The latest releases of PyO3 and rust numpy were just released. The
changelogs for both can be found at:

https://pyo3.rs/v0.18.0/changelog

and

https://github.com/PyO3/rust-numpy/blob/main/CHANGELOG.md

Since the two releases are tightly coupled this commit opts to update
them together instead of the normal dependabot workflow. Similarly some
of our usage (mainly around signatures and argument ordering) for
building a python interface using PyO3 has been deprecated. That usage
is also updated in this PR to avoid compilation warnings, which will be
treated as errors by clippy in CI.