Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-07-14

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All times shown according to UTC.

Time Nick Message
05:21 egonw_ joined #bioclipse
06:58 edrin joined #bioclipse
07:00 edrin hi
07:00 zarah ni hao edrin
07:06 olass joined #bioclipse
07:06 olass moin
07:06 zarah saluton olass
07:06 olass @seen egonw
07:06 zarah egonw was last seen 22 h 18 m 23 s ago in #bioclipse saying 'olass, jonalv: let's relocate'
07:06 olass hmm
07:16 edrin hi olass
07:24 sneumann joined #bioclipse
07:27 stain_ joined #bioclipse
07:35 olass hi edrin
08:10 jonalv joined #bioclipse
08:11 shk3 joined #bioclipse
08:30 masak joined #bioclipse
09:39 masak http://journal.stuffwithstuff.com/​2009/06/05/naming-things-in-code/
09:39 zarah masak's link is also http://tinyurl.com/pjlbc4
09:55 jonalv zarah: tell egonw regarding "Making your own feature Git repository" I could be wrong but I think that if I first do 'git repack -ad' and the do 'git prune' then 'git prune' will never do anything.
09:55 zarah Consider it noted.
09:56 * olass tried the command 'git lunch' but that did not resolve in git preparing lunch for him
09:56 * olass is disappointed
09:57 jonalv olass: maybe it can make coffe? :)
09:57 olass but I wanted lunch first
09:57 olass will try coffee later
11:03 shk3 probably git had a lunch for itself
11:03 shk3 not for you
12:05 stain olass: perhaps you need to pull in the lunch
12:05 stain distributed lunch
12:07 stain I pulled in the sandwich from the Spar downstairs and pulled in some vegetables and aioli from my repository at home - compiled it all here, and no unit test failures - just a bit of memory leakage of the aioli
12:08 olass stain: right :)
12:08 olass stain: maybe you could push a nice lunch for me?
12:08 olass not sandwiches, please
12:08 stain I've got a boiled egg
12:09 stain it does have some test failures though, it was not compiled with enough water resources, so some of it is not yet solid bytecode
12:10 stain did you go to ISMB in stockholm btw..?
12:30 masak jonalv: http://github.com/guides/fork-a-pro​ject-and-submit-your-modifications
12:30 zarah masak's link is also http://tinyurl.com/6o95se
12:54 olass stain: ISMB, no, was on holidays
12:54 olass besides, very expensive
12:55 olass too expensive for my prof
12:55 olass they must make a lot of money on that conf...
12:56 * olass is trying 'git push --200deg steak owen'
12:56 * olass expects the operation to take approx 1.5h
12:57 olass working from home makes some long-running tasks feasible
12:57 * olass is having brother+family on dinner soon
13:00 jonalv masak++
13:16 shk3 hi jonalv
13:16 masak shk3: he just went afk.
13:17 shk3 ok
13:32 jonalv olass: net.bioclispe.xom resdies in both egows cheminformatics repo and your core repo. Please choose one.
13:35 jonalv olass: ping
13:40 jonalv zarah: tell olass there are a bunch of plugins existing in mulitple repositotires now. Please order up the chaos and point out what should go where.
13:40 zarah Consider it noted.
13:52 shk3 joined #bioclipse
13:52 jonalv shk3: hi
13:52 jonalv shk3: did you ask for me?
13:52 shk3 yes
13:52 olass jonalv: pong
13:52 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
13:53 olass @msg
13:53 zarah olass: 12 m 45 s ago, jonalv said there are a bunch of plugins existing in mulitple repositotires now. Please order up the chaos and point out what should go where.
13:53 jonalv olass: it seems that net.bioclipse.servcies has been lost in the move...
13:53 shk3 I want to write a manager method (respectivly change an existing one)
13:53 shk3 to return partial results.
13:53 jonalv shk3: oh cool
13:53 olass jonalv: please send egonw a list of things to do
13:53 shk3 there is no documententation right now, it seems
13:53 olass he should resolve things, not me
13:53 olass this is his mess
13:53 shk3 could you give me some hints?
13:53 jonalv (I haven't thought about that for an eternity it feels like)
13:54 shk3 sorry
13:54 shk3 I would write documentation then
13:54 jonalv shk3: how far have you come?
13:54 shk3 well, I am at the start block
13:55 shk3 the wiki says:
13:55 shk3 There is also a pattern where the interface method takes a BioclipseJobUpdateHook and returns a BioclipseJob. Here the implementation takes an IPartialReturner and an IProgressMonitor
13:56 shk3 and that's it
13:56 shk3 I guess I need to use the IPartialReturner for actually returning results?
13:57 jonalv shk3: yes
13:57 shk3 do I need to implement that interface?
13:57 shk3 or is there an implementation I can use?
13:58 jonalv shk3: yes it's the callback. There should be an implementation you can build on I think. You still will probably want to implememnt the method that is called though
13:58 jonalv that's where you will handle the partial return
13:59 * jonalv has barely managed to get his git things up and running...
13:59 shk3 ok, i will look for the implementation and just try
13:59 shk3 I will come back to you if something is unclear
14:00 jonalv shk3: yes please
14:05 jonalv zarah: ask egonw Why are org.openscience.cdk.annotation and org.openscience.cdk.ioformats in core instead of in cheminformatics?
14:05 zarah Consider it noted.
14:07 shk3 jonalv: wiki says
14:07 shk3 There is also a pattern where the interface method takes a BioclipseJobUpdateHook and returns a BioclipseJob
14:08 shk3 so the BioclipseJob is really the return value and not a parameter (as it is in a method running as job and returning a result)?
14:09 jonalv zarah: tell egonw net.bioclipse.xom and probaly a few more are both in core and in cheminformatics for the moment. They need to be only at one place...
14:09 zarah Consider it noted.
14:10 jonalv shk3: there are two classes here. 1. BioclipseUiJob which is used as a paramater and 2. BioclipseJob which is returned
14:11 jonalv BioclipseUIJob is used for running something in the gui thread after a method has finnished while the BioclispeJob is a representation of the job which runs the code in a method run as a job. (if you see what I mean...)
14:11 olass @tell egonw: net.bc.xom should only be in bioclipse.core repo
14:11 zarah Consider it noted.
14:12 olass tell egonw: don't forget you promised to fix the qsar repo
14:12 masak olass: '@tell'
14:12 olass @tell egonw: don't forget you promised to fix the qsar repo
14:12 zarah Consider it noted.
14:12 shk3 ah ok
14:12 olass zarah: good boy
14:12 zarah olass: please rephrase or stop trying to be witty :)
14:12 olass zarah: good bot
14:12 zarah olass: eh... wha'?
14:13 shk3 so all results are returned via that PartialReturner?
14:13 shk3 last return of that is final result or so?
14:14 jonalv shk3: when you have done last return there is a method called done or finnished or soemthing like that which you should call
14:14 shk3 ok
14:14 shk3 thanks for the hint
14:14 jonalv shk3: one call to partialReturn should only contain the latest news not all that has been done up to that point
14:16 shk3 ah, I was wonderin about that
14:16 shk3 so the application collects results?
14:17 jonalv shk3: yes but if you want contiouns updates of somethign using the partial returns than you ahve to reimplement that method and do the collecting and updating yourelf off course
14:17 shk3 yes
14:18 shk3 I will try
14:19 jonalv shk3: good luck
14:39 CIA-54 bioclipse: jonalv * r11669 /bioclipse2/trunk/plugins/ (234 files in 63 dirs): StructureDB related plugins moved to GitHub
15:40 jonalv shk3: any progress?
15:41 shk3 sorry, got distracted
15:43 jonalv np
15:43 jonalv I just wondered :)
15:45 shk3 don't worry, I _will_ need you
15:46 shk3 perhaps you can help me with that:
15:46 shk3 I try writing a test, but I get could not get manager when I try to run it
15:47 shk3 it works from inside the plugin where the manager is in
15:47 shk3 but not from the test plugin.
15:47 shk3 can you think of a reason?
15:49 jonalv shk3: I guess it could be start otder of the plugins.
15:50 jonalv shk3: I take it you are writing a plugin test?
15:50 shk3 yes
15:50 jonalv and not a vanilla JUnit test...
15:51 shk3 plugin test
15:52 shk3 it's the finderTracker.waitForService(1000) in Activator returning null
15:54 jonalv shk3: yes sounds like start order of plugins to me
15:55 shk3 start order?
15:55 jonalv shk3: isn't there a wiki page about how to write plugin tests. Have you looked at it?
15:55 shk3 how is that influenced?
15:55 shk3 yes
15:55 shk3 i did quite a few of them and all work
15:55 shk3 but this one doesn't
15:55 shk3 must be some minor setting, I suppose
15:55 jonalv shk3: so, what's the difference? :)
15:56 shk3 if i only would know
16:37 edrin left #bioclipse
16:42 CIA-54 bioclipse: shk3 * r11670 /bioclipse2/trunk/plugins/​net.bioclipse.nmrshiftdb/ (3 files in 3 dirs): some cleanups
16:47 CIA-54 bioclipse: shk3 * r11671 /bioclipse2/trunk/plugins/net.bioclips​e.nmrshiftdb/src/net/bioclipse/nmrshif​tdb/business/INmrshiftdbManager.java: some cleanups
18:03 olass @seen egonw
18:03 zarah egonw was last seen 1 d 9 h 15 m 43 s ago in #bioclipse saying 'olass, jonalv: let's relocate'
18:15 egonw_ joined #bioclipse
19:00 sneumann joined #bioclipse
23:59 CIA-52 joined #bioclipse

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