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

Infrastructure and utilities bioBakery workflows
1

Hi,

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!!

2

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.

Thanks!
Lauren