sokrypton / sokrypton/ColabFold
Logic error in error handling for MMSeqs2 server connection
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Description
Hasn't actually affected me, but noticed while reading the code: in the submit() and status() methods defined in run_mmseqs2(), I believe the error_count=0 lines https://github.com/sokrypton/ColabFold/blob/0b6d4562030b057d8f6f5287497a2c007bdac548/colabfold/colabfold.py#L88 and https://github.com/sokrypton/ColabFold/blob/0b6d4562030b057d8f6f5287497a2c007bdac548/colabfold/colabfold.py#L115 should be outside their respective while loops.
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First steps
- Read the whole issue, then the project's contributing guide.
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- Fork the repository and make your change on a branch.
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Research direction
Open colabfold/colabfold.py and inspect run_mmseqs2(), especially the submit() and status() methods around lines 88 and 115. Trace how error_count behaves across each while loop and confirm that the completed change preserves the counter between retries in both methods.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 1/5
- Estimated time
- Under an hour
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 35/100