Camelia, the Perl 6 bug

IRC log for #cdk, 2008-03-06

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All times shown according to UTC.

Time Nick Message
00:31 CIA-18 jmol: hansonr * r9056 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties):
00:31 CIA-18 jmol: 11.5.13 VERSION
00:31 CIA-18 jmol: # bug fix: write PDB format incorrectly writes atoms with 4-length names
00:59 dleidert left #cdk
03:54 CIA-18 joined #cdk
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07:08 rojasm joined #cdk
07:29 Annzi joined #cdk
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08:28 egonw moin
08:38 * egonw is relocating to his other desk
09:03 jonalv joined #cdk
09:17 egonw joined #cdk
09:30 steinbeck joined #cdk
09:35 egonw coffee time
09:35 egonw hi steinbeck
09:35 egonw bbl
09:36 steinbeck moin egonw
09:59 jbrefort joined #cdk
10:26 masak joined #cdk
10:31 CIA-18 bioclipse: carl_masak * r5020 /bioclipse2/trunk/plugins/net.bioclips​e.biojava.business/src/net/bioclipse/b​iojava/business/BiojavaManager.java:
10:31 CIA-18 bioclipse: [BioJavaManager.java]
10:31 CIA-18 bioclipse: * removed @Override
10:31 CIA-18 bioclipse: * removed unused imports
10:35 steinbeck joined #cdk
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12:34 egonw rojasm: ping
12:45 steinbeck_ joined #cdk
13:05 * egonw is having fun with R
13:06 * egonw is fitting broad peaks with all sorts of functions
13:07 jpansanel hi
13:11 egonw hi jpansanel
13:33 rojasm egonw yes!
13:33 egonw was wondering what the next steps are...
13:33 egonw reaction/ branch can now be closed, right?
13:34 egonw so, what will be next to clean up?
13:34 egonw partial charges?
13:34 rojasm yes! I supose PC
13:34 rojasm partial charges
13:34 rojasm you mean we should remove and create a new one
13:34 egonw right
13:34 egonw yeah, remove reaction/
13:34 egonw and create (copy) a new branch charges/ or so
13:35 rojasm ok
13:35 egonw btw
13:35 egonw I had a charges/ branch in my subfolder...
13:35 egonw will have to check the state of that
13:37 egonw rojasm: mom.... will check this branch right now
13:38 egonw rojasm: ping...
13:39 egonw rojasm: it got some 10-15 relevant patches
13:39 egonw which I'd like to apply to the new charges branch
13:40 egonw it introduces a new interface called IPartialChargeCalculator
13:40 egonw and adds stubs for unit test classes
13:41 rojasm sorry. Maya with question
13:41 egonw np
13:41 dleidert joined #cdk
13:42 rojasm why new interface
13:42 rojasm charge is not a element or something like that
13:42 rojasm ist a descriptor
13:42 egonw it's an interface for the calculator, not the result
13:43 rojasm than I would make interface only for charge
13:43 rojasm with contains possible pi and sigma and total
13:43 egonw how's that different from IPartialChargeCalculator?
13:44 rojasm sorry I sow erroneus IPar... as PI
13:46 rojasm so we will use your charge branches?
13:46 egonw no
13:47 egonw because it is not src/main src/test compatible
13:47 rojasm oh yes
13:49 rojasm do I create? or you?
13:49 egonw please go ahead
13:49 rojasm perfect
13:49 egonw when you created it, I'll merge in my changes
13:58 rojasm svn delete -m "Deleting reaction branches" https://cdk.svn.sf.net/svnroot/cd​k/branches/miguelrojasch/reaction
13:59 rojasm to remove
13:59 egonw svn remove?
14:00 rojasm I think it is the same
14:00 rojasm del, remove, delete
14:01 rojasm is it correct?
14:01 CIA-18 bioclipse: carl_masak * r5021 /bioclipse2/trunk/plugins/net.bioclipse.core/src​/net/bioclipse/recording/JsScriptGenerator.java:
14:01 CIA-18 bioclipse: [JsScriptGenerator.java]
14:01 CIA-18 bioclipse: * variable names are displayed, not IDs
14:01 dleidert normally yes
14:03 rojasm to create a new branches do I have to use cp or import?
14:03 dleidert if you don't want to loose the history: cp
14:04 egonw svn copy
14:04 rojasm ok! thanks
14:05 CIA-18 cdk: miguelrojasch * r10333 /branches/miguelrojasch/reaction/: Deleting reaction brances
14:08 CIA-18 cdk: miguelrojasch * r10334 /branches/miguelrojasch/charges/: create a new branches for charge project
14:20 CIA-18 bioclipse: carl_masak * r5022 /bioclipse2/trunk/plugins/net.bioclipse.co​re.tests/net.bioclipse.recording/net/biocl​ipse/recording/ScriptGenerationTests.java:
14:20 CIA-18 bioclipse: [ScriptGenerationTests.java]
14:20 CIA-18 bioclipse: * renamed variable
14:20 CIA-18 bioclipse: * removed untestable part
14:21 egonw rojasm: done?
14:22 rojasm ok, thanks!
14:22 rojasm ups. ! yes done
14:23 rojasm aber not the interface
14:23 egonw no, will do that...
14:23 rojasm ok! perfect
14:25 * egonw is making a checkout of miguelrojasch/charges/
14:28 CIA-18 bioclipse: jonalv * r5023 /bioclipse2/trunk/plugins/net.bioclipse.core/sr​c/net/bioclipse/recording/RecordingAdvice.java: The recording now uses the getNamespace method when figuring out which manager has been called instead of as before the toString method.
14:35 CIA-18 cdk: egonw * r10335 /branches/miguelrojasch/charges/.project: Customized project name for Eclipse...
14:42 CIA-18 bioclipse: jonalv * r5024 /bioclipse2/trunk/plugins/net.bioclipse.core/sr​c/net/bioclipse/core/domain/BioObjectList.java: removed @Recorded from toArray methods on BioObjectList
14:49 rojasm egonw: do you want to create some new package for the creator staff?
14:50 egonw creator staff?
14:50 rojasm sorry! you said you want to create the IP..Creator interface
14:51 egonw ah...
14:51 egonw well... just await the patches
14:51 rojasm will it be together with the other interfaces as IAtom?
14:53 egonw can't remember :)
14:54 rojasm doesn't matter
15:02 egonw rojasm: this is more difficult than I had hoped...
15:02 rojasm mmm
15:02 egonw ok, me moves into manual hacking mode
15:03 rojasm I believe you
15:07 CIA-18 cdk: egonw * r10336 /branches/miguelrojasch/charges/src/ (4 files in 3 dirs): Applied patch 9863: 'Moved AtomTypeCharges to experimental; it's not unit tested, but not used either, so no harm'
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15:22 egonw rojasm: it's going slowly
15:22 egonw but I'm making progress
15:22 rojasm perfect thanks
15:23 CIA-18 cdk: egonw * r10337 /branches/miguelrojasch/charges/src/ (15 files in 4 dirs):
15:23 CIA-18 cdk: Applied patch 9864: 'Added an interface IPartialChargeCalculator and cleaned up
15:23 CIA-18 cdk: code by putting the GasteigerMarsiliPartialCharges parameters in the
15:23 CIA-18 cdk: constructor; also cleaned up some QSAR descriptor code wrt to setting the number
15:23 CIA-18 cdk: of max iterations to be used in the GM partial charge calculator'
15:30 CIA-18 cdk: egonw * r10338 /branches/miguelrojasch/charges/src/t​est/org/openscience/cdk/charges/Gaste​igerMarsiliPartialChargesTest.java: Applied patch 9866: 'Some work on the unit tests'
15:36 egonw grpmhh...
15:36 egonw SF svn is bloody slow again :(
15:40 steinbeck joined #cdk
15:40 CIA-18 cdk: egonw * r10339 /branches/miguelrojasch/charges​/src/test/org/openscience/cdk/ (2 files in 2 dirs): Applied patch 9899: 'Added stub for missing test class'
15:42 CIA-18 cdk: egonw * r10340 /branches/miguelrojasch/charges​/src/test/org/openscience/cdk/ (2 files in 2 dirs): Fixed some compile issues
15:44 CIA-18 bioclipse: jonalv * r5025 /bioclipse2/trunk/plugins/n​et.bioclipse.usermanager/: copied usermanager into bioclipse 2 repo
15:45 CIA-18 bioclipse: jonalv * r5026 /bioclipse2/trunk/plugins/net.​bioclipse.usermanager.tests/: copied usermanager.tests into bioclipse 2
16:03 egonw oi, that was a long hack again
16:03 CIA-18 cdk: egonw * r10341 /branches/miguelrojasch/charges/src/ (4 files in 3 dirs): Applied patch 9901: 'All class in the charges module now implement IPartialChargeCalculator; some other code clean up'
16:05 CIA-18 cdk: egonw * r10342 /branches/miguelrojasch/charges/​src/META-INF/charges.cdkdepends: Applied patch 9902: 'Cleaned up deps'
16:05 egonw and a quick one
16:06 CIA-18 bioclipse: carl_masak * r5027 /bioclipse2/trunk/plugins/net.bioclip​se.core/src/net/bioclipse/recording/ (3 files):
16:06 CIA-18 bioclipse: [BioObjectRecord.java]
16:06 CIA-18 bioclipse: * removed unused imports
16:06 CIA-18 bioclipse: [JsScriptGenerator.java]
16:06 CIA-18 bioclipse: [MethodRecord.java]
16:06 CIA-18 bioclipse: * started implementing list support
16:09 CIA-18 cdk: egonw * r10343 /branches/miguelrojasch/charges/src/ (2 files in 2 dirs): Applied patch 9903: 'No coverage errors anymore, added some unit tests and some stubs'
16:09 egonw ok, two left
16:11 CIA-18 cdk: egonw * r10344 /branches/miguelrojasch/charges/src/mai​n/org/openscience/cdk/qsar/descriptors/​atomic/PartialPiChargeDescriptor.java: Applied patch 9916: 'Fixed wrapping of charges'
16:12 CIA-18 bioclipse: jonalv * r5028 /bioclipse2/trunk/plugins/​net.bioclipse.usermanager/ (4 files in 3 dirs): Commented out logging code that doesn't work. jonalv needs to figure out how logging is done i bioclipse...
16:13 egonw ok, done
16:14 CIA-18 cdk: egonw * r10345 /branches/egonw/charge/: Removed branch; patches have been applied to miguelrojasch/charges/ which is based on today's trunk.
17:13 CIA-18 jmol: hansonr * r9057 /trunk/Jmol/src/org/jmol/ (util/Parser.java viewer/Jmol.properties viewer/Viewer.java): version=11.5.13 # bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN
17:15 CIA-18 jmol: hansonr * r9058 /branches/v11_4/Jmol/src/org/jmol/ (util/Parser.java viewer/Jmol.properties): version=11.4.RC9 # bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN
17:27 Annzi left #cdk
17:29 CIA-18 jmol: hansonr * r9059 /branches/v11_4/Jmol/src/o​rg/jmol/util/Parser.java: version=11.4.RC9 # bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN
17:29 CIA-18 jmol: hansonr * r9060 /trunk/Jmol/src/org/jmol/util/Parser.java: version=11.5.13 # bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN
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18:28 CIA-18 jmol: nicove * r9061 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
18:29 CIA-18 jmol: nicove * r9062 /trunk/Jmol/src/org/jmol/translation/Jmol/ (11 files): Update of .po files
18:40 CIA-18 jmol: nicove * r9063 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
18:54 CIA-18 jmol: aherraez * r9064 /trunk/Jmol/src/org/jmol/tr​anslation/JmolApplet/es.po: Spanish
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