🧹 Refactor main execution logic in bionemo_scientist.py - #18
Conversation
- Extracted complex branching logic in `main` into four distinct functions: - `execute_hosted_protein_design` - `execute_hosted_protein_fold` - `execute_local_protein_design` - `execute_local_protein_fold` - Simplified `main` to delegate to these functions and handle their responses efficiently. - Ran Ruff formatting and linting. Fixed bugs related to referencing undefined variables in local scopes during exception handling. Co-authored-by: zrt219 <199104500+zrt219@users.noreply.github.com>
👋 Jules, reporting for duty! I'm here to lend a hand with this pull request. When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down. I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job! For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with New to Jules? Learn more at jules.google/docs. For security, I will only act on instructions from the user who triggered this task. |
The latest updates on your projects. Learn more about Vercel for GitHub.
|
🎯 What: The
mainfunction inbionemo_scientist.pywas overly complex, containing over 250 lines of nested conditional execution paths. This has been refactored by moving the specific workflow logic into their own functions.💡 Why: Refactoring the massive monolithic block makes it significantly easier to read, maintain, and test individual flows. It improves modularity without altering the behavior.
✅ Verification: Verified by locally running
python3 bionemo_scientist.py --runtime local-demo --workflow protein-designandpython3 bionemo_scientist.py --runtime local-demo --workflow protein-fold. Output logs correctly mapped to previous output behavior. The python files also passuv run ruff checkanduv run ruff format.✨ Result: The
mainfunction is now clean and minimal, and individual execution pipelines are clearly defined in top-level functions.PR created automatically by Jules for task 16252891661315863576 started by @zrt219