Extension of transform module

[EnricoTrizio]

Description

Adding some preprocessing tools to the transform module, including descriptors computation and tools.

NB-1 Transform object are supposed not to have trainable parameters.
NB-2 Position-dependent descriptors are implemented only for cubic/orthorhombic cells.

The structure of the module is:

Tools

• Normalization
• Switching functions (new)
• Continuous Histogram (new, derivable histogram using KDE)

Descriptors, acting on positions

• Multiple descriptors (new, wrapper class to compute multiple descriptors on the same set of positions)
• Pairwise distances (new, computes ALL pairwise distances from a set of positions)
• Torsional angle (new, computes the torsional angle from a set of positions + index of 4 involved atoms)
• Coordination number (new, computes from a set of positions coordination numbers of elements of group A wrt group B)
• Eigs adjacency matrix (new, computes adjacency matrix eigenvalues. Could be moved to a tutorial)

Already implemented but likely to be kept out of this PR:

• Radius graph (compute graph inputs in the format: edge sources, edge destinations and edge distances)
• Radial distribution function (compute RDF from a set of position and optionally the integral of a peak)

Status

• Ready to go

[andrrizzi]

Looks good! I've left a few comment but it's only nitpicking.

For the structure, it looks ok to me, but I'd tend to have the least possible number of packages/modules called tools or utils. I might be missing the rationale here though. I usually use tools essentially as synonym for utils meaning "anything I don't know where else to put/how else to organize".

Maybe we could simply move all the transform/tools/*.py modules directly in transform/*.py. Some of the elements (like Inverse or Statistics) might deserve their own inverse.py or statistics.py module. This is mostly taste anyway. It might not be the prettiest structure to have a bunch of small modules inside a package but I usually find it helpful when I navigate codebases.