Pyo3 `Bound<'py, T>` api

[Michael-J-Ward]

Which issue does this PR close?

Part of #727

Rationale for this change

pyo3 has deprecated their gil-refs api.

See the blog announcement and the migration guide.

What changes are included in this PR?

Migrates to pyo3's Bound api

Are there any user-facing changes?

There should not be.