Improve imaginary frequency handling in QHACalc and PhononCalc

[Andrew-S-Rosen]

Summary

This PR is a continuation of #159. I do a few related things in this PR:

1. I changed how imaginary_freq_tol is interpreted. Since we haven't minted a new release yet, I was thinking more about the most user friendly interpretation of this keyword argument and decided that it should be a negative float rather than positive float. In this case, any frequency less than imaginary_freq_tol is flagged. The default is imaginary_freq_tol=0.0.
2. I added a keyword argument on_imaginary_modes: Literal["error", "warn", "ignore"] = "ignore" that gives the user flexibility on what happens when there are imaginary modes.
3. I fixed a small bug in an error message: the number of frequencies was reported incorrectly since I used n_freqs = len(frequencies) instead of n_freqs = frequencies.size

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