Added cleanup method to all classes

[nwlandry]

Fixes #195.

This PR

• Adds the cleanup() method to SimplicialComplex and DiHypergraph and fixes several bugs in the cleanup() method for Hypergraph.
• Adds unit tests.
• Fixes the strong node removal in Issue Strong node removal breaks the internal Hypergraph data structure #445.
• Adds the isolates() method to the DiNodeView class.
• Adds the connected kwarg to cleanup() for hypergraphs and simplicial complexes, which removes nodes/edges not in the largest component.
• is_frozen is now a property.

[codecov]

Codecov Report

Patch coverage: 98.16% and project coverage change: +0.89% 🎉

Comparison is base (ea1aaf6) 90.94% compared to head (7435da9) 91.83%.
Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #440      +/-   ##
==========================================
+ Coverage   90.94%   91.83%   +0.89%     
==========================================
  Files          59       60       +1     
  Lines        4076     4251     +175     
==========================================
+ Hits         3707     3904     +197     
+ Misses        369      347      -22     

Files Changed	Coverage Δ
xgi/core/simplicialcomplex.py	85.66% <96.22%> (+2.39%)	⬆️
xgi/core/dihypergraph.py	98.12% <100.00%> (+0.11%)	⬆️
xgi/core/diviews.py	83.60% <100.00%> (+0.18%)	⬆️
xgi/core/hypergraph.py	93.54% <100.00%> (+6.29%)	⬆️
xgi/utils/utilities.py	95.28% <100.00%> (+0.23%)	⬆️

... and 14 files with indirect coverage changes

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[maximelucas]

Thanks Nich, looks good. Good idea this connected argument!

It's a bit long so I didn't check every single line. Just a few comments.
Also same usual comment, not to fix now: it feels like we have a lot of (almost) redundant code between SC, HG, and DiHG.

[nwlandry]

Thanks Nich, looks good. Good idea this connected argument!

It's a bit long so I didn't check every single line. Just a few comments. Also same usual comment, not to fix now: it feels like we have a lot of (almost) redundant code between SC, HG, and DiHG.

I agree - my goal is to get things working and then we can focus on inheritance/sharing functionality. One of the issues that I ran into was that because SimplicialComplex uses frozen sets, we can only do strong node removal. At that point, it made sense to just implement remove_ node and remove_nodes_from in SimplicialComplex.

[maximelucas]

Thanks for the explanations, looks good :)

[nwlandry]

Thanks for the review, @maximelucas!! I appreciate it :)