Make simplify use mostly keyword-only args

[hyanwong]

Fixes #846

[benjeffery]

@hyanwong I just force-pushed to add tests for this and the other kwarg only methods. This is mainly so we don't add positional arguments in error in future.

[hyanwong]

Do we also want to make ts.trees() kwonly (and presumably most of the args to Tree.__init__)?

[hyanwong]

I've added the kw-only stuff to .trees() as well, @benjeffery (in a separate commit), as Jerome gave that the thumbs up

[jeromekelleher]

Looks good. I'm slightly nervous about making tracked_samples kw-only, though, as I have a feeling there's a fair bit of coding using that. Are we sure all the documentation examples are ok with this?

I guess tsinfer is a good yardstick - if we don't break any code in there in things like the validation suite, then maybe it's OK. Still, breaking peoples code gratuitously for the sake of neatness isn't good.

[hyanwong]

Looks good. I'm slightly nervous about making tracked_samples kw-only, though, as I have a feeling there's a fair bit of coding using that. Are we sure all the documentation examples are ok with this?

I could shift the asterisk so that tracked_samples can be positional? Whatever you prefer.

[jeromekelleher]

I could shift the asterisk so that tracked_samples can be positional? Whatever you prefer.

This is probably safer, I think. No point in breaking code for the sake of it.

[hyanwong]

I could shift the asterisk so that tracked_samples can be positional? Whatever you prefer.

This is probably safer, I think. No point in breaking code for the sake of it.

Done, with new changelog. Ready to merge, I think.

[jeromekelleher]

Great, thanks. It would be nice to test that trees([0]) is the same thing as trees(tracked_samples=[0]), just in case that asterisk gets moved by accident at some point.

[hyanwong]

Great, thanks. It would be nice to test that trees([0]) is the same thing as trees(tracked_samples=[0]), just in case that asterisk gets moved by accident at some point.

Added test_tracked_samples_is_first_arg

[benjeffery]

LGTM

[benjeffery]

Just as I was about to merge I noticed the tests were not quite right, fixed and force pushed.