Camelia, the Perl 6 bug

IRC log for #cdk, 2008-11-06

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All times shown according to UTC.

Time Nick Message
05:01 jbrefort joined #cdk
07:31 egonw joined #cdk
09:15 CIA-38 cdk: egonw * r13005 /cdk/branches/cdk-1.2.x/to​ols/extractTestStats.bsh: Better error reporting
09:16 CIA-38 cdk: egonw * r13006 /cdk/branches/cdk-1.2.x/src​/test/org/openscience/cdk/ (30 files in 2 dirs): Refactored CoverageTest to be JUnit4-based
10:04 jbrefort joined #cdk
10:27 thomasku joined #cdk
10:27 thomasku moin
10:27 zarah hi thomasku
10:29 egonw hi thomasku
10:29 zarah egonw: You have new messages. Write '@messages' to read them.
10:29 egonw @msg
10:29 zarah egonw: 18 h 7 m 59 s ago, edrin said sorry, we had 1000 of seminars today cant chat
10:30 thomasku hi egonw
10:31 egonw thanx for linking to your blog
10:34 CIA-38 cdk: egonw * r13007 /cdk/branches/cdk-1.2.x/src​/test/org/openscience/cdk/ (33 files in 2 dirs): Refactored CoverageAnnotationTest to be JUnit4-based
10:53 CIA-38 cdk: egonw * r13008 /cdk/branches/cdk-1.2.x/src​/test/org/openscience/cdk/ (3 files in 3 dirs): First module is now fully JUnit4
10:57 thomasku joined #cdk
11:27 CIA-38 cdk: egonw * r13009 /cdk/branches/cdk-1.2.x/src/test/​org/openscience/cdk/modulesuites/ (22 files): OK, many more module suites ported to JUnit4
11:45 jerome__ joined #cdk
11:45 jpansanel moin
11:45 zarah hi jpansanel
11:59 egonw hi jpansanel
12:06 CIA-38 cdk: egonw * r13010 /cdk/branches/cdk-1.2.x/src/test/​org/openscience/cdk/modulesuites/ (9 files): All easy modules are now JUnit4
12:06 CIA-38 cdk: egonw * r13011 /cdk/branches/cdk-1.2.x/src/t​est/org/openscience/cdk/qsar/ (5 files in 2 dirs): Fixed use of Assert: orgg.junit (JUnit4), not junit.framework (JUnit3)
12:06 CIA-38 cdk: egonw * r13012 /cdk/branches/cdk-1.2.x/src/tes​t/org/openscience/cdk/atomtype/ (5 files): Removed obsolete suite() methods
12:06 CIA-38 cdk: egonw * r13013 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/limitations/AlgorithmLimitations.java: Converted to JUnit4
12:16 malick joined #cdk
13:08 CIA-38 cdk: egonw * r13014 /cdk/branches/cdk-1.2.x/src/test/​org/openscience/cdk/modulesuites/ (4 files): Refactored to use JUnit4 instead of JUnit3
13:43 Julio joined #cdk
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13:53 CIA-38 cdk: egonw * r13015 /cdk/branches/cdk-1.2.x/src​/test/org/openscience/cdk/ (5 files in 2 dirs): Factored out last bits of junit.framework stuff: everything is now using JUnit4 org.junit. Ready to upgrade to JUnit4.5, which has Assume
14:35 jpansanel egonw : Is someone still working on strigi-chemical ?
14:37 egonw not actively at this moment, AFAIK
14:41 CIA-38 cdk: egonw * r13016 /cdk/branches/cdk-1.2.x/ (40 files in 2 dirs): Upgraded to JUnit 4.5
14:41 CIA-38 cdk: egonw * r13017 /cdk/branches/cdk-1.2.x/.classpath: Updated Eclipse's .classpath
14:41 CIA-38 cdk: egonw * r13018 /cdk/branches/cdk-1.2.x/src​/test/org/openscience/cdk/ (5 files in 5 dirs): Use assume for runSlowTests
14:42 CIA-38 cdk: egonw * r13019 /cdk/branches/cdk-1.2.x/src/test/o​rg/openscience/cdk/qsar/model/R2/ (CNNRegressionModelTest.java LinearRegressionModelTest.java): Use assume for runRModelTests
14:53 CIA-38 cdk: egonw * r13020 /cdk/branches/cdk-1.2.x/src/main/or​g/openscience/cdk/isomorphism/match​ers/smarts/AtomicNumberAtom.java: Fixed a NPE source (closes #2229168)
14:57 CIA-38 cdk: egonw * r13021 /cdk/branches/cdk-1.2.x/src/main/o​rg/openscience/cdk/tools/manipulat​or/AtomContainerManipulator.java: Applied suggestion by Syed: don't try to perceive and configure IPseudoAtom's
15:40 CIA-38 cdk: egonw * r13022 /cdk/branches/cdk-1.2.x/src/test/org/o​penscience/cdk/io/XYZWriterTest.java: Added unit tests for two bugs I reported: #2215775 and #2215774
15:44 Julio joined #cdk
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15:57 CIA-38 cdk: egonw * r13023 /cdk/branches/cdk-1.2.x/src/test/org/o​penscience/cdk/io/XYZWriterTest.java: 1. Fixed test to detect a TAB; 2. test neg values
15:57 CIA-38 cdk: egonw * r13024 /cdk/branches/cdk-1.2.x/src/main/org​/openscience/cdk/io/XYZWriter.java: More uniform output of values and output zeros when Point3d is UNSET (closes #2215774 and #2215775)
16:20 jonalv joined #cdk
16:20 egonw hi jonalv
16:20 jonalv hi egonw
16:21 jonalv hi zarah
16:27 CIA-38 cdk: egonw * r13025 /cdk/branches/cdk-1.2.x/src/main/org/openscience/c​dk/qsar/descriptors/molecular/MDEDescriptor.java: Fixed a NPE: updated for Element.atomicNumber defaulting to UNSET
16:32 zarah joined #cdk
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16:58 CIA-38 cdk: egonw * r13026 /cdk/branches/cdk-1.2.x/src/main/o​rg/openscience/cdk/Fragment.java: Removed: no serious functionality, not used (closes #2194603).
18:35 timvdm joined #cdk
18:58 egonw hi timvdm
19:07 timvdm hi egonw
19:08 timvdm does the cdk have a way to predict pKa?
19:09 egonw almost
19:09 timvdm are you implementing the SMARTS prediction method?
19:09 egonw some weeks ago I partially implemented a recent paper
19:09 CIA-38 cdk: egonw * r13027 /cdk/branches/cdk-1.2.x/src/test/org/open​science/cdk/io/cml/CMLRoundTripTest.java: Fixed setup method: should be static
19:09 egonw yes, using the decision tree
19:10 egonw published 2-3 weeks ago
19:10 CIA-38 cdk: egonw * r13028 /cdk/branches/cdk-1.2.x/src/test/org/open​science/cdk/io/cml/CMLRoundTripTest.java: Added test for bug #1713398
19:10 egonw but not all constructs were supported at the time, but Rajarshi extended the features of the SMARTS code
19:10 egonw but I have not had time to update the code yet
19:10 timvdm yes, I saw it in google reader
19:10 egonw good :)
19:11 CIA-38 cdk: egonw * r13029 /cdk/branches/cdk-1.2.x/src/test/org/open​science/cdk/io/cml/CMLRoundTripTest.java: Better testing
19:12 CIA-38 cdk: egonw * r13030 /cdk/branches/cdk-1.2.x/src/test/org/open​science/cdk/io/cml/CMLRoundTripTest.java: Tests for roundtripping of hydrogen count (see #1713398)
19:16 edrin joined #cdk
19:17 egonw hi edrin
19:17 edrin hi egonw
19:18 edrin was very busy today... in the morning diagnostics, in the afternoon students
19:21 edrin egonw: how are you doing?
19:36 egonw busy too... and got a cold coming up :(
20:59 egonw edrin: cu tomorrow!
20:59 edrin bye
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