Camelia, the Perl 6 bug

IRC log for #cdk, 2012-12-12

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All times shown according to UTC.

Time Nick Message
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13:15 commitbot [cdk] egonw pushed 1 new commit to cdk-1.4.x: http://git.io/lHvRig
13:15 commitbot cdk/cdk-1.4.x 5a5db14 John May: Generified comparators, removing redundant casts...
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13:29 commitbot [cdk] egonw pushed 1 new commit to cdk-1.4.x: http://git.io/VNQBOQ
13:29 commitbot cdk/cdk-1.4.x d7a55d3 John May: corrected handling of null value in the TreeNodeComparator. Previous if any node or atom were null the comparator would return '0' which is incorrect. If one is null and the other is not the objects are not equal....
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13:46 commitbot [cdk] egonw pushed 1 new commit to cdk-1.4.x: http://git.io/BEqk4g
13:46 commitbot cdk/cdk-1.4.x 704280a John May: Corrected canonical label sorting in the SmilesGenerator. This canonical labels are long and thus when the difference between two values is taken the result may be larger then the largest possible integer. This in rare cases cause the value to overflow and thus make the comparator non-transitive....
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14:12 commitbot [cdk] egonw pushed 1 new commit to cdk-1.4.x: http://git.io/SrGphA
14:12 commitbot cdk/cdk-1.4.x 6e8533a Egon Willighagen: Make sure the tests are also run with JUnit4...
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14:37 commitbot [cdk] egonw pushed 1 new commit to cdk-1.4.x: http://git.io/kDgfkg
14:37 commitbot cdk/cdk-1.4.x 40536af Egon Willighagen: OK, simple fix: reset the test graph before each test method call...
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14:49 commitbot [cdk] egonw pushed 1 new commit to cdk-1.4.x: http://git.io/cDGqNg
14:49 commitbot cdk/cdk-1.4.x 425c795 John May: Replaced subtraction based comparison. When the difference (which is a double) is converted to an integer the result may overflow. This overflow can occur in rare cases but would cause the comparator to be non-transitive....
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15:07 commitbot [cdk] egonw pushed 1 new commit to cdk-1.4.x: http://git.io/_nzYPg
15:07 commitbot cdk/cdk-1.4.x e5b1bc6 John May: Replaced subtraction based comparator. This comparator is unlikely to overflow but the safety of using the equalities ensures the proper behaviour of this comparator....
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15:30 commitbot [cdk] egonw pushed 1 new commit to cdk-1.4.x: http://git.io/4D0aAg
15:30 commitbot cdk/cdk-1.4.x ed399df John May: Corrected null handling on AtomContainer 2D centre comparison. Previous if either container was null the comparator would incorrectly return '0' indicating they were equal. The method was changed to always provide a minimum Point2d when an atom container is null. This will sort all null containers lower then non-null containers....
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15:55 commitbot [cdk] egonw pushed 1 new commit to master: http://git.io/bRlkeQ
15:55 commitbot cdk/master 6a323f0 John May: Generified comparators, removing redundant casts...
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16:05 commitbot [cdk] egonw pushed 1 new commit to master: http://git.io/zCKxCA
16:05 commitbot cdk/master 65ed12c John May: corrected handling of null value in the TreeNodeComparator. Previous if any node or atom were null the comparator would return '0' which is incorrect. If one is null and the other is not the objects are not equal....
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16:16 commitbot [cdk] egonw pushed 1 new commit to master: http://git.io/2kDbqQ
16:16 commitbot cdk/master 26a2f9b John May: Corrected canonical label sorting in the SmilesGenerator. This canonical labels are long and thus when the difference between two values is taken the result may be larger then the largest possible integer. This in rare cases cause the value to overflow and thus make the comparator non-transitive....
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16:22 commitbot [cdk] egonw pushed 2 new commits to master: http://git.io/bNiSFw
16:22 commitbot cdk/master 091336d Egon Willighagen: Make sure the tests are also run with JUnit4...
16:22 commitbot cdk/master f1e2e3d Egon Willighagen: OK, simple fix: reset the test graph before each test method call...
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16:32 commitbot [cdk] egonw pushed 3 new commits to master: http://git.io/CJlVQA
16:32 commitbot cdk/master f15ea9f John May: Replaced subtraction based comparison. When the difference (which is a double) is converted to an integer the result may overflow. This overflow can occur in rare cases but would cause the comparator to be non-transitive....
16:32 commitbot cdk/master 0968c90 John May: Replaced subtraction based comparator. This comparator is unlikely to overflow but the safety of using the equalities ensures the proper behaviour of this comparator....
16:32 commitbot cdk/master eda7ba7 John May: Corrected null handling on AtomContainer 2D centre comparison. Previous if either container was null the comparator would incorrectly return '0' indicating they were equal. The method was changed to always provide a minimum Point2d when an atom container is null. This will sort all null containers lower then non-null containers....
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17:21 commitbot [cdk] egonw pushed 9 new commits to master: http://git.io/6lnslQ
17:21 commitbot cdk/master bab373d John May: Added unit test for methods related to ShortestPathFingerprint. This include unit test for RandomNumber, SimpleAtomComparator, SimpleAtomCanonicalisation.
17:21 commitbot cdk/master 21adb90 John May: Move new classes from standard to fingerprint
17:21 commitbot cdk/master fd5fb30 John May: Removed redundant cast on comparator
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17:26 commitbot [cdk] egonw pushed 1 new commit to cdk-1.4.x: http://git.io/Y8ehNA
17:26 commitbot cdk/cdk-1.4.x 0d658df John May: Updated comparator on AtomPlacer. The comparator now uses the built in Integer comparator. To avoid null pointer exceptions the access to the weight value is wrapped in a private method which return the minimum integer value when the weight is not set (i.e. null).
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17:45 commitbot [cdk] egonw pushed 1 new commit to master: http://git.io/leVUmw
17:45 commitbot cdk/master 8d0642e John May: Updated comparator on AtomPlacer. The comparator now uses the built in Integer comparator. To avoid null pointer exceptions the access to the weight value is wrapped in a private method which return the minimum integer value when the weight is not set (i.e. null).
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18:34 commitbot [cdk] egonw pushed 1 new commit to master: http://git.io/oUGpHA
18:34 commitbot cdk/master 856781e John May: - Modified getTotalHydrogenCount(IAtomContainer) to actually provide the total hydrogen count. the only classes invoking this are AtomContainerSetManipulator and MoleculeSetManipulator the test on each of these were tested and worked as expected. - Added method to just count implicit hydrogens (as the pervious method actually did) - Modified existing unit test to reflect the change to total hydrogen count - Added three
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22:14 commitbot [cdk] egonw pushed 1 new commit to master: http://git.io/lMOsjA
22:14 commitbot cdk/master 962e33b Stephan Beisken: Added type check for the atom-atom mapping property....
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22:26 commitbot [cdk] egonw pushed 1 new commit to master: http://git.io/UjVO_w
22:26 commitbot cdk/master 1463387 Egon Willighagen: Fixed accepts() methods to also properly accept interfaces, fixing 7 testAcceptsAtLeastOneChemObjectClass() unit tests...
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23:45 commitbot [cdk] egonw pushed 3 new commits to master: http://git.io/G2OJMw
23:45 commitbot cdk/master 5baedfe John May: Gentrified IChemObject.getProperty() and provided a getProperty() which takes a class parameter so the method can be chained....
23:45 commitbot cdk/master 959f3fe John May: Added unit tests for the new getProperty(Object,Class) method....
23:45 commitbot cdk/master cc2af0f John May: Corrected method call on DebugChemObject...
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