 <p>This is more or less what you wrote. To be more precise:</p> <p>Yellowish line signal Cython command which are not directly translated to pure C code but which work by calling CPython API to do the job. Those line includes:</p> <ul> <li>Python object allocation</li> <li>calls to Python function and builtins</li> <li>operating on Python high level data stuctures (eg: list, tuples, dictionary)</li> <li>use of overloaded operation on Python types (eg: +, * in Python integers vs C int)</li> </ul> <p>In any case, this is a good indication that thing might be improved.</p>