enabled coverage for cython

[richardjgowers]

Fixes #443

Changes made in this Pull Request:

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[tylerjereddy]

I think @stefanv and the scikit-image team are quite interested in doing this for their library as well so cc'ing them here.

[richardjgowers]

@tylerjereddy I'm just seeing if it's as easy as these two lines... if it is I'll bring them in :)

[seb-buch]

@richardjgowers it basically is!.. with one caveat: lines with "cdef" are marked as "not covered" even if they actually are. This is a well known bug/issue (see cython/cython#1461).
Even with "embedsignature" set to true, I still have "false negative" for basically all definition lines.

[stefanv]

/cc @jni @soupault

[codecov]

Codecov Report

Merging #2029 into develop will increase coverage by <.01%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           develop    #2029      +/-   ##
===========================================
+ Coverage    88.59%   88.59%   +<.01%     
===========================================
  Files          143      143              
  Lines        17305    17361      +56     
  Branches      2649     2658       +9     
===========================================
+ Hits         15331    15381      +50     
- Misses        1376     1379       +3     
- Partials       598      601       +3

Impacted Files	Coverage Δ
package/MDAnalysis/coordinates/memory.py	94.28% <0%> (-0.11%)	⬇️
package/MDAnalysis/lib/__init__.py	100% <0%> (ø)	⬆️
package/MDAnalysis/lib/distances.py	87.88% <0%> (+0.24%)	⬆️

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[richardjgowers]

Hmm this is weird. When I run locally, the ascii table printout doesn't have any .pyx files, but if I look inside the .coverage file produced there are entries for .pyx files, so it's sort of working...

[orbeckst]

@Fenil3510 for your GSoC project proposal "Cythonizing ASCII Readers/Parser", the discussion here should be relevant.

[fenilsuchak]

I was researching on adding cython coverage, the codecov report here still doesn't track .pyx files. I ran the same locally with some minor changes(hacky) and the report covers .pyx files

Here's the HTML output

I have opened a separate PR for it as I will be working on this issue for my project.

[fenilsuchak]

This PR can be closed as #2255 solves it.