Clean up test suite output

[hakonanes]

Description of the change

This PR cleans up the test suite output by:

• Fixing causes for some Matplotlib warnings
• Silencing a numpy.log() warning
• Replace use of pytest.mark.xfail() with a pytest.raises(<error_type>): context. The replacement fullfills the same purpose as the former without cluttering the pytest output

I've also bumped the minimum version of diffpy.structure to 3.0.2 in setup.py. This ensures that Phase.from_cif() works on Windows with Python 3.10. I've added a changelog entry for this change.

Progress of the PR

• [n/a] Docstrings for all functions
• [x] Unit tests with pytest for all lines
• [x] Clean code style by running black via pre-commit

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 orix/__init__.py and in .zenodo.json.

[hakonanes]

Greath, thank you @harripj!

[hakonanes]

And also thank you for fixing the CIF reading on latest Windows in diffpy.structure.