Create Tree.as_dict_of_dicts() method for conversion to networkx.Graph/DiGraph

[winni2k]

This is a PR stub for the feature described in #456.

[codecov]

Codecov Report

Merging #457 into master will increase coverage by <.01%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #457      +/-   ##
==========================================
+ Coverage   87.31%   87.32%   +<.01%     
==========================================
  Files          21       21              
  Lines       15416    15423       +7     
  Branches     2996     2998       +2     
==========================================
+ Hits        13461    13468       +7     
  Misses        969      969              
  Partials      986      986

Flag	Coverage Δ
#c_tests	88.55% <100%> (ø)	⬆️
#python_c_tests	90.44% <100%> (ø)	⬆️
#python_tests	99.24% <100%> (ø)	⬆️

Impacted Files	Coverage Δ
python/tskit/trees.py	98.76% <100%> (ø)	⬆️

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[winni2k]

@jeromekelleher I think I have the basic functionality down now. Are there any tests or other features you'd like to see?

If not, then the next step is to remove all of those print statements, add some documentation and make an entry in the tutorial.

[jeromekelleher]

This is AWESOME thanks @winni2k! Some comments above.

[winni2k]

I've implemented all suggestions except for the Tree.as_edgelist() method. I think the dict_of_dicts approach is more flexible as it allows for branch length annotation, and I'm not sure the edge list would work with childless root nodes. See my comments above.

[jeromekelleher]

Looks great, thanks @winni2k. A few more minor comments and we're good to merge.

Can you squash the commits also please?

[winni2k]

All done

[jeromekelleher]

Great, thanks @winni2k. Can you rebase off upstream/master please? The PR is a little behind, and life is easier if the git history is linear.

[winni2k]

🥁