Camelia, the Perl 6 bug

IRC log for #cdk, 2009-01-28

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All times shown according to UTC.

Time Nick Message
02:54 Conrad joined #cdk
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08:30 jonalv joined #cdk
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08:52 egonw joined #cdk
09:10 egonw large set of patches pending...
09:11 * egonw is merging cdk-1.2.x with trunk
09:11 CIA-62 cdk: egonw * r13976 /cdk/trunk/src/test/org/openscien​ce/cdk/io/ChemObjectIOTest.java:
09:11 CIA-62 cdk: Test that for each IChemObject implementation, at least on object is accepted.
09:11 CIA-62 cdk: git-svn-id:
09:11 CIA-62 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12585 eb4e18e3-b210-0410-a6ab-dec725e4b171
09:11 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
09:12 shk3 joined #cdk
09:12 CIA-62 cdk: egonw * r13977 /cdk/trunk/src/test/org/openscien​ce/cdk/io/ChemObjectIOTest.java:
09:12 CIA-62 cdk: Added more testing
09:12 CIA-62 cdk: git-svn-id:
09:12 CIA-62 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12588 eb4e18e3-b210-0410-a6ab-dec725e4b171
09:12 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
09:13 CIA-62 cdk: egonw * r13978 /cdk/trunk/src/main/org/opensci​ence/cdk/io/ReaderFactory.java:
09:13 CIA-62 cdk: Java5 equivalent of the Java6 constructor (I think)
09:13 CIA-62 cdk: git-svn-id:
09:13 CIA-62 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12594 eb4e18e3-b210-0410-a6ab-dec725e4b171
09:13 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
09:14 CIA-62 cdk: egonw * r13979 /cdk/trunk/src/test/org/openscience/​cdk/io/formats/ChemFormatTest.java:
09:14 CIA-62 cdk: Added missing unit tests for getSupportedDataFeatures and getRequiredDataFeatures
09:14 CIA-62 cdk: git-svn-id:
09:14 CIA-62 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12595 eb4e18e3-b210-0410-a6ab-dec725e4b171
09:14 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
09:22 CIA-62 cdk: egonw * r13980 /cdk/trunk/src/main/org/op​enscience/cdk/io/formats/ (89 files):
09:22 CIA-62 cdk: Added annotation for testGetSupportedDataFeatures
09:22 CIA-62 cdk: git-svn-id:
09:22 CIA-62 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12596 eb4e18e3-b210-0410-a6ab-dec725e4b171
09:22 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
09:23 maclean joined #cdk
09:51 CIA-62 cdk: egonw * r13981 /cdk/trunk/src/main/org/op​enscience/cdk/io/formats/ (88 files):
09:51 CIA-62 cdk: Added annotation for testGetRequiredDataFeatures
09:51 CIA-62 cdk: git-svn-id:
09:51 CIA-62 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12597 eb4e18e3-b210-0410-a6ab-dec725e4b171
09:51 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
09:54 CIA-62 cdk: egonw * r13982 /cdk/trunk/src/test/org/openscience/cdk​/io/formats/ChemFormatMatcherTest.java:
09:54 CIA-62 cdk: Added test class for the IChemFormatMatcher interface
09:54 CIA-62 cdk: git-svn-id:
09:54 CIA-62 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12598 eb4e18e3-b210-0410-a6ab-dec725e4b171
09:54 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
10:07 CIA-62 cdk: egonw * r13983 /cdk/trunk/src/test/org/op​enscience/cdk/io/formats/ (46 files):
10:07 CIA-62 cdk: Extend ChemFormatMatcherTest if the tested object instanceof IChemFormatMatcher
10:07 CIA-62 cdk: git-svn-id:
10:07 CIA-62 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12599 eb4e18e3-b210-0410-a6ab-dec725e4b171
10:07 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
10:12 CIA-62 cdk: egonw * r13984 /cdk/trunk/src/test/org/openscience/cd​k/atomtype/StructGenMatcherTest.java: Overwriting default initialization methods from AbstractAtomTypeTest for the matcher; fixes NPEs all over the place, because AbstractAtomTypeTest.getFactory() was returning null
10:15 maclean joined #cdk
10:21 CIA-62 cdk: egonw * r13985 /cdk/trunk/src/test/org/openscience/cdk/io/ (22 files): Most readers now use SimpleChemObjectReaderTest
10:27 CIA-62 cdk: egonw * r13986 /cdk/trunk/src/test/org/openscience​/cdk/io/formats/JMEFormatTest.java:
10:27 CIA-62 cdk: Oops, JME is not a IChemFormatMatcher. Fixes many NPEs
10:27 CIA-62 cdk: git-svn-id:
10:27 CIA-62 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12602 eb4e18e3-b210-0410-a6ab-dec725e4b171
10:27 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
10:29 egonw blah... git-svn is so damn slow :(
10:30 maclean :[
10:30 maclean (zoom, scaling, and scale-to-fit almost implemented properly...)
10:31 egonw maclean: stefan told me about reaction stuff you were talking about...
10:31 egonw very much interested in that...
10:31 egonw Steffen Neumann too...
10:31 maclean the renderer (thinks that) it can render reactions, reactionsets, ...
10:31 maclean moleculesets
10:32 maclean and chemmodels, and molecules (atomcontainers)
10:32 maclean layout of reactions is a problem, I think, if they are not already laid out
10:33 CIA-62 cdk: egonw * r13987 /cdk/trunk/src/ (2 files in 2 dirs):
10:33 CIA-62 cdk: Renamed test method to be more meaningful. Fixes bug #2151934
10:33 CIA-62 cdk: git-svn-id:
10:33 CIA-62 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12610 eb4e18e3-b210-0410-a6ab-dec725e4b171
10:33 CIA-62 cdk: Author: rajarshi <rajarshi@eb4e18e3-b210-0410-a6ab-dec725e4b171>
10:38 maclean_ joined #cdk
10:40 CIA-62 cdk: egonw * r13988 /cdk/trunk/src/ (2 files in 2 dirs):
10:40 CIA-62 cdk: Ensured that if formal charge is not set, we don't crash. Added unit test. Fixes bug #2149621
10:40 CIA-62 cdk: git-svn-id:
10:40 CIA-62 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12611 eb4e18e3-b210-0410-a6ab-dec725e4b171
10:40 CIA-62 cdk: Author: rajarshi <rajarshi@eb4e18e3-b210-0410-a6ab-dec725e4b171>
10:43 CIA-62 cdk: egonw * r13989 /cdk/trunk/build.xml:
10:43 CIA-62 cdk: Updated so that dist-large includes common-cli. Fixes bug #2151521
10:43 CIA-62 cdk: git-svn-id:
10:43 CIA-62 cdk:  https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12612 eb4e18e3-b210-0410-a6ab-dec725e4b171
10:43 CIA-62 cdk: Author: rajarshi <rajarshi@eb4e18e3-b210-0410-a6ab-dec725e4b171>
10:46 CIA-62 cdk: egonw * r13990 /cdk/trunk/.gitignore: Ignore backup files
10:49 CIA-62 cdk: egonw * r13991 /cdk/trunk/develjar/.gitignore: Ignore doccheck.jar: used to spot JavaDoc errors, but it's not licensed to allow redistribution
10:51 maclean_ yay! rendered a reaction!
10:52 CIA-62 cdk: egonw * r13992 /cdk/trunk/work.txt: More patches from cdk1.2.x applies: 576 left to do :)
10:56 de__maas joined #cdk
11:09 Gpox joined #cdk
11:13 egonw maclean_++
11:14 maclean_ now trying to render bounding boxes
11:21 egonw make sure to this in the background layer
11:22 jbrefort joined #cdk
11:23 maclean_ egonw : really? hmmm.
11:23 de__maas left #cdk
11:24 maclean_ ok, done! :)
11:39 maclean_ oh great : apparently a reaction is modelled as a ChemModel with both a reaction set AND a molecule set.
11:40 egonw no, that is not the previously used convention
11:40 egonw the ReactionSet and MoleculeSet are mutually exclusive
11:43 maclean_ apparently not
11:43 maclean_ if written out with the cmlwriter, and then read back in...
11:43 maclean_ (at least, I think so - I will check and file a bug)
11:45 maclean_ also, Mappings are not written out (or read in?)
11:47 CIA-62 cdk: egonw * r13993 /cdk/trunk/ (284 files in 38 dirs):
11:47 CIA-62 cdk: Squash of many more commit merged; squashed because I lost internet
11:47 CIA-62 cdk: connectivity, and I have no clue how to 'continue' a half done 'git svn dcommit'
11:47 CIA-62 cdk: :( See the diff on the work.txt to the patches that are squased in this commit
12:04 maclean_ renderer patch uploaded for review!
12:13 egonw cheers
12:13 egonw maclean_: I'm heading for lunch now...
12:13 egonw and will join you around 1o'clock
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13:41 CIA-62 cdk: shk3 * r13994 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (4 files in 3 dirs): activated export
15:49 grandm44 joined #cdk
16:16 CIA-62 cdk: shk3 * r13995 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (3 files in 3 dirs): print works
16:55 carsten joined #cdk
17:23 CIA-62 cdk: shk3 * r13996 /jchempaint/trunk/src/main/org/opensci​ence/jchempaint/JChemPaintPanel.java: the exit works
17:32 egonw maclean: http://www.hmdb.ca/public/downlo​ads/current/metabolitecards.zip
17:32 zarah egonw's link is also http://tinyurl.com/cj7z57
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