Use uv for everything

[ecomodeller]

• Use dev dependency groups instead of optional dependencies (targeted to end users) in pyproject.toml.
• Use uv in all CI workflows
• Use uv run in Makefile
• Use src layout

A src layout is particularly valuable when developing libraries. It ensures that the library is isolated from any python invocations in the project root and that distributed library code is well separated from the rest of the project source.
https://docs.astral.sh/uv/concepts/projects/init/#libraries