sokrypton / sokrypton/ColabFold

updating local installation from v1.4 to v1.5

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Jupyter Notebook
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Description

Expected Behavior

COMPLETE: 100%|██████████| 150/150 [elapsed: 00:04 remaining: 00:00]

Current Behavior

ImportError Traceback (most recent call last)
in
11 from colabfold.utils import setup_logging
12 from colabfold.batch import get_queries, run, set_model_type
---> 13 from colabfold.plot import plot_msa_v1
14
15 import os

ImportError: cannot import name 'plot_msa_v1' from 'colabfold.plot' (/home/anaconda3/envs/Afld/lib/python3.7/site-packages/colabfold/plot.py)

Steps to Reproduce (for bugs)

Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally ypdate you local installation colabfold_batch to the newest version.
Please provide your input if you can share it.

ColabFold Output (for bugs)

Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.

Context

Providing context helps us come up with a solution and improve our documentation for the future.
Is there any way to update local alphafold installation directly or we need to make a totally new environment?

Your Environment

Include as many relevant details about the environment you experienced the bug in.

  • Git commit used
  • If you run it on a local system. Please add the server specifications
  • Operating system and version:

Contributor guide

Open the contributing guide

First steps

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

Research direction

Start with the local colabfold_batch installation and the colabfold.plot import shown in the traceback. Reproduce the v1.4-to-v1.5 update locally and verify that plot_msa_v1 is available or that the documented update path completes without the ImportError.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
bioinformatics, devops
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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