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Added changelog for 1.3.1

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@@ -166,3 +166,118 @@ This changelog is automatically generated from the:
* Set new methods to read new schemes of the reactions dictionary (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added testMethod value for Junit4 (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* For each data class, also test inherited methods for super classes implementing inherited superinterfaces (Egon Willighagen <egon.willighagen@gmail.com>)
+
+1.3.1
+-----------
+* Bumped version for 1.3.1 release (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added some extra lines, hopefully fixing the conflicts all the time (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed param name (Egon Willighagen <egonw@users.sourceforge.net>)
+* Updated the makefp3d target to work with the current build system (Egon Willighagen <egonw@users.sourceforge.net>)
+* Set up a branch for the 1.2.4 release (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixes bug 2898399. Updates to the SMARTS parser to handle proper matching for explicit hydrogens (including H, 1H, 2H and 3H). SMARTSQueryVisitor updated to take into account different isotopes of H. Also updated unit tests to take into account proper H matching. Added a unit test to further check H matching. (Rajarshi Guha <rajarshi.guha@gmail.com>)
+* Added tests to match hydrogens (mark_rynbeek <markr@ebi.ac.uk>)
+* Fixed junior issue 1816529: Missing Java5 generics for atomContainers() Iterator (Uli Köhler <ulikoehler@online.de>)
+* Reworked the tests for bug 2898032. Updated Javadocs for smiles generator (Rajarshi Guha <rajarshi.guha@gmail.com>)
+* Added unit test to confirm and check for bug 2898032 (Rajarshi Guha <rajarshi.guha@gmail.com>)
+* Fixed junior issue 1802586: Misuse of assertTrue for tested strings (Uli Köhler <ulikoehler@online.de>)
+* Made the AtomContainerPermutors IAtomContainer implementation independent (Egon Willighagen <egonw@users.sourceforge.net>)
+* Updated UIT to handle single atom queries and added a unit test for bug 2888845. Also updated Javadocs to specifically note behavior of single atom queries (Rajarshi Guha <rajarshi.guha@gmail.com>)
+* Fixed the dist-large target: removed to no longer existing .libdepends after the log4j module patch (Egon Willighagen <egonw@users.sourceforge.net>)
+* Implemented instantiating custom loggers; example in the unit test class (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added the use of the SystemOutLoggingTool as back up (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added a ILoggerTool implementation for STDOUT (Egon Willighagen <egonw@users.sourceforge.net>)
+* Dig up and updated the copyright history (Egon Willighagen <egonw@users.sourceforge.net>)
+* Factored out initialization of the tool, to allow reusing the code for other logger class names (Egon Willighagen <egonw@users.sourceforge.net>)
+* Moved the log4j.jar depending LoggingTool into a separate module (Egon Willighagen <egonw@users.sourceforge.net>)
+* Introduces the ILoggingTool interface and a factory so that CDK code no longer needs to depend on LoggingTool which depends on Apache's Log4j library. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added generation of java source jars (Peter Odéus <peter.odeus@gmail.com>)
+* Fixed matchers to allow XML without new lines (closes #2832835) (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added unit tests for detection of PubChem XML files. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed matchers to allow XML without new lines (closes #2832835) (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added unit tests for detection of PubChem XML files. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added reading of E/Z stereochemistry from double bonds in MDL V2000 molfiles. (Egon Willighagen <egon.willighagen@gmail.com>)
+* A minor fix to clean up a PDMD warning (Rajarshi Guha <rajarshi.guha@gmail.com>)
+* Overwrite unit tests, because there are no change events passed around at all for the NoNotification interface implementations (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added missing unit tests for IChemModel event propagation for the ICrystal field (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed propagation of change events to IChemModel when modifications are made in child IChemObjects (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed unit tests: the IChemModel.setFoo(null) should actually give a change event on the listener of the IChemModel, and not after unregistering of the Foo object. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Synchronized with the Blue Obelisk version (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added unit test to the function of the new IO setting to force 2D coordinate output. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added writer IO option to force writing of 2D coordinates if 3D coordinates are present too, which now are preferably outputted. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added unit test to verify that if 2D and 3D coordinates are available, the 3D coordinates are outputted. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Changed IBond.get/setStereo() to use a IBond.Stereo enumeration instead of an int (fixes #2855850): (Egon Willighagen <egon.willighagen@gmail.com>)
+* Fixed Taglets: only return HTML if the Tag is really given; the toString() method is given for all cases, not just when the tag is found (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added the Mannhold LogP descriptor (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added the Mannhold LogP descriptor to the ontology (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixeda bug which was causing various parts of the DescriptorEngine to fail - it was trying to instantiate a non-descriptor class which happens to reside in the descriptor package directory. This fix is a bit kludgy - ideally only descriptors should be in that directory (Rajarshi Guha <rajarshi.guha@gmail.com>)
+* Fixes ClassCastException when not IMolecule (Arvid Berg <goglepox@users.sourceforge.net>)
+* Upgraded to PMD 2.4.5 with many bug fixes, giving more accurate error reports (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added missing dependency on cdk-diff, being used in one of the unit tests (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed methods names to match those in the test class (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed test method name to match the expected patters, fixing a coverage test fail (Egon Willighagen <egonw@users.sourceforge.net>)
+* Removed duplicate code: MolecularFormulaTest now extends AbstractMolecularFormulaTest (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed test method annotation to point to the right method (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added missing @TestMethod annotation (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added modules that were missing from the PMD testing (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added modules that were missing from the doccheck testing (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added reference to IUPAC documentation about stereochemistry visualization. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
+* Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG (mark_rynbeek <markr@ebi.ac.uk>)
+* Added missing dependency introduced by the use of AbstractFingerprinterTest in test-standard. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Updated the unit test classes for all IFingerprinter implementations to use the new AbstractFingerprinter class; a few unit tests actually fail (Egon Willighagen <egonw@users.sourceforge.net>)
+* Extracted an AbstractFingerprinterTest with unit tests that should really apply to all IFingerprinter implementations (Egon Willighagen <egonw@users.sourceforge.net>)
+* Clean up of layout. (Jonathan Alversson <jonathan.alvarsson@gmail.com>)
+* Fix the unit test to not give a 'input must support mark' exception on some platforms, by wrapping the InputStream in a BufferedInputStream. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added missing dependencies (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added ioformats to modules to test (Egon Willighagen <egonw@users.sourceforge.net>)
+* Use StringBuilder to aggregate the field data, which gives an huge performance boost for SD file where multiline field data is found. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Use StringBuilder to aggregate the field data, which gives an huge performance boost for SD file where very much field data, like the ChEBI_complete.sdf (Egon Willighagen <egonw@users.sourceforge.net>)
+* Factored out steps in reading the SD file data block (Egon Willighagen <egonw@users.sourceforge.net>)
+* Bumped version, to make it clear this is not the 1.2.3 release (Egon Willighagen <egonw@users.sourceforge.net>)
+* Bumped version, to make it clear this is not the 1.3.0 release (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed registering on the cdk.threadnonsage tag (closes #2796362) (Egon Willighagen <egonw@users.sourceforge.net>)
+* Removed obsolete pattern from old svnrev tag (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed JavaDoc to remove traces of the old svnrev Tag (Egon Willighagen <egonw@users.sourceforge.net>)
+* Synchronized exception message with implementation (fixes #2844333) (Egon Willighagen <egonw@users.sourceforge.net>)
+* Made class private again, per authors request (Egon Willighagen <egonw@users.sourceforge.net>)
+* Any class will do, not just public, final and abstract (Egon Willighagen <egonw@users.sourceforge.net>)
+* Two further compile fixes after the merge with CDK 1.2.x (Egon Willighagen <egonw@users.sourceforge.net>)
+* Made the class public, to fix a compile problem introduced by the merge with CDK 1.2.x (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added ant task to calculate JavaNCSS code statistics (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added JavaNCSS 32.53 (LGPL 3.0) (Egon Willighagen <egonw@users.sourceforge.net>)
+* The Pauling Electronegativity is copied in configure as well. I can't see why not copy everything we have. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
+* Revert "added a test for bug 2831420": (Egon Willighagen <egonw@users.sourceforge.net>)
+* Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG (mark_rynbeek <markr@ebi.ac.uk>)
+* added a test for bug 2831420 (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
+* added a test for bug #2831420 (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
+* Made InChIGeneratorFactory a singleton. (jonalv <jonathan.alvarsson@gmail.com>)
+* Layout. (jonalv <jonathan.alvarsson@gmail.com>)
+* Added bug annotation (Rajarshi Guha <rajarshi.guha@gmail.com>)
+* test case for bug #2846213 (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
+* Fixed perception of N.planar3 where N.sp2 was detected, by now taking into account the given hydrogen count. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed perception of benzene with all single bond, but hydrogen count 1 and bonds flagged aromatic. In this case, the type is C.sp2 not C.sp3. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added assertions to unit test for values being not null (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added two unit tests for the same problem: carbon atom types are not correctly perceived if bond order info is SINGLE only, and hydrogen count and aromaticity flag is set. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Moved class into a org.openscience.cdk package, which seems to work now. I'm puzzled why it did not before. Solved several unit test fails. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Unsealed the XOM jar to allow having the CustomSerializer (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed Javadocs error (Rajarshi Guha <rajarshi.guha@gmail.com>)
+* Fixed a wrong javadoc tag. Also removed svn tag in the SMARTS parser JJT file, replaced with git tag (Rajarshi Guha <rajarshi.guha@gmail.com>)
+* Added support for 'public enum's (Egon Willighagen <egonw@users.sourceforge.net>)
+* corrected bug in bondtools.isStereo(IAtomContainer container, IAtom stereoAtom). A comparision of atom symbols in a nested loop was using the counter of the outer loop twice. Note it worked before, because there is a sort of fallback to Morgan numbers. fallback to morgan (fixes #2830287) (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
+* added a new test for bondtools (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
+* Fixed inconsistency between accepts() and write: also support writing of IAtomContainerSet and IAtomContainer as accepts() indicates (fixes #2827745) (Egon Willighagen <egonw@users.sourceforge.net>)
+* General test for testing consistency between write() and accepts(), testing that all accepted IChemObject's can also be written (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added unit test for bug #2826961: inconsistent atom typing for two SMILES. Unit test does not show a fail, ruling out a CDK bug (Egon Willighagen <egonw@users.sourceforge.net>)
+* Remove erroneous throws statement (Egon Willighagen <egonw@users.sourceforge.net>)
+* Bug found calculating the exact mass given a molecular formula when it is negative charged. (Miguel Rojas Cherto <miguelrojasch@gmail.com>)
+* Fixed reading of the cdk/dict/data/elements.owl database which is now in OWL (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixed issue 2458210: use assertNotNull(foo) etc instead of assertTrue(foo != null). (Uli Köhler <ulikoehler@online.de>)
+* Added minimum equivalents for BondManipulator.getMaximumBondOrder() methods (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fixes asserts: after removal *no* change should be recorded (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added IO option to disable generator of XML declaration statements in the output CML. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added generics, and consistified code by always returning a List<?> of the same '?'. (And some 80 chars fixes in the JavaDocs.) (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added unit tests to test that when a [Molecule|Reaction|Ring]Set has been removed from a ChemModel, the ChemModel should unregister as listener. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Added unit tests for event propagation from [Molecule|Reaction|Ring]Sets to ChemModel. (Egon Willighagen <egonw@users.sourceforge.net>)
+* More testing of flags. (Egon Willighagen <egonw@users.sourceforge.net>)
+* Fix for junior job id: [ 1837692 ] Test methods should throw only one Exception. (Paul Turner <paulturner@users.sourceforge.net>)
+* Fixed missing imports and wrapped to 80 chars (Egon Willighagen <egonw@users.sourceforge.net>)
+* Better excpetion handling in builder3d: (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
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