Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-01

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All times shown according to UTC.

Time Nick Message
04:50 Gpox joined #bioclipse
05:11 rojasm joined #bioclipse
05:51 thomas_ku joined #bioclipse
06:19 rojasm1 joined #bioclipse
06:51 CIA-49 bioclipse: goglepox * r6380 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (3 files in 3 dirs): Fixes AssertionFailedException and 'Resource does not exist' exceptions when closing editors to Virtual fiels on startup. Fix for bug #2030492
06:51 rojasm joined #bioclipse
07:13 olas joined #bioclipse
07:13 olas hi all
07:13 zarah hi olas
07:32 CIA-49 bioclipse: ospjuth * r6381 /bioclipse2/trunk/plugins/​net.sourceforge.jseditor/ (CVS/ META-INF/MANIFEST.MF icons/CVS/ scripts/ src-jseditor/): Cleanup, removed CVS folders.
07:47 CIA-49 bioclipse: ospjuth * r6382 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (13 files in 6 dirs): Cleared out all warnings.
07:50 CIA-49 bioclipse: ospjuth * r6383 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (5 files in 3 dirs): Set required environment to J2SE-1.5. I know this was problematic before but I'm willing to give it another try. Also converted lazystart to bundle-ActivationPolicy in manifest.
07:51 jonalv joined #bioclipse
07:52 jonalv mion
07:52 jonalv moin
07:52 zarah hi jonalv
07:53 CIA-49 bioclipse: ospjuth * r6384 /bioclipse2/trunk/plugins/net.​bioclipse.ui/build.properties: Removed unused fields in build.properties. Only warnings remaining is for plugin.xml, uses TabbedProerties internal class. No idea how to get around that.
08:06 shk3 joined #bioclipse
08:07 masak joined #bioclipse
08:13 CIA-49 bioclipse: ospjuth * r6385 /bioclipse2/trunk/plugins/​net.sourceforge.jseditor/ (20 files in 6 dirs): Cleared out all warnings from jseditor code by adapting to generics.
08:14 CIA-49 bioclipse: ospjuth * r6386 /bioclipse2/trunk/plugins/net.biocl​ipse.scripting.ui/build.properties: Added icons to build.properties.
08:15 CIA-49 bioclipse: ospjuth * r6387 /bioclipse2/trunk/plugins/net.b​ioclipse.core/build.properties: Added icons to build.properties.
08:16 CIA-49 bioclipse: ospjuth * r6388 /bioclipse2/trunk/plugins/net.​bioclipse.ui/build.properties: Added CSS for help to build.props.
08:16 egonw joined #bioclipse
08:39 jonalv A little script that now works in Bioclipse 2:
08:39 jonalv http://pastebin.com/m2b056dd9
08:41 CIA-49 bioclipse: goglepox * r6389 /bioclipse2/trunk/plugins/net.bioclipse.logg​er/src/net/bioclipse/logger/Activator.java:
08:41 CIA-49 bioclipse: writes logfile to users home directory on platforms other than macosx.
08:41 CIA-49 bioclipse: Got a better idea where it should be?
08:44 olas Gpox: it's fine with me
08:44 olas we could set a preference in Bioclipse in future versions with default to user.home
08:45 olas but for now it seems reasonable
08:46 * egonw thinks so too
08:48 Gpox logs to ~//Library/Logs/Bioclipse on mac
08:48 jonalv yey great success
08:49 jonalv Making all cdk methods run as jobs mean that getting childern on a huge file leading to OufOfMemory problem bnow longer crashes biocliupse
08:49 jonalv that was just a good side effect :)
08:50 egonw that means that getChildren() does not properly clean up resources?
08:51 jonalv egonw: I don't understand
08:51 jonalv what does clean up resources mean?
08:53 egonw remove pointers to the objects, so that the garbage collector can clean up tihngs
08:54 jonalv I will work on a few example js scripts for Biclipse 2 usign cdk then
08:54 olas great
08:56 CIA-49 bioclipse: ospjuth * r6390 /bioclipse2/trunk/plugins/net.bioclipse.jmol/s​rc/net/bioclipse/jmol/editors/JmolEditor.java: JmolEditor intances now gets name from the resource. Solves 2032536.
09:01 olas shk3: 2D coordinates is not working for me
09:01 shk3 egonw: the modelbuilder3d behaves strange
09:01 olas is I save to virtual file, it is still 3D
09:01 shk3 I get totally different fingerprints in the templateextractor and the builder
09:02 shk3 olas: will look at this
09:02 olas also, if I click in any text editor the option "create 2D coordinates" is there
09:02 olas it should not
09:02 shk3 tested with weired 2d coordinates and the cleanup works
09:02 shk3 but might be different with 3d
09:03 shk3 the visisbility is something which doesn't work for me
09:03 jonalv egonw: It must do some cleaning otherwsie Bioclipse wouldn't work after wards. After all it did throw an Out memory exception...
09:03 shk3 how do I restrict this to molecules?
09:03 shk3 also the validate cml should be restricted to xml/cml file extensions
09:03 shk3 but doesn't work for me
09:04 olas set it to use the cml/xml contenttype
09:04 olas that's what it's for
09:04 egonw shk3: check if the tExtractor and the builder actually use the same fingerprinter with the same settings...
09:04 egonw jonalv: ok
09:05 shk3 egonw: did so
09:05 shk3 seems to be the same
09:05 shk3 there must be some difference, but I can't find it
09:06 shk3 olas: could you have a look at the plugin.xml of net.bc.cml?
09:06 shk3 there is a visibleWhen in the menuContribution
09:06 shk3 but it complains about not finding the cml type
09:10 olas ok
09:10 olas cml will not be in 2.0-alpha
09:10 olas I'd be happy if you fixed the 2D coords first
09:10 shk3 working on this
09:10 shk3 but I have no idea how to do the visibility
09:11 olas I will delete your cml contenttype as we have one in core
09:11 olas ok?
09:11 olas shk3?
09:13 shk3 ok
09:13 shk3 if it is already there
09:13 shk3 btw, what do you mean with core?
09:13 shk3 there is no net.bc.core any longer, is there?
09:14 olas yes there is
09:14 olas but in core.ui I meant
09:14 olas working on this now
09:25 olas shk3: please fix bug JCP preferences
09:25 olas I commented on it
09:25 olas that is, 2033643
09:25 olas very important
09:29 CIA-49 bioclipse: shk3 * r6391 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui/src/net/bioclipse/cdk​/ui/handlers/Create2dHandler.java: also works with existing3d coordinates
09:31 CIA-49 bioclipse: shk3 * r6392 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): also works with existing3d coordinates
09:33 shk3 olas: two things to do with the 2d coordinates:
09:34 shk3 the menu visibility
09:34 shk3 and the file types
09:34 shk3 my manager method takes a string to indicate the file type (cml, mdl etc.)
09:34 shk3 is there/do we need a central definitions of these?
09:34 shk3 will look at the jcp preferences now
09:38 shk3 olas: you say "JCP prefs should be available from Bioclipse preferences"
09:38 shk3 I can't find them there
09:39 CIA-49 bioclipse: carl_masak * r6393 /bioclipse2/trunk/plugins/net.s​ourceforge.jseditor/plugin.xml: [jseditor] new, better run action
10:03 shk3 olas?
10:06 olas shk3: pong
10:06 olas any preferences for JCP should be in Bioclispe prefs
10:06 olas is that unclear?
10:06 olas we have a preferences dialog in Bioclipse with sections
10:06 olas plugins contribute preferencepages there
10:07 olas if JCP has preferences, this is what it should do.
10:07 olas you agree with me?
10:07 egonw agreed
10:07 olas (it was destined for shk3)
10:08 egonw for BC2.0, let's just assume the defaults?
10:08 olas sounds reasonable
10:08 egonw for the first alpha/RC at least?
10:08 olas yes
10:08 olas I just don't want any menu options that do not work
10:08 egonw I plan to do such pages for the CDK IO too
10:08 olas good
10:08 egonw right, those should be stripped
10:08 egonw btw: please take a sec to look at this unit test:
10:08 egonw http://cdk.pastebin.com/m7468f0c2
10:08 zarah egonw's link is also http://tinyurl.com/6oeqnt
10:08 olas bc2 will get nic efeatures when you start here, egonw
10:09 egonw olas: I hope so...
10:09 egonw otherwise we'll never become rich :)
10:09 olas haha
10:09 olas egonw: what to look for?
10:09 egonw please check the unit etst...
10:09 egonw that pastebine link I just posted
10:09 olas looking at it
10:09 olas doe sit pass?
10:10 olas for all OB  <-> CDK?
10:11 egonw yes
10:11 egonw no, not done that extensive testing :)
10:12 egonw but this test works :)
10:12 egonw anyway, perception is done by the CDK atom type matcher...
10:13 egonw which is quite solid
10:13 egonw I don't expect too much trouble...
10:13 egonw but it is nice to see that reflected in some stats, agreed
10:13 egonw anyway...
10:13 egonw a few more of these tests, and then I can merge with trunk
10:13 egonw pending Rajarshi's approval
10:23 shk3 olas: sorry for not answering
10:23 shk3 so the preferences are not yet in the bioclipse preferences?
10:23 shk3 this would need to be done?
11:22 olas shk3: yes
11:22 olas but not urgent
11:22 olas for the future, yes
11:22 olas today focus is on 2.0-alpha
11:22 olas shk3: please enumerate all cases when calculate2d action should be available
11:23 olas in context menu
11:26 shk3 net.bioclipse.cdk.ui.moleculeType ?
11:26 shk3 I would think this should be allright
11:27 shk3 the definition is in plugin.xml of net.bc.cdk.ui
11:29 egonw lunch, bbl
11:32 olas shk3: you misunderstand
11:32 olas shk3: if a molecule has 2d coordinates, it should not be available
11:32 olas hence cannot use that contenttype
11:32 olas IMO
11:33 olas but OK
11:33 olas for now I can settle with it
11:33 olas but still, the action is available when rich-click in texteditor.
11:33 olas not OK IMO
11:33 shk3 olas: sure?
11:34 shk3 why not regenerate 2d coordinates?
11:34 shk3 similar to cleanup in jcp
11:34 olas hmm
11:34 olas ok
11:35 olas then a dialog saying this would be good
11:35 shk3 with respect to the text editor:
11:35 shk3 i followed http://wiki.bioclipse.net/index.php​?title=How_to_add_menus_and_actions
11:35 zarah shk3's link is also http://tinyurl.com/55gl83
11:36 shk3 not sure how to restrict this to the navigator
12:05 * masak sets out to write http://wiki.bioclipse.net/index​.php?title=How_to_add_a_manager
12:07 egonw joined #bioclipse
12:08 egonw shk3: ping
12:08 egonw was just about to get to lunch when I saw your commit
12:08 egonw shk3: please revert that one
12:08 egonw I don't think the idea is to remove @pref from the JCP 2.3 application too, is it?
12:08 egonw instead, copy JCPGUI_stable.properties to JCPGUI_bioclipse.properties
12:08 egonw hack away in that copy, and have Bioclipse use JCPGUI_bioclipse.properties
12:09 egonw msg me, if you have questions and why and how
12:09 egonw olas: ping
12:09 egonw you broke CDK 1.0 btw...
12:09 shk3 a jcpgui-bioclipse.properties would need to be created, right?
12:09 shk3 me?
12:09 egonw you accidentally delete a whole lot of CDK 1.0 functionality
12:09 egonw shk3: yes
12:09 shk3 hm
12:09 egonw no, the broke CDK 1.0 was done by ola :)
12:10 shk3 ah
12:10 egonw bbl
12:10 egonw lunch time first
12:26 CIA-49 bioclipse: shk3 * r6394 /bioclipse2/trunk/plugins/net.bioclipse.​cdk10.jchempaint/src/net/bioclipse/cdk10​/jchempaint/ui/editor/MenuBarMaker.java: that's what it should be like
12:40 jonalv shk3: HAve you gotten my mail?
12:54 shk3 yes
12:55 shk3 so you did the release?
12:58 shk3 do you know how I can restrict a popup menu item to the resource view?
13:00 CIA-49 bioclipse: ospjuth * r6396 /bioclipse2/trunk/plugins/net.​bioclipse.ui/icons/sample.gif: Removed sample.gif since of no use to us.
13:03 CIA-49 bioclipse: ospjuth * r6395 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Commented out Import File as already existing.
13:04 CIA-49 bioclipse: carl_masak * r6397 /bioclipse2/trunk/plugins/net.bi​oclipse.scripting.ui/plugin.xml: [net.bioclipse.scripting.ui/plugin.xml] removed groovy and ruby for now
13:04 CIA-49 bioclipse: carl_masak * r6398 /bioclipse2/trunk/plugins/net.bioclipse.​ui/src/net/bioclipse/ui/Activator.java: [net.bioclipse.ui] whitespace
13:05 CIA-49 bioclipse: shk3 * r6399 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: added an icon
13:16 CIA-49 bioclipse: ospjuth * r6400 /bioclipse2/trunk/plugins/net.b​ioclipse.data.sampledata/data/ (8 files in 5 dirs): Removed unsupported resources and added sdf with 3D coords.
13:27 CIA-49 bioclipse: ospjuth * r6401 /bioclipse2/trunk/plugins/ne​t.bioclipse.data.sampledata/ (4 files in 3 dirs): Updated plugin.xml to reflect new data to install.
13:31 CIA-49 bioclipse: carl_masak * r6402 /bioclipse2/trunk/plugins/net.source​forge.jseditor/icons/run_script.gif: [net.sourceforge.jseditor] added icons/run_script.gif
13:33 CIA-49 bioclipse: ospjuth * r6403 /bioclipse2/trunk/plugins/net.bioclipse.jmol​/src/net/bioclipse/jmol/views/JmolView.java: Fix to display mols in Jmol when selected in SDFEditor with 3D coords SDFile.
13:57 CIA-49 bioclipse: jonalv * r6404 /bioclipse2/trunk/plugins/ne​t.bioclipse.data.sampledata/ (3 files in 2 dirs): added two js example scripts and fixed spelling error in plugin.xml
14:11 CIA-49 bioclipse: carl_masak * r6405 /bioclipse2/trunk/plugins/n​et.bioclipse.ui.business/: Initial import.
14:12 CIA-49 bioclipse: carl_masak * r6406 /bioclipse2/trunk/plugins/​net.bioclipse.ui.business/ (17 files in 8 dirs): Initial import.
14:17 CIA-49 bioclipse: carl_masak * r6407 /bioclipse2/trunk/plugins/net.bioc​lipse.ui.business/META-INF/spring/ (. context.xml): [net.bioclipse.ui.business] added META-INF/spring/context.xml
14:23 egonw joined #bioclipse
14:25 shk3 does anybody understand the menu stuff on popup:org.eclipse.ui.popup
14:25 shk3 wrong
14:25 shk3 should be
14:25 shk3 http://wiki.bioclipse.net/index.php?tit​le=How_to_add_menus_and_actions#Create_​a_popup_menu_item_that_uses_the_Command
14:25 zarah shk3's link is also http://tinyurl.com/55gl83
14:26 CIA-49 bioclipse: ospjuth * r6408 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (15 files in 3 dirs): Added a new intro section: "What can I do with Bioclipse 2.0-alpha".
14:31 shk3 olas: could you help me with the menu stuff?
14:35 CIA-49 bioclipse: carl_masak * r6409 /bioclipse2/trunk/plugins/net.bioclipse.​ui/src/net/bioclipse/ui/Activator.java: [net.bioclipse.ui.Activator] ws
14:40 CIA-49 bioclipse: carl_masak * r6410 /bioclipse2/trunk/plugins/net.bioclipse.sc​ripting.ui/src/net/bioclipse/scripting/ui/ (Activator.java business/JsConsoleManagerFactory.java): [net.bioclispe.scripting.ui] comment fixes
14:40 olas shk3: sorry, no time for that now
14:40 olas too close to release
14:41 shk3 hm ok, then you have to decide if you want it the release or not
14:42 olas I will test and decide
14:42 olas sry, this is really too late
14:43 olas but we'll send out a patch next week
14:43 olas that way we can test that procedure too :-)
14:43 olas we are running final tests now before build
14:44 olas I have written getting sterted...
14:44 olas and release notes
14:44 olas it's close now... :-)
14:44 olas ETA: 30-60 mins
14:44 egonw don't forget the tag!
14:45 olas will not
14:45 CIA-49 bioclipse: carl_masak * r6411 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/IUIManager.java:
14:45 CIA-49 bioclipse: [net.bioclipse.ui.business.IUIManager] added 'params' parameter to
14:45 CIA-49 bioclipse: @PublishedMethod annotations
14:50 CIA-49 bioclipse: jonalv * r6412 /bioclipse2/trunk/features/net.​bioclipse-feature/feature.xml: added net.bioclipse.ui.business to bioclipse feature
14:52 CIA-49 bioclipse: ospjuth * r6413 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (3 files in 3 dirs): Updated intro pages.
15:02 CIA-49 bioclipse: ospjuth * r6414 /bioclipse2/trunk/plugins/​net.bioclipse.ui/content/ (images/jseditor.png whatcanIdo.xhtml): Added jseditor to intro pages.
15:14 CIA-49 bioclipse: carl_masak * r6415 /bioclipse2/trunk/plugins/ (9 files in 5 dirs):
15:14 CIA-49 bioclipse: [net.bioclipse.scripting]
15:14 CIA-49 bioclipse: [net.bioclipse.scripting.ui]
15:14 CIA-49 bioclipse: Ruby and Groovy support removed altogether, pending the alpha release
15:20 olas masak++
15:20 masak had to be done, it seems
15:28 CIA-49 bioclipse: ospjuth * r6416 /bioclipse2/trunk/plugins/​net.bioclipse.ui.business/ (2 files in 2 dirs): Implemented OPEN and DELETE. Currently, delete fails with Javascript trace. masak?
15:28 masak will look at it
15:37 CIA-49 bioclipse: carl_masak * r6417 /bioclipse2/trunk/plugins/net.bioclipse.u​i.business/src/net/bioclipse/ui/business/ (IUIManager.java UIManager.java):
15:37 CIA-49 bioclipse: [IUIManager,UIManager]
15:37 CIA-49 bioclipse: * renamed s/delete/remove/ due to js keyword conflict
16:02 CIA-49 bioclipse: ospjuth * r6418 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.jchempaint/src/net/bioclipse/cdk10/j​chempaint/views/Java2DRendererView.java: Removed debug out.
16:18 CIA-49 bioclipse: ospjuth * r6419 /bioclipse2/trunk/ (25 files in 24 dirs): Set version to 2.0.0.alpha01.
16:26 olas we are close now...
16:31 egonw wait
16:31 egonw please reversion to:
16:32 egonw crap...
16:32 egonw let me think
16:32 egonw 2.0.0 must be larger than 2.0.0.bla
16:32 egonw never mind
16:32 egonw no idea how to do that
16:32 egonw wait, maybe I do:
16:32 egonw 2.0.0.0alpha01
16:33 egonw and later for actual 2.0.0.200808xx
16:33 egonw then the second is garanteed alphanumerically larger than the former
16:39 CIA-49 bioclipse: ospjuth * r6420 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: Commented out 2Daction and CDK navigatorcontent in Navigator.
16:40 masak egonw: sounds sane to me
16:41 jonalv olas: Windows version seem ok to me
16:41 masak using just dates as release numbers solves a whole lot of problems, btw. not saying that we should, just sayin'
16:41 egonw :)
16:42 egonw yeah, the eclipse people seem to be using that set up too...
16:42 egonw anyway...
16:42 egonw this alphanumerical order is actually immensly important for packagers
16:42 egonw to is useful to get used to it
16:44 olas noted
16:44 olas in next release
16:44 olas not now
16:44 olas too late
16:45 egonw ok, looking forward to download the alpha tonite, and seeing the tag commit ;)
16:45 egonw dinner time, bbl
16:45 egonw bye
16:51 CIA-49 bioclipse: carl_masak * r6421 /bioclipse2/trunk/plugins/net.bioc​lipse.ui/content/whatcanIdo.xhtml:
16:51 CIA-49 bioclipse: [whatcanido.xhtml]
16:51 CIA-49 bioclipse: * validated
16:51 CIA-49 bioclipse: * reworded
16:51 CIA-49 bioclipse: * fixed some typos
16:52 CIA-49 bioclipse: ospjuth * r6422 /bioclipse2/trunk/features/ (4 files in 2 dirs): Updated license and copyright.
16:54 CIA-49 bioclipse: ospjuth * r6423 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Version.
17:00 CIA-49 bioclipse: shk3 * r6424 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum/src/net/bioclipse/spectrum/dialogs/ (. AddMetadataDialog.java MappingFileCreationDialog.java): working on the spectrum editor
17:03 CIA-49 bioclipse: shk3 * r6425 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum/src/net/bioclipse/spectrum/editor/ (7 files): working on the spectrum editor
17:04 CIA-49 bioclipse: shk3 * r6426 /bioclipse2/trunk/plugins/net.bioclips​e.spectrum/src/net/bioclipse/spectrum/ (4 files in 3 dirs): working on the spectrum editor
17:05 CIA-49 bioclipse: shk3 * r6427 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (4 files in 3 dirs): working on the spectrum editor
17:07 CIA-49 bioclipse: carl_masak * r6428 /bioclipse2/tags/2.0-alpha-01/: This is Bioclipse 2.0.0-alpha-01.
17:08 masak three cheers for bioclipse! :)
17:09 CIA-49 bioclipse: carl_masak * r6429 /bot/trunk/zarah.pl: [zarah] "kick in the fork", requested by egonw++, added "mek" nick
17:13 masak @reload
17:13 CIA-49 bioclipse: carl_masak * r6430 /bot/trunk/zarah.pl: [zarah] implemented festive cheering functionality
17:13 masak @update
17:13 zarah joined #bioclipse
17:13 masak three cheers for bioclipse! :)
17:13 zarah hooray! hooray! hooray! :)
17:14 masak :)
17:14 masak zarah++
17:15 CIA-49 bioclipse: carl_masak * r6431 /bot/trunk/zarah.pl: [zarah] added "@reload"
17:35 olas WEEHOOOOOW!!!!
17:35 olas it's out
17:35 olas hope it works :-)
17:35 olas Now it's friday
17:37 olas bye
17:37 olas left #bioclipse
17:47 shk3 congratulations
19:07 edrin joined #bioclipse
19:16 egonw joined #bioclipse
19:19 egonw hi zarah
19:19 egonw zarah: do got no news for me?
19:19 zarah egonw: I did not understand that
19:19 Topic for #bioclipseis now An open source workbench for chemo- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 alpha released! See http://bioclipse.blogspot.com/
20:40 rojasm joined #bioclipse
23:21 edrin joined #bioclipse

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