Added Cython Coverage

[fenilsuchak]

Changes made in this Pull Request:

• Sorry, I messed up some commits in the last one. Anyway, even by forcing cython_linetrace = True the codecov report doesn't show coverage for .pyx files. Locally works perfectly with pytest-cov. The sample html output is here. Any suggestions?

PR Checklist

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

[codecov]

Codecov Report

Merging #2255 into develop will decrease coverage by 0.04%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           develop    #2255      +/-   ##
===========================================
- Coverage     89.7%   89.65%   -0.05%     
===========================================
  Files          160      172      +12     
  Lines        19769    21396    +1627     
  Branches      2783     2783              
===========================================
+ Hits         17733    19183    +1450     
- Misses        1440     1616     +176     
- Partials       596      597       +1

Impacted Files	Coverage Δ
package/MDAnalysis/lib/transformations.py	78.47% <0%> (-0.15%)	⬇️
package/MDAnalysis/analysis/encore/cutils.pyx	100% <0%> (ø)
package/MDAnalysis/lib/formats/libmdaxdr.pyx	80.9% <0%> (ø)
package/MDAnalysis/lib/c_distances.pyx	100% <0%> (ø)
package/MDAnalysis/lib/qcprot.pyx	100% <0%> (ø)
...alysis/analysis/encore/clustering/affinityprop.pyx	90.24% <0%> (ø)
package/MDAnalysis/lib/formats/cython_util.pyx	90% <0%> (ø)
package/MDAnalysis/lib/formats/libdcd.pyx	79.28% <0%> (ø)
package/MDAnalysis/lib/_cutil.pyx	98.81% <0%> (ø)
...e/dimensionality_reduction/stochasticproxembed.pyx	100% <0%> (ø)
... and 4 more

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[fenilsuchak]

Ok, probably I've traced the issue. Keeping the current changes as in this commit and building locally in editable mode with pip install -e package cython files are covered with coverage report visible but when I build it via pip install -v package as done by travis, the cython files aren't traced. Not sure of the exact reason why, but the search has been narrowed.

[richardjgowers]

Hmm interesting, try changing the travis build to -e ?

…

On Apr 19, 2019 at 08:35, <Fenil Suchak ***@***.***)> wrote: Ok, probably I've traced the issue. Keeping the current changes as in this commit and building locally in editable mode with pip install -e package cython files are covered with coverage report visible but when I build it via pip install -v package as done by travis, the cython files aren't traced. Not sure of the exact reason why, but the search has been narrowed. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub (#2255 (comment)), or mute the thread (https://github.com/notifications/unsubscribe-auth/ACGSGB7SJNHGJE6K6XEOTLLPRFY4PANCNFSM4HG3YKUQ).

[fenilsuchak]

Yuhu! .pyx covered in report!!

[fenilsuchak]

Travis failing due to doc in the _augment.pyx cython file. Not sure how to fix it. Any help would be appreciated

[zemanj]

@Fenil3510 Sphinx doesn't play nicely with Cython if embedsignature=True. Make sure to set embedsignature=False in the doc build and everything should work.

[fenilsuchak]

I believe codecov is failing due to low coverage of Cython files

[zemanj]

Definitely not your fault. I wouldn't trust codecove too much anyway. It often reports strange overall coverage values, such as a decrease even if the diff coverage is 100%...

…

On April 20, 2019 8:25:08 PM GMT+02:00, Fenil Suchak ***@***.***> wrote: I believe codecov is failing due to low coverage of Cython files -- You are receiving this because you commented. Reply to this email directly or view it on GitHub: #2255 (comment)

[richardjgowers]

Something strange is happening where we're getting the repo twice now...

e: seems like this isn't caused by this PR

[richardjgowers]

Ok looks good, +12 files in coverage which seems about right