add first draft of non-modularized code

[JessicaS11]

Adds the first draft of the code to the repo. This code is still under heavy development and will be undergoing a complete restructuring in the coming weeks to make it more modular (e.g. class-based architecture) and include an optional JupyterNotebook to run it step-by-step rather than as a single pipeline (current functionality to run it as a Python script from the command line will remain).

[JessicaS11]

The pre-commit and linter checks are (in my opinion) not worth fixing for this PR given that the code will change substantially, so we can implement these "best practice" habits as we go. I suspect we'll also run into the same sort of thing eventually with the typecheck (because there is no typing - where we specify that a given function outputs, for instance, a list of strings). But @hhollandmoritz, if it's a quick fix to get it to at least pip install, that would be super! If it's more than a quick fix or something you're not wanting to dive into, then we should just go ahead and get this merged as a starting point so you can start making the more critical changes.

[hhollandmoritz]

@JessicaS11 Well I don't know if it's "kosher" or not, but I was able to get it to install by changing the fallback version in the pyproject.toml file from "unkown" to "0.0.0" (since apparently "unknown" is not allowed). And by setting the dynamic dependencies to use the requirements.txt file rather than what was previously there ("numpy"). Again, not sure if this is how we plan to specify the dependencies longer-term, but python -m pip install . runs now.

And when I ran main.py it was able to load all the modules and crash out on the config file loading (because I didn't bother to change the file paths).

(Whether it works as expected, beyond that, I have no idea), but that seems like a good starting place to me.

I think we can merge.

[hhollandmoritz]

As @JessicaS11 stated the linter and ghactions are not worth fixing at this time. Pip install works, I am self-approving this merge.