Investigate and fix deprecation warnings encountered in tests

[gshank]

When we run our tests we get a fairly large number of deprecation warnings. Many of these seem to come from dependencies. We should investigate these warnings and see if we should 1) upgrade the dependency or 2) modify our code or 2) just wait.

Here are some examples of warnings. We should run the tests and collect all of them for investigation.

env/lib/python3.8/site-packages/packaging/version.py:127: DeprecationWarning: Creating a LegacyVersion has been deprecated and will be removed in the next major release

jinja2/runtime.py:679: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.

<class 'networkx.utils.decorators.argmap'> compilation 5:5: DeprecationWarning: write_gpickle is deprecated and will be removed in 3.0.Use pickle.dump(G, path, protocol)