[Doc/Feature] Refactor, doc update and behavior fix for graphs (#1983)

* Update graph

* Fix for dgl.graph

* from_scipy

* Replace canonical_etypes with relations

* from_networkx

* Update for hetero_from_relations

* Roll back the change of canonical_etypes to relations

* heterograph

* bipartite

* Update doc

* Fix lint

* Fix lint

* Fix test cases

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* Fix test

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* Use DGLError

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* rewrite sanity checks

* delete unnecessary checks

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Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>

examples/tensorflow/rgcn/entity_classify.py

@@ -66,7 +66,6 @@ def main(args):
         hg = dataset[0]
 
         num_rels = len(hg.canonical_etypes)
-        num_of_ntype = len(hg.ntypes)
         category = dataset.predict_category
         num_classes = dataset.num_classes
         train_mask = hg.nodes[category].data.pop('train_mask')
@@ -98,7 +97,7 @@ def main(args):
                 category_id = i
 
         # edge type and normalization factor
-        g = dgl.to_homo(hg)
+        g = dgl.to_homogeneous(hg, edata=['norm'])
 
     # check cuda
     if args.gpu < 0:

include/dgl/transform.h

@@ -89,15 +89,15 @@ ToBlock(HeteroGraphPtr graph, const std::vector<IdArray> &rhs_nodes, bool includ
  * * \c count : The array of edge occurrences per edge type.
  * * \c edge_map : The mapping from original edge IDs to new edge IDs per edge type.
  *
- * \note Example: consider the following graph:
+ * \note Example: consider a graph with the following edges
  *
- *     g = dgl.graph([(0, 1), (1, 3), (2, 2), (1, 3), (1, 4), (1, 4)])
+ *     [(0, 1), (1, 3), (2, 2), (1, 3), (1, 4), (1, 4)]
  *
  * Then ToSimpleGraph(g) would yield the following elements:
  *
- * * The first element would be the simple graph itself:
+ * * The first element would be the simple graph itself with the following edges
  *
- *       simple_g = dgl.graph([(0, 1), (1, 3), (1, 4), (2, 2)])
+ *       [(0, 1), (1, 3), (1, 4), (2, 2)]
  *
  * * The second element is an array \c count.  \c count[i] stands for the number of edges
  *   connecting simple_g.src[i] and simple_g.dst[i] in the original graph.

python/dgl/_deprecate/graph.py

@@ -4038,6 +4038,7 @@ class DGLGraph(DGLBaseGraph):
         self._node_frame = old_nframe
         self._edge_frame = old_eframe
 
+    @property
     def is_homogeneous(self):
         """Return if the graph is homogeneous."""
         return True

python/dgl/batch.py

@@ -397,7 +397,7 @@ def unbatch(g, node_split=None, edge_split=None):
                           for i in range(num_split)]
 
     # Create graphs
-    gs = [convert.heterograph(edge_dict, num_nodes_dict, validate=True, idtype=g.idtype)
+    gs = [convert.heterograph(edge_dict, num_nodes_dict, idtype=g.idtype)
           for edge_dict, num_nodes_dict in zip(edge_dict_per, num_nodes_dict_per)]
 
     # Unbatch node features

python/dgl/data/citation_graph.py

@@ -19,7 +19,7 @@ from .. import convert
 from .. import batch
 from .. import backend as F
 from ..convert import graph as dgl_graph
-from ..convert import to_networkx
+from ..convert import from_networkx, to_networkx
 
 backend = os.environ.get('DGLBACKEND', 'pytorch')
 
@@ -119,7 +119,7 @@ class CitationGraphDataset(DGLBuiltinDataset):
         test_mask = _sample_mask(idx_test, labels.shape[0])
 
         self._graph = graph
-        g = dgl_graph(graph)
+        g = from_networkx(graph)
 
         g.ndata['train_mask'] = generate_mask_tensor(train_mask)
         g.ndata['val_mask'] = generate_mask_tensor(val_mask)
@@ -794,13 +794,13 @@ class CoraBinary(DGLBuiltinDataset):
             for line in f.readlines():
                 if line.startswith('graph'):
                     if len(elist) != 0:
-                        self.graphs.append(dgl_graph(elist))
+                        self.graphs.append(dgl_graph(tuple(zip(*elist))))
                     elist = []
                 else:
                     u, v = line.strip().split(' ')
                     elist.append((int(u), int(v)))
             if len(elist) != 0:
-                self.graphs.append(dgl_graph(elist))
+                self.graphs.append(dgl_graph(tuple(zip(*elist))))
         with open("{}/pmpds.pkl".format(root), 'rb') as f:
             self.pmpds = _pickle_load(f)
         self.labels = []

python/dgl/data/gindt.py

@@ -157,7 +157,7 @@ class GINDataset(DGLBuiltinDataset):
 
                 self.labels.append(self.glabel_dict[glabel])
 
-                g = dgl_graph([])
+                g = dgl_graph(([], []))
                 g.add_nodes(n_nodes)
 
                 nlabels = []  # node labels

python/dgl/data/graph_serialize.py

@@ -86,8 +86,8 @@ def save_graphs(filename, g_list, labels=None):
     Create :code:`DGLGraph`/:code:`DGLHeteroGraph` objects and initialize node
     and edge features.
 
-    >>> g1 = dgl.graph(([0, 1, 2], [1, 2, 3])
-    >>> g2 = dgl.graph(([0, 2], [2, 3])
+    >>> g1 = dgl.graph(([0, 1, 2], [1, 2, 3]))
+    >>> g2 = dgl.graph(([0, 2], [2, 3]))
     >>> g2.edata["e"] = th.ones(2, 4)
 
     Save Graphs into file

python/dgl/data/karate.py

@@ -6,7 +6,7 @@ import networkx as nx
 from .. import backend as F
 from .dgl_dataset import DGLDataset
 from .utils import deprecate_property
-from ..convert import graph as dgl_graph
+from ..convert import from_networkx
 
 __all__ = ['KarateClubDataset', 'KarateClub']
 
@@ -56,7 +56,7 @@ class KarateClubDataset(DGLDataset):
         label = np.asarray(
             [kc_graph.nodes[i]['club'] != 'Mr. Hi' for i in kc_graph.nodes]).astype(np.int64)
         label = F.tensor(label)
-        g = dgl_graph(kc_graph)
+        g = from_networkx(kc_graph)
         g.ndata['label'] = label
         self._graph = g
         self._data = [g]

python/dgl/data/minigc.py

@@ -6,7 +6,7 @@ import numpy as np
 from .dgl_dataset import DGLDataset
 from .utils import save_graphs, load_graphs, makedirs
 from .. import backend as F
-from ..convert import graph as dgl_graph
+from ..convert import from_networkx
 from ..transform import add_self_loop
 
 __all__ = ['MiniGCDataset']
@@ -147,7 +147,7 @@ class MiniGCDataset(DGLDataset):
         # preprocess
         for i in range(self.num_graphs):
             # convert to DGLGraph, and add self loops
-            self.graphs[i] = add_self_loop(dgl_graph(self.graphs[i]))
+            self.graphs[i] = add_self_loop(from_networkx(self.graphs[i]))
         self.labels = F.tensor(np.array(self.labels).astype(np.int))
 
     def _gen_cycle(self, n):

python/dgl/data/rdf.py

@@ -300,7 +300,7 @@ class RDFGraphDataset(DGLBuiltinDataset):
         # convert to heterograph
         if self.verbose:
             print('Convert to heterograph ...')
-        hg = dgl.to_hetero(g,
+        hg = dgl.to_heterogeneous(g,
                                   ntypes,
                                   etypes,
                                   metagraph=mg)

python/dgl/data/reddit.py

@@ -8,7 +8,7 @@ import os
 from .dgl_dataset import DGLBuiltinDataset
 from .utils import _get_dgl_url, generate_mask_tensor, load_graphs, save_graphs, deprecate_property
 from .. import backend as F
-from ..convert import graph as dgl_graph
+from ..convert import from_scipy
 
 
 class RedditDataset(DGLBuiltinDataset):
@@ -140,7 +140,7 @@ class RedditDataset(DGLBuiltinDataset):
         # graph
         coo_adj = sp.load_npz(os.path.join(
             self.raw_path, "reddit{}_graph.npz".format(self._self_loop_str)))
-        self._graph = dgl_graph(coo_adj)
+        self._graph = from_scipy(coo_adj)
         # features and labels
         reddit_data = np.load(os.path.join(self.raw_path, "reddit_data.npz"))
         features = reddit_data["feature"]

python/dgl/data/sbm.py

@@ -8,7 +8,7 @@ import numpy.random as npr
 import scipy as sp
 
 from .dgl_dataset import DGLDataset
-from ..convert import graph as dgl_graph
+from ..convert import from_scipy
 from .. import batch
 from .utils import save_info, save_graphs, load_info, load_graphs
 
@@ -124,7 +124,7 @@ class SBMMixtureDataset(DGLDataset):
             pq = [generator() for _ in range(self._n_graphs)]
         else:
             raise RuntimeError()
-        self._graphs = [dgl_graph(sbm(self._n_communities, self._block_size, *x)) for x in pq]
+        self._graphs = [from_scipy(sbm(self._n_communities, self._block_size, *x)) for x in pq]
         self._line_graphs = [g.line_graph(backtracking=False) for g in self._graphs]
         in_degrees = lambda g: g.in_degrees().float()
         self._graph_degrees = [in_degrees(g) for g in self._graphs]

python/dgl/data/tu.py

@@ -100,7 +100,7 @@ class LegacyTUDataset(DGLBuiltinDataset):
         DS_graph_labels = self._idx_from_zero(
             np.genfromtxt(self._file_path("graph_labels"), dtype=int))
 
-        g = dgl_graph([])
+        g = dgl_graph(([], []))
         g.add_nodes(int(DS_edge_list.max()) + 1)
         g.add_edges(DS_edge_list[:, 0], DS_edge_list[:, 1])
 
@@ -296,7 +296,7 @@ class TUDataset(DGLBuiltinDataset):
         DS_graph_labels = self._idx_from_zero(
             loadtxt(self._file_path("graph_labels"), delimiter=",").astype(int))
 
-        g = dgl_graph([])
+        g = dgl_graph(([], []))
         g.add_nodes(int(DS_edge_list.max()) + 1)
         g.add_edges(DS_edge_list[:, 0], DS_edge_list[:, 1])
 

python/dgl/dataloading/dataloader.py

@@ -596,8 +596,11 @@ class EdgeCollator(Collator):
                 'graph has multiple or no edge types; '\
                 'please return a dict in negative sampler.'
             neg_srcdst = {self.g.canonical_etypes[0]: neg_srcdst}
+        # Get dtype from a tuple of tensors
+        dtype = F.dtype(list(neg_srcdst.values())[0][0])
         neg_edges = {
-            etype: neg_srcdst.get(etype, []) for etype in self.g.canonical_etypes}
+            etype: neg_srcdst.get(etype, (F.tensor([], dtype), F.tensor([], dtype)))
+            for etype in self.g.canonical_etypes}
         neg_pair_graph = heterograph(
             neg_edges, {ntype: self.g.number_of_nodes(ntype) for ntype in self.g.ntypes})
 

python/dgl/generators.py

@@ -38,12 +38,12 @@ def rand_graph(num_nodes, num_edges, idtype=F.int64, device=F.cpu(),
     rows = F.copy_to(F.astype(eids / num_nodes, idtype), device)
     cols = F.copy_to(F.astype(eids % num_nodes, idtype), device)
     g = convert.graph((rows, cols),
-                      num_nodes=num_nodes, validate=False,
-                      formats=formats,
+                      num_nodes=num_nodes,
                       idtype=idtype, device=device)
-    return g
+    return g.formats(formats)
 
-def rand_bipartite(num_src_nodes, num_dst_nodes, num_edges,
+def rand_bipartite(utype, etype, vtype,
+                   num_src_nodes, num_dst_nodes, num_edges,
                    idtype=F.int64, device=F.cpu(),
                    formats=['csr', 'coo', 'csc']):
     """Generate a random bipartite graph of the given number of src/dst nodes and
@@ -53,6 +53,12 @@ def rand_bipartite(num_src_nodes, num_dst_nodes, num_edges,
 
     Parameters
     ----------
+    utype : str, optional
+        The name of the source node type.
+    etype : str, optional
+        The name of the edge type.
+    vtype : str, optional
+        The name of the destination node type.
     num_src_nodes : int
         The number of source nodes, the :math:`|U|` in :math:`G=(U,V,E)`.
     num_dst_nodes : int
@@ -75,8 +81,7 @@ def rand_bipartite(num_src_nodes, num_dst_nodes, num_edges,
     eids = random.choice(num_src_nodes * num_dst_nodes, num_edges, replace=False)
     rows = F.copy_to(F.astype(eids / num_dst_nodes, idtype), device)
     cols = F.copy_to(F.astype(eids % num_dst_nodes, idtype), device)
-    g = convert.bipartite((rows, cols),
-                          num_nodes=(num_src_nodes, num_dst_nodes), validate=False,
-                          idtype=idtype, device=device,
-                          formats=formats)
-    return g
+    g = convert.heterograph({(utype, etype, vtype): (rows, cols)},
+                            {utype: num_src_nodes, vtype: num_dst_nodes},
+                            idtype=idtype, device=device)
+    return g.formats(formats)

python/dgl/heterograph_index.py

@@ -547,6 +547,9 @@ class HeteroGraphIndex(ObjectBase):
         """
         if order is None:
             order = ""
+        elif order not in ['srcdst', 'eid']:
+            raise DGLError("Expect order to be one of None, 'srcdst', 'eid', "
+                           "got {}".format(order))
         edge_array = _CAPI_DGLHeteroEdges(self, int(etype), order)
         src = F.from_dgl_nd(edge_array(0))
         dst = F.from_dgl_nd(edge_array(1))

python/dgl/nn/mxnet/conv/gatedgraphconv.py

@@ -76,8 +76,9 @@ class GatedGraphConv(nn.Block):
             is the output feature size.
         """
         with graph.local_scope():
-            assert graph.is_homogeneous(), \
-                "not a homograph; convert it with to_homo and pass in the edge type as argument"
+            assert graph.is_homogeneous, \
+                "not a homogeneous graph; convert it with to_homogeneous " \
+                "and pass in the edge type as argument"
             zero_pad = nd.zeros((feat.shape[0], self._out_feats - feat.shape[1]),
                                 ctx=feat.context)
             feat = nd.concat(feat, zero_pad, dim=-1)

python/dgl/nn/mxnet/conv/relgraphconv.py

@@ -229,8 +229,9 @@ class RelGraphConv(gluon.Block):
         mx.ndarray.NDArray
             New node features.
         """
-        assert g.is_homogeneous(), \
-            "not a homograph; convert it with to_homo and pass in the edge type as argument"
+        assert g.is_homogeneous, \
+            "not a homogeneous graph; convert it with to_homogeneous " \
+            "and pass in the edge type as argument"
         with g.local_scope():
             g.ndata['h'] = x
             g.edata['type'] = etypes