Processed alot of what pylint suggested. Might change the naming conventions rules tho, the short parameter names are an issue, but lets not get too strict..

changed the examples to work again, modified the run_system python function to handle stuff correctly, in a cleaner fashion

Changed the api code: removed all the functions that did a slightly different thing. put them into 1 function that has several options. Moreover, cleaned up code, test functions, and other functions throughout code