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- avoided internal warnings in case a file is not closed - read_fasta can now process a filename in addition to streams/handles
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@AlessioMilanese While this PR has various minor fixes, there is a major issue to address before it can be merged.
In
create_db, we sometimes have a problem with the logistic solver not converging duringclf.fit()(observed increate_db:estimate_function).I added a command line option
-N <int>to allow adjusting themax_iterparameter ofLogisticRegression. Alternatively, (or in addition), we could try catching the warning (in this PR warnings are treated as errors) and try to adjustmax_iterautomatically.