Default weight to 1 for unweighted graph during n2v (#789)

* Allow undirected graphs for n2v

graspologic/embed/n2v.py

@@ -130,7 +130,7 @@ def node2vec_embed(
         f"Completed. Ending time is {str(end)} Elapsed time is {str(start - end)}"
     )
 
-    labels = node2vec_graph.original_graph.nodes()
+    labels = list(node2vec_graph.original_graph.nodes())
     remapped_labels = node2vec_graph.label_map_to_string
 
     return (

graspologic/utils/utils.py

@@ -1004,7 +1004,7 @@ def remap_labels(
 
 
 def remap_node_ids(
-    graph: nx.Graph, weight_attribute: str = "weight"
+    graph: nx.Graph, weight_attribute: str = "weight", weight_default: float = 1.0
 ) -> Tuple[nx.Graph, Dict[Any, str]]:
     """
     Given a graph with arbitrarily types node ids, return a new graph that contains the exact same edgelist
@@ -1016,7 +1016,8 @@ def remap_node_ids(
         A graph that has node ids of arbitrary types.
     weight_attribute : str,
         Default is ``weight``. An optional attribute to specify which column in your graph contains the weight value.
-
+    weight_default : float,
+        Default edge weight to use if a weight is not found on an edge in the graph
     Returns
     -------
     Tuple[nx.Graph, Dict[Any, str]]
@@ -1030,10 +1031,18 @@ def remap_node_ids(
     if not isinstance(graph, nx.Graph):
         raise TypeError("graph must be of type nx.Graph")
 
+    if not nx.is_weighted(graph, weight=weight_attribute):
+        warnings.warn(
+            f'Graph has at least one unweighted edge using weight_attribute "{weight_attribute}". '
+            f'Defaulting unweighted edges to "{weight_default}"'
+        )
+
     node_id_dict = dict()
     graph_remapped = type(graph)()
 
-    for source, target, weight in graph.edges(data=weight_attribute):
+    for source, target, weight in graph.edges(
+        data=weight_attribute, default=weight_default
+    ):
         if source not in node_id_dict:
             node_id_dict[source] = str(len(node_id_dict.keys()))
 

tests/embed/test_n2v.py

@@ -1,7 +1,6 @@
 # Copyright (c) Microsoft Corporation and contributors.
 # Licensed under the MIT License.
 
-import io
 import networkx as nx
 import numpy as np
 import unittest
@@ -106,6 +105,34 @@ def test_node2vec_embedding_florentine_graph_correct_shape_is_returned(self):
         # vocab list should have exactly 34 elements
         self.assertEqual(len(vocab_list), 15)
 
+    def test_node2vec_embedding_unweighted_florentine_graph_correct_shape_is_returned(
+        self,
+    ):
+        graph = nx.florentine_families_graph()
+
+        model = gc.embed.node2vec_embed(graph)
+        model_matrix: np.ndarray = model[0]
+        vocab_list = model[1]
+        self.assertIsNotNone(model)
+        self.assertIsNotNone(model[0])
+        self.assertIsNotNone(model[1])
+
+        # model matrix should be 34 x 128
+        self.assertEqual(model_matrix.shape[0], 15)
+        self.assertEqual(model_matrix.shape[1], 128)
+
+        # vocab list should have exactly 34 elements
+        self.assertEqual(len(vocab_list), 15)
+
+    def test_node2vec_same_labels_are_returned(self):
+        graph = nx.florentine_families_graph()
+        node_ids = list(graph.nodes())
+
+        embedding, labels = gc.embed.node2vec_embed(graph)
+
+        for i in range(len(node_ids)):
+            self.assertEqual(node_ids[i], labels[i])
+
     def test_node2vec_embedding_barbell_graph_correct_shape_is_returned(self):
         graph = nx.barbell_graph(25, 2)
         for s, t in graph.edges():

tests/test_utils.py

@@ -1,7 +1,9 @@
 # Copyright (c) Microsoft Corporation and contributors.
 # Licensed under the MIT License.
 
+import logging
 import unittest
+import warnings
 from math import sqrt
 
 import networkx as nx
@@ -587,6 +589,21 @@ def test_remap_node_ids_invalid_typ_raises_typeerror(self):
             with pytest.raises(TypeError):
                 gus.remap_node_ids(graph=type())
 
+    def test_remap_node_ids_unweighted_graph_raises_warning(self):
+        with warnings.catch_warnings(record=True) as warnings_context_manager:
+            graph = nx.florentine_families_graph()
+
+            gus.remap_node_ids(graph)
+
+            self.assertEqual(len(warnings_context_manager), 1)
+            self.assertTrue(
+                issubclass(warnings_context_manager[0].category, UserWarning)
+            )
+            self.assertTrue(
+                "Graph has at least one unweighted edge"
+                in str(warnings_context_manager[0].message)
+            )
+
     def _assert_graphs_are_equivalent(self, graph, new_graph, new_node_ids):
         self.assertTrue(len(new_graph.nodes()) == len(graph.nodes()))
         self.assertTrue(len(new_graph.edges()) == len(graph.edges()))