Question: Installation problems. Numpy?

[allmanbrent]

Installation Problems? I had several issues while installing it. The first was that because I have spaces in some of my parent directories, the installation code could not point to the correct directories. I fixed this by changing the CURRENTPATH to '.'

I then was able to finish the installation, but ran into an issue with running collabfold_batch where packages seem incompatible.

Computational environment

• OS: $ uname -m x86_64

To Reproduce Steps to reproduce the behavior:

1. My directory setup looks like: Parent_dir ->colabfold_batch .....-update_intelmac.sh .....->colabfold_batch ..........->bin ..........->colabfold-conda ..........->conda
2. I navigate to the directory Parent_dir/colabfold_batch/colabfold_batch
3. I then execute the following line and am met with this error message

colabfold_batch --help
Traceback (most recent call last):
 File "/Users/beallma/miniconda3/bin/colabfold_batch", line 5, in <module>
     from colabfold.batch import main
  File "/Users/beallma/miniconda3/lib/python3.8/site-packages/colabfold/batch.py", line 33, in <module>
    from alphafold.common import protein, residue_constants
  File "/Users/beallma/miniconda3/lib/python3.8/site-packages/alphafold/common/protein.py", line 19, in <module>
     from alphafold.common import residue_constants
   File "/Users/beallma/miniconda3/lib/python3.8/site-packages/alphafold/common/residue_constants.py", line 774, in <module>
    restype_atom37_to_rigid_group = np.zeros([21, 37], dtype=np.int)
   File "/Users/beallma/miniconda3/lib/python3.8/site-packages/numpy/__init__.py", line 284, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'int

Expected behavior When I run collabfold_batch I expect to be directed to the help menu so I can see the parameterlist. Thank you for any help you can provide! I am looking forward to running this program locally because of the constraints on Google Colab. This seems like it will be a great resource.

[Dongchengzhi]

I have the same problem. In my opinion, my GNU compiler version (4.8.5) leads to this.

[gieses]

You can monkey patch the file in the error by replacing np.int with np.int32. Numpy API has changed and does not allow np.int anymore.

restype_atom37_to_rigid_group = np.zeros([21, 37], dtype=np.int)
-->
restype_atom37_to_rigid_group = np.zeros([21, 37], dtype=np.int32)

Also see https://github.com/sokrypton/ColabDesign/issues/115

[dbolser]

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