refine w/o TreeTime Error

[emmahodcroft]

This was introduced inadvertently because of concurrent development in refine in #282 and #283 that meant the two fixes were never tested together :)

#282 allows trees to be re-rooted without time-inference, but checks that the rooting instructions aren't Treetime arguments ("best", "min_dev", etc) (line 210-211, refine.py).

However, if you are running refine without time-inference (as I was working on in #283 ) and without the --root argument (just wanting internal node names), there's a default value for --root of "best" - so this check fails.

I am not keen to just get rid of the default being "best" for --root because this would change the behaviour of runs without any warning (and probably be hard to catch), if users have runs where they don't specify --root and are expecting it to default to "best".

I wouldn't even be in favour of a warning, really, since telling users "you specified 'best' and we are going to ignore it" make 0 sense when they didn't actually specify a root at all...

Perhaps instead, if there's no --timetree argument and args.root=='best', this is ignored and the run proceeds, and we could say something like "Adding internal node names without rerooting" (or "Adding internal node names with rerooting" if it's been specified correctly) to make the situation clear but unsurprising to users.

Happy to implement this if that sounds good, but wanted to check with @rneher & @PierreBarrat that this works alongside their original intention.

[rneher]

I would probably raise an error if something other than the default is specified and warn otherwise (mentioning that it was likely by default).

[emmahodcroft]

Worth noting that if you use --keep-root this solves this. But not sure we should have to require this. Will make a PR.

[emmahodcroft]

Closed by #349