filter_nodes for simplify

[jeromekelleher]

Here's a quick first pass for #2605.

I think it basically works, but would need more testing and a bit of implementation polish (mainly just properly working out whether a node is a sample).

The main limitation is that the input samples must be the original tree sequence samples. We could probably relax that a bit, I guess (make it a subset?) but I didn't think it through.

@hyanwong - do you want to try this out on your applications and maybe come up with some tests?

[codecov]

Codecov Report

Merging #2606 (5bcbc30) into main (5a3ebde) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #2606   +/-   ##
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  Coverage   93.91%   93.91%           
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  Files          27       27           
  Lines       27200    27200           
  Branches     1215     1215           
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  Hits        25544    25544           
  Misses       1622     1622           
  Partials       34       34           

Flag	Coverage Δ
c-tests	92.24% <ø> (ø)
lwt-tests	89.05% <ø> (ø)
python-c-tests	73.14% <ø> (ø)
python-tests	98.95% <ø> (ø)

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[hyanwong]

I think we decided that we should allow any set of nodes to be specified as samples, although I'd be happy simply to restrict it to ts.samples(), at least for the time being.

If we did allow different sample sets with filter_nodes=False, I think we said that the order of samples passed to the function should not be important (so that nodes never change their ID). Alternatively, we could simply error out if the node IDs provided as samples are not in ascending order.

[hyanwong]

I wasn't sure how to add extra functionality to this PR (or whether I have permission to), so I have opened up another PR with the commit in this PR as the first commit and a few tests added as extra commits: #2619. Hence I'm closing this

[mergify]

⚠️ The sha of the head commit of this PR conflicts with #2619. Mergify cannot evaluate rules on this PR. ⚠️