search

labsyspharm / scimap

Spatial Single-Cell Analysis Toolkit
https://scimap.xyz/
MIT License
71 stars 24 forks source link

np.warnings.filterwarnings('ignore') no longer supported by numpy #92

Closed milesbailey121 closed 6 months ago

milesbailey121 commented 6 months ago

Hi, I've been having an issue when running sm.pl.gate_finder() it throws AttributeError: module 'numpy' has no attribute 'warnings' This carries from np.warnings.filterwarnings('ignore') on line 148 in gate_finder().

I think I found a fix, it seem to have replaced this with the np.seterr('ignore') function in the newer versions of numpy

NumPy version = 1.26.4

Code Used: sm.pl.gate_finder (image_path, adata, marker_of_interest, from_gate = 5, to_gate = 9, increment = 0.1, point_size=10)

ajitjohnson commented 6 months ago

@milesbailey121, thank you for identifying this bug. I have updated the script according to your suggestion. Please install the latest version of the package (1.3.5) using pip install scimap --upgrade. It would be great if you could test the function and let me know if the issue is resolved. Thank you.

milesbailey121 commented 6 months ago

@ajitjohnson I've just checked with the latest version and it works perfectly. Thank you very much for resolving the issue!

ajitjohnson commented 6 months ago

thank you :)