Modernize packaging: migrate to pyproject.toml and support uv

[wshlavacek]

Current state

• Package is distributed via setup.py with setuptools
• Docker image exists (Dockerfile) but is dated (BioNetGen 2.3.1, anaconda3 base, bdist_wheel)
• No dependency upper bounds — upstream updates can break PyBNF
• Installation requires users to manage Python environments manually

Recommendations

1. Migrate setup.py to pyproject.toml — modern standard, better tooling support
2. Pin dependency upper bounds in pyproject.toml to prevent breakage
3. Support uv — users can then install with uvx pybnf or uv tool install pybnf with no Python knowledge required
4. Update the Dockerfile — freshen base image and BioNetGen version

This supersedes #212 (pre-compiled binary). The uv approach gives users the same "just run it" experience without fighting PyInstaller + dask incompatibilities.