Camelia, the Perl 6 bug

IRC log for #cdk, 2007-10-03

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All times shown according to UTC.

Time Nick Message
07:11 rojasm joined #cdk
07:19 carsten joined #cdk
07:25 masak joined #cdk
07:50 olas joined #cdk
08:05 jonalv joined #cdk
08:20 CIA-31 bioclipse: jonalv * r3888 /trunk/playground/plugins/ne​t.bioclipse.structuredb/src/ (4 files in 2 dirs): Now all dao tests for structure except update works. But the hasValuesEquals to method does not check the AtomContainer molecule. Not sure of how bad this is, it might give false positives and how bad would that be?
08:27 CIA-31 bioclipse: ospjuth * r3889 /trunk/plugins/net.bioclipse.cdk.jchemp​aint/src/net/bioclipse/plugins/bc_jchem​paint/editors/JCPMultiPageEditor.java: Uncommitted fixes to some selection and save problems.
08:28 CIA-31 bioclipse: ospjuth * r3890 /trunk/plugins/net.bioclip​se.jmol/logger.properties: Correction to an outcommented string, but still... who knows...
08:41 CIA-31 bioclipse: jonalv * r3891 /trunk/playground/plugins/ne​t.bioclipse.structuredb/src/ (2 files in 2 dirs): All dao tests passes. The bar is green! Party! ehm I mean time to write more tests...
08:41 CIA-31 bioclipse: jonalv * r3892 /trunk/playground/plugins/net.bioclipse.str​ucturedb.tests/tests/net/bioclipse/structur​edb/persistency/dao/StructureDaoTest.java: All dao tests passes. The bar is green! Party! ehm I mean time to write more tests...
09:19 jonalv where is egonw? Is he alright?
09:23 CIA-31 bioclipse: ospjuth * r3893 /trunk/ (2 files in 2 dirs): Moved to include in release 1.1.5
09:25 CIA-31 bioclipse: ospjuth * r3894 /trunk/features/net.bioclipse.s​tatistics-feature/feature.xml: Added net.bioclipse.chart to statistics feature
09:32 CIA-31 bioclipse: ospjuth * r3895 /trunk/plugins/net.bioclipse.chart/ (META-INF/MANIFEST.MF build.properties jars/pcmcopy1.1.jar): Fixed build path, removed unused dependencies and exported JfreeChart.jar
09:33 CIA-31 bioclipse: ospjuth * r3896 /trunk/plugins/net.bioclips​e.chart/src/net/bioclipse/ (chart/ChartUtils.java model/PcmXYDataset.java): Removed unused classes.
09:34 CIA-31 bioclipse: jonalv * r3897 /trunk/plugins/ (4 files in 4 dirs): Moved net.bioclipse.database to net.bioclipse.hibernate and net.bioclipse.database.hsqldb to net.bioclipse.hibernate.hsqldb
09:34 olas joined #cdk
09:34 CIA-31 bioclipse: ospjuth * r3898 /trunk/plugins/ (2 files in 2 dirs): Updated CP
09:41 jbrefort joined #cdk
09:56 CIA-31 bioclipse: ospjuth * r3899 /trunk/features/net.bioclipse-feature/feature.xml: Updated plugins and features for release with Eclipse 3.3
09:57 CIA-31 bioclipse: ospjuth * r3900 /trunk/plugins/net.bioclipse/ (META-INF/MANIFEST.MF bioclipse.product): Updated for release 1.1.5 with Eclipse 3.3
11:35 CIA-31 bioclipse: ospjuth * r3901 /trunk/features/net.bioclipse.chem​oinformatics-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:35 CIA-31 bioclipse: ospjuth * r3902 /trunk/plugins/net.bioclipse.bi​ojava.ui/META-INF/MANIFEST.MF: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:36 CIA-31 bioclipse: ospjuth * r3903 /trunk/features/net.bioclipse.bio​informatics-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:38 CIA-31 bioclipse: ospjuth * r3904 /trunk/features/net.bioclipse.s​tatistics-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:38 CIA-31 bioclipse: ospjuth * r3905 /trunk/features/net.bioclips​e.qsar-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:45 CIA-31 bioclipse: ospjuth * r3906 /trunk/features/net.bioclips​e.data-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:47 CIA-31 bioclipse: ospjuth * r3907 /trunk/features/net.bioclipse.data​.blueobelisk-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:56 CIA-31 bioclipse: ospjuth * r3908 /trunk/features/net.bioclips​e.qsar-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:56 CIA-31 bioclipse: ospjuth * r3909 /trunk/features/net.bioclipse.data​.blueobelisk-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
12:11 CIA-31 bioclipse: ospjuth * r3910 /trunk/bioclipsUpdateSite/site.xml: Finally got all dependencies right to build update site
12:28 rojasm left #cdk
12:35 CIA-31 bioclipse: jonalv * r3911 /trunk/playground/plugins/net.bioclipse.database/: Created database plugin
12:43 CIA-31 bioclipse: jonalv * r3912 /trunk/playground/plugins/ (net.bioclipse.database.demo/ net.bioclipse.hibernate.demo/): moved net.bioclipse.database.demo in playground to net.bioclipse.hibernate.demo
12:55 carsten joined #cdk
12:59 CIA-31 bioclipse: jonalv * r3913 /trunk/playground/plugins/net.bioclipse.empty/ (4 files in 3 dirs): moved views out of the plugins package
13:01 CIA-31 bioclipse: ospjuth * r3914 /trunk/features/net.bioclipse-feature/feature.xml: Updated even more deps for release 1.1.5 with Eclipse 3.3 to get export for multiple platforms working
13:08 CIA-31 bioclipse: jonalv * r3915 /trunk/playground/plugins/net.bioclipse.database/ (META-INF/MANIFEST.MF src/net/bioclipse/model/): Removed model stuff left from the empty plugin
13:08 CIA-31 jmol: hansonr * r8345 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties JmolConstants.java): version=11.3.28 critical bug fix for color command not coloring objects properly
13:39 CIA-31 blueobelisk: pansanel * r128 /structures/trunk/src/carbohydrates/index.xml: Adding many synonyms
13:39 CIA-31 blueobelisk: pansanel * r129 /structures/trunk/src/carbohydrates/ (23 files): Updating MP and BP
13:39 jpansanel hi carsteen
13:40 jpansanel -e
13:40 jpansanel I have added many saccharides to Chemical Structures
13:41 CIA-31 blueobelisk: pansanel * r130 /structures/trunk/xml/l10n.xml: Fix spelling
13:41 CIA-31 blueobelisk: pansanel * r131 /structures/trunk/TODO: Updating TODO
13:42 jpansanel carsten : you told me that you have some fix for chemical structures
13:42 carsten oh, yeeeees
13:42 jpansanel could you send me these fixes ?
13:42 carsten I forgot about that one .-)
13:42 jpansanel :)
13:43 carsten A    blueobelisk/smiles-spec/tru​nk/perhydroisoquinoline.gif
13:43 carsten what are those files for?
13:43 carsten jpansanel: ping me later today about that I have to go now
13:43 carsten I will be back at ~7pm
13:43 CIA-31 jmol: hansonr * r8346 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs):
13:43 CIA-31 jmol: version=11.3.28 VERSION
13:43 CIA-31 jmol: # critical bug fix for color command not coloring objects properly
13:43 CIA-31 jmol: # bondOrders 2.5 and -2.5 PartialTriple and partialTriple2
13:45 carsten c u later
14:05 CIA-31 cdk: rajarshi * r9004 /trunk/cdk/src/org/openscience/cdk/pha​rmacophore/PharmacophoreMatcher.java: Fixed some Javadoc tags
14:12 CIA-31 bioclipse: biocoder * r3916 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Removed test action
14:16 CIA-31 bioclipse: biocoder * r3917 /trunk/plugins/net.bioclipse.chart/src/​net/bioclipse/dialogs/ChartDialog.java: removed debug output
14:17 CIA-31 bioclipse: biocoder * r3918 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Removed debug output.
14:21 olas joined #cdk
14:23 CIA-31 bioclipse: ospjuth * r3919 /trunk/plugins/net.bioclip​se.statistics/plugin.xml: Commented out MatrixEditor as GridEditor is the one that works
14:35 CIA-31 bioclipse: ospjuth * r3920 /trunk/plugins/net.bioclipse.statistics/ (plugin.xml src/net/bioclipse/model/MatrixResource.java): Updated resource to use GridMatrixEditor by default with new id (as class and id should always be the same in plugin.xml)
14:52 CIA-31 bioclipse: ospjuth * r3921 /trunk/plugins/net.bioclipse/ (META-INF/MANIFEST.MF bioclipse.product): Updated even more deps for release 1.1.5 with Eclipse 3.3 to get export for multiple platforms working
14:59 CIA-31 bioclipse: jonalv * r3922 /trunk/playground/plugins/ (16 files in 10 dirs): Started fooling around with databasetype extension point
15:13 CIA-31 bioclipse: jonalv * r3923 /trunk/playground/plugins/net.bioclips​e.structuredb.tests/tests/net/bioclips​e/structuredb/DatabasesetupTest.java: removed superfluous test
15:31 olas left #cdk
16:35 CIA-31 jmol: nicove * r8347 /trunk/Jmol-FAH/projects/p3742.xyz.gz: Folding@Home
16:41 Nout joined #cdk
16:43 CIA-31 cdk: rajarshi * r9005 /trunk/cdk/src/org/openscience/cdk/pharmacophore/ (4 files): Fixed some Javadoc tags
16:53 CIA-31 cdk: rajarshi * r9006 /trunk/cdk/src/org/openscience/cdk/ph​armacophore/PharmacophoreUtils.java: Added code to read pharmacophore definitions from an XML file
16:55 CIA-31 cdk: rajarshi * r9007 /trunk/cdk/src/org/openscienc​e/cdk/test/MpcoreTests.java: Updated to call the new test routines for the pcore util methods
16:58 CIA-31 cdk: rajarshi * r9008 /trunk/cdk/src/data/pcore/ (. pcore.xml): Added a directory for pcore def docs. Added an example file
17:03 carsten joined #cdk
18:20 egonw joined #cdk
18:23 egonw moin
18:23 egonw hi Nout!
18:28 CIA-31 cdk: rajarshi * r9009 /trunk/cdk/src/META-INF/ (pcore.libdepends test-pcore.libdepends): updated build dependencies for the pcore module
18:33 CIA-31 cdk: rajarshi * r9010 /trunk/cdk/src/data/pcore/invalid1.xml: Added an exampleof an invalid pcore def file
18:36 CIA-31 cdk: rajarshi * r9011 /trunk/cdk/src/org/openscience/cdk/ph​armacophore/PharmacophoreUtils.java: removed some methods that dont have bodies for now
18:43 CIA-31 cdk: rajarshi * r9012 /trunk/cdk/src/org/openscience/cdk/test/ph​armacophore/PharmacophoreUtilityTest.java: Added tests for reading pcore def xml files
19:48 CIA-31 jmol: nicove * r8348 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version

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