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