Feature finder Implementation

[straussmaximilian]

FF Implementation - Draft

This is to integrate the AlphaPept Feature finding code.

Layout

alpharaw/
│
├── feature/                   # Source files
│   ├── centroids.py            # Connect centroids
│   └── finding.py          # API to call the FF
│   └── hills.py          # Hill Refinement
│   └── isotope_pattern.py          # Pre Isotope Patterns and Isotope Patterns from Hills
│   └── performance.py          # Helper function for performance, could be moved to AlphaBase at somre point

ToDO:

• Port initial code
• Get rid of AlphaPept settings and have them as arguments
• Revise the performance function and remove CUDA functionality > used from AlphaTims
• Use constants/ averagine model from alphabase > Used from AlphaPept for now
• Make API more streamlined
• Have integration test

Current Status: Working but somehow slower (?)

[straussmaximilian]

This is now a fully working integration

• This uses @threadpool from AlphaTims as a performance function, so it is dependent on alphatims
• I removed the networkx dependency by having ChatGPT rewrite the required function. This worked surprisingly well
• The notebook has some unit tests and a full integration test with the dataframe api
• I had to copy some chemistry functions - this introduces some redundancy. Feel free to replace with existing code if you have..

Runtime for the full file on my MacBook: ~20 minutes

[jalew188]

@straussmaximilian Thank you. It looks good. On windows, the speed seems quite slow. We can fix this later.