Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-24

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All times shown according to UTC.

Time Nick Message
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07:11 viklund hmm
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08:34 CIA-14 bioclipse: ospjuth * r4793 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (2 files in 2 dirs): Added dummy action for Proteins.
08:34 CIA-14 bioclipse: ospjuth * r4794 /branches/bioclipse2/bioinformatics/​plugins/net.bioclipse.biojava.ui.tes​t/src/net/bioclipse/biojava/ui/test/ (6 files in 2 dirs): Added more test for SequenceContentProvider.
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12:42 CIA-14 bioclipse: carl_masak * r4795 /branches/bioclipse2/core/plugins/net.biocl​ipse.recording/src/net/bioclipse/recording/ (JSScriptGenerator.java JsScriptGenerator.java):
12:42 CIA-14 bioclipse: [JSScriptGenerator -> JsScriptGenerator]
12:42 CIA-14 bioclipse: * Easier to read
13:33 CIA-14 bioclipse: carl_masak * r4796 /branches/bioclipse2/core/plugins/net.bi​oclipse.recording.tests/src/net/bioclips​e/recording/ScriptGenerationTests.java:
13:33 CIA-14 bioclipse: [ScriptGenerationTests.java]
13:33 CIA-14 bioclipse: * chased earlier name change
13:34 CIA-14 bioclipse: carl_masak * r4797 /branches/bioclipse2/core/plugins/​net.bioclipse.ui/src/net/bioclipse​/ui/views/ActionHistoryView.java:
13:34 CIA-14 bioclipse: [ActionHistoryView.java]
13:34 CIA-14 bioclipse: * chased earlier name change
13:35 jonalv joined #bioclipse
13:36 CIA-14 bioclipse: carl_masak * r4798 /branches/bioclipse2/ (5 files in 5 dirs):
13:36 CIA-14 bioclipse: [net.bioclipse.core]
13:36 CIA-14 bioclipse: [net.bioclipse.recording]
13:36 CIA-14 bioclipse: [net.bioclipse.biojava.business]
13:36 CIA-14 bioclipse: [net.bioclipse.springBasedPrototypePlugin]
13:36 CIA-14 bioclipse: * methods are subject to recording according to whitelisting
13:36 CIA-14 bioclipse:  (with the annotation @Recorded) instead of blacklisting
13:36 masak jonalv: I'm done
13:36 masak please update everything
13:36 edrin joined #bioclipse
13:37 CIA-14 bioclipse: jonalv * r4799 /branches/bioclipse2/core/plugins/ (2 files in 2 dirs): No need to implicitly start recording plugin now since the plugin is started when one of it's class files is loaded
13:43 edrin hi
13:47 masak hi edrin
13:48 masak olas: did you say you just wrote an installer wizard?
13:49 masak because I just ran an installer wizard for TOPALi, you know the multiple sequence alignment program
13:50 masak it was a bizarre experience
13:50 masak usually, in Mac OS, one just drags the .app folder to Applications
13:51 masak but TOPALi brought up a _wizard_ to do exactly that :/
13:51 olas masak:
13:51 olas masak: no
13:51 masak ok
13:51 olas I just made a NewSampleProjectWizard
13:51 masak ah
13:51 masak good
13:51 olas which contains sampleData
13:51 masak I see
13:52 masak nvm then :)
13:56 olas all: please see my mail to bioclipse-devel
13:57 viklund olas: looks good, go for it ;)
13:57 masak :)
14:02 masak olas: I'm thinking maybe we should adopt a style guide for bc2
14:02 masak I once wrote a style guide for tk, the product we wrote for IBG
14:02 masak here it is: http://masak.org/carl/tk/style-guide/
14:02 masak it's very XML/XPath-biased
14:03 masak we'd want to target Java :)
14:08 masak things like 80-character lines, indentation, (not using) tab characters
14:17 olas I like the idea
14:18 CIA-14 bioclipse: carl_masak * r4800 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
14:18 CIA-14 bioclipse: [ScriptingConsoleView.java]
14:18 CIA-14 bioclipse: * Bound SWT.ARROW_RIGHT to a more sensible action
14:18 masak we can put it in the wiki
14:21 olas please do
14:21 masak \o/
14:21 * masak does
14:38 masak ...and here we go: http://wiki.bioclipse.net/i​ndex.php?title=Style_guide
14:39 masak I'm sure I'll be able to think of a few more after reading some code written by others :P
15:08 CIA-14 bioclipse: ospjuth * r4801 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (10 files in 5 dirs): Added an extension point for installing data folders in the NewSampleDataProjectWizard. Wizard now operational.
15:13 CIA-14 bioclipse: ospjuth * r4802 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (data/AminoAcids/ data/amino_acids/ plugin.xml): Renamed to AminoAcids
15:16 CIA-14 bioclipse: ospjuth * r4803 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (data/Qresources/ data/ScriptingResources/ plugin.xml): Updated sample data folders and implemented EP.
15:23 CIA-14 bioclipse: ospjuth * r4804 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (2 files in 2 dirs): Updated EP implementation. This plugin now works.
15:38 egonw Uppsala... ack on the dir structure refactoring
15:39 egonw that will make running PMD easier too
15:46 masak wai~!
15:48 egonw huh?
15:49 masak (an expression of sudden joy and agitation)
15:49 egonw mmm... let's try that again...
15:49 egonw PMD!
15:49 masak wai~!
15:50 egonw heheheh
15:50 masak :)
16:12 olas egonw: Peter Murray-Dust?
16:12 egonw huh?
16:12 olas PMD?
16:12 egonw where did you find that?
16:12 egonw hahahah
16:12 egonw no...
16:12 olas :-)
16:13 egonw SVN: bioclipse/branches/bioclipse2/pmd.xml
16:13 olas what is it?
16:13 egonw see pmd.sf.net
16:14 olas oh
16:14 olas I see
16:26 CIA-14 bioclipse: Annzi * r4805 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.moss/: Initial import.
16:27 CIA-14 bioclipse: Annzi * r4806 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.moss/ (59 files in 8 dirs): Initial import.
16:31 egonw oi, goodies
16:31 egonw net.bioclipse.moss
16:31 egonw Annzi: no Cheat Sheet yet, I guess? :)
16:35 Annzi egonw: oh no I think I might be the only person in the world that understands this messy code :)
16:35 egonw oi...
16:36 egonw olas: that's why PMD is so interesting...
16:36 egonw Annzi: PMD will complaint then :)
16:37 jonalv what is this PMD?
16:37 egonw [2008-01-24 17:15:38] <egonw> see pmd.sf.net
16:37 egonw [2008-01-24 17:14:59] <egonw> SVN: bioclipse/branches/bioclipse2/pmd.xml
16:37 jonalv thx
16:37 masak wai~!
16:37 egonw cd bioclipse2/; ant -f pmd.xml
16:37 egonw masak: hehehe
16:37 masak :)
16:37 * egonw loves running jokes
16:38 * masak too
16:38 jonalv hm I need to check out bioclipse 2 first from the terminal...
16:38 jonalv oh it's a joke?
16:38 * jonalv is lost now
16:38 Annzi so am I!!
16:38 Annzi :)
16:38 masak jonalv: say PMD, and you'll see
16:39 jonalv pmd
16:39 masak wai~!
16:39 jonalv ?
16:39 masak :)
16:39 Annzi ??
16:39 masak :)
16:39 egonw jonalv: right, there you go :)
16:39 masak exactly.
16:39 jonalv pmd
16:39 masak exactly.
16:39 masak wai~!
16:39 masak (I like PMD.)
16:40 masak wai~!
16:40 jonalv so do we run it yet?
16:40 masak not regularly
16:40 jonalv I guess the idea is to run it on some server?
16:40 egonw not as in Bioclipse Nightly, no
16:40 masak but you can run it locally, on your box
16:40 egonw jonalv: indeed
16:40 masak jonalv: yes
16:41 jonalv we probably should get a nightly build server of some sort...
16:41 * egonw is off for basketbal, and a meeting in Leiden tomorrow
16:41 jonalv Running all JUnit tests as well
16:41 egonw jonalv: quite so
16:41 masak jonalv: would be great
16:41 egonw google for 'CDK Nightly"
16:41 egonw and you get an idea what we do with the chemistry development kit
16:42 jonalv yes I ahve seen that page but it was quite some time ago
16:42 egonw that server runs in Indiana, where Rajarshi Guha is
16:42 jonalv k
16:42 Annzi egonw: now I can finally answer your question...no ;)
16:43 Annzi or  statement that is
16:46 egonw ok, bye all
16:46 egonw have a nice weekend!
16:47 olas left #bioclipse
17:20 jonalv HEADS UP
17:21 jonalv now removing net.bioclipse.recording
17:21 jonalv It has been merged into net.bioclipse.core
17:22 Annzi left #bioclipse
17:23 jonalv now subclipse of course has to make my day even worse...
17:26 CIA-14 bioclipse: jonalv * r4807 /branches/bioclipse2/ (22 files in 9 dirs): Merged net.bioclipse.recording into net.bioclipse.core
17:27 CIA-14 bioclipse: jonalv * r4808 /branches/bioclipse2/core/plug​ins/net.bioclipse.recording/: removed net.bioclipse.recording
17:27 CIA-14 bioclipse: carl_masak * r4809 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
17:27 CIA-14 bioclipse: [JsConsoleView.java]
17:27 CIA-14 bioclipse: * Console now complains if R is not installed
17:35 CIA-14 bioclipse: jonalv * r4810 /branches/bioclipse2/core/plug​ins/net.bioclipse.core.tests/ (12 files in 9 dirs): moved recording tests into net.bioclipse.core.tests
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