sokrypton / sokrypton/ColabFold
Issues using forked alphafold for modifed colabfold
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Description
Expected Behavior
trying to test run a colabfold on a modified alphafold repo, should run batch.py on a test fasta file
Current Behavior
alphafold.common is not recognized, modulenotimported error
Steps to Reproduce (for bugs)
follow the steps on contribute.md for local changes
Context
Have tried updating the python path, importing manually with importlib
Your Environment
running on linux machine, a100, not docker compatible
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 contribute.md and the batch.py entry point, using the test FASTA file and the reported alphafold.common import error as the reproduction case. Check how the modified AlphaFold repository is made available on the Linux environment, including the attempted Python path and importlib approaches. Done means batch.py runs on the test FASTA without the ModuleNotFoundError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100