Numpy issues 2x - caught between a rock and a hard place?


I am on Ubuntu 20.04 and Python 3.8.10 and I ran into multiple issues with numpy for the wmgx workflow.

Initially, with numpy 1.24.4, I got an “AttributeError: module ‘numpy’ has no attribute ‘int’.” - this went away by downgrading to 1.20.3 and allowed me to run kneaddata without issues.

Now, however, a new error appeared in metaphlan “ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject” - it was suggested, that upgrading numpy will sort this, but this will again break the aforementioned issue.

Any ideas please? Many thanks!!

Hi, Thank you for including so many details in your post! We run Python 3.10.9 with numpy 1.25.1 and this works for the latest version of Kneaddata and MetaPhlAn.