Warning for draw_svg plot uses logging module instead of warnings #2870
Description
I came across a minor issue with the plotting code: the draw_svg warning for mutations above unplotted nodes uses the logging module instead of the warnings module, that we'd usually use for user warnings. I discovered this because I couldn't find a way to suppress it. The warning is currently this:
if len(unplotted) > 0:
logging.warning(
f"Mutations {unplotted} are above nodes which are not present in the "
"displayed tree, so are not plotted on the topology."
)If we were to use warnings instead, I'm guessing we'd do something like this? I'm not sure what stack level is appropriate here.
if len(unplotted) > 0:
warnings.warn(
f"Mutations {unplotted} are above nodes which are not present in the "
"displayed tree, so are not plotted on the topology.",
UserWarning,
stacklevel=2
)