Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-27

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All times shown according to UTC.

Time Nick Message
04:47 CIA-16 jmol: hansonr * r8681 /trunk/Jmol/src/org/jmol/ (10 files in 2 dirs):
04:47 CIA-16 jmol: version=11.3.49_dev
04:47 CIA-16 jmol: # bug fix: set perspectiveDepth off broken in 11.3.48
04:47 CIA-16 jmol: # bug fix: set scaleAngstromsPerInch not turning off perspectiveDepth
04:47 CIA-16 jmol: # bug fix: scaleAngstromsPerInch not in state
04:47 CIA-16 jmol: # bug fix: _firstFrame/_lastFrame variables mess up state
04:47 CIA-16 jmol: # bug fix: calculate surfaceDistance broken for 11.3.48
05:49 CIA-16 jmol: hansonr * r8682 /trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java:
06:22 CIA-16 jmol: hansonr * r8683 /trunk/Jmol/src/org/jmol/ (symmetry/SpaceGroup.java viewer/TransformManager11.java):
06:30 CIA-16 jmol: hansonr * r8684 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.49 VERSION
06:47 egonw joined #cdk
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08:30 steinbeck joined #cdk
08:30 steinbeck moin
08:35 egonw hi steinbeck
08:35 steinbeck Hi egonw
09:00 jonalv joined #cdk
09:02 egonw steinbeck: are you working on that clone() bug>
09:02 egonw ?
09:02 egonw it's assigned to you, but not sure if on purpose...
09:02 steinbeck I'm not working on any CDK bug at the moment. Too much admin stuff to do. :-)
09:03 egonw OK, good
09:03 egonw will fix that bug then
09:23 egonw http://chem-bla-ics.blogspot.com/2007/11/​be-in-my-advisory-board-1-being-good.html
09:23 jbrefort joined #cdk
09:54 CIA-16 cdk: egonw * r9509 /trunk/cdk/src/org/openscience/cdk/test/ (3 files in 3 dirs): Converted to JUnit4 tests.
10:04 carsten joined #cdk
10:07 CIA-16 cdk: egonw * r9510 /trunk/cdk/src/org/openscience​/cdk/test/ChemObjectTest.java: Added most basic JUnit test for #1838820.
10:08 alexandros_p joined #cdk
10:09 egonw hi alexandros_p
10:10 alexandros_p hello egonw
10:10 egonw steinbeck: that clone() bug is more nasty than I anticipated...
10:10 egonw steinbeck: the current ChemObject.clone() code *explicitly* and *only* clones IChemObject properties ...
10:11 steinbeck ack
10:11 steinbeck bad
10:11 steinbeck BRB
10:11 steinbeck left #cdk
10:12 egonw OK, me has to go now too...
10:12 egonw will be back later
10:18 steinbeck joined #cdk
10:33 thomas_ku joined #cdk
10:33 thomas_ku moin
10:38 CIA-16 bioclipse: ospjuth * r4338 /branches/bioclipse2/chemoinformatics/ne​t.bioclipse.jmol/src/net/bioclipse/jmol/ (2 files in 2 dirs): Updates for highlighting selections in Jmol from Outline
11:02 jpansanel moin
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13:22 CIA-16 cdk: egonw * r9511 /trunk/cdk/src/org/openscience/cdk​/io/DefaultChemObjectReader.java: Use ArrayList instead of Vector.
13:23 thomas_ku joined #cdk
13:24 egonw not bad
13:24 CIA-16 cdk: egonw * r9512 /trunk/cdk/src/org/openscience/cdk​/io/DefaultChemObjectWriter.java: Use ArrayList instead of Vector.
13:25 egonw very rough estimate indicates a 10% speed up :)
13:33 CIA-16 cdk: egonw * r9513 /trunk/cdk/src/org/openscience/cdk/io/ (DefaultChemObjectReader.java IChemObjectReader.java): Added the concept of 'reader mode' with values RELAXED and STRICT. For example, in STRICT mode, the MDLV2000Reader will fail when 'T' or 'D' element symbols are found.
13:42 masak joined #cdk
13:44 CIA-16 cdk: egonw * r9514 /trunk/cdk/src/org/openscie​nce/cdk/io/MDLReader.java: Make use of the new STRICT mode: complain if MDL v2000 or v3000 are attempted to be read with the MDLReader.
13:47 CIA-16 blueobelisk: pansanel * r195 /structures/trunk/src/heteroaromatics/ (13 files):
13:47 CIA-16 blueobelisk: Some missing french translations have been added
13:47 CIA-16 blueobelisk: Some files have been renamed according the usual name
13:49 CIA-16 cdk: egonw * r9515 /trunk/cdk/src/org/openscie​nce/cdk/io/MDLReader.java: Added a constructor with InputStream and Mode too.
13:50 steinbeck left #cdk
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14:25 CIA-16 bioclipse: jonalv * r4339 /branches/bioclipse2/bioinformatics/p​lugins/net.bioclipse.biojava.business​/src/net/bioclipse/biojava/business/ (BioJavaManager.java IBiojavaManager.java): Uppdated the IBioJavamanager interface
14:28 CIA-16 jmol: hansonr * r8685 /trunk/Jmol/src/org/jmol/m​odelset/ModelLoader.java: refactoring chains[] group3s[] ---> chainOf[] group3Of[]
15:02 CIA-16 blueobelisk: pansanel * r196 /structures/trunk/src/ketones/ (11 files):
15:02 CIA-16 blueobelisk: Some missing french translation have been added
15:02 CIA-16 blueobelisk: Some files have been renamed
15:07 CIA-16 bioclipse: carl_masak * r4340 /branches/bioclipse2/core/plugins/net.bio​clipse.core/src/net/bioclipse/core/views/ (3 files):
15:07 CIA-16 bioclipse: [net.bioclipse.core.views]
15:07 CIA-16 bioclipse: * General JavaDoc and internal documentation
15:07 CIA-16 bioclipse: * Restored 'verbose' functionality
15:12 CIA-16 blueobelisk: pansanel * r197 /structures/trunk/src/macrocycles/ (index.xml porphin.cml porphyrin.cml):
15:12 CIA-16 blueobelisk: Renaming correcly the molecule
15:12 CIA-16 blueobelisk: Adding the french translation
15:24 CIA-16 bioclipse: carl_masak * r4341 /branches/bioclipse2/core/plugins/ne​t.bioclipse.core/src/net/bioclipse/c​ore/views/ScriptingConsoleView.java:
15:24 CIA-16 bioclipse: [ScriptingConsoleView.java]
15:24 CIA-16 bioclipse: * more documentation
15:24 CIA-16 bioclipse: * added a few TODOs
15:24 CIA-16 blueobelisk: pansanel * r198 /structures/trunk/src/nitriles/ (7 files):
15:24 CIA-16 blueobelisk: Missing french translations have been added in index.xml
15:24 CIA-16 blueobelisk: cml files have been renamed according the usual name
15:25 CIA-16 blueobelisk: pansanel * r199 /structures/trunk/src/nitroalkanes/index.xml: Fix translations
16:02 CIA-16 cdk: egonw * r9516 /trunk/cdk/src/org/openscience/​cdk/test/io/MDLReaderTest.java: Fixed syntax: no V2000 format.
16:03 egonw only 484 commits to go for the big CDK party !
16:23 CIA-16 bioclipse: carl_masak * r4342 /branches/bioclipse2/core/plugins/ne​t.bioclipse.core/src/net/bioclipse/c​ore/views/ScriptingConsoleView.java:
16:23 CIA-16 bioclipse: [ScriptingConsoleView.java]
16:23 CIA-16 bioclipse: * reordered TODOs in priority order
16:44 CIA-16 cdk: egonw * r9517 /trunk/cdk/src/org/openscience/cdk/test/ (30 files in 21 dirs): Only IChemObjectReader.Mode.STRICT mode in JUnit tests: we don't want errors because the file was not correct
16:48 jpansanel strange
16:48 jpansanel the last revision of chemical-structure (r200)
16:48 jpansanel does  not appear on the IRC
16:55 LaserJock maybe the CDK blitz swamped CIA? :-)
17:04 CIA-16 jmol: nicove * r8686 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
17:12 CIA-16 bioclipse: carl_masak * r4343 /branches/bioclipse2/core/plugins/net.​bioclipse.core/src/net/bioclipse/core/ (3 files in 2 dirs):
17:12 CIA-16 bioclipse: [net.bioclipse.core.scripting]
17:12 CIA-16 bioclipse: [net.bioclipse.core.views]
17:12 CIA-16 bioclipse: * decoupled ScriptingEnvironments from their consoles
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18:08 carsten joined #cdk
18:21 egonw joined #cdk
18:55 CIA-16 cdk: rajarshi * r9518 /trunk/cdk/src/org/openscience/cdk/test/qsar/d​escriptors/molecular/ALOGPDescriptorTest.java: Added code to make sure that atoms are typed
18:57 egonw LaserJock: ready for tomorrow?
18:57 egonw I'm looking forward to your tutorial
19:01 CIA-16 cdk: rajarshi * r9519 /trunk/cdk/src/org/openscience/cdk/qs​ar/descriptors/molecular/ALOGP.java: Cleaned up most of the code - made the public calculate method not use globals, updated copyright, removed printing to stdout, correct handling of exceptions, added logging
19:01 LaserJock egonw: well, I'm not sure how exciting it'll be. Mostly Q&A type stuff
19:02 LaserJock egonw: I actually thought it was today and got up early for it :(
19:02 egonw not about making debs?
19:02 egonw and ppa?
19:11 LaserJock well yeah
19:11 LaserJock but there's only so much you can do in 1hr
19:11 LaserJock so it should be good
19:11 LaserJock but not an in-depth tutorial
19:11 LaserJock my general intro to packaging classes usually run 2hrs
19:14 egonw ah...
19:15 egonw well... I got some packaging experience...
19:15 egonw but no little about PPA
19:16 CIA-16 cdk: rajarshi * r9520 /trunk/cdk/src/org/openscience/cdk/test/sm​iles/smarts/parser/SMARTSSearchTest.java: Added tests that check for logical operations between bonds - currently fails
19:17 LaserJock egonw: then it'll probably be good for you
19:17 egonw good :)
19:18 egonw PPA sounds like an excellent next step for Debian/Ubuntu...
19:18 egonw allows me to create and distribute debs
19:18 egonw without having to find a sponsor
19:19 CIA-16 cdk: rajarshi * r9521 /trunk/cdk/src/org/openscience/cdk/test/sm​iles/smarts/parser/SMARTSSearchTest.java: Fixed an expected value
19:24 egonw cool: deb http://ppa.launchpad.net/egonw/ubuntu hardy main
19:24 egonw very cool!
19:25 egonw got my own (empty :) deb repository !
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19:47 CIA-16 cdk: rajarshi * r9522 /trunk/cdk/src/org/openscience/cdk/test/sm​iles/smarts/parser/SMARTSSearchTest.java: Added another test
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