Replace num_edges_per_tree by tree_edge_indices in TreeSet

[amontoison]

Improve the readability of what was done in #228.
I found that the need to update a variable first in various specific places (at the end of for loops) in the code was quite difficult to read and error-prone.
Things will become even more complex with #233, so I prefer to make these modifications first.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (45aa7aa) to head (7b67d58).
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff            @@
##              main      #237   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           15        15           
  Lines         1785      1781    -4     
=========================================
- Hits          1785      1781    -4     

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