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New features, typing, and build changes (#59)

* Added new functions to math_utils

* Linting and changed output for vibrations_utils.get_coupling

* Mayor changes to trajectory

Changed format of save trajectory
added __add__ and __iadd__ function

* cleaned up vibrations_utils

* added new functions to math_utils

* added new functionality to trajectroy

* fixed minor bug in get_area

* fixed minor bug in get_eigenvalues_in_Hz

* linting

* Added test_get_number_of_electrons

* Added cube file, need refactoring

* added CubefileParameters

* linting

* added function get_kinetic_energies

* added empty init file to fix reloading problem

* added some utility function

* added test_get_change_of_charge_density

* Added new function to output

* added visualise optimisation script which is command line executable

* added possibility to return Cartesian eigenvectors

* added tests AimsOutput

* update to filecrawler

* added new unit to units

* updated test_output

* updated test again

* fixed tests

* Fixed breaking change in arguments of output

* Fix break Dylan introduced

* added test_get_geometry_steps_of_optimisation

* added test_math_utils

* update to visualise_aims_optimisation

* some linting

* fixed parameters

* fixed minor bug in geometry

* Some fixes

fixed bug in get_force_components, added warning to get_parameters (this function is not very good)

* updated tests

* updated output

* Debugging tests for new functionality

* Fixed whitespace in final test and removed warning

* update geometry

* fixed elemental_colourmaps.yaml

* Formatting and function to add spin moments

* Fixed copying bug in parsing final KS states

* renamed bin to scripts

* added docstrings to mathutils

* Formatting and type hint fixes

* Started reformatting cube file

* Finished fixing cube module

* Further linting fixes and started fixing tests

* Fixed all tests

* Started re-adding some functionality to cube

* Started lint fixes for geometry

* F... (continued)

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Source Files on job 15263787048.1