There are a few outdated lines of code which need to be updated.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: Theparse_objmethod is deprecated; usemodel_validateinstead. 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.
There are a few outdated lines of code which need to be updated. The specific warnings in question -
BiopythonDeprecationWarning: This module has been DEPRECATED. Please use the CodonAdaptationIndex class in Bio.SeqUtils instead.BiopythonDeprecationWarning: This module has been DEPRECATED. Please use the CodonAdaptationIndex class in Bio.SeqUtils instead.PydanticDeprecatedSince20: Theparse_objmethod is deprecated; usemodel_validateinstead. Deprecated in Pydantic V2.0 to be removed in V3.0.