Camelia, the Perl 6 bug

IRC log for #cdk, 2008-03-27

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All times shown according to UTC.

Time Nick Message
04:12 CIA-11 bioclipse: rklancer * r5207 /bioclipse2/trunk/plugins/net.bioclipse.logger/: Initial import. net.bioclipse.logging is dead, long live net.bioclipse.logger!
04:21 CIA-11 bioclipse: rklancer * r5208 /bioclipse2/trunk/plugins/net.bioclipse.logger/ (19 files in 8 dirs): After a little fight with Subclipse, I have more files for you.
04:30 CIA-11 bioclipse: rklancer * r5209 /bioclipse2/trunk/ (3 files in 3 dirs):
04:30 CIA-11 bioclipse: Updated target platform and bioclipse.product to reflect net.bioclipse.logger;
04:30 CIA-11 bioclipse: updated command line args in bioclipse.product to a) enable assertions and b)
04:30 CIA-11 bioclipse: set default workspace location to ~/Library/Application Support/Bioclipse
04:30 CIA-11 bioclipse: Workspace/ for OS X users
04:32 CIA-11 bioclipse: rklancer * r5210 /bioclipse2/trunk/plugins/net.bioclipse​.biojava.ui.test/META-INF/MANIFEST.MF: cleanup: removed extraneous log4j imports (especially important b/c the new net.bioclipse.logger only exports org.apache.log4j at the moment, and none of the other log4j packages)
04:44 CIA-11 bioclipse: rklancer * r5211 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Oops fix to little problem with default workspace location on OS X - now goes to ~/Library/Application Support/Bioclipse/Default Workspace/ - not ~/Library/Application%20Support/​Bioclipse/Default%20Workspace...
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06:08 CIA-11 bioclipse: rklancer * r5212 /bioclipse2/trunk/plugins/net.bioclipse.logg​er/src/net/bioclipse/logger/Activator.java: fixed unnecessarily complicated usage pattern of enum
06:43 CIA-11 bioclipse: rklancer * r5213 /bioclipse2/trunk/plugins/net.bioclipse.logg​er/src/net/bioclipse/logger/Activator.java: can't leave well enough alone ... found a prettier idiom for the enum
06:56 CIA-11 bioclipse: rklancer * r5214 /bioclipse2/trunk/plugins/net.bioclipse.logg​er/src/net/bioclipse/logger/Activator.java: This idiom actually works...
07:45 jpansanel moin
07:47 Annzi joined #cdk
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07:54 thomas_ku_ moin
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10:00 CIA-11 bioclipse: carl_masak * r5215 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/n​et/bioclipse/ui/views/ScriptingConsoleView.java:
10:00 CIA-11 bioclipse: [ScriptingConsoleView.java]
10:00 CIA-11 bioclipse: * whitespace
10:09 CIA-11 bioclipse: ospjuth * r5216 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/META-INF/MANIFEST.MF: Added net.bioclispe.logger as dep in net.bioclipse.ui. Don't know if this is correct but it resolves cyclic dependencies after the latest commit by rklancer regarding net.bioclipse.logger.
10:31 CIA-11 bioclipse: jonalv * r5217 /bioclipse2/trunk/plugins/net​.bioclipse.usermanager.tests/ (2 files in 2 dirs): fixed borken test
10:32 steinbeck joined #cdk
10:33 egonw hi steinbeck
10:33 steinbeck moin
10:33 CIA-11 bioclipse: jonalv * r5218 /bioclipse2/trunk/plugins/net.​bioclipse.usermanager.tests/: added (by tests) generated data files to svn:ignore
10:39 jpansanel egonw : do you think that it could be possible to have a link between JCP and Jmol, so that you sketch a molecule into JCP and open Jmol to display it
10:40 jpansanel the interest is that by using the minimize function, you can convert it to 3D.
10:40 egonw yeah, it's called Bioclipse
10:40 jpansanel :o)
10:41 egonw seriously... that path is not easy, but Bioclipse does bits of it, using CDK, it's Builder3D (which currently only works for molecules without rings). and Jmol for 3D viz
10:41 jpansanel ok
10:43 jpansanel egonw , steinbeck : do you think we could build a project financed by the EU for Open Source and Life Science ?
10:44 steinbeck jpansanel: there maybe EU programmatic options for that
10:44 jpansanel I think so
10:44 egonw jpansanel: do you have a funding thingy in mind?
10:44 jpansanel yes
10:44 egonw thingy = program
10:44 steinbeck if you are interested, we should set-up a skype conference.
10:44 * egonw is interested
10:45 * steinbeck too
10:45 jpansanel the idea is to develop a suite of open source tools for the drug discovery
10:46 jpansanel I'm in touch with a consultant for european contract
10:46 jpansanel the base fees are payed by OSEA, a french agency
10:47 CIA-11 cdk: thomaskuhn * r10538 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/qsar/model/weka/ (15 files): Some clean up and upgrade to Java 5 standards
10:47 steinbeck jpansanel: for the sake of documentation, can we continue this by email?
10:47 jpansanel and it takes 3% of the amount of the project funds
10:47 jpansanel yes
10:47 CIA-11 cdk: thomaskuhn * r10539 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/renderers/ (4 files): Some clean up and upgrade to Java 5 standards
10:48 CIA-11 cdk: thomaskuhn * r10540 /cdk-taverna/trunk/src/test/java/or​g/openscience/cdk/applications/tave​rna/qsar/QSARDescriptorTest.java: Only test a few QSAR classes not all
10:48 CIA-11 cdk: thomaskuhn * r10541 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/stru​ctgen/StructureDiagramGenerator.java: Some clean up and upgrade to Java 5 standards
11:13 egonw btw, I make a full git repository of CDK history...
11:13 egonw will all tags and branches...
11:13 egonw about 200MB of patches
11:13 egonw compressed
11:13 egonw took my machine about 3 days
11:13 egonw to create from the SVN repos...
11:13 egonw just to ensure that no one else is repeating that excersise...
11:14 egonw will blog about it this weekend...
11:14 egonw oh, and feel free to make a vote in my blog about JCP development
12:08 jpansanel egonw : JCP applet is the only that is FLOSS
12:09 jpansanel It's a major feature for a private company developing FLOSS software.
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12:44 CIA-11 bioclipse: jonalv * r5219 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): test for situation where asking for info about loggedin user woithout being logged in
12:52 CIA-11 bioclipse: carl_masak * r5220 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/n​et/bioclipse/ui/views/ScriptingConsoleView.java:
12:52 CIA-11 bioclipse: [ScriptingConsoleView.java]
12:52 CIA-11 bioclipse: * converted all /* */ comments to Javadoc comments
12:52 CIA-11 bioclipse: * added further and more detailed comments everywhere
12:52 CIA-11 bioclipse: * reordered methods -- abstract ones last
13:28 CIA-11 bioclipse: carl_masak * r5221 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/n​et/bioclipse/ui/views/ScriptingConsoleView.java:
13:28 CIA-11 bioclipse: [ScriptingConsoleView.java]
13:28 CIA-11 bioclipse: * new line breaking solution
13:40 CIA-11 bioclipse: carl_masak * r5222 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/n​et/bioclipse/ui/views/ScriptingConsoleView.java:
13:40 CIA-11 bioclipse: [ScriptingConsoleView.java]
13:40 CIA-11 bioclipse: * minor tweaks of whitespace handling
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13:52 CIA-11 bioclipse: carl_masak * r5223 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/n​et/bioclipse/ui/views/ScriptingConsoleView.java:
13:52 CIA-11 bioclipse: [ScriptingConsoleView.java]
13:52 CIA-11 bioclipse: * a bit more Javadoc
13:52 CIA-11 bioclipse: Annzi * r5224 /bioclipse2/trunk/plugins/net.bioc​lipse.moss/src/net/bioclipse/moss/ (5 files in 3 dirs): Changes in file and path settings
13:57 CIA-11 bioclipse: carl_masak * r5225 /bioclipse2/trunk/plugins/net.bioclipse.core/sr​c/net/bioclipse/recording/RecordingAdvice.java:
13:57 CIA-11 bioclipse: [RecordingAdvice.java]
13:57 CIA-11 bioclipse: * inlined local variable
14:07 CIA-11 cdk: thomaskuhn * r10542 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/basicutilities/ (3 files): Some clean up and upgrade to Java 5 standards
14:07 CIA-11 cdk: thomaskuhn * r10543 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​bioclipse/BioclipseResultViewer.java: Some clean up and upgrade to Java 5 standards
14:08 CIA-11 cdk: thomaskuhn * r10544 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/fi​ngerprint/FingerprintCalculator.java: Some clean up and upgrade to Java 5 standards
14:08 CIA-11 cdk: thomaskuhn * r10545 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/fing​erprint/FingerprintCalculatorAPI.java: Remove unused old class was used with the API consumer
14:08 CIA-11 cdk: thomaskuhn * r10546 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/io/ (8 files): Some clean up and upgrade to Java 5 standards
14:08 CIA-11 cdk: thomaskuhn * r10547 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/io/action/ (3 files): Some clean up and upgrade to Java 5 standards
14:09 CIA-11 cdk: thomaskuhn * r10548 /cdk-taverna/trunk/src/main/java/org/ope​nscience/cdk/applications/taverna/jchemp​aint/action/JChemPaintEditorAction.java: Some clean up and upgrade to Java 5 standards
14:09 CIA-11 cdk: thomaskuhn * r10549 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​layout/StructureDiagramCreator.java: Remove unused old class
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14:09 CIA-11 cdk: thomaskuhn * r10550 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/modeling/ (3 files): Some clean up and upgrade to Java 5 standards
14:09 CIA-11 cdk: thomaskuhn * r10551 /cdk-taverna/trunk/src/main/java/org/ope​nscience/cdk/applications/taverna/qsar/ (6 files): Some clean up and upgrade to Java 5 standards
14:10 CIA-11 cdk: thomaskuhn * r10552 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/qs​ar/action/QSARDescriptorAction.java: Some clean up and upgrade to Java 5 standards
14:10 CIA-11 cdk: thomaskuhn * r10553 /cdk-taverna/trunk/src/main/java/org/open​science/cdk/applications/taverna/qsar/des​criptors/molecular/RuleOfFiveFilter.java: Some clean up and upgrade to Java 5 standards
14:10 CIA-11 cdk: thomaskuhn * r10554 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/qsar/model/weka/ (6 files): Some clean up and upgrade to Java 5 standards
14:11 CIA-11 cdk: thomaskuhn * r10555 /cdk-taverna/trunk/src/main/java/org/openscience/​cdk/applications/taverna/qsar/model/weka/action/ (10 files): Some clean up and upgrade to Java 5 standards
14:11 CIA-11 cdk: thomaskuhn * r10556 /cdk-taverna/trunk/src/main/java/or​g/openscience/cdk/applications/tave​rna/renderers/Draw2DStructure.java: Some clean up and upgrade to Java 5 standards
14:11 CIA-11 cdk: thomaskuhn * r10557 /cdk-taverna/trunk/src/main/java/org/openscien​ce/cdk/applications/taverna/scuflworkers/cdk/ (CDKScavenger.java CDKTask.java): Some clean up and upgrade to Java 5 standards
14:11 CIA-11 cdk: thomaskuhn * r10558 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/reac​tionenumerator/ReactionEnumerator.java: Some clean up and upgrade to Java 5 standards
14:11 CIA-11 cdk: thomaskuhn * r10559 /cdk-taverna/trunk/src/main/java/or​g/openscience/cdk/applications/tave​rna/tools/CloningCMLChemFile.java: Remove unused old class
14:11 CIA-11 cdk: thomaskuhn * r10560 /cdk-taverna/trunk/src/main/java/org/openscience/​cdk/applications/taverna/tools/TagMolecules.java: Some clean up and upgrade to Java 5 standards
14:12 CIA-11 cdk: thomaskuhn * r10561 /cdk-taverna/trunk/src/main/java/org/open​science/cdk/applications/taverna/smiles/ (SMILESGenerator.java SMILESParser.java SmilesTools.java): Some clean up and upgrade to Java 5 standards
14:12 CIA-11 cdk: thomaskuhn * r10562 /cdk-taverna/trunk/src/test/java/org​/openscience/cdk/applications/tavern​a/tools/CloningCMLChemFileTest.java: Remove unused old class
14:15 CIA-11 bioclipse: jonalv * r5226 /bioclipse2/trunk/plugins/​net.bioclipse.usermanager/ (5 files in 5 dirs): Fixed bug wigh login problem for editing account info. The UserManager in bioclipse 2 is mature enough for some heavy testing. No (currently) known bugs remains.
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14:51 CIA-11 bioclipse: ospjuth * r5227 /bioclipse2/trunk/plugins/net.bioclipse.biomoby/ (8 files in 3 dirs): Updated to Biomoby1.0.
14:52 CIA-11 bioclipse: ospjuth * r5228 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): Updates for moby1.0.
14:53 CIA-11 bioclipse: ospjuth * r5229 /bioclipse2/trunk/plugins/net.bioclipse.bio​moby.tests/src/net/bioclipse/biomoby/tests/ (22 files in 2 dirs): Refactored old tests to dedicated package, will be updated to Junit4.
15:02 CIA-11 cdk: thomaskuhn * r10563 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​qsar/AbstractAtompairDescriptor.java: Some clean up and upgrade to Java 5 standards
15:02 CIA-11 cdk: thomaskuhn * r10564 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/qsar/model/weka/ (5 files): Some clean up and upgrade to Java 5 standards
15:02 CIA-11 cdk: thomaskuhn * r10565 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/reac​tionenumerator/ReactionEnumerator.java: Some clean up and upgrade to Java 5 standards
15:02 CIA-11 cdk: thomaskuhn * r10566 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/renderers/ (4 files): Some clean up and upgrade to Java 5 standards
15:03 CIA-11 cdk: thomaskuhn * r10567 /cdk-taverna/trunk/src/test/java/org/​openscience/cdk/applications/taverna/ (CDKTavernaTestData.java CMLChemfileTest.java): Some clean up and upgrade to Java 5 standards
15:03 CIA-11 cdk: thomaskuhn * r10568 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/aromat​icity/DetectHueckelAromaticityTest.java: Some clean up and upgrade to Java 5 standards
15:04 CIA-11 cdk: thomaskuhn * r10569 /cdk-taverna/trunk/src/test/java/org/op​enscience/cdk/applications/taverna/io/ (3 files): Some clean up and upgrade to Java 5 standards
15:04 CIA-11 cdk: thomaskuhn * r10570 /cdk-taverna/trunk/src/test/java/org/o​penscience/cdk/applications/taverna/is​omorphism/SubstructureFilterTest.java: Some clean up and upgrade to Java 5 standards
15:05 CIA-11 cdk: thomaskuhn * r10571 /cdk-taverna/trunk/src/test/java/org/​openscience/cdk/applications/taverna/​jchempaint/JChemPaintEditorTest.java: Some clean up and upgrade to Java 5 standards
15:05 CIA-11 cdk: thomaskuhn * r10572 /cdk-taverna/trunk/src/test/java/org/opens​cience/cdk/applications/taverna/modeling/ (2 files): Some clean up and upgrade to Java 5 standards
15:05 CIA-11 cdk: thomaskuhn * r10573 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/qsar/ (4 files): Some clean up and upgrade to Java 5 standards
15:05 CIA-11 cdk: thomaskuhn * r10574 /cdk-taverna/trunk/src/test/java/org/open​science/cdk/applications/taverna/qsar/des​criptors/molecular/RuleOfFiveTest.java: Some clean up and upgrade to Java 5 standards
15:06 CIA-11 cdk: thomaskuhn * r10575 /cdk-taverna/trunk/src/test/java/org/opensci​ence/cdk/applications/taverna/qsar/descripto​rs/atomic/InductiveAtomicSoftnessTest.java: Some clean up and upgrade to Java 5 standards
15:06 CIA-11 cdk: thomaskuhn * r10576 /cdk-taverna/trunk/src/test/java/org/openscie​nce/cdk/applications/taverna/qsar/model/weka/ (6 files): Some clean up and upgrade to Java 5 standards
15:06 CIA-11 cdk: thomaskuhn * r10577 /cdk-taverna/trunk/src/test/java/org/open​science/cdk/applications/taverna/reaction​enumerator/ReactionEnumeratorTest.java: Some clean up and upgrade to Java 5 standards
15:07 CIA-11 cdk: thomaskuhn * r10578 /cdk-taverna/trunk/src/test/java/org/opensc​ience/cdk/applications/taverna/qsar/descrip​tors/atompair/PiContactDetectionTest.java: Some clean up and upgrade to Java 5 standards
15:07 CIA-11 cdk: thomaskuhn * r10579 /cdk-taverna/trunk/src/test/java/o​rg/openscience/cdk/applications/ta​verna/tools/TagMoleculesTest.java: Some clean up and upgrade to Java 5 standards
15:11 CIA-11 bioclipse: carl_masak * r5230 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/views/JsConsoleView.java:
15:11 CIA-11 bioclipse: [JsConsoleView.java]
15:11 CIA-11 bioclipse: * filtered tab completed manager methods to only those recorded
15:11 CIA-11 bioclipse: * jonalv++ for moral/l/l/technical support in times of hardship
15:37 Annzi left #cdk
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16:18 CIA-11 bioclipse: ospjuth * r5231 /bioclipse2/trunk/plugins/net.bioclipse.services/ (6 files in 4 dirs): Started working on databaseType and impl, and demonstrated menu contributed as objectContribution.
16:19 man-di left #cdk
16:32 CIA-11 bioclipse: jonalv * r5232 /bioclipse2/trunk/plugins/n​et.bioclipse.structuredb/: Initial movement of net.bioclipse.structuredb to bc2
16:34 CIA-11 bioclipse: jonalv * r5233 /bioclipse2/trunk/plugins/net.bioclipse.biojava.​business.tests/net.bioclipse.structuredb.tests/: Initial copying of net.bioclipse.structuredb.tests into bc2
16:57 Annzi left #cdk
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17:05 CIA-11 bioclipse: jonalv * r5234 /bioclipse2/trunk/plugins/net.​bioclipse.structuredb.tests/: Initial copying of net.bioclipse.structuredb.tests into bc2
17:08 CIA-11 bioclipse: jonalv * r5235 /bioclipse2/trunk/plugins/net.bioclipse.biojava.​business.tests/net.bioclipse.structuredb.tests/: reverted borken commit
17:12 CIA-11 bioclipse: jonalv * r5236 /bioclipse2/trunk/plugins/net.bioclipse.hsqldb/: Introduced net.bioclipse.hsqldb into bc2
19:32 CIA-11 bioclipse: Annzi * r5237 /bioclipse2/trunk/plugins/net.bioclipse.moss/doc/ (mossUsage.html readFiles.html): Added more help contents.
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20:19 egonw moin
20:19 egonw live from Arnhem central station
20:19 egonw with 15 mins of free wireless
20:19 egonw after watching a few minutes of MS Office demo talk :)
20:19 egonw anyway, good deal
20:36 CIA-11 bioclipse: rklancer * r5238 /bioclipse2/trunk/ (22 files in 22 dirs): cleanup: added entries to build.properties files so that more projects actually work when launched as part of exported binary distribution of Bioclipse (vs. only working when Bioclipse is launched from within Eclipse)
20:42 CIA-11 bioclipse: rklancer * r5239 /bioclipse2/trunk/ (10 files in 10 dirs): Cleanup - deleted obsolete logger.properties files from the root of several projects
21:12 CIA-11 bioclipse: rklancer * r5240 /bioclipse2/trunk/plugins/net.bioclipse.logg​er/src/net/bioclipse/logger/Activator.java: little fixups to style, made BcPath enum public (exposes USERHOME, WORKSPACE, INSTALL_AREA, and DEFAULT_LOG_DIR system property key-and-value pairs)
22:14 CIA-11 jmol: aherraez * r9210 /branches/v11_4/Jmol/src/org/jmo​l/translation/JmolApplet/es.po: Spanish
22:15 CIA-11 jmol: aherraez * r9211 /trunk/Jmol/src/org/jmol/tr​anslation/JmolApplet/es.po: Spanish
22:32 rojasm left #cdk

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