Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-11-24

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
07:47 egonw joined #bioclipse
07:49 Gpox joined #bioclipse
08:01 egonw_ joined #bioclipse
08:05 edrin joined #bioclipse
08:26 Gpox joined #bioclipse
08:27 CIA-53 bioclipse: egonw * r7811 /bioclipse2/trunk/features/net.biocl​ipse.speclipse_feature/feature.xml: Added CDK1.0 plugins, as they are no longer part of the Cheminformatics feature
09:01 CIA-53 bioclipse: goglepox * r7812 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java:
09:01 CIA-53 bioclipse: Changes to work with the merged jchempaint branch
09:01 CIA-53 bioclipse: of cdk
09:01 CIA-53 bioclipse: goglepox * r7813 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Uses the new Renderer object for rendering
09:13 jonalv joined #bioclipse
09:13 jonalv hi
09:13 zarah hi jonalv
09:22 egonw_ hi jonalv
09:22 jonalv so how far along did jchempaint get? :)
09:23 jonalv is there something I can test-run? :)
09:26 egonw_ yes, see:
09:26 egonw_ https://apps.sourceforge.net/mediawiki/cd​k/index.php?title=JChemPaintWorkshop2008
09:27 egonw_ there is a new update site up on pele
09:27 egonw_ https://apps.sourceforge.net/mediawiki/cdk/inde​x.php?title=JChemPaintWorkshop2008#JChemPaint_2.5.0_for_Bioclipse
09:27 egonw_ or just run Bioclipse from trunk with the JChemPaint feature :)
09:27 jonalv think I will do that :)
09:35 jonalv uhm net.bioclipse.cdk.jchempaint.view is not compiling for me...
09:36 jonalv egonw_: do you know anything about that?
09:37 egonw_ mom, checking
09:38 jonalv for example it can't find: org.openscience.cdk.renderer.Renderer
09:39 egonw_ I dont' get any errors here...
09:39 jonalv how irritating
09:39 egonw_ hang on
09:40 egonw_ let me check if I have Gpox' latest commits
09:40 egonw_ whcih I don't
09:40 jonalv k
09:41 jonalv Gpox: Why doesn't it compile for me?
09:41 egonw_ because you need the org.openscience.cdk.render from the jchempaint primary branch, I think
09:42 egonw_ or wait until the are synched again ...
09:42 egonw_ Gpox: ping
09:42 Gpox yes thats right
09:42 egonw_ Gpox: do you got anything pending to jchempaint-primary, or should I synchronize
09:45 Gpox yes i got some
09:45 Julio joined #bioclipse
09:46 egonw hi Julio
09:46 egonw Julio: you store more than 30 secs this time?
09:46 egonw store=stay
09:46 Julio hi
09:46 zarah hi Julio
09:46 * egonw wonders what is wrong with his keyboard... or whether he is still asleep...
09:46 Julio hi guys
09:46 egonw hi :)
09:46 jonalv hi Julio
09:47 egonw good that your connection is not lost directly again
09:47 * egonw still wonders what a 'nookie' is ...
09:47 jonalv Gpox: where did you go?
09:48 jonalv ah right
09:48 jonalv so I should just forget about having a look at jchempaint right now then?
09:48 egonw nope
09:48 egonw I'll sync
09:48 Julio I have a question about CDK, I posted it in the CDK chat room
09:49 jonalv Julio: I don't see a question just a statement about you having a question...
09:49 egonw jonalv: :)
09:50 edrin hi
09:50 zarah hi edrin
09:51 jonalv hi edrin
09:51 edrin hi jonalv
09:56 jonalv egonw: what the adress to the new update site?
09:56 egonw see that wiki page
09:56 jonalv + is there something about it on the Bioclipse site?
09:56 egonw nope
09:57 egonw not at this moment
09:57 egonw it's more for the daring people
09:57 egonw with experimental stuff, really
09:57 egonw Gpox: let me know when you are done patching in jcp-primary
09:58 edrin what are current bc2 release plans?
09:58 egonw december
09:59 egonw so, last friday before x-mas I guess :)
09:59 egonw edrin: if you want something in, you need to write unit testing
09:59 egonw CoverageTest and BlaManagerPluginTest
10:00 egonw http://wiki.bioclipse.net/index.php?title​=List_of_stable_managers_in_bioclipse_2.0
10:00 jonalv egonw: Update operation has failed
10:00 jonalv Error retrieving "plugins/org.eclipse.core.fi​lesystem.macosx_0.0.0.jar". [Server returned HTTP response code: "404 Not Found" for URL: http://pele.farmbio.uu.se/experimental/update/plu​gins/org.eclipse.core.filesystem.macosx_0.0.0.jar.]
10:00 jonalv Server returned HTTP response code: "404 Not Found" for URL: http://pele.farmbio.uu.se/experimental/update/plu​gins/org.eclipse.core.filesystem.macosx_0.0.0.jar.
10:00 jonalv
10:00 zarah egonw's link is also http://tinyurl.com/68dyxn
10:00 zarah jonalv's link is also http://tinyurl.com/5m3xbz
10:00 zarah jonalv's link is also http://tinyurl.com/5m3xbz
10:00 jonalv egonw: very experimental indeed... :)
10:02 Gpox egonw: i am done patching
10:02 egonw Gpox: tack
10:04 edrin egonw: i could adjust the wsdbfetch plugin wizard for retrieving EBI db entries if this is wanted
10:07 egonw jonalv: mmm... delta pack missing, I guess :)
10:08 jonalv egonw: yea so it would seeem...
10:08 egonw edrin: yes, that would be nice I think
10:08 egonw jonalv: please file a bug report
10:08 jonalv I will try to get usermanager over to the stable managers now...
10:10 egonw excellent
10:10 egonw please update the wiki page when done
10:15 jonalv egonw: will do :)
10:15 shk3 joined #bioclipse
10:24 jonalv egonw: wasn't the coverage test included with the abstractManager test?
10:25 egonw no
10:25 jonalv egonw: why not?
10:26 egonw because I rather have it spit up...
10:26 egonw though I do not have arguments against other options
10:27 jonalv hm okey. I just thought I was done after I had extended abstractManagerTest but obvkiiuoly I wasn't...
10:37 CIA-53 bioclipse: egonw * r7814 /bioclipse2/trunk/cdk-externals/trunk/ (40 files in 9 dirs): Synchronized with CDK's jchempaint-primary (rev 13241)
10:50 egonw Gpox: please check the commit I just made
10:50 gilleain joined #bioclipse
10:51 egonw Gpox: and have a loot at the ExtraGenerator
10:51 egonw because that one gives seven compile errors
10:52 egonw Gpox, gilleain: btw, please check the files you checked in to ensure they have copyright headers
10:54 Julio left #bioclipse
10:54 shk3 and module declarations
10:55 shk3 btw, the whole jcp project is experimental right now
10:56 shk3 nobody should complain about code in there
10:56 shk3 but we don't need a branch or so, right?
11:00 egonw no, we *should* complain
11:00 egonw otherwise it won't be improved...
11:00 egonw always complain
11:00 shk3 well, depends on
11:00 egonw just don't shout, be polite, etc...
11:00 shk3 I am heavily working on this
11:01 shk3 and I put in lots of TODOs
11:01 egonw don't blame people, just say where they can improve things
11:01 shk3 to find places where I now I need to do something
11:02 egonw if you want to commit unfinished stuff, use a branch
11:02 egonw that is...
11:02 egonw if others depend on something compiling...
11:05 * jonalv likes to now what's going if something is not compiling. That's just me... :)
11:05 shk3 well, whole jcp is unfinished
11:05 shk3 but compiles
11:05 egonw 'compiles' is the primary thing
11:05 jonalv honestly what is finnished?
11:05 egonw but anything beyond that can be commented on too
11:05 shk3 I think it is
11:05 CIA-53 bioclipse: egonw * r7815 /bioclipse2/trunk/cdk-externals/trunk/org.o​penscience.cdk.render/src/org/openscience/c​dk/renderer/generators/ExtraGenerator.java: Removed unused and broken class
11:05 egonw jonalv: dunno
11:05 shk3 at least for the jcp project right now
11:06 egonw jonalv: I do know what fiNished is :)
11:06 * egonw thinks shk3 should start making functionality lists
11:06 * jonalv wonders if software ever get finished
11:06 egonw umm
11:06 * egonw thinks jonalv should start making functionality lists
11:06 egonw shk3: sorry
11:07 egonw jonalv: when all functionality is implemented it is finished
11:07 egonw then comes the maintaince list
11:07 jonalv egonw: intresting...
11:07 egonw (and the snow keep falling)
11:07 egonw Gpox: ping
11:07 egonw or gilleain
11:07 Gpox yes
11:07 jonalv yea lucky you who are at home and don't need to bike home...
11:07 gilleain pong
11:07 egonw I got a IRenderingVisitor.visitModel() not found
11:08 egonw jonalv: yes :)
11:08 gilleain where/why/how?
11:08 egonw org.openscience.cdk.render -> RenderingModel
11:08 egonw gilleain: a fresh copy of jchempaint-primary into BC2 SVN
11:09 gilleain Ah. Arvid's "model" has been changed to my "ElementGroup".
11:09 gilleain so visitModel(Model m) becomes visitElementGroup(ElementGroup group)
11:10 gilleain Sorry. I know that changing the interfaces changes things downstream.
11:10 egonw yeah, no worries...
11:10 egonw ok, when I change the method call
11:10 gilleain But it isn't always clear beforehand what the interface needs to be, until the implementation is in place.
11:10 egonw it now complains that visitElementGroup cannot be applied to RenderingModel
11:10 egonw Gpox, gilleain: please check and fix
11:11 egonw as I am not sure how to proceed
11:11 egonw gilleain: indeed...
11:11 CIA-53 bioclipse: jonalv * r7816 /bioclipse2/trunk/plugins/ (6 files in 4 dirs): [usermanager] added "Bioclipse manager testing" to the usermanager
11:11 gilleain Is your visitElementGroup consuming an ElementGroup?
11:11 jonalv egonw: I hope you have winterdecks on the car now... :)
11:11 gilleain Or a Saab.
11:12 Gpox there is no RenderinModel it has been renamed to ElementGroup
11:13 gilleain By the way, Gpox : I think you were right - things are better if the generated IRenderingElements are not transformed to the origin.
11:14 shk3 egonw: how to track when a chemmodel changes?
11:14 egonw jonalv: winterdeck? what's that? winter tires with spikes?
11:14 jonalv sry yea
11:14 jonalv I am not awake yet either
11:14 egonw Gpox: oh, then I'll just remove that class
11:15 gilleain It means that there is one more addition per draw cycle, and when translating back to model space, but it is more consistent.
11:15 egonw yes, we got those
11:15 gilleain What do you think?
11:15 egonw shk3: register a listener?
11:15 egonw shk3: but maybe track state yourself...
11:15 egonw shk3: as you already know when you perform an edit
11:15 jonalv egonw: seems like they will be needed... :)
11:16 egonw yes, nice :)
11:17 jonalv just a quick check: Should org.openscience.cdk.render compile for me?
11:17 egonw after this comimt:
11:17 egonw (problem was that I copied in the new .render/ without deleting the old code)
11:17 CIA-53 bioclipse: egonw * r7817 /bioclipse2/trunk/cdk-externals/trunk/org.o​penscience.cdk.render/src/org/openscience/c​dk/renderer/elements/RenderingModel.java: Removed obsolete class
11:17 * jonalv is looking forward to see what jchempaint looks like now. :)
11:18 egonw jonalv: with that patch it should compile properly again
11:18 * jonalv is updating and testing
11:18 gilleain horrible is what it looks like.
11:18 egonw :)
11:18 jonalv oh how come?
11:18 gilleain refactoring/redesigning always makes things seem worse for a while.
11:18 jonalv okey
11:19 gilleain but things are better, I swear! :)
11:19 jonalv haha okey
11:19 egonw gilleain: the copyright header should be before the package line
11:19 gilleain http://gilleain.blogspot.com/2008/11/chalky.html
11:19 zarah gilleain's link is also http://tinyurl.com/59nemz
11:19 gilleain oh, really?
11:19 gilleain oh well.
11:19 egonw umm... yeah, sort of ...
11:19 shk3 egonw: there is only a IChemObjectListener, and that seems to be called all the time, even with hightlights
11:19 egonw just remember it boosts your svn stats :)
11:19 shk3 so need to do it myself
11:20 shk3 ok
11:20 egonw shk3: yeah... that needs to be split up
11:20 gilleain will fix.
11:20 egonw shk3: but did not have time to come up with a patch yet
11:21 jonalv wow many colors in this new editor...
11:22 egonw who did the Outline in the old JCP editor? Ola I guess??
11:23 jonalv that would be my guess as well
11:38 jonalv egonw: about bug #138
11:38 jonalv Is that the best we can do?
11:40 egonw with this bugzilla?
11:40 egonw it seems so
11:40 egonw what did you have in mind?
11:41 jonalv that we use the QA features...
11:41 jonalv it is there isn't it_
11:43 egonw have not really found them
11:43 egonw other than that a QA team can put a VERIFIED label
11:43 jonalv yea
11:44 jonalv and after it's verified it can be closed...
11:44 egonw but that's something you can already do...
11:44 egonw after you fixed it, assign it to someone from the QA team
11:45 jonalv egonw: no
11:45 egonw no?
11:45 jonalv you can not assign a fixed bug
11:45 egonw oh
11:45 gilleain There's a QA team?
11:45 egonw no
11:45 jonalv I can see use for one...
11:46 gilleain A metaphorical team, then. A theoretical team-construct?
11:46 egonw here's where the commercial support comes in
11:49 * jonalv heads out looking for something that can be eaten. cya
12:58 jonalv very quite here...
13:08 jonalv egonw: What was that about commercial support_
13:08 jonalv ?
13:11 charlgren joined #bioclipse
13:16 * egonw was away for lunch
13:16 egonw there is some 30cm snow now here
13:17 jonalv yea, I took a walk over to Blå and had a pizza...
13:17 jonalv it's snowing alrigt...
13:17 egonw ah nice
13:17 jonalv :/
13:17 egonw it just sort of stopped here
13:17 jonalv not here...
13:18 jonalv egonw: Do you know when olas will be back?
13:18 egonw I think next week
13:18 egonw I hope so
13:18 jonalv I am still not sure about the structuredb gui. I could use some input from you and olas...
13:19 egonw otherwise the BC2.0.0 will be really difficult
13:19 jonalv yea
13:19 egonw I'll be at UU Wed-Fri
13:19 egonw at your disposal
13:19 jonalv oh not tomorrow?
13:19 jonalv :)
13:19 egonw no
13:19 egonw Fien turns 5 tomorrow
13:19 jonalv oh aha :)
13:46 CIA-53 bioclipse: egonw * r7819 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (9 files in 3 dirs): Ported Ola's Outline to the new JChemPaintEditor
13:52 gilleain If I see things which are not bugs, but potential improvements to how the cdk does things, I should still make a bug report, correct? Or a feature request?
13:53 jonalv yea
13:53 gilleain yea which?
13:53 gilleain :)
13:54 gilleain yay, my screen is in readable mode again.
13:56 egonw gilleain: bug report, severity 'enhancement'
13:57 gilleain ahh. ok.
14:01 egonw gilleain: brilliant blog!
14:01 egonw how do I enable that in Bioclipse?
14:05 gilleain Oh, right, what, no.
14:06 gilleain You could do that in bioclipse.
14:06 gilleain if you re-wrote it.
14:06 gilleain :)
14:06 egonw ah :(
14:06 gilleain see : http://github.com/gilleain/renderlabs
14:06 zarah gilleain's link is also http://tinyurl.com/5zx4ck
14:07 gilleain I often make tiny experimental apps (single frame, no buttons, minimal interaction) to try out stuff.
14:08 egonw yes, very good
14:08 gilleain If you've ever seen processing (or proce55ing, as it used to be called)
14:08 egonw that's they way it should be
14:08 gilleain It's good because it forces me to think like a client of the cdk.
14:08 gilleain not like a cdk developer.
14:09 egonw processing?
14:09 egonw no, have not seen that
14:09 gilleain it's a scripting language on top of java for making applets/pictures/animations.
14:09 gilleain http://processing.org
14:11 egonw mmmm... looks interesting...
14:11 egonw you make graphics with java?
14:11 egonw in pro55esing?
14:12 gilleain you can write it in processing, or use the api in pure java.
14:13 egonw looks nice!
14:13 gilleain it's great for sketching out graphics things
14:13 egonw yeah, indeed
14:13 egonw I'm browsing the examples...
14:18 egonw joined #bioclipse
14:19 egonw grmphh...
14:19 gilleain shk3: commited it
14:19 egonw my java/ff crashes my X11 session way too often
14:19 egonw third time today now :(
14:20 gilleain :(
14:22 egonw quite so...
14:22 egonw first two times was with nmrshiftdb.org
14:22 egonw it's the applets :(
14:50 * jonalv heads over to the hospital now. will be back soon. Where soon depends on the amount of snow outside...
14:51 shk3 is it still snowing?
14:52 jonalv yes
14:52 egonw yes
14:55 shk3 wow
14:56 egonw gilleain: please check this commit:
14:56 gilleain ...
14:57 gilleain which commit?
14:59 egonw mom ...
14:59 egonw you just commited something to the same file
14:59 egonw which trips up svn
14:59 egonw should be around the corner now
15:00 egonw ah, on #cdk :)
15:29 CIA-53 bioclipse: egonw * r7820 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (19 files): Copied missing PNGs for the Outline from the cdk10.jchempaint plugin
16:05 egonw a huge tractor is making our road to the 55 snow free :)
16:20 CIA-53 bioclipse: egonw * r7821 /bioclipse2/trunk/plugins/net.biocl​ipse.core.tests/src/net/bioclipse/c​ore/tests/AbstractManagerTest.java: Fixed test: sum.length() isnot 0 results in a Boolean and is NotNull by default
16:21 CIA-53 bioclipse: egonw * r7822 /bioclipse2/trunk/plugins/net.bioclipse​.core.tests/src/net/bioclipse/core/test​s/coverage/AbstractCoverageTest.java: Added test for empty TestMethods annotation (fixes #143)
16:21 zarah bug #143 | http://tinyurl.com/55t8ok
17:11 edrin left #bioclipse
17:50 Gpox joined #bioclipse
19:23 CIA-53 bioclipse: egonw * r7823 /bioclipse2/trunk/plugins/net.biocl​ipse.core.tests/src/net/bioclipse/c​ore/tests/AbstractManagerTest.java: Extended testForFooJobImplementations to support foo(X, IFile, Y) too
19:32 CIA-53 bioclipse: egonw * r7824 /bioclipse2/trunk/plugins/net.biocl​ipse.core.tests/src/net/bioclipse/c​ore/tests/AbstractManagerTest.java: Fixed JavaDoc, to match the actual test
19:33 CIA-53 bioclipse: egonw * r7825 /bioclipse2/trunk/plugins/net.biocl​ipse.core.tests/src/net/bioclipse/c​ore/tests/AbstractManagerTest.java: Better testing: count params help fields, but only for methods which actually has parameters
19:58 CIA-53 bioclipse: egonw * r7826 /bioclipse2/trunk/plugins/net.biocl​ipse.core.tests/src/net/bioclipse/c​ore/tests/AbstractManagerTest.java: Factored out a method, for reuse later
19:59 CIA-53 bioclipse: egonw * r7827 /bioclipse2/trunk/plugins/net.biocl​ipse.core.tests/src/net/bioclipse/c​ore/tests/AbstractManagerTest.java: Added a method that assumes that any @Job method with a String as last parameter, has a matching method with the same signature, expect String becomes IFile, IProgressMonitor, Runnable (fixes #133)
19:59 zarah bug #133 | http://tinyurl.com/5epxwf
21:22 edrin joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary