Tree path length

[jeremyguez]

I give here a try at #2249. I commented out the last test (copied from TestMRCA) as the trees I generated with tskit.Tree.generate_balanced did not have a virtual node (don't know why). I added some assert comparing with self.t.depth() outputs, but not sure if it's a good idea.
@jeromekelleher

[codecov]

Codecov Report

Merging #2259 (65b4e8a) into main (5bff374) will decrease coverage by 11.76%.
The diff coverage is 20.00%.

❗ Current head 65b4e8a differs from pull request most recent head 6630dc1. Consider uploading reports for the commit 6630dc1 to get more accurate results

@@             Coverage Diff             @@
##             main    #2259       +/-   ##
===========================================
- Coverage   93.31%   81.54%   -11.77%     
===========================================
  Files          27       27               
  Lines       26035    25894      -141     
  Branches     1170     1170               
===========================================
- Hits        24294    21116     -3178     
- Misses       1711     4711     +3000     
- Partials       30       67       +37     

Flag	Coverage Δ
c-tests	92.23% <ø> (ø)
lwt-tests	89.05% <ø> (ø)
python-c-tests	71.94% <20.00%> (-0.02%)	⬇️
python-tests	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
python/tskit/trees.py	47.35% <20.00%> (-50.68%)	⬇️
python/tskit/cli.py	0.00% <0.00%> (-95.94%)	⬇️
python/tskit/vcf.py	9.67% <0.00%> (-90.33%)	⬇️
python/tskit/text_formats.py	10.25% <0.00%> (-89.75%)	⬇️
python/tskit/drawing.py	10.41% <0.00%> (-89.02%)	⬇️
python/tskit/combinatorics.py	13.70% <0.00%> (-85.66%)	⬇️
python/tskit/stats.py	35.13% <0.00%> (-64.87%)	⬇️
python/tskit/util.py	56.41% <0.00%> (-43.59%)	⬇️
python/tskit/metadata.py	79.52% <0.00%> (-19.50%)	⬇️
... and 2 more

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[jeromekelleher]

Looks great! Some minor comments, and we're good to go then.

[jeromekelleher]

Looks great, thanks @jeremyguez! I've one more suggestion above for testing the interface, and we're done then.

Can you squash your commits down to one then please? (See this guide if you're not familiar with squashing)

[jeromekelleher]

OK, looking good! Just one last formatting nitpick.

Just fyi, rather than adding another commit and squashing, this is a case where "amending" a commit is handy. git commit -a --amend should update the commit, and you can then force push to update the PR.

[jeromekelleher]

Fantastic, thanks @jeremyguez !

[jeremyguez]

Thanks for your help @jeromekelleher !