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IMP Manual  develop.4056850,2019/07/22
IMP gotchas

Below are suggestions prompted by bugs found in code submitted to IMP.

  • Never use 'using namespace' outside of a function; instead explicitly provide the namespace. (This avoids namespace pollution, and removes any ambiguity.)
  • Never use the preprocessor to define constants. Use const variables instead. Preprocessor symbols don't have scope or type and so can have unexpected effects.
  • Don't expect IMP::Object::get_name() names to be unique; they are there for human viewing. If you need a unique identifier associated with an object or non-geometric value, just use the object or value itself.
  • Pass other objects by value or by const & (if the object is large) and store copies of them.
  • Never expose member variables in an object which has methods. All such member variables should be private.
  • Don't derive a class from another class simply to reuse some code that the base class provides - only do so if your derived class could make sense when cast to the base class. As above, reuse existing code by pulling it into a function.
  • Clearly mark any file that is created by a script so that other people know to edit the original file.
  • Always return a const value or const reference if you are not providing write access. Returning a const copy means the compiler will report an error if the caller tries to modify the return value without creating a copy of it.
  • Include files from the local module first, then files from other IMP modules and finally outside includes. This makes any dependencies in your code obvious, and by including standard headers after IMP headers, any missing includes in the headers themselves show up early (rather than being masked by other headers you include).
    #include <IMP/mymodule/mymodule_exports.h>
    #include <IMP/mymodule/MyRestraint.h>
    #include <IMP/Restraint.h>
    #include <vector>
    
  • Use double variables for all computational intermediates.
  • Avoid using nested classes in the API as SWIG can't wrap them properly. If you must use use nested classes, you will have to do more work to provide a Python interface to your code.
  • Delay initialization of keys until they are actually needed (since all initialized keys take up memory within each particle, more or less). The best way to do this is to have them be static variables in a static function:
    FloatKey get_my_float_key() {
      static FloatKey k("hello");
      return k;
    }
    
  • One is the almost always the right number:
    • Information should be stored in exactly one place. Duplicated information easily gets out of sync.
    • A given piece of code should only appear once. Do not copy, paste and modify to create new functionality. Instead, figure out a way to reuse the existing code by pulling it into an internal function and adding extra parameters. If you don't, when you find bugs, you won't remember to fix them in all the copies of the code.
    • There should be exactly one way to represent any particular state. If there is more than one way, anyone who writes library code which uses that type of state has to handle all ways. For example, there is only one scheme for representing proteins, namely the IMP::atom::Hierarchy.
    • Each class/method should do exactly one thing. The presence of arguments which dramatically change the behavior of the class/method is a sign that it should be split. Splitting it can make the code simpler, expose the common code for others to use and make it harder to make mistakes by getting the mode flag wrong.
    • Methods should take at most one argument of each type (and ideally only one argument). If there are several arguments of the same types (eg two different double parameters) it is easy for a user to mix up the order of arguments and the compiler will not complain. int and double count as equivalent types for this rule since the compiler will transparently convert an int into a double.