mcveanlab / treeseq-inference

Work for the tree sequence inference paper.

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Minor - set "quiet" output for ARGweaver

hyanwong opened this issue · comments

if "quiet=False" on line 508 of plots.py, a whole ream of ARGweaver output is given. I think we should set this if e.g. args.verbosity>=2 (or logging level=debug), but not sure how to access this status from within the run_argweaver() routine. @jeromekelleher could you have a look and decide how to do it? Thanks

I think it's fine as it is --- I don't think we're ever going to be particularly interested in this output unless for debugging purposes, when we can just manually edit the source.

The alternative would be to save a ''verbosity'' instance variable in the Dataset class, and to make the various run_X methods instance methods rather than static. That way we could check the verbosity (if > 4 say) and set quiet to False.

I don't have a strong opinion either way. Initial impressions indicate that we're not going to be doing much testing with ARGWeaver as it's so slow...