sokrypton / sokrypton/ColabFold
A new error message with Colabfold batch
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- Jupyter Notebook
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Description
Hi,
Sorry for the trouble. Could you kindly help resolve this new error message with Colabfold batch please? Thank you,
AttributeError Traceback (most recent call last)
in <cell line: 0>()
3 import sys
4
----> 5 from colabfold.batch import get_queries, run
6 from colabfold.download import default_data_dir
7 from colabfold.utils import setup_logging
5 frames
/usr/local/lib/python3.11/dist-packages/jax/_src/lib/init.py in
74 version_str = jaxlib.version.version
75 version = check_jaxlib_version(
---> 76 jax_version=jax.version.version,
77 jaxlib_version=jaxlib.version.version,
78 minimum_jaxlib_version=jax.version._minimum_jaxlib_version)
AttributeError: partially initialized module 'jax' has no attribute 'version' (most likely due to a circular import)
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 by reproducing the import in the reported Colab notebook, beginning with from colabfold.batch import get_queries, run and the JAX traceback shown. Inspect the import path and installed JAX-related packages; the work is done when the ColabFold batch import completes without the circular-initialization AttributeError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100