Add optional check for imaginary modes in PhononCalc/QHACalc and return the frequencies

[Andrew-S-Rosen]

Summary

This is an updated attempt to check for imaginary modes. Supersedes #131.

The PR adds a new keyword argument imaginary_freq_tol to PhononCalc and QHACalc. If there are any imaginary frequencies with a magnitude greater than imaginary_freq_tol, an error will be raised. For PhononCalc and QHACalc, imaginary_freq_tol=None by default. The frequencies are also now returned when running PhononCalc and thereby closes #138.

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

[Andrew-S-Rosen]

@rul048: I am getting test failures in CI that look unrelated. I'm not quite sure what is going wrong with loading the TensorNet model. But these tests seem to pass locally for me. Please let me know if you suggest any changes. This PR is ready for review.

[Andrew-S-Rosen]

Moved into #159 to prevent merge conflicts.