Fix Orientations IO

[SCiarella]

This PR improves the Orientations class. In particular, this PR implements a Strategy design pattern to allow users to select which transformations to use and their order.

Previous methods of Orientations have been reformatted into the abstract classes Normalize, Conventional, and Symmetrize that perform their respective transformation. The user will then access Orientation.transformed_trajectory to get the result of any series of transformations, instead of using different _get* methods.

The specific outcomes of the PR are the following:

• closes #287 by granting control about which transformation to use and their order. This is done via set_transformation and execute_transformation
• closes #288 by allowing different primitive cells using the setter method Orientations.prim_to_conv_matrix
• closes #289 by allowing the user to exclude or include the Normalize transformation as needed.

The corresponding notebook has been updated.

[SCiarella]

Thanks @stefsmeets for the suggestions!

I'm wondering if we can simplify it a bit, from:

transforms = ['Normalize', 'Conventional', 'Symmetrize']
vasp_orientations.set_transformation(transforms)
transformed_traj = vasp_orientations.execute_transformations()

to

transforms = ['Normalize', 'Conventional', 'Symmetrize']
transformed_traj = vasp_orientations.transform(transforms)

I have used this approach, it makes total sense!

[SCiarella]

Moreover, this PR partially covers #286 because now rectilinear_plot uses Orientations.transformed_trajectory which can be any series of transformations. @tfamprikis can you check if this solves the problem described in #286?