diff options
| -rw-r--r-- | .SRCINFO | 4 | ||||
| -rw-r--r-- | PKGBUILD | 7 | ||||
| -rw-r--r-- | sagemath-networkx2.patch | 1464 |
3 files changed, 3 insertions, 1472 deletions
@@ -1,6 +1,6 @@ pkgbase = sagemath-git pkgdesc = Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab - pkgver = 8.3.beta7.r0.g010ba97de0 + pkgver = 8.3.beta8.r0.g6bccacc656 pkgrel = 1 url = http://www.sagemath.org arch = x86_64 @@ -105,7 +105,6 @@ pkgbase = sagemath-git source = sagemath-threejs.patch source = sagemath-ignore-warnings.patch source = sagemath-cremona.patch - source = sagemath-networkx2.patch source = sagemath-scipy-1.0.patch source = sagemath-singular-4.1.1.patch source = sagemath-lcalc-c++11.patch @@ -121,7 +120,6 @@ pkgbase = sagemath-git sha256sums = 2d13b15ad2d1511bb3d752a261497060a8901882b1c2fa9813219781b7a71d83 sha256sums = a4a6c87b46ff23b89608aca66d00427334502e8bfb5dfe68b94497d19be1c7ae sha256sums = 71cc42d168545d460bc7f67a30486ff1534093e2b4deeb83deda8ff5bd081e7b - sha256sums = c65d9259df0e416ab74fd8c269df7d10d620b973ffe5583038d3433316c67a32 sha256sums = 17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a sha256sums = 11a68f156647ba9f38cb01b2a5e4f9a6a78f6297f2a5a65fbfdfe32d4be69d0c sha256sums = 5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0 @@ -8,7 +8,7 @@ pkgbase=sagemath-git pkgname=(sagemath-git sagemath-jupyter-git) -pkgver=8.3.beta7.r0.g010ba97de0 +pkgver=8.3.beta8.r0.g6bccacc656 pkgrel=1 pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab" arch=(x86_64) @@ -37,7 +37,7 @@ makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhom source=(git://git.sagemath.org/sage.git#branch=develop sagemath-env.patch package.patch latte-count.patch sagemath-python3-notebook.patch test-optional.patch r-no-readline.patch fes02.patch sagemath-threejs.patch sagemath-ignore-warnings.patch sagemath-cremona.patch - sagemath-networkx2.patch sagemath-scipy-1.0.patch sagemath-singular-4.1.1.patch sagemath-lcalc-c++11.patch + sagemath-scipy-1.0.patch sagemath-singular-4.1.1.patch sagemath-lcalc-c++11.patch pari-ratpoints.patch::"https://github.com/sagemath/sage/commit/83458400.patch") sha256sums=('SKIP' '50992e8421595aee3fe84663cbc7417d8d010cbcc824851032f24930653c2950' @@ -50,7 +50,6 @@ sha256sums=('SKIP' '2d13b15ad2d1511bb3d752a261497060a8901882b1c2fa9813219781b7a71d83' 'a4a6c87b46ff23b89608aca66d00427334502e8bfb5dfe68b94497d19be1c7ae' '71cc42d168545d460bc7f67a30486ff1534093e2b4deeb83deda8ff5bd081e7b' - 'c65d9259df0e416ab74fd8c269df7d10d620b973ffe5583038d3433316c67a32' '17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a' '11a68f156647ba9f38cb01b2a5e4f9a6a78f6297f2a5a65fbfdfe32d4be69d0c' '5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0' @@ -95,8 +94,6 @@ prepare(){ patch -p1 -i ../fes02.patch # use Features to detect Cremona databases https://trac.sagemath.org/ticket/24718 patch -p1 -i ../sagemath-cremona.patch -# adapt to networkx 2 changes https://trac.sagemath.org/ticket/24374 - patch -p1 -i ../sagemath-networkx2.patch # use python2 sed -e 's|#!/usr/bin/env sage-python23|#!/usr/bin/env python2|' -e 's|#!/usr/bin/env python\b|#!/usr/bin/env python2|' -i src/bin/* diff --git a/sagemath-networkx2.patch b/sagemath-networkx2.patch deleted file mode 100644 index e0703142c28c..000000000000 --- a/sagemath-networkx2.patch +++ /dev/null @@ -1,1464 +0,0 @@ -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): |