Add the Bio module for test_parsimony

[hyanwong]

For some reason this didn't auto-install for me using setup.py. Not sure why it works in the CI testing suite, but it can't harm to add it to the dev requirements, surely.

[jeromekelleher]

For some reason this didn't auto-install for me using setup.py. Not sure why it works in the CI testing suite, but it can't harm to add it to the dev requirements, surely.

Setup.py only includes deps needed for installation, not for testing. Good to add Biopython to the development requirements all right though, thanks.

[hyanwong]

Ah - that explains it. Thanks for clarifying.

[codecov]

Codecov Report

Merging #268 into master will decrease coverage by 0.16%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #268      +/-   ##
==========================================
- Coverage    85.8%   85.64%   -0.17%     
==========================================
  Files          19       19              
  Lines       14068    13735     -333     
  Branches     2736     2665      -71     
==========================================
- Hits        12071    11763     -308     
+ Misses       1043     1022      -21     
+ Partials      954      950       -4

Flag	Coverage Δ
#c_tests	86.56% <ø> (-0.16%)	⬇️
#python_c_tests	89.9% <ø> (-0.04%)	⬇️
#python_tests	99.16% <ø> (-0.01%)	⬇️

Impacted Files	Coverage Δ
c/tskit/trees.c	90.38% <0%> (-0.2%)	⬇️
c/tskit/core.c	82.47% <0%> (-0.14%)	⬇️
python/_tskitmodule.c	83.22% <0%> (-0.14%)	⬇️
python/tskit/trees.py	98.57% <0%> (-0.01%)	⬇️

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[jeromekelleher]

Looks good - I rebased to bring it up to date. Will merge once CI goes through.

[jeromekelleher]

This isn't BioPython, it's a different package; change to 'biopython'

[hyanwong]

biopython is already in development.txt. So not sure why this didn't work before for me. But I guess this PR can simply be cancelled

[hyanwong]

Was the wrong module anyway