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PEP8: how can we avoid breaking API

See original GitHub issue

Parts of the library do not follow PEP8 names.

I took a look at /examples and compiled the names there imported:

class pymbar.MBAR (+ its methods)
class pymbar.PMF (+ its methods)
class pymbar.utils.DataError
class pymbar.utils.ParameterError
function pymbar.BAR
function pymbar.confidenceintervals.AndersonDarling
function pymbar.confidenceintervals.generateConfidenceIntervals
function pymbar.confidenceintervals.QQPlot
function pymbar.EXP
function pymbar.EXPGauss
function pymbar.timeseries.statisticalInefficiency
function pymbar.timeseries.subsampleCorrelatedData
function pymbar.utils.kn_to_n

These should either:

A. left alone for now, or B. be an alias to the PEP8-compliant name with a DeprecationWarning

We should probably include more names in that list, but the question is the same: how do we want to face these changes?

Issue Analytics

State:
Created 4 years ago
Comments:10 (5 by maintainers)

Top GitHub Comments

2reactions

mrshirtscommented, Feb 25, 2020

That seems like it might be a good path forward. There are a couple of actual improvements / bug fixes that have been found / we may find over the next couple weeks that we should backport as well.

Issue filed at #364 to make a list

0reactions

mrshirtscommented, Feb 28, 2020

Closing this, since the solution is #365