Camelia, the Perl 6 bug

IRC log for #cdk, 2008-12-17

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All times shown according to UTC.

Time Nick Message
05:18 jbrefort joined #cdk
07:23 carsten joined #cdk
08:44 egonw joined #cdk
09:25 jonalv joined #cdk
09:41 CIA-60 cdk: egonw * r13610 /cdk/branches/cdk-1.2.x/src/ma​in/org/openscience/cdk/debug/ (4 files):
09:41 CIA-60 cdk: Fixed methods to match that of the implemented interface; the method did not
09:41 CIA-60 cdk: overwrite the super method, effectively not implementing some interface methods,
09:41 CIA-60 cdk: but adding new methods. Bugs found by having proper unit testing
09:42 CIA-60 cdk: egonw * r13611 /cdk/branches/cdk-1.2.x/src/test/org/opens​cience/cdk/formula/AdductFormulaTest.java: Inherit from IAdductFormulaTest, instead of duplicating the tests.
09:43 CIA-60 cdk: egonw * r13612 /cdk/branches/cdk-1.2.x/src/te​st/org/openscience/cdk/debug/ (9 files): Added missing constructor unit tests
09:45 CIA-60 cdk: egonw * r13613 /cdk/branches/cdk-1.2.x/src​/test/org/openscience/cdk/ (5 files): Test the impl constructor only, not the IChemObjectBuilder wrapper, which is tested elsewhere
10:22 CIA-60 cdk: egonw * r13614 /cdk/branches/cdk-1.2.x/src​/test/org/openscience/cdk/ (12 files in 2 dirs): Added missing constructor unit tests
10:22 CIA-60 cdk: egonw * r13615 /cdk/branches/cdk-1.2.x/src/test/org/opensci​ence/cdk/debug/DebugReactionSchemeTest.java: Fixed test method name to match used convention
10:39 shk3 joined #cdk
11:07 egonw yeah, zero missing unit tests in datadebug :)
11:08 CIA-60 cdk: egonw * r13616 /cdk/branches/cdk-1.2.x/build.xml: Fixed check for up to dateness of test jars
11:09 CIA-60 cdk: egonw * r13617 /cdk/branches/cdk-1.2.x/src/test/org/opens​cience/cdk/formula/AdductFormulaTest.java: Test the impl constructor only, not the IChemObjectBuilder wrapper, which is tested elsewhere
11:10 CIA-60 cdk: egonw * r13618 /cdk/branches/cdk-1.2.x/src/ (5 files in 2 dirs): Added missing constructor unit tests
11:21 gilleain joined #cdk
11:38 CIA-60 cdk: shk3 * r13619 /jchempaint/trunk/src/main/org/openscience/jc​hempaint/action/ConvertToRadicalAction.java: that was not committed
11:57 jbrefort joined #cdk
12:22 CIA-60 cdk: egonw * r13620 /cdk/branches/cdk-1.2.x/src/test/org/open​science/cdk/debug/DebugReactionTest.java: Test the impl constructor only, not the IChemObjectBuilder wrapper, which is tested elsewhere
12:23 CIA-60 cdk: egonw * r13621 /cdk/branches/cdk-1.2.x/src/tes​t/org/openscience/cdk/nonotify/ (19 files): Adding missing constructor unit tests
12:23 CIA-60 cdk: egonw * r13622 /cdk/branches/cdk-1.2.x/src/test/org/opensc​ience/cdk/nonotify/NNPDBStructureTest.java: Added last two missing unit tests
12:35 CIA-60 cdk: egonw * r13623 /cdk/branches/cdk-1.2.x/src/test/org/opensc​ience/cdk/protein/data/PDBPolymerTest.java: Added missing unit test
12:49 egonw gilleain: ping
12:49 gilleain si?
12:49 egonw populate bug report
12:49 egonw testing fix
12:49 egonw just wanted to note
12:49 egonw better even to use interfaces as parameter
12:49 egonw so, I'm using List instead of ArrayList
12:50 gilleain eh?
12:50 egonw https://sourceforge.net/tracker2/?func=detail&am​p;aid=2339458&group_id=20024&atid=120024
12:52 gilleain suppose so.
12:52 CIA-60 cdk: egonw * r13624 /cdk/branches/cdk-1.2.x/src/main/org/o​penscience/cdk/layout/AtomPlacer.java: Use an interfaces instead of an implementation in APIs (closes #2339458)
13:08 CIA-60 cdk: egonw * r13625 /cdk/branches/cdk-1.2.x/src/ (3 files in 3 dirs): Adding missing R#N=R atom type (closes #2424511)
13:12 egonw shk3: what are your plans with your builder3d patch?
13:12 egonw I want to release 1.2.0 friday latest...
13:13 shk3 sorry
13:13 shk3 where in wiki should api changes be explained
13:13 shk3 ?
13:14 egonw https://apps.sourceforge.net/mediawiki/cdk​/index.php?title=CDK_1.2_TODO#API_Changes
14:24 zarah joined #cdk
14:24 CIA-60 cdk: egonw * r13626 /cdk/branches/cdk-1.2.x/src/test/org/openscie​nce/cdk/gui/smiles/SmilesGeneratorTest.java: Fixed tests: use MDLV2000Reader for MDL V2000 molfiles
14:25 CIA-60 cdk: egonw * r13627 /cdk/branches/cdk-1.2.x/src/ (30 files in 16 dirs): Bug annotation administration: cleaned up closed bug, by confirming that they are closed in the cdk1.2.x/ branch (closes #2103200)
14:27 zarah joined #cdk
14:28 gilleain joined #cdk
14:45 CIA-60 cdk: egonw * r13628 /cdk/branches/cdk-1.2.x/src​/main/org/openscience/cdk/ (31 files in 15 dirs): Added missing svn:keywords SVN annotation
14:57 CIA-60 cdk: egonw * r13629 /cdk/branches/cdk-1.2.x/src/main/or​g/openscience/cdk/qsar/descriptors/ (5 files in 2 dirs): Added missing svn:keywords SVN annotation
14:57 CIA-60 cdk: egonw * r13630 /cdk/branches/cdk-1.2.x/src​/main/org/openscience/cdk/ (5 files in 5 dirs): Fixed JavaDoc errors reported by Nightly: broken links and incorrect parameter names
15:03 shk3 egonw: done the api changes
15:03 egonw ok, please update the patch report with a link, and assign to rajarshi to ask him if he is happy about it
15:44 carsten joined #cdk
15:53 CIA-60 cdk: gilleain * r13631 /cdk/branches/jchempaint-primary/ (3 files in 3 dirs):
15:53 CIA-60 cdk: - Added a method to the Intermediate Renderer that takes a Visitor and a ChemModel.
15:53 CIA-60 cdk: - A very, very simple SVGGenerator class.
16:08 jbrefort joined #cdk
16:12 CIA-60 cdk: egonw * r13632 /cdk/branches/eoc21-jj1802589/: Merged with cdk1.2.x
16:32 CIA-60 cdk: egonw * r13633 /cdk/branches/cdk-1.2.x/ (116 files in 34 dirs):
16:32 CIA-60 cdk: Applied branch eoc21-jj1802589
16:32 CIA-60 cdk: Author: eoc21@users.sf.net
16:33 CIA-60 cdk: egonw * r13634 /cdk/branches/cdk-1.2.x/src/main/​org/openscience/cdk/aromaticity/ (2 files): Fixed typo in name Hueckel
16:37 CIA-60 cdk: egonw * r13635 /cdk-doc/ (. trunk/): Setting up location for documentation
16:41 CIA-60 cdk: egonw * r13636 / (cdk/branches/cdk-1.2.x/doc/website/ cdk-doc/trunk/website/): Moved the very old website from cdk1.2.x into cdk-doc
16:43 CIA-60 cdk: egonw * r13637 / (4 files in 4 dirs): Moved the other website stuff from cdk1.2.x into cdk-doc
16:44 CIA-60 cdk: egonw * r13638 / (4 files in 4 dirs): Moved the developers and user guides from cdk1.2.x into cdk-doc
16:46 CIA-60 cdk: egonw * r13639 /cdk-rfc/ (. trunk/): Set up a location of the Request For Comments archive
16:50 CIA-60 cdk: egonw * r13640 / (54 files in 2 dirs): Moved the RFCs into a separate archive
16:53 CIA-60 cdk: egonw * r13641 /cdk/branches/cdk-1.2.x/doc/ (4 files in 3 dirs): Moved guide related build tools to cdk-doc project
16:55 CIA-60 cdk: egonw * r13642 /cdk/branches/cdk-1.2.x/doc/RFC/: Removed empty dir
16:56 CIA-60 cdk: egonw * r13643 /cdk/branches/cdk-1.2.x/doc/design/: Moved design diagrams to cdk-doc
16:57 CIA-60 cdk: egonw * r13644 /cdk-doc/trunk/design/: Moved design diagrams to cdk-doc
16:57 CIA-60 cdk: egonw * r13645 /cdk-doc/trunk/ (4 files in 3 dirs): Moved guide related build tools to cdk-doc project
17:22 CIA-60 cdk: gilleain * r13646 / (6 files in 5 dirs): Export as SVG now (minimally) works.
17:46 egonw gilleain++
17:47 gilleain yeah, well, you haven't seen how i did it yet...
17:47 egonw hehehe
17:47 gilleain (I didn't use batik)
17:49 gilleain but i'm reading the page for it
19:29 CIA-60 cdk: egonw * r13648 /cdk/branches/cdk-1.2.x/AUTHORS: Added missing AUTHORS list
19:29 CIA-60 cdk: egonw * r13649 /cdk/branches/cdk-1.2.x/AUTHORS: Added three names that I remembered
19:33 CIA-60 cdk: egonw * r13650 /cdk/branches/cdk-1.2.x/AUTHORS: Added three names that I remembered
19:39 CIA-60 cdk: egonw * r13651 /cdk/branches/cdk-1.2.x/src/META​-INF/test-builder3d.cdkdepends: Added missing dependency
20:18 CIA-60 cdk: egonw * r13652 /cdk/branches/cdk-1.2.x/src/main/org/openscie​nce/cdk/charges/InductivePartialCharges.java: Ensure the Jmol atom type factory is instantiated
20:19 CIA-60 cdk: egonw * r13653 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/io/formats/ChemFormatMatcherTest.java: Added dummy method, to satisfy the coverage tester, with explanation is done differently
20:21 CIA-60 cdk: egonw * r13654 /cdk/branches/cdk-1.2.x/src/tes​t/org/openscience/cdk/charges/ (InductivePartialChargesTest.java PolarizabilityTest.java): Ignore to unimplemented methods; junit can report about Ignored tests
20:57 CIA-60 cdk: egonw * r13655 /cdk/branches/cdk-1.2.x/src/main/org/ope​nscience/cdk/io/cml/CMLCoreModule.java: Fixed NPE: not everything we read is an chemical element, and does not always have the concept Isotope...
21:11 CIA-60 cdk: egonw * r13656 /cdk/branches/cdk-1.2.x/src/main/org/​openscience/cdk/qsar/descriptors/atom​ic/IPAtomicLearningDescriptor.java: Restore hybridization after calculation; descriptor are not allowed to change the input structure
21:17 CIA-60 cdk: egonw * r13657 /cdk/branches/cdk-1.2.x/src/main/org/ope​nscience/cdk/qsar/DescriptorEngine.java: Also catch NoClassDefFoundError's, as alternatively thrown when a Class is not found
21:19 CIA-60 cdk: egonw * r13658 /cdk/branches/cdk-1.2.x/src/META-I​NF/test-qsarmolecular.cdkdepends: Adding missing depedency for the testjunk() test method in DescriptorEngineTest
21:23 CIA-60 cdk: egonw * r13659 /cdk/branches/cdk-1.2.x/src/ME​TA-INF/qsarprotein.cdkdepends: Added missing dependency on AtomContainerDiff for AminoAcidCountDescriptorTest
21:37 CIA-60 cdk: egonw * r13660 /cdk/branches/cdk-1.2.x/src/main/org/ope​nscience/cdk/io/cml/CMLCoreModule.java:
21:37 CIA-60 cdk: Reverted the use of the IsotopeFactory which was causing regressions; an
21:37 CIA-60 cdk: alterivative fix for the bug that triggered the introduction will be developed,
21:37 CIA-60 cdk: and that original bug report is reopened (closes #2442355, opens #1014344)
22:17 CIA-60 cdk: egonw * r13661 /cdk/branches/cdk-1.2.x/src/test/org/opens​cience/cdk/io/cml/cml23TestFramework.xml: Fixed path to schema
22:17 CIA-60 cdk: egonw * r13662 /cdk/branches/cdk-1.2.x/src/te​st/org/openscience/cdk/io/cml/ (3 files): Added test for reading isotope abundance and exact mass from CML
22:25 bag joined #cdk
22:35 CIA-60 cdk: egonw * r13663 /cdk/branches/cdk-1.2.x/src/ (4 files in 4 dirs): AtomParity no longer extends ChemObject (in agreement with IAtomParity, closes #2428901)

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