Fix shared flake8 rules

[eirikurj]

Purpose

Current flake8 rules are not applied as intended. The select statement only applies the patterns defined there, overwriting anything else, including the defaults. PR https://github.com/mdolab/.github/pull/45 removed E, F, W from the select, thus applying only A00, B patterns in our tests. To respect the defaults, but selectively enable values, we should instead use extend-select, to enable specific patterns.

There are two approaches possible:

1. Use the defaults and supplement them with extend-select for any patterns we want to enable. Then use extend-ignore to ignore some unwanted enabled patterns.
2. Continue to use select and manually specify every pattern we want to allow. Similarly, we need to use extend-ignore to ignore some unwanted enabled patterns.

This PR implements the former by removing any select statements, thus respecting all default patterns, but then selectively disabling certain patterns. The extend-select statement is not included in the current .flake8, as I am not aware of any special patterns we need to enable. The benefit of this approach is that we follow any defaults changed upstream, and we do not need to specifically enable plugin codes as we install them. They are automatically enabled as stated by the docs (see extend-select and select),

You usually do not need to specify this option as the default includes all installed plugin codes.

Open to discussions, comments, or concerns if there are any.

Expected time until merged

Soon as tests are not testing what we thought we are testing.

Type of change

• [x] Bugfix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (non-backwards-compatible fix or feature)
• [ ] Code style update (formatting, renaming)
• [ ] Refactoring (no functional changes, no API changes)
• [ ] Documentation update
• [x] Maintenance update
• [ ] Other (please describe)

Testing

Tested locally on several repositories. Please pull down and test locally as well.

Checklist

• [ ] I have run flake8 and black to make sure the Python code adheres to PEP-8 and is consistently formatted
• [ ] I have formatted the Fortran code with fprettify or C/C++ code with clang-format as applicable
• [ ] I have run unit and regression tests which pass locally with my changes
• [ ] I have added new tests that prove my fix is effective or that my feature works
• [ ] I have added necessary documentation

[A-CGray]

PR https://github.com/mdolab/.github/pull/45 removed E, F, W from the select, thus applying only A00, B patterns in our tests.

This is not true, the default list of errors flake8 checks includes a subset of the E, F, and W checks. PR #45 removed E, F and W from the select argument as this was enabling all E, F and W checks, including those that are not PEP compliant and in some cases contradict each other.

I agree with your conclusion, let's go with approach 1, maybe add in the extend-select line and comment it out so that it's obvious where to add things in future.

[eirikurj]

Added the extend-select commented out, as well as a comment.