Restructure folder for generators and linalg

[maximelucas]

Following #319

[codecov]

Codecov Report

Patch coverage: 97.34% and project coverage change: +0.05 🎉

Comparison is base (7ee8aa2) 90.29% compared to head (d848f70) 90.35%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #321      +/-   ##
==========================================
+ Coverage   90.29%   90.35%   +0.05%     
==========================================
  Files          36       41       +5     
  Lines        2926     2954      +28     
==========================================
+ Hits         2642     2669      +27     
- Misses        284      285       +1     

Impacted Files	Coverage Δ
xgi/drawing/draw.py	72.39% <ø> (ø)
xgi/generators/classic.py	94.73% <ø> (-1.53%)	⬇️
xgi/generators/uniform.py	93.91% <0.00%> (ø)
xgi/readwrite/xgi_data.py	94.00% <ø> (ø)
xgi/dynamics/synchronization.py	81.96% <60.00%> (+0.30%)	⬆️
xgi/generators/random.py	83.07% <96.00%> (ø)
xgi/generators/simplicial_complexes.py	96.47% <96.47%> (ø)
xgi/linalg/laplacian_matrix.py	97.82% <97.82%> (ø)
xgi/linalg/hodge_matrix.py	97.91% <97.91%> (ø)
xgi/generators/__init__.py	100.00% <100.00%> (ø)
... and 4 more

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[maximelucas]

It's already big enough to review I'd say.

Done:

• divided linalg into: hypergraph_matrix, hodge_matrix, and laplacian_matrix
• divided the generators into: classic, simple, lattice, random, uniform, simplicial_complexes
• merge the uniform and nonuniform random_hypergraph() (this resulted in not have the option to pass a desired degree like the uniform version had, but we could add an external function to convert p to degree)
• divided the tests accordingly

To do:

• rename generators consistently

[nwlandry]

Overall, looks good! Some high-level things:

• Can you update the docs to match the change in structure? In addition, can you move utils and linalg into their own folders and update with the new module names? For reference, see PR Add clustering coefficient definitions #316.
• The one nice thing about the uniform Erdös-Rényi hypergraph is that it had O(|V| +|E|) complexity which I needed for some larger hypergraphs. Is there a way to incorporate this in the random_hypergraph() function?

[nwlandry]

I don't know if I like the "hypergraph_matrix.py" name. Maybe break this into "incidence" and "adjacency"? But of course the intersection profile and degree matrices don't clearly belong to either. My concern is that these matrices aren't exclusively for hypergraphs in the way that we set them up.

[maximelucas]

Not exclusively for hypergraphs in the sense that they also work for simplicial complexes? But SCs are HGs O:)
We could just call it "matrix.py", or "structure". It's not so clear how to break into less than 5 files indeed.

[nwlandry]

Thanks for tackling this! A lot of good stuff here. I would say that the big thing is to add docs for the restructured files and there's just a few comments. Nice work!

[nwlandry]

Hi @maximelucas - I had the opportunity to look over this PR and looks great! I hope you don't mind that I did the following:

• I added the specific files relating to the modules that you added.
• I added the uniform_erdos_renyi_hypergraph back in, and I will add this as an issue so that eventually we can port it over to the random module as fast_random_hypergraph or something.

[maximelucas]

Perfect, thanks Nich!