Ref training nlist

[chrisiacovella]

Pull Request Summary

The last PR (#274) got closed accidentally and I can't reopen for some reason.
This relates to some of the changes suggested in Issue #269. Specifically, this streamlines the Neighborlist for training. The code has changed quite a bit since these initial classes had been sketched out, and this should hopefully make things clearer and make the code easier to read. This also will reduce the need to massage the config dict inputs related to the neighbor list cutoff that currently needs to be done.

Key changes

Notable points that this PR has either accomplished or will accomplish.

• The key logic used in what had been the NeighborList class is merged in the CalculateInteractingPairs class.
• The Neighborlist class has been removed.
• CalculateInteractingPairs is renamed NeighborListForTraining and moved to the neighbors.py file
• The PairList class has been moved to the neighbors.py file
• Update documentation to reflect the naming changes and locations of several key classes.

Associated Issue(s)

• NNP Factory Class Function Redesign #269

Pull Request Checklist

• Issue(s) raised/addressed and linked
• Includes appropriate unit test(s)
• Appropriate docstring(s) added/updated
• Appropriate .rst doc file(s) added/updated
• PR is ready for review

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 92.30769% with 8 lines in your changes missing coverage. Please review.

Project coverage is 85.33%. Comparing base (b594cfe) to head (f55d08e).

Additional details and impacted files

[chrisiacovella]

Since this was approved before being accidentally closed, I'm going to just go ahead and merge.