Camelia, the Perl 6 bug

IRC log for #cdk, 2013-03-24

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All times shown according to UTC.

Time Nick Message
06:03 jbrefort joined #cdk
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07:12 commitbot [cdk] egonw pushed 24 new commits to master: http://git.io/rbqeCg
07:12 commitbot cdk/master f5b4be1 John May: Introduced a new utility for computing the first shortest path and all shortest paths from a start to an end atom. This implementation replaces an existing static method in PathTools which has now been deprecated. Another helper class was added that simplifies the computation of all-vs-all shortest paths....
07:12 commitbot cdk/master 43224b8 John May: Improved terminology in javadoc and added @cdk.githash to production classes.
07:12 commitbot cdk/master 2f9e10e John May: Corrected constructor visibility
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09:01 commitbot [cdk] egonw pushed 1 new commit to master: http://git.io/py83XA
09:01 commitbot cdk/master 700bf50 John May: update DynamicFactory to be thread safe - when a constructor for given parameters is not found a lock is obtained before searching for an appropriate match....
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09:30 commitbot [cdk] egonw pushed 5 new commits to master: http://git.io/3h_e_A
09:30 commitbot cdk/master 5aaff49 John May: fixing failing coverage test in cdk-cip...
09:30 commitbot cdk/master 48861ee John May: adding mockito dependency to domain modules...
09:30 commitbot cdk/master e867e4b John May: annotations to satisfy coverage unit test...
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09:47 commitbot [cdk] egonw pushed 3 new commits to master: http://git.io/mj2i8A
09:47 commitbot cdk/master 1a3de8e John May: removed a line which tried to add a bond which didn't exist - the molecule has 3 atoms at indices 0, 1 and 2 (there is no 3)....
09:47 commitbot cdk/master abeff2e John May: factory call with interface...
09:47 commitbot cdk/master 53bc775 John May: resolved two regressions in builder3d due to null field values...
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10:23 commitbot [cdk] egonw pushed 6 new commits to master: http://git.io/e9CGXA
10:23 commitbot cdk/master efce85c John May: using reflection to correct unit test. Unit test order is non certain and so in this test the template may already be loaded (fail) - to avoid this we use reflection to create a new non-singleton instance and to excite the private loading of templates....
10:23 commitbot cdk/master f50a040 John May: resolved three unit test errors in cdk-builder3d, due to the SINGLE_OR_DOUBLE flag which if not erased was leading to different atom types and thus fingerprints when searching for templates....
10:23 commitbot cdk/master 3b8438f John May: replaced manipulator produce anonymous structures - the new method avoids cloning so all values will always be default and avoids issues from the previous commit...
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11:30 commitbot [cdk] egonw pushed 7 new commits to master: http://git.io/uRdRfA
11:30 commitbot cdk/master 1e065a3 John May: corrected caught exception, this exception changed in commit: 1ef89fb0...
11:30 commitbot cdk/master 9631e2e John May: when IMolecule was removed (27c6f7df) this conditional was broken. ICrystal was not a subclass of IMolecule but it is a subclass of IAtomContainer and so the first condition will match and writeCrystal is never called....
11:30 commitbot cdk/master 3ac357b John May: using array list instead of vector...
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11:59 commitbot [cdk] egonw pushed 4 new commits to master: http://git.io/H5qQ9w
11:59 commitbot cdk/master 63e3757 John May: moves MMFF94 parameter loading to a single (previously broken) method - resolves failing unit test...
11:59 commitbot cdk/master de0f6a3 John May: correct method name for inherited tests...
11:59 commitbot cdk/master f62103a John May: unit tests to ensure getCountFingerprint/getRawFingerprint throw an UnsupportedOperation exception, in the case of the only implementor (SignatureFingerprint) the methods are overridden...
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12:17 commitbot [cdk] egonw pushed 6 new commits to master: http://git.io/Ipro4Q
12:17 commitbot cdk/master 5564ad8 John May: test annotations...
12:17 commitbot cdk/master 22d8c66 John May: missing dependencies required by AbstractFingerprinterTest for Lingo and Signature fingerprinters....
12:17 commitbot cdk/master 2d828d7 John May: incorrect method name from super class...
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12:35 commitbot [cdk] egonw pushed 6 new commits to master: http://git.io/dkzIJA
12:35 commitbot cdk/master 243f448 John May: test for FragmentUtils.traverse()...
12:35 commitbot cdk/master 653efc6 John May: unit tests for MurckoFramgnter.getFrameworksAsContainers...
12:35 commitbot cdk/master 8d8f7d3 John May: unit test for MurckoFragmenter.getFragmentsAsContainers...
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12:50 commitbot [cdk] egonw pushed 2 new commits to master: http://git.io/Z5Mm7Q
12:50 commitbot cdk/master 8e9243e Egon Willighagen: Added a convenience method to get an isotope based on an element symbol and exact mass, returning null when nothing suitable is found...
12:50 commitbot cdk/master e69c387 John May: return the matching isotope closest to the provided exact mass...
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14:20 commitbot [cdk] egonw pushed 3 new commits to master: http://git.io/hBHDMg
14:20 commitbot cdk/master 9ad58d0 John May: correct mass number from exact mass...
14:20 commitbot cdk/master 9dbf86a John May: isRingSaturated check for SINGLE_OR_DOUBLE bond flag...
14:20 commitbot cdk/master b13ba75 Egon Willighagen: Restored the leading slash-less config file paths...
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14:56 commitbot [cdk] egonw pushed 1 new commit to master: http://git.io/E8gb2g
14:56 commitbot cdk/master 6624689 Egon Willighagen: Using the ClassLoader is important too...
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16:04 commitbot [cdk] egonw pushed 6 new commits to master: http://git.io/r1YKXQ
16:04 commitbot cdk/master cbae234 Egon Willighagen: Revert "Using the ClassLoader is important too"...
16:04 commitbot cdk/master 15e73b6 Egon Willighagen: Revert "Restored the leading slash-less config file paths"...
16:04 commitbot cdk/master 637f8cf Egon Willighagen: Revert "moves MMFF94 parameter loading to a single (previously broken) method - resolves failing unit test"...
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