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

updated grid code to be more clean, and have dedicated setup and cleanup functionalities. hopefully code will stay cleaner

updating scaling plots. added pool closing and joining at the end of the MP part because on astro2 I suddenly got the error of having too many open files

added fPIC to custom logging compiler. should solve issue on desktop pc. also fixed bug of precode requirement

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