Add ability to generate ER hypergraphs without multiedges

.github/workflows/test.yml

@@ -15,10 +15,10 @@ jobs:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

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>`
@@ -81,12 +86,6 @@ 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>`

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)
 

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

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

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