Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-13

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All times shown according to UTC.

Time Nick Message
06:28 olass joined #bioclipse
07:45 egonw joined #bioclipse
07:48 masak joined #bioclipse
07:49 masak OH HAI
07:49 zarah hi masak
07:52 masak hi zarah
07:58 egonw moin
07:58 zarah saluton egonw
08:06 olass moin egon
08:06 olass moin masak
08:06 olass moin zarah
08:07 masak moin olass
08:14 egonw masak: rednael now does multiple channels, with each one or more RSS feeds...
08:14 egonw masak: so it is ready for #bioclipse
08:14 masak egonw: kudos. go right ahead.
08:51 * egonw is going offline for some time
10:01 CIA-73 bioclipse: ospjuth * r9755 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (4 files in 3 dirs): Worked on bug #869: Added MolTableDescriber for associating BioList with opening in MolTable.
10:01 zarah bug #869 | http://tinyurl.com/d8y258
10:02 CIA-73 bioclipse: ospjuth * r9756 /bioclipse2/trunk/plugins/net.bioclipse​.ui.business/src/net/bioclipse/ui/busin​ess/describer/IBioObjectDescriber.java: Added possibility for IBioObjectDescribers to throw IBioclipseException.
10:02 masak olass: I'm going to look at your tickets later today.
10:02 olass thanks
10:02 * masak teleports home to bake lunch
11:01 masak joined #bioclipse
12:23 CIA-73 bioclipse: ospjuth * r9757 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Added shortname 'jcp' and '2d' to JCPeditor.
12:39 masak joined #bioclipse
13:14 CIA-73 bioclipse: ospjuth * r9758 /bioclipse2/trunk/plugins/net.bioclipse​.data/data/Javascripts/jmolExample.js: Added Jmol to echo Mass as calculated by cdk.
13:17 CIA-73 bioclipse: ospjuth * r9759 /bioclipse2/trunk/plugins/net.bioclipse​.data/data/Javascripts/jmolExample.js: Added comments to jmolExample.
13:18 CIA-73 bioclipse: ospjuth * r9760 /bioclipse2/trunk/plugins/net.b​ioclipse.data/data/Javascripts/ (extractsmiles.js extractsmilesAndMass.js): Added documentation for JS samples in sample data.
13:23 masak joined #bioclipse
13:39 olass hi masak
13:39 masak oh hai olass
13:39 olass are you looking through your bugs?
13:40 masak you can tell? :)
13:40 * olass is looking fwd to comments
13:40 olass and fixes too :)
13:40 * masak is going through bug mails and commit mails
13:40 * olass is working on his scripting presentation for the CDK workshop
13:40 olass scripting is nice!
13:40 masak olass: those are interesting problems, but I might have to hit you with a priority list tomorrow. we'll see.
13:41 olass very nice
13:41 olass masak: right
13:41 olass was expecting that
13:41 olass I'll be in UA tomorrow
13:41 masak I'm leaving on Wednesday.
13:41 olass so we can chat IRL
13:41 olass ok
13:41 masak good.
13:45 masak some are easy; those I will fix today.
13:45 CIA-73 bioclipse: ospjuth * r9761 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Changed implementation to BioList instead of ArrayList. See bug #880.
13:45 zarah bug #880 | http://tinyurl.com/c75es3
13:47 CIA-73 bioclipse: ospjuth * r9762 /bioclipse2/trunk/plugins/net.bioclipse​.data/data/Javascripts/downloadPDB.js: Added a script to download and visualize a PDB.
14:10 masak olass: wow, you've really been active submitting bugs...
14:10 olass :)
14:10 olass yes..
14:10 olass it's important
14:10 masak I try to reward you with as early and honest feedback as possible. :)
14:10 olass and more is up ;)
14:10 olass masak: thanks
14:10 masak aye, I just saw one more coming down the pipe. :)
14:10 olass most are minor bugs
14:11 * masak is thankful for that
14:11 olass hmm
14:11 olass about the R bug...
14:11 olass no
14:11 olass lets take it all tomorrow
14:11 masak yes. please.
14:11 olass (or if you comment in them)
14:11 olass :)
14:15 olass masak: about 871, it does not add parenthesis for cdk.fromSMILES
14:15 olass I commented in that bug
14:15 olass just FYI :)
14:15 masak olass: I noticed that too.
14:15 olass good
14:15 masak olass: it works for all methods in the js namespace, but not for those in the cdk namespace.
14:16 masak I don't know why -- well worth checking out.
14:16 olass it seems to work for jcp namespace too
14:16 olass jcp.setZoom for example
14:16 olass adds (
14:16 masak something wrong with the cdk namespace...
14:17 masak will investigate.
14:26 masak git++
14:26 CIA-73 bioclipse: carl_masak * r9763 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
14:26 CIA-73 bioclipse: [ScriptingConsoleView] special keys also move focus
14:26 CIA-73 bioclipse: The output text box previously didn't respond to special keys such as the
14:26 CIA-73 bioclipse: up/down arrows and Enter. Now it does -- it transfers control and focus to
14:26 CIA-73 bioclipse: the input box just as normal keys do.
14:26 CIA-73 bioclipse: Fixes bug #872.
14:27 zarah bug #872 | http://tinyurl.com/d4m7tq
14:39 masak Java's String.split method is weird.
14:39 CIA-73 bioclipse: ospjuth * r9764 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/IUIManager.java: Fixed inconsistent inline help, which had description in parameters annotation.
14:46 CIA-73 bioclipse: ospjuth * r9765 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/IUIManager.java: Small type in BioObject
14:47 CIA-73 bioclipse: carl_masak * r9766 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
14:47 CIA-73 bioclipse: [ScriptingConsoleView] now doesn't break R output
14:47 CIA-73 bioclipse: In absence of R output, the ScriptingConsoleView had regressed to not caring
14:47 CIA-73 bioclipse: for output which might not have a final newline. Fixed that, and learned a
14:47 CIA-73 bioclipse: bit about Java's String.split() in the process.
14:47 CIA-73 bioclipse: Fixes bug #857.
14:47 zarah bug #857 | http://tinyurl.com/cdjdrh
14:52 masak git++
14:53 CIA-73 bioclipse: carl_masak * r9767 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
14:53 CIA-73 bioclipse: [JsConsoleView] improved 'help' usage message
14:53 CIA-73 bioclipse: Whereas previously it gave two of its possible usages, it now gives all three.
14:53 CIA-73 bioclipse: Fixes bug #847.
14:53 zarah bug #847 | http://tinyurl.com/dmjk4n
15:01 * masak feels very productive today
15:02 CIA-73 bioclipse: ospjuth * r9768 /bioclipse2/trunk/plugins/net.bioclips​e.balloon.business/src/net/bioclipse/b​alloon/business/IBalloonManager.java: Cleaned up annotations and javadoc for balloon
15:05 olass masak: around?
15:05 masak olass: and about.
15:05 olass the focus lost bug is very iritating
15:06 masak olass: did you read my comments on that ticket?
15:06 olass nope
15:06 olass will do now
15:06 masak please do.
15:07 olass done
15:07 olass I see
15:07 olass however
15:08 olass see my comment
15:08 olass bug 870
15:08 olass bug #870
15:08 olass zarah?
15:08 olass @ping
15:08 zarah olass: pong
15:08 olass @bug 870
15:08 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=870
15:08 olass masak: commented
15:09 * masak looks
15:10 masak olass: no, you don't understand...
15:10 masak there is no appropriate place to do this.
15:10 masak not in the manager, not somewhere else.
15:11 olass not on a case by case basis?
15:11 olass if I want top enforce it?
15:11 olass to
15:11 masak olass: no, the problem... did you read my comment?
15:11 olass mom
15:12 olass a new comment?
15:12 masak no.
15:12 masak hm, actually...
15:12 masak maybe in the New World Order this can actually be solved...
15:12 masak I need to ask jonalv++.
15:12 olass ok
15:13 olass let's do it tomorrow
15:13 masak if the manager code knows it's been called from the console, we're fine.
15:13 masak but I don't know if we do.
15:13 olass ok
15:59 CIA-73 bioclipse: ospjuth * r9769 /bioclipse2/trunk/plugins/net.bioclipse.qsar/sr​c/net/bioclipse/qsar/business/QsarManager.java: Catch all exceptions when parsing resources.
16:56 CIA-73 bioclipse: ospjuth * r9770 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar/src/net/bioclipse/qsar/​descriptor/IDescriptorResult.java: Made some fields public to access values and labels of descriptorresults.
16:56 CIA-73 bioclipse: ospjuth * r9771 /bioclipse2/trunk/plugins/net.bioclipse.qsar/src​/net/bioclipse/qsar/business/IQsarManager.java: Added manager documentation for publishing help to JS.
16:57 CIA-73 bioclipse: ospjuth * r9772 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar/src/net/bioclipse/qsar/​descriptor/IDescriptorResult.java: Made error field public to access from descriptorresults.
16:58 CIA-73 bioclipse: ospjuth * r9773 /bioclipse2/trunk/plugins/net.biocl​ipse.data/data/Javascripts/qsar.js: Added a QSAR sample script
16:59 CIA-73 bioclipse: ospjuth * r9774 /bioclipse2/trunk/plugins/net.bioclips​e.data/data/Javascripts/jcpcustom.js: Added a sample script to demonstrate JCP scripting
20:37 CIA-73 bioclipse: ospjuth * r9775 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (DescriptorsPage.java ResponsesPage.java): Removed old SelectionProviderDelegate.

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