sokrypton / ColabFold

Making Protein folding accessible to all!
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AlphaFold2_advanced.ipynb numpy error #630

Open justinecwilliams opened 2 months ago

justinecwilliams commented 2 months ago

When running the first cell/installing dependencies of the AlphaFold2_advanced.ipynb notebook within google colab, I am getting a numpy error (below). Any ideas on how to resolve this? Thank you!


[<ipython-input-5-d249335626b2>](https://localhost:8080/#) in <cell line: 102>()
    100 
    101 import colabfold as cf
--> 102 import colabfold_alphafold as cf_af
    103 
    104 import json

3 frames
[/usr/local/lib/python3.10/dist-packages/numpy/__init__.py](https://localhost:8080/#) in __getattr__(attr)
    317 
    318         if attr in __former_attrs__:
--> 319             raise AttributeError(__former_attrs__[attr])
    320 
    321         if attr == 'testing':

AttributeError: module 'numpy' has no attribute 'int'.
`np.int` was a deprecated alias for the builtin `int`. To avoid this error in existing code, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations```
Ash100 commented 2 months ago

Same Issue

milot-mirdita commented 2 months ago

Is this the "new" advanced notebook: https://colab.research.google.com/github/sokrypton/ColabDesign/blob/gamma/af/examples/predict.ipynb

Or the old/retired advanced notebook: https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb

If it's the later please move to the standard notebook or Sergey's new advanced.