fix existing output directory issue

[omgol411]

Addressing #38

• output_dir overrides args.output in run_prism. If the former is None (default value), args.output is used
• os.makedirs(output_dir, exist_ok=True) handles existing output directory correctly.

Summary by CodeRabbit

• Bug Fixes
  • Improved output directory handling to ensure all output files (bead spread results, annotations, and precision data) are consistently written to the specified location.

[coderabbitai]

📝 Walkthrough

Walkthrough

The run_prism function refactors its output directory resolution logic. Instead of conditional checks on args.output, the function now unconditionally resolves output_dir when not provided and creates the directory explicitly, replacing all downstream references from args.output to the consistent output_dir variable.

Changes

Cohort / File(s)	Summary
Output Directory Resolution src/main.py	Refactored output directory handling: removed conditional logic that depended on os.path.exists(args.output), consolidated into explicit output_dir assignment and unconditional directory creation. All file write operations now consistently use the computed output_dir instead of args.output.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Poem

A rabbit hops through cleaner paths,
Where output folders bloom anew—
No conditions, just direct creation,
Consistency in every write,
A tidy warren, pure and bright! 🐰✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title 'fix existing output directory issue' directly relates to the changeset, which refactors output directory handling in run_prism to fix how output_dir is resolved and used.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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