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Teichlab / bbknn

Batch balanced KNN
MIT License
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Throwing exceptions with logg.info() arguments. #14

Closed milescsmith closed 5 years ago

milescsmith commented 5 years ago

BBKNN fails to run with the latest version of Scanpy due to its use of passing arguments that are no longer valid. I just did the simple thing of removing everything other than the message, which has restored its functionality.

ktpolanski commented 5 years ago

Thanks for the hot fix, I went into the Scanpy source code and found how they do logging now. This allows the keeping of timing in the logging, which I'm quite fond of. I'll patch up BBKNN soon in this fashion.

https://github.com/theislab/scanpy/blob/709bafb8ed600daf5f9ee995a0dc845ac1e7e605/scanpy/neighbors/__init__.py#L110-L118

ktpolanski commented 5 years ago

I pulled the most recent version of scanpy from pip, and it appears to still do the old logging. As such, if I update this now, any pip-installed scanpy (i.e. the overwhelming majority of them, if I were to guess) will stop working with BBKNN. I'll wait for the change to actually go live in pip and act on it then.