Speed up core logic using Rust

[jacobwhall]

This PR rewrites some of the core distance calculations in Rust, using crates such as kiddo (k-d trees) and rayon (parallelization) to faithfully re-implement this logic. The result is a drop-in replacement for the original, passing all tests and running significantly faster.

A few notes:

• I have used uv for dependency management and to run CI tests
• Maturin handles cross-platform compilation for package distribution
• Since I was already working in pyproject.toml, I went ahead and bumped the version to 0.4.0

I recommend releasing something like 0.4.0-alpha to ensure the package distributes correctly, and give end users the chance to test this package in their environments before making a full 0.4.0 release.

[jacobwhall]

I removed the progress_bar option, since it will need a reimplementation in Rust.