sokrypton / sokrypton/ColabFold

AlphaFold2_advanced.ipynb numpy error

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Description

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```

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First steps

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  3. Fork the repository and make your change on a branch.
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Research direction

Start with AlphaFold2_advanced.ipynb and rerun its first dependency-installation cell in Google Colab. Inspect the imports of colabfold and colabfold_alphafold around the reported NumPy compatibility error. Done means the first cell completes and the notebook imports without the numpy.int AttributeError.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, numpy, python
Domain
bioinformatics
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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