add cython code to coverage report

[kain88-de]

Cython has recently gained support for coverage our of box [1]. It might be worth to have that code covered as well since we aim to replace all CPython-extensions with Cython in the long run.

[1] http://blog.behnel.de/posts/coverage-analysis-for-cython-modules.html

[richardjgowers]

Yeah that looks like a good idea.

[souravsingh]

I would like to work on the issue.

[kain88-de]

@souravsingh sure just assign your self to the issue.

You should also look over the cython-mailing list for any problems that you will encounter.

Before you try to get a coverage report for MDAnalysis I suggest you create a small test cython project and try to get a working coverage report for your test project. That removes a lot of variables and should speed up testing since the compilation phase will be much shorter.

[kain88-de]

https://gitlab.com/logan/cython-template-project

This is an example repository that claims to have the coverage of cython files working. For anybody interested in taking this.

[orbeckst]

Maybe this commit attempt to add coverage in https://gitlab.com/logan/cython-template-project is helpful in that it lists some changes that seem to pertain to getting cython coverage.

[kain88-de]

Btw this works very well in combination with pytest See https://github.com/MDAnalysis/pytng

@utkbansal something you can look into after a complete transition to pytest

[utkbansal]

@kain88-de Sure

[richardjgowers]

https://medium.com/@dfdeshom/better-test-coverage-workflow-for-cython-modules-631615eb197a