Return ragged arrays in Environment Matching Code

[tommy-waltmann]

Description

This PR makes the point_environments property of the EnvironmentCluster and EnvironmentMotifMatch, as well as the cluster_environments property of EnvironmentCluster, return a list if numpy arrays of different sizes.

Motivation and Context

This is a more intuitive way to return the data to the user, and the padded zero vectors in the previous implementation were confusing.

Resolves: #981

How Has This Been Tested?

Tests have been added to ensure raggedness of the properties which have had their behavior changed.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds or improves functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation improvement (updates to user guides, docstrings, or developer docs)

Checklist:

• I have read the CONTRIBUTING document.
• My code follows the code style of this project.
• I have updated the documentation (if relevant).
• I have added tests that cover my changes (if relevant).
• All new and existing tests passed.
• I have updated the credits.
• I have updated the Changelog.

[tommy-waltmann]

In addition to the changes here, I think the restriction that the disjoint set data structure (EnvDisjointSet) have a max number of neighbors in any given environment can be lifted now. I didn't write that code though, so I'm not quite sure, @vyasr any thoughts?

[vyasr]

Hmm yeah I think that sounds right. The only reason that was needed was to properly size the output arrays and to control iteration bounds, but with a ragged array you can iterate properly over each subarray (environment) so it should be safe to stop tracking that. Let me know if you run into any issues with removing it, but I think it should be fine.

[b-butler]

I am not overly familiar with the environment matching code, but the changes look good.

[bdice]

A few small suggestions.