Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-12-03

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All times shown according to UTC.

Time Nick Message
06:11 egonw joined #bioclipse
06:15 sneumann_ joined #bioclipse
06:54 samuell joined #bioclipse
07:23 egonw joined #bioclipse
07:41 Gpox joined #bioclipse
07:56 sneumann_ joined #bioclipse
08:08 egonw samuell: http://feedproxy.google.com/~​r/talis/n2/~3/F57XQOrXgWo/941
08:08 zarah egonw's link is also http://tinyurl.com/ye3bn7y
08:09 samuell egonw: thx
08:41 CIA-65 bioclipse.cheminformatics: Arvid Berg 2.2.x * r06a344d / plugins/net.bioclipse.cdk.jchempaint/plugin.xml :
08:41 CIA-65 bioclipse.cheminformatics: Changed check for active editor if multipage.
08:41 CIA-65 bioclipse.cheminformatics: Using property tester to find out if JCP is the active editor in the mol table.
08:41 CIA-65 bioclipse.cheminformatics: Solves bug #1734 - http://bit.ly/4PKp5e
08:41 zarah bug #1734 | http://tinyurl.com/yct32b2
09:09 jonalv joined #bioclipse
09:36 samuell egonw: Just for testing, how close shifts would one typically be interested in? 0.1 difference? less?
09:37 * samuell grabs coffee
09:39 egonw proton NMR: .3
09:39 egonw carbon: 5
09:39 egonw samuell: but you can play with that, of course :)
09:41 sneumann_ We use 3 for 13C when doing 2D NMR
09:45 olass joined #bioclipse
09:45 egonw Gpox: ping
09:45 egonw hi olass
09:46 Gpox egonw: pong
09:46 olass hi
09:46 zarah hello olass, you fantastic person you
09:46 egonw Gpox: I ran into some patch reordering problems...
09:46 egonw there are circular deps in the IOldChemModelRelay patch :(
09:47 egonw Gpox: which means that I cannot move all patches in the current bioclipse-2.1.x branch into the proper locations :(
09:49 Gpox what kind of deps?
09:50 egonw this patch:
09:50 egonw "Moved all methods except the most important from IChemModelRelay to IOldChemModelRelay"
09:50 egonw (my hashes are different, rebased...)
09:50 egonw which gives a compile error
09:50 egonw about two update methods
09:51 egonw and makes renderextra fail
09:52 egonw Gpox: but we are not going to worry about this now...
09:52 egonw just wanted you to know...
09:52 egonw we'll have to do some patch rewriting in january, when we already wanted to make changes for BC 2.4 anyway
09:52 egonw practically means that I am moving the patches in bioclipse-2.1.x into 10-unsorted
09:53 egonw and then I'll rename a bunch of branches
09:53 egonw and start applying patches in your pele jcpprim repository
09:57 samuell egonw: Ok... .3 makes sense... since it seems like .1 is the smallest step
09:57 egonw .3 is about the computational accuracy you can acchieve with current methods...
09:57 egonw though some report closer to .2, I am not entirely convinced about those statistics
09:58 samuell egon: Oh, ok
09:58 samuell I mean "Ah, ok"
10:15 CIA-65 bioclipse.blipkit: Samuel Lampa master * rcac0e41 / (3 files in 2 dirs): Added rdf and pellet to product file, Improved manager help msg, and changed character to use for forcing type to atom - http://bit.ly/8TCsfE
10:23 egonw Gpox: update jchempaint-primary on pele
10:23 egonw Gpox: my schedule
10:23 egonw 1. rename branches (fix numbering, names reflecting purpose)
10:24 egonw 2. git format-patch and apply to a clean cdk 1.3.1, creating a cdk-jchempaint repository on the fly
10:24 egonw 3. your patches (I will use the format-patch route)
10:24 olass egonw: I will try to build 2.2.0.RC2 tomorrow, do you think it will be possible to sync JCP-primary with bioclipse-cheminformatics before then? Or is this not useful?
10:25 egonw and put them into the currently-called 10-unsorted
10:25 egonw yes, that would be very useful
10:25 egonw and yes, I hope to finish it today
10:25 olass egonw: super!
10:25 egonw that was the whole aim :)
10:25 * olass was not sure
10:26 olass it's hard to keep up with everything :)
10:26 egonw which is good
10:26 egonw you do not have to keep up with all these details
10:26 olass my brain is still cooling down from last week...
10:26 egonw indeed
10:27 egonw Gpox: shall I prefix the branches with "cdkjcp-" ?
10:28 Gpox thats ok
10:29 egonw I was hoping for more than 'ok'...
10:29 egonw does it make sense? is it useful?
10:29 egonw does it make things more clear?
10:29 egonw if not, I leave it out
10:29 egonw you have a better prefix perhaps?
10:30 Gpox isn't the whole repository cdkjcp?
10:31 egonw yes, I will name if cdk-jchempaint
10:31 egonw so, it does not add anything, does it?
10:33 Gpox no I don't think it does
10:35 CIA-65 bioclipse.cheminformatics: Egon Willighagen 2.2.x * rd394608 / plugins/net.bioclipse.cdk.busi​ness.test/META-INF/MANIFEST.MF : Remove unneeded versioning of imported plugins - http://bit.ly/6EVYlx
10:35 egonw ok, so not ok :)
10:35 Gpox yes. no cdkjcp- prefix
10:35 egonw ack
10:35 egonw thanx for the feedback
10:38 Gpox @pz 431 # fixed this, bioclipse now has support single electrons
10:38 zarah Cannot detect feed type
10:39 Gpox @pz 431 //like this then?
10:39 zarah Gpox: I couldn't find anything on '431 //like this then?' in the database.
10:41 egonw 1-required-patches-for-the-cdk-library
10:42 Gpox @pz 431 #bug
10:42 zarah Cannot detect feed type
10:43 egonw Gpox: 2-design-render ?
10:43 egonw with 3-impl-renderbasic ?
10:44 egonw or 3-implemention-renderbasic ?
10:44 egonw should I add 'of' ?
10:44 egonw like:
10:44 egonw 2-design-of-render ?
10:44 egonw and
10:44 egonw 3-implementation-of-renderbasic ?
10:44 * egonw is getting coffee
10:44 Gpox 2-render-api
10:45 egonw ok
10:45 egonw 3-renderbasic-impl ?
10:45 Gpox 3-render-imp-basic
10:45 egonw ok
10:45 Gpox *+l
10:45 egonw works for me
10:45 egonw huh?
10:45 Gpox 3-render-impl-basic
10:45 egonw ah :)
10:45 egonw sure
10:45 * egonw will make it so
10:46 Gpox zarah--
10:47 Gpox @pz 431
10:47 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=431
11:57 egonw_ joined #bioclipse
12:02 olass all: http://www.biomedcentral.com/1471-2105/10/397/
12:02 zarah olass's link is also http://tinyurl.com/y862u67
12:02 olass please update your CV's :)
12:38 sneumann_ joined #bioclipse
13:55 * samuell has to figure out if SPARQL can do arithmetic comparisons...
13:56 * jonalv is reminded of addition in Prolog
13:59 samuell Yep, figured it out in Prolog, at last, so now the time has came to SPARQL, since I want to try to do the same thing in pellet
14:03 egonw samuell: try to formulate things in OWL axioms
14:04 egonw or at least parts of the solution
14:04 samuell egonw: Yeah, suspected that's what is needed
14:04 egonw Gpox: I've updated pele; writing up an email to cdk-jchempaint
14:05 CIA-65 bioclipse.cheminformatics: Arvid Berg master * r6abb115 / (3 files in 2 dirs): Added modules and edits for radical support - http://bit.ly/5GucGo
14:05 CIA-65 bioclipse.cheminformatics: Arvid Berg master * r12c75ea / (3 files in 3 dirs): Implements radical support in JCP - http://bit.ly/5LxYx0
14:05 CIA-65 bioclipse.cheminformatics: Stefan Kuhn master * r4b02c61 / cdk-externals/trunk/org.openscience.cdk​.renderextra/src/org/openscience/cdk/re​nderer/generators/RadicalGenerator.java :
14:05 CIA-65 bioclipse.cheminformatics: the RadicalGenerator can render atoms with more than one single electron.
14:05 CIA-65 bioclipse.cheminformatics: Signed-off-by: Arvid Berg <goglepox@users.sourceforge.net>
14:05 egonw crap
14:05 CIA-65 bioclipse.cheminformatics: Added rendering of more than one for vertical alignment too. And reverse direction on vertical alignment. - http://bit.ly/6tt19I
14:06 CIA-65 bioclipse.cheminformatics: Egon Willighagen master * r8a91370 / (7 files in 6 dirs): Merge commit 'goglepox/2.2.x' - http://bit.ly/7q5G0V
14:06 egonw wrong branch :(
14:06 CIA-65 bioclipse.cheminformatics: Arvid Berg 2.2.x * r6abb115 / (3 files in 2 dirs): Added modules and edits for radical support - http://bit.ly/5GucGo
14:06 CIA-65 bioclipse.cheminformatics: Arvid Berg 2.2.x * r12c75ea / (3 files in 3 dirs): Implements radical support in JCP - http://bit.ly/5LxYx0
14:06 CIA-65 bioclipse.cheminformatics: Stefan Kuhn 2.2.x * r4b02c61 / cdk-externals/trunk/org.openscience.cdk​.renderextra/src/org/openscience/cdk/re​nderer/generators/RadicalGenerator.java :
14:06 CIA-65 bioclipse.cheminformatics: the RadicalGenerator can render atoms with more than one single electron.
14:06 CIA-65 bioclipse.cheminformatics: Signed-off-by: Arvid Berg <goglepox@users.sourceforge.net>
14:06 CIA-65 bioclipse.cheminformatics: Added rendering of more than one for vertical alignment too. And reverse direction on vertical alignment. - http://bit.ly/6tt19I
14:41 CIA-65 bioclipse.blipkit: Samuel Lampa master * ra1c7804 / plugins/net.bioclipse.blipkit/src/net/biocl​ipse/blipkit/business/JPLQueryWrapper.java : Added methods 'isList' and 'termArrayToList' - http://bit.ly/4n0moJ
14:41 CIA-65 bioclipse.blipkit: Samuel Lampa master * ra6a576b / plugins/net.bioclipse.blipkit/src/net/biocl​ipse/blipkit/business/JPLQueryWrapper.java : Handle (prolog style) lists as input type - http://bit.ly/91HBOU
14:57 samuell egonw: Is there a special manager method for reading OWL files, or how do I do?
15:00 * samuell feels like he only knows about these semantic things in theory, not how to do it in practice :( ... more to learn ...
15:09 egonw owl == rdf
15:10 egonw so, no need for a special reading code
15:11 CIA-65 bioclipse.cheminformatics: Arvid Berg 2.2.x * rb6dea2f / plugins/net.bioclipse.cdk.jchempaint.view/src/ne​t/bioclipse/cdk/jchempaint/view/SWTRenderer.java :
15:11 CIA-65 bioclipse.cheminformatics: Scale line width in SWT-renderer
15:11 CIA-65 bioclipse.cheminformatics: Solves bug #1747 - http://bit.ly/7aMMVU
15:11 zarah bug #1747 | http://tinyurl.com/yjaxcoq
15:39 shk3 joined #bioclipse
18:52 olass joined #bioclipse
18:52 CIA-65 bioclipse.statistics: Ola Spjuth 2.2.x * r3fa7335 / (2 files in 2 dirs): Updated version to 2.2.0.RC2. - http://bit.ly/5cHVTT
18:52 CIA-65 bioclipse.balloon: Ola Spjuth 2.2.x * r2158213 / (8 files in 8 dirs): Updated version to 2.2.0.RC2. - http://bit.ly/8nkUIR
18:53 CIA-65 bioclipse.core: Ola Spjuth 2.2.x * ra448fcd / features/net.bioclipse.birt_feature/feature.xml : Set version to 2.2.0.RC2. - http://bit.ly/7g9PZo
18:53 CIA-65 bioclipse.ds: Ola Spjuth 2.2.x * rd46cafa / (9 files in 9 dirs): Updated version to 2.2.0.RC2. - http://bit.ly/6TC1CY
18:54 CIA-65 bioclipse.qsar: Ola Spjuth 2.2.x * r5d18b44 / plugins/net.bioclipse.qsar.ui/src/net/bio​clipse/qsar/ui/editors/MoleculesPage.java :
18:54 CIA-65 bioclipse.qsar: Do not repopulate in pageChanged; avoids Exception.
18:54 CIA-65 bioclipse.qsar: Got an "Getter called on disposed observable" after moving to 3.5. - http://bit.ly/7venSA
18:54 CIA-65 bioclipse.qsar: Ola Spjuth 2.2.x * rfb5bd3a / (16 files in 16 dirs): Updated version to 2.2.0.RC2. - http://bit.ly/7IegNp
18:55 olass egonw: would be great if you could set ID to 2.2.0.RC2 for all plugins and all features in your repos where you are dictator
18:55 olass for tomorrow's RC2 build :)
18:58 * olass will go practice bandy now
18:58 olass see you tomorrow
18:58 olass bye
20:59 CIA-65 bioclipse.cheminformatics: Egon Willighagen 2.2.x * r153bee4 / features/net.bioclipse.chemoin​formatics_feature/feature.xml : Added new cdk.log4j plugin - http://bit.ly/75d18f
21:30 CIA-65 bioclipse.cheminformatics: Egon Willighagen 2.2.x * re0c066a / (16 files in 16 dirs): Bumped version to 2.2.0.RC2 - http://bit.ly/5TJc8O
21:33 CIA-65 bioclipse.joelib: Egon Willighagen 2.2.x * rf3c37ab / (4 files in 3 dirs): Bumped version to 2.2.0.RC2 - http://bit.ly/7NrY41
21:33 CIA-65 bioclipse.joelib: Egon Willighagen master * rf3c37ab / (4 files in 3 dirs): Bumped version to 2.2.0.RC2 - http://bit.ly/7NrY41
21:35 CIA-65 bioclipse.social: Egon Willighagen 2.2.x * r60539a2 / (4 files in 3 dirs): Bumped version to 2.2.0.RC2 - http://bit.ly/7Brhha
21:36 CIA-65 bioclipse.social: Egon Willighagen master * r60539a2 / (4 files in 3 dirs): Bumped version to 2.2.0.RC2 - http://bit.ly/7Brhha
21:38 CIA-65 bioclipse.statistics: Egon Willighagen master * r4526017 / (3 files in 3 dirs): Bumped version to 2.2.0.RC2 - http://bit.ly/7op5C4

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