Camelia, the Perl 6 bug

IRC log for #cdk, 2008-08-05

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All times shown according to UTC.

Time Nick Message
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05:18 CIA-34 cdk: egonw * r11857 /cdk/trunk/src/main/org/openscience/cd​k/fingerprint/MACCSFingerprinter.java: Fixed typo.
05:25 CIA-34 cdk: egonw * r11858 /cdk/trunk/src/main/org/opens​cience/cdk/qsar/descriptors/ (2 files in 2 dirs): Fixed two more NoModification fails
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07:04 egonw moin
07:04 zarah hi egonw
07:10 egonw http://news.bbc.co.uk/1/hi/magazine/7540427.stm
07:10 zarah egonw's link is also http://tinyurl.com/6gyzmr
07:10 egonw there are really people convinced that the earth is flat...
07:22 thomas_ku joined #cdk
07:23 thomas_ku moin
07:23 zarah hi thomas_ku
07:30 egonw hi thomas_ku
07:30 egonw thomas_ku: cool new fingerprinter in CDK trunk
07:30 egonw using the Inte:ligand SMARTS substructures
07:31 thomas_ku ok cool! I will have a look at it
07:31 thomas_ku how long is the fingerprint?
07:34 egonw 300-ish, I think
07:35 thomas_ku ok thats good
07:36 thomas_ku because If it is to long I will have memory problems
07:36 egonw hahahaha
07:36 thomas_ku but 300 bit is ok
07:36 thomas_ku the problem is, that the algorithm I am using currently only works with double values
07:37 thomas_ku and if I want to calc a 1000 bit vector that would mean 1000 double values per vector
07:39 thomas_ku 1000 * 8 byte * 185000 structures = 1411 MB RAM if I only want to hold them one times in memory
07:43 egonw that's why they invented BitSet :)
07:43 egonw stupid algorithm then...
07:44 thomas_ku yeah thats true but it is a fast algorithm
07:44 egonw would be faster if it would not eat that much memory
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09:49 jpansane1 moin
09:49 zarah hi jpansane1
10:35 egonw joined #cdk
10:38 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 7344, 78 fails + 48 errors (1.72%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk | CDK News paper online on pharmacophores: http://www.cdknews.org/
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12:54 shk3 hi all
12:54 zarah hi shk3
12:54 shk3 I have a problem understanding what nightly is doing.
12:54 shk3 looking at http://cheminfo.informatics.indiana.edu/~rgu​ha/code/java/nightly/test/result-extra.html
12:54 zarah shk3's link is also http://tinyurl.com/5w9jur
12:54 shk3 it should give me the test results for the extra module, shouldn't it?
12:55 shk3 it says:  Tests run: 37, Failures: 0, Errors: 0, Time elapsed: 1.355 sec
12:55 shk3 if I run the tests, in reports/result-extra.txt, I get
12:55 shk3 Tests run: 90, Failures: 3, Errors: 1, Time elapsed: 3.096 sec
12:56 shk3 where does that difference come from?
12:56 shk3 63 tests written today?
12:56 shk3 seems hard to believe...
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15:31 shk3 egonw: you have a minute?
15:32 egonw shk3: actually, just getting a nap
15:32 egonw ask me tonite
15:32 egonw or email me
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19:29 rguha joined #cdk
19:29 egonw hi rguha
19:30 rguha hi
19:30 zarah hi rguha
19:30 rguha hi zarah
19:30 egonw oh, rguha, meet zarah
19:30 egonw zarah is a bot from Uppsala
19:30 zarah egonw: you've just exceeded my capabilities :/
19:30 rguha what does the bot do?
19:30 egonw @tell rguha that he has a message
19:30 zarah Consider it noted.
19:30 egonw @slap yourself
19:30 zarah no, I'd rather not
19:31 egonw ummm
19:31 egonw @slap egonw
19:31 * zarah is overcome by a sudden desire to hurt egonw
19:31 rguha nice :)
19:31 zarah rguha: You have new messages. Write '@messages' to read them.
19:31 rguha @messages
19:31 zarah rguha: egonw said that he has a message
19:31 egonw well, you get the idea
19:31 rguha yes
19:31 egonw he's (she?) is learning
19:31 rguha who set it up? Ola?
19:31 egonw zarah will get supercow powers
19:31 zarah egonw: I did not understand that
19:31 egonw masak
19:31 egonw oh, rguha++
19:32 egonw @karma rguha
19:32 zarah rguha has a karma of 1
19:32 egonw I think that was the main aim of the bot :)
19:32 rguha @karma rguha
19:32 zarah rguha has a karma of 1
19:32 egonw ok, to work
19:32 rguha right
19:32 egonw Matt's branch is not good
19:32 rguha hmm, IBond is messes up
19:32 egonw the commit was far from clean
19:32 egonw see my email
19:32 rguha saw that
19:32 rguha also removed some methods that support multi-center bonds
19:32 egonw yeah, I think he branched an old trunk version
19:33 rguha hmm
19:33 rguha can we sync trunk into this branch?
19:33 rguha only stuff in interfaces has changed in the branch
19:34 egonw no, merging in SVN1.4 is not good enough
19:34 egonw better take a clean copy
19:34 egonw ha, he just replied
19:34 egonw "Can't, I'm in my lab. I was just waiting for some stuff to cool down."
19:35 rguha hmm
19:35 egonw OK, let's be bold, remove his branch, copy in a fresh one, and redo his commit properly?
19:35 rguha sounds good
19:35 egonw i'm in for some CDK hacking
19:35 egonw ok, here goes
19:35 rguha me too, sick of writing papers
19:36 egonw yeah, you've been writing a lot of them lately...
19:36 rguha networks are *very* cool
19:36 rguha been playing with Cytoscape - amazing peice of s/w
19:37 rguha let me know when you make the branch
19:37 egonw ah, good
19:37 egonw have not had the time for doing that
19:37 egonw been to the Cytoscape conference day, this Spring
19:37 egonw saw some science work based on it...
19:37 egonw I think we'll integrate it into Bioclipse next year
19:37 egonw ok, here goes...
19:37 rguha it's very interesting how mapping data to a network can lead to new views
19:38 rguha ok
19:38 CIA-34 joined #cdk
19:39 egonw rguha: I'll quickly run a svn log on the branch...
19:39 rguha ok
19:39 egonw to see from what he actually copied...
19:39 rguha its actually pretty recent
19:40 rguha I think he just deleted stuff (I don't know why)
19:40 egonw he might have applied the patch by Thomas?
19:40 rguha thomas said to delete his branch
19:40 egonw yeah, he just replied he had copied trunk@11861
19:40 rguha but log says 11849
19:41 egonw yeah, but he had uploaded a patch to SF before that
19:41 egonw yeah, sorry...
19:41 egonw that's what he wrote
19:41 egonw miscopied that
19:41 rguha oh ok
19:41 egonw 11861 was his commit
19:41 egonw ok, so something went wrong...
19:41 egonw will delete now
19:42 rguha ok
19:43 CIA-34 cdk: egonw * r11863 /cdk/branches/mesprague-iterators/: Delete branch, as something went wrong in the patching, and Rajarshi and I will now redo this patch.
19:44 CIA-34 cdk: egonw * r11864 /cdk/branches/speleo3-iterable/: Removed obsolete branch.
19:48 CIA-34 jmol: hansonr * r9672 /trunk/Jmol/src/org/openscience/j​mol/app/webexport/WebPanel.java: removal of .contains()
19:49 CIA-34 cdk: egonw * r11865 /cdk/branches/mesprague-iterators/:
19:49 CIA-34 cdk: Made a fresh branch: patching in this order:
19:49 CIA-34 cdk: 1. move APIs from cdk.interfaces to Iterable<?> (leaving broken code, but clean patch)
19:49 CIA-34 cdk: 2. update all code "Iterator<?> bla = foo.atoms()" to use things like "Iterator<?> bla = foo.atoms().iterator;"
19:49 CIA-34 cdk:  (not yet using the "for (? bla : foo.atoms())" syntax yet, but small clean patches)
19:49 CIA-34 cdk: 3. when all that is done, we'll replace Iterator<?> by "for ()" synxtax
19:55 egonw sorry, was called a way for a sec
19:57 rguha np
19:57 rguha still doing a co
19:57 matt_s joined #cdk
19:58 egonw hi matt_s!
19:58 rguha hello
19:58 zarah hi rguha
19:59 matt_s hows it going
20:00 egonw both checking out your branch
20:00 egonw well, the fresh version of it
20:00 egonw I just copied in a new copy of trunk...
20:00 egonw I do not have the impression you deliberately replaced Order back with double got IBond.getOrder()...
20:01 egonw and redoing the Iterable changes from a fresh copy is easier
20:02 egonw I seems you copied the correct version of trunk though
20:02 matt_s I don't know what happened. If I'm slow responding it means I had yo go back to the bench.
20:02 egonw no worries :)
20:03 egonw what's your day job anyway?
20:05 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 7344, 76 fails + 48 errors (1.69%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk | CDK News paper online on pharmacophores: http://www.cdknews.org/
20:05 egonw BTW, fail rate of the unit tests is finally going down in trunk...
20:05 matt_s I just started a 6-month contract helping an electroplating company implement some new processes and some new testing procedures. Periodically I get the urge to work with actual chemicals.
20:05 egonw :)
20:05 rguha a real chemist :)
20:05 egonw I left real chemistry after I blew up my vacuum hood :)
20:06 egonw (amongst other reasons)
20:09 matt_s I'm also working with a local university on some software for teaching undergrad comp-chem. That's what JGamess is for (the release is coming I swear).
20:09 egonw ah, ok...
20:09 egonw did I mention Bioclipse already?
20:09 CIA-34 cdk: egonw * r11866 /cdk/branches/mesprague-iterators/.project: Tuned for eclipse
20:09 egonw would be a perfect basis for something like that
20:10 rguha ok, co complete
20:10 egonw rguha: same here
20:10 rguha I assume we start on interfaces.*
20:10 egonw yes, see commit
20:10 * egonw is booting Eclipse and importing the branch
20:10 rguha is there a palce I can put up some text - summarizing usages of Iterator in interface.*
20:10 rguha we can then follow the usages
20:10 egonw what do you mean?
20:11 rguha there are 59 usages of Iterator<*> in interfaces.*
20:11 egonw cdk.pastebin.com
20:11 rguha Can I dump that report somewhere so we can divide it up
20:11 egonw http://cdk.pastebin.com
20:12 rguha http://cdk.pastebin.com/m4808a463
20:12 zarah rguha's link is also http://tinyurl.com/5v84wa
20:12 egonw let's do interface by interface, one interface per commit
20:13 rguha OK - I'll do files 1,3, ... in the list
20:13 egonw OK
20:13 egonw mmm...
20:13 egonw interfaces do not have counters
20:14 egonw better: you start at the top, I at the bottom?
20:14 rguha I meant I'll do the odd files in the list I pasted
20:15 egonw rigth, but there is not odd/even indicator
20:16 rguha OK, I'm starting IAdductFormula
20:16 rguha :)
20:16 rojasm joined #cdk
20:17 egonw hi rojasm
20:17 egonw rguha: I'm on IReactionSet
20:18 CIA-34 cdk: rajarshi * r11867 /cdk/branches/mesprague-iterators/src/main/org/​openscience/cdk/interfaces/IAdductFormula.java: Updated code to return Iterable rather than Iterator
20:20 CIA-34 cdk: egonw * r11868 /cdk/branches/mesprague-iterators/src/main/org​/openscience/cdk/interfaces/IReactionSet.java: Uses Iterable now
20:20 CIA-34 cdk: egonw * r11869 /cdk/branches/mesprague-iterators/src/main/org​/openscience/cdk/interfaces/IReactionSet.java: And the clean up of unused imports :(
20:21 egonw onto IMoleculeSet
20:22 egonw first two were easy :)
20:22 CIA-34 cdk: egonw * r11870 /cdk/branches/mesprague-iterators/src/main/or​g/openscience/cdk/interfaces/IReaction.java: Uses Iterable now
20:23 CIA-34 cdk: egonw * r11871 /cdk/branches/mesprague-iterators/src/main/org​/openscience/cdk/interfaces/IMoleculeSet.java: Uses Iterable now
20:23 CIA-34 cdk: rajarshi * r11872 /cdk/branches/mesprague-iterators/src/main/org/​openscience/cdk/interfaces/IAtomContainer.java: Updated code to return Iterable rather than Iterator
20:24 CIA-34 cdk: egonw * r11873 /cdk/branches/mesprague-iterators/src/main/org/ope​nscience/cdk/interfaces/IMolecularFormulaSet.java: Uses Iterable now
20:24 CIA-34 cdk: rajarshi * r11874 /cdk/branches/mesprague-iterators/src/main/org/op​enscience/cdk/interfaces/IAtomContainerSet.java: Updated code to return Iterable rather than Iterator
20:24 egonw seems I got the easy ones
20:24 egonw IMapping is next
20:25 CIA-34 cdk: egonw * r11875 /cdk/branches/mesprague-iterators/src/main/org/op​enscience/cdk/interfaces/IMolecularFormula.java: Uses Iterable now
20:25 CIA-34 cdk: rajarshi * r11876 /cdk/branches/mesprague-iterators/src/main/​org/openscience/cdk/interfaces/IBond.java: Updated code to return Iterable rather than Iterator
20:26 egonw IChemSequence
20:26 CIA-34 cdk: egonw * r11877 /cdk/branches/mesprague-iterators/src/main/o​rg/openscience/cdk/interfaces/IMapping.java: Uses Iterable now
20:26 CIA-34 cdk: rajarshi * r11878 /cdk/branches/mesprague-iterators/src/main/or​g/openscience/cdk/interfaces/IChemFile.java: Updated code to return Iterable rather than Iterator
20:26 egonw ok, done then...
20:26 egonw with step 1
20:27 CIA-34 cdk: rajarshi * r11879 /cdk/branches/mesprague-iterators/src/main/org/​openscience/cdk/interfaces/IChemSequence.java: Updated code to return Iterable rather than Iterator
20:27 egonw ok, that crossed my commit :)
20:27 rguha oops
20:27 egonw no worries
20:28 egonw OK, let's do step 2:
20:28 rguha okso I think we're done?
20:28 egonw [21:49] <CIA-34> cdk: 2. update all code "Iterator<?> bla = foo.atoms()" to use things like "Iterator<?> bla = foo.atoms().iterator;"
20:28 egonw [21:49] <CIA-34> cdk:  (not yet using the "for (? bla : foo.atoms())" syntax yet, but small clean patches)
20:28 egonw yes, done with step 1
20:28 egonw Eclipse counts 505 compile errors
20:29 rguha a good idea will be to go though the classes implementing a given interface
20:29 egonw due to the changes we made
20:29 rguha so I'll start with IAdductFormula and clean up the classes implementing that
20:29 egonw ok, so for all three implementations: data, datadebug and nonotify
20:29 egonw I'll start from the bottom again
20:29 rguha ok
20:30 egonw commits interface by interface again
20:30 rguha actually
20:30 rguha theres a problem
20:30 rguha no, sorry
20:30 egonw I expect problems
20:31 rguha well, the implemnenting classes will require that we implement the Iterable interface
20:31 egonw I guess we need custom Iterable<> implementations, not?
20:31 rguha right
20:31 egonw hehehe
20:31 rguha but for now, let stick to 2, which just updates the usages of the methods
20:31 egonw ok, nonotify and datadebug both inherit from data
20:31 rguha yes
20:31 egonw so, do the implementation in data first, then just wrap from datadebug and nonotify
20:31 rguha right
20:32 egonw ok, right
20:32 rguha but do you want to do the implementation at this point? Or change usage?
20:32 egonw right.... let's add 1a: fix the implementations
20:32 rguha ok
20:33 rguha so implementation now then?
20:33 matt_s I would implement the Iterable with an anonymous class
20:33 rguha an example?
20:34 rguha essentially IterableIterator?
20:34 matt_s public Iterable<IAtom> atoms(){
20:34 rguha aah ok
20:35 matt_s return new Iterable(){ public iterator(){...}}
20:35 egonw well.. but the Iterable has a iterator() method too, not?
20:35 egonw ah, OK
20:35 egonw ok, I'll have a go at Bond.java
20:36 egonw rguha: all classes that returned an Iterator already have an anynomous
20:36 egonw class
20:36 egonw which now implements Iterator<?>
20:36 rguha not really - they all had a speific Iterator class fror that type
20:36 egonw I'll use Bond.AtomsIterator as template
20:36 egonw oh, right
20:36 egonw that's not anonymous
20:36 egonw sorry, my bad
20:36 egonw ok, let's got for the internal class first then?
20:37 egonw then we can switch to anonymous class in a second set of patches
20:37 rguha in AdductFormula I'm using the following:
20:37 rguha public Iterable<IIsotope> isotopes() {
20:37 rguha return new Iterable() {
20:37 rguha public Iterator iterator() {
20:37 rguha return isotopesList().iterator();
20:37 rguha }
20:37 rguha };
20:37 rguha }
20:38 egonw sounds fine
20:38 egonw won't work for Bond
20:38 rguha btw, do we need to strictly do 1a and 2 separately?
20:38 egonw which uses IAtom[] internally
20:38 matt_s exactly. If the anonymous class doesn't make sense, I'm open to other suggestions. I tend to think this way because I do a lot of .net programming
20:38 rguha I would like to commit code that compiles and to do that I'll have to usages as well
20:39 egonw rguha: OK
20:39 egonw I'm on Bond.java then
20:39 rguha I'd say where we can use anon classes we do so, where we cant, we just make a private
20:39 rguha simpler code
20:39 egonw fine
20:39 egonw we'll check the full patch later anyway...
20:41 CIA-34 cdk: rajarshi * r11880 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (debug/DebugAdductFormula.java formula/AdductFormula.java): Updated code to implement Iterable and usages appropriately
20:41 egonw rguha: actually...
20:42 egonw the patch for Bond.java is really trivial...
20:42 egonw the internal classes can be re-used as they are...
20:42 egonw only the atoms() method had to change:
20:42 egonw -    public Iterator<IAtom> atoms() {
20:42 egonw -        return new AtomsIterator();
20:42 egonw +    public Iterable<IAtom> atoms() {
20:42 egonw +        return new Iterable<IAtom>() {
20:42 egonw +               public Iterator<IAtom> iterator() {
20:42 egonw +                       return new AtomsIterator();
20:42 egonw +               }
20:42 egonw +        };
20:42 egonw }
20:43 rguha excellent
20:43 rguha I'm working on all the implelenting classes of IAtom
20:43 egonw ok
20:44 rguha duh! there's no iterables in there
20:44 CIA-34 cdk: egonw * r11881 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (Bond.java debug/DebugBond.java): Synched with IBond API for Iterable changes
20:45 egonw I'm on ReactionSet
20:48 CIA-34 cdk: egonw * r11882 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (3 files in 3 dirs): Synched with IReactionSet API for Iterable changes
20:49 egonw rguha: which class are you doing now
20:49 egonw ?
20:49 egonw I'll do RingSet
20:49 egonw was thinking about MoleculeSet
20:49 egonw no, not RingSet
20:50 egonw Reaction
20:50 rguha AtomContainer - basically classes implementing IAtomContainer
20:51 egonw right
20:51 egonw which includes RingSet
20:51 rguha no, just Ring
20:52 egonw ok, then I'll of AtomContainerSet next
20:52 rguha ok
20:54 CIA-34 cdk: egonw * r11883 /cdk/branches/mesprague-iterators/src/m​ain/org/openscience/cdk/Reaction.java: Synched with IReaction API for Iterable changes
20:57 CIA-34 cdk: egonw * r11884 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (AtomContainerSet.java debug/DebugAtomContainerSet.java): Synched with IAtomContainerSet API for Iterable changes
21:02 CIA-34 cdk: egonw * r11885 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (MoleculeSet.java debug/DebugMoleculeSet.java): Synched with IAtomContainerSet API for Iterable changes
21:03 CIA-34 cdk: rajarshi * r11886 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (13 files in 2 dirs): Updated code to implement Iterable and usages appropriately
21:03 rguha OK, all implementing classes of IAtomContainer updated.
21:03 egonw excellent
21:04 rguha did you do all implementers of IBond?
21:04 egonw think so
21:04 egonw did I miss anything?
21:04 rguha I didn't check
21:04 egonw ok, I think I got all IAtomContainerSet bits too
21:04 egonw I'll update SVN
21:04 rguha ok
21:04 rguha i'll move onto IChemFile
21:04 egonw and let's see where we are
21:04 CIA-34 cdk: egonw * r11887 /cdk/branches/mesprague-iterators/src/​main/org/openscience/cdk/RingSet.java: Synched with IAtomContainerSet API for Iterable changes
21:05 egonw ok
21:06 egonw I'm on REactionSchem
21:07 CIA-34 cdk: rajarshi * r11888 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (ChemFile.java debug/DebugChemFile.java): Updated code to implement Iterable and usages appropriately
21:07 rguha ok, now on IMapping
21:08 egonw ok, FragmentAtom is for me then
21:08 CIA-34 cdk: egonw * r11889 /cdk/branches/mesprague-iterators/src/main​/org/openscience/cdk/ReactionScheme.java: Updated ReactionScheme for Iterator -> Iterable
21:08 egonw oh, and I *really* like the new syntax :)
21:09 CIA-34 cdk: rajarshi * r11890 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (Mapping.java debug/DebugMapping.java): Updated code to implement Iterable and usages appropriately
21:09 rguha now on IChemSequence
21:11 rguha indeed - and maybe one day we'll get closures :)
21:11 CIA-34 cdk: rajarshi * r11891 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (ChemSequence.java debug/DebugChemSequence.java): Updated code to implement Iterable and usages appropriately
21:11 rguha now on IMlecularFormula
21:11 egonw what was a closure again?
21:12 rguha anonymous function that can maintain state
21:12 rguha like generators in Python
21:12 egonw oh... that sounds ... umm...
21:12 rguha very good for iterating over infinite collections :)
21:12 rguha (or very large)
21:12 rguha how far are you up from the bottom?
21:13 egonw FragmentAtom
21:13 CIA-34 cdk: egonw * r11892 /cdk/branches/mesprague-iterators/src/mai​n/org/openscience/cdk/FragmentAtom.java: Updated FragmentAtom for Iterator -> Iterable
21:14 egonw infinite collections... that sounds like Petabyte QSAR data sets :)
21:14 egonw hahahaha
21:14 rguha :) or structure generation
21:15 egonw are all interface implementations updated now?
21:15 rguha I think so
21:15 egonw I still have one error on DebugmolceualrFormula
21:15 rguha running a compile to see what happens
21:16 egonw ok, bit of nasty stuff in there...
21:16 egonw on it...
21:16 rguha it's clean here
21:16 egonw results from a Map.keySet being returned
21:16 egonw sure?
21:16 rguha which function?
21:16 egonw did you commit all
21:16 egonw ?
21:16 rguha yes
21:16 egonw just reverted and doing another svn up
21:17 rguha i don't see any usage of Map in DebugMolecularFormula
21:17 egonw no, but in MolecularFormula there is
21:17 egonw did you touch that yet?
21:17 egonw if not, I'll fix it
21:18 rguha I think so
21:18 egonw don't see it in the 'svn log'
21:18 rguha hmm, there was no Iterable in there maybe
21:18 rguha I see the problem
21:18 rguha you can go ahead and fix it
21:18 egonw ok
21:19 rguha now the gargantuan task of updating usage :(
21:22 matt_s if you don't get to everything, I can do some of the update later tonight when I'm not up to my elbows in chromate solutions.
21:22 CIA-34 cdk: egonw * r11893 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (2 files in 2 dirs): Synched with IMolecularFormula API for Iterable changes
21:22 rguha sure, thanks
21:22 rguha i think it'll be a good idea to split up the work by modules
21:23 egonw ok, all data, datadebug, nonotify is clean for me now
21:23 egonw I'll try to run the unit tests for those three modules
21:23 matt_s email me the list of modules you want me to do.
21:24 rguha i'll cover the qsar modules
21:24 egonw I currently count 509 required updates
21:24 egonw fixes
21:24 egonw not bad...
21:25 egonw I've had literally thousands in past API changes :)
21:25 egonw rguha: let's update test-data, test-datadebug and test-nonotify first
21:26 egonw so that I can run the unit tests...
21:26 rguha aah ok
21:26 rguha hold on I just edited a number of test stuff
21:26 rguha let me do the committ
21:26 egonw ok
21:27 CIA-34 cdk: rajarshi * r11894 /cdk/branches/mesprague-iterators/src/ (4 files in 2 dirs): Updated usages of Iterator to use Iterable
21:27 rguha done
21:28 rguha I'll do test-nonotify
21:28 egonw ack
21:29 egonw most of test-datadebug and test-nonotify reuses tests from test-data
21:29 egonw btw, I'm just adding ".iterator()" right now
21:30 rguha clean
21:31 egonw no commit?
21:31 egonw it was already clean?
21:31 CIA-34 cdk: egonw * r11895 /cdk/branches/mesprague-iterator​s/src/test/org/openscience/cdk/ (7 files): Added missing .iterator()'s
21:32 rguha yes
21:32 egonw test results for test-data
21:32 egonw 11 errors, 1 fail
21:32 rguha hmm
21:33 rguha are you taking that one then?
21:33 egonw yes, looking into these 12
21:33 rguha ok
21:34 rguha test-datadebug is clean
21:35 egonw ok, one problem left
21:35 egonw but a nasty one
21:36 egonw NPE in this line:
21:36 egonw (middle one of:
21:36 egonw )
21:36 rguha which class?
21:36 egonw for (IAtomContainer container : atomContainers) {
21:36 egonw clone.addAtomContainer((IAtom​Container)container.clone());
21:36 egonw }
21:36 egonw RingSet
21:36 rguha hmm
21:37 egonw I'll commit the test fixes
21:39 CIA-34 cdk: egonw * r11896 /cdk/branches/mesprague-iterators/src/ (5 files in 3 dirs): Fixes for the Iterator -> Iterable changes
21:39 rguha any idea where the npe is from?
21:39 egonw no, not yet
21:39 rguha I can't see how it's related to Iterables
21:40 egonw I'll check the commit I made to the RingSet.clone() method to update it for Iterable...
21:40 rguha ok
21:42 egonw -               java.util.Iterator result = atomContainers();
21:42 egonw -               while (result.hasNext()) {
21:42 egonw -                       clone.addAtomContainer((IAtomContainer) ((IAtomContainer)result.next()).clone());
21:42 egonw +               for (IAtomContainer container : atomContainers) {
21:42 egonw +                       clone.addAtomContainer((IAtom​Container)container.clone());
21:43 egonw ok, there is a bug in the code I added:
21:43 egonw it should have said:
21:43 rguha aah right
21:43 egonw for (IAtomContainer container : atomContainers()) {
21:44 egonw nasty one... easy to overlook
21:44 egonw no idea that one could do this on bla[] too :)
21:44 egonw ok, that fixes that one too
21:45 egonw ok, onto running test-datadebug
21:45 CIA-34 cdk: egonw * r11897 /cdk/branches/mesprague-iterators/src/​main/org/openscience/cdk/RingSet.java: Iterate over atomContainers() not over the array; fixes the clone NPE
21:45 egonw ok, 100% success
21:45 egonw same for nonotify
21:45 egonw ok, I count 473 compile fixes left...
21:46 egonw rguha: by module, or by package?
21:46 rguha by package is easier to track
21:46 egonw latter is easier in Eclipse
21:46 egonw right
21:46 egonw I'll start from the bottom again
21:46 rguha I'm doing qsar.* right now
21:46 egonw and add .iterator() only
21:46 egonw ok
21:46 rguha right
21:46 egonw you're doing src/main, correct?
21:46 egonw then I'll actually continue with src/test
21:46 egonw ok?
21:48 rguha ok
21:48 rguha (though I did update a few from src/test)
21:49 egonw commited ?
21:49 egonw if not, please do
21:52 rguha yes, just committed
21:53 CIA-34 cdk: rajarshi * r11898 /cdk/branches/mesprague-iterators/​src/main/org/openscience/cdk/qsar/ (26 files in 5 dirs): Updated usages of Iterator to use Iterable
21:56 CIA-34 cdk: rajarshi * r11899 /cdk/branches/mesprague-iterators/src/m​ain/org/openscience/cdk/pharmacophore/ (PharmacophoreMatcher.java PharmacophoreUtils.java): Updated usages of Iterator to use Iterable
21:58 CIA-34 cdk: rajarshi * r11900 /cdk/branches/mesprague-iterators/src/main​/org/openscience/cdk/modeling/forcefield/ (BondStretching.java Torsions.java): Updated usages of Iterator to use Iterable
22:00 CIA-34 cdk: rajarshi * r11901 /cdk/branches/mesprague-iterators/src/mai​n/org/openscience/cdk/modeling/builder3d/ (AtomPlacer3D.java ForceFieldConfigurator.java): Updated usages of Iterator to use Iterable
22:02 egonw ok, committing all fixes for src/test
22:02 rguha ok
22:04 CIA-34 cdk: egonw * r11902 /cdk/branches/mesprague-iterator​s/src/test/org/openscience/cdk/ (63 files in 20 dirs): Updated for Iterator -> Iterable
22:05 egonw 326 errors left
22:05 egonw I got some 5 minutes left, before I have to do
22:05 rguha i'll be of soon
22:05 egonw I'm on cdk.io.*
22:05 rguha I've done packages that start with m,p,q in src/main
22:06 CIA-34 cdk: rajarshi * r11903 /cdk/branches/mesprague-iterators/src/ (2 files in 2 dirs): Updated usages of Iterator to use Iterable
22:09 CIA-34 cdk: egonw * r11904 /cdk/branches/mesprague-iterators​/src/main/org/openscience/cdk/io/ (15 files in 4 dirs): Updated cdk.io.* for Iterator -> Iterable
22:09 CIA-34 cdk: rajarshi * r11905 /cdk/branches/mesprague-iterators/s​rc/main/org/openscience/cdk/graph/ (8 files in 3 dirs): Updated usages of Iterator to use Iterable
22:09 CIA-34 cdk: egonw * r11906 /cdk/branches/mesprague-iterators/src/m​ain/org/openscience/cdk/isomorphism/mat​chers/QueryAtomContainerCreator.java: Updated cdk.isomorphism for Iterator -> Iterable
22:11 CIA-34 cdk: egonw * r11907 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (3 files in 2 dirs): Updated cdk.layout and cdk.iupac.parser for Iterator -> Iterable
22:14 CIA-34 cdk: egonw * r11908 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (3 files in 2 dirs): Updated cdk.libio and cdk.render for Iterator -> Iterable
22:15 egonw I think we're almost done
22:15 egonw well, still 260 left :)
22:16 rguha latest commit should clean up a good chunk
22:16 rguha can you do an updte and see how many are left
22:16 CIA-34 cdk: rajarshi * r11909 /cdk/branches/mesprague-iterators/src/mai​n/org/openscience/cdk/tools/manipulator/ (9 files): Updated usages of Iterator to use Iterable
22:17 egonw mom
22:18 egonw 202 left
22:18 CIA-34 cdk: egonw * r11910 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (2 files in 2 dirs): Updated cdk.controller cdk.geometry.GTools for Iterator -> Iterable
22:19 egonw cdk.reaction -> 69
22:19 CIA-34 cdk: egonw * r11911 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (4 files in 3 dirs): A few more updates for Iterator -> Iterable
22:20 egonw cdk.tools -> 61
22:20 CIA-34 cdk: rajarshi * r11912 /cdk/branches/mesprague-iterators/src​/main/org/openscience/cdk/tools/manip​ulator/ReactionSetManipulator.java: Updated usages of Iterator to use Iterable
22:20 egonw you tools, I reaction?
22:20 rguha ok
22:24 CIA-34 cdk: rajarshi * r11913 /cdk/branches/mesprague-iterators/src​/main/org/openscience/cdk/tools/manip​ulator/ReactionSetManipulator.java: yet more Updated usages of Iterator to use Iterable
22:27 egonw will update and count
22:28 egonw many cdk.reaction files in the commit...
22:28 CIA-34 cdk: egonw * r11914 /cdk/branches/mesprague-iterators/src/m​ain/org/openscience/cdk/reaction/type/ (33 files): Updated cdk.reaction for Iterator -> Iterable
22:28 egonw 113
22:29 egonw cdk.aromaticity
22:29 egonw cdk. charges
22:30 egonw cdk.formula
22:31 CIA-34 cdk: egonw * r11915 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (8 files in 2 dirs): Updated cdk.aromaticty and cdk.charges for Iterator -> Iterable
22:31 egonw cdk.inchi
22:32 egonw .ringsearch
22:32 egonw ok, got to go now
22:32 egonw should be around 95 left
22:33 egonw 79
22:33 CIA-34 cdk: egonw * r11916 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (5 files in 4 dirs): Updated cdk.inchi and cdk.ringsearch for Iterator -> Iterable
22:34 egonw .validate + .templates
22:34 egonw 69 left
22:34 egonw cu tomorrow
22:34 CIA-34 cdk: egonw * r11917 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (3 files in 2 dirs): Updated cdk.templates and cdk.validate for Iterator -> Iterable
22:35 egonw matt_s, rguha: it's really all just add ".iterator()"
22:35 egonw bye for now
22:35 rguha right
22:35 rguha bye
22:36 matt_s I'm going home. You guys have all the fun.
22:37 CIA-34 cdk: rajarshi * r11918 /cdk/branches/mesprague-iterators/s​rc/main/org/openscience/cdk/tools/ (8 files): yet more Updated usages of Iterator to use Iterable
22:40 rpohl66 joined #cdk
22:41 CIA-34 cdk: rajarshi * r11919 /cdk/branches/mesprague-iterators/src/​main/org/openscience/cdk/tools/manipul​ator/ReactionSchemeManipulator.java: Fixed a few missing conversions from Iterator to Iterable
22:43 CIA-34 cdk: rajarshi * r11920 /cdk/branches/mesprague-iterators/sr​c/main/org/openscience/cdk/tools/man​ipulator/ReactionManipulator.java: Fixed a few missing conversions from Iterator to Iterable
22:49 CIA-34 cdk: rajarshi * r11921 /cdk/branches/mesprague-iterators/src/mai​n/org/openscience/cdk/tools/manipulator/ (4 files): Updated missing usages of Iterator to Iterable
22:54 rpohl66 using latest cdk/trunk and jchem/trunk - when i bring up the test editor it seems that the display is highly zoomed in - only see black and white blobs - any suggestions?

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