Deprecation
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Description
There are a few outdated lines of code which need to be updated. The specific warnings in question -
- CodonUsageIndices.py throws the following error: `BiopythonDeprecationWarning: This module has been DEPRECATED. Please use the CodonAdaptationIndex class in Bio.SeqUtils instead.`
- CodonUsage.py also throws the same error: `BiopythonDeprecationWarning: This module has been DEPRECATED. Please use the CodonAdaptationIndex class in Bio.SeqUtils instead.`
- main.py throws the following error: `PydanticDeprecatedSince20: The `parse_obj` method is deprecated; use `model_validate` instead. Deprecated in Pydantic V2.0 to be removed in V3.0.`
- optimize.py doesn't seem to like the " \ | " string when printing out the logo.
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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
Read CodonUsageIndices.py, CodonUsage.py, main.py, and optimize.py, then reproduce the listed deprecation warnings and logo-printing problem. Trace each warning to its named file and verify that the deprecated calls are addressed and optimize.py prints the logo correctly without the reported string issue.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Refactor
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100