Modernized package by using pyproject.toml instead of setup.py

[stefdoerr]

This modernizes the python packaging of propka. It's also useful for newer tools like uv which don't work without the pyproject.toml file. With this change you can just do uv run pytest in the folder and it creates the env and runs the tests.

In theory I can also get rid of versioneer if you want by jsut adding setuptools-scm to the build-system (which would allow us to remove the remaining setup.py as well as the versioneer.py and version.py files). I didn't do it here to not intervene too much but if you want I am more than happy to add the change.

[Copilot]

Pull request overview

This PR modernizes PROPKA’s Python packaging by migrating project metadata and tool configuration into pyproject.toml, reducing reliance on legacy setup.py/setup.cfg configuration and improving compatibility with modern tooling (e.g., uv, PEP 517 builds).

Changes:

• Added pyproject.toml with PEP 621 project metadata, setuptools configuration, and tool configs (versioneer/coverage/yapf/mypy).
• Simplified setup.py to only provide Versioneer-driven version + cmdclass.
• Removed setup.cfg, added a dedicated long description markdown file, and updated MANIFEST.in pruning.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
setup.py	Reduced to minimal Versioneer integration for dynamic versioning.
setup.cfg	Removed in favor of pyproject.toml tool configuration.
pyproject.toml	New single source of truth for packaging metadata + tool configs.
MANIFEST.in	Prunes docs/tests; needs alignment with removed/added packaging files.
LONG_DESCRIPTION.md	New long description file referenced by pyproject.toml.

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[stefdoerr]

I fixed the suggestions of copilot. Let me know if you want me to also remove versioneer in favor of setuptools-scm https://setuptools-scm.readthedocs.io/en/latest/ which works without adding any files in the repository.