Merge pull request #16 from pedugnat/str-ids

Use str for node ids + generate_dynamic_graphs rename

Author: pedugnat

README.md

@@ -31,10 +31,10 @@ pip install -U dynnode2vec
 import pickle
 
 from dynnode2vec.dynnode2vec import DynNode2Vec
-from dynnode2vec.utils import generate_dynamic_graphs
+from dynnode2vec.utils import create_dynamic_graph
 
 # Create random graphs
-graphs = generate_dynamic_graphs(
+graphs = create_dynamic_graph(
   n_base_nodes=100, n_steps=50, base_density=0.05
 )
 

dynnode2vec/__init__.py

@@ -7,7 +7,7 @@
 
 from .biased_random_walk import BiasedRandomWalk, RandomWalks
 from .dynnode2vec import DynNode2Vec, Embedding
-from .utils import generate_dynamic_graphs
+from .utils import create_dynamic_graph
 
 
 def get_version() -> str:

dynnode2vec/biased_random_walk.py

@@ -26,7 +26,7 @@ def __init__(self, graph: nx.Graph) -> None:
         :param graph: graph to run walk on
         """
         self.graph = nx.convert_node_labels_to_integers(
-            graph, ordering="sorted", label_attribute="true_label"
+            graph, ordering="default", label_attribute="true_label"
         )
 
         self.mapping: Dict[int, Any] = nx.get_node_attributes(self.graph, "true_label")

dynnode2vec/utils.py

@@ -10,22 +10,23 @@
 
 def sample_nodes(graph: nx.Graph, k: int) -> List[int]:
     """
-    Sample nodes randomly from a graph.
+    Samples nodes randomly from a graph.
     """
     return random.sample(graph.nodes, k=k)
 
 
-def generate_dynamic_graphs(
+def create_dynamic_graph(
     n_base_nodes: int = 100, n_steps: int = 10, base_density: float = 0.01
 ) -> List[nx.Graph]:
     """
-    Generates a list of dynamic graphs, i.e. that depend on the previous graph.
+    Creates a list of graphs representing the evolution of a dynamic graph,
+    i.e. graphs that each depend on the previous graph.
     """
     # Create a random graph
     graph = nx.fast_gnp_random_graph(n=n_base_nodes, p=base_density)
 
     # add one to each node to avoid the perfect case where true_ids match int_ids
-    graph = nx.relabel_nodes(graph, mapping={n: n + 1 for n in graph.nodes()})
+    graph = nx.relabel_nodes(graph, mapping={n: str(n) for n in graph.nodes()})
 
     # initialize graphs list with first graph
     graphs = [graph.copy()]
@@ -38,9 +39,9 @@ def generate_dynamic_graphs(
             graph.remove_node(node)
 
         # add some more nodes
-        node_idx = max(graph.nodes) + 1
+        node_idx = max(map(int, graph.nodes)) + 1
         for i in range(2 * change_size):
-            graph.add_node(node_idx + i)
+            graph.add_node(str(node_idx + i))
 
         # add some edges for the new nodes
         for edge in zip(

tests/test_biased_random_walk.py

@@ -12,11 +12,16 @@
 
 @pytest.fixture(name="graphs")
 def fixture_graphs():
-    return dynnode2vec.utils.generate_dynamic_graphs(
+    return dynnode2vec.utils.create_dynamic_graph(
         n_base_nodes=30, n_steps=5, base_density=0.02
     )
 
 
+def add_random_weights(graph):
+    for *_, data in graph.edges(data=True):
+        data["weight"] = random.random()
+
+
 def test_init(graphs):
     brw = dynnode2vec.biased_random_walk.BiasedRandomWalk(graphs[0])
 
@@ -46,12 +51,11 @@ def test_generate_walk(graphs, ip, iq, weighted):
     # pylint: disable=invalid-name
     # make sure that tested node has at least one neighbor
     graph = graphs[0]
-    graph.add_edge(0, 1, weight=0.5)
+    graph.add_edge("0", "1")
 
     # add random weights to the graph for the weighted case
     if weighted:
-        for _, _, data in graph.edges(data=True):
-            data["weight"] = random.random()
+        add_random_weights(graph)
 
     brw = dynnode2vec.biased_random_walk.BiasedRandomWalk(graph)
     rng = random.Random(0)
@@ -74,8 +78,7 @@ def test_run(graphs, p, q, weighted):
 
     # add random weights to the graph for the weighted case
     if weighted:
-        for *_, data in graph.edges(data=True):
-            data["weight"] = random.random()
+        add_random_weights(graph)
 
     brw = dynnode2vec.biased_random_walk.BiasedRandomWalk(graph)
 

tests/test_dynnode2vec.py

@@ -12,7 +12,7 @@
 
 @pytest.fixture(name="graphs")
 def fixture_graphs():
-    return dynnode2vec.utils.generate_dynamic_graphs(
+    return dynnode2vec.utils.create_dynamic_graph(
         n_base_nodes=30, n_steps=5, base_density=0.02
     )