clean generic_graph.py (part 9) - edge and vertex handlers

[dcoudert]

In this ticket, we clean methods for adding/removing vertices/edges and enumerating neighbors. The main changes are:

• add parameter sort to method .vertices. This gives an alternative to list(G).
• in method delete_vertices, we add as first instruction vertices = list(vertices). This way we now allow to call this method with an iterator. Before, the method was not removing any vertex when called with an iterator. This will certainly help reducing further the number of calls to .vertices().
• in method vertex_iterator, we remove doctests related to former networkx backend
• change in method remove_multiple_edges that should make it faster
• PEP8 cleaning

CC: @tscrim @fchapoton

Component: graph theory

Author: David Coudert

Branch/Commit: 1c43e4e

Reviewer: Travis Scrimshaw

Issue created by migration from https://trac.sagemath.org/ticket/26666

[dcoudert]

Commit: 0070906

[dcoudert]

Branch: public/26666_generic_graph_part_9_edge_and_vertex

[dcoudert]

New commits:

0070906

trac #26666: generic_graph.py (part 9) - edge and vertex handlers

[fchapoton]

comment:2

2 trivial failing doctests in src/sage/graphs/bipartite_graph.py

[sagetrac-git]

Changed commit from 0070906 to ecfc5c6

[sagetrac-git]

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

7131aaa	trac #26666: fix doc
ecfc5c6	trac #26666: fix doctests in bipartite_graph.py

[dcoudert]

comment:4

oups, fixed.

[sagetrac-git]

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

44c76f2

trac #26666: avoid .vertices() in method clear

[sagetrac-git]

Changed commit from ecfc5c6 to 44c76f2

[dcoudert]

comment:7

We also avoid sorting vertices before removing them from the graph.

[tscrim]

comment:8

Just for clarity, I think it is better to add these parentheses: if (not sort) and key:

Since u and v are code inputs for the one-line descriptions, I think it would be better to do

-Delete all edges from `u` to `v`.
+Delete all edges from ``u`` to ``v``.

I think the OUTPUT: block for has_vertex is functionally useless and can be safely removed (it is essentially a copy of the one-line description).

Other than that LGTM.

[sagetrac-git]

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

1c43e4e

trac #26666: implement reviewer's comments

[sagetrac-git]

Changed commit from 44c76f2 to 1c43e4e

[dcoudert]

comment:10

i have implemented all you comments. Should be better now.

[tscrim]

Reviewer: Travis Scrimshaw

[tscrim]

comment:11

Thanks. LGTM.

[vbraun]

Changed branch from public/26666_generic_graph_part_9_edge_and_vertex to 1c43e4e