Add unit tests

README.md

@@ -88,6 +88,8 @@ The XGI package has been supported by NSF Grant 2121905, ["HNDS-I: Using Hypergr
 ## Other resources
 This library may not meet your needs and if this is this case, consider checking out these other resources:
 * [HyperNetX](https://pnnl.github.io/HyperNetX): A package in Python for representing, analyzing, and visualizing hypergraphs.
+* [Reticula](https://docs.reticula.network/): A package with a Python wrapper of C++ functions for representing, analyzing, and visualizing temporal and static graphs and hypergraphs.
 * [SimpleHypergraphs.jl](https://pszufe.github.io/SimpleHypergraphs.jl/v0.1/): A package in Julia for representing, analyzing, and generating hypergraphs.
+* [HyperGraphs.jl](https://github.com/lpmdiaz/HyperGraphs.jl): A package in Julia for representing, analyzing, and generating hypergraphs which may be oriented and weighted.
 * [hyperG](https://cran.r-project.org/package=HyperG): A package in R for storing and analyzing hypergraphs
 * [NetworkX](https://networkx.org/): A package in Python for representing, analyzing, and visualizing networks.

docs/source/api/readwrite/xgi.readwrite.json.rst

@@ -7,8 +7,8 @@ xgi.readwrite.json
 
    .. rubric:: Functions
 
-   .. autofunction:: read_hypergraph_json
-   .. autofunction:: write_hypergraph_json
+   .. autofunction:: read_json
+   .. autofunction:: write_json
 
 
 

tests/algorithms/test_assortativity.py

@@ -26,26 +26,37 @@ def test_dynamical_assortativity(edgelist1, edgelist6):
     assert abs(xgi.dynamical_assortativity(H1) - -0.0526) < 1e-3
 
 
-def test_degree_assortativity(edgelist1, edgelist6):
+def test_degree_assortativity(edgelist1, edgelist5):
     H1 = xgi.Hypergraph(edgelist1)
     assert -1 <= xgi.degree_assortativity(H1, kind="uniform") <= 1
     assert -1 <= xgi.degree_assortativity(H1, kind="top-2") <= 1
     assert -1 <= xgi.degree_assortativity(H1, kind="top-bottom") <= 1
 
-    H2 = xgi.Hypergraph(edgelist6)
+    H2 = xgi.Hypergraph(edgelist5)
     assert -1 <= xgi.degree_assortativity(H2, kind="uniform") <= 1
     assert -1 <= xgi.degree_assortativity(H2, kind="top-2") <= 1
     assert -1 <= xgi.degree_assortativity(H2, kind="top-bottom") <= 1
 
+    # test "exact" keyword
+    assert -1 <= xgi.degree_assortativity(H1, kind="uniform", exact=True) <= 1
+    assert -1 <= xgi.degree_assortativity(H1, kind="top-2", exact=True) <= 1
+    assert -1 <= xgi.degree_assortativity(H1, kind="top-bottom", exact=True) <= 1
+
 
 def test_choose_degrees(edgelist1, edgelist6):
     H1 = xgi.Hypergraph(edgelist1)
     k = H1.degree()
 
+    # test singleton edges
     with pytest.raises(XGIError):
         e = H1.edges.members(1)
         choose_degrees(e, k)
 
+    # invalid choice function
+    with pytest.raises(XGIError):
+        e = H1.edges.members(0)
+        choose_degrees(e, k, "test")
+
     e = H1.edges.members(0)
     assert np.all(np.array(choose_degrees(e, k)) == 1)
 

tests/classes/test_hypergraph.py

@@ -50,7 +50,8 @@ def test_contains(edgelist1):
     for node in unique_nodes:
         assert node in H
 
-    assert 0 not in H
+    # test TypeError handling
+    assert [1, 2, 3] not in H
 
 
 def test_string():

tests/classes/test_iddict.py

@@ -1,7 +1,7 @@
 import pytest
 
 import xgi
-from xgi.exception import IDNotFound
+from xgi.exception import IDNotFound, XGIError
 
 
 def test_iddict(edgelist1):
@@ -17,6 +17,17 @@ def test_iddict(edgelist1):
     with pytest.raises(IDNotFound):
         H.edges[4]
 
+    assert H.edges[0] == dict()
+
+    with pytest.raises(XGIError):
+        H._edge[None] = [1, 2, 3]
+
+    with pytest.raises(IDNotFound):
+        del H._node["test"]
+
+    with pytest.raises(TypeError):
+        H._node[[0, 1, 2]] = [0, 1]
+
 
 def test_neighbors():
     H = xgi.Hypergraph()

tests/linalg/test_matrix.py

@@ -317,6 +317,12 @@ def test_multiorder_laplacian(edgelist2, edgelist6):
         L1, node_dict1 = xgi.multiorder_laplacian(
             H1, orders=[1, 2], weights=[1, 1], index=True
         )
+
+    # different order and weight lengths
+    with pytest.raises(ValueError):
+        L1, node_dict1 = xgi.multiorder_laplacian(
+            H2, orders=[1, 2], weights=[1, 1, 1], index=True
+        )
     node_dict1 = {k: v for v, k in node_dict1.items()}
     assert L1.shape == (5, 5)
     assert np.all((L1.T == L1))
@@ -343,6 +349,9 @@ def test_multiorder_laplacian(edgelist2, edgelist6):
     assert L2[node_dict2[3], node_dict2[5]] == 0
     assert L2[node_dict2[3], node_dict2[6]] == 0
 
+    L2 = xgi.multiorder_laplacian(H2, orders=[1, 2], weights=[1, 1])
+    assert np.shape(L2) == (6, 6)
+
 
 def test_intersection_profile(edgelist2):
     el1 = edgelist2
@@ -370,6 +379,10 @@ def test_intersection_profile(edgelist2):
 
     assert P2[edge_dict2[2], edge_dict2[2]] == 3
 
+    P2 = xgi.intersection_profile(H1, order=2)
+    assert np.shape(P2) == (1, 1)
+    assert P2[0, 0] == 3
+
 
 def test_clique_motif_matrix(edgelist4):
     H1 = xgi.Hypergraph(edgelist4)
@@ -407,3 +420,24 @@ def test_empty():
     assert xgi.adjacency_matrix(H).shape == (0, 0)
     assert xgi.laplacian(H).shape == (0, 0)
     assert xgi.clique_motif_matrix(H).shape == (0,)
+
+    # with indices
+    data = xgi.incidence_matrix(H, index=True)
+    assert len(data) == 3
+    assert data[0].shape == (0,)
+    assert type(data[1]) == dict and type(data[2]) == dict
+
+    data = xgi.adjacency_matrix(H, index=True)
+    assert len(data) == 2
+    assert data[0].shape == (0, 0)
+    assert type(data[1]) == dict
+
+    data = xgi.laplacian(H, index=True)
+    assert len(data) == 2
+    assert data[0].shape == (0, 0)
+    assert type(data[1]) == dict
+
+    data = xgi.clique_motif_matrix(H, index=True)
+    assert len(data) == 2
+    assert data[0].shape == (0,)
+    assert type(data[1]) == dict

tests/readwrite/test_bipartite_edgelist.py

@@ -1,8 +1,10 @@
 import tempfile
+from typing import Type
 
 import pytest
 
 import xgi
+from xgi.exception import XGIError
 
 bipartite_edgelist_spaces_string = """0 0
 # Comment
@@ -56,6 +58,32 @@ def test_read_bipartite_edgelist(file_string, extra_kwargs):
 
 def test_parse_bipartite_edgelist():
     lines = ["0 0", "1 0", "2 0", "3 0", "4 1", "5 2", "6 2", "6 3", "7 3", "8 3"]
+    bad_lines1 = ["0", "1 0", "2 0", "3 0", "4 1", "5 2", "6 2", "6 3", "7 3", "8 3"]
+    bad_lines2 = [
+        "test 0",
+        "1 0",
+        "2 0",
+        "3 0",
+        "4 1",
+        "5 test",
+        "6 test",
+        "6 3",
+        "7 3",
+        "8 3",
+    ]
+    bad_lines3 = [
+        "0 0",
+        "1 0",
+        "2 0",
+        "3 0",
+        "4 1",
+        "5 test",
+        "6 test",
+        "6 3",
+        "7 3",
+        "8 3",
+    ]
+
     H = xgi.parse_bipartite_edgelist(lines, nodetype=int)
     assert list(H.nodes) == [0, 1, 2, 3, 4, 5, 6, 7, 8]
     assert list(H.edges) == ["0", "1", "2", "3"]
@@ -89,6 +117,18 @@ def test_parse_bipartite_edgelist():
         [3],
     ]
 
+    # test less than two entries per line
+    with pytest.raises(XGIError):
+        xgi.parse_bipartite_edgelist(bad_lines1)
+
+    # test failed nodetype conversion
+    with pytest.raises(TypeError):
+        xgi.parse_bipartite_edgelist(bad_lines2, nodetype=int)
+
+    # test failed edgetype conversion
+    with pytest.raises(TypeError):
+        xgi.parse_bipartite_edgelist(bad_lines3, edgetype=int)
+
 
 def test_write_bipartite_edgelist(edgelist1):
     _, filename = tempfile.mkstemp()

tests/readwrite/test_edgelist.py

@@ -50,6 +50,8 @@ def test_parse_edgelist():
         [1, 4, 7, 8],
         [2, 3],
     ]
+    with pytest.raises(TypeError):
+        xgi.parse_edgelist(["test 2", "2 3 4", "test 4 7 8", "2 3"], nodetype=int)
 
 
 def test_write_edgelist(edgelist1):