Camelia, the Perl 6 bug

IRC log for #cdk, 2009-01-30

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All times shown according to UTC.

Time Nick Message
07:08 edrin joined #cdk
07:35 jbrefort joined #cdk
08:02 Gpox joined #cdk
08:55 carsten joined #cdk
09:38 egonw joined #cdk
09:39 jonalv joined #cdk
11:12 shk3 joined #cdk
11:53 steinbeck joined #cdk
11:54 egonw yes
11:55 steinbeck Ah, does your private chat not work?
12:16 maclean joined #cdk
12:21 * maclean is branching... crossed fingers
12:21 maclean gah!
12:22 maclean dammit - how can a file already exist in a branch that is being created?
12:30 egonw git?
12:30 egonw can happen if you create a branch from a branch which you do not have checkout out at the moment
12:30 egonw e.g.
12:30 egonw when you branch CDK trunk, while having cdk1.2.x checked out
12:33 egonw shk3: https://translations.launchpad.​net/jchempaint/trunk/+pots/keys
12:33 egonw the .po's have been uploaded
12:39 * egonw is doing a bit of NL translation for JChemPaint
12:39 egonw Gpox: care from some Swedish?
12:51 egonw from=for
12:53 de__maas joined #cdk
13:04 egonw shk3: I made you owner of the JCP translations so that you can upload .po files too
13:06 maclean_ joined #cdk
13:07 maclean_ egonw: not git, svn. and I'm trying to commit my working copy as a branch. it complains about the HighlightGenerator already existing.
13:07 egonw ah...
13:07 egonw weird
13:07 shk3 thanks
13:07 egonw check with the SVN HTML frontend it really is a new branch you are creating
13:08 maclean_ well, it doesn't create it, as it fails half way through.
13:08 maclean_ gaaah.
13:09 maclean_ so no new branch shows up in the html view.
13:12 maclean_ Gpox : I've uploaded a patch that only covers the CDK only. I can't seem to branch due to my own incompetance, so could you try to use this patch?
13:14 Gpox will do
13:15 maclean_ cool, thanks.
14:09 CIA-62 cdk: egonw * r14000 /cdk/ (branches/trunk-messed-up/ trunk/): Moved away trunk, to make a clean new trunk branch
14:10 egonw oh, that's nice :)
14:10 egonw such a landmark commit to be the 14000th :)
14:13 maclean_ heh
14:13 CIA-62 cdk: egonw * r14001 /cdk/trunk/: Copied in a fresh trunk from CDK 1.2.x; a poor mans 'git rebase'... but then with keeping the later trunk patches, which I will do manually.
14:13 * egonw is curious to see how git-svn will handle these moves...
14:13 egonw let's see...
14:14 * egonw issues a 'git svn fetch; git svn rebase' on his 'master'
14:21 egonw ok, fetch worked:
14:21 egonw well... too much to paste
14:23 egonw rebase seems to have worked too
14:23 egonw guys... we have an almost up to date trunk :)
14:26 maclean_ yay
14:27 maclean_ (cutting down the cdk branch-jungle)++
14:28 egonw ok, and trunk-messed-up also looks good
14:29 rguha joined #cdk
14:29 rguha hi
14:29 zarah rguha: where have you been? I've been worried.
14:29 egonw ha rguha
14:29 maclean_ hi
14:29 zarah oh hai maclean_
14:29 maclean_ ohai
14:30 rguha egonw: regarding the merge with trunk - mightn't it be a good idea to first get all outstanding patches into 1.2.x and then merge that with trunk?
14:30 egonw no, because there is API changing stuff in trunk
14:30 egonw oh
14:30 egonw that way
14:30 egonw misread it the first time
14:30 rguha :)
14:31 egonw you mean the patches from the tracker, right?
14:31 rguha i was mainly thinking of the vflib branch - so many things can benefit
14:31 rguha right
14:31 egonw nah, rebase will take care of that
14:31 egonw I could not rebase anymore because of stupid merges and backports
14:31 rguha oh ok
14:31 egonw never backport to a branch, because that messes up rebaseing
14:31 rguha i'll keep that it mind
14:32 egonw I'm now figuring out which patches to apply...
14:32 rguha from the tracker?
14:32 egonw sorry... commit patches
14:32 egonw from old trunk
14:32 egonw aka
14:32 egonw trunk-messed-up
14:32 rguha oh ok
14:33 egonw $ cd oldtrunk/
14:33 egonw $ git init
14:33 egonw $ git pull ../../git-svn/cdk local-trunk-mess
14:33 rguha as Christoph mentioned, moving to Git overall might be a good thing
14:33 egonw yes, we'll do that
14:33 egonw once CDK 1.2.0 is out
14:33 egonw which is soon
14:33 rguha cool
14:33 rguha btw, will CDK 1.2.0 include the updated rendering code?
14:33 egonw only the ReaderFactory bug is a blocker
14:34 maclean_ heh, egonw :
14:34 maclean_ http://changelog.complete.org/arch​ives/586-rebase-considered-harmful
14:34 egonw no
14:34 zarah maclean_'s link is also http://tinyurl.com/5plbq3
14:34 egonw 1.2.1 may have
14:34 rguha so 1.2.0 won't have rendering?
14:34 egonw correct
14:34 rguha :(
14:34 egonw well...
14:34 maclean_ there was a mail from a cdk user about this : wondering why he couldn't use the molecule panel /molecule table etc
14:35 egonw the jchempaint-primary patch has not been reviewed yet
14:35 egonw I don't want to delay 1.2.0 for that
14:35 rguha hmm
14:35 rguha but if it's just the controller and renderer packages - couldn't that be fasttracked?
14:35 maclean_ http://www.nabble.com/MoleculeViewer2D.displa​y%28-cdk-1.1.4.jar-td21453271.html#a21453271
14:35 zarah maclean_'s link is also http://tinyurl.com/dz2fqq
14:36 rguha maclean_, oh right, yes, forgot about this
14:36 rguha this would be the best approach
14:37 maclean_ there is a pressing need for some kind of cdk-gui project, with all the stuff that was removed from trunk.
14:37 maclean_ shk3 and I discussed this before
14:37 rguha in fact given this idea, might it not be best to just delete controller, renderer etc from 1.2.x?
14:38 maclean_ hmmm
14:38 maclean_ hmmm
14:38 maclean_ not sure
14:39 rguha be back in 15 minutes
14:39 rguha \away
14:39 maclean_ s/\/\//
14:42 maclean_ ooh: I've never used 'call hierarchy' before, how neat.
14:48 shk3 egonw: just started translations on launchpad
14:48 egonw ok
14:48 egonw I already did some NL stuff
14:48 shk3 when I download the file, I get umlaute not endcoded in any way
14:48 shk3 is that ok?
14:48 egonw no idea
14:49 egonw I think you need to use Java escaping for that
14:49 egonw but best to ask Nico@Jmol
14:49 egonw or Angel
15:02 rguha joined #cdk
15:06 maclean_ aargh! godfordamt sourceforge. [:-(
15:06 egonw what's up?
15:07 Gpox maclean_: I still can't get this patch to work, maybe i am doing something wrong :/
15:08 maclean_ gpox: possibly not. are you getting objections to the HighlightGenerator?
15:08 maclean_ I think I may have screwed something up in my working copy...
15:08 Gpox i get them all over the place
15:08 maclean_ egonw: it was just me failing to use the bug tracker interface properly.
15:09 maclean_ (but it's still sf's fault, somehow :)
15:10 Gpox one thing i noticed is that is says revision 13973 but the latest for jcp-primary is  13974 a change to HighlightGenerator as it happens
15:10 maclean_ ahhhaahhh.
15:10 maclean_ hmmm.
15:10 egonw ah...
15:10 egonw svn cleanup
15:10 egonw that might help synch the SVN hists again
15:11 maclean_ perhaps if I update, then make the patch?
15:11 maclean_ svn cleanup, eh?
15:12 Gpox maybe, don't you use git?
15:13 CIA-62 cdk: gilleain * r14002 /cdk/branches/maclean-jchempaint/ (49 files in 10 dirs): Major renderer changes.
15:13 maclean_ aha!
15:14 maclean_ right. I cleanup-ed, and updated.
15:14 maclean_ Gpox : no, I would like to, but haven't done yet.
15:18 rguha looks like git will rule the world :)
15:19 Gpox maclean_: so dose maclean-jcheampaint cotains your changes to the Renderer?
15:19 maclean_ Gpox : yup
15:20 maclean_ Or, rather, I hope so.
15:20 Gpox it seams to be missing a few classes
15:21 Gpox IFontManager, IDrawVisitor, MappingGenerator, BoundsGenerator
15:23 maclean_ bother
15:25 maclean_ aargh. I can't switch to the new branch either.
15:30 maclean_ the missing classes were not versioned (for no obvious reason)
15:31 maclean_ but if I commit them, it will go to the jcp-primary branch, not the new branch
15:31 maclean_ and I can't switch, for no obvious reason.
15:32 rguha looking at outstanding bugs in 1.2.x I see that the proton partial charge descriptor is still there
15:32 rguha the last comment was to update to pad with NaN's
15:32 rguha was that done?
15:33 maclean_ right, I have a plan
15:39 egonw rguha: that that I know
15:40 CIA-62 cdk: gilleain * r14003 /cdk/branches/maclean-jchempaint/src​/main/org/openscience/cdk/renderer/ (5 files in 3 dirs): Missing classes.
15:40 maclean_ Gpox: there you go.
15:41 rguha egonw, ok, i'll go ahead and fix it
15:41 egonw thanx
15:46 Gpox maclean_: there is a font property in the RendererModel that should probably be used by the FontManager
15:49 maclean_ ah the custom font, yes?
15:49 maclean_ that is true.
15:50 maclean_ I'm not altogether happy with making a renderer taking a font manager in the constructor, bytheway
15:51 maclean_ but the alternative is to hold a reference to the font manager in the class that creates the RenderingVisitor, and then set it just before calling the appropriate paint(obj, visitor) method
15:52 maclean_ and it seems safer to just set it once, when making a renderer. but not so clean as before ("new Renderer()")
15:54 maclean_ Oh, and the RendererModel.useAntiAliasing could be used somewhere.
15:55 Gpox I think i do, i know i did use it at some point
15:56 maclean_ well, it could be made explicit by putting it in the DrawVisitor interface, so that the Renderer can call it.
16:00 maclean_ Oh, and about the IDrawVisitor interface - the logic behind that was that there may be visitors that don't draw the tree (PrintVisitor, DistanceSearchVisitor, for example) that don't need to set the renderer model.
16:00 de__maas left #cdk
16:00 maclean_ (could also move the setTransform method down to that interface from IRenderingVisitor)
16:03 Gpox and rename it as IDrawVisitor is what should be used when rendering
16:04 Gpox ElementVisitor would be a better name
16:05 Gpox or RenderingElementVisitor
16:06 maclean_ yes
16:06 maclean_ that last one, though long, is clearest.
16:10 Gpox or just Visitor and change visit(IRenderingElement) to visit(Object) ;)
16:12 maclean_ hmmm. I got into some endless recursion trouble with the PrintVisitor at one point.
16:17 CIA-62 cdk: shk3 * r14004 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (5 files in 3 dirs): activated the square selection (problem remaining: it's flicking)
16:18 CIA-62 cdk: shk3 * r14005 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (4 files in 4 dirs): activated the square selection
16:19 CIA-62 cdk: rajarshi * r14006 /cdk/branches/cdk-1.2.x/src/ (2 files in 2 dirs): Updated proton charge descriptpr so that it os fixed size . Updated docs and test. Fixes bug 203973
16:22 egonw rguha: ah, good
16:22 egonw that will be a nice test for the rebase :)
16:22 rguha :)
16:24 rguha btw, does anybody know how I can check out a single branch without do an svn co for the whole CDK project?
16:24 egonw co -N
16:24 egonw svn co -N cdk
16:24 egonw svn co -N cdk/branches
16:24 egonw svn co cdk/branches/cdk-1.2.x
16:25 rguha aah,thanks
16:25 egonw -N(orecurse)
16:30 CIA-62 cdk: shk3 * r14007 /cdk/branches/jchempaint-primary/sr​c/main/org/openscience/cdk/renderer​/selection/RectangleSelection.java: activated the square selection (no longer flicking)
16:37 egonw rguha: I think I have all relevant patches applied
16:37 rguha great
16:37 egonw checked the first of the two you mentioned...
16:37 egonw that one is one
16:37 egonw that one is in
16:37 egonw now checking the second
16:37 rguha ok
16:37 egonw commit 12508?
16:37 egonw that's a merge actually
16:38 egonw what's the real second commit you meant?
16:38 rguha one sec
16:39 rguha oops, I meant to write revs 12458 to 12507
16:39 rguha those were between two merges
16:40 egonw ok
16:40 egonw checkin
16:41 rguha and one more, just to be careful is rev 12263
16:41 egonw ah, good catch!
16:41 egonw that series of patches I do not have yet :(
16:42 egonw that was after a merge
16:42 rguha in general I think any commit that refers to a bugfix shouldbe checked\
16:42 egonw so it looked like commits in a branch
16:43 egonw well, I'm pretty sure the FPs for the builder3d need updating anyway
16:44 rguha ok - so all updates to fp code were in 1.2.x? I thought that some bits of builder3d had gone into trunk
16:44 egonw I merged most of the builder3d changes into 1.2.x
16:45 rguha ok
16:46 egonw well... it's rather bumpy right this way
16:46 egonw but already much improved to pure SVN
16:46 rguha well, if we move to git completely, I assume it'll be much smoother
16:47 egonw indeed
16:47 rguha i love branching in git :)
16:47 egonw I love merging in git
16:48 egonw oh... and what Gpox taught me: git rebase --interactive HEAD~5
16:48 egonw (replace 5 with what you like)
16:48 CIA-62 cdk: rajarshi * r14008 /cdk/branches/cdk-1.2.x/src/test/org/opensc​ience/cdk/io/random/RandomAccessTest.java: Updated file path in test
16:48 maclean_ what does that magic invocation do?
16:49 egonw merge, reorganize, delete local commits :)
16:49 egonw very handy in this cherry-picking of commits
16:49 maclean_ ah
16:49 egonw try it
16:50 maclean_ jooiiiin usss.
16:50 egonw :)
16:52 rguha lol
16:52 * maclean_ sudo port installs git-core
16:55 CIA-62 cdk: rajarshi * r14009 /cdk/branches/cdk-1.2.x/src/main/org/opensci​ence/cdk/io/random/RandomAccessReader.java: Some code cleanups. Got rid of unnecessary exceptions that closes bug 2487580
16:57 egonw rguha++
16:57 rguha :)
16:58 rguha btw, why was the p9olymer bug fix postponed?
16:59 egonw too difficult
16:59 egonw requires API changes
16:59 egonw at least some things
16:59 egonw IIRC
16:59 rguha is there no way to identify an atom not part of a monomer?
16:59 rguha is there a test for this bug?
17:00 rguha oops, see it now
17:03 rguha looks like the test does not really test the bug
17:04 egonw oh...
17:04 egonw not good
17:05 rguha updating now
17:06 rguha polymer.clone is messed up even with copying monomers!
17:06 egonw yes
17:06 egonw it's seriously messed up indeed
17:06 egonw hence the delay
17:07 CIA-62 cdk: rajarshi * r14010 /cdk/branches/cdk-1.2.x/src/test/or​g/openscience/cdk/PolymerTest.java: updated test to actually start testing for bug. Identifies serious problems
17:16 CIA-62 cdk: rajarshi * r14011 /cdk/branches/cdk-1.2.x/src/main/​org/openscience/cdk/Polymer.java: First fix to ensure that monomers and their attached atoms are properly cloned
17:17 rguha egonw, can you point me to some tests that fail because of the polymer bug?
17:18 egonw check Nightly
17:18 egonw MdataTests
17:19 egonw OK, commiting patches of old trunk to new tunk
17:19 egonw will then try the rebase
17:19 rguha fingers crossed
17:19 * egonw has fingers crossed
17:19 egonw hehehe
17:19 CIA-62 cdk: egonw * r14012 /cdk/trunk/src/main/org/openscience/cdk/m​odeling/builder3d/TemplateExtractor.java:
17:19 CIA-62 cdk: documentation
17:19 CIA-62 cdk: git-svn-id:
17:19 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12180 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:19 CIA-62 cdk: Author: shk3 <shk3@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:19 egonw actually hit enter before I saw your message
17:20 CIA-62 cdk: egonw * r14013 /cdk/trunk/src/ (2 files in 2 dirs):
17:20 CIA-62 cdk: added a convenience constructor to smilesgenerator, improved a test to test the aromaticity behaviour
17:20 CIA-62 cdk: git-svn-id:
17:20 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12181 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:20 CIA-62 cdk: Author: shk3 <shk3@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:21 CIA-62 cdk: egonw * r14014 /cdk/trunk/src/test/org/openscience/cdk/​atomtype/SybylAtomTypeMatcherTest.java:
17:21 CIA-62 cdk: Updated tests: findType(IAC, IAtom) cannot detect aromaticity; but findType(IAtomContainer) does, but not tested yet
17:21 CIA-62 cdk: git-svn-id:
17:21 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12184 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:21 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:22 CIA-62 cdk: egonw * r14015 /cdk/trunk/src/main/org/openscience/cdk/atomtype/ (EStateAtomTypeMatcher.java StructGenMatcher.java): (log message trimmed)
17:22 CIA-62 cdk: Added method to IAtomTypeMatcher to perceive types for all atoms in the
17:22 CIA-62 cdk: container; allowing some removal of redundant calculations, and the addition of
17:22 CIA-62 cdk: calculation of molecular properties, like aromaticity, as used in the Sybyl atom
17:22 CIA-62 cdk: type matcher
17:22 CIA-62 cdk: git-svn-id:
17:22 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12185 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:22 CIA-62 cdk: egonw * r14016 /cdk/trunk/src/main/org/openscience/cdk/ (2 files in 2 dirs):
17:22 CIA-62 cdk: Fixed a bunch of Javadoc errors
17:22 CIA-62 cdk: git-svn-id:
17:22 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12274 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:22 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:23 CIA-62 cdk: egonw * r14017 /cdk/trunk/src/main/org/openscience/c​dk/charges/StabilizationCharges.java: (log message trimmed)
17:23 CIA-62 cdk: removed "throws CDKException" from method
17:23 CIA-62 cdk: StructureResonanceGenerator.setR​eactions(List<IReactionProcess>
17:23 CIA-62 cdk: newReactionsList). And depending methods as
17:23 CIA-62 cdk: StabilizationCharges.calculatePositive. It was producing some incoherences:
17:23 CIA-62 cdk: org.openscience.cdk.charges.StabilizationCharges row 83: Unreachable catch block
17:23 CIA-62 cdk: for CDKException. This exception is never thrown from the try statement body.
17:24 CIA-62 cdk: egonw * r14018 /cdk/trunk/src/test/org/openscience/cdk/aromat​icity/CDKHueckelAromaticityDetectorTest.java:
17:24 CIA-62 cdk: Updated test to check that a aromatic molecle coming from two diferent sources (kekule and aromatic SMILES) gets represented internally as the same thing. Currently does not
17:24 CIA-62 cdk: git-svn-id:
17:24 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12754 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:24 CIA-62 cdk: Author: rajarshi <rajarshi@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:25 CIA-62 cdk: egonw * r14019 /cdk/trunk/src/test/org/openscience/cdk/aromat​icity/CDKHueckelAromaticityDetectorTest.java:
17:25 CIA-62 cdk: Rearranged the order of operations and provided a useful message. Added bug annotation
17:25 CIA-62 cdk: git-svn-id:
17:25 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12755 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:25 CIA-62 cdk: Author: rajarshi <rajarshi@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:25 CIA-62 cdk: egonw * r14020 /cdk/trunk/src/META-INF/test-standard.cdkdepends:
17:25 CIA-62 cdk: Added missing dep
17:25 CIA-62 cdk: git-svn-id:
17:25 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12756 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:25 CIA-62 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:26 CIA-62 cdk: egonw * r14021 /cdk/trunk/src/test/org/openscience/cdk/smiles/sm​arts/parser/visitor/SmartsQueryVisitorTest.java:
17:26 CIA-62 cdk: Added copyright info
17:26 CIA-62 cdk: git-svn-id:
17:26 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12914 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:26 CIA-62 cdk: Author: djiao <djiao@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:26 egonw quite a few patches to go
17:27 CIA-62 cdk: egonw * r14022 /cdk/trunk/src/ (2 files in 2 dirs):
17:27 CIA-62 cdk: added method to calculate the Total Mass Number given a IMolecularFormula
17:27 CIA-62 cdk: git-svn-id:
17:27 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@13160 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:27 CIA-62 cdk: Author: miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:27 CIA-62 cdk: shk3 * r14023 /jchempaint/trunk/po/ (5 files in 2 dirs): added german translations
17:27 CIA-62 cdk: egonw * r14024 /cdk/trunk/src/test/org/openscience/cdk/tools/ma​nipulator/MolecularFormulaManipulatorTest.java:
17:27 CIA-62 cdk: Correction of the solution
17:27 CIA-62 cdk: git-svn-id:
17:27 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@13161 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:27 CIA-62 cdk: Author: miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:28 CIA-62 cdk: egonw * r14025 /cdk/trunk/src/ (5 files in 5 dirs): Some compile fixes for fails that sneaked in during the previous trunk-messed-up patch commits
17:28 CIA-62 cdk: rajarshi * r14026 /cdk/branches/cdk-1.2.x/src/ (2 files in 2 dirs): Updated Polymer clone so that it properly clones atoms not associated with a monomer. Updated test case. Still have 16 fails in MdataTests
17:28 CIA-62 cdk: egonw * r14027 /cdk/trunk/src/main/org/openscience/cdk/m​odeling/builder3d/TemplateHandler3D.java:
17:28 CIA-62 cdk: problems with modelbuilder are due to atomtyping; writing and reading molecules as smiles helps
17:28 CIA-62 cdk: git-svn-id:
17:28 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12475 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:28 CIA-62 cdk: Author: shk3 <shk3@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:29 shk3 egonw: do you know who did the french etc. translations for jcp?
17:29 egonw I think Nico
17:29 CIA-62 cdk: egonw * r14028 /cdk/trunk/src/main/org/openscience/cdk/m​odeling/builder3d/TemplateHandler3D.java:
17:29 CIA-62 cdk: model builder working again
17:29 CIA-62 cdk: git-svn-id:
17:29 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12477 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:29 egonw oh, for jcp
17:29 CIA-62 cdk: Author: shk3 <shk3@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:29 egonw no, don't remember
17:29 egonw does the SVN log not say so?
17:29 egonw could have been Nico
17:29 * egonw is heading to dinner
17:30 egonw bbl
17:30 egonw commit remain coming for a while
17:30 egonw commit*s* remain coming for a while
17:30 CIA-62 cdk: egonw * r14029 /cdk/trunk/src/ (4 files in 3 dirs):
17:30 CIA-62 cdk: refactored a method
17:30 CIA-62 cdk: git-svn-id:
17:30 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12478 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:30 CIA-62 cdk: Author: shk3 <shk3@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:31 shk3 egonw: eet smaklig!
17:31 egonw eet smakelijk
17:31 shk3 almost dutch
17:31 egonw almost indeed
17:31 CIA-62 cdk: egonw * r14030 /cdk/trunk/src/test/org/openscience/cdk/tools/​manipulator/AtomContainerManipulatorTest.java:
17:31 CIA-62 cdk: refactored a method
17:31 CIA-62 cdk: git-svn-id:
17:31 CIA-62 cdk:  https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@12479 eb4e18e3-b210-0410-a6ab-dec725e4b171
17:31 CIA-62 cdk: Author: shk3 <shk3@eb4e18e3-b210-0410-a6ab-dec725e4b171>
17:32 egonw and don't ask me what a 'lijk' has to do with dinner :)
17:33 maclean_ "The dead but otherwise (mostly) intact body of a human or animal; corpse"...
17:33 egonw hardly ever used for animal actually
17:34 egonw a dead animal is not a 'lijk'... just a dead animal
17:34 egonw oh, it's done commiting
17:34 egonw OK, let's try rebase in action
17:35 carsten joined #cdk
17:36 egonw grpmh...
17:36 carsten moin
17:36 zarah hello carsten, you fantastic person you
17:36 carsten Ah, zarah is a bot :-)
17:38 maclean_ yup
17:50 CIA-62 cdk: rajarshi * r14031 /cdk/branches/cdk-1.2.x/src/main/​org/openscience/cdk/Polymer.java: Polymer.clone in much better shape - down to 4 fails in MdataTests
18:21 maclean_ rguha : the testPolymerClone method needs to test that the monomers are not shared, not just that the HashMaps are not not shared.
18:21 maclean_ I mailed a patch to egon, but I don't think he applied it.
18:22 maclean_ I'm re-forwarding it to the list...
18:22 rguha he mentioned that he had postponed it since it required changes to interfaces etc
18:23 maclean_ oh
18:23 maclean_ really?
18:23 rguha that's what was the note in the SF bug report
18:24 maclean_ I saw him say that, but didn't realize it was about that
18:24 rguha but it only requires a change to clone()
18:24 rguha there are bigger issues in BioPolymer (and I assume PDBPolymer)
18:25 maclean_ Ahh, no, that's a different thing, if you are referring to bug 2454890
18:26 rguha well 2454890 refers to just Polymer
18:26 rguha and I made that pending because I updated Polymer.clone which appears to fix the fails - the remainder are due to bugs in BioPolymer etc
18:26 maclean_ I'm talking about testing something that is not properly tested, not fixing a failing test...
18:27 maclean_ It's the old problem of deep cloning.
18:27 rguha oh ok - yes, I updated PolymerTest - I'll add the test that you mentioned
18:28 maclean_ cool
18:31 CIA-62 cdk: shk3 * r14032 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (JCPMenuTextMaker.java RenderPanel.java): some i18n related stuff, better code for status bar
18:33 CIA-62 cdk: rajarshi * r14033 /cdk/branches/cdk-1.2.x/src/test/or​g/openscience/cdk/PolymerTest.java: added a test to PolymerTest to ensure that the clone properly makes new monomers and bonds
18:34 rguha maclean_, I think the new test in PolymerTest correctly checks that the deep copy was OK
18:35 maclean_ ok, checking
18:36 CIA-62 cdk: rajarshi * r14034 /cdk/branches/cdk-1.2.x/src/test/or​g/openscience/cdk/PolymerTest.java: Added a bit more code to be more sure that the deep copy was OK
18:37 maclean_ I just use "git svn fetch" to get new chages, right?
18:37 CIA-62 cdk: rajarshi * r14035 /cdk/branches/cdk-1.2.x/src/test/or​g/openscience/cdk/PolymerTest.java: one more check to to make sure that the new atom is added correctly to the polymer and the monomer
18:37 rguha mm, not sure about git+svn
18:38 rguha I'm just working with the svn repo for 1.2.x
18:38 rguha so svn update should be enough
18:38 maclean_ oh
18:39 maclean_ right, yes, that seems like a better test.
18:40 maclean_ cloning object hierarchies is a real pain.
18:40 rguha true
18:40 maclean_ worse when they are heirarchies of inheritance hierarchies...
18:40 rguha I still wonder why the CDK needs to implement a whole hierarchy for proteins when we might reuse BioJava and implement adaptors
18:41 maclean_ indeed
18:41 maclean_ I think that would be a much better approach
18:41 maclean_ of course, we could equally ask why biojava doesn't use cdk atom classes...
18:42 maclean_ :)
18:42 rguha true :)
18:42 rguha hmm, might be a student project to implement adaptor classes ...
18:45 maclean_ bug priority 9 is highest, isn't it?
18:46 egonw OK, git-svn officially sucks
18:46 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
18:46 rguha maclean_, yes
18:46 maclean_ ah good
18:47 rguha egonw, the Polymer bug is updated and fixed. I made the bug report pending. When you get a chance can you close it
18:47 egonw cool!
18:47 egonw rguha++, maclean++
18:48 egonw BTW...
18:48 egonw rebase fails...
18:48 rguha so manual merges then?
18:48 egonw because git-svn does not pick up the moving around of thing :(
18:48 egonw will go offline now
18:49 egonw and do some more attempts with other methods later...
18:50 egonw I think I see a way of doing it...
18:50 egonw but possibly not with 'trunk'
18:50 egonw so it seems that when we move to git...
18:50 egonw I will propose to start from scratch...
18:50 rguha start what from scratch?
18:50 maclean_ ok, cool egonw: quick question
18:50 egonw and just put the whole SVN history up for download
18:50 maclean_ (stupid question)
18:50 egonw rguha: from the latest revision...
18:51 rguha hmm, no history :(
18:51 maclean_ I just do "git svn fetch", right?
18:51 egonw so, that we are sure to have a clean history...
18:51 egonw rguha: well... maybe not
18:51 maclean_ to get changes, that it
18:51 egonw yes
18:51 maclean_ hmmm
18:51 egonw got to go now...
18:51 rguha egonw, well if it makes branches/merging easier it's probably best to just take the hit
18:51 egonw maclean_: followed by:
18:51 egonw git svn rebase
18:51 maclean_ ahhaahaaaa.
18:51 maclean_ takk
18:51 egonw rguha: it would at least remove dangling branches
18:52 egonw rguha: try gitk
18:52 rguha egonw, aah ok
18:52 egonw and you'll see that the SVN backend sort of messes up the whole what comes from where...
18:52 egonw e.g.
18:52 rguha hmm
18:52 egonw git thinks the the current (new) trunk, actually comes from the old trunk...
18:52 egonw though that bit of history was actually removed...
18:53 rguha hmm, a fresh start sounds better
18:53 egonw so, that trick did not quite work...
18:53 egonw maybe if I make a checkout of only trunk, and no branches, that it starts relatively clean too...
18:53 rguha since 1.2.0 is close, why not just stick to SVN and then make a new start
18:53 rguha shifitng to git
18:54 egonw yes, I was thinking that too...
18:54 egonw ok, really going offline now
18:54 egonw watch a movie
18:54 rguha ok, bye
18:54 egonw cu tomorrow/next week
20:03 dleidert joined #cdk

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