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AI Fix Prompts for Seqmat

Copy any prompt below into Claude, ChatGPT, or your AI coding assistant to automatically fix the issue. Each prompt includes full context, code location, and step-by-step fix instructions.

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MEDIUM ⚒ significant #1

Simplify 1 high-complexity files

complexity refactoring quality
Expected outcome: All listed files reduced to medium or low complexity
Files to modify: seqmat/cli.py
Prompt (copy this into your AI assistant) 
These files in 'nicolasalynn__seqmat' have high cyclomatic complexity:

- **seqmat/cli.py**: complexity=57, max nesting=7, longest function=75 lines

For each file:
1. Break large functions into smaller, focused functions
2. Reduce nesting depth (extract early returns, use guard clauses)
3. Simplify conditional logic
4. Extract complex expressions into named variables