Replace copy_tree from distutils with copytree from shutil

[ikondov]

Closes #532

Summary

Major changes:

• Fix: replace copy_tree from deprecated distutils package with copytree from the shutil package

Todos

If this is work in progress, what else needs to be done?

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install