graph vertices cut off

[jasongrout]

Though #7299 helped, graph vertices are still cut off.

We can turn off clipping of the matplotlib scatterplot and add some bbox_extra_artists to the savefig which takes those artists into account when calculating the bounding box (when bbox_inches='tight').

---

First apply attachment: trac-9211-fix_cut_vertices_in_graphs.patch and then apply attachment: trac_9211_digraph_clipping.patch to $SAGE_ROOT/devel/sage. Finally apply attachment: trac_9211-fix_doctests.patch to $SAGE_ROOT/devel/sage.

CC: @rbeezer @kcrisman @kini

Component: graph theory

Author: Jason Grout

Reviewer: Punarbasu Purkayastha

Merged: sage-4.8.alpha1

Issue created by migration from https://trac.sagemath.org/ticket/9211

[jasongrout]

comment:1

Here is a good example showing the problem (still):

a=matrix([[1,2],[3,4]])

var('x y z w')
b=matrix([[x,y],[z,w]])

a.set_immutable()
b.set_immutable()

K=DiGraph({a:[b]})
show(K, vertex_size=800)

[jasongrout]

Attachment: trac-9211-graph-vertices-cut.patch.gz

[jasongrout]

comment:2

This patch depends on the matplotlib spkg at #9221. I don't know if the patch is very elegant. I'll trust the reviewer's comments on that. The problem is that it lets the scatter plot vertices extend beyond the frame (relying on the user adjusting the axes_pad option to extend the frame).

[jasongrout]

Author: Jason Grout

[jasongrout]

Work Issues: depends on #9221

[jasongrout]

comment:4

The patch doesn't work for multiple-edge graphs (they are drawn completely differently than graphs without multiple edges). In fact, we probably ought to draw all graphs using CircleCollection objects rather than scatter_plot or Circles.