#6041: [with spkg, needs work] update NetworkX to version 0.99
--------------------------+-------------------------------------------------
Reporter: mvngu | Owner: rlm
Type: enhancement | Status: new
Priority: major | Milestone: sage-4.0.1
Component: graph theory | Keywords:
--------------------------+-------------------------------------------------
Comment(by mvngu):
I managed to get all doctests in {{{sage/graphs/base/graph_backends.py}}}
to pass, but at the expense of deleting the following methods from the
class {{{NetworkXGraphBackend}}}. Here I assume that
{{{NetworkXGraphBackend}}} is an undirected graph without multiple edges.
1. {{{loops}}} -- This is irrelevant with the API changes in NetworkX
0.99, since the class {{{Graph}}} from NetworkX 0.99 allows for self-loops
without having to explicitly set it with a boolean.
1. {{{multiple_edges}}} -- Again irrelevant since the class {{{Graph}}}
doesn't allow multiple edges. Graphs with multiple edges should now be
constructed via the class {{{MultiGraph}}} (not directed), or
{{{MultiDiGraph}}} which allows for directed arcs.
Here's a diff of the changes to {{{sage/graphs/base/graph_backends.py}}}:
{{{
diff -r 21c6c829ea32 sage/graphs/base/graph_backends.py
--- a/sage/graphs/base/graph_backends.py Sat May 16 09:46:59 2009
-0700
+++ b/sage/graphs/base/graph_backends.py Tue May 19 23:47:29 2009
-0700
@@ -499,13 +499,12 @@
"""
if N is None:
import networkx
- N = networkx.XGraph()
+ N = networkx.Graph()
self._nxg = N
- def add_edge(self, u, v, l, directed):
+ def add_edge(self, u, v, l):
"""
- Add an edge (u,v) to self, with label l. If directed is True,
this is
- interpreted as an arc from u to v.
+ Add an edge (u,v) to self, with label l.
INPUT:
u,v: vertices
@@ -514,11 +513,11 @@
DOCTEST:
sage: G =
sage.graphs.base.graph_backends.NetworkXGraphBackend()
- sage: G.add_edge(1,2,'a',True)
+ sage: G.add_edge(1, 2, "a")
"""
self._nxg.add_edge(u, v, l)
- def add_edges(self, edges, directed):
+ def add_edges(self, edges):
"""
Add a sequence of edges to self. If directed is True, these are
interpreted as arcs.
@@ -529,7 +528,7 @@
DOCTEST:
sage: G =
sage.graphs.base.graph_backends.NetworkXGraphBackend()
- sage: G.add_edges([],True)
+ sage: G.add_edges([])
"""
for e in edges:
try:
@@ -537,7 +536,7 @@
except:
u,v = e
l = None
- self.add_edge(u,v,l,directed)
+ self.add_edge(u, v, l)
def add_vertex(self, name):
"""
@@ -589,7 +588,7 @@
"""
return self._nxg.degree(v)
- def del_edge(self, u, v, l, directed):
+ def del_edge(self, u, v, l):
"""
Deletes the edge (u,v) with label l.
@@ -600,9 +599,10 @@
DOCTEST:
sage: G =
sage.graphs.base.graph_backends.NetworkXGraphBackend()
- sage: G.del_edge(1,2,'a',True)
+ sage: G.add_edge(1, 2, "a")
+ sage: G.del_edge(1, 2, "a")
"""
- self._nxg.delete_edge(u, v, l)
+ self._nxg.delete_edge(u, v)
def del_vertex(self, v):
"""
@@ -649,16 +649,16 @@
DOCTEST:
sage: G =
sage.graphs.base.graph_backends.NetworkXGraphBackend()
- sage: G.get_edge_label(1,2)
+ sage: G.get_edge_label(1, 2)
Traceback (most recent call last):
...
- NetworkXError: Edge (1,2) requested via get_edge does not
exist.
+ NetworkXError: edge (1,2) not in graph
"""
return self._nxg.get_edge(u, v)
- def has_edge(self, u, v, l):
+ def has_edge(self, u, v):
"""
- True if self has an edge (u,v) with label l.
+ True if self has an edge (u,v).
INPUT:
u,v: vertex labels
@@ -669,10 +669,19 @@
DOCTEST:
sage: G =
sage.graphs.base.graph_backends.NetworkXGraphBackend()
- sage: G.has_edge(1,2,'a')
+ sage: G.has_edge(1, 2)
False
"""
- return self._nxg.has_edge(u, v, l)
+ return self._nxg.has_edge(u, v)
+
+ def has_selfloops(self):
+ """
+ Returns ``True`` if this graph has self-loops; ``False``
otherwise.
+ """
+ if self._nxg.number_of_selfloops() > 0:
+ return True
+ else:
+ return False
def has_vertex(self, v):
"""
@@ -781,8 +790,9 @@
DOCTEST:
sage: G =
sage.graphs.base.graph_backends.NetworkXGraphBackend()
+ sage: G.add_edges([(0,1), (0,2), (1,2)])
sage: G.iterator_nbrs(0)
- <generator object at ...>
+ <dictionary-keyiterator object at ...>
"""
return self._nxg.neighbors_iter(v)
@@ -802,7 +812,7 @@
sage: G.iterator_in_nbrs(0)
Traceback (most recent call last):
...
- AttributeError: 'XGraph' object has no attribute
'predecessors_iter'
+ AttributeError: 'Graph' object has no attribute
'predecessors_iter'
"""
return self._nxg.predecessors_iter(v)
@@ -822,7 +832,7 @@
sage: G.iterator_out_nbrs(0)
Traceback (most recent call last):
...
- AttributeError: 'XGraph' object has no attribute
'successors_iter'
+ AttributeError: 'Graph' object has no attribute
'successors_iter'
"""
return self._nxg.successors_iter(v)
@@ -839,49 +849,9 @@
DOCTEST:
sage: G =
sage.graphs.base.graph_backends.NetworkXGraphBackend()
sage: G.iterator_verts(0)
- <listiterator object at ...>
+ <generator object at ...>
"""
- return iter(self._nxg.prepare_nbunch(verts))
-
- def loops(self, new):
- """
- Get/set whether or not self allows loops.
-
- INPUT:
- new: boolean or None
-
- DOCTEST:
- sage: G =
sage.graphs.base.graph_backends.NetworkXGraphBackend()
- sage: G.loops(True)
- sage: G.loops(None)
- True
- """
- if new is None:
- return self._nxg.selfloops
- if new:
- self._nxg.allow_selfloops()
- else:
- self._nxg.ban_selfloops()
-
- def multiple_edges(self, new):
- """
- Get/set whether or not self allows multiple edges.
-
- INPUT:
- new: boolean or None
-
- DOCTEST:
- sage: G =
sage.graphs.base.graph_backends.NetworkXGraphBackend()
- sage: G.multiple_edges(True)
- sage: G.multiple_edges(None)
- True
- """
- if new is None:
- return self._nxg.multiedges
- if new:
- self._nxg.allow_multiedges()
- else:
- self._nxg.ban_multiedges()
+ return iter(self._nxg.nbunch_iter(verts))
def name(self, new):
"""
@@ -969,39 +939,24 @@
newd[perm[v]] = newtempd
self._nxg.adj = newd
- def set_edge_label(self, u, v, l, directed):
+ def set_edge_label(self, u, v, l):
"""
Label the edge (u,v) by l.
INPUT:
u,v: vertices
l: edge label
- directed: boolean
DOCTEST:
sage: G =
sage.graphs.base.graph_backends.NetworkXGraphBackend()
- sage: G.set_edge_label(1,2,'a',True)
+ sage: # G is empty graph, so it doesn't have the edge (1,2)
+ sage: G.set_edge_label(1, 2, "a")
+ sage: # add some edges to G
+ sage: G.add_edges([(1,2), (1,3), (2,3)])
+ sage: G.set_edge_label(1, 2, "b")
"""
- if not self.has_edge(u, v, None):
+ if not self.has_edge(u, v):
return
- if self.multiple_edges(None):
- if directed:
- self._nxg.succ[u][v] = [l]
- self._nxg.pred[v][u] = [l]
- else:
- self._nxg.adj[u][v] = [l]
- self._nxg.adj[v][u] = [l]
else:
- if directed:
- self._nxg.succ[u][v] = l
- self._nxg.pred[v][u] = l
- else:
- self._nxg.adj[u][v] = l
- self._nxg.adj[v][u] = l
-
-
-
-
-
-
-
+ self._nxg.adj[u][v] = l
+ self._nxg.adj[v][u] = l
}}}
But the following doctests failed:
{{{
sage -t -long "devel/sage-6041/sage/graphs/graph_bundle.py"
sage -t -long "devel/sage-6041/sage/graphs/graph_generators.py"
sage -t -long "devel/sage-6041/sage/graphs/planarity.pyx"
sage -t -long "devel/sage-6041/sage/graphs/graph_fast.pyx"
sage -t -long "devel/sage-6041/sage/graphs/graph_isom.pyx"
sage -t -long "devel/sage-6041/sage/graphs/schnyder.py"
sage -t -long "devel/sage-6041/sage/graphs/graph_coloring.py"
sage -t -long "devel/sage-6041/sage/graphs/graph.py"
sage -t -long "devel/sage-6041/sage/graphs/chrompoly.pyx"
sage -t -long "devel/sage-6041/sage/graphs/print_graphs.py"
sage -t -long "devel/sage-6041/sage/graphs/graph_plot.py"
sage -t -long "devel/sage-6041/sage/graphs/graph_list.py"
sage -t -long "devel/sage-6041/sage/graphs/graph_database.py"
sage -t -long "devel/sage-6041/sage/graphs/base/dense_graph.pyx"
sage -t -long "devel/sage-6041/sage/graphs/base/sparse_graph.pyx"
sage -t -long "devel/sage-6041/sage/graphs/base/c_graph.pyx"
sage -t -long "devel/sage-6041/sage/graphs/bipartite_graph.py"
sage -t -long "devel/sage-6041/sage/graphs/linearextensions.py"
sage -t -long "devel/sage-6041/sage/graphs/base/dense_graph.pyx"
sage -t -long "devel/sage-6041/sage/graphs/base/sparse_graph.pyx"
sage -t -long "devel/sage-6041/sage/graphs/base/c_graph.pyx"
}}}
It looks like anything under {{{sage/graphs/}}} that uses
{{{sage/graphs/base/graph_backends.py}}} should be changed accordingly.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/6041#comment:3>
Sage <http://sagemath.org/>
Sage - Open Source Mathematical Software: Building the Car Instead of
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