Camelia, the Perl 6 bug

IRC log for #cdk, 2008-05-22

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All times shown according to UTC.

Time Nick Message
03:04 CIA-31 joined #cdk
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04:24 egonw joined #cdk
04:24 egonw hi mansu
04:28 CIA-31 joined #cdk
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05:00 CIA-31 cdk: egonw * r11117 /cdk/trunk/src/test/org/openscienc​e/cdk/CoverageAnnotationTest.java: Be informative about which test is not found
05:12 rojasm joined #cdk
05:12 rojasm moin
05:25 egonw hi rojasm
05:25 CIA-31 cdk: egonw * r11118 /cdk/branches/cdk-1.0.x/src/org/opens​cience/cdk/libio/cml/Convertor.java: Removed J1.5 syntax
05:26 egonw you received my email with the 'tuned' patch?
05:39 rojasm yes
05:39 rojasm but I am still at home
05:39 * egonw too
05:39 egonw I was lucky last night again...
05:39 rojasm as soon as I am in the uni I will commit
05:39 egonw catched an earlier train in Utrecht...
05:39 egonw which had slight delay
05:39 egonw so, got home 30 minutes earlier :)
05:40 rojasm oo
05:40 rojasm :)
05:40 egonw I won't be at PRI until some 10:00
05:40 rojasm ok
05:41 CIA-31 cdk: egonw * r11119 /cdk/trunk/src/main/org/openscienc​e/cdk/config/AtomTypeFactory.java: Removed annotation for removed tests
05:41 CIA-31 cdk: egonw * r11120 /cdk/trunk/src/test/org/openscience/c​dk/DefaultChemObjectBuilderTest.java: Added missing unit tests
05:41 rojasm I will commit the patch (without updated the trunk or updating the trunk first? ) when I am there
05:42 egonw without a new sync
05:42 CIA-31 cdk: egonw * r11121 /cdk/trunk/src/ (6 files in 3 dirs): Moved test classes to test-data for classes that moved to data
05:42 rojasm perfect withouth
05:42 egonw your patch is, I think indepdendent
05:46 CIA-31 cdk: egonw * r11122 /cdk/trunk/src/test/org/openscience/cdk/formula/ (3 files): Added three missing tests
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06:21 rojasm joined #cdk
06:22 rojasm moin
06:23 egonw hi rojasm
06:24 egonw rojasm: after you applied the patch, might you please have a look at the CDK BTS, and set 'Assingee' to your account, to browse through the bugs assigned to you, and update the info for fixed bugs etc...
06:25 egonw e.g 1628465 can be closed
06:25 egonw and there are three other IP related bug reports
06:27 CIA-31 cdk: egonw * r11123 /cdk/trunk/src/test/org/openscience/cd​k/ringsearch/AllRingsFinderTest.java: Ignore this long running test
06:27 CIA-31 cdk: egonw * r11124 /cdk/trunk/src/test/org/openscience/cdk/tools/​manipulator/AtomContainerManipulatorTest.java: Unit test fix: compare double, double with a margin
06:27 * egonw is heading to the railway station
06:27 egonw bbl
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08:18 rojasm hi egonw!
08:19 rojasm when I apply the patch it asks me Reversed (or previously applied) patch detected! Assume -R?[n]
08:19 rojasm what is yes?
08:19 jonalv okey, so how do I do a substructurematch? (That is check if something is a substrucutre of something else) and while we are on it how do I do the corresponding operation for SMARTS?
08:20 egonw rojasm: then it reverts the patch...
08:20 rojasm than no
08:21 egonw depends on what the patch is...
08:21 egonw but when you reject the patch, or when it cannot apply it, it will create a .rej file
08:21 egonw and you should inspect those...
08:21 egonw jonalv: look for the UniversalIsomorphismChecker
08:21 egonw in cdk.isomorphism
08:21 rojasm ok
08:22 egonw jonalv: in src/test/org/openscience/cdk/isomorphism is a unit test class with example code
08:22 jonalv egonw, thank you :)
08:29 rojasm I think I miss completely all. egonw should it be a lot of work if I make the process again? and you inspect again the patch? :(
08:31 jonalv egonw, it sounds to me like isomorphism isn't exactly what I want. I mean it's a substructure search...
08:34 * jonalv guesses he should use the isSubgraph method which he missed at first read through :)
08:39 CIA-31 bioclipse: jonalv * r5663 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: implemented cdk.subStructureMatches
08:48 egonw jonalv: yes, the UIT has subgraph matching too, as you found out :)
08:49 egonw rojasm: yes, fine
08:52 jonalv egonw, I would greatly appreciate if you took a look at my code in Bioclipse sometime when you have the time because I am out doing things I don't know very much about now... :)
08:53 egonw jonalv: as in?
08:53 egonw you think you're work is finished?
08:53 egonw if so,
08:53 egonw please blog about it, and explain how people can set up a structuredb, import a SDF, and then do a sub structure search
08:54 jonalv egonw, my work is not finnished but parts of it are starting to work :)
08:55 egonw then you need to explain me how I can help you
08:55 jonalv you have time now? :)
09:01 egonw umm... depends
09:01 egonw if it's short
09:01 egonw I don't have time to boot BC2 at this moment
09:02 jonalv it takes that long? :)
09:03 jonalv Tell you what, I will write you a mail with a few things you can have a look at and you do it when you have time. Could that work?
09:03 egonw yes, that would work
09:29 CIA-31 bioclipse: ospjuth * r5664 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Some work to get SingleStructure tab working. Currently, molecules are not repainted.
09:38 CIA-31 bioclipse: carl_masak * r5665 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/views/JsConsoleView.java: [JsConsoleView] added a final newline at end of progress bar
10:39 thomas_ku joined #cdk
10:40 thomas_ku moin
10:43 egonw hi thomas_ku
10:59 thomas_ku_ joined #cdk
11:22 CIA-31 bioclipse: ospjuth * r5666 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Added repaint() commands that don't work, just to show what I've tried. Egon: please help!
11:26 CIA-31 jmol: hansonr * r9405 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): 11.5.38 VERSION
11:31 CIA-31 bioclipse: jonalv * r5667 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): Added substructuresearch method returning result in a list
12:18 CIA-31 bioclipse: ospjuth * r5668 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Force repaint when updating JCPModel by fooling the ControlListener that JCP has been resized. Not beautiful, but works.
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13:17 CIA-31 bioclipse: carl_masak * r5669 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
13:17 CIA-31 bioclipse: [JsThread] added isBusy() method
13:17 CIA-31 bioclipse: [JsConsoleView] now only tab completes on a non-busy js
13:20 thomas_ku joined #cdk
13:27 CIA-31 jmol: hansonr * r9406 /trunk/Jmol/src/org/jmol/viewer/Eval.java:
13:31 CIA-31 bioclipse: carl_masak * r5670 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/editors/ColorManager.java: [ColorManager] brought up to Java 1.5 standards
13:44 malick joined #cdk
13:56 egonw rojasm: ping
14:02 CIA-31 bioclipse: ospjuth * r5671 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (IJCPbasedMPE.java JCPPage.java): Added interface for JCPbasedMPEs so that JCP can know if contained in an MPE and act upon that.
14:03 CIA-31 bioclipse: egonw * r5672 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: If the selected entry has not changed, don't update the second view...
14:15 CIA-31 bioclipse: ospjuth * r5673 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.sdf​editor/src/net/bioclipse/cdk10/sdfeditor/editor/ (6 files): Adding index column for SDFileEditor, as requested per RFE 1968729.
14:20 CIA-31 bioclipse: jonalv * r5674 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/views/JsConsoleView.java: Cleaned up a bit in ConsoleProgressMonitor
14:21 CIA-31 bioclipse: jonalv * r5675 /bioclipse2/trunk/plugins/ (9 files in 5 dirs): Made progress monitor for substructureSearch
14:30 CIA-31 bioclipse: egonw * r5676 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: Overwrite oldIx at the right place...
14:30 CIA-31 bioclipse: egonw * r5677 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: Fixed nothing-has-been-selected-previously default (index of structures starts at 0); force a repaint, just in case, but does not help against the grey screen
14:30 CIA-31 bioclipse: egonw * r5678 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.sdfeditor/src/net/bioclipse/cdk10/sd​feditor/editor/StructureTablePage.java: Missing space; dump error instead of eating it
14:33 CIA-31 bioclipse: ospjuth * r5679 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: On change to StructTablePage, set selection according to currentModel.
14:57 CIA-31 bioclipse: ospjuth * r5680 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Selections are now synchronized between table and JCPpage in SDFileEditor.
15:42 CIA-31 bioclipse: ospjuth * r5681 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.sdf​editor/src/net/bioclipse/cdk10/sdfeditor/editor/ (3 files): Added sorting when click on headers in SDFileEditor, except on header for Structures. Solves 1968729.
16:38 malick left #cdk
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16:59 s_wolf hi there
17:02 s_wolf left #cdk
17:02 CIA-31 bioclipse: ospjuth * r5682 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.sdf​editor/src/net/bioclipse/cdk10/sdfeditor/editor/ (SDFEditor.java StructureTablePage.java): Attempt to fix "grey box bug" when switching to JCPpage in SDFileEditor. Egon: please verify that bug is squashed!
17:52 rojasm joined #cdk
19:35 CIA-31 cdk: archvile18 * r11125 /cdk/trunk/src/test/org/openscience/cdk​/smiles/DeduceBondSystemToolTest.java: Some test cases were buggy. Fixed now. Concerns bug [1969642] "DeduceBondSystemToolTests are failing"
19:37 CIA-31 cdk: archvile18 * r11126 /cdk/trunk/src/main/org/openscience/c​dk/smiles/DeduceBondSystemTool.java: Fixed two issues regarding UNSET hydrogen counts and PLANAR3 hybridization. Relates to bug [1969642] "DeduceBondSystemToolTests are failing".
19:41 CIA-31 bioclipse: ospjuth * r5683 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: Commented out cdk.ui contents in navigator, as CDK1o is used for SDF files and CML files.
19:44 CIA-31 bioclipse: ospjuth * r5684 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.ui/: Initial import.
22:24 CIA-31 jmol: hansonr * r9407 /trunk/Jmol/src/org/jmol/ (3 files in 3 dirs): 11.5.38 -- CIF reading of B factors
22:55 CIA-31 jmol: hansonr * r9408 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Eval.java): minor bug fix -- nonexistent ^

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