Remove TreeNode from the main workflow #360
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The following artifacts were built for this PR: empire-biplot.qzv, empire.qzv, empress-tree.qzv |
kwcantrell
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Aug 29, 2020
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Thanks @ElDeveloper! There is a odd satisfaction in removing TreeNode and completely removing the Tree class. I have a just a couple of comments.
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Thanks @kwcantrell all should be addressed. |
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Thanks @ElDeveloper |
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Use BPTree for all operations. In addition, I also removed the usage of
"EmpressNodeXXX" to refer to unnamed nodes.
This resulted in a lot of code being deleted, and a few tests being removed
since bp.parse_newick differs from TreeNode.read. The biggest thing being that
missing length values are by default assigned to 0.