structure the whole project

[timziebart]

Give a new basic structure to the project. Which folder structure is good and why? What elements are needed?

todo

• what to do about the periodic ckdtree?
• add a readme add README #11
• separate between interface functions and computing functions (see below)
• numbify everything with nb.jit decorator
• clean the code
• clean up test.py and separate choice of example, grid and backscaling (maybe more?)

[timziebart]

use directly the lower level viability calculation functions. Like this, the interfaces for the viability calculations can be separated out ...

e.g. introduce functions with _viability_kernel and _viability_capture_basin that do the actual calculations (and are used by topology_classification) while the functions viability_kernel and viability_capture_basin are the interfaces to the outside if somebody wants to calculate viability stuff only (not TSM).

[timziebart]

numba can't accept functions as parameters for nopython mode, so use factory functions instead (see here and make_run_function.