[Bugfix] edge order is not preserved when converting from edge list (d…

…mlc#262)

Jenkinsfile

@@ -34,6 +34,7 @@ def pytorch_unit_test(dev) {
 def mxnet_unit_test(dev) {
   withEnv(["DGL_LIBRARY_PATH=${env.WORKSPACE}/build", "PYTHONPATH=${env.WORKSPACE}/python"]) {
     sh "python3 -m nose -v --with-xunit tests/mxnet"
+    sh "python3 -m nose -v --with-xunit tests/graph_index"
   }
 }
 

python/dgl/graph_index.py

@@ -678,6 +678,25 @@ def from_scipy_sparse_matrix(self, adj):
         dst = utils.toindex(adj_coo.col)
         self.add_edges(src, dst)
 
+    def from_edge_list(self, elist):
+        """Convert from an edge list.
+
+        Paramters
+        ---------
+        elist : list
+            List of (u, v) edge tuple.
+        """
+        self.clear()
+        src, dst = zip(*elist)
+        src = np.array(src)
+        dst = np.array(dst)
+        num_nodes = max(src.max(), dst.max()) + 1
+        min_nodes = min(src.min(), dst.min())
+        if min_nodes != 0:
+            raise DGLError('Invalid edge list. Nodes must start from 0.')
+        self.add_nodes(num_nodes)
+        self.add_edges(utils.toindex(src), utils.toindex(dst))
+
     def line_graph(self, backtracking=True):
         """Return the line graph of this graph.
 
@@ -868,7 +887,10 @@ def create_graph_index(graph_data=None, multigraph=False, readonly=False):
         return graph_data
 
     if readonly and graph_data is not None:
-        gi = create_immutable_graph_index(graph_data)
+        try:
+            gi = create_immutable_graph_index(graph_data)
+        except:
+            gi = None
         # If we can't create an immutable graph index, we'll have to fall back.
         if gi is not None:
             return gi
@@ -879,19 +901,27 @@ def create_graph_index(graph_data=None, multigraph=False, readonly=False):
     if graph_data is None:
         return gi
 
+    # edge list
+    if isinstance(graph_data, (list, tuple)):
+        try:
+            gi.from_edge_list(graph_data)
+            return gi
+        except:
+            raise DGLError('Graph data is not a valid edge list.')
+
     # scipy format
     if isinstance(graph_data, scipy.sparse.spmatrix):
         try:
             gi.from_scipy_sparse_matrix(graph_data)
             return gi
         except:
-            raise Exception('Graph data is not a valid scipy sparse matrix.')
+            raise DGLError('Graph data is not a valid scipy sparse matrix.')
 
     # networkx - any format
     try:
         gi.from_networkx(graph_data)
     except:
-        raise Exception('Error while creating graph from input of type "%s".'
+        raise DGLError('Error while creating graph from input of type "%s".'
                          % type(graph_data))
 
     return gi

python/dgl/immutable_graph_index.py

@@ -8,7 +8,7 @@
 from ._ffi.function import _init_api
 from . import backend as F
 from . import utils
-from .base import ALL, is_all, dgl_warning
+from .base import ALL, is_all, dgl_warning, DGLError
 
 class ImmutableGraphIndex(object):
     """Graph index object on immutable graphs.
@@ -33,7 +33,7 @@ def add_nodes(self, num):
         num : int
             Number of nodes to be added.
         """
-        raise Exception('Immutable graph doesn\'t support adding nodes')
+        raise DGLError('Immutable graph doesn\'t support adding nodes')
 
     def add_edge(self, u, v):
         """Add one edge.
@@ -45,7 +45,7 @@ def add_edge(self, u, v):
         v : int
             The dst node.
         """
-        raise Exception('Immutable graph doesn\'t support adding an edge')
+        raise DGLError('Immutable graph doesn\'t support adding an edge')
 
     def add_edges(self, u, v):
         """Add many edges.
@@ -57,11 +57,11 @@ def add_edges(self, u, v):
         v : utils.Index
             The dst nodes.
         """
-        raise Exception('Immutable graph doesn\'t support adding edges')
+        raise DGLError('Immutable graph doesn\'t support adding edges')
 
     def clear(self):
         """Clear the graph."""
-        raise Exception('Immutable graph doesn\'t support clearing up')
+        raise DGLError('Immutable graph doesn\'t support clearing up')
 
     def is_multigraph(self):
         """Return whether the graph is a multigraph
@@ -592,6 +592,8 @@ def from_networkx(self, nx_graph):
     def from_scipy_sparse_matrix(self, adj):
         """Convert from scipy sparse matrix.
 
+        NOTE: we assume the row is src nodes and the col is dst nodes.
+
         Parameters
         ----------
         adj : scipy sparse matrix
@@ -601,6 +603,26 @@ def from_scipy_sparse_matrix(self, adj):
         out_mat = adj.tocoo()
         self._sparse.from_coo_matrix(out_mat)
 
+    def from_edge_list(self, elist):
+        """Convert from an edge list.
+
+        Paramters
+        ---------
+        elist : list
+            List of (u, v) edge tuple.
+        """
+        self.clear()
+        src, dst = zip(*elist)
+        src = np.array(src)
+        dst = np.array(dst)
+        num_nodes = max(src.max(), dst.max()) + 1
+        min_nodes = min(src.min(), dst.min())
+        if min_nodes != 0:
+            raise DGLError('Invalid edge list. Nodes must start from 0.')
+        data = np.ones((len(src),), dtype=np.int32)
+        spmat = sp.coo_matrix((data, (src, dst)), shape=(num_nodes, num_nodes))
+        self._sparse.from_coo_matrix(spmat)
+
     def line_graph(self, backtracking=True):
         """Return the line graph of this graph.
 
@@ -728,19 +750,27 @@ def create_immutable_graph_index(graph_data=None):
     # Let's create an empty graph index first.
     gi = ImmutableGraphIndex(F.create_immutable_graph_index())
 
+    # edge list
+    if isinstance(graph_data, (list, tuple)):
+        try:
+            gi.from_edge_list(graph_data)
+            return gi
+        except:
+            raise DGLError('Graph data is not a valid edge list.')
+
     # scipy format
     if isinstance(graph_data, sp.spmatrix):
         try:
             gi.from_scipy_sparse_matrix(graph_data)
             return gi
         except:
-            raise Exception('Graph data is not a valid scipy sparse matrix.')
+            raise DGLError('Graph data is not a valid scipy sparse matrix.')
 
     # networkx - any format
     try:
         gi.from_networkx(graph_data)
     except:
-        raise Exception('Error while creating graph from input of type "%s".'
+        raise DGLError('Error while creating graph from input of type "%s".'
                          % type(graph_data))
 
     return gi

tests/graph_index/test_basics.py

@@ -139,8 +139,19 @@ def test_predsucc():
     assert 2 in succ
     assert 0 in succ
 
+def test_create_from_elist():
+    elist = [(2, 1), (1, 0), (2, 0), (3, 0), (0, 2)]
+    g = create_graph_index(elist)
+    for i, (u, v) in enumerate(elist):
+        assert g.edge_id(u, v)[0] == i
+    # immutable graph
+    g = create_graph_index(elist, readonly=True)
+    for i, (u, v) in enumerate(elist):
+        print(u, v, g.edge_id(u, v)[0])
+        assert g.edge_id(u, v)[0] == i
 
 if __name__ == '__main__':
     test_edge_id()
     test_nx()
     test_predsucc()
+    test_create_from_elist()

tests/pytorch/test_graph.py

@@ -2,6 +2,7 @@
 import math
 import numpy as np
 import scipy.sparse as sp
+import networkx as nx
 import torch as th
 import dgl
 import utils as U
@@ -26,6 +27,16 @@ def test_graph_creation():
     g.ndata['h'] = 3 * th.ones((5, 2))
     assert U.allclose(3 * th.ones((5, 2)), g.ndata['h'])
 
+def test_create_from_elist():
+    elist = [(2, 1), (1, 0), (2, 0), (3, 0), (0, 2)]
+    g = dgl.DGLGraph(elist)
+    for i, (u, v) in enumerate(elist):
+        assert g.edge_id(u, v) == i
+    # immutable graph
+    g = dgl.DGLGraph(elist, readonly=True)
+    for i, (u, v) in enumerate(elist):
+        assert g.edge_id(u, v) == i
+
 def test_adjmat_speed():
     n = 1000
     p = 10 * math.log(n) / n
@@ -87,6 +98,7 @@ def test_incmat_speed():
 
 if __name__ == '__main__':
     test_graph_creation()
+    test_create_from_elist()
     test_adjmat_speed()
     test_incmat()
     test_incmat_speed()