add parameter to control output class

[corybrunson]

This PR introduces the return_class parameter to vietoris_rips() and cubical(). It defaults to "PHom" and can be set to "persistence" instead; for the latter option, {phutil} becomes a dependency. The PHom (and default) output should be unchanged, while the persistence output provides some metadata that the class understands.

The plan is to change the default to "persistence" in the next major release and eventually deprecate the "PHom" class and its option.

[astamm]

Why not starting the deprecation right now?

[corybrunson]

My thinking was that users would get a soft notice (introduction of options), then a soft warning (change of default), then a hard warning (deprecation). But i concede that i err toward being too gradual.

[astamm]

We could have the documentation here link to the documentation of as_persistence() and as_PHom().

[astamm]

Same comment here.

[corybrunson]

On this and the above comment, i lean toward non-duplication of hyperlinks, and i believe (or at least intended) that the persistence class is linked in the Details. But i would not object to this change.

[corybrunson]

On reflection, i'm with you.

[astamm]

Better to call phutil::as_persistence() than to actually import the function from {phutil}.

[corybrunson]

Good call. Feel free to make that change!

[corybrunson]

Never mind, i'm on it.

[corybrunson]

@astamm could you review again?

In particular, wrapping the soft-deprecation call in a helper function undermined its environment-sensitive design, so i dropped it into every place "PHom" is invoked. Please confirm that it works as expected. : )