moved around functions, fixed the super-help function, changed some of the tests for persistent_data

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 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

fixing errors: hdf5 file creation when there are no settings. and the setting export if there is a functio in it