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

added general run_system api binding, which will eventually replace the individual ones. this function runs a system, and depending on the input it will use a custom logging, a preloaded store, write log to file etc. I think it will be better to just write some if statements in a single function, and not have too many repeating code

Rewrote argument handling of population class, added export functions. Added python-c-bindings to return store and other small changes