search

MannLabs / alphamap

An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
https://mannlabs.github.io/alphamap/
Apache License 2.0
76 stars 18 forks source link

Potential performance issue: .apply slow in pandas 1.4.0 #72

Open TendouArisu opened 9 months ago

TendouArisu commented 9 months ago

Issue Description:

Hello. I have discovered a performance degradation in the .apply function of pandas version below 1.5. And I notice the repository depends on pandas 1.4.0 requirements.txt. I am not sure whether this performance problem in pandas will affect this repository. I found some discussions on pandas GitHub related to this issue, including #44172 and #45404. I also found that alphamap/preprocessing.py and alphamap/importing.py used the influenced api. There may be more files using the influenced api and more parts using pandas 1.4.0.

Suggestion

I would recommend considering an upgrade to a different version of pandas >= 1.5 or exploring other solutions to optimize the performance of .apply. Any other workarounds or solutions would be greatly appreciated. Thank you!

ibludau commented 4 months ago

Hi - thanks a lot for your comment and sorry for the long silence. we just created a new release which uses loose dependencies. could you please check if your performance issue still persists and let us know. thanks a lot - I hope we can improve your alphamap experience!