Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-07

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All times shown according to UTC.

Time Nick Message
04:35 masak joined #bioclipse
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06:14 Gpox joined #bioclipse
06:49 masak joined #bioclipse
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07:53 jonalv joined #bioclipse
07:55 jonalv moin
07:55 zarah hi jonalv
08:09 olas joined #bioclipse
08:10 * olas hates bike-thieves
08:23 egonw joined #bioclipse
08:27 malick joined #bioclipse
08:42 shk3 joined #bioclipse
09:46 CIA-49 bioclipse: goglepox * r6499 /bioclipse2/trunk/plugins/net.bioclips​e.scripting.ui/src/net/bioclipse/scrip​ting/ui/views/ActionHistoryView.java: Added scrollbar. Fixes 2041401
09:56 CIA-49 bioclipse: ospjuth * r6500 /bioclipse2/trunk/plugins/net.bioclip​se.ui/src/net/bioclipse/ui/contenttyp​es/CmlFileCoordinatesDescriber.java: changed type to dimension in deprecated contenttype.
09:57 CIA-49 bioclipse: ospjuth * r6501 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (6 files in 2 dirs): Fixed preferences intialization for update sites. Wiki paga available at http://wiki.bioclipse.net/index.php​?title=How_to_work_with_preferences. Closes 2040139.
09:57 zarah CIA-49's link is also http://tinyurl.com/5ps4sc
10:12 CIA-49 bioclipse: ospjuth * r6502 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Updated for renamed class to initialize prefs.
10:18 EskilA joined #bioclipse
10:53 CIA-49 bioclipse: shk3 * r6503 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum/src/ (6 files in 2 dirs): spectrum editor is roughly working
11:07 olas shk3: roughly? :-)
11:12 shk3 well, lots of things to tweak
11:12 shk3 but the open-change-save cycle works
11:12 shk3 I saw that the molecule content types are all in net.bioclipse.ui
11:12 shk3 are we putting all contenttypes in there?
11:15 olas shk3: no
11:15 olas just the ones that are global to many plugins
11:15 olas and sinc eUI is the (currently) only common dependency for all utilizing these, it seemed the only choice
11:16 shk3 hm, so where to put the cml-spectrum-type?
11:16 shk3 spectrum plugin?
11:16 olas in spectrum
11:16 shk3 ok
11:16 olas it is not relevant to most other plugins
11:16 olas but CML definitely is
11:16 olas if we add a dep to CML plugin, cml contenttype could be there
11:17 olas but currently we donät use CML-plugin in Bioclipse alpha
11:18 egonw joined #bioclipse
11:21 malick joined #bioclipse
11:33 shk3 does anybody know how to bind an editor to multiple content types?
11:43 olas look at JCP
11:43 olas it is bound to cml and mdl
11:44 olas just add 2 bindings
12:15 edrin joined #bioclipse
12:16 olas hi edrin
12:16 olas how are things going with XMPP services?
12:17 olas any outline for me?
12:18 jonalv I hate KTable!
12:20 edrin hi ola, will be available in 15 minutes
12:24 masak jonalv: what did KTable ever do to you?
12:24 jonalv not work
12:24 masak ah, a sin of omission :)
12:25 jonalv java.lang.UnsupportedClassVersionError: Bad version number in .class file
12:25 jonalv Why can't it say which class file?
12:25 masak love those bad numbers
12:26 jonalv it doesn't even say which class file only that some class file has a bad version... :(
12:26 jonalv How am I to know what?
12:29 masak remove the class files one by one, until the error message disappears :P
12:31 jonalv right..
12:38 shk3 I am trying to implement a describer following the ones in org.bc.ui
12:38 shk3 they extend TextContentDescriber
12:38 shk3 when I do this, I get:
12:38 shk3 Discouraged access: The type TextContentDescriber is not accessible due to restriction on required library /opt/eclipse/plugins/org.eclipse.cor​e.contenttype_3.3.0.v20080604-1400.j
12:38 shk3 any idea what this means and/or what to do?
12:52 olas have you imported the plugin in manifest?
12:52 olas or you might need to import other plugins to the plugin
12:59 jonalv Brunn is now running in Bioclispe 2! What remains is some cleanup. All jar files are double for the moment and Brunn should use the jar files shipped by Bioclipse 2! :)
13:00 masak jonalv++
13:03 shk3 can't find anything to import
13:04 shk3 there is no org.eclipse.core.contenttype library
13:04 shk3 if I do add in dependencies
13:06 shk3 hm,  I copied everything from net.bc.ui
13:06 shk3 and still complaining
13:07 shk3 it doesn't say it can't find it, but there are restrictions on the library
13:07 shk3 I don't know what his means
13:08 malick joined #bioclipse
13:10 olas jonalv++
13:10 masak shk3: it means that the library or plugin in question doesn't export what you're trying to import
13:11 olas "Thank go it's wednesday"-coffee in 5 mins for the Uppsala Team
13:11 jonalv w00t
13:11 jonalv lol
13:11 olas go=god, not Gene Ontology
13:11 masak yay!
13:11 masak thank Gene Ontology for that!
13:11 olas but beware
13:11 olas the cake I made yesterday is not superb...
13:12 jonalv that's good it wednesday! (_or_?)
13:12 olas a lemon cake
13:12 masak jonalv: that's good it grammar?
13:13 jonalv masak: I actually thought I wrote thanks good it\s wedensday :)
13:13 jonalv gah
13:13 masak zarah: thank jonalv
13:13 zarah jonalv: masak says thank you
13:13 jonalv zarah, masak thanks yourselves :)
13:13 zarah jonalv: eh... wha'?
13:14 jonalv zarah: never mind
13:14 zarah jonalv: please rephrase or stop trying to be witty :)
13:14 masak jonalv: eh... wha'?
13:14 jonalv masak: never mind
13:14 masak jonalv: please rephrase or stop trying to be witty :)
13:14 jonalv masak: oh shut up
13:15 shk3 masak: but it works in ui
13:16 masak shk3: yes. strange.
13:16 masak @update
13:16 CIA-49 bioclipse: carl_masak * r6504 /bot/trunk/zarah.pl: [zarah] replies appropriately to "never mind"
13:16 zarah joined #bioclipse
13:17 masak zarah: never mind.
13:17 zarah masak: please rephrase or stop trying to be witty :)
13:17 * zarah never minds
13:18 masak @update
13:18 CIA-49 bioclipse: carl_masak * r6505 /bot/trunk/zarah.pl: [zarah] slight "never mind" fix
13:18 zarah joined #bioclipse
13:47 masak zarah: never mind
13:47 * zarah never minds
14:14 CIA-49 bioclipse: carl_masak * r6506 /bioclipse2/trunk/plugins/net.bioc​lipse.biojava.ui/src/net/bioclipse​/biojava/ui/editors/Aligner.java:
14:14 CIA-49 bioclipse: [Aligner] consensus sequence is now drawn last.
14:14 CIA-49 bioclipse: this solves a few graphical problems.
14:17 edrin sorry olas, I am currently completely spamed with stuff here
14:21 masak stuff--
14:21 CIA-49 bioclipse: ospjuth * r6507 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (4 files in 3 dirs): Added new icons for JCP outline.
14:22 CIA-49 bioclipse: ospjuth * r6508 /bioclipse2/trunk/plugins/net.bioc​lipse.logger/META-INF/MANIFEST.MF: Updated version.
14:47 CIA-49 bioclipse: jonalv * r6509 /bioclipse2/trunk/features/net.​biclipse.usermanager-feature/: Initial import of usermanager feature
14:47 CIA-49 bioclipse: jonalv * r6510 /bioclipse2/trunk/features/net​.biclipse.usermanager-feature/ (.project build.properties feature.xml): Initial import of usermanager feature
15:05 malick left #bioclipse
15:09 shk3 olas: you have a minute?
15:10 shk3 or jonalv?
15:15 jonalv shk3: maybe :)
15:20 shk3 ok
15:21 shk3 it's about the 2d coordinates
15:21 shk3 I used Commands (the new way) as explained in the wiki.
15:21 shk3 but I can't find out how to restrict the menu item to molecule popups.
15:21 shk3 is anybody willing to help with that?
15:22 jonalv I haven't done that...
15:22 shk3 if not, I would go for  Actions (the old way)
15:22 jonalv olas: will be back later, maybe he can help you then... :)
15:23 shk3 ok
15:29 CIA-49 bioclipse: carl_masak * r6511 /bioclipse2/trunk/plugins/net.bi​oclipse.cdk10.jchempaint/icons/ (14 files): [n.b.c10.jcp] added icons for atom types and bonds. deleted old icons
15:33 masak @tell olas r6511 contains the new atom and bond icons.
15:33 zarah Consider it noted.
15:53 edrin olas: available?
16:09 edrin olas?
16:09 edrin ping
16:09 edrin test
16:22 egonw edrin: yes, we hear you :)
16:23 edrin sorry, i was away
16:24 edrin very busy these days, got a double position in diagnostics this month and will run around the whole day. it's over in September again
16:24 shk3 was there a major redesign at sourceforge?
16:24 edrin there is going to be one i think
16:25 shk3 the project pages loook ... well... strange
16:25 shk3 seems like it's done
16:25 edrin egonw: good thing is
16:26 edrin the work of the last year got accepted!
16:26 edrin finally...
16:26 egonw congrats!
16:26 edrin :)
16:26 edrin thanks
16:26 edrin today I got the acc...
16:27 edrin on the other hand in pubmed a new article appeared today, where they do the same stuff we are currently working on
16:27 egonw yes, that happens
16:27 egonw some progress is just in the air
16:31 edrin eh
16:32 edrin do you mean something specific?
16:33 edrin egonw?
16:33 egonw no
16:34 egonw just that some research questions are just in the air...
16:34 egonw and then you can have multiple groups do the same thing
16:40 edrin my current article was accepted in eukaryotic cell
16:42 edrin want you to see a preview?
16:43 egonw not sure if I will be able to read it :)
16:43 edrin there are interesting pictures :)
16:46 edrin anyway, may next published aim is the xmpp articel
16:47 egonw that sounds excellent
16:50 edrin yea
16:51 edrin :)
16:51 edrin I hope you like this
16:52 olas hi edrin, hi egonw
16:52 zarah olas: You have new messages. Write '@messages' to read them.
16:52 olas @msg
16:52 zarah olas: masak said r6511 contains the new atom and bond icons.
16:54 edrin hey olas
16:55 olas brb in 5 mins
16:56 shk3 hey olas
17:12 edrin olas: sorry, i have to leave now
17:12 edrin cu tomorrow, i will do xmpp this weekend
17:13 olas edrin: ok
17:14 olas I have tons of otehr stuff to do so no worries :-)
17:14 edrin :(
17:14 edrin cu
17:14 edrin left #bioclipse
17:15 shk3 olas: i have something problem I want to get rid of
17:15 shk3 I need a minute of you time.
17:16 olas shk3: sure
17:16 olas what is it?
17:16 shk3 [16:21] <shk3> it's about the 2d coordinates
17:16 shk3 [16:21] <shk3> I used Commands (the new way) as explained in the wiki.
17:16 shk3 [16:21] <shk3> but I can't find out how to restrict the menu item to molecule popups.
17:16 shk3 do you have any idea?
17:17 shk3 if not, i will do it with an action
17:17 olas I wanted to look into this but have not had time
17:17 shk3 (the old way)
17:17 olas I think I created a bug and assigned to me
17:17 shk3 ah
17:17 shk3 so i wait if you can find something
17:17 olas well
17:18 olas actually I assigned that bug to gilleain...
17:18 olas but I promise to look at it tomorrow
17:18 olas (please remind me)
17:18 shk3 gilleain hasn't been here today
17:18 olas it is a key feature to have actions/commands sorted out
17:18 shk3 yes
17:18 olas and I will try it tomorrow
17:18 shk3 is there any advantage over actions?
17:18 olas today I made preferences :-)
17:18 olas yes
17:19 olas more in xml
17:19 olas more configurable
17:19 olas more reusable
17:19 olas actually, I think the more specified in XML the better
17:19 olas the old JMOL actions (there were >30) were replaced by 1 action and a ne wCommand
17:20 egonw olas, shk3: this might be related:
17:20 egonw http://beb4ch.com/2008/08/04/e​clipse-rcp-visiblewhen-thingy/
17:20 olas so REALLY good in that case
17:20 zarah egonw's link is also http://tinyurl.com/5ptxte
17:20 olas yes
17:20 olas that's what shk3: didnät get to work
17:20 olas didn't
17:20 egonw ack
17:21 olas contenttypes/commands/actions are tricky
17:21 olas but VERY powerful
17:21 olas and if we sort this out and write a wiki page, things will be smoother
17:21 olas but as it's new ground it takes a while
17:21 olas but we're getting there!
17:22 olas shk3: please push gilleain to updgrade the CML contenttypes to not read full file
17:22 olas that is important
17:22 olas and as soon as we get the create2D action in place, we can add more actions :-)
17:22 olas Gpox is working hard on JCP-SWT
17:23 olas he's well on the way
17:23 olas egonw: looking forward to when you come here and give him more input/directions
17:23 egonw yes, me too...
17:23 egonw it's really soon now, but still so far away
17:24 egonw btw, rguha gave feedback on the sybyl atom type patch
17:24 olas I did see your OWL-atom types patch was accepted
17:24 egonw one was nasty
17:24 olas :-)
17:24 olas which one?
17:24 egonw the one that said, please stop using the old CDK atom type list...
17:24 egonw so, I did...
17:24 egonw but that got about 500 regressions :)
17:24 egonw so, fixing those now
17:24 olas aah
17:24 egonw anyway... it's good
17:24 egonw already found a bug in the old list
17:24 olas yes
17:24 egonw so effecting the old atom typing code...
17:25 olas and after this, it will be testing aginst OB?
17:25 olas I think that is important
17:25 egonw no, after that I need to bang out a few atom type perception bugs first
17:25 egonw and then OB :)
17:25 shk3 great that jcp is making progress
17:25 shk3 I didn't do anything, I must admit
17:25 olas yes, Gpox is really good
17:25 shk3 too much to do
17:25 olas it's ok
17:25 olas you have other stuff to worry about as well
17:26 egonw I haven't had time for JCP clean up stuff too...
17:26 egonw the todo list is on a yellow postit attached to my laptop :)
17:26 shk3 I saw this visibleWhen, but I couldn't sort out how it works
17:26 egonw but does not help
17:26 shk3 it's complicated
17:26 olas I think Gpox has learnd a lot about SWT and editing
17:27 egonw Gpox++
17:27 olas looks like he's making progress at least :-)
17:27 shk3 btw: from egon's link "There are other variables you could use. The full list is avalilabe if you check the source code of the class org.eclipse.ui.workbench.IScources."
17:27 shk3 great documentation
17:27 egonw ah, I'm happy to hear that it is useful
17:28 egonw ok, I think that last commit fixes most of the 500 regressions...
17:28 egonw PLANAR3 hybridization was not read from the OWL yet :(
17:28 egonw took me an hour to discover that :(
17:28 egonw ok, got to catch the train now...
17:28 egonw bbl
17:28 egonw bye
17:45 olas karma olas
17:45 zarah olas has a karma of 1
17:45 olas left #bioclipse
17:45 CIA-49 bioclipse: ospjuth * r6512 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (6 files in 4 dirs): Ask if users want's to update on startup if there are updates available. Checkbox to remember and not ask again.
17:49 olas joined #bioclipse
17:57 olas @tell masak masak++ for icons!
17:57 zarah Consider it noted.
17:58 olas @tell jonalv I think you have a dependency in usermanager plugin to another plugin in the brunn feature, while the brunn feature depends on the usermanager feature
17:58 zarah Consider it noted.
18:10 olas @tell masak Feedback on icons: IMO carbon is too black compared to red/blue (who look a bit too bright IMO). It is also hard to distinguish between single-double-tripple bonds due to too thin lines (more focus on bonds than atoms in that case). But a very good start!
18:10 zarah Consider it noted.
18:13 olas karma masak
18:13 zarah masak has a karma of 2
18:13 CIA-49 bioclipse: ospjuth * r6513 /bioclipse2/trunk/plugins/net.bioclipse.cdk​10.jchempaint/src/net/bioclipse/cdk10/jchem​paint/outline/StructureLabelProvider.java: Updated for JCP to use new icons (gif -> png) by masak++.
18:14 olas karma masak
18:14 zarah masak has a karma of 3
18:28 olas bye for today
18:28 olas left #bioclipse
18:28 CIA-49 bioclipse: ospjuth * r6514 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (about.ini about.mappings about.properties): Branded Bioclipse feature.
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