included functions from publication

[maximelucas]

I added two functions I made here: https://github.com/maximelucas/HOI_shape_sync_differently/blob/main/utils.py

• shuffle_hyperedges(H, order, p): shuffle hyperedges with a given probability
• node_swap(H, nid1, nid2, order): swap node membership in edges of given order
• added tests for both

I put them in a new file generators/randomizing.py.

[codecov]

Codecov Report

Patch coverage: 92.06% and project coverage change: +0.01 🎉

Comparison is base (d7e59cc) 90.95% compared to head (d4dbaf0) 90.97%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #400      +/-   ##
==========================================
+ Coverage   90.95%   90.97%   +0.01%     
==========================================
  Files          47       48       +1     
  Lines        3882     3944      +62     
==========================================
+ Hits         3531     3588      +57     
- Misses        351      356       +5     

Impacted Files	Coverage Δ
xgi/generators/randomizing.py	91.80% <91.80%> (ø)
xgi/generators/__init__.py	100.00% <100.00%> (ø)

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[nwlandry]

Overall looks good! My biggest question would be if you could mirror some of the same syntax in the double_edge_swap method of the hypergraph class. No worries if it doesn't make sense.

[maximelucas]

Good point, let me have a look. You mean like the docstrings and variable names?

Btw, should we also move double_edge_swap to randomizing.py? Or should we at least have them in the same file? Since they're similar in ideas.

[nwlandry]

I see double edge swap as a fundamental edge operation so I would keep in in Hypergraph for now. I didn't look very closely, but the contents of node_swap() seem to have similarities to what is implemented in double_edge_swap(). Either node_swap() could call double_edge_swap() or just use some of the same algorithm/variable names. But maybe there's not as direct a correspondence as I thought.

[maximelucas]

Finally had a better look.

• functionality: they are similar but different. double_edge_swap() picks two nodes and two edges, and swaps the membership of those two nodes in those two edges. node_swap() also picks two nodes, but then swaps their membership in all edges that they are part of, not just two.

• naming: It's your function, but looping over all the edges that contain them. Because of that, it felt more natural for me to call it "node swap" rather than edge swap. Your function is more "symmetric" wrt to nodes and edges, I guess it could also be called "double_node_swap"?

• location: to me in might make more sense conceptually to put both of them in randomizing.py? I understand that you see the swap as a fundamental operation. hypergraph.py now contains almost only methods to remove/add nodes/edges/attributes, "creating structure". In my mind, the two swap functions take an existing structure, and modify it by switching things around. In my case, I wrote node_swap() with randomization in mind, to degree sequences intact but changing degree correlations between orders. Maybe yours is less random as you pick the edges to use.

• implementation: node_swap() is clearly based on your implementation of double_edge_swap() (variable names, structure, etc.). I added a few initial checks to make sure that the queried nodes exist etc. Conceptually it could be implemented as a loop where each iteration uses your function in practice I remember I thought that would be more of a hassle than anything.

Happy to change anything, let me know what you think.

[nwlandry]

@maximelucas: I'm good with you merging it, thanks for the additional clarification. We can probably revisit whether double_edge_swap should be in the Hypergraph class.