Simplify dihypergraph

HOW_TO_CONTRIBUTE.md

@@ -7,8 +7,8 @@ Please note we have a [code of conduct](/CODE_OF_CONDUCT.md), please follow it i
 ## Pull Request process
 
 1. Download the dependencies in the developer [requirements file](/requirements/developer.txt).
-2. [Optional, but STRONGLY preferred] Add unit tests for features being added or bugs being fixed.
-3. [Optional, but STRONGLY preferred] Include any new method/function in the corresponding docs file.
+2. Add unit tests for features being added or bugs being fixed.
+3. Include any new method/function in the corresponding docs file.
 4. Run `pytest` to verify all unit tests pass.
 5. Identify the unnecessary imports in the
    1. source code by running `pylint xgi/ --disable all --enable W0611`

README.md

@@ -125,7 +125,7 @@ This library may not meet your needs and if this is this case, consider checking
 * [halp](http://murali-group.github.io/halp): A Python package with directed and undirected hypergraph implementations and several algorithms.
 * [Hypergraph Analysis Toolbox (HAT)](https://hypergraph-analysis-toolbox.readthedocs.io): A Python/Matlab package for hypergraph construction, visualization, and analysis (Especially for Pore-C data).
 * [Hypergraphx](https://hypergraphx.readthedocs.io): A Python for representing, analyzing, and visualizing hypergraphs.
-* [HyperNetX](https://hypernetx.readthedocs.io/en/latest/): A Python package for representing, analyzing, and visualizing hypergraphs.
+* [HyperNetX](https://hypernetx.readthedocs.io): A Python package for representing, analyzing, and visualizing hypergraphs.
 * [NetworkX](https://networkx.org): A Python package for representing, analyzing, and visualizing networks.
 * [Reticula](https://docs.reticula.network): A Python package wrapping C++ functions for representing, analyzing, and visualizing temporal and static graphs and hypergraphs.
 

docs/source/api/core.rst

@@ -11,5 +11,4 @@ core functionality
    ~xgi.core.dihypergraph
    ~xgi.core.simplicialcomplex
    ~xgi.core.views
-   ~xgi.core.diviews
    ~xgi.core.globalviews

docs/source/api/core/xgi.core.diviews.DiEdgeView.rst → docs/source/api/core/xgi.core.views.DiEdgeView.rst

@@ -1,7 +1,7 @@
-xgi.core.diviews.DiEdgeView
-===========================
+xgi.core.views.DiEdgeView
+=========================
 
-.. currentmodule:: xgi.core.diviews
+.. currentmodule:: xgi.core.views
 
 .. autoclass:: DiEdgeView
    :show-inheritance:

docs/source/api/core/xgi.core.diviews.DiNodeView.rst → docs/source/api/core/xgi.core.views.DiNodeView.rst

@@ -1,7 +1,7 @@
-xgi.core.diviews.DiNodeView
-===========================
+xgi.core.views.DiNodeView
+=========================
 
-.. currentmodule:: xgi.core.diviews
+.. currentmodule:: xgi.core.views
 
 .. autoclass:: DiNodeView
    :show-inheritance:

docs/source/api/core/xgi.core.views.rst

@@ -13,4 +13,6 @@
 
         IDView
         NodeView
-        EdgeView
+        EdgeView
+        DiNodeView
+        DiEdgeView

docs/source/using-xgi.rst

@@ -12,7 +12,7 @@ Published work
 2024
 ----
 
-Nicholas W. Landry, Ilya Amburg, Mirah Shi, and Sinan Aksoy, "Filtering higher-order datasets", *Journal of Physics: Complexity* **5** 015006 (2024).
+Nicholas W. Landry, Ilya Amburg, Mirah Shi, and Sinan Aksoy, "Filtering higher-order datasets", *Journal of Physics: Complexity* **5**, 015006 (2024).
 
 :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>`
@@ -22,7 +22,7 @@ Nicholas W. Landry, Jean-Gabriel Young, and Nicole Eikmeier, "The simpliciality
 :bdg-link-primary-line:`Paper <https://doi.org/10.1140/epjds/s13688-024-00458-1>`
 :bdg-link-primary-line:`Code <https://github.com/nwlandry/the-simpliciality-of-higher-order-networks>`
 
-Leonie Neuhäuser, Michael Scholkemper, Francesco Tudisco, and Michael T. Schaub, "Learning the effective order of a hypergraph dynamical system", *Science Advances* **10**,eadh4053 (2024).
+Leonie Neuhäuser, Michael Scholkemper, Francesco Tudisco, and Michael T. Schaub, "Learning the effective order of a hypergraph dynamical system", *Science Advances* **10**, eadh4053 (2024).
 
 :bdg-link-primary-line:`Paper <https://doi.org/10.1126/sciadv.adh4053>`
 :bdg-link-primary-line:`Code <https://git.rwth-aachen.de/netsci/publication-2023-learning-the-effective-order-of-a-hypergraph-dynamical-system>`
@@ -67,11 +67,17 @@ Gonzalo Contreras-Aso, Regino Criado, and Miguel Romance, "Beyond directed hyper
 :bdg-link-primary-line:`Paper <https://arxiv.org/abs/2403.11825>`
 :bdg-link-primary-line:`Code <https://github.com/goznalo-git/DirectedHyperCentrality>`
 
-Robin Delabays, Giulia De Pasquale, Florian Dörfler, Yuanzhao Zhang, "Hypergraph reconstruction from dynamics", arXiv:2402.00078 (2024).
+Robin Delabays, Giulia De Pasquale, Florian Dörfler, and Yuanzhao Zhang, "Hypergraph reconstruction from dynamics", arXiv:2402.00078 (2024).
 
 :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>`
@@ -90,7 +96,7 @@ Iacopo Iacopini, Márton Karsai, and Alain Barrat, "The temporal dynamics of gro
 :bdg-link-primary-line:`Paper <https://arxiv.org/abs/2306.09967>`
 :bdg-link-primary-line:`Code <https://github.com/iaciac/temporal-group-interactions>`
 
-Yuanzhao Zhang, Per Sebastian Skardal, Federico Battiston, Giovanni Petri, Maxime Lucas, "Deeper but smaller: Higher-order interactions increase linear stability but shrink basins", arXiv:2309.16581 (2023).
+Yuanzhao Zhang, Per Sebastian Skardal, Federico Battiston, Giovanni Petri, and Maxime Lucas, "Deeper but smaller: Higher-order interactions increase linear stability but shrink basins", arXiv:2309.16581 (2023).
 
 :bdg-link-primary-line:`Paper <https://arxiv.org/abs/2309.16581>`
 :bdg-link-primary-line:`Code <https://github.com/maximelucas/basins_and_triangles>`

tests/algorithms/test_shortest_path.py

@@ -1,8 +1,6 @@
 import numpy as np
-import pytest
 
 import xgi
-from xgi.exception import XGIError
 
 
 def test_single_source_shortest_path_length(edgelist1):

tests/core/test_dihypergraph.py

@@ -162,7 +162,7 @@ def test_add_edge_warns_when_overwriting_edge_id():
     H2.add_edge(([3, 4], [5, 6, 7]))
     with pytest.warns(Warning):
         H2.add_edge(([5, 6], [8]), id=0)
-    assert H2._edge_out == {0: {1, 2}, 1: {3, 4}}
+    assert {i: e["in"] for i, e in H2._edge.items()} == {0: {1, 2}, 1: {3, 4}}
 
 
 def test_add_edge_with_id():
@@ -241,7 +241,7 @@ def test_add_edges_from_format2():
     H1 = xgi.DiHypergraph([({1, 2}, {3}), ({2, 3, 4}, {1})])
     with pytest.warns(Warning):
         H1.add_edges_from([(({1, 3}, {2}), 0)])
-    assert H1._edge_out == {0: {1, 2}, 1: {2, 3, 4}}
+    assert {i: e["in"] for i, e in H1._edge.items()} == {0: {1, 2}, 1: {2, 3, 4}}
 
 
 def test_add_edges_from_format3():
@@ -280,7 +280,7 @@ def test_add_edges_from_format4():
     H1 = xgi.DiHypergraph([({1, 2}, {3}), ({2, 3, 4}, {1})])
     with pytest.warns(Warning):
         H1.add_edges_from([(({0, 1}, {2}), 0, {"color": "red"})])
-    assert H1._edge_out == {0: {1, 2}, 1: {2, 3, 4}}
+    assert {i: e["out"] for i, e in H1._edge.items()} == {0: {3}, 1: {1}}
 
 
 def test_add_edges_from_dict(diedgedict1):
@@ -388,7 +388,7 @@ def test_copy_issue128():
 def test_remove_node_weak(diedgelist1, diedgelist2):
     H = xgi.DiHypergraph(diedgelist1)
 
-    # node in the tail
+    # # node in the tail
     assert 1 in H
     H.remove_node(1)
     assert 1 not in H
@@ -615,7 +615,6 @@ def test_cleanup(dihypergraph1):
     assert "test" not in cleanDH
     assert set(cleanDH.nodes) == {"a", "b", "c", "d"}
     assert set(cleanDH.edges) == {"e1", "e2", "e3"}
-    edges = cleanDH.edges.dimembers()
     assert cleanDH.edges.dimembers("e1") == ({"a", "b"}, {"c"})
     assert cleanDH.edges.dimembers("e2") == ({"b"}, {"c", "d"})
     assert cleanDH.edges.dimembers("e3") == ({"b"}, {"c"})
@@ -649,5 +648,9 @@ def test_cleanup(dihypergraph1):
     assert cleanDH.edges.dimembers(1) == ({1}, {2, 3})
     assert cleanDH.edges.dimembers(2) == ({1}, {2})
 
-    assert cleanDH._edge_in == xgi.dual_dict(cleanDH._node_out)
-    assert cleanDH._edge_out == xgi.dual_dict(cleanDH._node_in)
+    node_in = {i: n["in"] for i, n in cleanDH._node.items()}
+    node_out = {i: n["out"] for i, n in cleanDH._node.items()}
+    edge_in = {i: e["in"] for i, e in cleanDH._edge.items()}
+    edge_out = {i: e["out"] for i, e in cleanDH._edge.items()}
+    assert edge_in == xgi.dual_dict(node_out)
+    assert edge_out == xgi.dual_dict(node_in)