Camelia, the Perl 6 bug

IRC log for #cdk, 2008-11-21

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All times shown according to UTC.

Time Nick Message
00:12 tim joined #cdk
00:31 tim joined #cdk
01:03 cpyang joined #cdk
06:53 jbrefort joined #cdk
08:03 egonw joined #cdk
08:22 CIA-37 cdk: shk3 * r13168 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (5 files): added a toolbar
08:30 CIA-37 cdk: gilleain * r13169 /cdk/branches/jchempaint-primary/ (9 files in 9 dirs): Removing the unused module package. Removed empty packages.
08:33 carsten joined #cdk
08:37 CIA-37 cdk: goglepox * r13170 /cdk/branches/jchempaint-primary/src/main​/org/openscience/cdk/renderer/generators/ (3 files): Changed to use cdk logger
08:44 CIA-37 cdk: shk3 * r13171 /jchempaint/trunk/src/main/org/o​penscience/jchempaint/resources/ (47 files in 2 dirs): changing symbols sort of works
10:03 jonalv joined #cdk
10:04 egonw ha jonalv
10:04 egonw will you come for lunch?
10:05 jonalv egonw: I just mailed you and said that I wouldn't
10:05 jonalv I realised that I probably could squeese down some miso soup though...
10:05 jonalv =)
10:05 egonw oh, sorry... not received yet
10:05 egonw jonalv: I guess we need to make a reservation, not?
10:06 jonalv egonw: yea
10:06 egonw forgot to do that earlier...
10:06 jonalv I am not working today anyway
10:06 egonw what's the name of the place again?
10:06 jonalv I feel that I wouldn't be able to concentrate and would just be complaining...
10:06 jonalv Yukikos
10:07 jonalv Yukikos sushi
10:07 egonw do you have Carl's number?
10:07 jonalv Carl has no mobile phone
10:07 egonw grmph...
10:07 jonalv mail him
10:08 egonw done
10:10 jonalv hokey
10:10 egonw ah, carl just walked in
10:10 jonalv good :)
10:10 egonw we have a reservation at 12:00
10:10 egonw you'll join for soup?
10:10 jonalv I stil wonder if I should join you
10:10 egonw it would be tempting to try sushi...
10:10 egonw which might indeed not be a good idea
10:10 jonalv yea...
10:11 jonalv perhaps I will try a small sushi too. I am actually able to open my mouth a bit better today it only hurts to swallow
10:11 egonw ok, let's meet at 12:00 at the restaurant then
10:11 jonalv and wel the tooth hurts as well off course but I can chew at the other half of my mouth and Yukikos is not at all far away from home...
10:12 jonalv okey you convinced me. I will boost up on pain medicine for this one... :/
10:12 egonw :)
10:12 egonw not sure if I convinced you...
10:13 egonw at least I did not try..
10:13 egonw I think the sushi did
10:13 egonw :)
10:17 jonalv you convinced me by just talking of it. :)
10:19 jonalv afk
10:30 CIA-37 cdk: goglepox * r13172 /cdk/branches/jchempaint-primary/src/main/org/o​penscience/cdk/renderer/ISimpleRenderer2D.java:
10:30 CIA-37 cdk: Changed API to conform to the new way.
10:30 CIA-37 cdk: setBounds(...) takes care of the transforming and
10:30 CIA-37 cdk: paintMolecule(...) renders the AtomContainer using
10:30 CIA-37 cdk: the IRenderingVisitor
10:32 shk3 joined #cdk
10:32 CIA-37 cdk: shk3 * r13173 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (6 files in 2 dirs): more work on jcp
10:32 CIA-37 cdk: gilleain * r13174 /cdk/branches/jchempaint-primary/src/ (14 files in 4 dirs): Restored Color.
10:32 gilleain joined #cdk
10:36 egonw sushi time
11:56 gilleain joined #cdk
12:00 jbrefort joined #cdk
12:10 carsten joined #cdk
12:11 CIA-37 cdk: goglepox * r13175 /cdk/branches/jchempaint-primary/src/main/org/o​penscience/cdk/renderer/ISimpleRenderer2D.java: Reverting chages to interface we will do this later maybe.
12:34 CIA-37 cdk: shk3 * r13176 /jchempaint/trunk/ (.classpath META-INF/MANIFEST.MF): more work on jcp
12:50 CIA-37 cdk: gilleain * r13177 /cdk/branches/gilleain-jchempaint/sr​c/main/org/openscience/cdk/renderer/ (8 files in 3 dirs): Fixed scaling.
13:25 egonw joined #cdk
13:57 jpansanel moin
13:57 zarah hi jpansanel
14:03 timvdm joined #cdk
14:04 egonw hi timvdm
14:04 timvdm hi egonw
14:18 CIA-37 cdk: gilleain * r13178 /cdk/branches/jchempaint-primary/src/ (4 files in 2 dirs): Painting text background.
14:38 CIA-37 cdk: shk3 * r13179 /cdk/branches/jchempaint-primary/ (13 files in 8 dirs): compiles via ant
14:39 CIA-37 cdk: shk3 * r13180 /jchempaint/trunk/ (11 files in 5 dirs): working on the scripts
15:06 CIA-37 cdk: shk3 * r13181 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (4 files in 2 dirs): moved classes to jcp, added module declarations
15:06 CIA-37 cdk: shk3 * r13182 /jchempaint/trunk/ (5 files in 3 dirs): build.xml generates a jar
15:06 gilleain joined #cdk
15:07 CIA-37 cdk: gilleain * r13183 /cdk/branches/gilleain-jchempaint/sr​c/test/org/openscience/cdk/renderer/ (2 files): Minor changes.
15:12 CIA-37 cdk: gilleain * r13184 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/ (3 files): Merged changes.
15:19 CIA-37 cdk: shk3 * r13185 /jchempaint/trunk/build.xml: the jar file works
15:21 CIA-37 cdk: goglepox * r13186 /cdk/branches/jchempaint-primary/src/main​/org/openscience/cdk/renderer/generators/ (3 files):
15:21 CIA-37 cdk: Added IGenerator interface for generators
15:21 CIA-37 cdk: it has one method generate(IAtomContainer, Point2d)
15:21 CIA-37 cdk: goglepox * r13187 /cdk/branches/jchempaint-primary/src/main/o​rg/openscience/cdk/renderer/Renderer.java:
15:21 CIA-37 cdk: Implemented a general renderer class.
15:21 CIA-37 cdk: It takes care of generators and connecting them
15:21 CIA-37 cdk: with AtomContainer and IRenderingVisitor.
15:21 CIA-37 cdk: egonw * r13188 /jchempaint/trunk/ (ant.properties.template build.props build.xml): Renamed properties file, and made it a template, which you'll have to copy to ant.properties
15:24 CIA-37 cdk: egonw * r13189 /jchempaint/trunk/: Ignore the local ant.properties created from the ant.properties.template
15:31 CIA-37 cdk: gilleain * r13190 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (2 files in 2 dirs): Initial refactoring of the Renderer2DModel into separate ControllerParameters and RenderingParameters classes.
15:38 CIA-37 cdk: egonw * r13191 /jchempaint/trunk/src/main/org/openscienc​e/jchempaint/application/JChemPaint.java: Gave it the JChemPaint title
15:39 CIA-37 cdk: egonw * r13192 /jchempaint/trunk/.gitignore: Ignore the local copy of ant.properties.template with git too
15:57 CIA-37 cdk: gilleain * r13193 /cdk/branches/jchempaint-primary/src/ (11 files in 3 dirs): Clean up of the Controller2DModules.
16:04 CIA-37 cdk: shk3 * r13194 /jchempaint/trunk/ (build-applet.xml build.xml): small changes in build scripts
18:08 tim joined #cdk
18:47 egonw joined #cdk
20:05 CIA-37 cdk: egonw * r13195 /cdk/branches/cdk-1.2.x/src/test/org/openscienc​e/cdk/atomtype/mapper/AtomTypeMapperTest.java: Added missing unit test.
20:05 CIA-37 cdk: egonw * r13196 /cdk/branches/cdk-1.2.x/src/main/org/openscie​nce/cdk/charges/InductivePartialCharges.java: Keep the original stacktrace.
20:05 CIA-37 cdk: egonw * r13197 /cdk/branches/cdk-1.2.x/src/test/org/openscienc​e/cdk/charges/InductivePartialChargesTest.java: Fixed NPE in test: added missing 3D coords
20:15 CIA-37 cdk: egonw * r13198 /cdk/branches/cdk-1.2.x/src/main/org​/openscience/cdk/io/PDBReader.java: Fixed testing of accepted interface: also test for superclasses, so that NNChemFile is recognized as IChemFile too
20:50 CIA-37 cdk: egonw * r13199 /cdk/branches/cdk-1.2.x/src/main/org/ope​nscience/cdk/qsar/model/R2/RModel.java: Fixed failing MqsarTest suite: added test up front for required R_HOME and LD_LIBRARY_PATH being set
20:54 CIA-37 cdk: egonw * r13200 /cdk/branches/cdk-1.2.x/ (70 files in 15 dirs): Git-Eclipse insisted on fixing the chmods
21:23 CIA-37 cdk: miguelrojasch * r13201 /cdk/branches/cdk-1.2.x/src/test/org/opensc​ience/cdk/formula/rules/RDBERuleTest.java: Test for bug: 2322906
21:32 CIA-37 cdk: egonw * r13202 /cdk/branches/cdk-1.2.x/src/test/org/op​enscience/cdk/qsar/descriptors/atomic/P​artialTChargeMMFF94DescriptorTest.java: Fixed test: first six atoms are all carbons, and then all hydrogens come. That's how the test molecule is constructed, and reorded expected values accordingly
21:33 CIA-37 cdk: egonw * r13203 /cdk/branches/cdk-1.2.x/src/main/org/openscience/c​dk/modeling/builder3d/ForceFieldConfigurator.java: Do not silently eat exceptions
21:52 CIA-37 cdk: egonw * r13204 /cdk/branches/cdk-1.2.x/src/main/or​g/openscience/cdk/modeling/builder3​d/MMFF94BasedAtomTypePattern.java: Synchronized pattern with output of current HOSECodeGenerator for water-like oxygens
21:53 CIA-37 cdk: egonw * r13205 /cdk/branches/cdk-1.2.x/src/test/org/op​enscience/cdk/qsar/descriptors/atomic/P​artialTChargeMMFF94DescriptorTest.java: Method is not as accurate as originally thought; or at least not anymore. The atom type percepion is implemented in a complex way, making it very sensitive to very many things
21:54 CIA-37 cdk: egonw * r13206 /cdk/branches/cdk-1.2.x/src/main/org/o​penscience/cdk/qsar/descriptors/atomic​/PartialTChargeMMFF94Descriptor.java: Clone the object, so to not modify the passes IAtom and IAtomContainer
22:16 CIA-37 cdk: egonw * r13207 /cdk/branches/cdk-1.2.x/src/test/org/ope​nscience/cdk/qsar/descriptors/atomic/Ato​mHybridizationVSEPRDescriptorTest.java: Added assertAtomTypesPerceived calls, showing three missing atom types; bugs reported
22:30 CIA-37 cdk: egonw * r13208 /cdk/branches/cdk-1.2.x/src/test/org/ope​nscience/cdk/qsar/descriptors/molecular/ (2 files): Added more thorough testing
22:51 CIA-37 cdk: egonw * r13209 /cdk/branches/cdk-1.2.x/src/test/or​g/openscience/cdk/qsar/descriptors/​molecular/XLogPDescriptorTest.java: Removed outcommented code
22:52 CIA-37 cdk: egonw * r13210 /cdk/branches/cdk-1.2.x/src/test/or​g/openscience/cdk/qsar/descriptors/​molecular/XLogPDescriptorTest.java: Added tests to ensure atom types are perceived
22:52 CIA-37 cdk: egonw * r13211 /cdk/branches/cdk-1.2.x/src/test/org/o​penscience/cdk/qsar/descriptors/molecu​lar/AminoAcidCountDescriptorTest.java: It is a molecular descriptor, but only makes really sense for peptides
22:53 CIA-37 cdk: egonw * r13212 /cdk/branches/cdk-1.2.x/src/main/org/​openscience/cdk/qsar/descriptors/mole​cular/AminoAcidCountDescriptor.java: Proper length of descriptor result type
23:01 CIA-37 cdk: egonw * r13213 /cdk/branches/cdk-1.2.x/src/main/org/opensci​ence/cdk/renderer/color/CPKAtomColors.java: Fixed a NPE: atomic number can be null
23:02 CIA-37 cdk: egonw * r13214 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/renderer/color/CPKAtomColorsTest.java: Fixed test: CPKAtomColors.PINK is not the same as Color.PINK
23:29 CIA-37 cdk: egonw * r13215 /cdk/branches/cdk-1.2.x/src/main/org/open​science/cdk/layout/TemplateHandler.java: Also output the stacktrace
23:29 CIA-37 cdk: egonw * r13216 /cdk/branches/cdk-1.2.x/src/META-​INF/test-qsarprotein.cdkdepends: Added missing dependency

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