james-vincent

Which version of python does this assume? Python version is not detailed in the readme. James Vincent, PhD Bioinformatics Software Curator Dept. of BCMP, Harvard Medical School — BioGrids.org --...

What produces the original issue: unrecognized arguments: --use-gpu-relax Is this really not an available argument for some versions/commits? Or, is this argument not available when a GPU is not detected?...

Yes, please do open a PR. We would love to have this implemented. I'm not sure how anyone deploys to a shared system otherwise.

Thanks for the quick response. I'm the go between for a user. This user reports: I should note I get the same error with tomograms which have not been denoised....

It's scipy.spatial, no scipy.special: pairwise_dist = scipy.spatial.distance.cdist(a, b, metric='euclidean')

I don't understand the comment. The issue I am reporting is that confidence.py does not import scipy.spatial. Should it?

It seems after installing AF2 I have two copies of scipy, one in regular site-packages and one that comes with jax: find ./ -name scipy -type d ./lib/python3.7/site-packages/jax/_src/scipy ./lib/python3.7/site-packages/jax/_src/third_party/scipy ./lib/python3.7/site-packages/jax/scipy...

Forgot to add, jax is correct version also: python.af2complex -c 'import jax;print(jax.__version__)' 0.3.25

The numpy version after instalaltion of AF2 2.3.1 did not match the version listed in af2complex requirements.txt. I reinstalled and set numpy==1.21.6. Now the example job runs correctly.

Same issue here still. Any update?