[WIP] Refactor core module with logging and I/O improvements

[Copilot]

• Address deprecation warnings - replace np.fromstring with modern alternatives
• Fix inconsistent logging format (use built-in parameter substitution)
• Fix docstring formatting issues (return types, typos, grammar)
• Improve error messages (replace assertions with descriptive ValueErrors, use f-strings consistently)
• Add try-finally block for timer in wannierization loop
• Fix validation logic using hasattr instead of getattr
• Optimize memory usage in file parsing (avoid string concatenation)
• Change generic Exception to ValueError for consistency

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