Upgrade python version

Upgraded nomad-lab to Python 3.9 and bumped a few dependency version.

Changelog: Changed

• updated to python 3.9
• only bumped what was necessary in this first step
• add a mypy.ini to remove longer and longer arg-based config from pylint calls
• some minor code fixes due to new version of mypy and pylint

With 3.9, i mean that we now build and run with 3.9. The min required is only 3.8. I guess, we could go even higher, if this is successful.