Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-23

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All times shown according to UTC.

Time Nick Message
02:31 CIA-18 cdk: rajarshi * r9945 /trunk/cdk/src/org/openscience/cdk/qsar/d​escriptors/molecular/BCUTDescriptor.java: Fixed a bug where it was returning too many values in the DoubleArrayResult
05:21 jbrefort joined #cdk
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07:06 rojasm left #cdk
07:24 CIA-18 cdk: egonw * r9946 /trunk/cdk/src/org/openscience/cdk​/test/CoverageAnnotationTest.java: Be happy about classes with just constants
07:25 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 5214, 77 fails + 44 errors (2.3%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
07:25 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 5214, 77 fails + 44 errors (2.3%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
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07:54 egonw_ hi rojasm
07:55 egonw_ rojasm: feel free to add any test you already have... please do, that is...
07:55 egonw_ the sooner they get in, the sooner I can start working on fixing missing atom types
07:55 egonw_ and maybe, even, we can finalize the reaction patch this friday...
07:56 rojasm Yes! sorry I had for today two presentations and I could not finish
07:56 rojasm I will finish today
07:58 egonw_ obviously, only when you really have time...
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08:32 CIA-18 bioclipse: ospjuth * r4764 /branches/bioclipse2/bioinformatics/plugins/​net.bioclipse.biojava.business/src/net/biocl​ipse/biojava/business/BiojavaManager.java: Implemented DNAtoProtein and ProteinToDNA
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09:48 CIA-18 bioclipse: jonalv * r4765 /branches/bioclipse2/core/plugins/net.bi​oclipse.recording.tests/src/net/bioclips​e/recording/ScriptGenerationTests.java: Simple reference generation test
10:35 CIA-18 bioclipse: ospjuth * r4766 /branches/bioclipse2/bioinformatics/p​lugins/net.bioclipse.biojava.business​/src/net/bioclipse/biojava/business/ (BiojavaHelper.java BiojavaManager.java IBiojavaManager.java): Updated translation functionality. All except RNA I/O now works.
10:35 CIA-18 bioclipse: ospjuth * r4767 /branches/bioclipse2/bioinformatics/plug​ins/net.bioclipse.biojava.business.tests​/tests/net/bioclipse/biojava/business/ (BiojavaHelperTest.java BiojavaManagerTest.java): All tests now passes except those who require RNA input.
10:36 CIA-18 bioclipse: ospjuth * r4768 /branches/bioclipse2/bioinformatics/​plugins/net.bioclipse.biojava.ui/src​/net/bioclipse/biojava/ui/actions/ (5 files): Wrote translation actions for manager except for those who require RNA input.
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12:49 CIA-18 bioclipse: jonalv * r4769 /branches/bioclipse2/ (8 files in 6 dirs): Created Bioclipse Exception and used it in the biojava manager
13:19 CIA-18 bioclipse: jonalv * r4770 /branches/bioclipse2/core/plugins/net.biocl​ipse.recording/src/net/bioclipse/recording/ (JSScriptGenerator.java Record.java): Simple reference support for script generation
13:41 CIA-18 bioclipse: jonalv * r4771 /branches/bioclipse2/core/plugins/​net.bioclipse.ui/src/net/bioclipse​/ui/views/ActionHistoryView.java: added newline between statements when opening editor with generated script
13:42 CIA-18 jmol: egonw * r8928 /trunk/Jmol/src/org/jmol/ada​pter/smarter/Resolver.java: CIF should be checked first, as it is more precise than PDB
13:44 CIA-18 jmol: egonw * r8929 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Added note on CIF/PDB format checking fix; not sure if I should bump version number
14:16 CIA-18 bioclipse: carl_masak * r4772 /branches/bioclipse2/core/plugins/net.bi​oclipse.recording.tests/src/net/bioclips​e/recording/ScriptGenerationTests.java:
14:16 CIA-18 bioclipse: [ScriptGenerationTests.java]
14:16 CIA-18 bioclipse: * new test about escaping of \n, \t etc
14:19 CIA-18 jmol: egonw * r8930 /branches/v11_4/Jmol/src/org/ope​nscience/jmol/app/About_nl.html: Added NL translation of About dialog
14:20 CIA-18 jmol: egonw * r8931 /branches/v11_4/Jmol/src/org/jmo​l/adapter/smarter/Resolver.java: svn-merged commit 8928: 'CIF should be checked first, as it is more precise than PDB'
14:22 CIA-18 jmol: egonw * r8932 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: Added two commits: CIF reading fix (8931) and NL translation of About (8930)
14:25 CIA-18 bioclipse: carl_masak * r4773 /branches/bioclipse2/core/plugins/net.bi​oclipse.recording.tests/src/net/bioclips​e/recording/ScriptGenerationTests.java:
14:25 CIA-18 bioclipse: [ScriptGenerationTests.java]
14:25 CIA-18 bioclipse: * corrected test a bit
14:26 CIA-18 bioclipse: carl_masak * r4774 /branches/bioclipse2/core/plugins/net.bioclipse.r​ecording/src/net/bioclipse/recording/Record.java:
14:26 CIA-18 bioclipse: [Record.java]
14:26 CIA-18 bioclipse: * satisfied escaping test
14:38 CIA-18 bioclipse: carl_masak * r4775 /branches/bioclipse2/core/plugins/net.bi​oclipse.recording.tests/src/net/bioclips​e/recording/ScriptGenerationTests.java:
14:38 CIA-18 bioclipse: [ScriptGenerationTests.java]
14:38 CIA-18 bioclipse: * test now wants a lower-case first letter on made-up identifiers
14:38 CIA-18 bioclipse: * one test fails
14:40 CIA-18 cdk: thomaskuhn * r9947 /trunk/paper/cdk-taverna/bmc_article.tex: A first attempt to start writing the article.
14:41 CIA-18 cdk: thomaskuhn * r9948 /trunk/paper/cdk-taverna/bmc_article.bib: Add some Taverna papers
14:42 CIA-18 bioclipse: carl_masak * r4776 /branches/bioclipse2/core/plugins/net.bioclipse.r​ecording/src/net/bioclipse/recording/Record.java:
14:42 CIA-18 bioclipse: [Record.java]
14:42 CIA-18 bioclipse: * satisfied test from r4775
14:42 CIA-18 bioclipse: * all tests now pass
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15:21 CIA-18 bioclipse: carl_masak * r4777 /branches/bioclipse2/core/plugins/net.bioclipse.r​ecording/src/net/bioclipse/recording/Record.java:
15:21 CIA-18 bioclipse: [Record.java]
15:21 CIA-18 bioclipse: * Removed extraneous space in stringification
15:22 CIA-18 bioclipse: carl_masak * r4778 /branches/bioclipse2/core/plugins/net.bioclipse.r​ecording/src/net/bioclipse/recording/Record.java:
15:22 CIA-18 bioclipse: [Records.java]
15:22 CIA-18 bioclipse: * removed extraneous quotes in stringification
15:26 CIA-18 bioclipse: ospjuth * r4779 /branches/bioclipse2/bioinformatics/plugins/net​.bioclipse.biojava.business/src/net/bioclipse/b​iojava/domain/BiojavaSequenceCollection.java: Caught an NPE.
15:31 CIA-18 bioclipse: carl_masak * r4780 /branches/bioclipse2/core/plugins/net.bioclipse.l​ogging/src/net/bioclipse/logging/Activator.java:
15:31 CIA-18 bioclipse: [Activator.java]
15:31 CIA-18 bioclipse: * changed one ArrayList -> List (program against interfaces)
15:31 CIA-18 bioclipse: * rewrote while/iterator loop into foreach loop
15:31 CIA-18 bioclipse: * removed unused imports
15:31 CIA-18 bioclipse: carl_masak * r4781 /branches/bioclipse2/core/plugins/net.bioclipse.r​ecording/src/net/bioclipse/recording/Record.java:
15:31 CIA-18 bioclipse: [Record.java]
15:31 CIA-18 bioclipse: * removed unused import
15:33 CIA-18 bioclipse: carl_masak * r4782 /branches/bioclipse2/core/plugins/net.biocl​ipse.recording.tests/src/net/bioclipse/reco​rding/integrationTests/RecordingTest.java:
15:33 CIA-18 bioclipse: [RecordingTest.java]
15:33 CIA-18 bioclipse: * added generic types to raw types
15:40 CIA-18 bioclipse: ospjuth * r4783 /branches/bioclipse2/bioinformatics/pl​ugins/net.bioclipse.biojava.ui.test/: Initial import.
15:40 CIA-18 bioclipse: ospjuth * r4784 /branches/bioclipse2/bioinformatics/p​lugins/net.bioclipse.biojava.ui.test/ (17 files in 9 dirs): Initial import.
15:42 CIA-18 bioclipse: carl_masak * r4785 /branches/bioclipse2/core/plugins/ne​t.bioclipse.ui/src/net/bioclipse/ui/​editors/keyword/KeywordEditor.java:
15:42 CIA-18 bioclipse: [KeywordEditor.java]
15:42 CIA-18 bioclipse: * ArrayList -> List (code against interfaces)
15:42 CIA-18 bioclipse: * added generics
15:42 CIA-18 bioclipse: * removed debug comments
15:43 CIA-18 bioclipse: ospjuth * r4786 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (3 files in 3 dirs): Updated contentProvider to support unit tests.
15:49 CIA-18 bioclipse: carl_masak * r4787 /branches/bioclipse2/ (4 files in 4 dirs):
15:49 CIA-18 bioclipse: [build.properties in net.bioclipse.core,
15:49 CIA-18 bioclipse:  net.bioclipse.r,
15:49 CIA-18 bioclipse:  net.bioclipse.scripting,
15:49 CIA-18 bioclipse:  net.bioclipse.springBasedPrototypePlugin]
15:49 CIA-18 bioclipse: * included plugin.xml
16:21 CIA-18 bioclipse: egonw * r4788 /branches/bioclipse2/ (9 files in 3 dirs): Added PMD QA set up
17:45 CIA-18 bioclipse: jonalv * r4789 /branches/bioclipse2/ (8 files in 5 dirs):
17:45 CIA-18 bioclipse: Introduced BioObjectList that implements the Collection interface List.
17:45 CIA-18 bioclipse: Later on we should try to make it recordable as well. (no help from Spring this time though)
18:07 CIA-18 bioclipse: carl_masak * r4790 /branches/bioclipse2/bioinformatics/plugins​/net.bioclipse.biojava.business/src/net/bio​clipse/biojava/domain/BioObjectList.java:
18:07 CIA-18 bioclipse: [BioObjectList.java]
18:07 CIA-18 bioclipse: * removed @Overrides
18:18 CIA-18 bioclipse: jonalv * r4791 /branches/bioclipse2/ (7 files in 5 dirs): Moved the BioObjectList into net.bioclipse.recording. The best would be to have it in net.bioclipse.core but there is a circular reference problem. Maybe we should merge some plugins into one?
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18:25 CIA-18 bioclipse: carl_masak * r4792 /branches/bioclipse2/core/plugins/net.​bioclipse.recording/src/net/bioclipse/​recording/domain/BioObjectList.java:
18:25 CIA-18 bioclipse: [BioObjectList.java]
18:25 CIA-18 bioclipse: * removed @Overrides
18:30 Annzi left #cdk

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