Sunday, October 07, 2012

CDK 1.4.12: the changes, the authors, and the reviewers

I was just about to write up the changes of CDK 1.4.14 I uploaded to SourceForge last week, when I noticed that I forgot the blog the changes for CDK 1.4.13 and 1.4.12. Well, fortunately, those two releases are identical, caused by me fighting the SourceForge file system. So, first I will post the changes of that release then.

This release contains a few patches to improve the packaging on Debian, now reports the version too in the JavaDoc window title along with a few other JavaDoc fixes, adds the atom type, has bug fixes for the MolecularFormulaManipulator, DebugChemObjectBuilder, and the NonotificationChemObjectBuilder, and add roundtripping of aromaticity in the CML format. All in all, unless you were affected by one of the fixed bugs, this release is not overly interesting.

But, also a big welcome to Tomáš Pluskal as a new CDK patch author!

The changes
  • Use properties for jar locations 13c63cd
  • Report the CDK version *and* the date 4e85157
  • Set the encoding (patch by Onkar Shinde ) 08b9d92
  • Removed output to STDOUT 4e0f4a3
  • Split out Doxygen generation, so that creating JavaDoc does not require Doxygen 7ac0705
  • Synchronized referral to vecmath to all list vecmath*.jar 0050e24
  • Refactored to have jar file names as properties and thus customizable, and split out development targets into devel.xml, reducing the dependencies for compiling the CDK (via the taskdef, it dependend on JavaNCSS too) 18d4cb2
  • Fixed pointing to the development libraries, using the same customizable approach as in the rest of the build.xml a22f151
  • Fixed the labeling, which was the wrong way around c7ac530
  • Added roundtripping of atom-based aromaticity (fixes #1709130) 56b8f9c
  • Throw an IllegalArgumentException instead of a NullPointerException when an atom is configured of an unknown element 75b58bf
  • Added a missing dependency 8a041b5
  • Throw an exception when the given atom is not found in the chemmodel (fixes #3530861) 04f686f
  • Fixed the @cdk.githash links dd9cdb8
  • Fixed the target to be called 99c2171
  • Fixed the module assignment 77d8bd6
  • Fixed the same problem as in DefaultChemObjectBuilder (see commit 3d0b0e5f329e9256638ce18e4b5024e2d348474a and 2a2aecc077add716309591e2fae9832dfcfc64cf) b5caeba
  • Added proper module assignment for RandomGenerator 57117c3
  • Added a note about atom types to be perceived before using this class (closes #3513957) 6a1100c
  • Updated for the bug fix in commit 37ca43cc4ea0f0a7efaf10edbbe60ef57a44e8ce 74ee663
  • Updated test for the bug fix in commit 37ca43cc4ea0f0a7efaf10edbbe60ef57a44e8ce to include the implicit hydrogens. 948f02f
  • Added atom type 631c399
  • Added a unit test for the perception of (bug #3529082) 232657a
  • Added a new author 32b1b33
  • Updated the README (fixes #3538451) 378ffa9
  • Added Nina's modifcations to ensure that getting a molecular formula includes implicit hydrogens. Addressed bug 2983334. Also updated a unit test to take into account that H's are being considered 37ca43c
  • Updated a method based on Ninas suggestion to avoid modifiying a atom container when looping over it. This avoids a concurrent modification exception. Also updated some Javadocs eba09ca
  • Change the getHTML method to return the elements in the Hill System order (bug #3432131). 3f3fab5
The authors
28  Egon Willighagen
  3  Rajarshi Guha
  1  John May
  1  Tomas Pluskal
The reviewers
5  Egon Willighagen 
3  Rajarshi  Guha 
3  John May 
1  Nina Jeliazkova 

As always, I made these overviews with these scripts.