Remove rotate_from_matrix

[viljarjf]

Description of the change

Removes ReciprocalLatticeVector.rotate_from_matrix, and "manually" rotate instead where it was used

Progress of the PR

• Docstrings for all functions
• Unit tests with pytest for all lines
• [] Clean code style by running black (some unrelated files were formatted when I ran black)

For reviewers

• The PR title is short, concise, and will make sense 1 year later.
• New functions are imported in corresponding __init__.py.
• New features, API changes, and deprecations are mentioned in the
  unreleased section in CHANGELOG.rst.
• Contributor(s) are listed correctly in credits in diffsims/release_info.py and
  in .zenodo.json.