Biocsetup

- Rename github actions to `run-tests` & `publish-pypi`.

- Minor changes to improve user experience.
- Replace `myst_nb` and `myst_parser`.

- Uses PyScaffold with Markdown extension for base project structure
- Configures GitHub Actions for testing and PyPI publishing
- Sets up pre-commit hooks
- Configures documentation with:
- MyST-NB for Jupyter notebook support
- Furo theme
- Type hints documentation
- Adds Ruff configuration for consistent code formatting
- Creates README