Dependencies and packaging

[aaTman]

Note: I am using my main forked branch here but the headache of closing a PR and reopening with a new branch name isn't worth it to me. Treat it as if the name was chore/add-dependency-and-packaging-mananging.

Previously, atmos was only able to be used in a scripting fashion. This PR includes the following changes and updates:

• Rearranges the directory tree to align with typical python packages
• Adds a pyproject.toml with all required dependencies and build-system to allow for packaging atmos
• Adds a uv.lock lockfile for uv based dependency management
• Updates README.md to include installation instructions
• Adds .python-version with a minimum version of 3.11 to allow for numpy>=2.4.6 and numba>=0.65.1

I tested this both on a virtual environment self-contained in the cloned repo, and in another virtual environment independent of it with uv pip install -e . which was successful.