scipy 1.4 causes some test failures due to deprecation warnings. Some of them arise from networkx code (already fixed upstream), here we fix the ones that come from sage code

CC: @kiwifb @timokau @isuruf

Component: packages: standard

Author: Antonio Rojas

Branch: a676e5a

Reviewer: François Bissey

Issue created by migration from https://trac.sagemath.org/ticket/29115