deprecate parameter copy in networkx_graph

[rajat1433]

Done in this ticket:

• deprecate parameter copy of method networkx_graph. This parameter was useful for the _nxg backend that we don't have anymore.
• remove remaining pieces of calls to ._backend._nxg
• remove deprecated class NetworkXGraphDeprecated. It should have been removed in remove deprecated classes NetworkXGraphDeprecated and NetworkXDiGraphDeprecated #27166, but has been forgotten.

CC: @dcoudert

Component: graph theory

Author: Rajat Mittal

Branch/Commit: cefb5fb

Reviewer: David Coudert

Issue created by migration from https://trac.sagemath.org/ticket/27491

[rajat1433]

Branch: u/gh-rajat1433/27491_networkx_graph

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

1228fba

bug fix

[sagetrac-git]

Commit: 1228fba

[rajat1433]

Author: Rajat Mittal

[rajat1433]

Reviewer: dcoudert

[dcoudert]

comment:4

This is a very good catch. However, what you propose to do is not what should be done.

In #27166, we removed deprecated networkx backends, but we forgot to update other parts.

• In file src/sage/graphs/base/graph_backends.pyx: remove class NetworkXGraphDeprecated

• in method networkx_graph: remove parameter copy and update the code so that the method always returns a networkx graph.

• the name of this ticket will have to be updated accordingly

[sagetrac-git]

Changed commit from 1228fba to 3b48ef2

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

3b48ef2

copy removed

[rajat1433]

New commits:

3b48ef2

copy removed

[rajat1433]

comment:8

I am not able to locate _backend._nxg in any backend file in the networkx_graph method

        try:
            return self._backend._nxg
        except Exception:

can you point the location or does it always throw an error , if so we can remove it.

[dcoudert]

comment:9

We don't have this backend anymore. This is a remaining of the very first releases of Sagemath that we have not fully removed yet (I forgot to do it in #27166).

You can also remove this from trees.pyx

#        from networkx import MultiGraph
#        G = Graph(self.vertices)
#        cdef object XG = G._backend._nxg
#
#        for i from 2 <= i <= self.vertices:
#            vertex1 = i - 1
#            vertex2 = self.current_level_sequence[i - 1] - 1
#            XG.add_edge(vertex1, vertex2)
#
#        return G

        # Currently, c_graph does not have all the same functionality as networkx.
        # Until it does, we can't generate graphs using the c_graph backend even
        # though it is twice as fast (for our purposes) as networkx.

[sagetrac-git]

Changed commit from 3b48ef2 to ba0855a

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

ba0855a

removed unnecessary code

[rajat1433]

Changed reviewer from dcoudert to David Coudert

[dcoudert]

comment:12

I was a little to fast. To be clean, we should add a deprecation warning for parameter copy.

Could you:

• put back parameter copy as input parameter, but without documentation. So

-    def networkx_graph(self):
+    def networkx_graph(self, copy=True):

• and add the following at the very beginning of the method

+        if copy is not True:
+            deprecation(27491, "parameter copy is removed")

Then, in one year, we will completely remove this parameter.

Another small modification:

-        N.add_nodes_from(self.vertices())
+        N.add_nodes_from(self)

Method vertices sorts vertices by default, and returns a list of vertices. Method add_nodes_from can take an iterator as input. So we save the creation of the list.

I changed the description of this ticket to be consistent with what it does.

[sagetrac-git]

Changed commit from ba0855a to cefb5fb

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

cefb5fb

deprecated copy

[rajat1433]

comment:14

deprecated the copy parameter.

[dcoudert]

comment:15

LGTM

[vbraun]

Changed branch from u/gh-rajat1433/27491_networkx_graph to cefb5fb