Bug fix for rapidsai#1899 - added test and bug fix to ensure a graph …

…that has not been renumbered is handled correctly by cugraph.subgraph()

python/cugraph/cugraph/community/subgraph_extraction.py

@@ -11,19 +11,19 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import cudf
+
 from cugraph.community import subgraph_extraction_wrapper
 from cugraph.utilities import (ensure_cugraph_obj_for_nx,
                                cugraph_to_nx,
                                )
 
-import cudf
-
 
 def subgraph(G, vertices):
     """
     Compute a subgraph of the existing graph including only the specified
-    vertices.  This algorithm works for both directed and undirected graphs,
-    it does not actually traverse the edges, simply pulls out any edges that
+    vertices.  This algorithm works for both directed and undirected graphs, and
+    does not traverse the edges, but instead it simply pulls out any edges that
     are incident on vertices that are both contained in the vertices list.
 
     Parameters
@@ -66,10 +66,12 @@ def subgraph(G, vertices):
     result_graph = type(G)()
 
     df = subgraph_extraction_wrapper.subgraph(G, vertices)
+    src_names = "src"
+    dst_names = "dst"
 
     if G.renumbered:
-        df, src_names = G.unrenumber(df, "src", get_column_names=True)
-        df, dst_names = G.unrenumber(df, "dst", get_column_names=True)
+        df, src_names = G.unrenumber(df, src_names, get_column_names=True)
+        df, dst_names = G.unrenumber(df, dst_names, get_column_names=True)
 
     if G.edgelist.weights:
         result_graph.from_cudf_edgelist(

python/cugraph/cugraph/tests/test_subgraph_extraction.py

@@ -15,24 +15,20 @@
 
 import numpy as np
 import pytest
+import networkx as nx
 
 import cudf
 import cugraph
 from cugraph.tests import utils
 
 
-# Temporarily suppress warnings till networkX fixes deprecation warnings
-# (Using or importing the ABCs from 'collections' instead of from
-# 'collections.abc' is deprecated, and in 3.8 it will stop working) for
-# python 3.7.  Also, this import networkx needs to be relocated in the
-# third-party group once this gets fixed.
-import warnings
-
-with warnings.catch_warnings():
-    warnings.filterwarnings("ignore", category=DeprecationWarning)
-    import networkx as nx
+################################################################################
+# pytest setup - called for each test function
+def setup_function():
+    gc.collect()
 
 
+################################################################################
 def compare_edges(cg, nxg):
     edgelist_df = cg.view_edge_list()
     assert cg.edgelist.weights is False
@@ -71,10 +67,9 @@ def nx_call(M, verts, directed=True):
     return nx.subgraph(G, verts)
 
 
+################################################################################
 @pytest.mark.parametrize("graph_file", utils.DATASETS)
 def test_subgraph_extraction_DiGraph(graph_file):
-    gc.collect()
-
     M = utils.read_csv_for_nx(graph_file)
     verts = np.zeros(3, dtype=np.int32)
     verts[0] = 0
@@ -87,8 +82,6 @@ def test_subgraph_extraction_DiGraph(graph_file):
 
 @pytest.mark.parametrize("graph_file", utils.DATASETS)
 def test_subgraph_extraction_Graph(graph_file):
-    gc.collect()
-
     M = utils.read_csv_for_nx(graph_file)
     verts = np.zeros(3, dtype=np.int32)
     verts[0] = 0
@@ -101,7 +94,6 @@ def test_subgraph_extraction_Graph(graph_file):
 
 @pytest.mark.parametrize("graph_file", utils.DATASETS)
 def test_subgraph_extraction_Graph_nx(graph_file):
-    gc.collect()
     directed = False
     verts = np.zeros(3, dtype=np.int32)
     verts[0] = 0
@@ -130,8 +122,6 @@ def test_subgraph_extraction_Graph_nx(graph_file):
 
 @pytest.mark.parametrize("graph_file", utils.DATASETS)
 def test_subgraph_extraction_multi_column(graph_file):
-    gc.collect()
-
     M = utils.read_csv_for_nx(graph_file)
 
     cu_M = cudf.DataFrame()
@@ -162,3 +152,22 @@ def test_subgraph_extraction_multi_column(graph_file):
     for i in range(len(edgelist_df_res)):
         assert sG2.has_edge(edgelist_df_res["0_src"].iloc[i],
                             edgelist_df_res["0_dst"].iloc[i])
+
+
+# FIXME: the coverage provided by this test could probably be handled by another
+# test that also checks using renumber=False
+def test_subgraph_extraction_graph_not_renumbered():
+    """
+    Ensure subgraph() works with a Graph that has not been renumbered
+    """
+    graph_file = utils.RAPIDS_DATASET_ROOT_DIR_PATH / "karate.csv"
+    gdf = cudf.read_csv(graph_file, delimiter = " ",
+                        dtype=["int32", "int32", "float32"], header=None)
+    verts = np.array([0, 1, 2], dtype=np.int32)
+    sverts = cudf.Series(verts)
+    G = cugraph.Graph()
+    G.from_cudf_edgelist(gdf, source="0", destination="1", renumber=False)
+    Sg = cugraph.subgraph(G, sverts)
+
+    assert Sg.number_of_vertices() == 3
+    assert Sg.number_of_edges() == 3

python/cugraph/pytest.ini

@@ -4,9 +4,11 @@ addopts =
            --benchmark-max-time=0
            --benchmark-min-rounds=1
            --benchmark-columns="mean, rounds"
-           --benchmark-gpu-disable
-           --cov=cugraph
-           --cov-report term-missing:skip-covered
+           ## for use with rapids-pytest-benchmark plugin
+           #--benchmark-gpu-disable
+           ## for use with pytest-cov plugin
+           #--cov=cugraph
+           #--cov-report term-missing:skip-covered
 
 markers =
           managedmem_on: RMM managed memory enabled