Camelia, the Perl 6 bug

IRC log for #cdk, 2009-02-06

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All times shown according to UTC.

Time Nick Message
06:45 carsten joined #cdk
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09:57 CIA-62 cdk: shk3 * r14077 /jchempaint/trunk/ (14 files in 3 dirs): more status bar stuff
09:59 egonw shk3: ha, launchpad is paying off :)
09:59 egonw there now seems to be a arabic translation of JChemPaint :)
09:59 egonw that rocks :)
10:00 shk3 and a cornish one
10:00 egonw المعين غير صالح SMILES
10:00 egonw cornish??
10:00 egonw what's that?
10:01 shk3 what they speak in cornwall
10:01 shk3 well, spoke
10:01 egonw hahaha...
10:01 egonw cool
10:01 shk3 last native speaker did in 18xx
10:01 egonw :)
10:01 egonw I'm sure he did not translate it, or ... ?
10:01 egonw (or she)
10:01 shk3 she
10:01 shk3 an old lady
10:01 egonw yes, sure :)
10:01 shk3 and it's debated if shw really spoke it
10:02 shk3 maybe she just shouted a few words at the curious
10:02 shk3 nobody to prove her wrong, after all
10:06 Gpox joined #cdk
10:43 CIA-62 cdk: shk3 * r14078 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (3 files): cleaned up the menu classes a lot (code duplications etc.)
10:44 CIA-62 cdk: shk3 * r14079 /jchempaint/trunk/src/main/org/openscience/jc​hempaint/resources/JCPGUI_stable.properties: added the showX item to the popup menu (advantage: if you have hidden the menu bar, you can actually get it back)
10:45 CIA-62 cdk: egonw * r14080 /cdk/branches/cdk-1.2.x/src/test/​org/openscience/cdk/modulesuites/ (MextraTests.java MfingerprintTests.java): Fixed organization of tests: DistanceMomentTest and TanimotoTest are no longer in extra bug in fingerprint
10:52 CIA-62 cdk: shk3 * r14081 /jchempaint/trunk/src/main/org/openscie​nce/jchempaint/JChemPaintMenuBar.java: removed unused constructor
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12:14 CIA-62 cdk: egonw * r14082 /cdk/trunk/ (4 files in 2 dirs): Uploaded JNI-InChI 0.5
12:14 CIA-62 cdk: egonw * r14083 /cdk/trunk/ (.classpath META-INF/MANIFEST.MF): Updated Eclipse config files
12:15 CIA-62 cdk: egonw * r14084 /cdk/trunk/src/ (2 files in 2 dirs): Added InChIKey generation support
12:39 Gpox joined #cdk
12:47 CIA-62 cdk: egonw * r14085 /cdk/branches/cdk-1.2.x/ (24 files in 19 dirs): Merge branch 'newJNIInchI' into local1.2
12:51 egonw grmph...
12:52 egonw not good
12:58 maclean not good?
13:01 maclean er....wtf? wait a second - why is the controller hub using the highlight radius when doing getClosestAtom??
13:02 egonw it's not, is it?
13:02 egonw it uses the highlight radius when to decide if something should be highlighted...
13:02 maclean nuh-uh
13:02 egonw ok, file a bug report...
13:03 maclean or just fix it?
13:03 maclean it's like half a line
13:03 egonw ok, please do
13:03 maclean oki
13:10 CIA-62 cdk: gilleain * r14086 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (ControllerHub.java HighlightModule.java): Testing for highlight distance was happening in two places, and not scaled correctly either.
13:12 egonw maclean++
13:12 egonw nice fix
13:12 maclean heh, wait though...
13:12 egonw that radius check in controllerhub was not supposed to be there
13:12 maclean no indeed.
13:13 egonw one thing I do not understand though
13:13 egonw why do you scale world coords?
13:13 egonw correct for scale in screen coords I would understand
13:13 egonw but should highlight radius in world coord not always be the same...
13:13 egonw ah...
13:13 egonw wait
13:14 egonw that's to correct for the units used in the world space...
13:14 egonw sure
13:15 CIA-62 cdk: gilleain * r14087 /cdk/branches/jchempaint-primary/src/main/org/​openscience/cdk/controller/ControllerHub.java: Well known distance calculation speedup is to use the square of the distance. This avoids calculating the square root, but it exactly equivalent.
13:15 maclean egonw: that's right
13:15 CIA-62 cdk: egonw * r14088 /cdk/branches/cdk-1.2.x/ (24 files in 19 dirs): Reverting previous patch... was not a clean merge :(
13:15 maclean :(
13:28 egonw OK, another try...
13:28 egonw thanx got I am living in a git world
13:28 egonw no idea how I could have done this easily with just svn
13:28 egonw ok, make that
13:28 egonw "thank god"
13:29 egonw not that it really matters, I'm atheist
13:29 egonw well, not really...
13:29 maclean agnostic?
13:29 egonw I'm one of those guys who just has not seen convincing evidence he exists or not
13:29 egonw right
13:29 egonw that's the word
13:30 CIA-62 cdk: egonw * r14089 /cdk/branches/cdk-1.2.x/ (4 files in 2 dirs): Uploaded JNI-InChI 0.5
13:31 CIA-62 cdk: egonw * r14090 /cdk/branches/cdk-1.2.x/ (.classpath META-INF/MANIFEST.MF): Updated Eclipse config files
13:31 egonw ok, that's going much better
13:31 egonw (or she)
13:32 egonw still snowing here
13:32 CIA-62 cdk: egonw * r14091 /cdk/branches/cdk-1.2.x/src/ (2 files in 2 dirs): Added InChIKey generation support
13:33 maclean cool
13:45 CIA-62 cdk: egonw * r14092 /cdk-eclipse/trunk/src/main/net/sf/cdk/t​ools/eclipse/EclipseProjectCreator.java: Support JNI-InChI 0.5
13:45 egonw btw... note the commit number
13:46 egonw this means that in the last half year or so (10000 commit)
13:46 egonw we had 40% commits...
13:46 egonw or...
13:46 egonw in the last year, the CDK productivity was about on par with the 7 years before that
13:47 maclean how many of those are my "forgot cdk.module annotation", though :)
13:48 maclean (more seriously, well done developers!)
13:48 egonw maclean: true, also duplicate commits due to more branching
13:49 egonw the first happened in the past too
13:49 egonw and both just reflect better testing
13:49 egonw so, do add to the equation
13:50 maclean possibly more fine-grained changes, also
13:50 egonw better reviewing
13:52 CIA-62 cdk: shk3 * r14093 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (3 files in 2 dirs): selection change events can be listened to
13:52 CIA-62 cdk: shk3 * r14094 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (4 files in 2 dirs): selection change events are listened to for updating status bar (very cool feature)
13:56 CIA-62 cdk: shk3 * r14095 /cdk/branches/jchempaint-primary/src/main/​org/openscience/cdk/io/ReaderFactory.java: to get some more commits, I revert this change which should not be committed
13:57 maclean :)
13:58 maclean shk3: mini-feature request - could the reported masses in the status bar not be in such precise precision (2 significant digits, perhaps?)
13:59 maclean "C6 (Mass 123.9719507308571805618356)" looks a bit odd, you see.
13:59 shk3 this is a problem i will look at
13:59 shk3 the problem is: I once had a method which gave correct IUPAC masses
13:59 shk3 but some peopel (the guy from the netherlands for example) said we should not have that
14:00 shk3 and get the mass via the i-don't-know-which tool
14:00 shk3 from the i-don't-know-which xml files
14:00 shk3 and you see the result
14:00 egonw 1. what has that to do with how many digits you output?
14:00 egonw 2. I'm from Sweden
14:00 egonw from/in
14:00 shk3 did I talk about you ;-)
14:00 shk3 ?
14:00 egonw dunno
14:01 egonw Miguel?
14:01 shk3 seriously, will look at it
14:01 egonw who else?
14:01 egonw 50% chance
14:01 egonw actaully
14:01 shk3 might even be a conversion problem or so
14:01 egonw you were refering to Miguel
14:01 egonw not sure why
14:01 shk3 so not sure about the real reason
14:01 shk3 I will come back and blame you if I know the reason
14:02 shk3 :-)
14:02 maclean ok, dudes whatever - it was just a suggestion!
14:02 shk3 goint to do some bioclipse bugs now
14:02 egonw maclean: I second that one...
14:03 egonw shk3: please use 4 digits
14:04 shk3 well, there is some detail we need to discuss
14:04 shk3 but I will write to the mailing list next week
14:05 maclean ok. I like the reporting on the selection though, it is a great feature shk3++
15:26 CIA-62 cdk: shk3 * r14096 /cdk/branches/cdk-1.2.x/src/test/org/ope​nscience/cdk/io/ReaderFactoryTest.java: added a test which tests that the readerfactory on a smiles file returns null (and does not throw an exception, which it does right now)
15:40 CIA-62 cdk: egonw * r14097 /cdk-eclipse/trunk/src/main/net/sf/cdk/t​ools/eclipse/EclipseProjectCreator.java: Make sure to export the pkg too where the Activator is located, so that it actually can be used
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17:29 CIA-62 cdk: goglepox * r14098 /cdk/branches/jchempaint-primary/s​rc/main/org/openscience/cdk/render​er/font/AbstractFontManager.java: getFontSizeForZoom now returns smallest or largest if zoom is outside map range
17:58 CIA-62 cdk: djiao * r14099 /cdk/trunk/src/main/org/openscience/cdk​/smiles/smarts/parser/SMARTSParser.jjt: cdk.bug 2490336 fixed
19:06 CIA-62 cdk: gilleain * r14100 /cdk/branches/jchempaint-primary/src/main/o​rg/openscience/cdk/renderer/Renderer.java: Uses the zoom as well as the scale when calculating screen use.
19:26 CIA-62 cdk: egonw * r14101 /cdk/branches/cdk-1.2.x/src/main/org/openscien​ce/cdk/smiles/smarts/parser/SMARTSParser.jjt:
19:26 CIA-62 cdk: cdk.bug 2490336 fixed
19:26 CIA-62 cdk: git-svn-id:
19:26 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@14099 eb4e18e3-b210-0410-a6ab-dec725e4b171
19:26 CIA-62 cdk: Author: djiao <djiao@eb4e18e3-b210-0410-a6ab-dec725e4b171>
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19:59 CIA-62 cdk: gilleain * r14102 /cdk/branches/jchempaint-primary/src/main/org/open​science/cdk/controller/AlterBondStereoModule.java: Fixed to account for the change in the Hub methods getClosestAtom and getClosestBond. Since they no longer take highlighting into account, it is necessary to check if a bond or an atom is closer.
20:10 CIA-62 cdk: egonw * r14103 /cdk/branches/cdk-1.2.x/src/main/org/o​penscience/cdk/io/ReaderFactory.java: Fixed NPE: when no format has been detected, the reader == null
20:28 CIA-62 cdk: egonw * r14104 /cdk/branches/cdk-1.2.x/src/ (2 files in 2 dirs): Support writing of IAtomContainer too (fixes #2543530)
20:35 CIA-62 cdk: egonw * r14105 /cdk/branches/cdk-1.2.x/src/main/org/openscie​nce/cdk/renderer/color/CDK2DAtomColors.java: Backported NPE fix from jchempaint-primary: atomic number can be null
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