Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-05

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All times shown according to UTC.

Time Nick Message
05:42 masak joined #cdk
05:51 jpansane1 joined #cdk
06:02 CIA-16 bioclipse: carl_masak * r4123 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java:
06:02 CIA-16 bioclipse: [FunctionsTest.java]
06:02 CIA-16 bioclipse: * corrected misspelled function name
06:03 CIA-16 bioclipse: carl_masak * r4124 /trunk/playground/plugins/net.bioclipse.expressi​on/src/net/bioclipse/expression/Calculator.java:
06:03 CIA-16 bioclipse: [Calculator.java]
06:03 CIA-16 bioclipse: * implemented point notation for functions
06:43 CIA-16 bioclipse: carl_masak * r4125 /trunk/playground/plugins/ (4 files in 2 dirs):
06:43 CIA-16 bioclipse: * implemented proof-of-concept where all variables are passed by value
06:43 CIA-16 bioclipse:  to the functions
06:43 CIA-16 bioclipse: * all tests now pass
06:46 CIA-16 bioclipse: carl_masak * r4126 /trunk/playground/plugins/ (4 files in 2 dirs):
06:46 CIA-16 bioclipse: * reverted last commit
06:46 CIA-16 bioclipse: * we're now undecided again
07:11 CIA-16 jmol: nicove * r8569 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
07:42 jonalv joined #cdk
07:51 thomas_ku joined #cdk
07:51 thomas_ku moin
08:26 egonw joined #cdk
08:31 jbrefort joined #cdk
08:35 CIA-16 bioclipse: carl_masak * r4127 /trunk/playground/plugins/ (4 files in 2 dirs):
08:35 CIA-16 bioclipse: [net.bioclipse.expression]
08:35 CIA-16 bioclipse: [net.bioclipse.expression.tests]
08:35 CIA-16 bioclipse: * merged in r4125 again
08:35 CIA-16 bioclipse: * deleted package net.bioclipse.expression.ast, no longer need
08:35 CIA-16 bioclipse:  symbolic expressions
08:38 CIA-16 bioclipse: carl_masak * r4128 /trunk/playground/plugins/net.biocli​pse.expression/META-INF/MANIFEST.MF:
08:38 CIA-16 bioclipse: [MANIFEST.MF]
08:38 CIA-16 bioclipse: * chased changes from last commit
09:06 CIA-16 bioclipse: jonalv * r4129 /trunk/playground/plugins/ (2 files in 2 dirs): Wrote test for exception being thrown when supressed variable is used in expressions
09:23 CIA-16 bioclipse: jonalv * r4130 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java: Wrote functions tests for suppressed variables
09:37 CIA-16 bioclipse: carl_masak * r4131 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java:
09:37 CIA-16 bioclipse: [FunctionsTest.java]
09:37 CIA-16 bioclipse: * removed pesky annotations
09:41 CIA-16 bioclipse: carl_masak * r4132 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java:
09:41 CIA-16 bioclipse: [FunctionsTest.java]
09:41 CIA-16 bioclipse: * fixed typo
09:49 CIA-16 bioclipse: carl_masak * r4133 /trunk/playground/plugins/ (3 files in 2 dirs):
09:49 CIA-16 bioclipse: [FunctionsTest.java]
09:49 CIA-16 bioclipse: [VariablesTest.java]
09:49 CIA-16 bioclipse: * further typo fixing
09:49 CIA-16 bioclipse: [Calculator.java]
09:49 CIA-16 bioclipse: * introduced suppressed variables
10:04 CIA-16 bioclipse: carl_masak * r4134 /trunk/playground/plugins/ (2 files in 2 dirs):
10:04 CIA-16 bioclipse: [VariablesTest.java]
10:04 CIA-16 bioclipse: * further typo fixing
10:04 CIA-16 bioclipse: [Calculator.java]
10:04 CIA-16 bioclipse: * first half of suppressed variables impl
10:14 CIA-16 bioclipse: carl_masak * r4135 /trunk/playground/plugins/net.bioclipse.​expression/src/net/bioclipse/expression/ (Calculator.java SuppressedVariableException.java):
10:14 CIA-16 bioclipse: [Calculator.java]
10:14 CIA-16 bioclipse: * implemented second half of suppressed vars
10:14 CIA-16 bioclipse: [SuppressedVariablesException.java]
10:14 CIA-16 bioclipse: * new exception to distinguish from other Calculator exceptions
12:18 dleidert joined #cdk
12:21 CIA-16 bioclipse: ospjuth * r4136 /trunk/plugins/net.bioclipse.rhino/ (5 files in 3 dirs): Added an extension point and interface for adding scripting commands to Rhino.
12:21 CIA-16 bioclipse: ospjuth * r4137 /trunk/plugins/net.bioclipse.rhino/​src/net/bioclipse/plugins/bc_rhino/ (2 files in 2 dirs): Adapted plugin to use new extension point
12:23 CIA-16 bioclipse: ospjuth * r4138 /trunk/playground/plugins/​net.bioclipse.biomoby.ui/ (3 files in 2 dirs): Added an extension to provide BioMoby scripting commands for Rhino
12:37 CIA-16 bioclipse: ospjuth * r4139 /trunk/plugins/net.bioclipse.biojava.ui/ (5 files in 4 dirs): Use new scripting extension point in net.bioclipse.rhino to add scripting commands for BioJava
13:19 CIA-16 bioclipse: ospjuth * r4140 /trunk/plugins/net.bioclipse.rhino/ (2 files in 2 dirs): Added 'console' as namespace when scripting, and command available is now: 'console.write("hello world");'
13:32 jpansane1 hi
13:35 egonw hi jpansane1
13:37 CIA-16 cdk: egonw * r9367 /branches/egonw/remove-non-cdkatomtype-code/: Branch for development of a patch to remove arom detection based on no-cdk-atom-type code.
13:37 CIA-16 bioclipse: jonalv * r4141 /trunk/playground/plugins/ (3 files in 3 dirs): The test database now uses the database aliases so the connection url for it is on localhost/testServer. This technique will be necessary in order to work with multiple databases later on.
13:49 CIA-16 bioclipse: ospjuth * r4142 /trunk/plugins/net.bioclipse.biojava.ui/ (2 files in 2 dirs): Fix BioJava scripting commands
13:49 CIA-16 cdk: egonw * r9368 /branches/egonw/remove-non-​cdkatomtype-code/.project: Customized name, to please my Eclipse install
14:19 CIA-16 cdk: egonw * r9369 /trunk/cdk/src/org/openscience/cdk/​test/smiles/SmilesParserTest.java:
14:19 CIA-16 cdk: Updated tests for the fact that bond orders are *no longer* worked out by the
14:19 CIA-16 cdk: SMILES parser, but left for a post processing step. Rationale: the SMILES
14:19 CIA-16 cdk: explicitly did not contain them, so they should not be added to the output.
14:19 CIA-16 cdk: Effect: must faster SMILES parser.
14:28 CIA-16 cdk: egonw * r9370 /branches/egonw/remove-non-cdkatom​type-code/src/org/openscience/cdk/​test/smiles/SmilesParserTest.java: Synched with trunk/ r9369
14:42 CIA-16 bioclipse: jonalv * r4144 /trunk/playground/plugins/​net.bioclipse.structuredb/ (5 files in 3 dirs): renamed StructuredbDataBaseType -> Structuredb and added map for applicationcontexts. Right now the pedulum is swinging in the one-separate-applicationcontext-for-each-database direction...
14:53 CIA-16 cdk: egonw * r9371 /branches/egonw/remove-non-cdkatom​type-code/src/org/openscience/cdk/ (38 files in 21 dirs): Removed the old HueckelAromaticityDetector
15:07 CIA-16 cdk: egonw * r9372 /trunk/cdk/src/org/openscience/cdk/t​est/modulesuites/MosjvmtsTests.java: Removed obsolete test suite.
15:08 CIA-16 bioclipse: jonalv * r4145 /trunk/playground/plugins/n​et.bioclipse.structuredb/: svn:ignore...
15:10 CIA-16 bioclipse: jonalv * r4146 /trunk/playground/plugins/net.​bioclipse.structuredb.tests/: svn:ignore...
15:11 CIA-16 bioclipse: jonalv * r4147 /trunk/playground/plugins/net.bioclip​se.usermanager/META-INF/MANIFEST.MF: manifest configs...
15:12 CIA-16 cdk: egonw * r9373 /branches/egonw/remove-non-cdkatomt​ype-code/src/org/openscience/cdk/te​st/modulesuites/MosjvmtsTests.java: Synched with trunk/ r9372
15:25 CIA-16 cdk: egonw * r9374 /trunk/cdk/build.xml: Removed reference to the removed osjvmts module
15:35 CIA-16 cdk: egonw * r9375 /branches/egonw/remove-non-​cdkatomtype-code/build.xml: Synched with trunk/ r9374
16:04 CIA-16 bioclipse: jonalv * r4148 /trunk/playground/plugins/ (2 files in 2 dirs): added method for getting a list of account ids for an accounttype name
16:06 CIA-16 cdk: egonw * r9376 /branches/egonw/remove-non-cdkatomtype-code/src/or​g/openscience/cdk/fingerprint/Fingerprinter.java: Have to do atom type perception, otherwise aromaticity detection will not work :)
16:06 CIA-16 bioclipse: jonalv * r4149 /trunk/playground/plugins/net.bioclipse.structured​b/src/net/bioclipse/structuredb/Structuredb.java: Made Structuredb a UsermanagerEventListener since it should respond to login / logout events. Not entirely sure what it will do though...
16:32 CIA-16 bioclipse: ospjuth * r4150 /trunk/plugins/net.bioclipse.biojava.ui/ (2 files in 2 dirs): Tried to get visualization working from scripts. Seems Eclipse has changed selections in 3.3... we should not rely on this method in Bioclipse2! Problem unresolved.
16:36 CIA-16 bioclipse: ospjuth * r4151 /trunk/plugins/net.bioclipse.rhino/ (4 files in 3 dirs):
16:36 CIA-16 bioclipse: Added BioResource scripting tools and Editor scripting tools. Example features:
16:36 CIA-16 bioclipse: myres=bioresource.create(content);
16:36 CIA-16 bioclipse: myres=bioresource.create("myseq.seq", content);
16:36 CIA-16 bioclipse: editor.open(myres);
16:36 CIA-16 bioclipse: Note: Selections are not triggered and hence no views are able to display created resources. They are however opened in correct editor. Unresolved problem (appeared in Eclipse 3.3). Should be resolved in Bioclipse2.
16:37 CIA-16 bioclipse: ospjuth * r4152 /trunk/playground/plugins/net.biocli​pse.biomoby.ui/META-INF/MANIFEST.MF: Exported packages to get scripting to work.
16:39 CIA-16 bioclipse: ospjuth * r4153 /trunk/plugins/net.bioclipse/src/net/​bioclipse/views/BioResourceView.java: Tried to adapt for IStructuredSelection but unable to resolve selection problem from a script.
16:47 CIA-16 cdk: egonw * r9377 /branches/egonw/remove-non-cdkatom​type-code/src/org/openscience/cdk/​atomtype/CDKAtomTypeMatcher.java: Fixed recognition of C.sp2 when ISAROMATIC flag was set (e.g. using mdl:bondorder=4)
16:48 CIA-16 cdk: egonw * r9378 /trunk/cdk/src/org/openscience/cdk​/atomtype/CDKAtomTypeMatcher.java: Fixed recognition of C.sp2 when ISAROMATIC flag was set (e.g. using mdl:bondorder=4)
16:59 CIA-16 bioclipse: ospjuth * r4154 /trunk/plugins/net.bioclipse/src/net/​bioclipse/views/BioResourceView.java: Created a RefreshRunnable to update TreeViewer from GUI thread. Still doesn't work...
16:59 CIA-16 bioclipse: ospjuth * r4155 /trunk/plugins/net.bioclipse.rhino/src/net/b​ioclipse/plugins/bc_rhino/EditorTools.java: Tried to refresh using new runnable. No, doesn't do the trick.
17:39 CIA-16 bioclipse: ospjuth * r4156 /trunk/plugins/net.bioclipse.biojava.ui/src/n​et/bioclipse/plugins/views/SequenceView.java: Removed debug outs
17:41 CIA-16 bioclipse: ospjuth * r4157 /trunk/plugins/net.bioclipse.webservices/ (4 files in 3 dirs): Added scripting namespace for webservices plugin. Only method available now: 'mypdb=ws.downloadPDB("1ale");'
18:40 dleidert joined #cdk
19:36 CIA-16 jmol: nicove * r8570 /trunk/Jmol-FAH/projects/ (p3729.xyz.gz p4102.xyz.gz): Folding@Home
19:39 egonw joined #cdk
19:39 egonw he thomas_ku
20:06 thomas_ku he egonw
20:06 thomas_ku I will go offline now!
20:06 thomas_ku But be online tomorrow again
20:06 egonw ack ,bye
20:06 thomas_ku so cu than!
20:07 thomas_ku have a nice night!
20:07 egonw you too

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