[WIP] Draft of generalized RustBCA python wrapper(s)

[drobnyjt]

Thank you for your contribution to rustBCA!

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• Opened an issue
• Referenced the relevant issue number(s) below
• Provided a description of the changes below
• Ensured all tests pass and added any necessary tests for new code

Fixes #277

Description

This PR adds a new way to run RustBCA - a Python wrapper that takes an input-file-shaped dictionary and runs RustBCA without generating or parsing an input file.

This comes in two flavors: rustbca_py(input_file, geometry_mode) which produces identical output files to the standalone code and rustbca_local_py(input_file, geometry_mode) which produces a dict from this Rust struct:

pub struct FinishedParticlesContainer {
    sputtered: Vec<bool>,
    implanted: Vec<bool>,
    atomic_number: Vec<usize>,
    mass: Vec<f64>,
    energy: Vec<f64>,
    x: Vec<f64>,
    y: Vec<f64>,
    z: Vec<f64>,
    ux: Vec<f64>,
    uy: Vec<f64>,
    uz: Vec<f64>,
}

All of this is made possible with the newest version of PyO3 and the pythonize crate, which allows one to serialize/deserialize python dicts to structs that implement serde (de)serialization.

Tests

I've added tests that compare the output of the two new functions to the standalone code to make_input_file_and_run.py.

Todo

• both functions should return a PyErr as appropriate (this is more idiomatic than the int flag suggested in issue [feature] General python binding for rustbca #277)
• implement other geometry types (currently only has 1D)
• clean up module imports etc.