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Teichlab / bbknn

Batch balanced KNN
MIT License
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error during ridge_regression #53

Closed JuliaChristiaanse closed 1 year ago

JuliaChristiaanse commented 1 year ago

Hi there,

First of all, thank you for this great package! It has been very helpful for my graduation project so far. I am currently following the bbknn tutorial notebook, but I get an error at the ridge_regression part of the tutorial. "AttributeError: module 'numpy' has no attribute 'int'."

"np.int was a deprecated alias for the builtin int. To avoid this error in existing code, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information. The aliases was originally deprecated in NumPy 1.20;""

I get this error when following your tutorial notebook with my own dataset. I am quite new to scRNAseq analysis and I am simply wondering if it's my package management that's wrong or that it might be something else?

Anyway, grateful in advance for your reply!

Greetings,

Julia

ktpolanski commented 1 year ago

It would appear that np.int() got removed in numpy 1.20.0. I've found the offending line and switched it to int() as pre the recommendation.

You can either downgrade numpy to a pre-1.20.0 version, or uninstall BBKNN and install it straight from GitHub with the change applied. There are a couple other tweaks in place which will at some point be released as 1.6.0, but it should work like your existing version.

JuliaChristiaanse commented 1 year ago

I tried with a numpy pre-1.20.0 version, but that did not solve the problem. But updating the bbknn package worked like a charm :D Thank you !