Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-02

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All times shown according to UTC.

Time Nick Message
03:57 stain joined #bioclipse
05:23 olass joined #bioclipse
06:27 Gpox joined #bioclipse
06:39 rojasm joined #bioclipse
07:07 egonw joined #bioclipse
07:08 egonw moin
07:08 zarah saluton egonw
08:06 shk3 joined #bioclipse
08:06 egonw hi shk3!
08:07 egonw how was your holiday?
08:07 shk3 horrible
08:08 egonw really? sorry to hear that
08:09 jonalv joined #bioclipse
08:11 shk3 how is the bc release doing?
08:11 shk3 did you decide on the change workspace stuff?
08:12 egonw we have a status meeting today
08:12 egonw ask ola about the WS changing stuff... that's his call
08:13 egonw he's here, and I expect him online soon
08:13 shk3 ok
08:14 shk3 i will wait for the result
08:14 shk3 have other stuff to do anyway
08:23 olass joined #bioclipse
08:26 olass shk3: about the switch workspace...
08:27 olass The action is not working, right?
08:27 olass ynithing I can do to help?
08:27 olass are you working on it?
08:28 shk3 the action is working for me
08:28 shk3 let me just test again
08:29 shk3 updating bioclipse
08:30 shk3 might take a while
08:35 shk3 olass: you want the dialog only to appear if the choose workspace action had been called, right?
08:36 olass shk3: what do you mean?
08:36 olass when else can it be shown?
08:36 shk3 no choose workspace dialog at normal startup
08:36 olass oh yes, not on startup please
08:36 shk3 ?
08:36 olass yes
08:36 olass right
08:36 shk3 will try to do this
08:36 olass excellent
08:36 shk3 still updating
08:37 olass I know, it takes time
08:37 shk3 how is the rest of bc2 going
08:37 shk3 ?
08:37 olass we will have s status meeting today
08:37 egonw olass: I sort of like to be asked the WS on start at... can we make this false by default, but optional?
08:37 olass sounds good
08:37 olass and yes
08:37 olass advanced users like that
08:37 shk3 will try this
08:37 olass nivoce users will be scared
08:37 egonw or will it automatically ask a WS, when I already have one Bioclipse booted, asking me for another one, the first being blocked...
08:38 olass sounds complicated
08:38 shk3 indeed
08:38 olass can we maybe add this in 2.1?
08:38 olass or...
08:38 olass have anyone tried it now?
08:38 egonw I think it worked on my machine... .
08:39 egonw but that's Kubuntu too
08:39 olass egonw: with released versions, I-
08:39 olass I mena, not started from Eclipse?
08:39 shk3 It's NOT working from eclipse
08:40 olass shk3: that was regarding multiple Bioclipse accessing the same WS
08:40 shk3 ah
08:41 shk3 we could put a lock file in the workspace or so
08:41 shk3 but this is dangerous if bc crashes without being closed properly
08:41 shk3 the ws then stays locked
08:41 shk3 and average users will be confused
08:41 shk3 I would not like to do this
08:41 jonalv uhm, all users would be confused I would say
08:42 shk3 well, expert users might lock for a .lock file or so
08:42 jonalv yea expert users on the linux platform perhaps...
08:43 olass please, not now
08:43 de__maas joined #bioclipse
08:43 olass post 2.0 in a branch maybe
10:19 masak joined #bioclipse
10:52 shk3 joined #bioclipse
11:25 egonw Bioclipse crashing is certainly confusing to the user
11:25 shk3 can I revert the revert for the whole of bioclipse?
11:26 shk3 or do I need to do it file by file?
11:26 egonw shk3: please ask ola when he is back
11:26 masak shk3: there's -R on 'svn revert', if that's your question.
11:26 zarah masak: You have new messages. Write '/msg zarah @messages' to read them.
11:27 masak zarah: OH RLY?
11:27 zarah masak: you've just exceeded my capabilities :/
11:27 masak zarah: massage
11:27 zarah masak: 1 d 1 h 29 m 41 s ago, jonalv said zarah should give a link the the Bioclipse planet on the commando @planet
11:27 masak jonalv: patches welcome. :P
11:27 masak or tickets. just not free-floating @tells.
11:27 * jonalv mumbles something unhearable
11:28 jonalv masak: oh you like tickes better do you
11:28 shk3 svn revert is for local stuff, isn't it?
11:28 masak jonalv: aye.
11:28 masak shk3: aye.
11:28 jonalv masak: I thought you would create a ticket if you liked the idea...
11:28 shk3 anyway, i can do it
11:28 masak jonalv: no, that's not the way it works.
11:28 masak it's a bit of quid pro quo, you know.
11:28 jonalv masak: did you like the idea?
11:29 masak if you throw out a random feature request, I'd like you to go through the minimal amount of work needed to record your idea.
11:29 masak _then_ you'll get your wish.
11:29 masak deal?
11:29 jonalv masak: actually I think I would like you oppinion on the idea...
11:29 masak this will tidy up operations, for example making you do the work of actually pasting the URL into th request.
11:30 masak jonalv: I'm not against it.
11:30 jonalv I don't even remember that url. That is why I wanted zarah to know it in the first place...
11:30 masak I have nothing to add to that.
11:31 egonw planet.bioclipse.net
11:31 egonw htt://planet.bioclipse.net
11:31 egonw http://planet.bioclipse.net
11:31 egonw even that
11:31 masak egonw: thanks.
11:31 egonw btw... /me makes a mental note to make rednael post Planet Bioclipse posts here
11:32 egonw maybe I should file a ticket against myself for this
11:32 egonw :)
11:32 jonalv yes good idea. Why is not rednael in here by the way?
11:33 egonw because 1) the code is not good enough yet to support more than one channel
11:33 jonalv is it an uninteractive bot?
11:33 egonw 2) we are not using git yet
11:33 egonw correct
11:33 jonalv aha
11:33 egonw it just spit, does not eat
11:34 jonalv zarah drinks too
11:34 jonalv @botbear
11:34 jonalv @botbeer
11:34 jonalv :)
11:34 zarah ;)
11:34 jonalv |lol|
11:34 masak I like separating discussion (zarah) and mindless reporting (rednael).
11:34 masak I didn't think I would, but I do.
11:36 de__maas left #bioclipse
11:37 CIA-58 bioclipse: carl_masak * r9554 /bot/trunk/zarah.pl: [zarah] now does @planet url reporting
11:37 jonalv zarah: reboot
11:37 jonalv masak: that is the way to do things right...
11:37 jonalv ?
11:37 zarah joined #bioclipse
11:37 jonalv @planet
11:37 masak jonalv: aye.
11:37 zarah jonalv: http://planet.bioclipse.net
11:37 jonalv masak++
11:38 masak 7-line change. :)
11:38 jonalv hehe
11:38 masak the operative line was this:
11:38 masak $dialogue->reply()->( 'http://planet.bioclipse.net' );
11:38 masak zarah rocks.
11:39 masak zarah: you're the cool one!
11:39 zarah masak: no, YOU are the cool one! :)
11:39 egonw @planet
11:39 zarah egonw: http://planet.bioclipse.net
12:04 masak egonw: once we switch from CIA-whatever to rednael, we can integrate an 'egonw++' system for commits in those messages.
12:04 masak looking forward to that. :)
12:04 egonw :)
12:09 jonalv egonw: you just blew a big hole to the funniest thing of today...
12:09 egonw huh?
12:09 jonalv egonw: you know...
12:09 jonalv :)
12:09 egonw actually, no... you overestimate me
12:10 jonalv egonw: a certain mailing list...
12:10 egonw please come over
12:10 egonw and explain
12:10 jonalv really?
12:10 egonw I know what ML your are talking about
12:10 jonalv okey...
12:10 egonw but no clue about the hole or the wind that came from it...
12:10 egonw actually... not sure if I do want to know about it
12:18 masak egonw: seems I'm ineligible for GSoC scholarship this year, since I've already signed up as a mentor for Perl 6. :/
12:22 egonw ic, bad mistake
12:23 egonw expensive mistake too :)
12:25 masak you could say that. :)
12:26 masak on the other hand, the two things I'll probably be mentoring are difficult to hand over to someone else.
12:26 masak both will be GSoC projects on software that I've created, in some sense.
12:28 CIA-58 bioclipse: goglepox * r9555 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: added new method to create SDFIndex and use it for numberOfEntriesInSDF(...)
12:28 CIA-58 bioclipse: goglepox * r9556 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeViewerContentProvider.java: New content provider using SDFIndex
12:29 CIA-58 bioclipse: goglepox * r9557 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculesEditor.java: Fixed indentation
12:30 CIA-58 bioclipse: goglepox * r9558 /bioclipse2/trunk/plugins/ (6 files in 4 dirs):
12:30 CIA-58 bioclipse: Changed IMoleculesEditorModel.getMoleculeAt(index)
12:30 CIA-58 bioclipse: to return ICDKMolecule
12:30 CIA-58 bioclipse: goglepox * r9559 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Added createSDFIndex(...)
12:30 CIA-58 bioclipse: goglepox * r9560 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeViewerContentProvider.java: Added conversion from IChemFile to IMolecule and fixed null check
12:31 CIA-58 bioclipse: goglepox * r9561 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (3 files): Changed from MoleculeTableContentProvider to MoleculeViewerContentProvider
12:31 CIA-58 bioclipse: goglepox * r9562 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/JCPCellPainter.java: Removed a lot of extra lines and some formatting
12:32 CIA-58 bioclipse: goglepox * r9563 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/MoleculeTableViewer.java: Added size config for rowHederColumnWidthConfig
12:32 CIA-58 bioclipse: goglepox * r9564 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeViewerContentProvider.java: Changed reference for hidden fields
12:32 CIA-58 bioclipse: goglepox * r9565 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeViewerContentProvider.java: Cleaned up retrieval of IMolecule now uses generics
12:33 CIA-58 bioclipse: goglepox * r9566 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeViewerContentProvider.java: Fixed conversion of columnindex.
12:33 CIA-58 bioclipse: goglepox * r9567 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeViewerContentProvider.java: Adds NUMBER_OF_PROPERTIES by default when changing input.
12:34 CIA-58 bioclipse: goglepox * r9568 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Added better progress reporting.
12:34 CIA-58 bioclipse: goglepox * r9569 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Added null check when adapting
12:35 CIA-58 bioclipse: goglepox * r9570 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Added input changed operations to 'saveAs'. Fixes bug #492
12:35 zarah bug #492 | http://tinyurl.com/cgf6a6
12:35 CIA-58 bioclipse: goglepox * r9571 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (3 files): Added interface for handling columns
12:35 CIA-58 bioclipse: goglepox * r9572 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/MoleculeTableViewer.java: Changed from require a specific contentprovider to usage of a number of interfaces
12:36 CIA-58 bioclipse: goglepox * r9573 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculesEditor.java: Added handling for SMILES-files
12:38 olass joined #bioclipse
13:14 shk3 I can't run the exported bioclipse:
13:14 shk3 The Bioclipse executable launcher was unable to locate its companion shared library.
13:14 shk3 Does it work for you?
13:14 olass shk3: never seen that
13:14 olass will try tomorrow
13:14 shk3 could anybody try now?
13:15 shk3 please?
13:15 shk3 would like to work on the workspace stuff
13:15 olass shk3: just export and run bioclipse?
13:15 olass only core feature?
13:15 olass sure
13:15 shk3 yes
13:16 shk3 the default export
13:16 olass exporting
13:16 olass hmm, problems in net.bioclipse.dot
13:16 olass hmm, problems in net.bioclipse.doc
13:16 olass mom
13:20 CIA-58 bioclipse: ospjuth * r9574 /bioclipse2/trunk/plugins/net.b​ioclipse.doc/build.properties: Removed . from source build since no src to build anyway and export complained about this.
13:20 olass shk3: exporting succeeds, and bioclipse runs
13:20 olass maybe you should reinstall eclipse?
13:20 olass use 3.4.2
13:21 shk3 hm ok
13:21 shk3 too bad
13:21 olass why?
13:22 shk3 extra trouble
13:23 olass :)
13:23 olass exporting is always trouble
13:23 olass and detective work
13:47 shk3 olass: just committed the switch workspace stuff
13:47 shk3 I tested as far as possible
13:47 olass works?
13:47 shk3 could you do an export and see if it works exported?
13:47 olass sure
13:47 CIA-58 bioclipse: shk3 * r9575 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): re-added the switch workspace stuff
13:48 shk3 there is one detail remaining, but I would like to see if it works before
13:49 olass need to clean up some to test
13:49 olass will take 5-10 mins
13:50 shk3 sure
13:56 jonalv joined #bioclipse
13:56 jonalv oh hai...
13:57 egonw welcome back
13:58 jonalv thanks :)
14:13 masak jonalv: http://meta.wikimedia.org/wiki/Help:Table
14:13 zarah masak's link is also http://tinyurl.com/3cpu3t
14:25 masak http://producingoss.com/
14:26 masak allegedly a nice book.
14:26 masak and it's freely downloadable!
14:42 shk3 egonw?
14:42 egonw yes, what's up?
14:43 shk3 did you see bug #2697568
14:43 shk3 ?
14:43 shk3 would be great if you could comment on that.
14:43 egonw CDK?
14:43 shk3 yes
14:44 egonw seen it indeed...
14:44 egonw I think that's indeed a CML use case which did not have much attention yet
14:44 egonw do you think you can write a unit test for it?
14:45 shk3 I talked to some people in Jena who want to use jcp, so I would be interested in a fix.
14:45 shk3 shouldn't be a problem really.
14:45 shk3 sure I can do a test.
14:45 egonw thanx
14:45 egonw please assign to Miguel, him being the primary user of reactions in the CDK
14:45 egonw and ask his opinion
14:45 shk3 I could either do the suggested solution
14:46 shk3 or one holding the ref ids and replacing them after everything is read.
14:46 shk3 that Miguel Rojas?
14:46 egonw yes
14:46 shk3 or the jmol one?
14:46 shk3 ok
14:49 shk3 which branch should I work in?
14:57 shk3 egonw?
14:57 shk3 sorry, I am still confused with branches and git
14:57 egonw depends...
14:57 egonw not sure if it qualifies as true bug
14:57 egonw or merely a missing feature
14:57 egonw (plenty of those)
14:58 egonw so, pick what you like
14:58 olass shk3: please explain this to me
14:58 shk3 I need mor fundamental advice
14:58 egonw but since you have downstream users who are interested in the fix, I suggest 1.2.x
14:58 shk3 what do I do in git?
14:58 olass what does the code in ApplicationActionBarAdvisor
14:58 olass shk3?
14:58 shk3 mom
14:58 egonw shk3: what do you want it to do?
14:59 shk3 olass: applicationActionBarAdiviser just adds the menu item
14:59 shk3 egonw: put the test (and perhaps a fix) to the CMLReader somewhere
14:59 shk3 somewhere should be where it should go
14:59 shk3 olass: does it work?
14:59 olass no idea
14:59 olass haven't tested yet
15:00 shk3 ok
15:00 shk3 the really relevant code is
15:00 shk3 net.bc.core.Activator
15:00 shk3 starting l 70
15:00 olass shk3: why have you removed lines in bioclipse.product?
15:01 olass they define the default workspace
15:01 shk3 because if it is set there, it can not be changed later
15:01 olass shk3: please...
15:01 shk3 we need this @nodefault or so in bioclipse.product
15:01 shk3 to set it later
15:01 shk3 after start
15:02 olass shk3: I wrote in the email that we should have a default workspace on first startup
15:02 egonw git will not tell you in which branch you should put it...
15:02 egonw shk3: you have to decide that yourself
15:02 shk3 we have that
15:02 shk3 olass
15:02 olass where is that defined?
15:02 shk3 in net.bc.core.Activator
15:02 shk3 read from line 70 there
15:02 shk3 lots of comments in there
15:03 olass I see no lines like the ones you removed
15:03 shk3 egonw: I thought you could tell me
15:03 shk3 olass: which file?
15:03 olass [17:05] < shk3> in net.bc.core.Activator
15:03 shk3 ok
15:04 shk3 it is (should be) like this:
15:04 olass line 70 and on
15:04 egonw shk3: do cdk-1.2.x then
15:04 shk3 // fetch the Location that we will be modifying
15:04 shk3 Location instanceLoc = Platform.getInstanceLocation();
15:04 shk3 // if the location is already set, we start from eclipse
15:04 shk3 if(!instanceLoc.isSet()){
15:04 shk3 // remember=true means we do a restart from "switch workspace" and therefore
15:04 shk3 // get the workspace location from dialog, if not, we use the default one.
15:04 shk3 boolean remember = PickWorkspaceDialog.isRememberWorkspace();
15:04 shk3 if(remember){
15:04 shk3 instanceLoc.set(new URL("file", null, PickWorkspaceDialog.getLas​tSetWorkspaceDirectory()), false);
15:05 shk3 PickWorkspaceDialog.setRememberWorkspace( false );
15:05 shk3 }else{
15:05 shk3 instanceLoc.set(new URL("file", null, PickWorkspaceDialog.getWorkspacePathSuggestion()), false);
15:05 shk3 }
15:05 shk3
15:05 shk3 }
15:05 * egonw is heading home now
15:05 egonw bye
15:05 shk3 this is line 67 to 82
15:05 shk3 do you have that?
15:05 shk3 egonw: ok, will try
15:05 shk3 i have a git checkout
15:05 shk3 saying git branch -a gives me
15:05 shk3 an asterisk in front of cdk-1.2.x
15:05 shk3 so I can work in this checkout, right?
15:05 shk3 :-(
15:06 egonw shk3: try
15:07 egonw git checkout -b local-1.2.x cdk-1.2.x
15:07 egonw checkout -b will create you a new branch
15:08 egonw shk3: you have seen the wiki page I wrote?
15:08 shk3 no
15:08 shk3 which one?
15:09 shk3 olass: any progress? if you just start, you should get no dialog, but the default workspace. If you do the switch workspace, it should ask.
15:09 shk3 that's what I intended.
15:09 egonw https://apps.sourceforge.net/mediawiki/c​dk/index.php?title=Development_with_Git
15:09 egonw shk3: that one
15:10 shk3 thanks
15:10 shk3 will read through it
15:11 shk3 olass: don't worry about the use of that remember flag right now
15:11 shk3 I will clean that up once I know it works.
15:11 olass shk3: I am updating now
15:12 olass shk3: will test, but if it fails I will ask you to revert and commit again. ok?
15:13 * olass is concerned about core stability
15:13 olass almost there...
15:13 olass shk3: tomorrow there will be a release
15:14 olass would be great to have switch workspace in there
15:14 olass so people can test it
15:14 shk3 should be no problem
15:14 olass ok, exporting
15:14 shk3 great
15:19 olass @ping
15:19 zarah olass: pong
15:19 stain olass: I'm going to a core stability class in my gym
15:19 olass joined #bioclipse
15:20 olass shk3: it seems to work fine
15:20 olass need to run now
15:20 olass shk3++
15:20 olass bye
15:21 shk3 good to hear
15:21 shk3 will do one modification
15:21 shk3 and then it can go into the release
15:21 edrin joined #bioclipse
15:39 CIA-58 bioclipse: shk3 * r9576 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Improvement in Switch Workspace: If remember is checked, the new workspace will be used in the future (till another workspace is choosen via Switch Workspace and/or remember unchecked).
17:00 olass joined #bioclipse
17:05 shk3 joined #bioclipse
17:10 edrin left #bioclipse
18:06 egonw joined #bioclipse
18:09 olass joined #bioclipse
18:09 olass hi
18:09 zarah saluton olass
18:17 egonw hi olass
18:28 olass hi egonw
20:46 edrin joined #bioclipse
20:46 edrin zarah tell egonw http://www.youtube.com/watch?v=ZUBQknWU​EYU&amp;eurl=http%3A%2F%2Fwww.spiegel.d​e%2Fnetzwelt%2Fweb%2F0%2C1518%2C616948-​7%2C00.html&amp;feature=player_embedded
20:46 zarah edrin's link is also http://tinyurl.com/d9sp7f
20:46 zarah Consider it noted.
20:50 ilogger2 joined #bioclipse

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