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```
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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