Add depth method to tree class

[daniel-goldstein]

Now t.depth(u) returns the depth of node u in tree t, where depth is defined as the number of nodes on the path from u to the root, not including u.

[daniel-goldstein]

@jeromekelleher Should I be using a uint32_t (or some other int type) for depth and cast it to an unsigned int when building the python value?

[codecov]

Codecov Report

Merging #554 into master will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #554      +/-   ##
==========================================
+ Coverage   87.18%   87.20%   +0.01%     
==========================================
  Files          21       21              
  Lines       16233    16251      +18     
  Branches     3184     3187       +3     
==========================================
+ Hits        14153    14171      +18     
  Misses       1020     1020              
  Partials     1060     1060              

Flag	Coverage Δ
#c_tests	88.37% <100.00%> (+0.01%)	⬆️
#python_c_tests	90.30% <100.00%> (+0.01%)	⬆️
#python_tests	99.19% <100.00%> (+<0.01%)	⬆️

Impacted Files	Coverage Δ
c/tskit/trees.c	90.89% <100.00%> (+0.03%)	⬆️
python/_tskitmodule.c	83.95% <100.00%> (+0.02%)	⬆️
python/tskit/trees.py	98.64% <100.00%> (+<0.01%)	⬆️

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[jeromekelleher]

Excellent! Just a few very minor comments.

[jeromekelleher]

@petrelharp, do you agree with this definition of Tree.depth(u):

Returns the number of nodes on the path from u to root.

I think the PR is uncontroversial otherwise, no need to look over it.

[jeromekelleher]

Actually, now that I look at it that definition is wrong! Maybe "Returns the number of nodes on the path from u to root, not including u. Thus, the depth of u is 0 if u is a root."

[daniel-goldstein]

Good catch! In the code I used the wording "above u" but I think it's better to just be more explicit and say not including u.

[jeromekelleher]

Good catch! In the code I used the wording "above u" but I think it's better to just be more explicit and say not including u.

"Above" is tricky, because a lot of people think of trees with the root at the bottom (I don't know where they got that from!), so it's good to avoid it if you can. Sometimes it just makes things unreadable if you don't choose a direction though.

[petrelharp]

Returns the number of nodes on the path from u to root, not including u. Thus, the depth of u is 0 if u is a root.

I agree with this, except that it should say "from u to a root". (probably what you meant to write).