbolser genehack: I think I need to remove some dodgy local commits before I can rebase
08:37 dbolser btw, how do I folup on my pull request?
08:37 dbolser folup is a new word meaning 'follow up'
09:05 kblin dbolser: you can do the removing during the rebase
09:05 kblin it's called git rebase -i
10:09 dbolser kblin: ty
10:54 kblin dbolser: that and git add -i are my favourite git commands
11:32 dbolser kblin: to be clear, a remote rebase is done against a specific local branch?
11:32 dbolser I can't see how it would be otherwise but...
11:37 dbolser I just delete the pick line to skip that commit?
11:39 dbolser Could not apply ec01fac...
11:39 dbolser what is the normal usecase here?
11:39 dbolser also... I assume I'm rebasing against origin
11:42 dbolser I'm reading some local commits (git-log) that are "Merge branch 'master' of git://github.com/bioperl/bioperl-live" ... these are previous 'pulls' that I won't see once I learn how to rebase?
11:46 kblin er, hang on
11:56 kblin flaky connection here
14:46 Dezin joined #bioperl
14:46 Dezin anyone here?
14:46 dbolser no
14:47 dbolser only joking
14:47 Dezin would you know how to use SearchResultEventBuilder?
14:47 dbolser Dezin: how did you find us?
14:47 dbolser not off the top of my head
14:48 Dezin do you mean bioperl or the chat?
14:49 dbolser chat
14:50 Dezin my boss knew about it and he told me
14:50 dbolser what do you want to do?
14:50 dbolser cool
14:50 Dezin im trying to make the searchio result object only load the top few hits
14:50 dbolser http://www.bioperl.org/wiki/HOWTO:SearchIO ?
14:51 Dezin yeah i was already looking at that
14:51 dbolser ic
14:51 dbolser people will come in later (stateside)
14:51 Dezin sounds good
14:55 Dezin i feel like i need to create an event using SearchResultEventBuilder that makes the factory call result_end
14:56 Dezin **end_result
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15:47 dbolser HEAD^ is the parent of HEAD ... meaning the repo just before the last commit?
16:28 dbolser git diff foo origin/HEAD^ # nae diff
16:28 dbolser git diff foo origin/master # couple changes
16:29 dbolser how to bring foo in line with origin master?
16:29 dbolser why do I have branches named origin and master and foo?
16:39 rbuels dbolser: you don't have branches named origin, probably.  that's probably the name of a remote
16:40 rbuels dbolser: are you trying to diff a branch versus some other branch?
16:40 rbuels dbolser: or what?
16:41 dbolser rbuels: on my github fork of bp-live, I have a bugfix branch
16:41 dbolser on our webserver, I have head of 'origin'
16:42 dbolser wow, I'm getting more and more confused
16:42 dbolser git branch
16:42 dbolser * (no branch) foo master origin
16:42 rbuels origin is a very suspicious name for a head.  it sounds to me like somebody has messed some stuff up.
16:42 dbolser who would do that?!?!?
16:42 * dbolser feels ashamed
16:42 rbuels a raccoon
16:42 rbuels rascals.
16:42 dbolser deafferret
16:42 rbuels him too.
16:43 dbolser so ... what is this (no branch) business?
16:43 dbolser I think I prolly created a branch called origin by mistake at some point, so I'd like to see if there is anything worth keeping in that branch before nuking it
16:43 rbuels dbolser: it means you have done something like 'git checkout some_very_weird_thing' and your working copy's checkout is on something that is not a branch
16:44 rbuels well first, fix your working copy.  git checkout master.
16:44 dbolser Switched to branch "master"
16:44 rbuels 'git branch' lists what branches there are
16:44 rbuels in your local copy
16:44 dbolser foo
16:44 dbolser * master
16:44 dbolser origin
16:44 dbolser git diff --stats master origin ?
16:45 rbuels git log ^origin/master foo will tell you if there are any commits on foo that are not in origin/master
16:45 rbuels the carat says 'exclude commits that are also in this thing'
16:45 dbolser ic
16:45 pyrimidine joined #bioperl
16:45 * rbuels waves hello at pyrimidine
16:45 dbolser rbuels: I think that foo is just an out of date origin/master
16:45 pyrimidine o/
16:46 rbuels dbolser: if there is nothing worthwhile in foo, delete it with 'git branch -d foo'
16:46 dbolser Dezin: pyrimidine is the person to ask I think
16:46 pyrimidine may have to use -D
16:46 pyrimidine (if the branch is useless and hasn't been merged in)
16:46 dbolser rbuels: all I see is ... Merge branch 'master' of git://github.com/bioperl/bioperl-live
16:46 rbuels useless.
16:46 rbuels delete.
16:47 dbolser git branch rm foo
16:47 rbuels no.  -d
16:47 pyrimidine git branch -d foo
16:47 rbuels you probably just made a branch named 'rm'
16:47 rbuels lol
16:47 * dbolser swoons
16:47 dbolser indeed
16:47 dbolser error: The branch 'rm' is not an ancestor of your current HEAD.
16:47 dbolser If you are sure you want to delete it, run 'git branch -D rm'.
16:47 pyrimidine yep
16:47 rbuels yep
16:48 * dbolser swoons again
16:48 dbolser ok, same goes for foo
16:48 dbolser just *master and origin now
16:48 pyrimidine right.  the branch hasn't been merged back to master
16:49 pyrimidine so -d won't work.  Have to force the delete with -D
16:49 dbolser I know this is dumb but, ancestor means ... earlier version... but it contains ... what? changes that I haven't commited yet?
16:49 dbolser or ...
16:49 dbolser changes that I haven't pre-commited via a merge since origin has moved on?
16:50 dbolser it isn't yet an ancestor?
16:50 dbolser but it could be if I merged it... right?
16:50 pyrimidine don't think of origin as the branch
16:50 pyrimidine think of origin/master as the branch
16:51 dbolser thanks guys, unfortunately I just got 'the call'
16:51 dbolser pyrimidine: to make things slightly more confusing I actually do have a branch called 'origin'
16:51 dbolser (probably leading to my increased confusion)
16:51 pyrimidine yep
16:51 rbuels yes.  don't name branches origin.
16:51 dbolser shows the same commits as foo had
16:52 pyrimidine easy enough to rename that, IIRC
16:52 dbolser Deleted branch origin.
16:52 dbolser night
16:52 pyrimidine ok
16:52 dbolser ty
16:52 dbolser pyrimidine: did you get my pull request?
16:52 pyrimidine not yet
16:53 dbolser spaces in feature types are not well supported by bp_seqfeature_delete
16:53 dbolser dbolser/debug_bp_seqfeature_delete
16:53 dbolser night
16:53 pyrimidine pull reqs are acting strangely for organizations, not sure why
16:53 pyrimidine dbolser: okay, will look at it.  'Night~
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17:00 * pyrimidine notices an amazing correlation btwn announcing the intent to make a point release and the upswing of commits and new code to try getting into said release
17:00 pyrimidine buncha procrastinators :)
17:01 rbuels haha
17:14 pyrimidine re: pull requests and organizations: http://support.github.com/discussions/organi​zation-issues/109-pull-request-organizations
17:14 pyrimidine so it's being addressed
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17:27 kblin boy, some people really manage to find a lot of the foot-shooting power inherent in git
17:28 pyrimidine :)
17:34 rbuels yes, i hanged myself with git a couple of times while learning
17:37 kblin so thre's a few things that helped me along..
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17:52 * Fiona waves and says hello
17:52 pyrimidine kblin: if you have any references feel free to add them to the wiki page.
17:52 pyrimidine Fiona: o/
17:53 Fiona hey pyrimidine
17:54 pyrimidine :)
17:56 Fiona I'm new to irc, and even more new to bioperl
17:56 Fiona Good god thats bad English ><
17:57 pyrimidine s'okay
17:57 rbuels 'more newer' i think is what you were looking for
17:57 rbuels that's what i usually say
17:58 Fiona rbuels:  probably
17:58 Fiona I'm doing a masters research project (and really struggling) that requires me to use bioperl, so i thought i might pick up some tips from watching in here
17:59 rbuels Fiona: it's a good idea to hang out in here, yes
18:00 Fiona my project is on comparison of p. syringae ff5 and b728a strains
18:01 * pyrimidine once worked remotely with a Fiona who worked on Pseudomonas
18:01 pyrimidine funny, that
18:01 Fiona really?
18:01 pyrimidine Fiona Brinkman
18:02 Fiona any of you heard of a david studholme?
18:02 rbuels when i'm comparing pseudomonas strains, i usually start with taste and mouthfeel.  i swish it around in the glass ...  does it have "legs"?
18:02 pyrimidine I helped with the P. aeruginosa annotation way back
18:02 kblin pyrimidine: yeah, flaky internet connection right now, got a phone call, so GPRS dropped
18:03 pyrimidine kblin: np
18:05 kblin are reciepe-style instructions ok?
18:05 pyrimidine kblin: sure
18:05 kblin ok
18:06 pyrimidine though I'm wondering if a bioperl-related git cookbook is in order...
18:07 kblin of course most of this stuff can be found elsewhere
18:07 pyrimidine linkouts are probably better, then
18:08 pyrimidine particularly if the remote is up-to-date
18:08 * kblin nods
18:08 kblin not sure if they can be found in connection, but I'm happy to check
18:09 kblin mostly, as a beginner you just don't know that there's a command to do whatever you need
18:09 kblin once you found the command, the manpage usually is pretty good
18:10 pyrimidine agreed
18:10 pyrimidine I think things of use are mainly where one commonly runs into problems
18:11 pyrimidine merge conflicts, keep up-to-date with forks and branches, etc
18:11 kblin like you can happily forget that you're in the middle of a rebase, do some commits, then some time later you try to start a new rebase, git tells you there's one already running, so you abort it and poof your commits are gone
18:11 kblin git reflog saves the day here, if you know about it
18:11 pyrimidine yep, happened to me
18:11 pyrimidine reflog does help
18:13 kblin but I agree, I think the wiki should mainly have some common situations and maybe some best practices
18:13 kblin like you don't want to have a branch called origin, because that will confuse the heck out of you and everybody trying to help
18:14 pyrimidine or have a remote called 'master' :P
18:14 kblin hehe, yeah, same thing
18:14 Fiona i have to go now. I will be back later tonight
18:14 pyrimidine Fiona: ok
18:20 kblin hm, I guess I could prettify http://www.bioperl.org/wiki/T​alk:Using_Git#Helping_a_noob...
18:22 kblin not sure if it's a workflow you'd recommend, though
18:27 pyrimidine kblin: I think that's a good start
18:27 pyrimidine the changes from svn are what catch users off-guard the most
18:29 kblin the main difference from the current description is that I use one clone with two remotes, where the current guide suggests to do a seperate clone for the fork
18:30 pyrimidine TIMTOWTDI
18:30 pyrimidine (probably why the pythonistas like hg more :)
18:32 kblin that, and because it's done in python
18:33 kblin but I think the multiple remotes thing works in hg as well
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21:03 Yksi hello
21:16 dnewkirk hi
21:18 Yksi hey dnewkirk
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