Revert "Add unit tests (#147)"

This reverts commit be89732.

README.md

@@ -88,8 +88,6 @@ 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_json
-   .. autofunction:: write_json
+   .. autofunction:: read_hypergraph_json
+   .. autofunction:: write_hypergraph_json
 
 
 

tests/algorithms/test_assortativity.py

@@ -26,37 +26,26 @@ def test_dynamical_assortativity(edgelist1, edgelist6):
     assert abs(xgi.dynamical_assortativity(H1) - -0.0526) < 1e-3
 
 
-def test_degree_assortativity(edgelist1, edgelist5):
+def test_degree_assortativity(edgelist1, edgelist6):
     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(edgelist5)
+    H2 = xgi.Hypergraph(edgelist6)
     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

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

tests/classes/test_iddict.py

@@ -1,7 +1,7 @@
 import pytest
 
 import xgi
-from xgi.exception import IDNotFound, XGIError
+from xgi.exception import IDNotFound
 
 
 def test_iddict(edgelist1):
@@ -17,17 +17,6 @@ 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

@@ -317,12 +317,6 @@ 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))
@@ -349,9 +343,6 @@ 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
@@ -379,10 +370,6 @@ 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)
@@ -420,24 +407,3 @@ 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

@@ -3,7 +3,6 @@
 import pytest
 
 import xgi
-from xgi.exception import XGIError
 
 bipartite_edgelist_spaces_string = """0 0
 # Comment
@@ -57,32 +56,6 @@ 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"]
@@ -116,18 +89,6 @@ 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

@@ -51,10 +51,6 @@ def test_parse_edgelist():
         [2, 3],
     ]
 
-    # This will fail because the "test" node ID can't be converted to int
-    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):
     _, filename = tempfile.mkstemp()

tests/readwrite/test_hypergraph_json.py

@@ -0,0 +1,114 @@
+import tempfile
+
+import xgi
+
+json_string = """
+{
+    "hypergraph-data": {
+      "name": "test",
+      "author": "Nicholas Landry"
+    },
+    "node-data": {
+      "1": {
+        "color": "blue"
+      },
+      "2": {
+        "color": "yellow"
+      },
+      "3": {
+        "color": "cyan"
+      },
+      "4": {
+        "color": "green"
+      }
+    },
+    "edge-data": {
+      "edge1": {
+        "weight": 2
+      },
+      "edge2": {
+        "weight": 4
+      },
+      "edge3": {
+        "weight": -1
+      }
+    },
+    "edge-dict": {
+      "edge1": [
+        "1",
+        "2"
+      ],
+      "edge2": [
+        "2",
+        "3",
+        "4"
+      ],
+      "edge3": [
+        "1",
+        "4"
+      ]
+    }
+  }
+"""
+
+
+def test_read_hypergraph_json():
+    _, filename = tempfile.mkstemp()
+    with open(filename, "w") as file:
+        file.write(json_string)
+
+    H1 = xgi.read_hypergraph_json(filename, nodetype=int)
+    H2 = xgi.read_hypergraph_json(filename)
+
+    assert list(H1.nodes) == [1, 2, 3, 4]
+    assert list(H1.edges) == ["edge1", "edge2", "edge3"]
+
+    assert list(H2.nodes) == ["1", "2", "3", "4"]
+    assert H1["name"] == "test"
+    assert H1["author"] == "Nicholas Landry"
+    assert [H1.edges.members(id) for id in H1.edges] == [[1, 2], [2, 3, 4], [1, 4]]
+    assert [H2.edges.members(id) for id in H2.edges] == [
+        ["1", "2"],
+        ["2", "3", "4"],
+        ["1", "4"],
+    ]
+
+    assert H1.nodes[1]["color"] == "blue"
+    assert H1.edges["edge2"]["weight"] == 4
+
+
+def test_write_hypergraph_json(edgelist1):
+    _, filename = tempfile.mkstemp()
+    H1 = xgi.Hypergraph(edgelist1)
+
+    H1["name"] = "test"
+    H1["author"] = "Nicholas Landry"
+
+    node_attr_dict = {
+        1: {"name": "Leonie"},
+        2: {"name": "Ilya"},
+        3: {"name": "Alice"},
+        4: {"name": "Giovanni"},
+    }
+    xgi.set_node_attributes(H1, node_attr_dict)
+
+    edge_attr_dict = {
+        0: {"weight": 1},
+        1: {"weight": 2},
+        2: {"weight": 3},
+        3: {"weight": -1},
+    }
+    xgi.set_edge_attributes(H1, edge_attr_dict)
+
+    xgi.write_hypergraph_json(H1, filename)
+
+    H2 = xgi.read_hypergraph_json(filename, nodetype=int, edgetype=int)
+
+    assert H1.nodes == H2.nodes
+    assert H1.edges == H2.edges
+    assert [H1.edges.members(id) for id in H1.edges] == [
+        H2.edges.members(id) for id in H2.edges
+    ]
+    assert H2.nodes[2] == {"name": "Ilya"}
+    assert H2.edges[1] == {"weight": 2}
+    assert H2["name"] == "test"