Issues using forked alphafold for modifed colabfold

[michaelhla]

Expected Behavior

trying to test run a colabfold on a modified alphafold repo, should run batch.py on a test fasta file

Current Behavior

alphafold.common is not recognized, modulenotimported error

Steps to Reproduce (for bugs)

follow the steps on contribute.md for local changes

Context

Have tried updating the python path, importing manually with importlib

Your Environment

running on linux machine, a100, not docker compatible

[michaelhla]

have also tried working directly in a colab notebook but Bio.SCOP not found when running import colabfold.batch

[milot-mirdita]

Are you using our alphafold fork: https://github.com/steineggerlab/alphafold

If not please replay your changes onto our fork. ColabFold is not meant to be run with DeepMind's AF2.

[michaelhla]

yeah just following instructions here, seems to be your af fork: https://github.com/sokrypton/ColabFold/blob/main/Contributing.md