Replacing the non-test .todense() methods with .toarray()
Replacing the test .todense() methods with .toarray()
Fixing redundant np.asarray(X.toarray()) in metrics
Additional .todense() -> .toarray() fixes
Fixing small formatting issue in doctest
Merge pull request #3169 from mjbommar/issue-3167-eradicate-todense

PR re: issue 3167 to eradicate .todense()