Camelia, the Perl 6 bug

IRC log for #cdk, 2008-09-06

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

All times shown according to UTC.

Time Nick Message
05:34 egonw joined #cdk
05:39 jbrefort joined #cdk
05:45 CIA-14 cdk: egonw * r12184 /cdk/trunk/src/test/org/openscience/cdk/​atomtype/SybylAtomTypeMatcherTest.java: Updated tests: findType(IAC, IAtom) cannot detect aromaticity; but findType(IAtomContainer) does, but not tested yet
05:46 CIA-14 cdk: egonw * r12185 /cdk/trunk/src/main/org/openscience/cdk/atomtype/ (7 files):
05:46 CIA-14 cdk: Added method to IAtomTypeMatcher to perceive types for all atoms in the
05:46 CIA-14 cdk: container; allowing some removal of redundant calculations, and the addition of
05:46 CIA-14 cdk: calculation of molecular properties, like aromaticity, as used in the Sybyl atom
05:46 CIA-14 cdk: type matcher
06:51 CIA-14 cdk: egonw * r12186 /cdk/trunk/src/test/org/openscience/cdk/atomtype/ (6 files): Added missing unit tests
06:52 CIA-14 cdk: egonw * r12187 /cdk/trunk/src/main/org/openscience/cdk/atomtype/ (6 files): Added unit test annotation
07:00 bag joined #cdk
09:50 carsten joined #cdk
13:08 dleidert joined #cdk
17:40 egonw joined #cdk
18:31 CIA-14 cdk: egonw * r12188 /cdk/branches/cdk-1.2.x/src/test/org/ope​nscience/cdk/coverage/CoverageTest.java: Don't fail in a missing test class, but count and report them
18:32 CIA-14 cdk: egonw * r12189 /cdk/branches/cdk-1.2.x/src/test/org/opensc​ience/cdk/geometry/GeometryToolsTest.java: Added unit test for bug #2094881
18:32 CIA-14 cdk: egonw * r12190 /cdk/branches/cdk-1.2.x/src/main/org/open​science/cdk/geometry/GeometryTools.java: Applied bug fix by Thorsten, see #2094881
18:38 CIA-14 cdk: egonw * r12191 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcherTest.java: Updated tests: findType(IAC, IAtom) cannot detect aromaticity; but findType(IAtomContainer) does, but not tested yet
18:38 CIA-14 cdk: egonw * r12192 /cdk/branches/cdk-1.2.x/src/mai​n/org/openscience/cdk/atomtype/ (7 files):
18:38 CIA-14 cdk: Added method to IAtomTypeMatcher to perceive types for all atoms in the
18:38 CIA-14 cdk: container; allowing some removal of redundant calculations, and the addition of
18:38 CIA-14 cdk: calculation of molecular properties, like aromaticity, as used in the Sybyl atom
18:38 CIA-14 cdk: type matcher
18:39 CIA-14 cdk: egonw * r12193 /cdk/branches/cdk-1.2.x/src/tes​t/org/openscience/cdk/atomtype/ (6 files): Added missing unit tests
18:40 CIA-14 cdk: egonw * r12194 /cdk/branches/cdk-1.2.x/src/mai​n/org/openscience/cdk/atomtype/ (6 files): Added unit test annotation
19:41 CIA-14 cdk: egonw * r12195 /cdk/branches/cdk-1.2.x/pmd/migrating.xml: Also test for migration to JUnit4
19:42 CIA-14 cdk: egonw * r12196 /cdk/branches/cdk-1.2.x/ (5 files in 2 dirs): Don't do the Vector check on the qm module, as it actually defines a (mathematical) Vector class, messing up the PMD test
19:42 CIA-14 cdk: egonw * r12197 /cdk/branches/cdk-1.2.x/pmd/migrating-qm.xml: Now really exclude the ReplaceVectorWithList test
19:43 CIA-14 cdk: egonw * r12198 /cdk/branches/cdk-1.2.x/pmd/custom-test.xml: Make sure to test for JUnit4 migration for test modules too
20:13 CIA-14 cdk: egonw * r12199 /cdk/branches/cdk-1.2.x/src​/main/org/openscience/cdk/ (10 files in 3 dirs): Cleaned up code: Vector->List
20:14 CIA-14 cdk: egonw * r12200 /cdk/branches/cdk-1.2.x/build.props: No JCP version; updated CDK one to indicate branch
20:29 CIA-14 cdk: egonw * r12201 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcherTest.java: Added unit tests for differences in behaviour of findMatchingAtomType(IAtomContainer, IAtom) and findMatchingAtomTypes(IAtomContainer)
20:29 CIA-14 cdk: egonw * r12202 /cdk/branches/cdk-1.2.x/src/main/org/opensci​ence/cdk/atomtype/SybylAtomTypeMatcher.java: Not only the atom type name, but the hybridization too must be set for the hueckel aromaticity to work
21:52 CIA-14 cdk: egonw * r12203 /cdk/branches/cdk-1.2.x/src/ (14 files in 10 dirs): API change: all IRingSet.getX() methods now return an IRingSet (closeing #2080973)
22:02 bag joined #cdk
22:10 CIA-14 cdk: egonw * r12204 /cdk/branches/cdk-1.2.x/src/main/org/ope​nscience/cdk/tools/IValencyChecker.java: Removed method; the hydrogenAdder should be used for that, not a IValencyChecker
22:11 CIA-14 cdk: egonw * r12205 /cdk/branches/cdk-1.2.x/src​/main/org/openscience/cdk/ (7 files in 4 dirs): Removed/replaced deprecated code
22:28 CIA-14 cdk: egonw * r12206 /cdk/branches/cdk-1.2.x/src/main/org/op​enscience/cdk/graph/SpanningTree.java: Don't return the first atom, if no path is found (closes #2044675)
23:04 CIA-14 cdk: egonw * r12207 /cdk/branches/cdk-1.2.x/src/ (2 files in 2 dirs): Added unit test; it's not a SMILES parsing problem, but a bond order deduction issue (regarding #1363882)
23:05 CIA-14 cdk: egonw * r12208 /cdk/branches/cdk-1.2.x/src/test/ (2 files in 2 dirs): Added unit test for bug #1535055

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