Sunday, September 18, 2011

CDK 1.4.3: the changes, the authors, and the reviewers

CDK 1.4.3 is the third update in 1.4 series, aimed fixing bugs, though this series can also be updated with new functionality. The users can be assured that the project has a peer-review process, and an extensive test suite to ensure functionality meets standards. Mind you, we are still in need of many, many more tests, but that's another story.

This update release has a mix of things. First, it contain another big batch of atom types by Nimish, Asad, and Gilleain. If our counting is right, only one atom type remains. It takes the number of atom types known by the CDK software over 300. This release also contains a few bug fixes. For example, it was noticed that some test classes were not automatically run, which when hooked in resulted in 5 failing unit tests (out of a few hundred). These bugs in IReactionScheme implementations, DebugMolecularFormula, and NNMapping are not regressions, and were present in earlier 1.3 and 1.4 releases too, but are now fixed. The scope was only minor and probably therefore not noticed before. Furthermore, a thread-safety bug was fixed and setting the background color in 2D depictions.

New functionality in this release is the ArrowElement, which is fixing a bug in the CDK-JChemPaint patch, and the silent module, that will replace the nonotify module in master (if a removal patch gets accepted). Earlier timings showed excellent performance, and all users are encouraged to use this implementation when the listening model of the core interfaces is not used.

The changes
  • Ported ArrowElement from renderextra to renderbasic 8650700
  • Added missing cloning of the properties aeaa993
  • Removed add/removeListener() calls 496f242
  • Removed notifyChanged() calls 822189e
  • Implemented the silent module as a nonotify replacement, copied from the data module, with tests copied from test-nonotify. 78fb9c8
  • Added two missing tests to overwrite the notifying default implementation 294cecf
  • Added missing call to super d81fc3d
  • Fixed getting the isotope count for a particular isotope df8e31e
  • Added missing test classes to the nonotify test suite bb2e41f
  • Added missing test classes to the datadebug test suite 6bea1fa
  • Ru final 220d183
  • S final 55ed20d
  • Br final 81c629a
  • Zn final 8cf1d4d
  • V final 862b91d
  • Al final fed0c1a
  • Added Ag+ and Ag-* atom types (addressing #3388240) 033fb9f
  • Added missing test class d98ec5b
  • Se atom type test cases added 55c6a83
  • Se atom type cases added ad7753a
  • Se atom type added 02e65a4
  • Unit test for one of the current S atom types 82c2c4a
  • Ti final ee1ac09
  • Removed obsoleted code by Ni patch 682d0a1
  • Ni final 8026156
  • Sr final 458d1aa
  • Pb final 6207b4f
  • Tl final ae54e0c
  • Hooked in Mg atom type detection 81ce6e5
  • Mg final c562129
  • Hooked in Gadolinum atom type perception 00e9aac
  • Gd final 770dc99
  • Removed hybridization state: you cannot create five orbitals starting from four ef34cca
  • Sb final 9b1fe00
  • Mo final a8c44bc
  • Pt final cc46f63
  • Cu final 177e5bd
  • Fixed OpenJavaDocCheck reporting: added two missing property values 3152dd0
  • B final e159e5b
  • Ca Atom type test case added 517dd0c
  • Ca Atom type data added b91943a
  • Ca Atom type added 6c3f09f
  • No longer caches the background color, fixing that when the value in the model changes *after* passing it to the visitor it is not updated too e4786fa
  • thread safety c4067cd
The Authors
Again with the note that Nimish work is reflected by the patches by Gilleain and Asad.

21  Egon Willighagen
21  Gilleain Torrance
  3  Syed Asad Rahman
  1  Jonathan Alvarsson

The Reviewers

21  Egon Willighagen
  7  Gilleain Torrance
  1  Rajarshi Guha

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