Camelia, the Perl 6 bug

IRC log for #cdk, 2007-12-20

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All times shown according to UTC.

Time Nick Message
00:19 CIA-17 jmol: hansonr * r8828 /trunk/Jmol/src/org/jmol/ (11 files in 3 dirs): version=11.3.62_dev # bug fix: calculate hbonds broken
00:51 CIA-17 jmol: hansonr * r8829 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): version=11.3.62_dev # bug fix: calculate hbonds broken in 11.3.58 (missing model field in BioPolymer)
01:45 CIA-17 jmol: gutow * r8830 /trunk/Jmol/src/org/ (2 files in 2 dirs): Update of help instructions for testing web export pages locally
05:37 CIA-17 jmol: hansonr * r8831 /trunk/Jmol/src/org/jmol/ (14 files in 5 dirs):
05:37 CIA-17 jmol: version=11.3.62_dev
05:37 CIA-17 jmol: # bug fix: calculate hbonds for trajectories
05:37 CIA-17 jmol: # code: distinction between file-derived or connected hbonds and calculated hydrogen bonds
05:42 CIA-17 jmol: hansonr * r8832 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.62 VERSION
06:14 CIA-17 cdk: egonw * r9639 /trunk/cdk/build.xml: Forgot to upload the changed build.xml to reflect the new qsarmolecular module
06:26 CIA-17 cdk: egonw * r9640 /trunk/cdk/src/META-INF/test-pcore.cdkdepends: Added missing dependency
06:30 CIA-17 jmol: nicove * r8833 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
07:39 CIA-17 cdk: egonw * r9641 /trunk/cdk/src/META-INF/tes​t-qsarmolecular.cdkdepends: Added a missing dependency
07:54 CIA-17 cdk: egonw * r9642 /trunk/cdk/src/org/openscience/cdk​/test/qsar/descriptors/molecular/ (2 files): For now, not in extending MolecularDescriptorTest
07:56 CIA-17 cdk: egonw * r9643 /trunk/cdk/src/ (81 files in 3 dirs): Moved the rest of the molecular descriptors to the qsarmolecular module
07:59 steinbeck joined #cdk
08:00 CIA-17 cdk: egonw * r9644 /trunk/cdk/src/org/openscience/cdk/test/qsar/des​criptors/molecular/MolecularDescriptorTest.java: Put test for super.descriptor in separate method, to make the problem more pronounced
08:18 jpansanel moin
08:23 olas joined #cdk
08:23 CIA-17 bioclipse: ospjuth * r4568 /trunk/playground/plugins/net.bioclipse.​biomoby.ui/src/net/bioclipse/biomoby/ui/ (6 files in 3 dirs): Updates to caching and javadoc
08:37 jpansanel olas : what's the date for the release 1.2 of bioclipse ?
08:37 jpansanel olas : also congratulation for the prize at the Trophee du Libre
08:37 jpansanel !
08:40 olas thanks jpansanel
08:40 olas I think 1.2.0 will be released today or tomorrow
08:40 olas depending on the final tests
08:49 jpansanel olas: how do you include the chemical-structure project into bioclipse ?
08:51 olas we include it as a menu option
08:51 olas you can select from the menu "Install chemical-structures"
08:52 olas it is a separate checkbox when you install from the update-site
08:52 olas I think egonw has updated it for 1.2.0
08:52 jpansanel ok
08:52 olas it's really great
08:52 olas a lot of structures to browse around
08:53 jpansanel can I do something for making this update easier ?
08:53 olas Very informative in my classes :-)
08:53 jpansanel :)
08:53 olas hmm, I don't think so at the moment
08:53 olas it's pretty straight-forward
08:54 olas but you should probably ask egonw for details
08:54 jpansanel ok
08:54 * olas will be afk for some 30 mins
09:22 jbrefort joined #cdk
09:25 jpansanel bonjour jean
09:27 egonw moin
09:28 jbrefort salut jérôme
09:31 egonw jpansanel: we could set up a svn:externals...
09:32 egonw but let's do that after 1.2.0
09:32 egonw don't have time for any fixin
09:32 egonw ' today
09:32 egonw the version in there is pretty recent, IIRC
09:45 jpansanel moin egonw
09:45 egonw hi jpansanel
09:49 jpansanel I was to a ruby conference last night
09:49 jpansanel excellent :)
09:49 olas we have a ruby console in Biuclipse2 :-)
09:50 olas I think that means support for scripting Bioclipse with ruby in some way...
09:50 egonw yes, saw the commit...
09:50 olas but I'll have to ask masak about that
09:50 egonw *very* cool
09:50 egonw sounds like tmie for the net.bioclipse.rubidium plugin
09:51 olas What masak is doing is that he includes various scripting engines and then you can pick your favourite
09:51 egonw olas: please contact Rich
09:51 olas yea, or better if masak does that
09:51 olas will tell him to do that
09:51 olas I know he reads Rich's blog
10:02 * egonw needs to do some admin stuff... will be back later...
10:10 steinbeck left #cdk
10:15 CIA-17 joined #cdk
10:19 egonw_ joined #cdk
10:19 CIA-17 cdk: egonw * r9645 /trunk/cdk/src/org/openscience/cdk/test/qsar/des​criptors/molecular/MolecularDescriptorTest.java: More testing: are the parameters properly given and consistent
11:16 masak joined #cdk
12:54 CIA-17 cdk: egonw * r9646 /trunk/cdk/src/ (3 files in 2 dirs): Fixed a few more deps
12:55 thomas_ku joined #cdk
12:55 egonw thomas_ku: will my InChI patch be part of the new 1.7.0-targeted CDK-Taverna?
12:56 CIA-17 cdk: egonw * r9647 /trunk/cdk/src/META-INF/tes​t-valencycheck.cdkdepends: Another missing dep
12:56 thomas_ku moin
12:58 egonw btw, T1.7 looks nice
12:58 egonw you can see the multithreading in action :)
12:58 * egonw thinks this should be fun times for thomas...
12:58 egonw I have not tried to run a WF against a PubChem SD file...
12:59 egonw but that might just be possible now...
13:00 egonw though I am not sure how to write a T2 activity yet
13:01 thomas_ku egonw: sorry got a call
13:01 egonw np
13:01 thomas_ku I didn't test T1.7 up to now
13:01 thomas_ku so I can't tell you more
13:01 egonw it's CDK 1.0 based, right?
13:01 thomas_ku Will try it tomorrow
13:01 egonw if so, remove the IPMolecularTest.java
13:02 egonw and corresponding worker
13:02 thomas_ku it is based on the latest branch of the cdk1.0.x
13:02 egonw not stable
13:02 egonw see my blog
13:02 egonw and similar for bond and atom
13:03 thomas_ku saw it
13:03 thomas_ku but will not get it today
13:03 thomas_ku and yes your inchi stuff will go get in with the next release
13:04 egonw mmm... should do the InChI generator too...
13:05 thomas_ku that would be great
13:17 egonw if (ret == INCHI_RET.OKAY) {
13:17 egonw inchiList.add(gen.getInchi());
13:17 egonw } else {
13:17 egonw comment.add(gen.getMessage());
13:17 egonw }
13:17 egonw thomas_ku: is that like you intend with the commetn output?
13:18 thomas_ku thats ok
13:22 egonw WTF??
13:23 thomas_ku ?
13:23 thomas_ku what?
13:23 egonw I copy paste SMILESGeneratorTest into .inchi
13:23 egonw and then it can no longer find the package where the CDKTestCases is ???
13:24 thomas_ku ahm mom
13:24 thomas_ku did you try a clean?
13:25 egonw worth a try
13:26 thomas_ku did you copied the file to the test directory or to the scr main directory?
13:26 egonw no, checked that
13:27 thomas_ku no idea than...
13:27 thomas_ku can you commit the file
13:28 thomas_ku than I can check myself
13:28 egonw the clean helped
13:28 egonw sometimes Eclipse just messes up
13:28 thomas_ku strange...
13:32 egonw ok, worker seems to work...
13:32 egonw this is the test I have:
13:32 egonw for (String element : result) {
13:32 egonw if (!element.startsWith("InChI=1/")) {
13:32 egonw correctResult = false;
13:32 egonw System.out.println("result is not an InChI: " + element);
13:32 egonw }
13:32 egonw i++;
13:32 egonw }
13:33 thomas_ku It is OK
13:33 egonw :)
13:33 CIA-17 cdk: egonw * r9648 /branches/egonw/cdk-taverna-mb/src/ (2 files in 2 dirs): Added InChI generator worker
13:33 egonw btw, filed a bug report...
13:34 egonw you got somewhere SMILE... but that should be SMILES
13:34 egonw menu string
13:34 egonw or port name or so
13:36 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 4466 test, 96 fails + 30 errors (2.82%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
13:36 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 4466 test, 96 fails + 30 errors (2.82%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
13:37 thomas_ku Oh thanks will look for this
13:39 egonw or did I email that?
13:39 thomas_ku you mentioned it before some days ago
13:39 thomas_ku not sure where
13:39 egonw I did file this: http://sourceforge.net/tracker/inde​x.php?func=detail&aid=1844235&a​mp;group_id=20024&atid=120024
13:40 egonw but that is about me failing to get cdk-taverna working in 1.6.2
13:42 thomas_ku yeah I saw that and did you tried it with the small change I have done on the server side after we talked about this the last time?
13:43 thomas_ku I have really no idea where your problem is comming from!! up to now I can't reproduce it
13:44 egonw yes, I did
13:44 egonw ok, then please close the bug...
13:44 egonw if I still have the problem with the 1.7 version, I'll file a new one...
13:45 masak egonw: olas jsut told me about your thoughts on rubidium
13:45 masak sounds interesting
13:45 masak I think I'd like that too
13:45 masak any ideas pmn wjere tp start
13:45 egonw yeah, talk to Rich... might he interesting for him to support...
13:45 masak egonw: ok, I will
13:45 egonw good for his business, good for ours
13:46 masak yes.
13:46 thomas_ku egonw: that I will not work with 1.7.0 it ok
13:46 thomas_ku because we haven't a version for this!!
13:46 egonw no, I know...
13:47 egonw I meant, let's disregard that bug, and wait for the 1.7 version
13:47 egonw with a focus on -wait- :)
13:47 thomas_ku yeah but I fear we won't get a new version this year...
13:47 egonw once you got around to releasing a CDK-Taverna for 1.7... I'll check again, and if still have the problem, I will file a new bug...
13:47 thomas_ku Ok
14:09 thomas_ku have to go now
14:09 thomas_ku cu
14:09 egonw bye
14:17 CIA-17 cdk: egonw * r9649 /trunk/cdk/src/org/openscience/cdk/test/qsar/des​criptors/molecular/MolecularDescriptorTest.java: 1. Fixed method name according to scheme; 2. added more testing, now for the descriptor specification, and descriptor type
14:20 * egonw wonders when Nightly will rerun again...
14:20 egonw OK, we're past the 4500 unit tests for trunk now
14:38 CIA-17 cdk: egonw * r9650 /trunk/cdk/src/org/openscience/cdk/test/ (2 files in 2 dirs): Added missing unit test class, found with the coverage testing
14:51 egonw only 350 commits away from the big 10.000 commits
14:52 CIA-17 cdk: egonw * r9651 /trunk/cdk/src/org/openscience/cdk/ (4 files in 3 dirs): Renamed the ALogP descriptor to use the same scheme as the rest of the CDK
14:55 CIA-17 cdk: egonw * r9652 /trunk/cdk/src/org/openscienc​e/cdk/test/CoverageTest.java: It's not just the core module that it is testing anymore...
15:01 CIA-17 cdk: egonw * r9653 /trunk/cdk/src/org/openscience/cdk/test/qsar/des​criptors/molecular/MolecularDescriptorTest.java: Additional testing; there are rather simplistic though
15:05 jbrefort joined #cdk
15:13 steinbeck joined #cdk
15:17 egonw hi steinbeck
15:21 rojas1 left #cdk
15:21 steinbeck hi
15:25 CIA-17 jmol: hansonr * r8834 /trunk/Jmol/src/org/jmol/ (7 files in 2 dirs): version=11.3.63_dev # bug fix: "within()" upgrade for boundbox: within(boundbox), within(boundbox,atomExpression)
15:29 carsten joined #cdk
15:36 egonw http://chem-bla-ics.blogspot.com/2007/12​/molecular-qsar-descriptors-in-cdk.html
15:36 egonw more obligatory reading :)
16:01 steinbeck left #cdk
16:44 CIA-17 jmol: hansonr * r8835 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs): version=11.3.63_dev # bug fix: multiframe draw with labels different for each frame not properly saved in state
16:46 egonw bye all
16:46 * egonw is going to play basketball and then go home
16:46 egonw no idea when I are allowed back online again
17:27 CIA-17 jmol: hansonr * r8836 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties): version=11.3.63_dev # bug fix: print {atomSet}.color -- .color returning bounding box!
17:47 CIA-17 cdk: rajarshi * r9654 /trunk/cdk/src/org/openscience/cdk/qsar/descr​iptors/molecular/CarbonTypesDescriptor.java: Fixed so that we return the proper type of the DescriptrResult
17:52 rguha joined #cdk
17:58 CIA-17 jmol: hansonr * r8837 /trunk/Jmol/src/org/jmol/g3d/Graphics3D.java: version=11.3.63_dev # bug fix: background color off when not white and ends in "FF"
18:16 CIA-17 cdk: rajarshi * r9655 /trunk/cdk/src/org/openscience/cdk/qsar/desc​riptors/molecular/AtomCountDescriptor.java: Updted atom count descriptor to assume that an if getHydrogenCount() on an atom returns UNSET, then the implicit H count is 0. Avoids NPE's
18:50 CIA-17 jmol: hansonr * r8838 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs):
18:50 CIA-17 jmol: version=11.3.63_dev structure bug; quaternion command by itself
18:50 CIA-17 jmol: # bug fix: models with turns crash jmol if not first model loaded
18:50 CIA-17 jmol: # bug fix: quaternion command by itself not switching to most recent quaternion
19:53 CIA-17 cdk: rajarshi * r9656 /trunk/cdk/src/org/openscience/​cdk/qsar/descriptors/molecular/ (BCUTDescriptor.java BondCountDescriptor.java): Updated code to return the proper parameter types
19:54 jbrefort joined #cdk
20:16 CIA-17 jmol: hansonr * r8839 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties): version=11.3.63_dev # bug fix: subsets not properly handling restrict
20:32 carsten joined #cdk
20:39 CIA-17 jmol: hansonr * r8840 /trunk/Jmol/src/org/jmol/viewer/Viewer.java: version=11.3.63_dev # bug fix: subsets not restricting hover
20:58 CIA-17 cdk: rajarshi * r9657 /trunk/cdk/tools/nightly.py: Added code to generate a page showing which JUnit failures were fixed and which are new fails. Also updated code to use pickle for persistence. Makes life easier
22:13 CIA-17 jmol: hansonr * r8841 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties):
22:13 CIA-17 jmol: version=11.3.63_dev # bug fix: moveto alternative format missing necessary 0 rotationRadius requirement
22:13 CIA-17 jmol: # moveTo ...... {atomExpression} 0 [zoomOrZoomFactor]
22:13 CIA-17 jmol: # where [zoomOrZoomFactor] is n, +n, -n, *n, /n, or 0 (to indicate fill screen)
22:55 CIA-17 jmol: hansonr * r8842 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs): version=11.3.63_dev # bug fix: polyhedra .... translucent 0.3 green

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