search

martinez-zacharya / MOP-UP

A pipeline that constructs bipartite protein-sharing networks for bacteriophages to analyze host-range, taxonomy and horizontal gene transfer.
1 stars 0 forks source link

Default installation of Numpy breaks MOP-UP #3

Closed nelsonruth11 closed 1 year ago

nelsonruth11 commented 1 year ago

Hello,

I installed MOP-UP following the directions in the readme. I then ran it on a small file with the command

python3 mop-up.py test /path/mve/mve_test.faa @ /path/analysis/mopup/mop_out/

which immediately threw an error "AttributeError: module 'numpy' has no attribute 'bool'".

I downgraded Numpy to v1.23.5 (conda install numpy=1.23.5) and MOP-UP ran successfully. It appears as of Numpy 1.20 np.int and np.bool have been deprecated then entirely removed at version 1.24.0.

Anyways, thanks for the tool and love the profile pic. -Nelson

martinez-zacharya commented 1 year ago

Thank you for finding this bug and also figuring out the fix! I've changed the .yml file to set up the conda environment to specifically use numpy=1.23.5.