FOR_DEVELOPERS

one iteration is:

  - adapt files in pyOpenMS/pyopenms/pxds

  - adapt unittests and maybe memoryleaktests

  - run in this directory:

    1) generate_code_and_cythonize.bat

    2) python setup.py build_ext --inplace

    3) run_unittests_with_local_pyopenms.bat

    4) maybe: run_memleak_tests.bat


about the unittests / testcoverage:

   the unittests have docstrings with sections
   """
      @tested
      ClassA.method1
      .method2
      .mehtod3
      .__init__
      ClassB.method_a
      ....
      @end 
   """

   these have to be maintained by the developers and 
   declare which classes and methods from the wrappings
   are tested in the corresponding module /class/method.

   the script check_test_coverage.py loads _pyOpenMS.pyd,
   extracts all wrapped classes and their methods and
   compares them with the delcared ones.

   at the end the script gives an overview over missing
   tests.
   

about the code generator:

    the generator parses .pxd files. that are cython files
    which describe the signatures of used c++ classes and their
    methods.

    the generator then builds cython code for python classes,
    the methods of these classes delegate to the corresponding
    c++ methods and perform type conversions for input arguments
    and the return value.
    
    if you add an #ignore comment to a class or method in a .pxd
    file the class or method will be ignored by the code generator

    for template classes you have to specify a comment
    #inst=<A,...> at the end of "cppclass .." line in the .pxd file.
    this describes the classes for instatiating the class.
    at the moment this only works for one instantiation.

    --> see pyOpenMS\cython_code\pxd\MSExperiment.pxd

    the script build_cython_file.py stirs the code generation process

    the generated cython code is in pyOpenMS/_pyOpenMS.pyx

    if you want to extend the code generator:

      - PXDParser.py should be able to parse all pxd statements
        unless nested declarations (as inner ::iterator types).

      - Most probably you have to extend the conversion functions
        in DelegateClassGenerator.py