Refactor Phylogenetics - Githubissues

datasnakes / OrthoEvolution

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

https://orthoevolution.readthedocs.io/en/master/

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Refactor Phylogenetics #154

Open sdhutchins opened 4 years ago

sdhutchins commented 4 years ago

What are you trying to accomplish?

Improve the Phylogenetics API and code style.

What is the error or issue?

The code is not using a number of Python's best practices.

TODO

[ ] Refactor ETE3PAML
[x] Refactor PhyML
[x] ~~Remove pexpect from Phylip in favor of subprocess~~ Refactor Phylip
[ ] Consider deprecating PhyloTree
[ ] Refactor CodemlRun

sdhutchins commented 4 years ago

@grabear I think I can have this done by Friday - I know we were wanting to do documentation after you got #152 done, but I feel confident I can knock this out close that point.

sdhutchins commented 3 years ago

Will work on this over the weekend.