Convert nexus tests to use dendropy

[jeromekelleher]

Closes #1785

Add dendropy to various requirements lists and refactor the tests to use pytest a little better

Hopefully this sets the foundation for following up with label changes etc.

@jeetsukumaran would you mind taking a quick look and seeing if the dendropy usage looks OK to you please?

[codecov]

Codecov Report

Merging #1836 (b3ff095) into main (d7514b8) will decrease coverage by 0.00%.
The diff coverage is n/a.

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@@            Coverage Diff             @@
##             main    #1836      +/-   ##
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- Coverage   93.43%   93.43%   -0.01%     
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  Files          27       27              
  Lines       24808    24804       -4     
  Branches     1094     1094              
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- Hits        23179    23175       -4     
  Misses       1594     1594              
  Partials       35       35              

Flag	Coverage Δ
c-tests	92.20% <ø> (+<0.01%)	⬆️
lwt-tests	89.14% <ø> (ø)
python-c-tests	94.53% <ø> (-0.01%)	⬇️
python-tests	98.75% <ø> (-0.01%)	⬇️

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Impacted Files	Coverage Δ
python/_tskitmodule.c	91.68% <0.00%> (-0.01%)	⬇️
python/tskit/trees.py	97.84% <0.00%> (-0.01%)	⬇️
python/tskit/drawing.py	99.42% <0.00%> (-0.01%)	⬇️
python/tskit/tables.py	98.79% <0.00%> (ø)
python/tskit/__init__.py	100.00% <0.00%> (ø)
c/tskit/tables.c	90.30% <0.00%> (+<0.01%)	⬆️

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[jeetsukumaran]

At first glance, this works fine. One caution is the expectation that every node (including internal nodes) on the dendropy tree have a non-None taxon attribute. This assumes that: (a) tskit emits internal node labels, and (b) dendropy parses these internal node labels as Taxon objects and assigns them to the taxon attribute of the corresponding node. The latter is not default behavior with dendropy (it parses them as labels), but, as you have done in the tests, setting suppress_internal_node_taxa=False gets it there. Just a note to keep in mind with test setup/administration.

[jeromekelleher]

OK great, thanks @jeetsukumaran. I'll merge this and push a batch up updates to improve the nexus handling then.