Part 3 PyO3 0.21 upgrade: Remove usage of deprecated numpy crate APIs

[itamarst]

Description

numpy has switched a number of APIs to use PyO3's new Bound<> API. We should use numpy's new replacement APIs instead of the deprecated ones.

Search for "#15215" to find places where deprecation is manually suppressed; there should be none left when this PR is merged.

[itamarst]

Ah, looks like Ritchie did most of these already, so there's just one instance of numpy APIs left.

[ritchie46]

Yes, I think it would also be worth it to use the bounded API wherever we can. This can increase perf by 25% according to their benchmarks. So we should see if we can remove all GilRef API usages (even if not deprecated yet).

[itamarst]

The other APIs are also deprecated, it's just the deprecation warnings are suppressed by the gil-refs feature in the pyo3 crate to make upgrades easier.

This issue is specifically about the numpy. Switching to Bound<> for pyo3 crate APIs is what I will start on next (i.e. next 5 minutes 😁).