path: root/sagemath-networkx2.patch

diff --git a/build/pkgs/networkx/SPKG.txt b/build/pkgs/networkx/SPKG.txt
index c70a3c1..ca598bb 100644
--- a/build/pkgs/networkx/SPKG.txt
+++ b/build/pkgs/networkx/SPKG.txt
@@ -10,65 +10,4 @@ BSD
 
 == Upstream Contact ==
 
-See http://networkx.lanl.gov/
-
-== Dependencies ==
- * numpy
- * scipy
-
-== Option Dependencies ==
- * matplotlib
-
-== Special Update/Build Instructions ==
- * remove the src/doc/data directory containing various pngs
-
-== Changelog ==
-
-=== networkx-1.6 (Daniel Krenn, April 1, 2012) ===
-
-* upgraded to 1.6 release
-* removed previous patches, since they are fixed in this version
-
-=== networkx-1.2.p2 (Dima Pasechnik, November 26, 2011) ===
-
-* removed symbolic links to work around tar bugs on Cygwin
-
-=== networkx-1.2.p1 (Ben Edwards, August 10, 2010) ===
-
-* Patches small readwrite which allows for the reading of gml
-  graphs using matplotlibs version of pyparser.
-
-=== networkx-1.2 (Ben Edwards, July 20,2010) ===
-
-* upgraded to 1.2 release
-* removed previous patch which is fixed in this version
-
-=== networkx-1.1 (Ben Edwards, July 20,2010) ===
- * upgraded to the 1.1 release
- * Added patch that fixes bug in random_powerlaw_graph, reported upstream
-   should be fixed in networkx-1.2
-
-=== networkx-1.0.1 (Gregory McWhirter, January 27, 2010) ===
- * upgraded to the 1.0.1 release (see #7608)
- * deleted obsolete patches to nx_pylab.py
-
-=== networkx-0.99.p1 (Jason Grout, September 1st, 2009) ===
- * patch matplotlib routines to use numpy instead of the now-deprecated matplotlib.numerix
-
-=== networkx-0.99.p0 (Michael Abshoff, January 28th, 2009) ===
- * cleanup SPKG.txt
- * cleanup spkg-install
-
-=== networkx-0.99 (Robert Miller, Dec. 23rd, 2008) ===
- * upgraded to the 0.99 release
-
-=== networkx-0.36.p1 (Michael Abshoff, Jan. 31st, 2008) ===
- * remove .svn directories (#2009)
-
-=== networkx-0.36.p0 ===
- * add hg repo, check in files
-
-=== networkx-0.36 ===
- * update to the 0.36 release (Robert Miller)
- * remove src/doc/data directory to cut down the size (Michael Abshoff)
-
+https://networkx.github.io/
diff --git a/build/pkgs/networkx/checksums.ini b/build/pkgs/networkx/checksums.ini
index 3ca7296..0216ba0 100644
--- a/build/pkgs/networkx/checksums.ini
+++ b/build/pkgs/networkx/checksums.ini
@@ -1,4 +1,4 @@
 tarball=networkx-VERSION.tar.gz
-sha1=ac24380b13dfe92633370ad2091c0c04b6d098a2
-md5=6ef584a879e9163013e9a762e1cf7cd1
-cksum=1278894037
+sha1=cbd567e3ad8cf4d2f382b72f05a1af8fc508a815
+md5=7655d7aba670b1573c3adb90f8830c1e
+cksum=3151275585
diff --git a/build/pkgs/networkx/package-version.txt b/build/pkgs/networkx/package-version.txt
index 0b1ce62..879b416 100644
--- a/build/pkgs/networkx/package-version.txt
+++ b/build/pkgs/networkx/package-version.txt
@@ -1 +1 @@
-1.11.p0
+2.1
diff --git a/src/sage/graphs/base/graph_backends.pyx b/src/sage/graphs/base/graph_backends.pyx
index 2edc256..bef61a6 100644
--- a/src/sage/graphs/base/graph_backends.pyx
+++ b/src/sage/graphs/base/graph_backends.pyx
@@ -1,9 +1,9 @@
+# -*- coding: utf-8 -*-
 r"""
 Backends for Sage (di)graphs.
 
 This module implements :class:`GenericGraphBackend` (the base class for
-backends) and :class:`NetworkXGraphBackend` (a wrapper for `NetworkX
-<http://networkx.lanl.gov/>`__ graphs)
+backends).
 
 Any graph backend must redefine the following methods (for which
 :class:`GenericGraphBackend` raises a ``NotImplementedError``)
@@ -48,12 +48,16 @@ Classes and methods
 -------------------
 """
 
-#*******************************************************************************
-#        Copyright (C) 2008 Robert L. Miller <rlmillster@gmail.com>
+# ****************************************************************************
+#       Copyright (C) 2008 Robert L. Miller <rlmillster@gmail.com>
+#                     2018 Julian Rüth <julian.rueth@fsfe.org>
 #
-# Distributed  under  the  terms  of  the  GNU  General  Public  License (GPL)
-#                         http://www.gnu.org/licenses/
-#*******************************************************************************
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 from __future__ import absolute_import
 
 from .c_graph cimport CGraphBackend, CGraph
@@ -690,12 +694,6 @@ cdef class GenericGraphBackend(SageObject):
             multiedges = (<CGraphBackend> self)._multiple_edges
             directed   = (<CGraphBackend> self)._directed
             loops      = (<CGraphBackend> self)._loops
-        elif isinstance(self, NetworkXGraphBackend):
-            data_structure = "implementation"
-            implementation = "networkx"
-            multiedges =  self._nxg.is_multigraph()
-            directed   =  self._nxg.is_directed()
-            loops      =  bool(self._nxg.number_of_selfloops)
         else:
             raise Exception
 
@@ -800,9 +798,9 @@ class NetworkXGraphDeprecated(SageObject):
             sage: X.multiedges = True
             sage: G = X.mutate()
             sage: G.edges()
-            [(1, 2), (2, 3)]
+            MultiEdgeDataView([(1, 2), (2, 3)])
             sage: G.edges(data=True)
-            [(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]
+            MultiEdgeDataView([(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})])
 
         """
         import networkx
@@ -868,11 +866,11 @@ class NetworkXDiGraphDeprecated(SageObject):
             sage: X.multiedges = True
             sage: G = X.mutate()
             sage: G.edges()
-            [(1, 2), (2, 1), (2, 3)]
+            OutMultiEdgeDataView([(1, 2), (2, 1), (2, 3)])
             sage: G.edges(data=True)
-            [(1, 2, {'weight': 7}),
-             (2, 1, {7: {}, 8: {}}),
-             (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]
+            OutMultiEdgeDataView([(1, 2, {'weight': 7}),
+                                  (2, 1, {8: {}, 7: {}}),
+                                  (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})])
 
         """
         import networkx
@@ -899,735 +897,3 @@ class NetworkXDiGraphDeprecated(SageObject):
 from sage.misc.persist import register_unpickle_override
 register_unpickle_override('networkx.xgraph','XGraph', NetworkXGraphDeprecated)
 register_unpickle_override('networkx.xdigraph','XDiGraph', NetworkXDiGraphDeprecated)
-
-class NetworkXGraphBackend(GenericGraphBackend):
-    """
-    A wrapper for NetworkX as the backend of a graph.
-
-    TESTS::
-
-        sage: import sage.graphs.base.graph_backends
-
-    """
-
-    _nxg = None
-
-    def __init__(self, N=None):
-        """
-        Initialize the backend with NetworkX graph N.
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            doctest:...: DeprecationWarning: This class is not supported anymore and will soon be removed
-            See http://trac.sagemath.org/18375 for details.
-            sage: G.iterator_edges([],True)
-            <generator object at ...>
-        """
-        if N is None:
-            import networkx
-            N = networkx.MultiGraph()
-        self._nxg = N
-        from sage.misc.superseded import deprecation
-        deprecation(18375,"This class is not supported anymore and will "
-                    "soon be removed")
-
-    def __setstate__(self,state):
-        r"""
-        Fix the deprecated class if necessary.
-        """
-        for k,v in state.iteritems():
-            self.__dict__[k] = v
-        if isinstance(self._nxg, (NetworkXGraphDeprecated, NetworkXDiGraphDeprecated)):
-            from sage.misc.superseded import deprecation
-            deprecation(18375,"You unpickled an object which relies on an old "
-                        "data structure. Save it again to update it, for it "
-                        "may break in the future.")
-            self._nxg = self._nxg.mutate()
-
-    def add_edge(self, u, v, l, directed):
-        """
-        Add an edge (u,v) to self, with label l.  If directed is True, this is
-        interpreted as an arc from u to v.
-
-        INPUT:
-
-        - ``u,v`` -- vertices
-        - ``l`` -- edge label
-        - ``directed`` -- boolean
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.add_edge(1,2,'a',True)
-        """
-
-        if u is None: u = self.add_vertex(None)
-        if v is None: v = self.add_vertex(None)
-
-        if l:
-            self._nxg.add_edge(u, v, weight=l)
-        else:
-            self._nxg.add_edge(u, v)
-
-    def add_edges(self, edges, directed):
-        """
-        Add a sequence of edges to self.  If directed is True, these are
-        interpreted as arcs.
-
-        INPUT:
-
-        - ``edges`` -- list/iterator of edges to be added.
-        - ``directed`` -- boolean
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.add_edges([],True)
-        """
-        for e in edges:
-            try:
-                u,v,l = e
-            except ValueError:
-                u,v = e
-                l = None
-            self.add_edge(u,v,l,directed)
-
-    def add_vertex(self, name):
-        """
-        Add a labelled vertex to self.
-
-        INPUT:
-
-        - ``name``: vertex label
-
-        OUTPUT:
-
-        If ``name=None``, the new vertex name is returned. ``None`` otherwise.
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.add_vertex(0)
-        """
-        if isinstance(self._nxg, (NetworkXGraphDeprecated, NetworkXDiGraphDeprecated)):
-            self._nxg = self._nxg.mutate()
-
-        retval = None
-        if name is None: # then find an integer to use as a key
-            i = 0
-            while self.has_vertex(i):
-                i=i+1
-            name = i
-            retval = name
-
-        self._nxg.add_node(name)
-
-        return retval
-
-    def add_vertices(self, vertices):
-        """
-        Add labelled vertices to self.
-
-        INPUT:
-
-        - ``vertices``: iterator of vertex labels. A new label is created, used and returned in
-          the output list for all ``None`` values in ``vertices``.
-
-        OUTPUT:
-
-        Generated names of new vertices if there is at least one ``None`` value
-        present in ``vertices``. ``None`` otherwise.
-
-        EXAMPLES::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.add_vertices([1,2,3])
-            sage: G.add_vertices([4,None,None,5])
-            [0, 6]
-        """
-        vertices = list(vertices)
-        nones = vertices.count(None)
-        vertices = [v for v in vertices if v is not None]
-        self._nxg.add_nodes_from(vertices)
-
-        new_names = []
-        i = 0
-        while nones > 0:
-            while self.has_vertex(i):
-                i += 1
-            self._nxg.add_node(i)
-            new_names.append(i)
-
-            nones -= 1
-            i += 1
-
-        return new_names if new_names != [] else None
-
-    def degree(self, v, directed):
-        """
-        Return the total number of vertices incident to `v`.
-
-        INPUT:
-
-        - ``v`` -- a vertex label
-        - ``directed`` -- boolean
-
-        OUTPUT:
-
-            degree of v
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.add_vertices(range(3))
-            sage: G.degree(1, False)
-            0
-        """
-        return self._nxg.degree(v)
-
-    def in_degree(self, v):
-        """
-        Return the in-degree of `v`.
-
-        INPUT:
-
-        - ``v`` -- a vertex label
-
-        OUTPUT:
-
-            degree of v
-
-        TESTS::
-
-            sage: G = DiGraph(digraphs.Path(5),implementation="networkx")
-            doctest:...: DeprecationWarning: The 'implementation' keyword is deprecated, and the graphs has been stored as a 'c_graph'
-            See http://trac.sagemath.org/18375 for details.
-            sage: G = G._backend
-            sage: G.in_degree(0)
-            0
-            sage: G.in_degree(4)
-            1
-        """
-        return self._nxg.in_degree(v)
-
-    def out_degree(self, v):
-        """
-        Return the out-degree of `v`.
-
-        INPUT:
-
-        - ``v`` -- a vertex label
-
-        OUTPUT:
-
-            degree of v
-
-        TESTS::
-
-            sage: G = DiGraph(digraphs.Path(5),implementation="networkx")
-            doctest:...: DeprecationWarning: The 'implementation' keyword is deprecated, and the graphs has been stored as a 'c_graph'
-            See http://trac.sagemath.org/18375 for details.
-            sage: G = G._backend
-            sage: G.out_degree(0)
-            1
-            sage: G.out_degree(4)
-            0
-        """
-        return self._nxg.out_degree(v)
-
-    def del_edge(self, u, v, l, directed):
-        """
-        Delete the edge `(u,v)` with label `l`.
-
-        INPUT:
-
-        - ``u,v`` -- vertices
-        - ``l`` -- edge label
-        - ``directed`` -- boolean
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.del_edge(1,2,'a',True)
-        """
-        import networkx
-        try:
-            if self._nxg.is_multigraph():
-                for k,d in self._nxg.edge[u][v].iteritems():
-                    if d.get('weight',None) == l:
-                        self._nxg.remove_edge(u,v,k)
-                        break
-            else:
-                if l is None or self._nxg.edge[u][v].get('weight',None) == l:
-                    self._nxg.remove_edge(u,v)
-        except (KeyError, networkx.NetworkXError):
-            pass
-
-
-    def del_vertex(self, v):
-        """
-        Delete a labelled vertex in self.
-
-        INPUT:
-
-        - ``v`` -- vertex label
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.del_vertex(0)
-            Traceback (most recent call last):
-            ...
-            NetworkXError: The node 0 is not in the graph.
-        """
-        self._nxg.remove_node(v)
-
-    def del_vertices(self, vertices):
-        """
-        Delete labelled vertices in self.
-
-        INPUT:
-
-        - ``vertices`` -- iterator of vertex labels
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.del_vertices([1,2,3])
-            Traceback (most recent call last):
-            ...
-            NetworkXError: The node 1 is not in the graph.
-        """
-        for v in vertices:
-            self._nxg.remove_node(v)
-
-    def get_edge_label(self, u, v):
-        """
-        Return the edge label of `(u,v)`.
-
-        INPUT:
-
-        - ``u,v`` -- vertex labels
-
-        OUTPUT:
-            label of `(u,v)`
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.get_edge_label(1,2)
-            Traceback (most recent call last):
-            ...
-            NetworkXError: Edge (1,2) requested via get_edge_label does not exist.
-        """
-        cdef dict E
-        try:
-            E = self._nxg.edge[u][v]
-        except KeyError:
-            from networkx import NetworkXError
-            raise NetworkXError("Edge (%s,%s) requested via get_edge_label does not exist."%(u,v))
-
-        if self._nxg.is_multigraph():
-            return [ e.get('weight',None) for e in E.itervalues() ]
-        else:
-            return E.get('weight',None)
-
-    def has_edge(self, u, v, l):
-        """
-        True if self has an edge (u,v) with label l.
-
-        INPUT:
-
-        - ``u,v`` -- vertex labels
-        - ``l`` -- label
-
-        OUTPUT:
-            boolean
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.has_edge(1,2,'a')
-            False
-        """
-        if not self._nxg.has_edge(u, v):
-            return False
-        if l is None:
-            return True
-        cdef dict E = self._nxg.adj[u][v]
-        if self._nxg.is_multigraph():
-            return any(e.get('weight', None) == l
-                       for e in E.itervalues())
-        else:
-            return any(e == l for e in E.itervalues())
-
-    def has_vertex(self, v):
-        """
-        True if self has a vertex with label v.
-
-        INPUT:
-
-        - ``v`` -- vertex label
-
-        OUTPUT:
-            boolean
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.has_vertex(0)
-            False
-        """
-        return self._nxg.has_node(v)
-
-    def iterator_edges(self, vertices, labels):
-        """
-        Iterate over the edges incident to a sequence of vertices. Edges are
-        assumed to be undirected.
-
-        INPUT:
-
-        - ``vertices`` -- a list of vertex labels
-        - ``labels`` -- boolean
-
-        OUTPUT:
-            a generator which yields edges, with or without labels
-            depending on the labels parameter.
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.iterator_edges([],True)
-            <generator object at ...>
-        """
-        if labels:
-            for u,v,d in self._nxg.edges_iter(data=True):
-                if u in vertices or v in vertices:
-                    yield (u,v,d.get('weight',None))
-        else:
-            for u,v in self._nxg.edges_iter():
-                if u in vertices or v in vertices:
-                    yield (u,v)
-
-    def _iterator_in_edges_with_labels(self, vertices):
-        """
-        Iterate over the incoming edges incident to a sequence of vertices.
-        Special case, only for internal use.
-
-        EXAMPLES::
-
-            sage: g = DiGraph(graphs.PetersenGraph(), implementation="networkx")._backend
-            doctest:...: DeprecationWarning: The 'implementation' keyword is deprecated, and the graphs has been stored as a 'c_graph'
-            See http://trac.sagemath.org/18375 for details.
-            sage: sorted(list(g.iterator_in_edges([0,1], True)))
-            [(0, 1, None), (1, 0, None), (2, 1, None), (4, 0, None), (5, 0, None), (6, 1, None)]
-        """
-        for u,v,d in self._nxg.in_edges_iter(vertices,data=True):
-            yield (u,v,d.get('weight',None))
-
-    def iterator_in_edges(self, vertices, labels):
-        """
-        Iterate over the incoming edges incident to a sequence of vertices.
-
-        INPUT:
-
-        - ``vertices`` -- a list of vertex labels
-        - ``labels`` -- boolean
-
-        OUTPUT:
-            a generator which yields edges, with or without labels
-            depending on the labels parameter.
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: i = G.iterator_in_edges([],True)
-        """
-        if self._nxg.is_directed():
-            if labels:
-                return self._iterator_in_edges_with_labels(vertices)
-            else:
-                return self._nxg.in_edges_iter(vertices)
-        else:
-            return self.iterator_edges(vertices,labels)
-
-    def _iterator_out_edges_with_labels(self, vertices):
-        """
-        Iterate over the outbound edges incident to a sequence of vertices.
-        Special case, only for internal use.
-
-        EXAMPLES::
-
-            sage: g = DiGraph(graphs.PetersenGraph(), implementation="networkx")._backend
-            doctest:...: DeprecationWarning: The 'implementation' keyword is deprecated, and the graphs has been stored as a 'c_graph'
-            See http://trac.sagemath.org/18375 for details.
-            sage: sorted(list(g.iterator_out_edges([0,1], True)))
-            [(0, 1, None), (0, 4, None), (0, 5, None), (1, 0, None), (1, 2, None), (1, 6, None)]
-        """
-        for u,v,d in self._nxg.out_edges_iter(vertices,data=True):
-            yield (u,v,d.get('weight',None))
-
-    def iterator_out_edges(self, vertices, labels):
-        """
-        Iterate over the outbound edges incident to a sequence of vertices.
-
-        INPUT:
-
-        - ``vertices`` -- a list of vertex labels
-        - ``labels`` -- boolean
-
-        OUTPUT:
-            a generator which yields edges, with or without labels
-            depending on the labels parameter.
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: i = G.iterator_out_edges([],True)
-        """
-        if self._nxg.is_directed():
-            if labels:
-                return self._iterator_out_edges_with_labels(vertices)
-            else:
-                return self._nxg.out_edges_iter(vertices)
-        else:
-            return self.iterator_edges(vertices,labels)
-
-    def iterator_nbrs(self, v):
-        """
-        Iterate over the vertices adjacent to v.
-
-        INPUT:
-
-        - ``v`` -- vertex label
-
-        OUTPUT:
-            a generator which yields vertex labels
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.add_vertex(0)
-            sage: G.iterator_nbrs(0)
-            <dictionary-keyiterator object at ...>
-        """
-        return self._nxg.neighbors_iter(v)
-
-    def iterator_in_nbrs(self, v):
-        """
-        Iterate over the vertices u such that the edge (u,v) is in self
-        (that is, predecessors of v).
-
-        INPUT:
-
-        - ``v`` -- vertex label
-
-        OUTPUT:
-            a generator which yields vertex labels
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.iterator_in_nbrs(0)
-            Traceback (most recent call last):
-            ...
-            AttributeError: 'MultiGraph' object has no attribute 'predecessors_iter'
-        """
-        return self._nxg.predecessors_iter(v)
-
-    def iterator_out_nbrs(self, v):
-        """
-        Iterate over the vertices u such that the edge (v,u) is in self
-        (that is, successors of v).
-
-        INPUT:
-
-        - ``v`` -- vertex label
-
-        OUTPUT:
-            a generator which yields vertex labels
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.iterator_out_nbrs(0)
-            Traceback (most recent call last):
-            ...
-            AttributeError: 'MultiGraph' object has no attribute 'successors_iter'
-        """
-        return self._nxg.successors_iter(v)
-
-    def iterator_verts(self, verts):
-        """
-        Iterate over the vertices v with labels in verts.
-
-        INPUT:
-
-        - ``vertex`` -- vertex labels
-
-        OUTPUT:
-            a generator which yields vertices
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.iterator_verts(0)
-            <generator object bunch_iter at ...>
-        """
-        return self._nxg.nbunch_iter(verts)
-
-    def loops(self, new=None):
-        """
-        Get/set whether or not self allows loops.
-
-        INPUT:
-
-        - ``new`` -- can be a boolean (in which case it sets the value) or
-          ``None``, in which case the current value is returned. It is set to
-          ``None`` by default.
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.loops(True)
-            sage: G.loops(None)
-            True
-        """
-        if new is None:
-            return self._loops
-        if new:
-            self._loops = True
-        else:
-            self._loops = False
-
-    def multiple_edges(self, new=None):
-        """
-        Get/set whether or not self allows multiple edges.
-
-        INPUT:
-
-        - ``new`` -- can be a boolean (in which case it sets the value) or
-          ``None``, in which case the current value is returned. It is set to
-          ``None`` by default.
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.multiple_edges(True)
-            sage: G.multiple_edges(None)
-            True
-        """
-        from networkx import Graph,MultiGraph,DiGraph,MultiDiGraph
-        if new is None:
-            return self._nxg.is_multigraph()
-        if new == self._nxg.is_multigraph():
-            return
-        if new:
-            if self._nxg.is_directed():
-                self._nxg = MultiDiGraph(self._nxg)
-            else:
-                self._nxg = MultiGraph(self._nxg)
-        else:
-            if self._nxg.is_directed():
-                self._nxg = DiGraph(self._nxg)
-            else:
-                self._nxg = Graph(self._nxg)
-
-    def name(self, new=None):
-        """
-        Get/set name of self.
-
-        INPUT:
-
-        - ``new`` -- can be a string (in which case it sets the value) or
-          ``None``, in which case the current value is returned. It is set to
-          ``None`` by default.
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.name("A NetworkX Graph")
-            sage: G.name(None)
-            'A NetworkX Graph'
-        """
-        if new is None:
-            return self._nxg.name
-        self._nxg.name = new
-
-    def num_edges(self, directed):
-        """
-        The number of edges in self
-
-        INPUT:
-
-        - ``directed`` -- boolean
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.num_edges(True)
-            0
-            sage: G.num_edges(False)
-            0
-        """
-        return self._nxg.size()
-
-    def num_verts(self):
-        """
-        The number of vertices in self
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.num_verts()
-            0
-        """
-        return self._nxg.order()
-
-    def relabel(self, perm, directed):
-        """
-        Relabel the vertices of self by a permutation.
-
-        INPUT:
-
-        - ``perm`` -- permutation
-        - ``directed`` -- boolean
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.relabel([],False)
-        """
-        from networkx import relabel_nodes
-        name = self._nxg.name
-        self._nxg = relabel_nodes(self._nxg,perm)
-        self._nxg.name = name
-
-    def set_edge_label(self, u, v, l, directed):
-        """
-        Label the edge (u,v) by l.
-
-        INPUT:
-
-        - ``u,v`` -- vertices
-        - ``l`` -- edge label
-        - ``directed`` -- boolean
-
-        TESTS::
-
-            sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
-            sage: G.set_edge_label(1,2,'a',True)
-        """
-        if not self.has_edge(u, v, None):
-            return
-        if self.multiple_edges(None):
-            self._nxg[u][v].clear()
-            self._nxg[u][v][0] = dict(weight=l)
-            if directed is False:
-                self._nxg[v][u].clear()
-                self._nxg[v][u][0] = dict(weight=l)
-        else:
-            self._nxg[u][v]['weight'] = l
-            if directed is False:
-                self._nxg[v][u]['weight'] = l
diff --git a/src/sage/graphs/bipartite_graph.py b/src/sage/graphs/bipartite_graph.py
index a831f9a..738f571 100644
--- a/src/sage/graphs/bipartite_graph.py
+++ b/src/sage/graphs/bipartite_graph.py
@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 r"""
 Bipartite graphs
 
@@ -27,10 +28,14 @@ TESTS::
 
 #*****************************************************************************
 #         Copyright (C) 2008 Robert L. Miller <rlmillster@gmail.com>
+#                       2018 Julian Rüth <julian.rueth@fsfe.org>
 #
-# Distributed  under  the  terms  of  the  GNU  General  Public  License (GPL)
-#                         http://www.gnu.org/licenses/
-#*****************************************************************************
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 from __future__ import print_function
 from __future__ import absolute_import
 from six import iteritems
@@ -1421,7 +1426,7 @@ class BipartiteGraph(Graph):
             sage: G = graphs.CycleGraph(4)
             sage: B = BipartiteGraph([(u,v,2) for u,v in G.edges(labels=0)])
             sage: B.matching(use_edge_labels=True)
-            [(0, 3, 2), (1, 2, 2)]
+            [(1, 2, 2), (0, 3, 2)]
             sage: B.matching(use_edge_labels=True, value_only=True)
             4
             sage: B.matching(use_edge_labels=True, value_only=True, algorithm='Edmonds')
@@ -1480,7 +1485,7 @@ class BipartiteGraph(Graph):
             g = networkx.Graph()
             if use_edge_labels:
                 for u, v in W:
-                    g.add_edge(u, v, attr_dict={"weight": W[u, v]})
+                    g.add_edge(u, v, weight=W[u, v])
             else:
                 for u, v in L:
                     g.add_edge(u, v)
diff --git a/src/sage/graphs/digraph.py b/src/sage/graphs/digraph.py
index 5e67a6d..7151554 100644
--- a/src/sage/graphs/digraph.py
+++ b/src/sage/graphs/digraph.py
@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 r"""
 Directed graphs
 
@@ -112,6 +113,50 @@ graphs. Here is what they can do
 Methods
 -------
 """
+
+# ****************************************************************************
+#       Copyright (C) 2010      Alexandre Blondin Masse <alexandre.blondin.masse at gmail.com>
+#                               Carl Witty <cwitty@newtonlabs.com>
+#                               Gregory McWhirter <gmcwhirt@uci.edu>
+#                               Minh Van Nguyen <nguyenminh2@gmail.com>
+#                     2010-2011 Robert L. Miller <rlm@rlmiller.org>
+#                     2010-2015 Nathann Cohen <nathann.cohen@gmail.com>
+#                               Nicolas M. Thiery <nthiery@users.sf.net>
+#                     2011      Johannes Klaus Fichte <fichte@kr.tuwien.ac.at>
+#                     2012      Javier López Peña <vengoroso@gmail.com>
+#                     2012      Jim Stark <jstarx@gmail.com>
+#                     2012      Karl-Dieter Crisman <kcrisman@gmail.com>
+#                     2012      Keshav Kini <keshav.kini@gmail.com>
+#                     2012      Lukas Lansky <lansky@kam.mff.cuni.cz>
+#                     2012-2015 Volker Braun <vbraun.name@gmail.com>
+#                     2012-2017 Jeroen Demeyer <jdemeyer@cage.ugent.be>
+#                     2012-2018 David Coudert <david.coudert@inria.fr>
+#                     2013      Emily Gunawan <egunawan@umn.edu>
+#                     2013      Gregg Musiker <musiker@math.mit.edu>
+#                     2013      Mathieu Guay-Paquet <mathieu.guaypaquet@gmail.com>
+#                     2013-2014 Simon King <simon.king@uni-jena.de>
+#                     2014      Clemens Heuberger <clemens.heuberger@aau.at>
+#                               Erik Massop <e.massop@hccnet.nl>
+#                               R. Andrew Ohana <andrew.ohana@gmail.com>
+#                               Wilfried Luebbe <wluebbe@gmail.com>
+#                     2014-2015 André Apitzsch <andre.apitzsch@etit.tu-chemnitz.de>
+#                               Darij Grinberg <darijgrinberg@gmail.com>
+#                               Travis Scrimshaw <tscrim at ucdavis.edu>
+#                               Vincent Delecroix <20100.delecroix@gmail.com>
+#                     2014-2017 Frédéric Chapoton <chapoton@math.univ-lyon1.fr>
+#                     2015      Michele Borassi <michele.borassi@imtlucca.it>
+#                     2015-2017 John H. Palmieri <palmieri@math.washington.edu>
+#                               Jori Mäntysalo <jori.mantysalo@uta.fi>
+#                     2016      Dima Pasechnik <dimpase@gmail.com>
+#                     2018      Meghana M Reddy <mreddymeghana@gmail.com>
+#                               Julian Rüth <julian.rueth@fsfe.org>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 from __future__ import print_function, absolute_import
 
 from copy import copy
@@ -753,7 +798,7 @@ class DiGraph(GenericGraph):
             self.allow_multiple_edges(multiedges,check=False)
             self.allow_loops(loops,check=False)
             self.add_vertices(data.nodes())
-            self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True))
+            self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True))
         elif format == 'igraph':
             if not data.is_directed():
                 raise ValueError("A *directed* igraph graph was expected. To "+
@@ -2817,9 +2862,8 @@ class DiGraph(GenericGraph):
         INPUT:
 
         - ``implementation`` -- Use the default Cython implementation
-          (``implementation = default``), the default NetworkX library
-          (``implementation = "NetworkX"``) or the recursive NetworkX
-          implementation (``implementation = "recursive"``)
+          (``implementation = default``), or the default NetworkX library
+          (``implementation = "NetworkX"``)
 
         .. SEEALSO::
 
@@ -2843,12 +2887,7 @@ class DiGraph(GenericGraph):
 
         Using the NetworkX implementation ::
 
-            sage: D.topological_sort(implementation = "NetworkX")
-            [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10]
-
-        Using the NetworkX recursive implementation ::
-
-            sage: D.topological_sort(implementation = "recursive")
+            sage: list(D.topological_sort(implementation = "NetworkX"))
             [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10]
 
         ::
@@ -2860,21 +2899,6 @@ class DiGraph(GenericGraph):
             TypeError: Digraph is not acyclic; there is no topological
             sort.
 
-        .. note::
-
-           There is a recursive version of this in NetworkX, it used to
-           have problems in earlier versions but they have since been
-           fixed::
-
-              sage: import networkx
-              sage: D = DiGraph({ 0:[1,2,3], 4:[2,5], 1:[8], 2:[7], 3:[7],
-              ....:   5:[6,7], 7:[8], 6:[9], 8:[10], 9:[10] })
-              sage: N = D.networkx_graph()
-              sage: networkx.topological_sort(N)
-              [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10]
-              sage: networkx.topological_sort_recursive(N)
-              [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10]
-
         TESTS:
 
         A wrong value for the ``implementation`` keyword::
@@ -2893,12 +2917,9 @@ class DiGraph(GenericGraph):
             else:
                 raise TypeError('Digraph is not acyclic; there is no topological sort.')
 
-        elif implementation == "NetworkX" or implementation == "recursive":
+        elif implementation == "NetworkX":
             import networkx
-            if implementation == "NetworkX":
-                S = networkx.topological_sort(self.networkx_graph(copy=False))
-            else:
-                S = networkx.topological_sort_recursive(self.networkx_graph(copy=False))
+            S = networkx.topological_sort(self.networkx_graph(copy=False))
             if S is None:
                 raise TypeError('Digraph is not acyclic; there is no topological sort.')
             else:
diff --git a/src/sage/graphs/generators/degree_sequence.py b/src/sage/graphs/generators/degree_sequence.py
index baa8836..bcea8db 100644
--- a/src/sage/graphs/generators/degree_sequence.py
+++ b/src/sage/graphs/generators/degree_sequence.py
@@ -5,17 +5,17 @@ Graphs with a given degree sequence
 The methods defined here appear in :mod:`sage.graphs.graph_generators`.
 """
 
-###########################################################################
+# ****************************************************************************
+#       Copyright (C) 2006 Robert L. Miller <rlmillster@gmail.com>
+#                          Emily A. Kirkman
+#                     2009 Michael C. Yurko <myurko@gmail.com>
 #
-#           Copyright (C) 2006 Robert L. Miller <rlmillster@gmail.com>
-#                              and Emily A. Kirkman
-#           Copyright (C) 2009 Michael C. Yurko <myurko@gmail.com>
-#
-# Distributed  under  the  terms  of  the  GNU  General  Public  License (GPL)
-#                         http://www.gnu.org/licenses/
-###########################################################################
-
-# import from Sage library
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 from sage.graphs.graph import Graph
 from sage.misc.randstate import current_randstate
 
@@ -162,12 +162,8 @@ def DegreeSequenceConfigurationModel(deg_sequence, seed=None):
     ::
 
         sage: G = graphs.DegreeSequenceConfigurationModel([3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3])
-        sage: sorted(G.edges(labels=False))
-        [(0, 2), (0, 10), (0, 15), (1, 6), (1, 16), (1, 17), (2, 5), (2, 19),
-        (3, 7), (3, 14), (3, 14), (4, 9), (4, 13), (4, 19), (5, 6),
-        (5, 15), (6, 11), (7, 11), (7, 17), (8, 11), (8, 18), (8, 19),
-        (9, 12), (9, 13), (10, 15), (10, 18), (12, 13), (12, 16), (14, 17),
-        (16, 18)]
+        sage: len(G.edges())
+        30
         sage: G.show()  # long time
 
     REFERENCE:
diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
index 8d85f90..016cac2 100644
--- a/src/sage/graphs/generators/families.py
+++ b/src/sage/graphs/generators/families.py
@@ -5,18 +5,18 @@ Families of graphs
 The methods defined here appear in :mod:`sage.graphs.graph_generators`.
 """
 
-###########################################################################
+# ****************************************************************************
+#       Copyright (C) 2006 Robert L. Miller <rlmillster@gmail.com>
+#                          Emily A. Kirkman
+#                     2009 Michael C. Yurko <myurko@gmail.com>
+#                     2016 Rowan Schrecker <rowan.schrecker@hertford.ox.ac.uk>
 #
-#           Copyright (C) 2006 Robert L. Miller <rlmillster@gmail.com>
-#                              and Emily A. Kirkman
-#           Copyright (C) 2009 Michael C. Yurko <myurko@gmail.com>
-#
-#           Copyright (C) 2016 Rowan Schrecker <rowan.schrecker@hertford.ox.ac.uk>
-#            (Rowan Schrecker supported by UK EPSRC grant EP/K040251/2)
-#
-# Distributed  under  the  terms  of  the  GNU  General  Public  License (GPL)
-#                         http://www.gnu.org/licenses/
-###########################################################################
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 from __future__ import print_function, division
 import six
 from six.moves import range
@@ -197,22 +197,13 @@ def BalancedTree(r, h):
     gracefully::
 
         sage: graphs.BalancedTree(1, 10)
-        Balanced tree: Graph on 2 vertices
-
-        sage: graphs.BalancedTree(-1, 10)
-        Balanced tree: Graph on 1 vertex
+        Balanced tree: Graph on 11 vertices
 
     Similarly, we usually want the tree must have height `h \geq 1`
     but the algorithm also degenerates gracefully here::
 
         sage: graphs.BalancedTree(3, 0)
         Balanced tree: Graph on 1 vertex
-
-        sage: graphs.BalancedTree(5, -2)
-        Balanced tree: Graph on 0 vertices
-
-        sage: graphs.BalancedTree(-2,-2)
-        Balanced tree: Graph on 0 vertices
     """
     import networkx
     return Graph(networkx.balanced_tree(r, h), name="Balanced tree")
diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
index 3b1dd88..fda843a 100644
--- a/src/sage/graphs/generic_graph.py
+++ b/src/sage/graphs/generic_graph.py
@@ -317,6 +317,98 @@ can be applied on both. Here is what it can do:
 Methods
 -------
 """
+
+# ****************************************************************************
+#
+#       Copyright (C) 2010      Alexandre Blondin Masse <alexandre.blondin.masse at gmail.com>
+#                               Ben Edwards <bedwards@cs.unm.edu>
+#                               Carl Witty <cwitty@newtonlabs.com>
+#                               Gregory McWhirter <gmcwhirt@uci.edu>
+#                               Johan Sebastian Rosenkilde Nielsen <j.s.r.nielsen@mat.dtu.dk>
+#                               Minh Van Nguyen <nguyenminh2@gmail.com>
+#                               Mitesh Patel <qed777@gmail.com>
+#                               Sebastian Pancratz <sage@pancratz.org>
+#                               Tom Boothby <boothby@u.washington.edu>
+#                     2010-2011 Robert L. Miller <rlm@rlmiller.org>
+#                               Fidel Barrera-Cruz <fidel.barrera@gmail.com>
+#                               Leif Leonhardy <not.really@online.de>
+#                               Rob Beezer <beezer@ups.edu>
+#                     2010-2012 Dmitrii Pasechnik <dimpase@gmail.com>
+#                               Jason Grout <jason-sage@creativetrax.com>
+#                     2010-2013 Burcin Erocal <burcin@erocal.org>
+#                     2010-2014 Mike Hansen <mhansen@gmail.com>
+#                     2010-2015 Nicolas M. Thiery <nthiery@users.sf.net>
+#                     2010-2016 Nathann Cohen <nathann.cohen@gmail.com>
+#                     2010-2017 J. H. Palmieri <palmieri@math.washington.edu>
+#                     2010-2018 Christian Stump <christian.stump@univie.ac.at>
+#                               Vincent Delecroix <20100.delecroix at gmail.com>
+#                     2011      Anne Schilling <anne@math.ucdavis.edu>
+#                               Diego de Estrada <destrada@dc.uba.ar>
+#                               Eviatar Bach <eviatarbach@gmail.com>
+#                               Geoffrey Ehrman <gehrman@gmail.com>
+#                               Ivan Andrus <darthandrus@gmail.com>
+#                               Michael Orlitzky <michael@orlitzky.com>
+#                     2011-2012 Lukas Lansky <lansky@kam.mff.cuni.cz>
+#                     2011-2013 Robert Miller <rlm@rlmiller.org>
+#                     2011-2015 André Apitzsch <andre.apitzsch@st.ovgu.de>
+#                               Andrey Novoseltsev <novoselt@gmail.com>
+#                     2011-2018 Jeroen Demeyer <jdemeyer@cage.ugent.be>
+#                     2012      Dan Drake <drake@kaist.edu>
+#                               Javier López Peña <vengoroso@gmail.com>
+#                               Karl-Dieter Crisman <kcrisman@gmail.com>
+#                               Keshav Kini <keshav.kini@gmail.com>
+#                               Lauren Keough <s-lkeough1@math.unl.edu>
+#                               Nathan Carter <ncarter@bentley.edu>
+#                               Punarbasu Purkayastha <ppurka@gmail.com>
+#                               Stefano Leucci <leucci.stefano@gmail.com>
+#                     2012-2013 Frederic Chapoton <chapoton at math.univ-lyon1.fr>
+#                     2012-2015 Jernej Azarija <jernej.azarija@gmail.com>
+#                                Volker Braun <vbraun.name@gmail.com>
+#                     2012-2018 Julian Rueth <julian.rueth@gmail.com>
+#                     2013      Alexandre Prusch Züge <alexandrezuge@gmail.com>
+#                               Austin Roberts <austinis@math.washington.edu>
+#                               Birk Eisermann <eisermbi@fastmail.fm>
+#                               Uros Slana <urossla@gmail.com>
+#                     2013-2014 R. Andrew Ohana <andrew.ohana@gmail.com>
+#                               Simon King <simon.king@uni-jena.de>
+#                     2013-2018 Darij Grinberg <darijgrinberg@gmail.com>
+#                               Frédéric Chapoton <chapoton@math.univ-lyon1.fr>
+#                     2014      Emmanuel Charpentier <emm.charpentier@free.fr>
+#                               Erick Matsen <matsen@fhcrc.org>
+#                               Erik Massop <e.massop@hccnet.nl>
+#                               Florian Oosterhof <f.m.oosterhof@student.tue.nl>
+#                               Jean-Pierre Flori <jean-pierre.flori@ssi.gouv.fr>
+#                               Ralf Stephan <ralf@ark.in-berlin.de>
+#                               Robert Lipshitz <lipshitz@math.columbia.edu>
+#                               Thierry Monteil <sage@lma.metelu.net>
+#                     2014-2015 Wilfried Luebbe <wluebbe@gmail.com>
+#                     2014-2017 Travis Scrimshaw <tscrim at ucdavis.edu>
+#                     2014-2018 David Coudert <david.coudert@inria.fr>
+#                               Jori Mäntysalo <jori.mantysalo@uta.fi>
+#                     2015      David Einstein <deinst@gmail.com>
+#                               François Bissey <francois.bissey@canterbury.ac.nz>
+#                               Michele Borassi <michele.borassi@imtlucca.it>
+#                               Sergios Lenis <sergioslenis@gmail.com>
+#                     2015-2016 Janoš Vidali <janos.vidali@fmf.uni-lj.si>
+#                     2015-2018 Dima Pasechnik <dimpase@gmail.com>
+#                     2016      Jeremias Epperlein <jeremias.epperlein@gmail.com>
+#                               Marco Cognetta <cognetta.marco@gmail.com>
+#                               Peleg Michaeli <freepeleg@gmail.com>
+#                     2016-2018 Sébastien Labbé <slabqc@gmail.com>
+#                     2017      Emile Nadeau <nadeau.emile@gmail.com>
+#                               John Cremona <john.cremona@gmail.com>
+#                               Lokesh Jain <lokeshj1703@gmail.com>
+#                               Zachary Gershkoff <zgershkoff@gmail.com>
+#                     2017-2018 Moritz Firsching <moritz@math.fu-berlin.de>
+#                     2018      Erik M. Bray <erik.bray@lri.fr>
+#                               Meghana M Reddy <mreddymeghana@gmail.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 from __future__ import print_function, absolute_import, division
 from six.moves import range, zip
 from six import itervalues, iteritems, integer_types
@@ -376,18 +468,6 @@ class GenericGraph(GenericGraph_pyx):
         """
         for k,v in iteritems(state):
             self.__dict__[k] = v
-        from sage.graphs.base.graph_backends import NetworkXGraphBackend
-        if isinstance(self._backend, NetworkXGraphBackend):
-            from sage.misc.superseded import deprecation
-            deprecation(1000,"You unpickled an object which relies on an old "
-                        "data structure. Save it again to update it, for it "
-                        "may break in the future.")
-            g = self._backend._nxg
-            if g.is_directed():
-                from sage.graphs.digraph import DiGraph as constructor
-            else:
-                from sage.graphs.graph   import Graph   as constructor
-            self._backend = constructor(g)._backend
 
     def __add__(self, other):
         """
@@ -13130,18 +13210,18 @@ class GenericGraph(GenericGraph_pyx):
              6: 1/3, 7: 1/3, 8: 0, 9: 1/3, 10: 1/3, 11: 0}
 
             sage: (graphs.FruchtGraph()).clustering_coeff(weight=True)
-            {0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0.0,
+            {0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0,
             3: 0.3333333333333333, 4: 0.3333333333333333,
             5: 0.3333333333333333, 6: 0.3333333333333333,
-            7: 0.3333333333333333, 8: 0.0, 9: 0.3333333333333333,
-            10: 0.3333333333333333, 11: 0.0}
+            7: 0.3333333333333333, 8: 0, 9: 0.3333333333333333,
+            10: 0.3333333333333333, 11: 0}
 
             sage: (graphs.FruchtGraph()).clustering_coeff(nodes=[0,1,2])
             {0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0.0}
 
             sage: (graphs.FruchtGraph()).clustering_coeff(nodes=[0,1,2],
             ....:   weight=True)
-            {0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0.0}
+            {0: 0.3333333333333333, 1: 0.3333333333333333, 2: 0}
 
             sage: (graphs.GridGraph([5,5])).clustering_coeff(nodes=[(0,0),(0,1),(2,2)])
             {(0, 0): 0.0, (0, 1): 0.0, (2, 2): 0.0}
@@ -14592,20 +14672,14 @@ class GenericGraph(GenericGraph_pyx):
                 G = self.networkx_graph(copy=False)
             G.add_nodes_from(self.vertices())
 
+            degree = self.out_degree if self.is_directed else self.degree
             if vert is None:
-                closeness = networkx.closeness_centrality(G,vert,
-                                                          distance = 'weight'
-                                                          if by_weight
-                                                          else None)
-                return {v:c for v,c in iteritems(closeness) if c != 0}
+                closeness = networkx.closeness_centrality(G, vert, reverse=True, distance = 'weight' if by_weight else None)
+                return {v:c for v,c in iteritems(closeness) if degree(v) != 0}
             closeness = {}
-            degree = self.out_degree if self.is_directed else self.degree
             for x in v_iter:
                 if degree(x) != 0:
-                    closeness[x] = networkx.closeness_centrality(G, x,
-                                                             distance = 'weight'
-                                                             if by_weight
-                                                             else None)
+                    closeness[x] = networkx.closeness_centrality(G, x, reverse=True, distance='weight' if by_weight else None)
             if onlyone:
                 return closeness.get(vert, None)
             else:
diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py
index cd00df0..07a2a04 100644
--- a/src/sage/graphs/graph.py
+++ b/src/sage/graphs/graph.py
@@ -83,6 +83,8 @@ AUTHORS:
 
 - Amritanshu Prasad (2014-08): added clique polynomial
 
+- Julian Rüth (2018-06-21): upgrade to NetworkX 2
+
 Graph Format
 ------------
 
@@ -409,12 +411,17 @@ Methods
 -------
 """
 
-#*****************************************************************************
-#      Copyright (C) 2006 - 2007 Robert L. Miller <rlmillster@gmail.com>
+
+# ****************************************************************************
+#       Copyright (C) 2006-2007 Robert L. Miller <rlmillster@gmail.com>
+#                          2018 Julian Rüth <julian.rueth@fsfe.org>
 #
-# Distributed  under  the  terms  of  the  GNU  General  Public  License (GPL)
-#                         http://www.gnu.org/licenses/
-#*****************************************************************************
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 from __future__ import print_function
 from __future__ import absolute_import
 import six
@@ -1199,7 +1206,7 @@ class Graph(GenericGraph):
             self.allow_loops(loops, check=False)
             self.allow_multiple_edges(multiedges, check=False)
             self.add_vertices(data.nodes())
-            self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True))
+            self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True))
         elif format == 'igraph':
             if data.is_directed():
                 raise ValueError("An *undirected* igraph graph was expected. "+
@@ -4585,8 +4592,7 @@ class Graph(GenericGraph):
             ....: , (1,2,3), (1,3,3), (2,3,3)]
             sage: g = Graph(edge_list, loops=True, multiedges=True)
             sage: g.matching(use_edge_labels=True)
-            [(0, 3, 3), (1, 2, 6)]
-
+            [(1, 2, 6), (0, 3, 3)]
 
         TESTS:
 
@@ -4621,18 +4627,18 @@ class Graph(GenericGraph):
             g = networkx.Graph()
             if use_edge_labels:
                 for u, v in W:
-                    g.add_edge(u, v, attr_dict={"weight": W[u, v]})
+                    g.add_edge(u, v, weight=W[u, v])
             else:
                 for u, v in L:
                     g.add_edge(u, v)
             d = networkx.max_weight_matching(g)
             if value_only:
                 if use_edge_labels:
-                    return sum(W[u, v] for u, v in six.iteritems(d) if u < v)
+                    return sum(W[min(u, v), max(u, v)] for u, v in d)
                 else:
-                    return Integer(len(d) // 2)
+                    return Integer(len(d))
             else:
-                return [(u, v, L[u, v]) for u, v in six.iteritems(d) if u < v]
+                return [(u, v, L[min(u, v), max(u, v)]) for u, v in d]
 
         elif algorithm == "LP":
             g = self
@@ -6261,7 +6267,7 @@ class Graph(GenericGraph):
         return networkx.number_of_cliques(self.networkx_graph(copy=False), vertices, cliques)
 
     @doc_index("Clique-related methods")
-    def cliques_get_max_clique_graph(self, name=''):
+    def cliques_get_max_clique_graph(self):
         """
         Return the clique graph.
 
@@ -6276,10 +6282,6 @@ class Graph(GenericGraph):
             Currently only implemented for undirected graphs. Use to_undirected
             to convert a digraph to an undirected graph.
 
-        INPUT:
-
-        -  ``name`` - The name of the new graph.
-
         EXAMPLES::
 
             sage: (graphs.ChvatalGraph()).cliques_get_max_clique_graph()
@@ -6292,7 +6294,7 @@ class Graph(GenericGraph):
             sage: (G.cliques_get_max_clique_graph()).show(figsize=[2,2])
         """
         import networkx
-        return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), name=name, create_using=networkx.MultiGraph()))
+        return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), create_using=networkx.MultiGraph()))
 
     @doc_index("Clique-related methods")
     def cliques_get_clique_bipartite(self, **kwds):