Use PEP8 for Python API, Python use case and Python notebooks

[akenmorris]

I've noticed our Python API and use cases use a variety of different and inconsistent coding styles. Luckily Python, unlike C++, has a well defined standard coding style called PEP8 that many packages follow (e.g. scipy, numpy, etc).

https://www.python.org/dev/peps/pep-0008/

https://www.pythonlikeyoumeanit.com/Module5_OddsAndEnds/Writing_Good_Code.html

Some packages like SciPy even disallow non-PEP8 code:

https://docs.scipy.org/doc/scipy/reference/dev/contributor/pep8.html

If you use a python IDE like PyCharm, this is easy to enforce since it will point out all code that violates PEP8:

There is also a tool, autopep8:

https://pypi.org/project/autopep8/0.8/

I'm sure there are others as well.

This is just my recommendation. Feel free to overrule my suggestion and close this issue.

[cchriste]

I just got bit by this for the umpteenth time because my editor always uses spaces, but some of our python files are indented using tabs. From PEP8 https://www.python.org/dev/peps/pep-0008/#tabs-or-spaces:

Tabs or Spaces?
Spaces are the preferred indentation method.

Tabs should be used solely to remain consistent with code that is already indented with tabs.

Python 3 disallows mixing the use of tabs and spaces for indentation.

Python 2 code indented with a mixture of tabs and spaces should be converted to using spaces exclusively.

In addition, our python code has a mix of 2- and 4-space indents. From PEP8 https://www.python.org/dev/peps/pep-0008/#indentation:

Indentation
Use 4 spaces per indentation level.

While I am generally not a fan of coding standards (ex: monitors keep getting wider but we still shouldn't use more than 79 characters on a line??), I am in support of coding consistency.

[cchriste]

I've not tried any of the utilities that homogenize python code, but here's a brief script for anyone feeling intrepid:

~/code/ShapeWorks $ find . -name "*.py" -exec <pep8it> {} \; -print 

[jadie1]

The refactored use cases have all been fixed to use spaces only in the pymodule_nb_changes branch. We will run the autopep8 on them again to be sure just before creating a PR.