remove the old cp2kcube class and add type hints

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 45.01%. Comparing base (5e512e3) to head (4c42f00). Report is 21 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #66 +/- ## ========================================== + Coverage 43.60% 45.01% +1.40% ========================================== Files 32 32 Lines 2002 1906 -96 ========================================== - Hits 873 858 -15 + Misses 1129 1048 -81 ```

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