jbloomlab / phydms

phylogenetic analyses informed by deep mutational scanning data
GNU General Public License v3.0
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Lint the code #38

Closed skhilton closed 4 years ago

skhilton commented 4 years ago

This PR does two things

  1. Lint the code to make it pep8 compliant
  2. Add flake8 to the travis build to check for pep8 compliance.

The vast majority of the code changes are purely cosmetic. Of the top of my head I can think only two categories of changes that I wanted to run by you

  1. One of the flags that was raised was about "bare" except: statements. I believe I replaced all of those with either except Exception: or except ValueError but let me know if you have a better way of handling that
  2. I changed a docstring test so that it all fit on one line. Specifically, testing the DiscreteGamma function with three categories instead of four.

After you look this over, but before were merge, I can update the CHANGELOG and the version and etc.