#7608: upgrade NetworkX to version 1.0.1
---------------------------------+------------------------------------------
Reporter: ylchapuy | Owner: jason
Type: enhancement | Status: needs_review
Priority: major | Milestone: sage-4.3.4
Component: graph theory | Keywords:
Author: Gregory McWhirter | Upstream: N/A
Reviewer: Minh Van Nguyen | Merged:
Work_issues: |
---------------------------------+------------------------------------------
Changes (by newvalueoldvalue):
* reviewer: => Minh Van Nguyen
* author: => Gregory McWhirter
Comment:
The reason why gsmcwhirter's patch
[http://trac.sagemath.org/sage_trac/attachment/ticket/7608/trac_7608
-networkx-folded.patch trac_7608-networkx-folded.patch] is so large is
that most of it is about removing trailing white spaces. Maybe I don't
understand pickling enough to see why gsmcwhirter doesn't provide any
(valid) examples in the following code:
{{{
+class NetworkXGraphDeprecated(SageObject):
+ """
+ Class for unpickling old networkx.XGraph formats
+
+ DOCTEST:
+ sage: import sage.graphs.base.graph_backends
+ """
+
+ def __init__(self):
+ """
+ Issue deprecation warnings for the old networkx XGraph formats
+ """
+ import warnings
+ from sage.misc.misc import deprecation
+ warnings.warn("Your graph object is saved in an old format since
networkx\
+ was updated to 1.0.1. You can re-save your graph by
typing\
+ graph.save(filename) to make this warning go away.",
+ DeprecationWarning, stacklevel=2)
+ deprecation("Your graph object is saved in an old format since
networkx\
+ was updated to 1.0.1. You can re-save your graph by
typing\
+ graph.save(filename) to make this warning go away.")
+
+ def mutate(self):
+ """
+ Change the old networkx XGraph format into the new one.
+
+ OUTPUT:
+
+ - The networkx.Graph or networkx.MultiGraph corresponding to the
+ unpickled data.
+ """
+ import networkx
+ new_adj = {}
+
+ for node1, edges in self.adj.iteritems():
+ new_adj[node1] = {}
+ for node2, weights in edges.iteritems():
+ new_adj[node1][node2] = {}
+ if weights is not None:
+ try:
+ for weight in weights:
+ new_adj[node1][node2][weight] = {}
+ except TypeError:
+ new_adj[node1][node2]['weight'] = weight
+
+ if self.multiedges:
+ G = networkx.MultiGraph(new_adj)
+ else:
+ G = networkx.Graph(new_adj)
+
+ return G
+
+class NetworkXDiGraphDeprecated(SageObject):
+ """
+ Class for unpickling old networkx.XDiGraph formats
+
+ DOCTEST:
+ sage: import sage.graphs.base.graph_backends
+ """
+
+ def __init__(self):
+ """
+ Issue deprecation warnings for the old networkx XDiGraph formats
+ """
+ import warnings
+ from sage.misc.misc import deprecation
+ warnings.warn("Your digraph object is saved in an old format
since networkx\
+ was updated to 1.0.1. You can re-save your digraph by
typing\
+ digraph.save(filename) to make this warning go
away.",
+ DeprecationWarning, stacklevel=2)
+ deprecation("Your digraph object is saved in an old format since
networkx\
+ was updated to 1.0.1. You can re-save your digraph by
typing\
+ digraph.save(filename) to make this warning go
away.")
+
+ def mutate(self):
+ """
+ Change the old networkx XDiGraph format into the new one.
+
+ OUTPUT:
+
+ - The networkx.DiGraph or networkx.MultiDiGraph corresponding to
the
+ unpickled data.
+ """
+ import networkx
+ new_adj = {}
+
+ for node1, edges in self.adj.iteritems():
+ new_adj[node1] = {}
+ for node2, weights in edges.iteritems():
+ new_adj[node1][node2] = {}
+ if weights is not None:
+ try:
+ for weight in weights:
+ new_adj[node1][node2][weight] = {}
+ except TypeError:
+ new_adj[node1][node2]['weight'] = weight
+
+ if self.multiedges:
+ G = networkx.MultiDiGraph(new_adj)
+ else:
+ G = networkx.DiGraph(new_adj)
+
+ return G
+
+from sage.structure.sage_object import register_unpickle_override
+register_unpickle_override('networkx.xgraph','XGraph',
NetworkXGraphDeprecated)
+register_unpickle_override('networkx.xdigraph','XDiGraph',
NetworkXDiGraphDeprecated)
}}}
[http://www.sagemath.org/doc/developer/conventions.html This section] of
the Developer's Guide explains the policy regarding doctests and examples.
See also [http://www.sagemath.org/doc/developer/trac.html these
guidelines]. You need to explain why the following functions don't have
doctests/examples:
{{{
+ 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.
+ """
+ try:
+ assert(not isinstance(self._nxg, (NetworkXGraphDeprecated,
NetworkXDiGraphDeprecated)))
+ except AssertionError:
+ self._nxg = self._nxg.mutate()
+
+ for u,v,d in self._nxg.in_edges_iter(vertices,data=True):
+ yield (u,v,d.get('weight',None))
}}}
and
{{{
+ 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.
+ """
+ try:
+ assert(not isinstance(self._nxg, (NetworkXGraphDeprecated,
NetworkXDiGraphDeprecated)))
+ except AssertionError:
+ self._nxg = self._nxg.mutate()
+
+ for u,v,d in self._nxg.out_edges_iter(vertices,data=True):
+ yield (u,v,d.get('weight',None))
}}}
Nevertheless, the proposed changes to upgrade NetworkX to 1.0.1 have been
in demand for a long time. I'm happy with the changes, but you need to
address the issues I listed above.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/7608#comment:30>
Sage <http://www.sagemath.org>
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