Camelia, the Perl 6 bug

IRC log for #cdk, 2009-03-10

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All times shown according to UTC.

Time Nick Message
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08:46 CIA-62 cdk: miguelrojasch * r14389 /cdk/branches/cdk-1.2.x/src/test/org​/openscience/cdk/tools/manipulator/M​olecularFormulaManipulatorTest.java: Removed cdk.bug tag fixed by Egonw
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08:49 CIA-62 cdk: miguelrojasch * r14390 /cdk/branches/cdk-1.2.x/src/test/org​/openscience/cdk/tools/manipulator/M​olecularFormulaManipulatorTest.java: Removing @cdk.bug tag 1944604 from the javadoc. It is already closed
08:52 CIA-62 cdk: miguelrojasch * r14391 /cdk/branches/cdk-1.2.x/src/test/org​/openscience/cdk/tools/manipulator/M​olecularFormulaManipulatorTest.java: Removing @cdk.bug 2276507 from the javadoc. It is already closed
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10:33 thomas_ku moin
10:33 zarah oh hai thomas_ku
12:00 CIA-62 cdk: shk3 * r14392 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (9 files in 2 dirs): added tracking of implicit hydrogens
12:01 CIA-62 cdk: shk3 * r14393 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (15 files in 5 dirs): activated tracking of implicit hydrogens, menu items work etc.
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13:09 CIA-62 cdk: goglepox * r14394 /cdk/branches/jchempaint-primary/src/main/org/op​enscience/cdk/renderer/RenderingParameters.java: Set defaultBondColor to black
13:10 CIA-62 cdk: goglepox * r14395 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/g​enerators/BasicAtomGenerator.java: Only horizontal alignment for carbon
13:10 CIA-62 cdk: goglepox * r14396 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/g​enerators/BasicBondGenerator.java: Use default bond color
13:11 CIA-62 cdk: goglepox * r14397 /cdk/branches/jchempaint-primary/s​rc/main/org/openscience/cdk/render​er/generators/RingGenerator.java: Ported from bioclipse: egonw Reset the isAromatic var when checking the bonds
13:12 CIA-62 cdk: goglepox * r14398 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/g​enerators/SelectionGenerator.java: Draw selections for bonds
13:12 CIA-62 cdk: goglepox * r14399 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/s​election/IChemObjectSelection.java: Removed select(IAtomContainer) from interface
13:13 egonw Gpox++ for his hard work
13:13 CIA-62 cdk: goglepox * r14400 /cdk/branches/jchempaint-primary/s​rc/main/org/openscience/cdk/render​er/selection/ShapeSelection.java:
13:13 CIA-62 cdk: Moved clear() form select(IAtomContainer) to select(IChemModel).
13:13 CIA-62 cdk: And made select(IAtomContainer) private as it dose not clear selection anylonger
13:16 Gpox egonw: ok i have syncronized my changes from bc-cdk to jcp-primary
13:16 egonw ok, excellent
13:16 Gpox are your changes zyncronized?
13:17 egonw which changes? synched between?
13:18 Gpox bc-cdk -> cdk
13:18 Gpox git log cdk-external/trunk
13:19 egonw no, I have not yet updated cdk-external ...render and ...control yet
13:19 egonw but wasn't the point to wait for your above patches?
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13:19 egonw Gpox: I think I lost you...
13:19 Gpox yes, i mean commits to cdk-external/trunk
13:20 egonw I do not think I have anything to commit there
13:20 egonw other than the synch with jcp-prim
13:21 Gpox r9243 Fixed drawing of naphtalenes by fixed chosing where to put the double bonds (fixes #640)
13:22 Gpox just making sure no fixes are lost
13:22 egonw ah...
13:22 egonw ok, you did not port that one?
13:22 egonw neither did I
13:22 egonw can you port that one too, please?
13:37 CIA-62 cdk: goglepox * r14401 /cdk/branches/jchempaint-primary/src/main/org/​openscience/cdk/controller/ControllerHub.java: Ported from bioclipse: egonw Fixed drawing of naphtalenes by fixed chosing where to put the double bonds
13:40 Gpox egonw: done. Don't think there is anything else
13:41 Gpox there seams to be some changes in the org.openscience.cdk.standart plugin in jchempaint-primary
13:46 egonw mom
13:46 egonw checking
13:47 egonw 9062 is in upstream too
13:47 egonw is that the one you mean, or another?
13:49 Gpox no the other way from jcp-primary
13:50 egonw huh?
13:50 egonw sorry, really tired... you have to be rather explicit with things today
13:52 Gpox when you update cdk-external ..render, ...control and ...standart
13:53 egonw I did not intend to update standard...
13:54 egonw should I?
13:54 egonw in that case, I update to CDK 1.1.6...
13:55 egonw but that will bring in some API changes in SDF writing...
13:55 egonw which I had not in mind doing today...
13:56 Gpox I get compile errors when I use ...render and ...control from jchempaint-primary, indicating API changes in ReactionSetManipulator
14:00 egonw ack...
14:00 egonw shk3: did you yet make a patch for that for cdk 1.2.x too?
14:01 egonw this complicates things...
14:01 shk3 the patch is for 1.2
14:03 egonw I only saw the IReactionSet patch yet...
14:03 egonw not the patch for ReactionSetManipulator
14:05 shk3 ah, will make one for that as well
14:05 egonw thanx
14:05 Gpox ICDKChangeListener.zoomFactorChanged
14:06 shk3 yes
14:06 shk3 added that
14:15 egonw shk3: I asked Rajarshi to review your patch too, and submitted my comments
14:15 Gpox Come to think about it, now that everything is ported back to jcp-primary i can just fix those two problems localy and get hacking on selection handling
14:16 egonw Gpox: OK
14:16 egonw then I'll wait until those patches by shk3 are integrated into cdk1.2.x, OK?
14:17 Gpox ok
15:15 shk3 egonw: you said a reaction can be in the reactionset several times
15:16 shk3 I suppose it can.
15:16 egonw at least the code is not clear about it, neither is the JavaDoc
15:16 shk3 But looking at the code for AtomContainerSet it doesn't look like it handles an AtomContainer
15:16 egonw but your code makes a choice...
15:16 shk3 being in it several times
15:16 shk3 yes
15:16 shk3 see the point
15:16 egonw does it enfore it?
15:17 shk3 Just get the suspicion AtomContainerSet is not good in that respect
15:17 shk3 neither nor
15:17 shk3 I think
15:17 shk3 Code is:
15:17 shk3 for (int i = 0; i < atomContainerCount; i++) {
15:17 shk3 if (atomContainers[i] == atomContainer)
15:17 shk3 removeAtomContainer(i);
15:17 shk3 }
15:17 shk3 So it jumps the atomcontainer right behind the one removed
15:17 shk3 I think
15:19 egonw I would welcome the symmetry... so you could bring the assymmetry up on the mailing list...
15:19 egonw ask the original design of IReactionSet what the intention was
15:20 egonw yes, clear bug in AtomContainerSet
15:20 egonw you can add duplicates, but it would only remove the first instance of it..
15:20 egonw that does not sounds good
15:20 shk3 well, if they are right behind each other
15:20 shk3 if they are separated, the get removed
15:21 egonw yes, indeed
15:21 egonw good catch...
15:21 egonw nasty situation
15:21 egonw OK, so AtomContainerSet does allow duplicates
15:21 shk3 looks like
15:21 egonw and removed duplicates... if the code was OK
15:21 shk3 can't find any code preventing it at least
15:21 egonw the fix is fairly easy: start count at the end and down to zero
15:22 shk3 that should do it
15:22 shk3 shall I write a test?
15:22 egonw yes, please do
15:23 egonw I'll file a bug report
15:23 egonw just for reference
15:25 egonw https://sourceforge.net/tracker2/?func=detail&am​p;aid=2679343&amp;group_id=20024&amp;atid=120024
15:25 egonw shk3: please annotate the unit test with @cdk.bug 2679343
15:26 CIA-62 cdk: shk3 * r14402 /cdk/branches/cdk-1.2.x/src/test/org/openscience/​cdk/interfaces/AbstractAtomContainerSetTest.java: added a test for bug #2679343
15:27 CIA-62 cdk: gilleain * r14403 /jchempaint/trunk/src/main/org/openscienc​e/jchempaint/action/CopyPasteAction.java: Fixes a compile error caused by api changes to IChemObjectSelection ported from bioclipse-cdk.
15:28 egonw [16:25:52] <egonw> shk3: please annotate the unit test with @cdk.bug 2679343
15:28 shk3 on its way
15:28 egonw ok :)
15:28 shk3 hope it was ok to commit that directly
15:28 CIA-62 cdk: shk3 * r14404 /cdk/branches/cdk-1.2.x/src/test/org/openscience/​cdk/interfaces/AbstractAtomContainerSetTest.java: added a test for bug #2679343
15:28 egonw was not sure if the message got lost in between the flood of ocmmit messages
15:28 CIA-62 cdk: gilleain * r14405 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/g​enerators/SelectionGenerator.java: Minor patch to ensure that bond selections are drawn correctly in swing-jchempaint.
15:28 egonw shk3: yes, but fixes in cdk1.2.x is fine
15:29 egonw in particular unit tests etc
15:29 egonw I'll review those patches via email
15:30 egonw btw, in case you wonder... this @cdk.bug annotation is used to calculate the bug statistics on Nightly
15:30 egonw to see which open bugs have tests, which closed bugs do not have tests, etc
15:33 shk3 hm, your fix makes another test fail
15:33 shk3 investigating that...
15:34 shk3 ah >= 0, not >0
15:34 egonw which fix?
15:34 shk3 of course
15:34 shk3 the count down
15:34 shk3 but was stupidity of mine
15:34 egonw ic...
15:34 shk3 looks good now
15:35 egonw well, I think it's the most common source of bugs in informatics :)
15:35 shk3 show I commit?
15:35 shk3 show=shall
15:35 egonw yes
15:37 CIA-62 cdk: shk3 * r14406 /cdk/branches/cdk-1.2.x/src/main/org/o​penscience/cdk/AtomContainerSet.java: fixes bug #2679343
15:47 CIA-62 cdk: egonw * r14407 /cdk-rfc/trunk/8.xml: Typo (see bug #2596042)
15:49 CIA-62 cdk: egonw * r14408 /cdk/branches/cdk-1.2.x/src/ (6 files in 4 dirs): Made the IPseudoAtom behavior regarding exact mass, formal and partial charge in agreement with IAtom as described by RFC #8 (closes #2596042)
15:53 egonw dinner time
15:53 egonw bye
15:54 egonw (going looking for houses after that)
16:02 CIA-62 cdk: rajarshi * r14409 /cdk/branches/cdk-1.2.x/src/test/org/open​science/cdk/smiles/SmilesParserTest.java: Added unit test for bug 2596061. Note that it doesnt test for all the things that Andrew noted. See discussion on bug report
16:13 CIA-62 cdk: rajarshi * r14410 /cdk/branches/cdk-1.2.x/src/test/org/open​science/cdk/smiles/SmilesParserTest.java: Updated smiles parser test for pseudo atom to check mass number
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18:09 CIA-62 cdk: rajarshi * r14411 /cdk/branches/cdk-1.2.x/src/test/org/open​science/cdk/smiles/SmilesParserTest.java: Added a cdk.bug annotation for the test that checks hard coded H's
18:14 CIA-62 cdk: rajarshi * r14412 /cdk/branches/cdk-1.2.x/src/test/org/open​science/cdk/smiles/SmilesParserTest.java: Added another unit test to check for hard coded H's
18:16 CIA-62 cdk: rajarshi * r14413 /cdk/branches/cdk-1.2.x/src/main/org/op​enscience/cdk/smiles/SmilesParser.java: Fixed bug 2679607 to properly handle the Hn symbol
19:07 CIA-62 cdk: miguelrojasch * r14414 /cdk/branches/cdk-1.2.x/src/ (2 files in 2 dirs): Capability to parser a molecular formula string containing charge signal. E.g. [O3S]2-
19:17 CIA-62 cdk: miguelrojasch * r14415 /cdk/branches/cdk-1.2.x/src/main/or​g/openscience/cdk/tools/manipulator​/MolecularFormulaManipulator.java: Correction for when the charge is positive. It is not possible to create a Integer from a string like "+1"
19:49 CIA-62 cdk: miguelrojasch * r14416 /cdk/branches/cdk-1.2.x/src/main/or​g/openscience/cdk/tools/manipulator​/MolecularFormulaManipulator.java: Set value 1 when contains only the signal for specify the charge.
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