Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-06-09

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All times shown according to UTC.

Time Nick Message
04:02 egonw joined #bioclipse
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06:09 egonw joined #bioclipse
06:10 annzi joined #bioclipse
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06:17 CIA-70 bioclipse.cheminformatics: Arvid Berg 2.4.x * redc067e / (3 files in 3 dirs): Added BasicSceneGenerator to jcp widgets - http://bit.ly/aCYFje
06:17 CIA-70 bioclipse.cheminformatics: Egon Willighagen 2.4.x * ra2d7a8e / (15 files in 7 dirs): Updated for CDK-JChemPaint 12 API changes - http://bit.ly/9F3Jqq
06:17 CIA-70 bioclipse.cheminformatics: Arvid Berg master * r93d208a / (3 files in 3 dirs): Added BasicSceneGenerator to jcp widgets - http://bit.ly/bhH0Gf
06:17 egonw moin
06:17 zarah hello egonw, you fantastic person you
06:17 CIA-70 org.openscience.cdk: Egon Willighagen bioclipse2.4 * ra19e5e3 / (32 files in 23 dirs): Uploaded CDK-JChemPaint 12 - http://bit.ly/aY1hwE
06:17 egonw @tell Gpox please note the upload of CDK-JCP 12
06:17 zarah Consider it noted.
06:19 CIA-70 org.openscience.cdk: Arvid Berg bioclipse2.4 * r98cd2bd / plugins/org.openscience.cdk.renderbasic/src/org/op​enscience/cdk/renderer/AtomContainerRenderer.java : Removed scale and zoom form renderer and replaced with values form the generator parameters - http://bit.ly/94CPvh
06:19 CIA-70 org.openscience.cdk: Arvid Berg bioclipse2.4 * rb453c27 / plugins/org.openscience.cdk.renderextra/src​/org/openscience/cdk/renderer/Renderer.java : Removed scale and zoom form renderer and replaced with values form the generator parameters - http://bit.ly/bd4Std
06:21 annzi joined #bioclipse
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06:59 Gpox joined #bioclipse
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08:47 jonalv joined #bioclipse
08:51 jonalv oh hai
08:51 zarah saluton jonalv
09:14 sneumann_ good morning!
09:14 sneumann_ what happened to hudson ?
09:14 sneumann_ http://pele.farmbio.uu.se/hudson/
09:14 zarah sneumann_'s link is also http://tinyurl.com/yf9nyk4
09:14 sneumann_ pretty empty :-(
09:14 egonw joined #bioclipse
09:15 sneumann_ what happened to hudson ?
09:15 sneumann_ http://pele.farmbio.uu.se/hudson/
09:15 zarah sneumann_'s link is also http://tinyurl.com/yf9nyk4
09:15 sneumann_ pretty empty :-(
09:16 jonalv Gpox?
09:18 egonw offline, because I have not figured out how to hide the admin functionality...
09:18 egonw sneumann_: never mind how much I trust you, you are not going to get free, public admin rights ;)
09:19 egonw otherwise...
09:19 egonw Gpox' Hudson is still on his machine, not the instance running on pele
09:22 sneumann_ is the admin rights fixed to some URL ?
09:23 egonw good idea!
09:23 sneumann_ you could add a rewrite rule to only allow access from inside
09:23 egonw not sure though... would have to check
09:23 sneumann_ or put in some /hudson/admin/.htaccess
09:23 egonw but I'll keep that in mind
09:23 sneumann_ was just trying to convince someone here to write unit tests :;-)
09:24 jonalv egonw, Gpox: Did someone of you do fixes for ola's repos? Who do I pull from?
09:24 egonw ah, well those would not be online yet anyway...
09:24 egonw sneumann_: but perhaps use the CDK nightly build
09:24 egonw not using Hudson, though
09:24 sneumann URL ?
09:24 egonw http://pele.farmbio.uu.se/supernightly/
09:24 zarah egonw's link is also http://tinyurl.com/ku2bhf
09:25 egonw jonalv: I have not yet
09:26 Gpox jonalv: I have
09:26 Gpox going through my changes now, will ping you when pushed
09:26 jonalv Gpox: do you remember which repos?
09:26 jonalv okey
09:26 jonalv cool
09:27 Gpox metapring, ds and qsar
09:27 Gpox did you have changes ot qsar?
09:28 jonalv (where was it the log file was on Mac again?)
09:29 jonalv Gpox: did I have changes at qsar? I am not sure I understand what you mean
09:29 Gpox *to
09:30 jonalv uhm I don't know. Did I make changes?
09:30 jonalv no idea
09:31 jonalv since when?
09:31 Gpox you had some local changes yesterday I think
09:32 jonalv to qsar?
09:33 jonalv hm
09:33 jonalv hang on
09:33 jonalv no it doesn't look like it
09:33 jonalv could you just remind me where I can find the log file?
09:34 jonalv I am stuck without a stacktrace on claes machine and I am sort of hoping he log file might contain something
09:34 Gpox either in home or in ~/Library/Logs/Bioclipse
09:34 egonw sneumann: ping
09:35 egonw Gpox: do, you fixed metaprint2d, ds, and qsar wrt CDK-JCP 12?
09:35 Gpox working on commits right now
09:35 egonw ok, will not touch anything there then
09:44 * jonalv is back at his computer (working on two machines at the smae time )
09:44 jonalv Gpox: will yo send me pull requests when you are done with em then?
09:48 splicer joined #bioclipse
09:48 egonw hi splicer
09:48 splicer hi
09:48 zarah saluton splicer
09:49 splicer hehe.. even that.. thansk
09:49 splicer thanks
09:49 egonw you're from umea?
09:49 splicer yes
09:50 egonw welcome :)
09:50 egonw zarah is our smart bot
09:50 splicer I better stop answering her then
09:51 egonw :)
09:51 egonw masak: we should really say something about zarah in the channel title...
09:51 egonw and perhaps remove the reference to the bioclipse2 beta :)
09:51 masak egonw: feel free.
09:51 * egonw is no operator
09:52 egonw why not, he wonders...
09:52 * masak neither
09:52 * jonalv is no operator either
09:52 * jonalv seems to remember edrin being op
09:52 splicer CIA is a bot too right?
09:55 jonalv splicer: yea
09:57 egonw CIA routes commit messages here
10:00 egonw s_wolf: ping
10:02 Gpox jonalv: pull requests sent
10:07 jonalv Gpox: it does not apply nicely, at least not for qsar
10:08 jonalv Gpox: should I go back to olas and then apply your patches?
10:09 * jonalv tries that
10:10 Gpox wait, seams egon alrady added fix
10:13 * jonalv waits
10:13 Gpox did a force upadte of my branch
10:14 Gpox it should apply now
10:15 egonw I fixed bioclipse.cheminformatics
10:16 s_wolf egonw: pong
10:16 s_wolf hi
10:16 egonw hej! see #metware
11:05 egonw jonalv: ping
11:05 egonw jonalv: nvm
11:08 CIA-70 bioclipse.metabolomics: Egon Willighagen master * r063166b / plugins/net.bioclipse.metfrag/META-INF/MANIFEST.MF : Fixed dependencies: Standard InChI, and nu.xom and CMLDOM in the new 2.4.x way, using Import-Package - http://bit.ly/cTr4KR
11:08 CIA-70 bioclipse.metabolomics: Egon Willighagen master * r70c96a1 / (7 files in 4 dirs): Set version numbers to 2.4.0.RC1 - http://bit.ly/do59VO
11:20 mgerlich joined #bioclipse
12:02 egonw Gpox: ping
12:02 Gpox pong
12:03 egonw at what places are generators aggregated?
12:04 egonw it seems RingGenerator is not registered somewhere...
12:04 egonw causing a JCP editor to fail to open
12:04 Gpox there is a problem with the ReadOnlyRenderinParameterWrapper
12:05 egonw yes
12:05 egonw which becomes visible when rendering parameters are not known :)
12:05 egonw found to missing rendering params returned with getRenderingParameters
12:05 egonw but...
12:05 egonw the one I am looking at right now, *is*
12:06 Gpox they are aggregated at a lot of places, jchempainteditorwidget, jchempaintwidget createGenerators, jcpcellrenderer
12:16 egonw Gpox: I found the problem now
12:16 egonw ok, there will be a cdk-jcp 13 release soon
12:16 masak joined #bioclipse
12:17 CIA-70 bioclipse.cheminformatics: Egon Willighagen 2.4.x * rbabd368 / plugins/net.bioclipse.cdk.jchempaint/sr​c/net/bioclipse/cdk/jchempaint/business​/JChemPaintGlobalPropertiesManager.java : Do not try to set a parameter which is not used; fixing a ClassCastException - http://bit.ly/9Q2UOm
12:36 egonw Gpox: ping
12:36 Gpox pong
12:36 egonw Gpox: gilleain was worried about the removal of the DEFAULT_SCALE
12:36 egonw to I am going to revert that bit in your patch
12:37 egonw OK?
12:37 Gpox sure I just did what you said :)
12:38 egonw yeah, blame it on me :)
12:38 egonw Gpox++
12:46 egonw Gpox: will finish CDK-JCP 13 at home
12:46 egonw leaving now
13:25 edrin joined #bioclipse
13:44 CIA-70 bioclipse.core: Claes Andersson 2.4.x * re04fc7a / plugins/net.bioclipse.core/src/net/bioclipse/manag​ers/business/AbstractManagerMethodDispatcher.java :
13:44 CIA-70 bioclipse.core: Add message to exception
13:44 CIA-70 bioclipse.core: Adds detailed message to exception thrown in
13:44 CIA-70 bioclipse.core: AbstractMethodDispatcher.java - http://bit.ly/ddIaRE
14:23 egonw joined #bioclipse
14:24 egonw Gpox: ping
14:24 Gpox pong
14:24 egonw I have a number of fixes...
14:24 egonw but I want to remove the ReadOnlyRenderingParameter
14:25 egonw because it does not extend the wrapped class, it causes all those ClassCastExceptions
14:25 egonw instead, I want to just throw an error...
14:25 egonw which its set() method now does...
14:25 egonw does that make sense?
14:26 Gpox yes I know, it was only one way to solve the missing parameter problem, that is the other solution
14:31 egonw now that there is the getDefault() and set() methods, it should be fine, I guess
14:31 Gpox get?
14:35 egonw what do you mean?
14:37 Gpox is there a get method or do you need to do model.getParameter().getValue()?
14:42 egonw yeah, will add a method for that too...
14:42 egonw are you also OK with these shorter names:
14:42 egonw public T getValue(IRenderingParameter<T>)
14:43 egonw public set(IRenderingParameter<T>, T)
14:43 egonw public T getDefault(IRenderingParameter<T>)
14:43 egonw and the fourth:
14:43 egonw public IRenderingParameter<T> get(IRenderingParameter<T>)
14:43 Gpox yes
14:49 Gpox I would sugest public T get(Class<IRenteringParapeter<T>) and public IRenderingParameter<T> getParameter(Class<IRenderingParameter<T>>) more in line with the set
14:49 egonw ok
14:50 Gpox the set, get and getDefault returns/pass-in the value T and if you wan the parameter object you do the longer getParameter
14:50 egonw yes
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