Camelia, the Perl 6 bug

IRC log for #cdk, 2008-05-05

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
04:22 CIA-30 cdk: rajarshi * r10806 /cdk/trunk/src/ (2 files in 2 dirs): Added a test case to highlight estate atom typing from SMILES string
04:31 CIA-30 cdk: rajarshi * r10807 /cdk/trunk/src/test/org/openscienc​e/cdk/qsar/descriptors/molecular/M​omentOfInertiaDescriptorTest.java: Added a test case to catch absence of 3D coordinates
04:53 CIA-30 cdk: rajarshi * r10808 /cdk/trunk/src/test/org/openscience/cdk/aromat​icity/CDKHueckelAromaticityDetectorTest.java: Added a test for bug 1957684
04:54 CIA-30 cdk: rajarshi * r10809 /cdk/trunk/src/test/org/openscience/cdk/aromat​icity/CDKHueckelAromaticityDetectorTest.java: Added the actual assertion!
05:17 egonw joined #cdk
05:59 jbrefort joined #cdk
06:51 rojasm joined #cdk
07:01 CIA-30 cdk: miguelrojasch * r10810 /cdk/branches/miguelrojasch-CMLReact/src/main/o​rg/openscience/cdk/reaction/ReactionCycle.java: elimination ReactionCycle which doesn't make the correct function yet.
07:04 jpansanel moin
07:05 rojasm moin
07:15 egonw joined #cdk
07:16 CIA-30 cdk: miguelrojasch * r10811 /cdk/branches/miguelrojasch-CMLReact/src​/test/org/openscience/cdk/tools/manipula​tor/ReactionSchemeManipulatorTest.java: added missing tests
07:18 thomas_ku joined #cdk
07:19 CIA-30 cdk: miguelrojasch * r10812 /cdk/branches/miguelrojasch-charges/src/test/org/​openscience/cdk/modulesuites/MreactionTests.java: added ReactionEngine to modulesuites
07:25 thomas_ku moin
07:27 rojasm moin thomas_ku
07:36 egonw rojasm: did you get my replies on the branch posts?
07:36 egonw well, for one of them, actually
07:56 rojasm yes
07:56 rojasm I am working now with him
08:04 CIA-30 cdk: miguelrojasch * r10813 /cdk/branches/miguelrojasch-CMLRe​act/src/test/org/openscience/cdk/ (3 files in 2 dirs): added miss ReactionChainTest
08:14 thomas_ku egonw: around?
08:22 masak joined #cdk
08:24 jonalv joined #cdk
08:34 masak joined #cdk
08:37 egonw thomas_ku: yes, I am now
08:38 thomas_ku egonw: if I want to do some qsar calculation and I load the molecules from an sdf file, do I need to do an atom type perception or is it done automatically?
08:39 egonw no, this is not done automatically...
08:39 egonw are you using the DescriptorEngine?
08:39 egonw a separate worker would be good, actually...
08:39 egonw wanted to do that for a while...
08:39 egonw IMolecule(s) in, and two outputs...
08:40 egonw one IMolecule(s) for molecules with all atom types recognized
08:40 thomas_ku I use the qsar classes directly!
08:40 egonw one IMolecule(s) for molecules with at least one atom type *not* recognized
08:40 egonw thomas_ku: indeed, I now remember...
08:40 thomas_ku So i will get wrong results if I do not atomtype perception before I calculate qsar descriptors?
08:41 egonw bit sure abaut that...
08:41 egonw about
08:42 thomas_ku bit sure? so you don'T now? or what does this mean?
08:43 egonw haha...
08:43 egonw bit->not
08:43 thomas_ku ok
08:43 egonw sorry... had a shift in hand positions...
08:43 thomas_ku no problem...
08:43 egonw thomas_ku: there is not such atom typer worker yet, right?
08:44 thomas_ku no up to now not! But I will than build one
08:44 thomas_ku and I have to check wether all my calculated results are wrong...
08:44 thomas_ku because I allready started the calculation of qsar descriptor for 185000 molecules...
08:44 egonw ok, make sure to:
08:45 egonw do aromaticity detection
08:45 egonw for which you need atom type detection
08:45 egonw make sure to have 3D coorindates
08:45 egonw and explicit hydrogens
08:45 egonw anyway... nice test for the T2 enactment engine :)
08:46 thomas_ku I will ran these things on the old encatment...
08:46 egonw make sure to make a screenshot when it is working on it... with partial completion of workers :)
08:46 thomas_ku this is not spectaculas because I use nested worker and than you will not see much....
08:47 egonw oh... :(
08:47 rojasm egonw: Sorry for that I will make now
08:47 egonw thomas_ku: may I request a release after you made the atom type perception node?
08:48 egonw I haven't had time to get the build system for the update site to work here properly...
08:48 thomas_ku ok but not this week because I will fly to christoph on thursday...
08:48 egonw but love to start using CDK-Taverna for some of my work...
08:49 egonw it's a shame really...
08:49 egonw the fact that you cannot push a button to make a release
08:49 thomas_ku yes i now....
08:49 egonw thomas_ku: you don't do developers snapshot updates, do you?
08:49 thomas_ku currently not....
08:51 CIA-30 cdk: miguelrojasch * r10814 /cdk/branches/miguelrojasch-CMLReact/src/ (4 files in 2 dirs): added missed test in REactionManipulator and ReactionSetMAnipulator to do happy TESTCASE function
08:52 rojasm egonw: with the command ant -lib develjar/junit-4.3.1..jar -logfile ant.log test-all
08:52 rojasm the reports will be not create
08:52 egonw how so?
08:52 egonw what error do you get?
08:52 rojasm I need to do only ant -lib develjar/junit-4.3.1..jar test-all
08:52 rojasm for the first creates the ant.log file
08:53 egonw no, the '-logfile ant.log' is important
08:53 egonw yes, it should indeed
08:53 rojasm but not the directory
08:53 egonw it will also create the directory
08:53 rojasm reporst/*.txt
08:53 rojasm mmm
08:53 egonw because the -logfile will only copy what was normally sent to STDOUT to the log file
08:53 rojasm I supposed too
08:53 rojasm I tried again
08:54 rojasm and maybe we can today merge finally both branches :(
08:59 egonw let's see...
08:59 rojasm I will make again a merging between trunk to branch
08:59 egonw I still need to browse the patch...
09:08 thomas_ku egonw: the atomtype perceptor throws an execption if it couldn't detect an atomtype?
09:09 egonw no, it should return a null..
09:09 egonw I suggest to write a local iteration of the atoms
09:09 egonw and check if the method returns a null
09:10 egonw findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
09:10 egonw will update the JavaDoc to make this clear
09:11 thomas_ku do I have to set the atom type after this method call to the atom or is this done within the perception?
09:11 egonw no, it is not set...
09:11 egonw well, good point...
09:11 egonw so, you would run it over all atoms
09:12 egonw and configure the atom if not null
09:12 egonw no, better not configuer...
09:12 egonw just use the IAtom's setAtomTypeName()
09:15 rojasm rojasm ping
09:15 egonw rojasm: wondering if you're still awake? :)
09:16 rojasm I am
09:16 rojasm I was a moment out side
09:16 rojasm to test how far is ma wiffi
09:17 rojasm you are right
09:17 rojasm It was a mistake from me
09:17 rojasm like always
09:17 rojasm I submit the differences
09:18 CIA-30 cdk: thomaskuhn * r10815 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/database/p​gchem/IterativeMoleculeFromDBReader.java: Remove some old code
09:18 rojasm egown but Should I do a merge between trunk to branch again
09:18 rojasm first
09:19 egonw yes, if you want to report updated bug count differences
09:19 CIA-30 cdk: thomaskuhn * r10816 /cdk-taverna/trunk/src/main/java/org​/openscience/cdk/applications/tavern​a/atomtype/AtomTypePerceptor.java: Add an atom type perceptor worker
09:20 thomas_ku egonw: just commited a first version could you please have a short look on it?
09:20 thomas_ku I do not have set up a test for it up to now
09:21 * egonw is updating from SVN
09:21 thomas_ku egonw: do I have to use the CDKHueckelAromaticityDetector to detect the aromaticity?
09:22 egonw yes
09:22 thomas_ku ok thanks
09:23 egonw thomas_ku: check the source of the file...
09:23 egonw do you note that $Revision$ is not filled out?
09:23 egonw you'll have to set the svn:keywords...
09:23 egonw I'll do a commit to fix for that
09:24 egonw thomas_ku: "Percepted" -> "Perceived"
09:24 thomas_ku I'll use subclipse how do I use the svn:keywords?
09:24 thomas_ku oh thanks
09:24 egonw no idea
09:25 egonw but I'll do it :0
09:25 egonw :0 -> :)
09:26 egonw using throw new CDKException() to put something in notAll is a bit dirty...
09:26 egonw but don't see problems otherwise...
09:26 egonw actually I do...
09:27 egonw you should atom type atoms *after* the not-perceived element too...
09:27 egonw hang on...
09:27 egonw I'll code up something
09:27 thomas_ku thanks
09:33 egonw thomas_ku: you develop in Eclipse too?
09:33 egonw it does not pick up the CDK classes here...
09:33 thomas_ku yes...
09:34 thomas_ku ah why?
09:34 egonw no idea
09:34 egonw it does not seem to expect a cdk-all.jar or so...
09:34 thomas_ku ah I fear I no...
09:34 egonw does it depend on a cdk project?
09:35 thomas_ku or
09:35 thomas_ku do you have the maven plugin installed?
09:35 egonw no
09:35 egonw was giving to much trouble
09:35 thomas_ku thats the problem...
09:35 egonw ok
09:36 thomas_ku than you could just try to add the cdk trunk to the project just for now!
09:36 thomas_ku but you will not be able to test and compile things than I fear...
09:49 CIA-30 cdk: egonw * r10817 /cdk-taverna/trunk/src/main/java/org​/openscience/cdk/applications/tavern​a/atomtype/AtomTypePerceptor.java: Do not stop perception after the first NULL
09:50 egonw please verify if it correctly compiled
09:50 egonw s/d/s/
09:52 thomas_ku ok will check
09:52 thomas_ku thanks anyway!!
09:53 thomas_ku looks good!
09:53 thomas_ku thanks
10:36 CIA-30 cdk: miguelrojasch * r10818 /cdk/branches/miguelrojasch-CMLReact/ (633 files in 99 dirs): Merged the branch.miguelrojasch-CMLReact from cdk.trunk, rev:10813
10:41 * egonw is making a mirror of his WIN partition using Linux
10:41 egonw just in case WIN dirties itself again, making it unbootable again
10:58 rojasm joined #cdk
10:58 CIA-30 cdk: egonw * r10819 /cdk-taverna/trunk/src/ (334 files in 55 dirs): Fixed svn:keywords
11:01 thomas_ku thanks egon!!
11:02 thomas_ku egonw: so what do I need to do if I want to commit a change? do I need to change something than?
11:03 egonw no, automagically done
11:03 egonw that's what that svn:keywords property is for
11:03 thomas_ku you are the best
11:03 thomas_ku I have to update....
11:10 thomas_ku egonw: ok but how do I use the svn keywords within eclipse? with subclipse? do I have to do something special?or did you changed something that it will work automatically now?
11:10 egonw you do not have to do anything...
11:11 egonw it will automatically updated those Revision, Author etc info when you commit
12:04 CIA-30 joined #cdk
12:12 egonw rojasm: ping...
12:12 egonw rojasm: is there anything I can do regarding clean up of code, e.g. 1: move Manipulators to cdk.tools.manipulator, 2. move IReactionScheme to cdk.interface, 3. ... you name it...
12:13 egonw 4. IP clean up: split algorithms from QSAR wrappers...
12:13 egonw 5. proofread papers
12:14 egonw it's only two months before the end of my current postdoc year... 6 weeks for you, Miguel :)
12:14 egonw time flies
12:25 rojasm joined #cdk
12:35 CIA-31 joined #cdk
12:41 rojasm egonw around?
12:42 egonw yes
12:42 rojasm could you help me, please. because I can not find what I doing wrong
12:43 rojasm This message I didn't see :(
12:44 rojasm I know :(
12:44 rojasm I am working with that :( not fast How I expected
12:45 rojasm but I want today finish today with the emerging
12:46 egonw rojasm: boot skype
13:05 CIA-31 cdk: miguelrojasch * r10822 /cdk/branches/miguelrojasch-CMLReact/s​rc/test/org/openscience/cdk/reaction/ (12 files in 2 dirs): remove abstract from class test
13:14 rojasm as soon as the test-all is finish a mail to the devel-list
13:14 egonw ok, excelletn
13:38 rojasm joined #cdk
13:44 CIA-31 bioclipse: ospjuth * r5544 /bioclipse2/trunk/plugins/net.bioclipse​.biomoby.tests/src/net/bioclipse/biomob​y/tests/services/TestDropActions.java: Adapted drop test to use new ServiceManagerHelper.
13:45 steinbeck joined #cdk
13:55 rojasm egonw: sent the email to devel-list
13:56 egonw rojasm: thanx
14:05 rojasm egonw: with D-moduel=reaction test-module should it create the cdk-reaction.txt report too
14:05 CIA-31 cdk: rajarshi * r10823 /cdk/trunk/src/test/org/openscience/cdk/ (2 files in 2 dirs): Added bug id to the unit tests. Also replaced the molecule in the aromaticity with CDK source code rather than SMILES parsing. The aromaticity bug is fixed when CDK source format is used
14:06 egonw yes
14:13 CIA-31 cdk: rajarshi * r10824 /cdk/trunk/src/test/org/openscience/cdk/aromat​icity/CDKHueckelAromaticityDetectorTest.java: Made the test a little more thoroigh
14:13 CIA-31 cdk: miguelrojasch * r10825 /cdk/branches/miguelrojasch-CMLRe​act/src/test/org/openscience/cdk/ (3 files in 2 dirs): changed name spelling which was incorrect
14:17 egonw rojasm: do I understand correctly that your branch introduces new fails?
14:18 rojasm yes
14:18 rojasm it does
14:19 egonw +Testcase: testNPEWithBridgedRingsBug1772609(org.openscie​nce.cdk.layout.StructureDiagramGeneratorTest)
14:19 egonw that one is weird...
14:19 egonw any idea why that is happening?
14:19 egonw +Testcase: testMDMoleculeCustomizationRoundtripping(or​g.openscience.cdk.libio.md.MDMoleculeTest)
14:19 egonw or that one?
14:19 CIA-31 cdk: miguelrojasch * r10826 /cdk/branches/miguelrojasch-CMLReact/src/test/org/​openscience/cdk/modulesuites/MreactionTests.java: added the mechanisms test in the MreactionTests file
14:20 rojasm I do again
14:20 rojasm maybe I did a mistake somewhere
14:20 egonw I'm running test-all for trunk and your branch too
14:20 rojasm ok thanks
14:22 CIA-31 cdk: rajarshi * r10827 /cdk/trunk/src/test/org/openscience​/cdk/smiles/SmilesParserTest.java: Added a test for bug 1957958 in which a substituted pyridine parses OK and has identifiable atom types, but aromaticity detection indicates that the molecule is non-aromatic which is wrong
14:23 CIA-31 cdk: rajarshi * r10828 /cdk/trunk/src/test/org/openscience/cdk/ (3 files in 3 dirs): Fixed cdk.bug tags
14:26 rojasm if I want to create again but only a determined test-....jar, is it some command for that
14:26 rojasm because the -Dmodule if I understood correctly only is for running the test which are already packed in the .jar
14:27 rojasm isnt it?
14:27 egonw right
14:27 CIA-31 bioclipse: jonalv * r5545 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): Refactoring of HSQLDB-connecting. Now uses jdbc:hsqldb:file protocol instead of instantiating a server on my own.
14:27 egonw rm dist/jar/cdk-reaction.jar
14:27 egonw ant -Dmodule=reaction compile-module
14:27 egonw ummm
14:27 egonw you need to add an additional option there...
14:27 rojasm perfect thanks again
14:27 rojasm the lib junit?
14:28 egonw ant -Dsource=main -Dmodule=reaction compile-module
14:28 egonw and the test-reaction:
14:28 egonw ant -Dsource=test -Dmodule=test-reaction compile-module
14:38 egonw $ diff -u trunk.results branch.results | grep "^+" | grep -v "IP"
14:38 egonw +++ branch.results      2008-05-05 16:37:58.000000000 +0200
14:38 egonw +Testcase: test3Amino2MethylPyridine(org.openscience.cdk.​aromaticity.CDKHueckelAromaticityDetectorTest)
14:38 egonw +Testcase: testCoverage(org.openscienc​e.cdk.FormulaCoverageTest)
14:38 egonw +Testcase: testMDMoleculeCustomizationRoundtripping(or​g.openscience.cdk.libio.md.MDMoleculeTest)
14:39 egonw first one is because rajarshi fixed that after your last merge of trunk to branch
14:40 egonw second one: missing unit tests:
14:40 egonw MolecularFormulaManipulator: missing the expected test method: testGetString_IMolecularFormula_arrayString
14:40 egonw MolecularFormulaManipulator: missing the expected test method: testPutInOrder_arrayString_IMolecularFormula
14:40 egonw MolecularFormulaManipulator: missing the expected test method: testGetHillString_IMolecularFormula
14:40 egonw MolecularFormulaManipulator: missing the expected test method: testGenerateOrderEle
14:40 egonw rojasm: please add those
14:40 egonw last one seems to be a missing dep
14:41 egonw rojasm: please add cdk-formula.jar to META-INF/libiomd.cdkdepends
14:41 CIA-31 bioclipse: jonalv * r5546 /bioclipse2/trunk/plugins/net.bioclipse.hsql​db/src/net/bioclipse/hsqldb/HsqldbUtil.java: removed "file:" from path to database file
14:41 egonw the rest is IP stuff...
14:41 egonw which I do not care about at this moment...
14:41 egonw that's for the next step
14:42 rojasm ok
14:46 CIA-31 cdk: rajarshi * r10829 /cdk/trunk/src/test/org/openscience​/cdk/smiles/SmilesParserTest.java: Added explicit atom typing
14:54 CIA-31 cdk: miguelrojasch * r10830 /cdk/branches/miguelrojasch-CMLReact/​src/test/org/openscience/cdk/formula/​MolecularFormulaManipulatorTest.java: added missed test for MolecularFormulaManipulatorTest
14:55 CIA-31 cdk: miguelrojasch * r10831 /cdk/branches/miguelrojasch-CMLReact/src/test/org/​openscience/cdk/modulesuites/MreactionTests.java: added the reaction ElectronImpactSBEReactionTest in MreactionTest which was missed
14:57 CIA-31 cdk: miguelrojasch * r10832 /cdk/branches/miguelrojasch-CMLReac​t/src/META-INF/libiomd.cdkdepends: added cdk-formula.jar to cdkdepends for libiomd
14:58 rojasm done I try again to see the differences
15:14 CIA-31 cdk: miguelrojasch * r10833 /cdk/branches/miguelrojasch-CMLReact/src/ (4 files in 3 dirs): rename test ElectronImpactSDBReactionTest
15:19 egonw rojasm: the cdk-formula depends has to go into the test-libiomd.cdkdepends
15:30 CIA-31 bioclipse: ospjuth * r5547 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (.classpath .settings/ META-INF/MANIFEST.MF): Removed J2SE-1.5 requirement as that messes up things on Mac.
15:31 rojasm I put already, isn't it?
15:31 rojasm :(
15:31 rojasm oh no
15:32 egonw no, you put it in libiomd.cdkdepends instead...
15:32 rojasm oooo
15:32 rojasm sorry
15:32 rojasm I will change now
15:34 CIA-31 cdk: miguelrojasch * r10834 /cdk/branches/miguelrojasch-CMLReact/src/META-INF/ (libiomd.cdkdepends test-libiomd.cdkdepends): added cdk-formula.jar to cdkdepends for test-libiomd and removed it from libiomd
15:34 egonw ok, got to go home now
15:34 egonw already later than planned...
15:34 egonw bye all... stupid ASN reading thingy... :(
15:34 egonw bloddy itches
15:35 rojasm mmm! do you think after that I can commit them
15:35 rojasm one to one for trunk
15:35 rojasm Or you want to check again
15:35 egonw rojasm: please make a diff like:
15:36 egonw svn diff https://cdk.svn.sf.net/bla/trunk https://cdk.svn.sf.net/bla/br​anches/miguelrojasch-CMLReact
15:36 egonw and put that somewhere up for download...
15:36 egonw maybe as patch on SF
15:36 egonw I will look at it tonite then...
15:36 rojasm ok!
15:37 rojasm I will do it then
16:10 CIA-31 bioclipse: jonalv * r5548 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Switched to using ICDKMolecule instead IMolecule. It better represents the abstraction level we are at.
16:49 CIA-31 bioclipse: ospjuth * r5549 /bioclipse2/trunk/plugins/net.bi​oclipse.structuredb.tests/tests/ (4 files in 2 dirs): Added 2 CML files to replace Mol files as parsing of MOLfiles seems broken in CDKManager. Updated Test for these files.
17:01 carsten joined #cdk
17:24 CIA-31 bioclipse: jonalv * r5550 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Work on importing sdf files into the structuredb. It doesn't quite work yet
17:29 thomas_ku joined #cdk
17:38 CIA-31 bioclipse: jonalv * r5551 /bioclipse2/trunk/plugins/net.bioclipse.str​ucturedb.tests/tests/net/bioclipse/structur​edb/business/StructuredbManagerTest.java: fixed a few setup things
17:43 dleidert joined #cdk
17:52 CIA-31 cdk: miguelrojasch * r10835 /cdk/branches/miguelrojasch-CMLRe​act/src/test/org/openscience/cdk/ (47 files in 4 dirs): added missed test
18:13 CIA-31 bioclipse: ospjuth * r5552 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Added test for bug 1958097 (MOL-files not detected by CDKManager)
18:15 egonw joined #cdk
18:24 CIA-31 bioclipse: ospjuth * r5553 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added correct MDLFormatV2000 and V3000 to support mol-files (aka MDL-files). Test now passes.
18:24 CIA-31 cdk: miguelrojasch * r10836 /cdk/branches/miguelrojasch-CMLRe​act/src/test/org/openscience/cdk/ (3 files in 3 dirs): Merged the branch.miguelrojasch-CMLReact from cdk.trunk, rev:10835
18:30 rojasm done I am doing the diff
18:31 rojasm but now I dont have errors in formula or reaction
18:37 egonw compiling after update
19:05 rojasm egonw: I did the comparation
19:06 rojasm should I sent you per mail?
19:06 egonw fine
19:18 egonw rojasm: I'd like to see the svn diff
19:18 egonw btween the two branches
19:19 egonw to be precise:
19:19 egonw svn diff https://cdk.svn.sourceforge​.net/svnroot/cdk/cdk/trunk https://cdk.svn.sourceforge.net/svnroot/​cdk/cdk/branches/miguelrojasch-CMLReact
19:19 rojasm yes I sent now
19:23 rojasm egonw I sent the result of your script described in your blog
19:23 egonw yes, but I want a diff showing the code differences
19:23 rojasm the other line you wrote I initiate more of 10 minutes
19:23 rojasm and still is running
19:23 egonw ok
19:31 rojasm sent
19:33 rojasm egonw: what do you think?
19:43 egonw yeah, I'm happy with it
19:44 rojasm :)
19:44 rojasm should I commit one per one
19:45 egonw no, do it in one go
19:45 rojasm oh I like that if it is possible
19:45 egonw patch -n 0 < trunk.branch.diff
19:45 egonw or so...
19:50 rojasm sorry what do you mean with patch -n 0 < trunk.branch.diff. You
19:50 egonw patch -p0
19:51 egonw the -p0 is for removal of some prefixes
19:51 rojasm in trunk directory right?
19:51 egonw yes
19:52 egonw make sure all patches are applied
19:52 rojasm and then do commit
19:52 egonw no nothing is rejected
20:04 rojasm egonw: strange because it says that p is invalid character which in internet is the same example
20:07 egonw what command are you using exactly?
20:08 rojasm ack
20:09 rojasm I was putting behind svn
20:09 rojasm patch -p0 < diff.trunk.branch
20:09 egonw ah :)
20:12 rojasm and now How I check if all patch are done?
20:13 egonw find . -name "*.reject"
20:13 egonw and do a:
20:13 egonw svn diff > trunk.diff
20:13 egonw and then diff the trunk.diff against your trunk.branch.diff
20:14 egonw which should work, I think
20:14 egonw also check your patch for file removals
20:14 egonw which end up as zero sized files in your trunk/ checkout
20:22 rojasm I did:
20:22 rojasm dind . -name ".reject"
20:22 rojasm svn diff > trunk.diff
20:22 rojasm and then
20:23 rojasm diff -u trunk.diff diff.trunk.branch > diff.final
20:24 rojasm sorry again. ! and than I would look for files which are size zeor?
20:24 rojasm zero?
20:27 rojasm Now I see in my eclipse the changes after 2 min
20:30 egonw yes, zero length
20:30 egonw basically indicating removed files
20:30 egonw but not yet svn removed
20:31 rojasm done
20:31 rojasm than I should compare with the new trunk and the branches again if they are completely the same?
20:34 egonw that will only work after you commited...
20:34 egonw btu that would indeed be a good idea
20:35 rojasm ok I do first a test-all
20:35 egonw ok
20:39 egonw_ joined #cdk
20:43 rojasm shit some thing was wrong
20:44 rojasm I miss some commits
20:44 rojasm noo
20:47 rojasm ups false looked
20:48 rojasm egonw can I commit the changes?
20:54 egonw_ yes
20:55 CIA-31 cdk: miguelrojasch * r10837 /cdk/trunk/src/ (100 files in 29 dirs): merging from branches.miguelrojasch-charges to trunk
21:03 egonw rojasm: cheers! one down, one to go :)
21:04 CIA-31 cdk: egonw * r10838 /cdk/trunk/src/test/org/openscience/​cdk/io/PCCompoundASNReaderTest.java: Fixed test file path
21:04 rojasm ok
21:05 rojasm I will finish today for the other branch
21:05 CIA-31 cdk: egonw * r10839 /cdk/trunk/src/test/org/openscienc​e/cdk/modulesuites/MioTests.java: Enabled test for the PubChem ASN reader
21:05 egonw rojasm: I will go to bed soon
21:06 egonw please email me the 'svn diff', so that I can check it on the train tomorrow...
21:06 rojasm ja clar
21:06 egonw and do email to the cdk-devel the unit test changed statistics again
21:06 egonw oh...
21:06 CIA-31 cdk: egonw * r10840 /cdk/trunk/src/data/asn/pubchem/list.asn: Added PubChem ASN list thingy
21:06 egonw you might summarize the 'svn diff' on the mailing list too, by listing all touched files:
21:07 rojasm ok
21:07 CIA-31 cdk: egonw * r10841 /cdk/trunk/src/data/asn/pubchem/list.asn: Fixed consistency of file
21:07 egonw grep Inded branch.trunk.svn.diff
21:07 egonw grep Index ...
21:07 egonw make sure to explain how people can create the 'svn diff' themselves...
21:08 rojasm ok I will try
21:08 CIA-31 cdk: egonw * r10842 /cdk/trunk/src/ (3 files in 3 dirs): Added an iterating PC-Substances reader
21:09 CIA-31 cdk: rajarshi * r10843 /cdk/trunk/src/test/org/openscience/cdk​/atomtype/CDKAtomTypeMatcherTest.java: Added a test case for bug 1957958, in which we make a pyridine as if it came from a SMILES string, i.e., with all single bonds, no explicit hydrogens and all atoms marked as SP2
21:11 egonw rojasm: don't forget to remove the branch ...
21:16 rojasm ja clar
21:16 rojasm aber first I look it all is correct
21:20 egonw ack
21:32 CIA-31 cdk: rajarshi * r10844 /cdk/trunk/src/test/org/openscienc​e/cdk/graph/SpanningTreeTest.java: Added a test case for pyridine
21:34 CIA-31 cdk: egonw * r10845 /cdk/trunk/src/main/org/openscience/c​dk/atomtype/CDKAtomTypeMatcher.java: Removed use of getHydrogenCount
21:39 egonw good night
21:39 egonw bye
22:00 CIA-31 cdk: rajarshi * r10846 /cdk/trunk/src/main/net/sf/cdk/t​ools/doclets/CDKSVNTaglet.java: Updated source URL for Javadocs

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary