Draft: Add pre-commit hooks for Ruff and blacken-docs with global exclusions

[jeipollack]

Summary

This PR introduces pre-commit hooks to enforce code quality and documentation formatting across the WaveDiff repository.

Closes #194

The configuration includes:

• Ruff for linting and automatic fixes
• blacken-docs for formatting Markdown and reStructuredText files
• Trailing-whitespace, YAML, and TOML checks
• Global exclusions have been added to prevent formatting or linting of:
  • Jupyter notebooks (*.ipynb)
  • Historical directories under papers/

What’s Changed

• .pre-commit-config.yaml updated with hooks and global exclude
• Reformatted configuration and documentation files according to hooks
• Updated several files where minor formatting fixes were applied
• No code logic was modified; all changes are formatting or configuration.

How to Test / Verify

1. Install pre-commit if not already installed:

• pip install pre-commit

2. Install hooks:

• pre-commit install

3. Run hooks on all files:

• pre-commit run --all-files

4. Verify that:

• No files under papers/ or Jupyter notebooks are modified
• All .py, .md, .rst, .yaml, .toml files conform to the defined hooks

Scope

• Repository-wide pre-commit hooks and formatting enforcement
• Global exclusions prevent historical data and notebooks from being reformatted

Reviewer Notes

• Ensure .pre-commit-config.yaml matches the project conventions and desired hooks
• Confirm that global exclusions work as intended
• CI will automatically enforce these hooks for future commits

Next Steps

• After merge, all developers should run:
• pre-commit install
• Add/update instructions in CONTRIBUTING.md about pre-commit usage
• Consider adding hooks to CI for push validation