kage installation error

[cgroza]

I install kage via pip3 which works fine:

pip3 install kage-genotyper

However, when I try to run it I get:

cgroza@ubuntu:~$ kage
Traceback (most recent call last):
  File "/home/cgroza/.local/bin/kage", line 5, in <module>
    from kage.command_line_interface import main
  File "/home/cgroza/.local/lib/python3.10/site-packages/kage/command_line_interface.py", line 29, in <module>
    from kmer_mapper.command_line_interface import map_bnp
  File "/home/cgroza/.local/lib/python3.10/site-packages/kmer_mapper/command_line_interface.py", line 12, in <module>
    warnings.filterwarnings("ignore", category=np.VisibleDeprecationWarning) 
  File "/home/cgroza/.local/lib/python3.10/site-packages/numpy/__init__.py", line 410, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'VisibleDeprecationWarning'

[ivargr]

Hi!

Thanks for asking. I think this might be related to numpy recently having released version 2.0.0, and we have unfortunately not specified that KAGE requires version 1. Could you try force installing Numpy version 1 and see if that solves the issue? I.e. run pip3 install numpy==1.24 and then trying to run kage again.

If that solves the issue, I'll release a fix when I'm back from vacation next week.

[baozg]

It resolved in my part!