Fixing pseudo packing functions

[jgostick]

Fixes #916 Fixes #757 Fixes #649 Fixes #647 Fixes #575

[jgostick]

Got pseudo_gravity_packing working well, the clearance and mode args now work. And adding new spheres to existing structures works...

[codecov[bot]]

Codecov Report

Merging #922 (d3417c0) into dev (f053893) will decrease coverage by 0.2%. Report is 22 commits behind head on dev. The diff coverage is 84.1%.

Additional details and impacted files

@@           Coverage Diff           @@
##             dev    #922     +/-   ##
=======================================
- Coverage   83.1%   83.0%   -0.2%     
=======================================
  Files         36      36             
  Lines       4577    4662     +85     
=======================================
+ Hits        3807    3872     +65     
- Misses       770     790     +20     

[jgostick]

Now that we have declared the dev branch to be "version 3" I think we can merge this PR.