Enable ruff rule PD

[afuetterer]

What does this PR do?

Discussion at #2450

1. Mostly it is something like this:

documents.Document.values.tolist()

-->

documents.Document.to_numpy().tolist()

Refs:

• https://docs.astral.sh/ruff/rules/pandas-use-of-dot-values/
• https://pandas.pydata.org/pandas-docs/stable/whatsnew/v0.24.0.html#accessing-the-values-in-a-series-or-index

Summary:

$ ruff check --statistics
25      PD011   pandas-use-of-dot-values
 1      PD015   pandas-use-of-pd-merge

The tests were passing in my fork.

Before submitting

• This PR fixes a typo or improves the docs (if yes, ignore all other checks!).
• Did you read the contributor guideline?
• Was this discussed/approved via a Github issue? Please add a link to it if that's the case.
• Did you make sure to update the documentation with your changes (if applicable)?
• Did you write any new necessary tests?