Merge pull request #4 from jermainewang/master

Sync with latest commit

include/dgl/graph.h

-// DGL Graph interface
-#ifndef DGL_DGLGRAPH_H_
-#define DGL_DGLGRAPH_H_
+/*!
+ *  Copyright (c) 2018 by Contributors
+ * \file dgl/graph.h
+ * \brief DGL graph index class.
+ */
+#ifndef DGL_GRAPH_H_
+#define DGL_GRAPH_H_
 
-#include <stdint.h>
+#include <vector>
+#include <cstdint>
 #include "runtime/ndarray.h"
 
 namespace dgl {
@@ -17,7 +22,7 @@ class GraphOp;
 struct Subgraph;
 
 /*!
- * \brief Base dgl graph class.
+ * \brief Base dgl graph index class.
  *
  * DGL's graph is directed. Vertices are integers enumerated from zero. Edges
  * are uniquely identified by the two endpoints. Multi-edge is currently not
@@ -41,7 +46,7 @@ class Graph {
   } EdgeArray;
 
   /*! \brief default constructor */
-  Graph(bool multigraph = false) : is_multigraph_(multigraph) {}
+  explicit Graph(bool multigraph = false) : is_multigraph_(multigraph) {}
 
   /*! \brief default copy constructor */
   Graph(const Graph& other) = default;
@@ -192,7 +197,7 @@ class Graph {
    * \return the id arrays of the two endpoints of the edges.
    */
   EdgeArray InEdges(IdArray vids) const;
-  
+
   /*!
    * \brief Get the out edges of the vertex.
    * \note The returned src id array is filled with vid.
@@ -347,4 +352,4 @@ struct Subgraph {
 
 }  // namespace dgl
 
-#endif  // DGL_DGLGRAPH_H_
+#endif  // DGL_GRAPH_H_

include/dgl/graph_op.h

-// Graph operations
+/*!
+ *  Copyright (c) 2018 by Contributors
+ * \file dgl/graph_op.h
+ * \brief Operations on graph index.
+ */
 #ifndef DGL_GRAPH_OP_H_
 #define DGL_GRAPH_OP_H_
 
+#include <vector>
 #include "graph.h"
 
 namespace dgl {

include/dgl/runtime/README.md

-# C API and runtime
-
-Borrowed and adapted from TVM project.

include/dgl/runtime/c_backend_api.h

@@ -7,8 +7,8 @@
  *  used by compiled tvm operators, usually user do not need to use these
  *  function directly.
  */
-#ifndef TVM_RUNTIME_C_BACKEND_API_H_
-#define TVM_RUNTIME_C_BACKEND_API_H_
+#ifndef DGL_RUNTIME_C_BACKEND_API_H_
+#define DGL_RUNTIME_C_BACKEND_API_H_
 
 #include "c_runtime_api.h"
 
@@ -136,4 +136,4 @@ TVM_DLL int TVMBackendRunOnce(void** handle,
 #ifdef __cplusplus
 }  // TVM_EXTERN_C
 #endif
-#endif  // TVM_RUNTIME_C_BACKEND_API_H_
+#endif  // DGL_RUNTIME_C_BACKEND_API_H_

include/dgl/runtime/c_runtime_api.h

 /*!
  *  Copyright (c) 2016 by Contributors
- * \file tvm/runtime/c_runtime_api.h
+ * \file dgl/runtime/c_runtime_api.h
  * \brief TVM runtime library.
  *
  *  The philosophy of TVM project is to customize the compilation
@@ -15,8 +15,8 @@
  *   - Use TVMFuncListGlobalNames to get global function name
  *   - Use TVMFuncCall to call these functions.
  */
-#ifndef TVM_RUNTIME_C_RUNTIME_API_H_
-#define TVM_RUNTIME_C_RUNTIME_API_H_
+#ifndef DGL_RUNTIME_C_RUNTIME_API_H_
+#define DGL_RUNTIME_C_RUNTIME_API_H_
 
 // Macros to do weak linking
 #ifdef _MSC_VER
@@ -530,4 +530,4 @@ TVM_DLL int TVMStreamStreamSynchronize(int device_type,
 #ifdef __cplusplus
 }  // TVM_EXTERN_C
 #endif
-#endif  // TVM_RUNTIME_C_RUNTIME_API_H_
+#endif  // DGL_RUNTIME_C_RUNTIME_API_H_

include/dgl/runtime/device_api.h

 /*!
  *  Copyright (c) 2016 by Contributors
- * \file tvm/runtime/device_api.h
+ * \file dgl/runtime/device_api.h
  * \brief Abstract device memory management API
  */
-#ifndef TVM_RUNTIME_DEVICE_API_H_
-#define TVM_RUNTIME_DEVICE_API_H_
+#ifndef DGL_RUNTIME_DEVICE_API_H_
+#define DGL_RUNTIME_DEVICE_API_H_
 
 #include <string>
 #include "packed_func.h"
@@ -180,4 +180,4 @@ class DeviceAPI {
 constexpr int kRPCSessMask = 128;
 }  // namespace runtime
 }  // namespace tvm
-#endif  // TVM_RUNTIME_DEVICE_API_H_
+#endif  // DGL_RUNTIME_DEVICE_API_H_

include/dgl/runtime/module.h

 /*!
  *  Copyright (c) 2017 by Contributors
- * \file tvm/runtime/module.h
+ * \file dgl/runtime/module.h
  * \brief Runtime container of the functions generated by TVM,
  *  This is used to support dynamically link, load and save
  *  functions from different convention under unified API.
  */
-#ifndef TVM_RUNTIME_MODULE_H_
-#define TVM_RUNTIME_MODULE_H_
+#ifndef DGL_RUNTIME_MODULE_H_
+#define DGL_RUNTIME_MODULE_H_
 
 #include <dmlc/io.h>
 #include <memory>
@@ -174,4 +174,4 @@ inline const ModuleNode* Module::operator->() const {
 }  // namespace tvm
 
 #include "packed_func.h"
-#endif  // TVM_RUNTIME_MODULE_H_
+#endif  // DGL_RUNTIME_MODULE_H_

include/dgl/runtime/ndarray.h

 /*!
  *  Copyright (c) 2017 by Contributors
- * \file tvm/runtime/ndarray.h
+ * \file dgl/runtime/ndarray.h
  * \brief Abstract device memory management API
  */
-#ifndef TVM_RUNTIME_NDARRAY_H_
-#define TVM_RUNTIME_NDARRAY_H_
+#ifndef DGL_RUNTIME_NDARRAY_H_
+#define DGL_RUNTIME_NDARRAY_H_
 
 #include <atomic>
 #include <vector>
@@ -422,4 +422,4 @@ inline bool NDArray::Load(dmlc::Stream* strm) {
 
 }  // namespace runtime
 }  // namespace tvm
-#endif  // TVM_RUNTIME_NDARRAY_H_
+#endif  // DGL_RUNTIME_NDARRAY_H_

include/dgl/runtime/packed_func.h

 /*!
  *  Copyright (c) 2017 by Contributors
- * \file tvm/runtime/packed_func.h
+ * \file dgl/runtime/packed_func.h
  * \brief Type-erased function used across TVM API.
  */
-#ifndef TVM_RUNTIME_PACKED_FUNC_H_
-#define TVM_RUNTIME_PACKED_FUNC_H_
+#ifndef DGL_RUNTIME_PACKED_FUNC_H_
+#define DGL_RUNTIME_PACKED_FUNC_H_
 
 #include <dmlc/logging.h>
 #include <functional>
@@ -1212,4 +1212,4 @@ inline PackedFunc Module::GetFunction(const std::string& name, bool query_import
 }
 }  // namespace runtime
 }  // namespace tvm
-#endif  // TVM_RUNTIME_PACKED_FUNC_H_
+#endif  // DGL_RUNTIME_PACKED_FUNC_H_

include/dgl/runtime/registry.h

 /*!
  *  Copyright (c) 2017 by Contributors
- * \file tvm/runtime/registry.h
+ * \file dgl/runtime/registry.h
  * \brief This file defines the TVM global function registry.
  *
  *  The registered functions will be made available to front-end
@@ -22,8 +22,8 @@
  *   });
  * \endcode
  */
-#ifndef TVM_RUNTIME_REGISTRY_H_
-#define TVM_RUNTIME_REGISTRY_H_
+#ifndef DGL_RUNTIME_REGISTRY_H_
+#define DGL_RUNTIME_REGISTRY_H_
 
 #include <string>
 #include <vector>
@@ -141,4 +141,4 @@ class Registry {
 
 }  // namespace runtime
 }  // namespace tvm
-#endif  // TVM_RUNTIME_REGISTRY_H_
+#endif  // DGL_RUNTIME_REGISTRY_H_

include/dgl/runtime/serializer.h

 /*!
  *  Copyright (c) 2017 by Contributors
- * \file tvm/runtime/serializer.h
+ * \file dgl/runtime/serializer.h
  * \brief Serializer extension to support TVM data types
  *  Include this file to enable serialization of DLDataType, DLContext
  */
-#ifndef TVM_RUNTIME_SERIALIZER_H_
-#define TVM_RUNTIME_SERIALIZER_H_
+#ifndef DGL_RUNTIME_SERIALIZER_H_
+#define DGL_RUNTIME_SERIALIZER_H_
 
 #include <dmlc/io.h>
 #include <dmlc/serializer.h>
@@ -48,4 +48,4 @@ struct Handler<DLContext> {
 
 }  // namespace serializer
 }  // namespace dmlc
-#endif  // TVM_RUNTIME_SERIALIZER_H_
+#endif  // DGL_RUNTIME_SERIALIZER_H_

include/dgl/runtime/threading_backend.h

 /*!
  *  Copyright (c) 2018 by Contributors
- * \file tvm/runtime/threading_backend.h
+ * \file dgl/runtime/threading_backend.h
  * \brief Utilities for manipulating thread pool threads.
  */
-#ifndef TVM_RUNTIME_THREADING_BACKEND_H_
-#define TVM_RUNTIME_THREADING_BACKEND_H_
+#ifndef DGL_RUNTIME_THREADING_BACKEND_H_
+#define DGL_RUNTIME_THREADING_BACKEND_H_
 
 #include <functional>
 #include <memory>
@@ -82,4 +82,4 @@ int MaxConcurrency();
 }  // namespace runtime
 }  // namespace tvm
 
-#endif  // TVM_RUNTIME_THREADING_BACKEND_H_
+#endif  // DGL_RUNTIME_THREADING_BACKEND_H_

include/dgl/runtime/util.h

 /*!
  *  Copyright (c) 2017 by Contributors
- * \file tvm/runtime/util.h
+ * \file dgl/runtime/util.h
  * \brief Useful runtime util.
  */
-#ifndef TVM_RUNTIME_UTIL_H_
-#define TVM_RUNTIME_UTIL_H_
+#ifndef DGL_RUNTIME_UTIL_H_
+#define DGL_RUNTIME_UTIL_H_
 
 #include "c_runtime_api.h"
 
@@ -50,4 +50,4 @@ enum TVMStructFieldKind : int {
 }  // namespace intrinsic
 }  // namespace ir
 }  // namespace tvm
-#endif  // TVM_RUNTIME_UTIL_H_
+#endif  // DGL_RUNTIME_UTIL_H_

include/dgl/scheduler.h

-// DGL Scheduler interface
+/*!
+ *  Copyright (c) 2018 by Contributors
+ * \file dgl/scheduler.h
+ * \brief Operations on graph index.
+ */
 #ifndef DGL_SCHEDULER_H_
 #define DGL_SCHEDULER_H_
 
-#include "runtime/ndarray.h"
 #include <vector>
+#include "runtime/ndarray.h"
 
 namespace dgl {
 
@@ -25,8 +29,8 @@ namespace sched {
  */
 std::vector<IdArray> DegreeBucketing(const IdArray& vids);
 
-} // namespace sched
+}  // namespace sched
 
-} // namespace dgl
+}  // namespace dgl
 
-#endif // DGL_SCHEDULER_H_
+#endif  // DGL_SCHEDULER_H_

python/dgl/__init__.py

 from . import backend
 from . import data
 from . import function
-from . import generator
 from . import nn
 
 from ._ffi.runtime_ctypes import TypeCode
@@ -10,6 +9,5 @@ from ._ffi.base import DGLError, __version__
 
 from .base import ALL
 from .batched_graph import *
-from .generator import *
-from .graph import DGLGraph, __MSG__, __REPR__
+from .graph import DGLGraph
 from .subgraph import DGLSubGraph

python/dgl/backend/mxnet.py

@@ -46,8 +46,14 @@ def from_numpy(np_data):
 def pack(tensors):
     return F.concat(*tensors, dim=0)
 
-def unpack(x, indices_or_sections=1):
-    return th.split(x, indices_or_sections)
+def unpack(x, split_sizes_or_sections=1):
+    if isinstance(split_sizes_or_sections, list):
+        np_arr = x.asnumpy()
+        indices = np.cumsum(split_sizes_or_sections)
+        res = np.split(np_arr, indices[:-1])
+        return [tensor(arr, dtype=x.dtype) for arr in res]
+    else:
+        return F.split(x, split_sizes_or_sections)
 
 # TODO this doesn't exist for symbol.
 def shape(x):
@@ -66,7 +72,10 @@ def unique(x):
     return mx.nd.array(tmp, ctx=x.context, dtype=x.dtype)
 
 def gather_row(data, row_index):
-    return data[row_index,]
+    if isinstance(row_index, F.NDArray):
+        return F.take(data, row_index)
+    else:
+        return data[row_index,]
 
 scatter_row = mx.nd.contrib.index_copy
 
@@ -114,6 +123,27 @@ def get_context(x):
 def _typestr(arr_dtype):
     return arr_dtype
 
+def get_tvmtype(arr):
+    arr_dtype = arr.dtype
+    if arr_dtype == np.float16:
+        return TVMType('float16')
+    elif arr_dtype == np.float32:
+        return TVMType('float32')
+    elif arr_dtype == np.float64:
+        return TVMType('float64')
+    elif arr_dtype == np.int16:
+        return TVMType('int16')
+    elif arr_dtype == np.int32:
+        return TVMType('int32')
+    elif arr_dtype == np.int64:
+        return TVMType('int64')
+    elif arr_dtype == np.int8:
+        return TVMType('int8')
+    elif arr_dtype == np.uint8:
+        return TVMType('uint8')
+    else:
+        raise RuntimeError('Unsupported data type:', arr_dtype)
+
 def zerocopy_to_dlpack(arr):
     """Return a dlpack compatible array using zero copy."""
     return arr.to_dlpack_for_read()

python/dgl/backend/pytorch.py

@@ -93,23 +93,24 @@ def get_context(arr):
         return TVMContext(
                 TVMContext.STR2MASK[arr.device.type], arr.device.index)
 
-def _typestr(arr_dtype):
+def get_tvmtype(arr):
+    arr_dtype = arr.dtype
     if arr_dtype in (th.float16, th.half):
-        return 'float16'
+        return TVMType('float16')
     elif arr_dtype in (th.float32, th.float):
-        return 'float32'
+        return TVMType('float32')
     elif arr_dtype in (th.float64, th.double):
-        return 'float64'
+        return TVMType('float64')
     elif arr_dtype in (th.int16, th.short):
-        return 'int16'
+        return TVMType('int16')
     elif arr_dtype in (th.int32, th.int):
-        return 'int32'
+        return TVMType('int32')
     elif arr_dtype in (th.int64, th.long):
-        return 'int64'
+        return TVMType('int64')
     elif arr_dtype == th.int8:
-        return 'int8'
+        return TVMType('int8')
     elif arr_dtype == th.uint8:
-        return 'uint8'
+        return TVMType('uint8')
     else:
         raise RuntimeError('Unsupported data type:', arr_dtype)
 
@@ -130,20 +131,6 @@ def zerocopy_from_numpy(np_data):
     """Return a tensor that shares the numpy data."""
     return th.from_numpy(np_data)
 
-    '''
-    data = arr_data
-    assert data.is_contiguous()
-    arr = TVMArray()
-    shape = c_array(tvm_shape_index_t, tuple(data.shape))
-    arr.data = ctypes.cast(data.data_ptr(), ctypes.c_void_p)
-    arr.shape = shape
-    arr.strides = None
-    arr.dtype = TVMType(_typestr(data.dtype))
-    arr.ndim = len(shape)
-    arr.ctx = get_context(data)
-    return arr
-    '''
-
 def nonzero_1d(arr):
     """Return a 1D tensor with nonzero element indices in a 1D vector"""
     assert arr.dim() == 1

python/dgl/base.py

 """Module for base types and utilities."""
+from __future__ import absolute_import
+
+import warnings
+
+from ._ffi.base import DGLError
 
 # A special argument for selecting all nodes/edges.
 ALL = "__ALL__"
@@ -6,5 +11,4 @@ ALL = "__ALL__"
 def is_all(arg):
     return isinstance(arg, str) and arg == ALL
 
-__MSG__ = "__MSG__"
-__REPR__ = "__REPR__"
+dgl_warning = warnings.warn

python/dgl/data/citation_graph.py

@@ -206,10 +206,33 @@ def get_gnp_generator(args):
         return nx.fast_gnp_random_graph(n, p, seed, True)
     return _gen
 
+class ScipyGraph(object):
+    """A simple graph object that uses scipy matrix."""
+    def __init__(self, mat):
+        self._mat = mat
+
+    def get_graph(self):
+        return self._mat
+
+    def number_of_nodes(self):
+        return self._mat.shape[0]
+
+    def number_of_edges(self):
+        return self._mat.getnnz()
+
+def get_scipy_generator(args):
+    n = args.syn_gnp_n
+    p = (2 * np.log(n) / n) if args.syn_gnp_p == 0. else args.syn_gnp_p
+    def _gen(seed):
+        return ScipyGraph(sp.random(n, n, p, format='coo'))
+    return _gen
+
 def load_synthetic(args):
     ty = args.syn_type
     if ty == 'gnp':
         gen = get_gnp_generator(args)
+    elif ty == 'scipy':
+        gen = get_scipy_generator(args)
     else:
         raise ValueError('Unknown graph generator type: {}'.format(ty))
     return GCNSyntheticDataset(

python/dgl/data/utils.py

 """Dataset utilities."""
+from __future__ import absolute_import
 
-import os
+import os, sys
 import hashlib
 import warnings
 import zipfile
@@ -125,17 +126,22 @@ def extract_archive(file, target_dir):
     target_dir : str
         Target directory of the archive to be uncompressed
     """
+    if os.path.exists(target_dir):
+        return
     if file.endswith('.gz') or file.endswith('.tar') or file.endswith('.tgz'):
         archive = tarfile.open(file, 'r')
     elif file.endswith('.zip'):
         archive = zipfile.ZipFile(file, 'r')
     else:
         raise Exception('Unrecognized file type: ' + file)
+    print('Extracting file to {}'.format(target_dir))
     archive.extractall(path=target_dir)
     archive.close()
 
 def get_download_dir():
-    dirname = '_download'
+    """Get the absolute path to the download directory."""
+    curr_path = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
+    dirname = os.path.join(curr_path, '../../../_download')
     if not os.path.exists(dirname):
         os.makedirs(dirname)
     return dirname