Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-13

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All times shown according to UTC.

Time Nick Message
05:37 ilogger2_ joined #bioclipse
08:00 Gpox joined #bioclipse
08:09 masak joined #bioclipse
08:18 CIA-55 bioclipse: egonw * r9283 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Added unit test for bug #691
08:18 zarah bug #691 | http://tinyurl.com/cd6q6j
08:20 ilogger2 joined #bioclipse
08:54 olass joined #bioclipse
08:55 olass moin
08:55 zarah saluton olass
08:55 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
08:55 olass @msg
08:55 zarah olass: 20 h 12 m 14 s ago, masak said http://en.wikipedia.org/wiki/Scrum_(development)
08:55 masak saluton olas
08:55 olass hola masak
08:55 olass masak++ for the link
08:56 masak I'll get back to you when I've read the book.
08:56 olass masak: when was the last time you had a toffifee?
08:56 masak Scrum seems nice. especially once we get Real Users.
08:56 olass yes
08:56 olass can I borrow your book?
08:56 masak olass: I think I bought some a month or two ago in a non-programming-related context.
08:56 masak olass: certainly.
08:57 masak I'll bring it next week.
08:57 olass thanks but no rush. when you have read it
08:57 masak fine.
08:57 masak that might be a while, though.
09:12 CIA-55 bioclipse: ospjuth * r9284 /bioclipse2/trunk/plugins/net.bioclips​e.qsar/schema/descriptorProvider.exsd:
09:12 CIA-55 bioclipse: Uppdated EP to support listedvalues for descriptor parameters. This allows for a
09:12 CIA-55 bioclipse: full set of descriptors + parameters to produce large number of combinations
09:12 CIA-55 bioclipse: matching other software in QSAR. Now we can easily beat them by numbers.
09:16 jonalv joined #bioclipse
09:16 jonalv o/
09:17 * jonalv has updated and restarted his Windows machine and is checking out Bioclipse now... Gonna do some Winodws testing...
09:17 * jonalv is just afraid that Windows did not update everything and that one more restart (or more) is gonna be necessary...
09:28 shk3 joined #bioclipse
09:47 jonalv` joined #bioclipse
10:22 maclean joined #bioclipse
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10:29 shk3 joined #bioclipse
10:34 jonalv joined #bioclipse
10:43 egonw joined #bioclipse
10:50 egonw jonalv: ping
10:50 jonalv egonw: pong
10:51 egonw where is the code that makes the console output the chem formula?
10:51 jonalv cdkmolecule.toString
10:53 egonw tack
10:54 jonalv np
11:39 egonw olass: will you put an release on the update site today?
11:39 olass I was hoping not having to
11:39 olass takes time
11:40 olass but if you have a strong argument...
11:40 egonw there are many bug fixes
11:40 egonw and would be good if these got tested
11:40 egonw by our beta user community
11:40 egonw all three of them :)
11:40 olass sam + who else?
11:41 egonw peter maas
11:41 egonw lars
11:41 egonw or not?
11:41 egonw btw, I won a bioclipse soul with my Jmol blog:
11:41 olass no updates that lars wants to test
11:41 olass anything peter wants to test?
11:41 egonw http://friendfeed.com/e/84e1b9c1-6759-7bf5-2161-38​eda80a8531/Bioclipse-a-powerful-Jmol-application/
11:41 zarah egonw's link is also http://tinyurl.com/cqylnv
11:42 egonw the mol table I'd say
11:42 egonw peter will also want to test atom typing, I think
11:42 olass it's already in beta3
11:42 olass moltable
11:42 olass no updates since that
11:42 olass but sure
11:42 egonw well, at least JCP got a lot of fixes
11:42 egonw and a few in the cdk manager
11:42 egonw too
11:42 egonw and the jmol console
11:43 olass I am just asking if beta testers really will test them. Sam and Lars will not.
11:43 olass if so, I'd love to take the time
11:43 olass and if you say that they will test it, I will get the release out
11:43 egonw mom
11:43 egonw will count the beta3 downloads
11:43 olass that does not matter to my decision
11:44 egonw it will test the update site better?
11:44 egonw please?
11:44 olass :)
11:44 olass as long as an updated chemoinfo feature does rely on changes in bioclispe core it is moderately
11:44 egonw 205 downloads
11:44 olass easy
11:44 olass hmm, not bad
11:44 egonw so, there are certainly more beta testers than just Sam, Lars and Peter
11:45 olass right, you convinced me
11:45 egonw btw, 3 downloads for sparc/solaris :)
11:45 olass just don't think there are as many visible bug fixes that the beta3 testers will test
11:45 olass haha
11:45 olass not bad
11:45 olass ok, updating
11:45 egonw thanx!
11:45 olass Gpox: any commits up for today?
11:46 olass shk3: and from you?
11:46 olass masak: and yo?
11:46 olass jonalv: and you?
11:46 olass jonalv is testing on windows
11:46 shk3 in bioclipse?
11:46 shk3 no, nothing in particular
11:47 * olass is awaiting answer from Gpox, masak, and jonalv
11:47 * jonalv has not started testing yet...
11:47 olass ack
11:47 * jonalv heads over to Ackis for chalgrens presentation now
11:47 masak olass: no, no commits from me today.
11:48 * olass is awaiting answer from Gpox
11:48 jonalv olass: I had to fix that aswell... :)
11:48 egonw masak: did you get my forward on Jmol console autocomplete?
11:48 stain myGrid office going silly: http://picasaweb.google.com/st​ian.mygrid/RedNoseDayAtMyGrid#
11:48 masak egonw: yes, interesting.
11:48 zarah stain's link is also http://tinyurl.com/bb4b58
11:48 masak egonw: though I don't know exactly how to proceed with it.
11:48 egonw ha, it's red nose day today?
11:49 egonw oh no...
11:49 egonw that looks bad...
11:49 egonw stain: that can't be good :(
11:58 stain it's bad stuff
11:58 stain but everybody says I look good with the wig (the only one) - so I don't know if I should interpret that that my normal hairdo is a bit out of shape..
11:59 olass stain: maybe you just had a good hair day with the wig?
12:00 olass Gpox: around?
12:00 Gpox olass: yes
12:00 olass Gpox: If you have any commits on the way within an hour or so, let me know
12:00 olass will be a friday release today of cheminfo
12:01 olass on update site
12:01 olass I am happy to wait for you
12:01 olass if things are in late stages
12:01 olass Gpox: let me know
12:01 Gpox it would be nice to get the new selection stuff in
12:01 olass yes
12:01 stain always good strategy to do some late-submits and then a friday release! ;)
12:01 olass amen!
12:02 olass makes the weekend a bit brighter
12:02 stain and then you know that you'll have some work to do on Monday
12:02 olass yes...
12:02 egonw stain: you do not work during the weekends?
12:03 stain the Taverna team has a policy not to do releases on fridays.. but it happens quite often still, because the Monday release gets delayed due to those last-minute-commits
12:03 olass well, we have beta releases
12:03 olass so for us it's ok if the release has bugs
12:04 stain egonw: I follow the scandinavian work practices in weekends :)
12:04 olass stain: nice to hear that
12:04 stain even during the week - I am the only one working 8-16
12:04 stain university style is 10-18 ..
12:05 olass hmmm
12:05 olass not for scientists
12:05 olass we work *a lot* more
12:05 olass Gpox: is it possible to get selections in friday release? how much time do you need today?
12:19 * olass interprets Gpox silence as he is working hard on it ;)
12:26 egonw Gpox: ping me if I need to update anything or so
12:45 edrin joined #bioclipse
12:52 olass stain, egonw: Are you good with XML schema?
12:52 egonw a bit
12:52 olass is there a way of referencing elements that are not top level elements?
12:53 olass i.e. in DocumentRoot
12:53 egonw not sure what you mean
12:53 olass it seems the only way for me to make an element visible to a subsubsubelement is to place it in the DocumentRoot
12:54 CIA-55 bioclipse: egonw * r9285 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Added unit test for bug #621
12:54 zarah bug #621 | http://tinyurl.com/dafnlx
12:54 egonw are you talking XML schema
12:54 olass yes
12:54 egonw or DOM?
12:54 olass XSD
12:54 CIA-55 bioclipse: egonw * r9286 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Fixed output of formula with no hydrogens (fixes #621)
12:54 zarah bug #621 | http://tinyurl.com/dafnlx
12:54 egonw where does DocumentRoot come in?
12:55 egonw I always thought you cannot define in XML Schema what the root element must be
12:55 CIA-55 bioclipse: egonw * r9287 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeTableContentProvider.java: Fatal exceptions should be at least warn
12:55 olass egonw: well, you can have multiple elements in the top level in XSD
12:56 CIA-55 bioclipse: egonw * r9288 /bioclipse2/trunk/cdk-externals/trun​k/org.openscience.cdk.io/src/org/ope​nscience/cdk/io/MDLV2000Reader.java: Fixed a NPE source: 'null == 2' causes an exception, so first test for nullness
12:57 olass and it seems to me teh only way in order to reference them in other elements
12:57 olass egonw: guess you have never been in that situation?
12:57 olass that you need to reference another element in an XSD?
12:57 steinbeck joined #bioclipse
12:58 olass hi steinbeck
12:59 egonw olass: elements ahve to be defined indeed
12:59 egonw that is done as top elements, AFAIK
12:59 egonw hi stain
12:59 egonw hi steinbeck
12:59 egonw (wrong autocomplete :)
12:59 olass egonw: nope, not a necessity as top elements
13:00 olass well, defined maybe, but not declared
13:01 egonw olass: no clue
13:01 olass stain: are you good with XSD?
13:01 egonw you can send me the schema, if you want me to have a look at it...
13:01 egonw the error messages might give me a hint on how to get it working
13:03 olass no
13:03 olass this is not the case
13:03 olass I am working on design
13:04 olass and I do have error messages here too
13:04 olass you just get visibility errors
13:04 olass which is fine
13:04 * olass is readng W3C source
13:06 steinbeck Hi all
13:06 zarah saluton steinbeck
13:08 egonw Gpox: ping
13:08 Gpox egonw: pong
13:08 egonw steinbeck: enjoying the view?
13:08 egonw on strassbourgh?
13:09 egonw Gpox: IPseudoAtoms need to have the label rendered
13:09 egonw not the symbol
13:09 egonw where do I fix that?
13:11 steinbeck egonw: yes, exactly.
13:11 egonw :)
13:12 Gpox it is fixed in jcp-primary
13:12 egonw ah, excellent :)
13:12 egonw that was easy
13:13 Gpox egonw: i have committed my changes to jcp-primary, there is only three compile problems.
13:14 egonw you're on it?
13:14 egonw or do you need my assistence with that?
13:14 Gpox shk3: why a zoomFactorChanged(...) on ICDKChangeListener ?
13:15 Gpox i need your help
13:16 egonw rajarshi @ NIH now official: http://blog.rguha.net/?p=206
13:17 egonw mine, or shk3's ?
13:17 Gpox ReactionSetManipulator.getReleva​ntReaction(IReactionSet,String) dose not exist. I got control and render plugins from jcp-primary and the rest form cdk-externals from bioclipse
13:18 egonw Gpox: right... that patch you need to manually apply to CDK in Bioclipse
13:18 egonw get it from:
13:18 egonw ...
13:18 egonw http://sourceforge.net/tracker/inde​x.php?func=detail&aid=2675819&a​mp;group_id=20024&atid=320024
13:18 zarah egonw's link is also http://tinyurl.com/c4omos
13:20 Gpox ok
13:20 masak egonw: what is 'sysout-TAB'?
13:20 egonw masak: in Eclipse java editor you type: sysout
13:20 egonw then Ctrl-SPACE
13:20 masak ah.
13:20 masak I see.
13:20 egonw but since the JS console has TAB...
13:20 egonw I sort of misstyped
13:21 masak egonw: nowadays, it also has Ctrl+Space.
13:21 egonw yes, yes :)
13:21 egonw some extra advertisement never hurts?
13:21 egonw :)
13:21 masak I'll see what I can do.
13:22 masak it doesn't feel very highly prioritized...
13:22 masak ...but would be nice, of course.
13:25 Gpox the GeometryTools.getClosestAtom(...,IAtom toIgnore) i can patch myself in bioclipse.
13:26 egonw Gpox: and please send the patch to stefan too
13:26 egonw shk3: I think it is better to remove that parameter and have the code pass a proper container without that atom
13:27 egonw shk3: Gpox actually had a Collection<IAtom> instead of IAtomContainer which makes sense I think
13:28 Gpox egonw: i thing that method can be done away with is another way, it seams to be used in strange ways i will have to have a look at it
13:29 egonw ok
13:29 Gpox that leaves ICDKChangeListener.zoomFactorChanged()
13:32 shk3 well, this is to notify about zoom changes via mouse wheel
13:32 shk3 for updating status bar
13:34 Gpox shouldn't this be done via the controller?
13:35 egonw Gpox: all other events are passes in that way too...
13:35 egonw like selection...
13:35 egonw it sounds like a proper place to put it...
13:36 egonw why would you like to see it go via the controller?
13:38 masak The XML Specification, carefully annotated by Tim Bray. A great read, and invaluable for anyone with more than a passing interest in XML. http://www.xml.com/axml/testaxml.htm
13:38 zarah masak's link is also http://tinyurl.com/23twqp
13:39 masak it's full of nice little insights, at least for me.
13:39 masak "One of the nice things about XML is markup can easily be distinguished from text because it always begins either with the character < (in which case it ends with the character >) or the character & (in which case it ends with the character ;)."
13:39 masak huh. :)
13:40 egonw well... that's nonsense
13:40 Gpox While it is nice that the RendererModel has events that can be listened for when properties change. This change go via the IMouseEventRealy  and ZoomModule to the RendererModel and then to the application
13:40 masak egonw: please elaborate.
13:41 egonw <This is not= valid XML, so must be plain text with a single " somewhere. It's not even well-formed.>
13:41 egonw &nor is this a entity;
13:41 masak egonw: I think well-formedness is assumed.
13:41 egonw hahaha... a recursive defintion...
13:41 masak egonw: I was quoting slightly out of context.
13:41 egonw very useful :)
13:42 masak egonw: no, listen.
13:42 masak the quotation was from the annotated part.
13:42 masak he's basically explaining the spec.
13:42 masak no definitions involved.
13:42 egonw Gpox: please explain your suggestion on the mailing list
13:42 egonw as to document the design
13:43 egonw masak: OK, your quote was too much out of context... fine
13:43 masak egonw: I was just trying to explain what I liked about the annotations. I didn't expect the Spanish inquisition.
13:44 egonw hahaha :)
13:44 egonw look who's talking :)
13:44 masak true. :)
13:46 Gpox egonw: will do
13:46 Gpox egonw: Can you update org.openscience.cdk.render and control in bioclipse fro jcp-primary
13:46 egonw Gpox: tack
13:46 egonw yes, now?
13:49 Gpox yes
13:49 egonw ack
13:50 Gpox egonw: ping me when you are done, so i can commit to bioclipse
13:50 egonw yes, working on it
13:56 egonw Gpox: jchempaint-primary does not compile for me yet
13:56 egonw working on that...
13:56 Gpox ControllerHub?
13:57 egonw yes, a getClosestAtom() call
13:57 Gpox update again
13:57 egonw ack
13:57 Gpox fixed it
14:04 egonw Gpox: commit pending...
14:06 CIA-55 bioclipse: egonw * r9289 /bioclipse2/trunk/cdk-externals/trunk/ (57 files in 11 dirs): Uploaded latest code from jchempaint-primary (rev 14490)
14:15 egonw Gpox: back to you
14:16 Gpox yeah the Reaction patch is not just to applay
14:16 egonw ok
14:17 Gpox for one it is in cdk fromat
14:17 egonw I'll try
14:17 egonw yes, that is a problem indeed
14:17 egonw maybe I should have both use src/main ...
14:17 egonw will consider that
14:19 * egonw is applying shk3 patch to CDK in Bioclipse SVN
14:27 shk3 I managed to add children to specmol files
14:28 shk3 how can I make these to open in jchempaint/spectrum editor?
14:28 shk3 totally lost with that right now
14:30 egonw Gpox: ok, patch pending
14:32 shk3 hm, the sdf children don't open
14:32 shk3 wasn't that the point with the children stuff?
14:32 egonw Gpox: are they supposed to?
14:33 CIA-55 bioclipse: egonw * r9290 /bioclipse2/trunk/cdk-externals/trunk/ (4 files in 3 dirs): Applied shk3's CDK patch #2675819
14:33 egonw Gpox: back to you
14:34 edrin hi
14:34 zarah hi edrin
14:34 egonw hi edrin
14:34 edrin hi egonw
14:35 edrin could you continue with the second version?
14:36 egonw yes, soon I think
14:40 egonw did you make the modifications you wanted to make?
14:40 edrin no
14:45 CIA-55 bioclipse: goglepox * r9291 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Changed to use Single/Multi selection
14:46 egonw olass: how much time to Gpox and I have left, or is it already too late?
14:46 olass dunno
14:46 olass how much you have?
14:46 * egonw nothing...
14:46 egonw helping Gpox with his list of patches
14:46 olass Gpox: how long?
14:47 olass I'll do release as soon as you are done
14:47 olass ping me
14:47 egonw olass: CDK plugins have new version numbers
14:47 egonw all of them
14:47 olass ok
14:47 egonw the external ones that is...
14:47 olass feature updated?
14:47 egonw it's version?
14:48 egonw no
14:48 egonw shall I?
14:48 CIA-55 bioclipse: goglepox * r9292 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (3 files in 3 dirs):
14:48 CIA-55 bioclipse: Fixed syncing with between outline and editor.
14:48 CIA-55 bioclipse: Compares only the contained ChemObject of CDKChemObject
14:49 egonw 2.0.0.B20090313?
14:51 CIA-55 bioclipse: goglepox * r9293 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Removed settings passed to the renderer model as they are overwritten by the JCPPrefereses
14:51 CIA-55 bioclipse: goglepox * r9294 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/handlers/RemoveHandler.java: Changed LogicalSelection to EMPTY_SELECTION
14:52 CIA-55 bioclipse: goglepox * r9295 /bioclipse2/trunk/cdk-externals/trunk/org.open​science.cdk.standard/src/org/openscience/cdk/ (event/ICDKChangeListener.java geometry/GeometryTools.java): Patching GeometryTools and ICDKChangeEvent from jchempaint-primary
14:52 CIA-55 bioclipse: goglepox * r9296 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/icons/jcp/ (8 files): Added + sign to icons that add stuff bug #546
14:52 zarah bug #546 | http://tinyurl.com/c8822z
14:53 CIA-55 bioclipse: goglepox * r9297 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/handlers/RemoveHandler.java: Added IChemModelRelay to undo call
14:56 egonw Gpox: done?
14:57 Gpox shk3: i got compile error in MakeReactantOrProductInNewReactionEdit in latest bioclipse
14:57 shk3 mom
14:57 egonw Gpox: I'll check
14:58 CIA-55 bioclipse: goglepox * r9298 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint/src/net/bioclipse/cdk/jchempaint/undoredo/ (6 files): Updated SWT undo/ redo with IChemModelRelay
14:59 egonw shk3: it seems your patch was missing a method...
14:59 shk3 mom
15:02 shk3 let me check
15:07 shk3 updating
15:07 shk3 might take a while
15:07 shk3 can anybody comment on the child stuff?
15:07 shk3 I need to open children in editors
15:07 egonw Gpox: please remove the class for now
15:07 egonw Gpox: we do not do reactions in Bioclipse anyway
15:07 shk3 this seems not to be intended right now
15:08 shk3 wait a second
15:08 egonw Gpox: and we can reinstate it later
15:08 shk3 I think it's that method which I wasn't sure about
15:08 shk3 but I get confused with my 10 cdk checkouts
15:08 egonw Gpox: or shall I do that?
15:09 egonw Gpox: then olass can actually make the release
15:10 shk3 can you post the line which fails
15:10 shk3 ?
15:10 egonw 75
15:10 egonw and 99
15:10 Gpox to late already gone :)
15:10 egonw Gpox: yes that's fine
15:10 egonw Gpox: thanx
15:10 egonw shk3: we'll just fix it after the update site release...
15:11 egonw Gpox: everything set then?
15:11 egonw Gpox: have not seen your commit yet
15:11 CIA-55 bioclipse: goglepox * r9299 /bioclipse2/trunk/cdk-externals/trunk/o​rg.openscience.cdk.control/src/org/open​science/cdk/controller/undoredo/MakeRea​ctantOrProductInNewReactionEdit.java: Removed MakeReactantOrProductInNewReactionEdit
15:11 egonw ah, there it is :)
15:11 Gpox olass: all set
15:13 CIA-55 bioclipse: egonw * r9300 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Bumped feature number
15:14 jonalv joined #bioclipse
15:15 jonalv oh hai
15:15 zarah privet jonalv
15:15 egonw hej jonalv
15:15 * jonalv left his Windows computer online during the day
15:15 jonalv it was downloading Bioclipse...
15:15 jonalv now the hard drive is full
15:15 egonw hahahaha
15:16 jonalv it had something like 15GB free space...
15:16 jonalv I have no idea what has happened
15:16 jonalv but working with a Windows machine without free harddrive space is a pain
15:16 egonw I guess you are now part of the illegal-movie-torrent-network seeder
15:16 jonalv ah
15:17 jonalv yes it seems very strange...
15:17 egonw I mean... Bioclipse is not *that* big
15:17 jonalv I probably got some virus yea...
15:17 shk3 ok, the offending method probably was
15:18 shk3 ReactionSetManipulator.getRe​levantReaction(IReactionSet, IAtomContainer)
15:18 shk3 I was not sure about this since
15:18 shk3 I found and
15:18 shk3 ReactionSetManipulator.getRe​levantReaction(IReactionSet, IMolecule)
15:18 shk3 somewhere and thought these could be unified
15:18 shk3 but I can't find the later method right now
15:18 shk3 no idea which branch it was in
15:19 egonw file a bug report to make ReactionSetManipulator.getRelevantReaction() take an IAtomContainer
15:19 jonalv there is also the possibility that tortoise svn went crazy...
15:20 shk3 but I can't find that method any longer
15:20 shk3 it was in one of the 100 branches
15:21 * jonalv is gonna restart to a real operating system and have a look at the disk and see what all that space actually is...
15:23 shk3 ah, it's in 1.2 branch
15:24 egonw jonalv++ for booting Linux
15:25 CIA-55 bioclipse: goglepox * r9301 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Changed name from 'Recalculate' to 'Clean Up'
15:25 jonalv egonw: what paramater do I give ls to see the size of a catalogue?
15:25 egonw huh?
15:26 egonw catalogue?
15:26 jonalv ls -lh says that the folder file is 4kb
15:26 egonw du -hs or so
15:26 Gpox du -sh
15:26 jonalv I want the recursive size of the folder..
15:26 egonw du -h
15:26 jonalv oki
15:26 jonalv thanks
15:26 olass egonw: sry, been in tel
15:27 egonw olass: np
15:27 olass egonw: about SoC
15:27 olass I will not have time
15:28 egonw no, neither do I
15:28 egonw and think think we would get it anyway
15:28 olass ok, that setles it for this year IMO?
15:28 olass right
15:28 egonw yes, think so
15:29 egonw jonalv: kdirstat
15:29 egonw has a nice graphical overivew
15:29 egonw see: http://www.linuxhaxor.net/2008/01/24/gra​phical-disk-usage-display-with-kdirstat/
15:29 zarah egonw's link is also http://tinyurl.com/d44wsy
15:29 jonalv egonw: I think du -sh will do the trick... :)
15:29 egonw jonalv: ack
15:29 jonalv I don't want more thatn of those processes running. It already takes forever...
15:29 egonw hehehe
15:30 jonalv I think tortoise svn went totally amok and chewed up all available space...
15:30 egonw phew...
15:30 jonalv uhm there are windows users here right_
15:30 jonalv what svn implementation are you uisng_
15:30 jonalv ?
15:32 olass egonw: status for release today?
15:32 olass Gpox: ?
15:32 egonw ready to go
15:33 olass ok
15:33 olass will update then
15:33 egonw [16:11:49] <Gpox> olass: all set
15:33 egonw [16:11:49] <Gpox> olass: all set
15:33 egonw [16:11:49] <Gpox> olass: all set
15:33 zarah [16:11:49] <Gpox> olass: all set
15:33 olass could someone do last minute testing?
15:33 egonw [16:11:49] <Gpox> olass: all set
15:33 egonw [16:11:49] <Gpox> olass: all set
15:33 egonw [16:11:49] <Gpox> olass: all set
15:33 zarah [16:11:49] <Gpox> olass: all set
15:33 egonw crap
15:33 olass pastebin
15:33 egonw ok, sorry
15:33 egonw I pasted the things
15:33 egonw but it did not show up
15:33 egonw but that was apparently because it autohit RETURN :)
15:33 jonalv my Bioclipse checkout is 4.5 GB :/
15:33 jonalv tortoise--
15:34 egonw svn --
15:34 egonw maybe it is checking out all tags and branches too :)
15:34 jonalv egonw: but still...
15:38 olass jonalv: why are you not using git?
15:39 olass MOHAHAHA
15:39 jonalv olass: I don't know....
15:40 jonalv I am updating my local svn checkout of Bioclispe now. I am gonan copy the stufff from it onto my windows disk and then restart windows. That's probaly the fastest way to give the latest Bioclipse a test run in Windows for me...
15:40 jonalv olass: Or are you working on a beta 4 today?
15:41 jonalv olass: In that case I could just test run that one.... :)
15:41 olass yes
15:41 olass beta4 in progress
15:41 jonalv olass: ETA?
15:41 olass dunno
15:41 olass beta4 is just cheminfo on update site
15:41 olass if it works out of the box
15:41 olass if probs, then next week
15:41 * olass has little time left
15:41 olass or sunday
15:41 * olass will work on sunday as well
15:41 olass stain: it's the scandinavian weekend
15:42 olass we always work sundays
15:42 * olass is updating everything
15:47 shk3 egonw: which branch did you apply my patch to?
15:47 egonw bioclipse
15:47 shk3 ah, no cdk branch
15:47 shk3 ?
15:48 egonw no
15:48 shk3 ok, so I will keep discussing it in the tracker?
15:49 egonw yes
15:49 egonw Gpox++
15:50 egonw for the +'s on the icons
15:50 egonw nice!
15:51 shk3 could anybody please comment on this child thing?
15:52 shk3 are children in the navigtor supposed to open in editors?
15:52 egonw shk3: I wish I could, but I got no clue about how this works in BC2
15:52 shk3 did anybody ever do this/think about this?
15:56 egonw Gpox: do you know how that works?
15:57 Gpox no
15:58 shk3 so we don't have it right now?
16:00 jonalv what is windows doing? the hard drive is going full speed... but I am not using all memory...
16:00 * jonalv feels very uncomfortable...
16:06 olass I'm not sure I'll be able to get release out today
16:06 olass we need a patch as well for core feature
16:06 egonw how can I help
16:06 olass will see how fast it goes
16:07 olass you can't
16:07 olass sry
16:07 egonw ok :(
16:07 olass it's just one hour too late
16:07 olass but no worries
16:07 olass I might have time torrow
16:07 olass else it's sunday
16:07 egonw ack
16:08 olass will try now though...
16:08 egonw great
16:08 egonw olass++
16:12 CIA-55 bioclipse: ospjuth * r9302 /bioclipse2/trunk/plugins/ (13 files in 12 dirs): set version to beta4 2.0.0.B20090313
16:13 egonw edrin: ping
16:13 edrin yes?
16:13 egonw finally doing the CML schema thing...
16:13 edrin ah :)
16:13 egonw but I cannot find that regexp on line 1208
16:13 egonw actually
16:13 egonw nowhere in the schemata
16:14 egonw they all have escaped -'s
16:14 edrin hm
16:14 jonalv the eclipse zip file I have downloaded is protected by password
16:14 jonalv this is so strange...
16:14 edrin egonw: and this means?
16:14 egonw that I have no clue *where* to fix the problem
16:15 edrin maybe we were using an outdated version?
16:15 edrin egonw: well, i changed the regular expression as you wrote in your email in the .xsd and then the scomp tool was not complaining anymore
16:16 egonw sure
16:16 egonw but in the schemas used by the CDK services, there is nothing to fix
16:16 egonw they are all ok
16:16 egonw at least regarding the - not being escaped
16:16 Gpox shk3: http://scribbledideas.blogspot.com/2006/06/buil​ding-common-navigator-_115067357450703178.html
16:16 zarah Gpox's link is also http://tinyurl.com/br53dn
16:17 edrin ic, the .xsd i was using with scomp was another version?
16:17 egonw possibly
16:17 edrin egonw: did you try the .xsd of the services with scomp?
16:17 edrin does it report errors?
16:17 egonw no
16:17 egonw I don't have an scomp executable
16:18 egonw and did not have time to work out yet which Java class in the xmlbeans jar to call
16:18 edrin you can download it from xmlbeans. it is a console program
16:18 edrin executable
16:19 egonw URL?
16:19 edrin http://xmlbeans.apache.org/
16:19 egonw sure
16:19 egonw where I can download the scomp util
16:20 edrin http://xmlbeans.apache.org/s​ourceAndBinaries/index.html
16:20 egonw the website is rather uninformative regarding that
16:20 zarah edrin's link is also http://tinyurl.com/cy4q6y
16:20 edrin it's probably in the zip
16:20 edrin of the lib
16:20 edrin at least it was in the one i downloaded
16:20 egonw so, no link for just the scomp util?
16:20 edrin http://www.apache.org/dyn/c​loser.cgi/xmlbeans/binaries
16:20 edrin no
16:20 egonw as said, I already have the xmlbeans jar
16:20 zarah edrin's link is also http://tinyurl.com/adjmpp
16:21 edrin yes, but it's in the download
16:21 edrin http://apache.mirror.iphh.net/xml​beans/binaries/xmlbeans-2.4.0.zip
16:21 zarah edrin's link is also http://tinyurl.com/bqmjt7
16:24 egonw https://bugs.launchpad.net/ubun​tu/+source/xmlbeans/+bug/342349
16:25 edrin :)
16:26 edrin http://xmlbeans.apache.org/doc​s/2.4.0/guide/tools.html#scomp
16:26 zarah edrin's link is also http://tinyurl.com/df7wzt
16:26 edrin egonw: that's the command you need: scomp -srconly -src ..\src -d ..\xsb EasyPO.xsd
16:26 * edrin is back in 10 min
16:28 * olass is building a patch for bc core
16:28 olass damn
16:28 olass every friday ends like this
16:29 olass was supposed to go early today
16:30 olass I have no chance to verify things the right way now
16:30 olass will be one chance
16:30 olass let's hope it works
16:31 jonalv egonw: in what eclipse component do I find org.eclipse.wst.xml.core.cataloguecontributions?
16:32 jonalv our devlopment environment is not entirely easy to set up on a new computer... :(
16:32 egonw check the META-INF?
16:32 egonw should be in the deps
16:33 jonalv no I don't think it is. There is no error in the META-INF only plugin.xml
16:33 jonalv I am trying with downloading some stuff to eclispe now.. :)
16:33 egonw check the xml_feature plugins
16:34 egonw org.eclipse.wst.[common.emf|sse.ui|validation]
16:35 jonalv egonw: how do I install that?
16:35 egonw web tools package
16:35 egonw or so...
16:35 jonalv from the ganymede install site I can't find that
16:35 egonw from the default ganymedes update site
16:35 jonalv and web tools
16:35 jonalv oki trying with web tools
16:37 * jonalv hasn't even managed to start Eclipse with the chemoinformatics feature in windows yet... :(
16:39 jonalv egonw: the web tools didn't help...
16:39 egonw jonalv: I have
16:40 egonw WST Common Core
16:40 egonw WST Common UI
16:40 egonw WST XML Core
16:40 egonw WST XML User Documentation
16:40 egonw I guess tieh XML COre is the important one
16:40 egonw oh...
16:40 egonw or maybe:
16:40 egonw XSD - XML Schema Definition Runtime
16:40 egonw XSD Edit
16:40 egonw the latter probably not...
16:40 egonw but who knows
16:41 egonw and I also have:
16:41 jonalv yea...
16:41 egonw Eclipse XML Editors and Tools
16:41 egonw which sounds rather promosing :)
16:43 olass hmm
16:43 olass egonw: it doesn't look good
16:43 olass JCP is not centered in editor
16:43 egonw ok :(
16:43 olass is it for you?
16:43 egonw yes, fine with that for the beta
16:44 olass with what?
16:44 egonw it has many other improvements that make up for it easily
16:44 olass is it not centered for you?
16:44 egonw the moltable is fine
16:44 egonw sometimes not
16:44 olass JCP
16:44 olass moltable ahs no improvements in this
16:44 egonw I noticed a displacement at some point
16:44 olass :(
16:44 olass ok
16:44 egonw but nothing worrying in my case so far
16:44 egonw olass: sure it has
16:44 egonw it must
16:44 egonw have
16:44 olass I see several bugs after opening 2 files
16:44 egonw it shares the rendering engine, right?
16:44 olass no
16:44 olass well
16:44 egonw new or old
16:45 olass haven't even tried moltable
16:45 egonw are you sure these were not there in the previous version too?
16:45 olass yes
16:45 olass 110%
16:45 olass in JCP mol was always placed in center
16:45 olass now it is not
16:45 jonalv gah
16:45 olass but selections is nice!
16:45 jonalv it still won't start
16:45 egonw indeed
16:45 egonw and that's what I like to see tested
16:45 olass Gpox++ for hard work on selections
16:45 olass ok
16:47 jonalv olass: I can't get the chemoinformatics feature to run on my windows installation.  Iam missing some stupid Eclipse component. I am waiting for your latest build instead and will do testing with that one...
16:47 olass ack
16:48 jonalv bbl
16:48 jonalv afk
16:50 olass ok
16:50 olass egonw: update out
16:50 olass seems to run on Mac
16:50 egonw olass++
16:50 olass just hit update site
16:50 olass and try
16:50 olass I hope nothing is broken
16:50 olass if anyone finds broken stuff, it is easy to revert to old update site
16:51 olass send me an SMS if so
16:51 olass must run off now
16:51 olass will be online on sunday
16:51 olass bye for now
16:51 egonw bye!
16:51 egonw thanx!
16:52 CIA-55 bioclipse: ospjuth * r9303 /bioclipse2/trunk/plugins/ (7 files in 7 dirs): set version to beta4 2.0.0.B20090313
16:55 * egonw is away for dinner
17:23 edrin egonw: did the scomp tool work?
18:50 CIA-55 bioclipse: shk3 * r9304 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.jchempaint/META-INF/MANIFEST.MF: exports the activator
18:50 CIA-55 bioclipse: shk3 * r9305 /bioclipse2/trunk/plugins/net.bioclipse.specmol/ (4 files in 4 dirs): very basic child editing
19:31 edrin left #bioclipse
21:32 CIA-33 joined #bioclipse

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