Skip to content

⚡ Bolt: [performance improvement] optimize DataFrame iteration in verify utility#80

Open
alinelena wants to merge 1 commit into
mainfrom
bolt/optimize-dataframe-iteration-13598759025420501430
Open

⚡ Bolt: [performance improvement] optimize DataFrame iteration in verify utility#80
alinelena wants to merge 1 commit into
mainfrom
bolt/optimize-dataframe-iteration-13598759025420501430

Conversation

@alinelena

Copy link
Copy Markdown
Contributor

💡 What: Replaced slow df.iterrows() loop with C-optimized df.to_dict("records") when building cross-reference dictionaries for Parquet validation.
🎯 Why: df.iterrows() is an anti-pattern that creates a new Pandas Series object for every row, making iteration across large omol-25 datasets significantly slow.
📊 Impact: Converting to native Python dicts upfront and iterating them reduces overall processing overhead, improving speed and drastically decreasing memory allocation per row during iteration.
🔬 Measurement: Run python -m pytest tests/test_verify_processed_omol25.py and verify all tests pass smoothly. Optionally execute the utility on a large Parquet/XYZ pair and compare execution times.


PR created automatically by Jules for task 13598759025420501430 started by @alinelena

Replaced slow `df.iterrows()` with `df.to_dict("records")` in `verify_processed_omol25.py` to significantly speed up property checking and cross-referencing against Parquet files. Updated the downstream helper `get_dump_entry` to directly use native python dictionaries.

Co-authored-by: alinelena <3306823+alinelena@users.noreply.github.com>
@google-labs-jules

Copy link
Copy Markdown
Contributor

👋 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 @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!

New to Jules? Learn more at jules.google/docs.


For security, I will only act on instructions from the user who triggered this task.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant