Camelia, the Perl 6 bug

IRC log for #cdk, 2008-08-13

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All times shown according to UTC.

Time Nick Message
05:04 bag joined #cdk
05:24 jbrefort joined #cdk
05:41 CIA-34 cdk: egonw * r12001 /cdk-qa/trunk/projects/080808-0001/ (README mol2.cdk.txt): Rerun after lactam is fine as N.am too
06:24 CIA-34 cdk: egonw * r12002 /cdk/trunk/src/main/org/openscience/cdk/ (2 files in 2 dirs): Fixed a few PMD migration problems
06:40 CIA-34 cdk: egonw * r12003 /cdk/trunk/src/main/org/openscience/cdk/ (io/cml/CMLHandler.java isomorphism/AtomMappingTools.java): Fixed a few PMD migration problems
07:44 egonw joined #cdk
08:05 jonalv joined #cdk
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08:13 maclean joined #cdk
08:18 CIA-34 cdk: egonw * r12004 /cdk/trunk/src/main/org/op​enscience/cdk/ringsearch/ (FiguerasSSSRFinder.java SSSRFinder.java): Fixed a few PMD migration problems
08:22 CIA-34 cdk: egonw * r12005 /cdk/trunk/src/test/org/openscience/cdk/atomt​ype/CDKAtomTypeMatcherTestFileReposTest.java: Removed two problematic files: one with a R atom; other unvalidated
08:43 CIA-34 cdk: egonw * r12006 /cdk/trunk/src/main/org/openscience/cdk/validate/ (ValidationReport.java ValidatorEngine.java): Fixed a few PMD migration problems
08:45 CIA-34 cdk: egonw * r12007 /cdk/trunk/src/ (3 files in 3 dirs): Added extra atom typing test, which apparently I never added to any suite
08:49 CIA-34 cdk: egonw * r12008 /cdk/trunk/src/test/data/mdl/zinc_1309609.sdf: One of the ZINC entries from the 1000 structures test set we are allowed to use
08:54 CIA-34 cdk: egonw * r12009 /cdk/trunk/src/test/org/openscience/cdk/atomt​ype/CDKAtomTypeMatcherTestFileReposTest.java:
08:54 CIA-34 cdk: ZINC8 test file from CDK's ZINC1000 test set does not show null's in the atom
08:54 CIA-34 cdk: typing: so, the ZINC1000 QA .sdf must be broken. Indeed, I did found
08:54 CIA-34 cdk: irregularities in it in the past, and noted last week that at least several ZINC
08:54 CIA-34 cdk: id's are no longer present in ZINC8
09:15 gilleain joined #cdk
09:26 CIA-34 cdk: gilleain * r12010 /cdk/trunk/src/ (3 files in 3 dirs): Fix to PDBReader (bug id : 2046633). The problem was that the CONECT records in a PDB file are fully redundant so that a bond between atom 1 and atom 10 is both 1->10 and 10->1.
09:27 maclean joined #cdk
09:36 egonw joined #cdk
10:18 CIA-34 cdk: egonw * r12011 /cdk/trunk/src/main/org/openscience/c​dk/atomtype/CDKAtomTypeMatcher.java: Added missing unit test annotation.
10:18 egonw maclean: btw, be careful with minor updates in actual code changes
10:19 egonw try to not have those, because it's noise with respect to the actual code changes
10:19 egonw your last commit removed ';' in PubChemXMLHelper
10:19 egonw but when browsing the commit, I wondered why that class would need to be changed for a PDB fix
10:19 egonw well, this one was rather obvious what was going one...
10:20 maclean Ah, right. I see. So do a separate commit for minor things then?
10:20 egonw but the more whitespace and other insignification layout changes cloud the actual coding fixes
10:20 egonw yes
10:20 maclean Okay, will do.
10:20 egonw thanx :)
10:20 egonw and please bug others if you see them do it too
10:21 maclean Btw, that semicolon completely confused me - I thought it was an inner class with the same name as the enclosing class.
10:21 egonw mom
10:22 egonw where do you see that inner class?
10:22 maclean I thought that the constructor was a class definition, or something. I was just confused, is all.
10:23 egonw ah, ok
10:26 egonw oh, btw... nice patch!
10:27 maclean Thanks. btw : I've made a blog (my first!) at gilleain.blogspot.com. Chris said something about a blue obelisk feed?
10:27 egonw ah, yes
10:27 egonw ok, excellent!
10:27 egonw http://cb.openmolecules.net/
10:27 maclean takk.
10:39 egonw http://cb.openmolecules.net/​blog_search.php?blog_id=188
10:39 zarah egonw's link is also http://tinyurl.com/6ogy9e
10:39 maclean aha. I have truly joined the blagoblag.
10:41 egonw yeah, no way out anymore
10:41 maclean :)
11:02 CIA-34 cdk: egonw * r12012 /cdk/trunk/src/META-INF/test-core.libdepends: Added missing dependency
11:02 thomas_ku joined #cdk
11:46 CIA-34 cdk: egonw * r12013 /cdk-qa/trunk/projects/080813-00001/ (8 files): Modification on 080808-00001 to compare against ZINC8, which has better defined sdf files (all atom types are now perceived by the CDK)
11:49 thomas_ku moin
11:49 zarah hi thomas_ku
12:00 CIA-34 cdk: egonw * r12014 /cdk/trunk/src/ (4 files in 3 dirs): Added the N.thioamide atom type (as Sybyl's N.am := N.amide + N.thioamide)
13:16 CIA-34 cdk: egonw * r12015 /cdk/trunk/src/main/org/openscience/c​dk/dict/data/cdk-sybyl-mappings.owl: Sybyl does not seem to care much about charges
13:27 CIA-34 cdk: egonw * r12016 /cdk/trunk/src/ (2 files in 2 dirs): Consider amide too: O=C-N(R)(R) where R is non-hydrogen
14:38 CIA-34 cdk: thomaskuhn * r12017 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/art2aCla​ssification/Art2aClassificator.java:
14:38 CIA-34 cdk: Remove some bugs from the algorithm:
14:38 CIA-34 cdk: -Improved the serialization
14:38 CIA-34 cdk: -Solved a bug within check for network convergence
14:38 CIA-34 cdk: -Improved the random selection of vector. Now able to switch between random random and deterministic random
14:41 CIA-34 cdk: thomaskuhn * r12018 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/da​tabase/pgchem/GetMoleculesFromDB.java: Clean up imports
14:44 CIA-34 cdk: thomaskuhn * r12019 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/data​base/pgchem/GetQSARVectorFromDB.java: Removed a bug: The molecue ID was part of the fingerprint vector. Improved the clean up of the components of each vector. All components which contains a Double.NaN will be removed.
14:45 CIA-34 cdk: thomaskuhn * r12020 /cdk-taverna/trunk/src/main/java/org/open​science/cdk/applications/taverna/database​/pgchem/IterativeGetMoleculeFromDB.java: Clean up imports
14:46 CIA-34 cdk: thomaskuhn * r12021 /cdk-taverna/trunk/src/main/java/org/ope​nscience/cdk/applications/taverna/inchi/ (InChIGeneratorWorker.java InChIParser.java): Clean up imports and update to Java 5
14:52 CIA-34 cdk: thomaskuhn * r12022 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/io/ (11 files): Some clean up
14:55 CIA-34 cdk: thomaskuhn * r12023 /cdk-taverna/trunk/src/main/java/org​/openscience/cdk/applications/tavern​a/io/iterative/IteratingReader.java: Remove unused variable
14:55 CIA-34 cdk: thomaskuhn * r12024 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​isomorphism/SubstructureFilter.java: Add a suppress warnings
14:57 CIA-34 cdk: thomaskuhn * r12025 /cdk-taverna/trunk/src/main/java/org​/openscience/cdk/applications/tavern​a/jchempaint/JChemPaintEditor.java: Add a suppress warnings
14:58 CIA-34 cdk: thomaskuhn * r12026 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/modeling/ (2 files): Add a suppress warnings
15:51 CIA-34 cdk: shk3 * r12027 /cdk/branches/cdk-1.0.x/src/org/openscien​ce/cdk/renderer/color/CPKAtomColors.java: Hydrogens now black (bug #2033634) - no idea where the white came from
15:59 shk3 this commit actually was in in net.bioclipse.cdk10
15:59 shk3 Are the repositories the same?
15:59 shk3 confused
16:11 shk3 jonalv: do you have an idea about thie svn?
16:12 jonalv sry?
16:12 jonalv shk3: what's the problem?
16:12 shk3 i commited a change in net.bc.cdk10
16:13 jonalv you must have strayed over into cdk
16:13 shk3 and the message here tells about /cdk/branches/cdk-1.0.x/src
16:13 shk3 me?
16:13 jonalv yea
16:13 shk3 never :-)
16:13 shk3 had that suspicion, but can't see how it happened
16:13 shk3 so the svn reps are independent?
16:14 jonalv there is an svn:externals in the bioclispe repo and Eclipse just let's you commit to the cdk repo wihthout being very explicit. The abstraction actually holds. Very sneaky... :)
16:15 shk3 ah, and this holds for update as well?
16:16 shk3 so it's one repository effectivly?
16:16 jonalv almost
16:16 jonalv you still need a user and a password on the cdk repo in order to get to commit :)
16:16 jonalv but since both are on sf they are the same :)
16:17 shk3 sneaky
16:17 shk3 indeed
16:17 jonalv yea but actually quite nice too :)
16:17 shk3 definitly
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18:03 thomas_ku joined #cdk
18:03 CIA-34 cdk: thomaskuhn * r12028 /cdk-taverna/trunk/src/main/java/org/ope​nscience/cdk/applications/taverna/qsar/ (5 files): Add a suppress warnings
18:03 CIA-34 cdk: thomaskuhn * r12029 /cdk-taverna/trunk/src/main/java/org/open​science/cdk/applications/taverna/qsar/des​criptors/molecular/RuleOfFiveFilter.java: Add a suppress warnings
18:05 CIA-34 cdk: thomaskuhn * r12030 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/qsar/model/ART2A​Classificator/ART2AClassificatorWorker.java: Improve the worker for the ART2a classification to match the possibility of the classificator
18:15 CIA-34 cdk: thomaskuhn * r12031 /cdk-taverna/trunk/src/main/java/or​g/openscience/cdk/applications/tave​rna/qsar/model/ART2AClassificator/ (6 files in 4 dirs): Move to the tools package
19:03 CIA-34 cdk: thomaskuhn * r12032 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​qsar/model/ART2AClassificator/tools/ (3 files in 2 dirs): Add a new Worker: This worker compares two or more ART2a classification results. The output of this worker is a csv file and a PDF file with charts of the comparison
19:03 CIA-34 cdk: thomaskuhn * r12053 /cdk-taverna/trunk/src/test/java/org​/openscience/cdk/applications/tavern​a/smiles/SMILESGeneratorTest.java: Add a suppress warnings
19:03 CIA-34 cdk: thomaskuhn * r12033 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​qsar/model/ART2AClassificator/tools/ (4 files): Add a new series of worker: These worker allows an leaf one out iteration over all components of the fingerprint vector.
19:04 CIA-34 cdk: thomaskuhn * r12052 /cdk-taverna/trunk/src/test/java/org/open​science/cdk/applications/taverna/reaction​enumerator/ReactionEnumeratorTest.java: Add a suppress warnings
19:04 CIA-34 cdk: thomaskuhn * r12054 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/tool​s/ConvertFingerprintItemListToCSV.java: Add a new worker which stores a fingerprint vector as csv file
19:04 CIA-34 cdk: thomaskuhn * r12055 /cdk-taverna/trunk/src/test/java/org/open​science/cdk/applications/taverna/tools/Co​nvertFingerprintItemListToCSVTest.java: Add a unit test for the new worker which stores a fingerprint vector as csv file
19:20 bag joined #cdk
19:25 CIA-34 cdk: thomaskuhn * r12056 /cdk-taverna/trunk/src/main/java/org/open​science/cdk/applications/taverna/layout/: Remove empty package
19:27 CIA-34 cdk: thomaskuhn * r12057 /cdk-taverna/trunk/src/test/java/org/op​enscience/cdk/applications/taverna/qsar​/model/ART2AClassificator/tools/Compare​ART2AClassificationResultsTest.java: Add a unit test for the new Compare ART2a classification worker
19:28 CIA-34 cdk: thomaskuhn * r12058 /cdk-taverna/trunk/src/test/resources/data/ART2A/ (4 files): add some new test files for the art2a classification
19:28 CIA-34 cdk: thomaskuhn * r12059 /cdk-taverna/trunk/pom.xml: Add a JFreeChart dependency
21:56 edrin joined #cdk

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