Update cube.py

[nwinner]

Summary

• Feature 1: Spherical masks of the cube data is now supported
• Feature 2: Using spherical masks, atomic site averages and totals are now supported natively. These can be used, respectively, for getting the average electrostatic potential around a site using a V_HARTREE file from CP2K or the total spin on a site using a SPIN_DENSITY file from CP2K. These features are useful as an alternative to Bader partitioning for these properties when the bader executable is not available.
• Fix 1: Previously, cube files were loaded using for loops, which was prohibitively slow for files >1Gb. Now it is done with numpy and is much faster.

TODO (if any)

• While not necessary, it would be nice to support multiprocessing for the atomic site functions. These can be pretty expensive when the cube files are >1Gb. I previously used the multiprocessing module for this, but ran into some errors while trying it out. It was exceeding the memory available for the Drone, and since the Drone is supposed to be automatic/not require user modifications, I removed multiprocessing for robustness, but it would be nice to have it back at some point.
• New tests for the class methods have not been added yet.

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[coveralls]

Coverage decreased (-0.7%) to 82.995% when pulling 270e3d9 on nwinner:patch-2 into df0f9ba on materialsproject:master.

[shyuep]

Thanks!