Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-11-28

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All times shown according to UTC.

Time Nick Message
05:50 masak joined #bioclipse
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07:37 masak there are errors in bc2's net.bioclipse.ui plugin
07:37 masak can anyone confirm this?
07:38 masak I have one error in net.bioclipse.ui.BioclipseActivator, and one in net.bioclipse.ui.editors.pdb.PDBEditor.java
07:39 masak hm -- nevermind. turns out I had an old net.bioclipse.logging
07:49 CIA-18 bioclipse: carl_masak * r4344 /branches/bioclipse2/core/plugins/ (7 files in 5 dirs):
07:49 CIA-18 bioclipse: [net.bioclipse.core]
07:49 CIA-18 bioclipse: [net.bioclipse.ui]
07:49 CIA-18 bioclipse: * moved all ConsoleViews from core to ui
07:49 masak ...because proper separation makes me happy :)
08:04 steinbeck joined #bioclipse
08:04 steinbeck moin
08:09 masak moin
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09:04 CIA-45 bioclipse: carl_masak * r4346 /branches/bioclipse2/core/plugins/ (net.bioclipse.core.spring.osgi/ net.bioclipse.spring.osgi/):
10:03 kaskelot joined #bioclipse
10:03 kaskelot herro
10:03 masak olas, egonw: could one of you add kaskelot++ to the bioclipse project once he gets an SF account?
10:06 * jonalv summons edrin
10:07 * olas will do it
10:07 masak goodie
10:08 olas masak: kaskelots SF user?
10:08 * jonalv is trying to figure out what edrins magical JarClasspathLoader does and if he can bend the magic for his own purposes
10:09 masak olas: he's here, you can ask him :)
10:09 * masak suspects kaskelot's in the middle of creating a user account
10:09 egonw kaskelot: are you?
10:09 olas kaskelot?
10:10 kaskelot hello folks
10:10 kaskelot my user is updatebjarni
10:10 miguelrojasc1 left #bioclipse
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10:11 egonw hi rojasm
10:11 olas kaskelot: done
10:11 rojasm hi egonw
10:12 kaskelot \o/
10:12 EskilA_ joined #bioclipse
10:14 CIA-45 bioclipse: updatebjarni * r4347 /branches/bioclipse2/core/​plugins/net.bioclipse.r/: Initial import.
10:14 rojasm egonw: about the MolecularFormula. What do you think is the best? wenn add(IIsotope) than compare not instance but if the Isotope exists with some QueryIsotope for example
10:14 egonw oh, goody
10:15 CIA-45 bioclipse: updatebjarni * r4348 /branches/bioclipse2/core/plugins/net.bioclipse.r/ (11 files in 6 dirs): Initial import.
10:15 egonw rojasm: let's move to #cdk
10:15 olas A new Bioclipse developer! \o/
10:16 CIA-45 bioclipse: updatebjarni * r4349 /branches/bioclipse2/core/plugins/n​et.bioclipse.core/src/net/bioclipse​/core/scripting/JsEnvironment.java: Added R related nonsense, to be fixed.
10:16 egonw olas: I need a tutorial how to set up particular projects in Bioclipse... such as a QSAR project...
10:16 egonw with net.bioclipse.r in mind, this is of particular interest...
10:16 egonw olas: you know of a good tutorial, perhaps?
10:19 olas egonw: will be solved in Bioclipse2, I'm actually looking at it right now
10:20 olas for Bioclipse1 there is no info
10:20 egonw sure it will be solved...
10:20 egonw was asking about BC2
10:20 olas great
10:20 olas hmm
10:20 egonw want to learn how it works...
10:20 olas yes
10:20 olas I have a book
10:20 egonw pleaes point me to the material you are looking at...
10:20 egonw ah, crap
10:20 egonw umm...
10:20 olas Eclipse help is good
10:20 egonw shall we make a deal? ...
10:20 olas a deal?
10:20 egonw I scan that Bioclipse article in Eclipse Magazine... and you scan ...
10:20 egonw the book...
10:21 egonw perhaps...
10:21 egonw ?
10:21 egonw :)
10:21 * olas has to run to the plane in 10 mins
10:21 olas sorry, no time now
10:21 olas earliest on monday
10:21 olas no, tuesday
10:21 egonw olas: I think the proper way of boarding does not involve chasing a plane on the runway
10:21 olas Need to scan it in Uppsala
10:21 * olas is extremely fast
10:21 egonw :)
10:22 olas no seriously, I'd be very happy if dou'd learn that cause that means one less thing for me to do
10:22 olas a lot on the list now
10:23 olas what I advice you to do is:
10:23 olas Check out the R-plugin named StatEt from SVN
10:23 olas and look how they set up the R-project
10:23 olas It involves a "nature"
10:23 olas and a nature.decorator
10:24 olas Class implements IProject
10:24 * olas will do a small unfinished commit
10:26 egonw ok, thanxx
10:27 jonalv olas: got a few minuites?
10:27 olas no
10:27 jonalv okey...
10:27 olas well
10:27 olas wait
10:27 CIA-45 bioclipse: ospjuth * r4350 /branches/bioclipse2/core/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/wizards/ (. NewQSARRProjectWizard.java): Tried a NewQSARProjectWizard. Does not work, for egon to look at. Please also move from ui plugin.
10:27 olas maybe 5 mins
10:27 jonalv lol
10:27 jonalv It's about the JSEnvironment
10:28 jonalv Do you think that you can instead of making a namespace of a class with static methods make a namespace of an object immplementing a known interface?
10:29 olas I don't know
10:29 olas try it
10:29 jonalv I don't understand your code well enough...
10:30 jonalv olas: maybe you need run for your plane now...
10:30 olas soon soon
10:31 * olas is eating
10:31 masak olas: bonne chance en France!
10:31 olas does that mean: good luck?
10:31 masak yes
10:31 olas jonalv: I don't understand what you want to achieve
10:32 olas and "my code" is just an extension point implementation
10:32 jonalv you don't understand my question or you don't understand why I ask it?
10:32 olas the rest is edrins code
10:32 olas both
10:32 olas please elaborate
10:32 jonalv If we are to use AOP we can't use static methods on a class we need an instance...
10:32 jonalv and besides static methods are ugly...
10:33 jonalv That's prerry much all of it...
10:34 masak that's why it's called _object_ oriented programming, not _class_ oriented programming
10:36 olas dno't mind me
10:37 olas I just did a dirtty hack to make it work
10:37 olas please change it in any way you like
10:37 masak olas: ...sure, if it's even possible
10:37 olas can't help you from IRC
10:37 egonw olas: make sure to blog from france on the meeting
10:38 olas they have a live streaming
10:38 olas so you can see me if you like
10:38 egonw oh, cool :)
10:38 olas I will surely blog
10:38 egonw will blog about the stream...
10:38 egonw so that the complete ODOSOS community is watching you....
10:39 olas blog about the blog too :-)
10:39 egonw sure
10:39 olas gotta run now
10:39 egonw have fun
10:39 olas bye all
10:39 olas left #bioclipse
10:40 CIA-45 bioclipse: updatebjarni * r4351 /branches/bioclipse2/core/plugins/net​.bioclipse.core/META-INF/MANIFEST.MF: Dependency upon r.
10:41 egonw kaskelot: that does not sound like a good idea
10:41 kaskelot ?
10:41 egonw R should be optional
10:42 egonw not a hard dependency
10:42 kaskelot well, right now the code depends on r, so it doesn't work without the dependency
10:42 egonw right, your plugin should depend on it...
10:42 egonw but not .core
10:43 kaskelot you bioclipse folks can discuss this, I'm off for SNIC now
10:43 jonalv egonw, Is probably right.
10:44 kaskelot masak wanted me to put a line of test code in JsEnvironment and commit, so this is how it needs to be to work for the moment
10:44 steinbeck left #bioclipse
10:44 * jonalv thinks the extenstion points system is somewhat complicated to work with. And that is not even mentioning osgi-services...
10:44 * kaskelot -> SNIC
10:44 * jonalv @lunch
10:45 jonalv masak, did you heat up the sauna? ;)
10:46 * masak is too far into the smoke to see his computer
10:59 CIA-45 bioclipse: ospjuth * r4352 /branches/bioclipse2/core/plugins/net.bioclip​se.ui/src/net/bioclipse/ui/QsarProject.java: Missing project stub for egon.
11:29 edrin joined #bioclipse
11:52 edrin hi
12:04 masak hi edrin, jonalv was looking for you a few hours ago
12:08 edrin ok
12:08 edrin i'm now here
12:09 masak jonalv isn't, though
12:09 masak I'll let you know when he is
12:10 masak I'm not sure he still has something to ask, actually. it might be that he has traced the source of his problems away from rhino
12:10 masak we'll see
12:10 masak here he is now
12:11 jonalv tada :)
12:11 edrin magical
12:11 jonalv I am trying to figure out how your magical dynamic package loading is working...
12:12 jonalv Maybee I shuold try to explain what I want to do
12:12 edrin ok
12:12 jonalv Currently a JS name space is coupled to a class with static methods
12:13 jonalv What I want to do is couple it to an object instead
12:13 edrin ok
12:13 jonalv The problem is that this object should be of a certain interface
12:13 edrin are you trying to do an input/output object?
12:13 jonalv Question is though how the script plugin can now of this interface
12:14 jonalv not sure, what would that mean?
12:14 edrin you could pass to and get as a result from a script?
12:14 edrin that's what I wanted to add to the scripting plugin next
12:14 jonalv yes Definitly pass it but perahsp get something else back...
12:14 jonalv but that's not all
12:15 jonalv I want to do a service object
12:15 masak it's more general than I/O
12:15 edrin that was my plan, too
12:15 jonalv That is an object which you call methods on
12:15 jonalv So the methods wouldn't be statical on a class but on objects
12:16 edrin sorry, there is a visitor now, i can't help you now
12:16 jonalv to quote masak: "that's why it is called object oriented programming and not class oriented"
12:16 edrin maybe you can write me an email and i'll tell you what I might know
12:16 jonalv you have a visitor?
12:16 edrin it's not alien
12:16 edrin an alien
12:16 masak :)
12:17 masak edrin: nobody suggested that
12:17 jonalv what's your mail adress?
12:17 jonalv hm or I could post it to the bioclipse dev
12:17 jonalv that meakes actually more sence..
12:17 edrin yes, sure, but i will not read it now
12:17 masak jonalv: do that
12:17 edrin cu
13:29 CIA-45 bioclipse: carl_masak * r4353 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
13:29 CIA-45 bioclipse: [ScriptingConsoleView.java]
13:29 CIA-45 bioclipse: * beginnings of multi-line commands support
13:29 CIA-45 bioclipse: * "2 +\n2" now works
13:29 CIA-45 bioclipse: * shortened a few long lines
13:30 CIA-45 bioclipse: carl_masak * r4354 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (plugin.xml src/net/bioclipse/ui/Perspective.java):
13:30 CIA-45 bioclipse: [net.bioclipse.ui]
13:30 CIA-45 bioclipse: * corrected a few lingering RhinoConsoleView -> JsConsoleView
13:41 CIA-45 bioclipse: carl_masak * r4355 /branches/bioclipse2/core/plugins/net.b​ioclipse.ui/src/net/bioclipse/ui/views/ (3 files):
13:41 CIA-45 bioclipse: [net.bioclipse.ui.views]
13:41 CIA-45 bioclipse: * method name refactoring
14:02 CIA-45 bioclipse: carl_masak * r4356 /branches/bioclipse2/core/plugins/ (4 files in 2 dirs):
14:02 CIA-45 bioclipse: [net.bioclipse.core.Activator]
14:02 CIA-45 bioclipse: [net.bioclipse.ui]
14:02 CIA-45 bioclipse: * moved creation of sessions from consoles to Activator
14:02 CIA-45 bioclipse: [ScriptingConsoleView.java]
14:02 CIA-45 bioclipse: * now catches fatal exceptions in eval method
14:03 CIA-45 bioclipse: carl_masak * r4357 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
14:03 CIA-45 bioclipse: [ScriptingConsoleView.java]
14:03 CIA-45 bioclipse: * removed finished TODO
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14:55 edrin test
15:03 masak ...anything but that
15:13 CIA-45 bioclipse: carl_masak * r4358 /branches/bioclipse2/core/plugins/net​.bioclipse.core/META-INF/MANIFEST.MF:
15:13 CIA-45 bioclipse: [net.bioclipse.core]
15:13 CIA-45 bioclipse: * now exports net.bioclipse.core
15:13 CIA-45 bioclipse: * because Activator needs to be seen from other packages
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