[DOC] initial docs

docs/source/conf.py

+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../python'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'DGL'
+copyright = '2018, DGL Team'
+author = 'DGL Team'
+
+# The short X.Y version
+version = '0.0.1'
+# The full version, including alpha/beta/rc tags
+release = '0.0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = ['.rst', '.md']
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'dgldoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'dgl.tex', 'dgl Documentation',
+     'DGL Team', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'dgl', 'dgl Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'dgl', 'dgl Documentation',
+     author, 'dgl', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------

docs/source/index.rst

+.. DGL documentation master file, created by
+   sphinx-quickstart on Fri Oct  5 14:18:01 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to DGL's documentation!
+===============================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+Get Started
+-----------
+.. toctree::
+   :maxdepth: 2
+
+   install/index
+   tutorials/index
+
+API Reference
+-------------
+.. toctree::
+   :maxdepth: 2
+
+   api/python/index
+
+Index
+-----
+* :ref:`genindex`

docs/source/install/index.rst

+Install DGL
+============
+
+At this stage, we recommend installing DGL from source. To quickly try out DGL and its demo/tutorials, checkout `Install from docker`_.
+
+Get source codes
+----------------
+First, download the source files from github. Note you need to use the ``--recursive`` option to
+also clone the submodules.
+
+.. code:: bash
+
+    git clone --recursive https://github.com/jermainewang/dgl.git
+
+You can also clone the repository first and type following commands:
+
+.. code:: bash
+
+    git submodule init
+    git submodule update
+
+
+Build shared library
+--------------------
+Before building the library, please make sure the following dependencies are installed
+(use ubuntu as an example):
+
+.. code:: bash
+
+    sudo apt-get update
+    sudo apt-get install -y python
+
+We use cmake (minimal version 2.8) to build the library.
+
+.. code:: bash
+
+    mkdir build
+    cd build
+    cmake ..
+    make -j4
+
+Build python binding
+--------------------
+DGL's python binding depends on following packages (tested version):
+
+* numpy (>= 1.14.0)
+* scipy (>= 1.1.0)
+* networkx (>= 2.1)
+
+To install them, use following command:
+
+.. code:: bash
+
+    pip install --user numpy scipy networkx
+
+There are several ways to setup DGL's python binding. We recommend developers at the current stage
+use environment variables to find python packages.
+
+.. code:: bash
+
+    export DGL_HOME=/path/to/dgl
+    export PYTHONPATH=$DGL_HOME$/python:${PYTHONPATH}
+    export DGL_LIBRARY_PATH=$DGL_HOME$/build
+
+The ``DGL_LIBRARY_PATH`` variable is used for our python package to locate the shared library
+built above. Use following command to test whether the installation is successful or not.
+
+.. code:: bash
+
+    python -c 'import dgl'
+
+Install from docker
+-------------------
+TBD

docs/source/tutorials/index.rst

+Tutorials
+=========
+
+TBD: Get started on DGL

python/dgl/__init__.py

@@ -9,7 +9,7 @@ from ._ffi.function import register_func, get_global_func, list_global_func_name
 from ._ffi.base import DGLError, __version__
 
 from .base import ALL
-from .batch import batch, unbatch
+from .batched_graph import *
 from .generator import *
 from .graph import DGLGraph, __MSG__, __REPR__
 from .subgraph import DGLSubGraph

python/dgl/batch.py → python/dgl/batched_graph.py

@@ -10,6 +10,8 @@ from . import graph_index as gi
 from . import backend as F
 from . import utils
 
+__all__ = ['BatchedDGLGraph', 'batch', 'unbatch', 'split']
+
 class BatchedDGLGraph(DGLGraph):
     """The batched DGL graph.
 
@@ -74,15 +76,15 @@ class BatchedDGLGraph(DGLGraph):
 
     # override APIs
     def add_nodes(self, num, reprs=None):
-        """Add nodes."""
+        """Add nodes. Disabled because BatchedDGLGraph is read-only."""
         raise RuntimeError('Readonly graph. Mutation is not allowed.')
 
     def add_edge(self, u, v, reprs=None):
-        """Add one edge."""
+        """Add one edge. Disabled because BatchedDGLGraph is read-only."""
         raise RuntimeError('Readonly graph. Mutation is not allowed.')
 
     def add_edges(self, u, v, reprs=None):
-        """Add many edges."""
+        """Add many edges. Disabled because BatchedDGLGraph is read-only."""
         raise RuntimeError('Readonly graph. Mutation is not allowed.')
 
     # new APIs
@@ -146,7 +148,7 @@ def split(graph_batch, num_or_size_splits):
     pass
 
 def unbatch(graph):
-    """Unbatch the graph and return a list of subgraphs.
+    """Unbatch and return the list of graphs in this batch.
 
     Parameters
     ----------

python/dgl/nx_adapt.py

-"""Utility functions for networkx adapter."""
-from __future__ import absolute_import
-
-from collections import MutableMapping
-
-import networkx as nx
-import networkx.convert as convert
-
-class NodeDict(MutableMapping):
-    def __init__(self, add_cb, del_cb):
-        self._dict = {}
-        self._add_cb = add_cb
-        self._del_cb = del_cb
-    def __setitem__(self, key, val):
-        self._add_cb(key)
-        self._dict[key] = val
-    def __getitem__(self, key):
-        return self._dict[key]
-    def __delitem__(self, key):
-        self._del_cb(key)
-        del self._dict[key]
-    def __len__(self):
-        return len(self._dict)
-    def __iter__(self):
-        return iter(self._dict)
-
-class AdjOuterDict(MutableMapping):
-    def __init__(self, add_cb, del_cb):
-        self._dict = {}
-        self._add_cb = add_cb
-        self._del_cb = del_cb
-    def __setitem__(self, key, val):
-        val.src = key
-        self._dict[key] = val
-    def __getitem__(self, key):
-        return self._dict[key]
-    def __delitem__(self, key):
-        for val in self._dict[key]:
-            self._del_cb(key, val)
-        del self._dict[key]
-    def __len__(self):
-        return len(self._dict)
-    def __iter__(self):
-        return iter(self._dict)
-
-class AdjInnerDict(MutableMapping):
-    def __init__(self, add_cb, del_cb):
-        self._dict = {}
-        self.src = None
-        self._add_cb = add_cb
-        self._del_cb = del_cb
-    def __setitem__(self, key, val):
-        if self.src is not None and key not in self._dict:
-            self._add_cb(self.src, key)
-        self._dict[key] = val
-    def __getitem__(self, key):
-        return self._dict[key]
-    def __delitem__(self, key):
-        if self.src is not None:
-            self._del_cb(self.src, key)
-        del self._dict[key]
-    def __len__(self):
-        return len(self._dict)
-    def __iter__(self):
-        return iter(self._dict)
-
-class AdjInnerDictFactory(object):
-    def __init__(self, cb1, cb2):
-        self._cb1 = cb1
-        self._cb2 = cb2
-    def __call__(self):
-        return AdjInnerDict(self._cb1, self._cb2)
-
-def nx_init(obj,
-            add_node_cb,
-            add_edge_cb,
-            del_node_cb,
-            del_edge_cb,
-            graph_data,
-            **attr):
-    """Init the object to be compatible with networkx's DiGraph.
-
-    Parameters
-    ----------
-    obj : any
-        The object to be init.
-    add_node_cb : callable
-        The callback function when node is added.
-    add_edge_cb : callable
-        The callback function when edge is added.
-    graph_data : graph data
-        Data to initialize graph. Same as networkx's semantics.
-    attr : keyword arguments, optional
-        Attributes to add to graph as key=value pairs.
-    """
-    # The following codes work for networkx 2.1.
-    obj.adjlist_outer_dict_factory = None
-    obj.adjlist_inner_dict_factory = AdjInnerDictFactory(add_edge_cb, del_edge_cb)
-    obj.edge_attr_dict_factory = dict
-
-    obj.root_graph = obj
-    obj.graph = {}
-    obj._node = NodeDict(add_node_cb, del_node_cb)
-
-    obj._adj = AdjOuterDict(add_edge_cb, del_edge_cb)
-    obj._pred = dict()
-    obj._succ = obj._adj
-
-    if graph_data is not None:
-        convert.to_networkx_graph(graph_data, create_using=obj)
-    obj.graph.update(attr)

python/dgl/subgraph.py

@@ -6,7 +6,6 @@ import networkx as nx
 from . import backend as F
 from .frame import Frame, FrameRef
 from .graph import DGLGraph
-from .nx_adapt import nx_init
 from . import utils
 
 class DGLSubGraph(DGLGraph):