Move occ_tol to init in OrderDisorderedStructureTransformation

[Tinaatucsd]

Summary

Major changes:

• fix 1: Fixed incompatibility between OrderDisorderedStructureTransformation and StandardTransmuter:
• Previously, occ_tol was a method parameter in apply_transformation, making it unconfigurable when used with StandardTransmuter (which only passes transformation and optionally extend_collection parameters when calling append_transformation)
• Moved occ_tol to class initialization to allow proper configuration when used in transformation chains

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

[jmmshn]

Thanks @Tinaatucsd, it looks like occ_tol should have been placed as an attribute of the class since only the first two parameters are called by the alchemy part of the code.

https://github.com/materialsproject/pymatgen/blob/296a0ec856b22da847b2ccd0e55e146e071cb8fd/src/pymatgen/alchemy/materials.py#L123C1-L126C1

This was an oversight on my part. Thanks for finding this!