Jekyll2026-04-23T19:38:27+00:00http://egonw.github.io/blog/feed/by_tag/rse.xmlchem-bla-icsChemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.Egon WillighagenThings to check before you consider submitting a (final) CDK patch #12009-07-31T00:10:00+00:002009-07-31T00:10:00+00:00http://egonw.github.io/blog/2009/07/31/things-to-check-before-you-considerMark the final in the above title; if you merely seek advice on your patch, feel free to send them in whatever state. However, if you bring up your patch for peer review, make sure to have gone through the following steps, in random order:

  • be prepared for peer review feedback
  • realize your code will have to be LGPL or LGPL-compatible
  • make sure the copyright lines are properly updated (see Making patches; Attribution; Copyright and License.)
  • your code is fully unit tested
  • your code does not cause PMD failures
  • your code is fully JavaDoc-umented
    • no empty templates
    • JavaDoc for every class field, method and class
    • use of {@link}
    • use of CDK tags @cdk.bug, @cdk.cite, etc
    • period at the end of the first sentence
    • …
  • make sure all the code still compiles
  • make your code readable
    • 80 characters per line
    • variable names that reflect their purpose and nature
    • no code complexity errors with PMD
    • camelCasing as custom in Java
    • comment your code where appropriate, explaining what your code is supposed to do
    • …

These are reasons to reject your patch, so better make sure to not have to be reminded of that. The build environment comes with some code to make these checks easier (though not the fixing). For example, say I introduced a new module uff (for the UFF force field):

$ cd cdk/
$ ant clean dist-all test-dist-all
$ ant -Dmodule=uff test-module
$ ant -f javadoc.xml -Dmodule=uff doccheck-module
$ ant -f pmd.xml -Dpmd.test=custom -Dmodule=uff test-module
$ ant -f pmd.xml -Dpmd.test=custom -Dmodule=test-uff test-module
]]>Egon Willighagen