Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-09

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All times shown according to UTC.

Time Nick Message
05:06 egonw joined #bioclipse
06:32 olass joined #bioclipse
06:34 CIA-58 bioclipse: ospjuth * r9718 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (InformationPage.java QsarEditor.java): Added InformationPage with general metadata information input fields.
06:40 edrin joined #bioclipse
06:40 edrin good morning
06:41 edrin olass
06:41 olass hi edrin
06:50 Gpox joined #bioclipse
06:51 Gpox joined #bioclipse
07:12 egonw joined #bioclipse
07:12 edrin hi egonw
07:12 egonw hej edrin
07:13 edrin olass: goto #xws ?
07:13 CIA-58 bioclipse: goglepox * r9719 /bioclipse2/trunk/plugins/net.bioclipse.u​i.business/src/net/bioclipse/ui/business/ (IUIManager.java UIManager.java):
07:13 CIA-58 bioclipse: Added closeActiveEdtior() and closeEditor(...)
07:13 CIA-58 bioclipse: Resolves bugs 827, 828
07:13 CIA-58 bioclipse: goglepox * r9720 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/IUIManager.java: Removed trailing spaces
07:17 masak joined #bioclipse
07:39 jonalv joined #bioclipse
07:40 jonalv hi
07:40 zarah oh hai jonalv
07:46 jonalv olass: ehlo
07:47 olass hej
07:47 jonalv olass: so are we gonna test run your new build soon?
07:47 olass when done, yes
07:48 masak oh hai olass
07:48 olass ETA 1 hour or so
07:48 jonalv okey how far away do you think that is?
07:48 olass hi masak
07:48 jonalv oki
07:48 olass if create2d/3d works
07:49 olass jonalv: will you look at the failing tests today?
07:49 jonalv olass: I am thinking about that
07:49 olass good
07:49 egonw olass: shk3 reported 3d to be working again
07:49 jonalv olass: I am afraid it's not as easy as it looks though...
07:49 egonw olass: balloon seems working
07:49 olass egonw: balloon: good
07:49 egonw but the created ,sdf opens in 2D moltable
07:50 olass egonw: shk3: teh bugs are not marked as fixed
07:50 olass egonw: that is fine I guess
07:50 olass after all, this is desired behaviour for sdf
07:50 egonw and frame next is not working
07:50 olass file bug to jonalv
07:51 * olass is building beta4
07:51 jonalv huh a bug, for me?
07:51 egonw but the outline is working
07:51 egonw but highlighting atoms not
07:52 jonalv egonw: jmol?
07:52 egonw I have to agree... Jmol in Bioclipse is rather tricky to work with
07:52 jonalv egonw: selections synchronization only works when looking at one small molecule
07:52 egonw jonalv: I can demo, if oyu like
07:52 egonw ah, that would explain
07:52 egonw suck too
07:53 olass egonw: do you have the bugs for generate2d/3d or does stefan have them?
07:53 olass please mark as fixed
07:53 olass (if fixed)
07:53 egonw 825 is mine
07:53 olass oh
07:53 olass they are
07:53 jonalv egonw: That is all I have managed yet. Jmol in Bioclipse is a bit of a hack I am afraid...
07:53 olass :)
07:53 olass sry
07:53 egonw but that was never about create3D
07:53 egonw because that was not a problem with the action
07:53 olass whatever
07:54 olass it was a bug
07:54 olass and its solved
07:54 egonw no
07:54 egonw it is not
07:54 olass it is not?
07:54 olass explain
07:54 egonw please read the bug report comments
07:54 egonw that's what they are for
07:55 olass read it
07:55 olass and?
07:55 olass I see no other bug opened
07:56 olass hence my guess would be that this is a bug and it's still open
07:56 egonw why would I need to open another bug, if there is only one?
07:56 egonw yes, but you might notice the actual bug report
07:56 olass if it's not the same bug for example
07:56 egonw the bug report was about the created file not openend properly
07:56 egonw it still is
07:56 olass ok
07:56 egonw so, yes, it is not closed because it is not fixed yet
07:57 olass ok
08:00 jonalv olass, egonw: I am looking at the cdk methods loadMolecules and loadMolecule. They trouble me because they need to return stuff and yet they are taking progressMonitors. What is the behavior that is sought for here?
08:00 egonw shouldn't any time consuming stuff not block the GUI??
08:01 olass jonalv: I agree with egonw... these can be time-consuming tasks
08:02 jonalv egonw, olass : yes but explain to me how a method can both return and not block the gui... :/
08:03 egonw jonalv: ah, because the method can be used from the GUI too...
08:03 egonw good point...
08:03 egonw olass: he has a good point here...
08:03 jonalv if you are to return something to the gui thread the gui thread can't really go and do other stuff while waiting. The return can come at any time...
08:03 olass you could add a callback
08:03 egonw jonalv++
08:03 olass Gpox++ suggested this to get feedback while parsing large sdfiles
08:04 egonw jonalv: one more reason to split GUI calls and JS calls
08:04 olass for example, having read 100 it could return them but still continue to parse the rest 10.000
08:04 jonalv yes it's the pattern used when doing BioclipseGUIJob calls
08:05 olass jonalv: well, that's just at the end, right?
08:05 jonalv olass: uhm, hpw would you do that? The java construct return aborts a method...
08:05 olass no, not return
08:05 olass add, in addition to progressmonitor, a callback
08:05 olass Gpox: it was your suggestion, you should explain for jonalv
08:05 * olass is not as good a software engineer
08:06 jonalv olass: Ah like a collector?
08:06 stain using a callback?
08:06 jonalv olass: that is not something that translates well to JavaScript I am afraid... :/
08:06 stain pass in an extra callback-parameter, and then do callback.receiveResults(firstHundreds);
08:07 olass right
08:07 olass (something along those lines)
08:07 stain it's the old indirection of control pattern
08:08 jonalv yes
08:08 olass three cheers for old control patterns
08:08 zarah hooray! hooray! hooray! :)
08:08 stain just to be the grumpy, bearded guy with the "We had it all worked out in the 70s!" attitude
08:08 olass :)
08:08 stain I know what you need - the singleton factory pattern!
08:08 masak would that be 'inversion of control'? just checking.
08:09 stain masak: yes, sorry.. my beard is rusty
08:09 jonalv yes sadly enough I wasn't around back then and noone of the guys who where has been my teachers so I am doomed to rediscover all of it... :)
08:09 masak stain: :)
08:09 masak don't rediscover! read Gang of Four!
08:09 jonalv masak: and in what way is that not to discover?
08:10 stain I remember reading GoF as a Python-developer and I couldn't understand why you would need even half of those tings
08:10 stain now that I'm programming in a type-disabled language like Java I understand much more
08:10 masak jonalv: sounded to me you wanted to do it by trial-and-error.
08:10 jonalv masak: no
08:10 masak stain: amen.
08:10 jonalv masak: that would be reinvent
08:10 masak indeed.
08:10 masak don't do that either.
08:11 shk3 joined #bioclipse
08:11 jonalv but I am not sure we want to do that when running the stuff from JavaScirpt...
08:12 olass right
08:12 olass that is another question
08:12 olass and one for you to chew on
08:12 olass with Gpox
08:12 olass and masak
08:12 masak nod.
08:12 jonalv masak: are there gather and take constructs in JavaScript? :)
08:12 masak jonalv: don't think so. :/
08:13 masak that's likely a Perl 6 invention.
08:13 masak (by the way, gather/take + recursion. it rocks.)
08:15 egonw masak, jonalv: joining for a cup of coffee?
08:15 masak egonw: sure.
08:15 jonalv egonw: oki
08:19 olass shk3: please look att bug #834
08:30 shk3 I don't think the builder3d can do coordinates without hydrogen.
08:30 shk3 it's not totally clear,
08:30 shk3 but I don't think it makes sense to generate coordinates for an incomplete molecule.
08:32 olass shk3: please assign bug to egonw for comments
08:32 olass shk3: and please look at bug 838
08:33 olass shk3: I recently submitted a few bugs regarding generate2D/3D
08:33 olass you've made good progress though
08:33 olass but still some cases are not handled
08:48 olass jonalv: I don't understand the following:
08:48 olass As for testing it I guess just seeing that the view is not there when not that plugin is there but present when the plugin is should be enough.
08:48 olass what do you mean?
08:52 shk3 neither do I
08:52 shk3 sounds confus(ed|ing)
08:53 shk3 olass: I still have problems with the data plugins
08:53 shk3 if I commit the speclipse one, could you test it?
08:54 olass sure. No deps to other speclipse plugins, right?
08:54 shk3 no
08:54 shk3 only to data etc.
08:57 olass name of plugin?
08:57 olass net.bc.data.speclipse?
08:57 shk3 yes
08:57 shk3 committing
08:58 CIA-58 bioclipse: shk3 * r9721 /bioclipse2/trunk/plugins/net.bioclipse​.specmol/net.bioclipse.data.speclipse/: Initial import.
08:59 * shk3 is to a meeting
09:00 CIA-58 bioclipse: shk3 * r9722 /bioclipse2/trunk/plugins/net.bioclipse​.specmol/net.bioclipse.data.speclipse/ (128 files in 17 dirs): Initial import of speclipse sample data project
09:01 olass jonalv: about net.bc.jmol.cdk... does it contain anything for beta4?
09:01 jonalv olass: no idea,
09:01 * jonalv is in meeting with masak and egonw
09:02 olass jonalv: did you see the above?
09:02 olass [10:51] < olass> jonalv: I don't understand the following:
09:02 olass [10:51] < olass> As for testing it I guess just seeing that the view is not there when not that plugin is there but present when the plugin is should be enough.
09:02 olass jonalv: no rush, answer when you are back
09:02 jonalv olass: oki
09:02 * jonalv afk
09:05 olass jonalv: reopened bug #475 so you can answer there for the record
09:13 jonalv okey olass so I look at #475 now
09:13 jonalv @pz 475
09:13 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=475
09:13 olass just need a clarification what you meant
09:13 olass did not get it
09:14 CIA-58 bioclipse: ospjuth * r9723 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (ApplicationWorkbenchAdvisor.java actions/UpdateAction.java): Removed duplicated UpdateAction. Solves bug #820.
09:14 zarah bug #820 | http://tinyurl.com/c2betl
09:14 olass ok
09:15 olass I'm ready to build beta4
09:15 olass Gpox: any commits close?
09:15 olass anyone else?
09:15 olass first
09:15 olass second
09:15 olass ...and third. There goes beta4.
09:16 * olass is updating just to be sure
09:17 olass and shk3: checking out data.speclipse too
09:18 olass shk3: around?
09:18 olass why did you commit to inside net.bc.specmol?
09:18 olass shk3: please fix
09:19 * olass is checking out anyway
09:30 * olass is replacing B20090407 with B20090409
09:33 CIA-58 bioclipse: ospjuth * r9724 /bioclipse2/trunk/ (38 files in 36 dirs): Updated B20090407 to B20090400 for beta4 release.
09:34 CIA-58 bioclipse: ospjuth * r9725 /bioclipse2/trunk/plugins/ (6 files in 6 dirs): Updated balloon from B20090407 to B20090409 for beta4 release.
09:34 CIA-58 bioclipse: ospjuth * r9726 /bioclipse2/trunk/features/ (11 files in 11 dirs): Updated features from B20090407 to B20090409 for beta4 release.
09:34 CIA-58 bioclipse: ospjuth * r9727 /bioclipse2/trunk/plugins/ (6 files in 6 dirs): Updated xws4j and hivpred.client from B20090407 to B20090409 for beta4 release.
09:35 grandm44 joined #bioclipse
09:35 CIA-58 bioclipse: shk3 * r9728 /bioclipse2/trunk/plugins/net.bioclipse​.specmol/net.bioclipse.data.speclipse/: should not go here
09:36 CIA-58 bioclipse: ospjuth * r9729 /bioclipse2/trunk/plugins/ (11 files in 10 dirs): Updated qsar from B20090407 to B20090409 for beta4 release.
09:37 masak git++
09:37 masak it's not that it's extremely good, it's just... right in so many ways.
09:37 jonalv git++
09:37 jonalv and fast
09:37 masak SVN--
09:38 CIA-58 bioclipse: shk3 * r9730 /bioclipse2/trunk/plugins/ne​t.bioclipse.data.speclipse/: Initial import.
09:39 masak also, ack++, but no -- on grep, because it's still useful sometimes.
09:39 masak same with (Perl 6)++ and Perl 5.
09:41 CIA-58 bioclipse: shk3 * r9731 /bioclipse2/trunk/plugins/ne​t.bioclipse.data.speclipse/ (127 files in 16 dirs): Initial import of speclipse sample data project
09:42 masak ok, this is controversial, but I feel kind of strongly about it: I don't think a commit with commented-out code is a good commit.
09:42 masak there, I said it.
09:43 masak there are ways to make it less bad, for example adding a comment about why the commented-out code is commented out.
09:43 masak but plain, unexplained commented out code is the Junk DNA of programming.
09:43 shk3 does that refer to me?
09:43 masak shk3: no :)
09:43 shk3 I support this, btw
09:43 * masak pats shk3
09:43 shk3 this commented-out code is a mess
09:44 jonalv masak: are there ways to make it a good commit as well?
09:44 shk3 it stays there forever
09:44 jonalv masak: like removing the code intead?
09:44 shk3 nobody knows what it is about
09:44 masak jonalv: aye.
09:44 shk3 I can't be used anyway
09:44 shk3 worse is to commit classes which are excluded from build
09:45 jonalv I agree, I have stumbled upon lot's of classes with big commented blocks that I don't know what tot do about...
09:45 masak also, I tend to remove comments of the type "add 1 to the variable i".
09:45 masak and I don't feel guilty about that at all.
09:45 egonw I wish we had a Pelezille field "Need Advice"
09:45 masak egonw: make a category! :)
09:46 jonalv egonw: hm so you use that when a bug needs advice from someone else?
09:46 masak or a severity level, if that's possible.
09:46 egonw right
09:46 egonw no, severity level has different semantics
09:46 jonalv egonw: how would that work?
09:47 olass I regularly commit commented-out code
09:47 * egonw is exploring the flag concept of bugzilla
09:47 olass since I might be working on something that is not 100% ready
09:47 egonw olass--
09:48 egonw that's what branches are for
09:48 olass egonw: are you saying that all your ciommits in SVN are 100% finished?
09:48 egonw olass: how did you add that Milestone thingy in Pelezilla?
09:49 olass don't remember
09:49 olass it took me a while...
09:49 egonw olass: yes, I desparately trying to
09:49 egonw this why I like git so much
09:49 egonw because it allows me to try that sanely
09:49 jonalv olass: it's more that those commented lines tend to stay around forever...
09:50 olass that is another thing
09:50 olass that should be frowned upon
09:50 jonalv olass: perhaps but one thing leads to another...
09:50 olass no please stop disturbing me from work
09:50 jonalv lol
09:50 jonalv olass: this is work
09:51 olass such matters should be discussed in a meeting
09:51 olass IRC is not appropriate for this
09:51 olass it's too slow
09:51 masak olass: learn to type faster.
09:51 olass shk3: sorry, can't get your plugin to run
09:51 olass masak: no, it's slow because I wait for you guys ;)
09:51 shk3 do the other data plugins work for you?
09:51 jonalv maybe masak is used to working on projects where irc is the only available form of communication...
09:51 shk3 for me, none of them works.
09:51 olass shk3: yes
09:52 olass mom
09:52 shk3 what's the error?
09:52 masak olass: touché. :)
09:52 steinbeck joined #bioclipse
09:52 jonalv hi steinbeck
09:52 masak olass: I think I used to commit code with commented-out code in it. I stopped, and became a more harmonic programmer in the process.
09:52 olass masak: probably a good idea
09:52 jonalv masak++ /harmonic programmer
09:53 olass jonalv-- //For giving karma with incorrectly commented out comment
09:53 masak you should write code as if the next person to read it is an easily annoyed axe murderer who knows where you live.
09:53 egonw Gpox: crap...
09:53 egonw my mistake
09:53 egonw wrong jchempaint ML
09:54 egonw masak++
09:55 masak actually, that was a slight paraphrase. http://www.codinghorror.com​/blog/archives/001137.html
09:55 zarah masak's link is also http://tinyurl.com/6eezm2
09:55 jonalv olass: I am sorry for that. I get careless when writing on irc. Uo know that I tend to spel bad here. Does that really warant a karma reduction? :(
09:55 olass shk3: sorry, don't have time to look at data.speclipse more
09:55 egonw masak: that is actually said to be the reason why peer-review works...
09:55 olass jonalv++ //no
09:55 egonw not because of the peer-review itself
09:55 olass just wanted to scare you!
09:55 egonw but of the possible and like consequences
09:55 masak egonw: aye. just the threat of peer review helps.
09:55 egonw peer-review++
09:55 egonw git++
09:56 egonw cdk-workshop++
09:56 olass ok, exporting beta4 now as B20090409
09:56 jonalv egonw: did you just that steinbeck entered? :)
09:56 jonalv |see that
09:56 jonalv olass++
09:57 olass wil put on pele
09:57 egonw no, for the email he sent that 30 participants will join the interactiving hacking part of the WS
09:57 olass for testing
09:57 * jonalv will start testing it after lunch then :)
09:57 egonw steinbeck: really nice list of participants!
09:57 egonw steinbeck: I think Nico Adams will show up too
09:58 egonw steinbeck++ for the extra dinner :)
09:58 egonw oh, goodies...
09:58 egonw so much looking forward to it
09:58 egonw CDK++
09:58 masak RDF++
09:58 masak OWL++
09:58 egonw egonw: shut up, wrong channel
09:59 masak (talking to oneself)++
09:59 egonw bioclipse++ for perfect CDK, RDF and OWL integration
09:59 egonw zarah: can you keep up?
09:59 zarah egonw: are you talking to *me*?
09:59 masak egonw: she can. :)
09:59 egonw yes, DeNiro!
09:59 masak zarah: you're a smart girl.
09:59 zarah masak: So they keep telling me. Over.
09:59 olass egonw: in work-mood today?
10:00 egonw no, used up all my energe on Mon-Tue
10:00 olass right
10:00 egonw and exhausted all last reserves on Wed
10:00 egonw I'm in blind typing mode
10:00 * masak is doing small tasks today, cleaning up code along the way
10:00 egonw no thinking... that's become impossible
10:00 * olass computer is screaming from building beta4
10:00 egonw so just a flood of useless statements
10:00 masak thinking is way overrated.
10:00 egonw that is.
10:00 egonw it is good for my typing skills
10:01 olass don't think, prototype!
10:01 egonw and therefore for my programming skills :)
10:01 egonw it's good for bioclipse
10:04 shk3 olass: could you just tell me which sort of error you get?
10:04 olass I don't see the newwizard
10:07 egonw OK, I added to PZ a 'Action Needed' field
10:07 egonw with values:
10:07 egonw ---
10:07 egonw Needs a Unit Test
10:07 egonw Needs a Stacktrace
10:07 egonw Needs Further Information
10:08 olass sounds good, how do we use it?
10:08 olass email devel-ml?
10:08 egonw and complements Status and Resolution with info on what is required
10:08 egonw ack
10:08 shk3 olass: i put it into speclipse category
10:08 olass shk3: that category is where?
10:08 olass remember that there is no dep to a spectrum plugin
10:09 shk3 yes, that's a problem
10:09 shk3 will put it in sample data
10:09 olass but you probably should have that dep
10:09 olass if you like
10:09 olass do as you wish, this is your domain :)
10:10 CIA-58 bioclipse: shk3 * r9732 /bioclipse2/trunk/plugins/net.bio​clipse.data.speclipse/plugin.xml: changed category
10:10 shk3 could you try again?
10:10 olass not now
10:10 olass building beta4
10:10 olass maybe in afternoon
10:10 olass what error do you get btw?
10:11 olass @lunch
10:12 shk3 could not run wizard or so
10:12 shk3 totally uninformative
10:13 shk3 wait a second
10:13 shk3 works now
10:13 shk3 no idea why
10:43 CIA-58 bioclipse: ospjuth * r9733 /bioclipse2/trunk/features/net.bio​clipse.xws4j_feature/feature.xml: Removed net.bc.services; this is not in 2.0
10:43 CIA-58 bioclipse: ospjuth * r9734 /bioclipse2/trunk/features/se.uu.fa​rmbio.hivpred_feature/feature.xml: Set deps to correct version of xws and core.
10:48 CIA-58 bioclipse: ospjuth * r9735 /bioclipse2/trunk/plugins/n​et.bioclipse.actionHistory/ (META-INF/MANIFEST.MF build.properties): Updated id and build.props for beta4.
10:49 CIA-58 bioclipse: ospjuth * r9736 /bioclipse2/trunk/features/net.biocli​pse.experimental_feature/feature.xml: Set ID to B20090400 for beta4 release.
10:56 maclean joined #bioclipse
10:56 maclean
10:57 maclean I have a question that may well invoke the answer "That information is on the wiki", coupled with a dismissive wave of a hand
10:57 maclean It is this : what do I do if I get an "invalid thread access" error when invoking a method from a manager
10:59 maclean specifically, I implemented 'jcp.snapshot(String filepath)' and it doesn't like calling client.getArea() in the JCPWidget.
11:01 maclean Hmmm. And response came there none...
11:01 Gpox check updateView() in jcpmanager
11:01 maclean Aha! (I spoke too soon :)
11:01 maclean tack, Gpox.
11:05 maclean I had tried SafeRunner, which I found elsewhere, but I had forgotten about Runnables.
11:17 CIA-58 bioclipse: ospjuth * r9737 /bioclipse2/trunk/plugins/net.​bioclipse.bibtexml/plugin.xml: Made bibtexml parser operate on xml by default.
11:20 CIA-58 bioclipse: ospjuth * r9738 /bioclipse2/trunk/plugins/se.uu.f​armbio.hivpred.client/about.ini: Feature branding image had the wrong file extension.
11:21 maclean olass : I think that you disapproved of saving snapshot images of jmol to the workspace - do you feel the same way about jcp? (I suppose: yes)
11:21 olass yes..
11:21 olass do you disagree?
11:22 olass I'm not strongly against
11:22 olass but please the same behaviour for both
11:22 olass maclean: is this feature soon here?
11:22 maclean soon as I can actually make it testable
11:22 olass well
11:22 olass :)
11:22 olass will go on update site in the next batch :)
11:23 maclean I can imagine that users might want either : saving inside or outside the workspace.
11:23 maclean It's just that eclipse is set up such that it is easier to program saving inside...
11:32 CIA-58 bioclipse: shk3 * r9739 /bioclipse2/trunk/plugins/net.bioclip​se.cdk.ui/src/net/bioclipse/cdk/ui/ha​ndlers/Create2dHandlerWithReset.java: fixes bug #838
11:32 zarah bug #838 | http://tinyurl.com/ca98vj
11:38 CIA-58 bioclipse: ospjuth * r9740 /bioclipse2/trunk/features/ (9 files in 9 dirs): Updated feature dependencies from 0407 to 0409. Don't know why this was not detected in my earlier update.
11:39 olass ok, last call
11:39 olass any commits with ETA less than 10 minutes?
11:39 olass shk3?
11:39 olass Gpox?
11:39 olass maclean?
11:43 * masak is back
11:44 egonw masak: groovy is really grooby
11:44 egonw 10.times { groovy }
11:44 masak egonw: glad you like it.
11:44 egonw can I borrow the book over weekend?
11:44 egonw will drop beanshell for the CDK book
11:44 egonw in favor of groovy
11:46 * jonalv is back and backlogged now :)
11:46 * olass is building beta4 again
11:46 olass now for the final time
11:46 olass and will upload to SF
11:46 olass (just FYI)
11:46 egonw olass++
11:47 egonw 2.0.beta4 added to PZ
11:48 olass egonw++
11:56 edrin @pz #840
11:56 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=840
12:06 egonw jonalv: reading material ChemAxiom: http://wwmm.ch.cam.ac.uk/blogs/adams/?p=219
12:06 zarah egonw's link is also http://tinyurl.com/d8eg42
12:09 shk3 back from lunch
12:10 shk3 no commits
12:10 maclean olass : no nearby commits, sorry.
12:10 olass no worries
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12:15 maclean hmmm. saving a snapshot seems to work, inasmuch as it produces a file, which can be exported and opened.
12:15 maclean but the quickimage plugin has problems with it :(
12:15 egonw bugger...
12:16 olass ouch
12:16 olass maclean: why so?
12:16 maclean might have to flush an output stream or so
12:16 olass can you fix it?
12:16 olass is it your or my fault?
12:16 olass maclean?
12:16 maclean oh your fault, of course :)
12:16 olass if mine, file me a bug
12:16 maclean (joke! :)
12:17 olass :)
12:17 egonw fortunately there are update sites
12:18 egonw OK, I give up
12:18 egonw going home
12:19 maclean oh? giving up on what?
12:20 jonalv egonw: is it something we have done?
12:21 egonw no, trying to focus on the grant application
12:21 egonw but too tired
12:21 egonw going home now
12:21 egonw get some sleep
12:21 egonw and continue afterwards
12:21 egonw can't get beyond procrastinating now...
12:21 egonw it's not that I am doing nothing...
12:21 egonw but he asks this, other he asks that
12:22 masak olass: in my Bioclipse installation, updates are turned off by default.
12:22 masak olass: something called SKIP_UPDATE_ON_STARTUP
12:22 maclean egonw : good call - single task things! :)
12:22 maclean (seriously)
12:22 masak olass: how do I turn updates on?
12:22 masak maclean: indeed.
12:22 egonw yes, single thing: sleep
12:22 egonw masak: so, can I borrow the book?
12:23 masak egonw: sure thing.
12:23 olass masak: please give me the verbose startup log in a pastebin
12:23 egonw tack
12:23 masak olass: will do, but I think the relevant line is this:
12:23 masak DEBUG - Skipped updating due to preference setting.
12:23 olass there you have it
12:23 masak egonw: np. just don't spill coffee in it. :)
12:23 olass check your preference
12:23 masak olass: ack, but where?
12:23 egonw mmm... just by accident I found a very nice inkscape feature
12:24 olass uncheck the box
12:24 masak olass: which box?
12:24 olass hmm
12:24 olass good question...
12:24 egonw jonalv: in case I forgot later...
12:24 olass masak: I don't find the box either
12:24 masak olass: found "Automatic Updates" in Eclipse Preferences. I checked that box.
12:24 egonw jonalv: can you, at some point, tell me which structuredb tests only depend and test manager methods
12:25 masak trying again and seeing if that changes things.
12:25 egonw and are not tainted by manager implementation details?
12:25 jonalv egonw: what inkscape feature?
12:25 masak nope, that wasn't it.
12:25 egonw fading of anyobject in a certain direction
12:25 jonalv egonw: sure I just need to fully understand you question... :)
12:25 olass masak: file me a bug please for the missing checkbox
12:26 masak olass: will do.
12:26 jonalv egonw: oh
12:26 masak olass++
12:26 olass masak++ //good catch
12:40 maclean olass : err...the most recent update deleted the .project file from net.bioclipse_feature - is that right?
12:41 maclean I should say - /my/ most recent update, it may have been a while ago.
12:41 olass net.bioclipse_feature was renamed a while ago
12:41 olass net.bioclipse_feature was renamed a while ago to net.bioclipse.core_feature
12:41 maclean ohhh.
12:41 olass you might need to get the new from SVN
12:41 maclean I C
12:49 maclean Oh, and I was intending to submit a bug report about this, but I find no way to create a new folder in Bioclipse (unless it's a child of an existing folder) as the New Folder wizard asks for a parent, but if you only have Virtual...
12:49 jonalv maclean: the top items are projects...
12:49 maclean ohhhh
12:49 * jonalv just realised how unintuitive that is... :/
12:50 maclean right. I used to know that, but I forgot.
12:51 olass yes I know
12:51 olass the concept of a Workspace is not trivial
12:51 masak also, people who write '==true' in if statements should be tied to a chair and forced to read the JLS.
12:51 olass But we do have a cheatsheet
12:51 olass that guides you through these basic tasks
12:51 jonalv masak +1
12:52 maclean masak : who? who? :)
12:52 masak maclean: no names. (olass)
12:52 maclean Begins with "O" and ends with "lass", eh?
12:52 masak kinda.
12:53 olass masak: what is JLS?
12:53 masak olass: see? that's the problem. :)
12:53 maclean java language specification
12:53 olass right...
12:53 olass masak: are you reviewing my code in secrecy?
12:53 masak olass: no.
12:53 olass masak++
12:53 olass masak--
12:54 masak I'm reviewing it quite openly.
12:54 olass sry (was too fast)
12:54 maclean Hmmm. It seems that it is /Virtual that gives the image stuff problems. It works otherwise.
12:54 masak that's ok.
12:54 olass masak++
12:54 olass maclean: /Virtual is a blessing and a pain
12:54 masak mostly pain.
12:54 olass agreed
12:54 maclean <s>blessing</s>
12:54 olass actually
12:54 olass not much in use
12:55 olass and scheduled for removal in favor of a file-based temp dir
12:55 olass howecer, post 2.0
12:55 olass (maybe should be in 2.0 ?)
12:55 jonalv olass: "not much in use"? What do you mean?
12:55 jonalv olass: I use it all the time!
12:55 olass do you?
12:56 jonalv + all my scripts do
12:56 maclean A real Virtual supporter!
12:56 olass ok
12:56 jonalv hm or not _all_ but some...
12:56 olass jonalv: but it would be ok with you if we moved to file-based temp dir?
12:56 jonalv olass: yea that wouldn't be a problem
12:57 maclean http://gilleain.tumblr.com/post/94503094
12:57 zarah maclean's link is also http://tinyurl.com/d67gon
13:01 CIA-58 bioclipse: gilleain * r9741 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (4 files in 3 dirs): Snapshot method to capture an image of what is displayed on the JCP editor.
13:02 olass could someone tag SVN with 2.0.0.B20090409 ?
13:03 olass (actually before 9741 if possible but not super-important)
13:03 jonalv masak: please?
13:03 maclean ah. was that commit not a good idea?
13:03 olass no worries
13:03 olass I never said anything so my bad
13:03 olass and the commit looks nice!
13:04 masak jonalv: oki.
13:04 shk3 2.0.0.B20090409?
13:04 maclean no, I think you did say something about a branch.
13:04 shk3 did you not stick to 2.0.0.B20090407?
13:04 olass shk3: no
13:04 olass shk3: please backlog
13:04 olass and see commits earlier today
13:04 * masak tags the version
13:04 olass danke
13:04 shk3 "Updated B20090407 to B20090400 for beta4 release."
13:05 shk3 so you did this on the 0th of april?
13:06 * masak likes that date
13:06 maclean Midnight on the night between 30th March and 1st April?
13:06 maclean Or 31st.. er..
13:07 masak maclean: no, there's an actual day there. but it's an easter egg, so you have to unlock it first.
13:07 CIA-58 bioclipse: shk3 * r9742 /bioclipse2/trunk/net.bioclipse​.speclipse-updatesite/site.xml: updated the update site for 2.0.0.B20090407
13:07 maclean :)
13:16 CIA-58 bioclipse: carl_masak * r9743 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/net​/bioclipse/ui/dialogs/UpdatesAvailableDialog.java: [UpdatesAvailableDialog] replaced tabs -> spaces
13:18 CIA-58 bioclipse: carl_masak * r9744 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/net​/bioclipse/ui/dialogs/UpdatesAvailableDialog.java:
13:18 CIA-58 bioclipse: [UpdatesAvailableDialog] code cleanup
13:18 CIA-58 bioclipse: - removed unused imports, commented-out code (with no reason given for
13:18 CIA-58 bioclipse:  commenting it out), unused widgets, and '== true' in tests
13:18 CIA-58 bioclipse: - renamed constants to all-uppercase
13:18 CIA-58 bioclipse: - lots of whitespace improvements (aligning, spaces around ops)
13:24 CIA-58 bioclipse: carl_masak * r9745 /bioclipse2/tags/2.0.0.B20090409/: created tag 2.0.0.B20090409
13:26 masak olass: r9745.
13:27 olass masak++
13:28 masak it's actually very easy to make an SVN tag. if you do it right, you don't even have to check something out.
13:29 masak I re-realised this halfway through checking out trunk, and all branches and tags.
13:29 masak same thing goes for branches.
13:29 masak (but SVN still sucks.)
13:31 * maclean types "svn help suck" ...hmmm doesn't work
13:32 maclean "svn suck less"
13:32 olass maclean: depends on where you typed it
13:32 masak @google svn sucks
13:32 zarah masak: http://atomized.org/2005/09/subversion-sucks/
13:36 masak good rant.
13:41 maclean hmmm. possibly.
13:42 maclean heh. this is the 'agile branch strategy' :
13:42 maclean http://4.bp.blogspot.com/_eu8I42x_suU​/RvrwamFZOQI/AAAAAAAAA48/BqRz6zJK070/​s1600-h/agile_branching_strategy.jpg
13:42 zarah maclean's link is also http://tinyurl.com/cezyqz
13:44 maclean okay, the point in the text next to it was "...it becomes completely and utterly unmanageable...", so fair enuff.
13:49 masak haha.
13:50 * masak hugs git
14:23 CIA-58 bioclipse: shk3 * r9746 /bioclipse2/trunk/ (7 files in 7 dirs): Updated B20090407 to B20090409 for beta4 release.
14:30 shk3 Speclipse update site updated
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18:13 edrin left #bioclipse
18:19 CIA-58 bioclipse: ospjuth * r9747 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (7 files): Removed SelectionProvider, should use the one provided with EMF.
18:42 CIA-58 bioclipse: ospjuth * r9748 /bioclipse2/trunk/plugins/net.biocl​ipse.qsar.ui/src/net/bioclipse/qsar​/ui/editors/InformationPage.java: Added viewers for references and units.
18:54 CIA-58 bioclipse: ospjuth * r9749 /bioclipse2/trunk/bioclipse-updatesite/site.xml: Updated update-site for beta4.
18:54 CIA-58 bioclipse: ospjuth * r9750 /bioclipse2/trunk/experime​ntal-updatesite/site.xml: Updated experimental update-site for beta4.
19:47 CIA-58 bioclipse: ospjuth * r9751 /bioclipse2/trunk/plugins/net.bioclip​se.qsar.ui/src/net/bioclipse/qsar/ui/ (3 files in 3 dirs): Fixed parsing to handle BibTexML entries as well in QSAR builder. Also fixed exceptions if molecules do not exist.
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