Camelia, the Perl 6 bug

IRC log for #cdk, 2008-03-05

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All times shown according to UTC.

Time Nick Message
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04:48 CIA-18 cdk: rajarshi * r10301 /trunk/cdk/src/main/org/openscience/cdk/​io/iterator/IteratingSMILESReader.java: Updated constructors to allow one to specify a IChemObjectBuilder to build the actual molecules with. Useful if you want to use the NN* classes
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05:10 CIA-18 cdk: rajarshi * r10302 /trunk/cdk/src/main/org/openscience/​cdk/fingerprint/Fingerprinter.java: Updates to improve performance when building the String version of paths - avoid adding strings, and replaced them with StringBuilder calls
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06:57 rojasm moin
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07:33 CIA-18 cdk: miguelrojasch * r10303 /branches/miguelrojasch/reaction/ (42 files in 10 dirs): Synchronized with trunk; merged 10291:10302
07:35 rojasm egonw: around?
07:58 CIA-18 cdk: miguelrojasch * r10304 /branches/miguelrojasch/reaction/sr​c/test/org/openscience/cdk/tools/St​ructureResonanceGeneratorTest.java: added Test if the aromaticity is perserved by the resonance
08:25 CIA-18 cdk: miguelrojasch * r10305 /branches/miguelrojasch/reaction/src/ (2 files in 2 dirs): update the isomorphism to QueryAtomContainerCreator.create​SymbolAndBondOrderQueryContainer to distinguish between aromatics compounds
08:36 CIA-18 cdk: miguelrojasch * r10306 /branches/miguelrojasch/reaction/src/t​est/org/openscience/cdk/modulesuites/ (MformulaTests.java MreactionTests.java): update the coverage test to junit4
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08:49 jpansanel moin
09:13 egonw rojasm: I am now
09:21 CIA-18 cdk: miguelrojasch * r10307 /branches/miguelrojasch/reaction/src​/test/org/openscience/cdk/formula/Mo​lecularFormulaManipulatorTest.java: added missed test
09:24 rojasm hi egonw
09:24 rojasm solved thanks
09:24 rojasm thanks for the quaryAtomContainer
09:24 rojasm It works perfect now
09:24 rojasm free errors :)
09:24 egonw excellent :)
09:25 egonw that suprises me, because the test I wrote for it last nite does not work well...
09:25 egonw but too tired to pinpoint the problem :)
09:25 egonw ok... but that's really good news
09:25 rojasm mmm. I only tested for the resonancetest
09:26 egonw so... please merge reaction/ into trunk/ then
09:29 CIA-18 cdk: miguelrojasch * r10308 /branches/miguelrojasch/reaction/src/ (3 files in 3 dirs): added ReactionEngineTest
09:31 CIA-18 cdk: miguelrojasch * r10309 /branches/miguelrojasch/reaction/src/test​/org/openscience/cdk/reaction/type/Radica​lChargeSiteInitiationReactionTest.java: removed testMethod which was not used anymore
09:33 rojasm egonw could you please write the line which is necessary to merge form reaction/ into trunk/ so I can copy and shave before I do some bigggg mistake :)
09:35 egonw svn diff https://cdk.svn.sf.net/svnroot/cdk/trunk/cdk https://cdk.svn.sf.net/svnroot/cd​k/branches/miguelrojasch/reaction > reaction.patch
09:35 egonw then cd into trunk/cdk
09:35 egonw and apply the patch
09:35 egonw let me check if there is a better way...
09:38 egonw http://kenkinder.com/svnmerge/
09:38 rojasm ok thanks
09:38 egonw not sure if that is going to give help
09:39 egonw I'd go for the above...
09:39 egonw shall I do it?
09:39 egonw an alternative is this:
09:40 egonw check with commits were applied to reaction, using svn log reaction/
09:40 egonw and apply those one by one to trunk
09:40 egonw I get the feeling that merging changed from trunk/ into the branch/ is making things needlessly more complicated...
09:52 CIA-18 cdk: miguelrojasch * r10310 /branches/miguelrojasch/reaction/s​rc/test/org/openscience/cdk/reacti​on/ReactionSpecificationTest.java: New test for ReactionSpecificationTest
10:11 rojasm egonw: if I try to merge from miguelrojasch/reaction repository to my directory trunk/cdk and than commit is not easier?
10:12 egonw using what command?
10:12 rojasm cd myDirectory/trunk/cdk
10:12 rojasm svn merge -r 10302:HEAD https://cdk.svn.sourceforge.net/svnroo​t/cdk/branches/miguelrojasch/reaction
10:12 rojasm svn commit
10:12 egonw no, because that will not commit the changes you made before 10302
10:13 rojasm than from I created the branch
10:13 rojasm 9608
10:13 egonw later actually...
10:13 egonw but that won't work either
10:13 rojasm :(
10:13 egonw because that includes merging in commits made to trunk...
10:13 egonw viz. commit 10303
10:13 egonw the sync
10:14 rojasm mmm
10:14 rojasm so you suggest one to one
10:14 egonw right
10:14 egonw that might be the best approach
10:14 egonw apply reaction/ branch commit one by one, using:
10:14 egonw cd trunk/cdk
10:15 egonw svn merge -c 10309 https://cdk.svn.sourceforge.net/svnroo​t/cdk/branches/miguelrojasch/reaction
10:15 egonw etc
10:15 egonw that's how I kept cdk_1.0.x/ and trunk/ in sync
10:16 dleidert joined #cdk
10:17 egonw rojasm: first relevant patch is 10255
10:17 rojasm after 'miguelrojasch/reaction' the java file, right?
10:17 egonw run: svn log -r 10255:HEAD reaction/
10:18 egonw huh?
10:18 egonw what do you mean?
10:18 rojasm nothing, sorry false looked
10:21 rojasm egonw: using svn merge -c 10309 https://cdk.svn.sourceforge.net/svnroo​t/cdk/branches/miguelrojasch/reaction from trunk/cdk only merges the last update
10:22 egonw yes
10:22 egonw one by one
10:22 rojasm ups
10:22 egonw use that 'svn log' command to see which you'll have to merge
10:22 rojasm ok
10:22 egonw I see 10255, 10267, 10268
10:22 egonw 269, 272
10:22 egonw 273
10:23 egonw no, not that last one
10:23 egonw 274 275 276 287
10:23 egonw 288
10:23 egonw 290 292
10:23 egonw not 292, another sync
10:23 egonw 293
10:23 egonw 294
10:23 egonw 295
10:24 egonw 304
10:24 egonw 305
10:24 egonw 306
10:24 egonw 307
10:24 egonw 308
10:24 egonw 309
10:24 egonw 310
10:24 egonw that's it
10:25 rojasm and starting from smaller or the bigger. Or it doesn't matter
10:27 egonw yes, it matters
10:27 egonw and you can best update Eclipse after each merge
10:27 egonw to make sure there are no compile errors
10:31 CIA-18 cdk: miguelrojasch * r10311 /trunk/cdk/src/test/org/ope​nscience/cdk/reaction/type/ (2 files): Synchronized with miguelrojasch/reaction; merged 10267
10:32 CIA-18 cdk: miguelrojasch * r10312 /trunk/cdk/src/test/org/openscience/cdk/reac​tion/type/SharingChargeDBReactionTest.java: Synchronized with miguelrojasch/reaction; merged 10268
10:34 CIA-18 cdk: miguelrojasch * r10313 /trunk/cdk/src/main/org/openscience​/cdk/config/data/cdk_atomtypes.xml: Synchronized with miguelrojasch/reaction; merged 10269
10:35 CIA-18 cdk: miguelrojasch * r10314 /trunk/cdk/src/main/org/openscience​/cdk/config/data/cdk_atomtypes.xml: Synchronized with miguelrojasch/reaction; merged 10272
10:36 egonw rojasm: suggestion: include the origal commit message too
10:36 egonw I normally have something like:
10:36 CIA-18 cdk: miguelrojasch * r10315 /trunk/cdk/src/ (3 files in 3 dirs): Synchronized with miguelrojasch/reaction; merged 10274
10:36 egonw "Applied patch 10272 from the reaction branch: 'here goes to original message'"
10:37 CIA-18 cdk: miguelrojasch * r10316 /trunk/cdk/src/main/org/openscience​/cdk/config/data/cdk_atomtypes.xml: Synchronized with miguelrojasch/reaction; merged 10275
10:37 egonw rojasm: ping
10:38 CIA-18 cdk: miguelrojasch * r10317 /trunk/cdk/src/test/org/ope​nscience/cdk/reaction/type/ (2 files): Synchronized with miguelrojasch/reaction; merged 10276
10:40 CIA-18 cdk: miguelrojasch * r10318 /trunk/cdk/src/main/org/ope​nscience/cdk/reaction/type/ (31 files): Synchronized with miguelrojasch/reaction; merged 10287
10:40 rojasm egonw yes
10:40 rojasm not good?
10:40 egonw sort of:
10:40 egonw [2008-03-05 11:36:26] <egonw> rojasm: suggestion: include the origal commit message too
10:40 egonw [2008-03-05 11:36:32] <egonw> I normally have something like:
10:40 egonw [2008-03-05 11:37:01] <egonw> "Applied patch 10272 from the reaction branch: 'here goes to original message'"
10:41 egonw yes, it's good... but could be better, IMO :)
10:41 rojasm :)
10:44 CIA-18 cdk: miguelrojasch * r10319 /trunk/cdk/src/ (5 files in 3 dirs): Applied patch 10288 from the reaction branch: 'added new dictionary for reactions'
10:46 CIA-18 cdk: miguelrojasch * r10320 /trunk/cdk/src/main/org/openscience/c​dk/dict/data/reaction-processes.owl: Applied patch 10290 from the miguelrojasch/reaction branch: 'added the rest of reaction ID into the dictionary'
10:48 CIA-18 cdk: miguelrojasch * r10321 /trunk/cdk/src/main/org/openscience/c​dk/dict/data/reaction-processes.owl: Applied patch 10293 from the miguelrojasch/reaction branch: 'added empty schemas necessaries for the dictionary.'
10:49 CIA-18 cdk: miguelrojasch * r10322 /trunk/cdk/src/main/org/openscience/c​dk/dict/data/reaction-processes.owl: Applied patch 10294 from the miguelrojasch/reaction branch: 'complemented the mechanism onto Dictionary'
10:50 CIA-18 cdk: miguelrojasch * r10323 /trunk/cdk/src/ (6 files in 4 dirs): Applied patch 10295 from the miguelrojasch/reaction branch: 'added two new reactions for radical site ionization with it is charged'
10:55 rojasm egonw: I didn't receive. What email did you sent me und when?
10:56 rojasm :(
10:56 egonw by snail mail
10:59 CIA-18 cdk: miguelrojasch * r10324 /trunk/cdk/src/ (71 files in 9 dirs): Applied patch 10291 from the miguelrojasch/reaction branch: 'added new engine for ReactionProcess's which takes the parameters from the Dictionary.'
11:01 CIA-18 cdk: miguelrojasch * r10325 /trunk/cdk/src/test/org/openscience/cdk/to​ols/StructureResonanceGeneratorTest.java: Applied patch 10304 from the miguelrojasch/reaction branch: 'added Test if the aromaticity is perserved by the resonance'
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11:02 CIA-18 cdk: miguelrojasch * r10326 /trunk/cdk/src/ (2 files in 2 dirs): Applied patch 10305 from the miguelrojasch/reaction branch: 'update the isomorphism to QueryAtomContainerCreator.create​SymbolAndBondOrderQueryContainer to distinguish between aromatics compounds'
11:04 CIA-18 cdk: miguelrojasch * r10327 /trunk/cdk/src/test/org/ope​nscience/cdk/modulesuites/ (MformulaTests.java MreactionTests.java): Applied patch 10306 from the miguelrojasch/reaction branch: 'update the coverage test to junit4'
11:05 CIA-18 cdk: miguelrojasch * r10328 /trunk/cdk/src/test/org/openscience/cdk/for​mula/MolecularFormulaManipulatorTest.java: Applied patch 10307 from the miguelrojasch/reaction branch: 'added missed test'
11:06 CIA-18 cdk: miguelrojasch * r10329 /trunk/cdk/src/ (3 files in 3 dirs): Applied patch 10308 from the miguelrojasch/reaction branch: added ReactionEngineTest'
11:07 CIA-18 cdk: miguelrojasch * r10330 /trunk/cdk/src/test/org/openscience/cdk/reaction/t​ype/RadicalChargeSiteInitiationReactionTest.java: Applied patch 10309 from the miguelrojasch/reaction branch: 'removed testMethod which was not used anymore'
11:09 CIA-18 cdk: miguelrojasch * r10331 /trunk/cdk/src/test/org/openscience/cdk/​reaction/ReactionSpecificationTest.java: Applied patch 10310 from the miguelrojasch/reaction branch: 'New test for ReactionSpecificationTest'
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12:21 egonw bbl
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12:44 CIA-18 bioclipse: jonalv * r5009 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Renamed R extension point. R plugin now starts again
13:29 CIA-18 bioclipse: ospjuth * r5010 /bioclipse2/trunk/plugins/net.bioclipse.core/src/n​et/bioclipse/core/business/IBioclipseManager.java: Added base interface for managers
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14:17 CIA-18 bioclipse: ospjuth * r5011 /bioclipse2/trunk/plugins/net.bioclipse.services/ (9 files in 4 dirs): Adapted activator for logging and Spring OSGI and added simple serviceManager.
14:40 jpansanel man-di : If you meet dleidert, can you tell him that the release 0.5.1 of Mychem fix all the warning ?
14:40 jpansanel thanls
15:30 CIA-18 bioclipse: jonalv * r5012 /bioclipse2/trunk/plugins/ (9 files in 7 dirs): Changed all managers to make them extend IBioclipseManager and changed so that the namespace in the scriptinglanguage now depends on the method getNamespace on the managers instead of on the thier toString
15:34 CIA-18 bioclipse: egonw * r5013 / (bioclipse/trunk/plugins/ trunk/plugins/): Moved into new hierarchy.
15:35 CIA-18 bioclipse: egonw * r5014 / (bioclipse/trunk/features/ trunk/features/): Moved into new hierarchy.
15:36 CIA-18 bioclipse: egonw * r5015 / (bioclipse/trunk/playground/ trunk/playground/): Moved into new hierarchy.
15:37 CIA-18 bioclipse: egonw * r5016 / (bioclipse/trunk/tools/ trunk/tools/): Moved into new hierarchy.
15:38 CIA-18 bioclipse: egonw * r5017 / (bioclipse/trunk/makeHelpWebsite.pl trunk/makeHelpWebsite.pl): Moved into new hierarchy.
15:39 CIA-18 bioclipse: egonw * r5018 /xsw/ (. branches/ tags/ trunk/): Set up hierarchy for Edrin's XSW stuff
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15:55 egonw dleidert: do you know a good tool to validate RDF and/or OWL docs under Debian or Ubuntu?
15:55 egonw dleidert: can't find a working XML Schema or RelaxNG for any of the two, for use with xmllint
15:56 egonw literatlly have to leave in 2 minutes...
15:56 egonw so if not something comes to mind...
15:56 dleidert Is RDF registered with IANA? Then you could search for an RFC
15:56 egonw RFCs don't come with XML Schema's do they??
15:57 dleidert no, but they normally contain the information where to find them
15:57 dleidert rfc 3870
15:57 egonw ok, good enough pointer for now...
15:57 egonw will check that tonight
15:57 egonw thanx
15:57 egonw bye now
15:58 dleidert http://www.ietf.org/rfc/rfc3870.txt [1]
15:58 dleidert seems to point to what you are looking for
15:58 dleidert bye
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17:38 CIA-18 bioclipse: jonalv * r5019 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/n​et/bioclipse/ui/views/ScriptingConsoleView.java: A fix for bug: [ 1903065 ] Scripting consoles don't line break properly in Linux
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17:55 CIA-18 jmol: hansonr * r9052 /branches/v11_4/Jmol/src/org/jmol/viewer/ (Jmol.properties Viewer.java): version=11.4.RC9_dev # bug fix: write PDB format incorrectly writes atoms with 4-length names
17:56 CIA-18 jmol: hansonr * r9053 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs):
17:56 CIA-18 jmol: version=11.5.13_dev write command/PDB
17:56 CIA-18 jmol: # new feature: MODEL/ENDMDL records in write PDB (still no TER records)
17:56 CIA-18 jmol: # bug fix: write PDB format incorrectly writes atoms with 4-length names
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18:20 CIA-18 cdk: egonw * r10332 /trunk/cdk/src/META-INF/tes​t-qsarmolecular.cdkdepends: Added missing dependency
19:46 carsten joined #cdk
19:46 carsten jpansanel: hey, a new release
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23:34 dleidert egonw: ping
23:37 CIA-18 jmol: hansonr * r9054 /trunk/Jmol/src/org/ (5 files in 4 dirs): version=11.5.13_dev # application menu: Write state moved to main export menu; Export PDF to image writing
23:47 CIA-18 jmol: hansonr * r9055 /trunk/Jmol/src/org/openscien​ce/jmol/app/ImageTyper.java: version=11.5.13_dev # application menu: Write state moved to main export menu; Export PDF to image writing

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