Add ability to generate ER hypergraphs without multiedges (#596)

* Add ability to generate ER hypergraphs without multiedges * update * Fix #361 * Revert "Fix #361" This reverts commit 28cbbf3. * Update test.yml * fix non-multi-edge probability * formatting * Update xgi/generators/uniform.py Co-authored-by: Maxime Lucas <[email protected]> * Update using-xgi.rst * Response to review * Update uniform.py * Update xgi/generators/uniform.py Co-authored-by: Maxime Lucas <[email protected]> * Update xgi/generators/uniform.py Co-authored-by: Maxime Lucas <[email protected]> * Update xgi/generators/uniform.py Co-authored-by: Maxime Lucas <[email protected]> * Update xgi/generators/uniform.py Co-authored-by: Maxime Lucas <[email protected]> * Update xgi/generators/uniform.py Co-authored-by: Maxime Lucas <[email protected]> * Update xgi/generators/uniform.py Co-authored-by: Maxime Lucas <[email protected]> * updates --------- Co-authored-by: Maxime Lucas <[email protected]>
xgi-org · Oct 10, 2024 · f2e2241 · f2e2241
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diff --git a/docs/source/using-xgi.rst b/docs/source/using-xgi.rst
@@ -27,6 +27,11 @@ Nicholas W. Landry, Ilya Amburg, Mirah Shi, and Sinan Aksoy, "Filtering higher-o
 :bdg-link-primary-line:`Paper <https://doi.org/10.1088/2632-072X/ad253a>`
 :bdg-link-primary-line:`Code <https://github.com/nwlandry/filtering-higher-order-datasets>`
 
+Nicholas W. Landry, William Thompson, Laurent Hébert-Dufresne, and Jean-Gabriel Young, "Reconstructing networks from simple and complex contagions", Physical Review E **110**, L042301 (2024).
+
+:bdg-link-primary-line:`Paper <https://doi.org/10.1103/PhysRevE.110.L042301>`
+:bdg-link-primary-line:`Code <https://github.com/nwlandry/complex-network-reconstruction>`
+
 Nicholas W. Landry, Jean-Gabriel Young, and Nicole Eikmeier, "The simpliciality of higher-order networks", *EPJ Data Science* **13**, 17 (2024).
 
 :bdg-link-primary-line:`Paper <https://doi.org/10.1140/epjds/s13688-024-00458-1>`
@@ -86,12 +91,6 @@ Robin Delabays, Giulia De Pasquale, Florian Dörfler, and Yuanzhao Zhang, "Hyper
 :bdg-link-primary-line:`Paper <https://arxiv.org/abs/2402.00078>`
 :bdg-link-primary-line:`Code <https://github.com/TaylorBasedHypergraphInference/THIS>`
 
-Nicholas W. Landry, William Thompson, Laurent Hébert-Dufresne, and Jean-Gabriel Young, "Complex contagions can outperform simple contagions for network reconstruction with dense networks or saturated dynamics", arXiv:2405.00129
-
-:bdg-link-primary-line:`Paper <https://arxiv.org/abs/2405.00129>`
-:bdg-link-primary-line:`Code <https://github.com/nwlandry/complex-network-reconstruction>`
-
-
 Maxime Lucas, Luca Gallo, Arsham Ghavasieh, Federico Battiston, and Manlio De Domenico, "Functional reducibility of higher-order networks", arXiv:2404.08547 (2024).
 
 :bdg-link-primary-line:`Paper <https://arxiv.org/abs/2404.08547>`

diff --git a/tests/generators/test_uniform.py b/tests/generators/test_uniform.py
@@ -1,5 +1,6 @@
 import numpy as np
 import pytest
+from scipy.special import comb
 
 import xgi
 from xgi.exception import XGIError
@@ -150,14 +151,29 @@ def test_uniform_HPPM():
 def test_uniform_erdos_renyi_hypergraph():
     m = 2
     n = 10
-    k = 2
-    H1 = xgi.uniform_erdos_renyi_hypergraph(n, m, k, seed=0)
+    p = 1
+    H1 = xgi.uniform_erdos_renyi_hypergraph(n, m, p, seed=0)
+    ne1 = H1.num_edges
+    H1.merge_duplicate_edges(rename="tuple")
+    ne2 = H1.num_edges
+    assert ne1 == ne2
+    assert ne1 == comb(n, m)
 
     assert H1.num_nodes == 10
     assert xgi.unique_edge_sizes(H1) == [2]
 
+    H2 = xgi.uniform_erdos_renyi_hypergraph(n, m, p, seed=0, multiedges=True)
+    print(H2.edges)
+    ne1 = H2.num_edges
+    H2.merge_duplicate_edges()
+    ne2 = H2.num_edges
+    assert ne1 != ne2
+    assert ne1 == n**m - n  # remove loopy edges
+
     # test that the seed works
-    H2 = xgi.uniform_erdos_renyi_hypergraph(n, m, k, seed=0)
+    p = 0.1
+    H1 = xgi.uniform_erdos_renyi_hypergraph(n, m, p, seed=0)
+    H2 = xgi.uniform_erdos_renyi_hypergraph(n, m, p, seed=0)
 
     assert H1.edges.members(dtype=dict) == H2.edges.members(dtype=dict)
 

diff --git a/xgi/core/dihypergraph.py b/xgi/core/dihypergraph.py
@@ -1039,8 +1039,7 @@ def cleanup(self, isolates=False, relabel=True, in_place=True):
 
             convert_labels_to_integers(_DH, in_place=True)
 
-        if not in_place:
-            return _DH
+        return _DH
 
     def freeze(self):
         """Method for freezing a dihypergraph which prevents it from being modified

diff --git a/xgi/core/hypergraph.py b/xgi/core/hypergraph.py
@@ -1487,8 +1487,7 @@ def cleanup(
 
             convert_labels_to_integers(_H, in_place=True)
 
-        if not in_place:
-            return _H
+        return _H
 
     def freeze(self):
         """Method for freezing a hypergraph which prevents it from being modified

diff --git a/xgi/core/simplicialcomplex.py b/xgi/core/simplicialcomplex.py
@@ -848,8 +848,7 @@ def cleanup(self, isolates=False, connected=True, relabel=True, in_place=True):
 
             convert_labels_to_integers(_S, in_place=True)
 
-        if not in_place:
-            return _S
+        return _S
 
     def freeze(self):
         """Method for freezing a simplicial complex