Convert to src layout

[mdpiper]

I asked Claude to convert the Python source in this repository from a single-file layout to a src layout. This is what it came up with:

• Move diffusion_model.py into src/diffusion_model/__init__.py as an installable package
• Extract the __main__ block into src/diffusion_model/__main__.py so python -m diffusion_model
  continues to work
• Update pyproject.toml to use the setuptools packages.find discoverer pointed at src/, and
  add pythonpath = ["src"] for pytest
• Add .venv/ to .gitignore

I think it's curious that Claude put all the functions into the module definition file __init__.py, but I guess it makes sense instead of having a named module like model.py and a stub definition file that imports functions from the named module file.

[mcflugen]

Move diffusion_model.py into src/diffusion_model/init.py as an installable package

I’d prefer not to move the implementation directly into src/diffusion_model/__init__.py.

I generally try to keep __init__.py as small as possible: version metadata, __all__, and maybe re-exporting public functions/classes from private modules. Putting much more than that there makes imports less predictable and blurs the distinction between package API and package internals. __init__.py can also quickly become a junk drawer.

Extract the main block into src/diffusion_model/main.py so python -m diffusion_model
continues to work

For python -m diffusion_model, I think __main__.py should also stay minimal, e.g.

from diffusion_model._cli import main

if __name__ == "__main__":
    raise SystemExit(main())

The CLI code itself should be wrapped in a main() function, even if it stays in the same module for now.

Update pyproject.toml to use the setuptools packages.find discoverer pointed at src/, and
add pythonpath = ["src"] for pytest

I’m also hesitant about adding this to pyproject.toml:

[tool.pytest.ini_options]
pythonpath = ["src"]

I’d rather have tests run against the installed package so packaging errors are caught during testing and adding src directly to PYTHONPATH can mask those issues.

Add .venv/ to .gitignore

Adding .venv/ to .gitignore is harmless, though maybe a little out of scope for this PR.

[mdpiper]

@mcflugen Thank you for reviewing this PR. Everything worked, but it had a bad smell. Would you like to make changes, or would prefer I do so?

[mcflugen]

Would you like to make changes, or would prefer I do so?

You go for it!