Cimport consistency

[Hakarishirenai]

Fixes #3908

Changes made in this Pull Request:

• Have updated all cimport numpy from np to cnp

PR Checklist

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

[Hakarishirenai]

@hmacdope can you give it a look ?

[hmacdope]

Seem to be a large number of test failures @Hakarishirenai? You will have to go through and have a look at each one and fix it. Do you know how to run the tests locally? Have a look on the contributing page and tests guide for some tips if not.

[Hakarishirenai]

Sure, will give it a look and try fixing them!

[codecov]

Codecov Report

Base: 93.48% // Head: 93.52% // Increases project coverage by +0.03% 🎉

Coverage data is based on head (a501dcf) compared to base (0c4f823).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #3978      +/-   ##
===========================================
+ Coverage    93.48%   93.52%   +0.03%     
===========================================
  Files          190      190              
  Lines        24951    25028      +77     
  Branches      3527     3542      +15     
===========================================
+ Hits         23326    23407      +81     
+ Misses        1102     1100       -2     
+ Partials       523      521       -2     

Impacted Files	Coverage Δ
package/MDAnalysis/lib/_augment.pyx	100.00% <100.00%> (ø)
package/MDAnalysis/lib/_cutil.pyx	100.00% <100.00%> (ø)
package/MDAnalysis/lib/formats/cython_util.pyx	100.00% <100.00%> (ø)
package/MDAnalysis/lib/formats/libdcd.pyx	91.11% <100.00%> (ø)
package/MDAnalysis/lib/formats/libmdaxdr.pyx	87.92% <100.00%> (ø)
package/MDAnalysis/lib/qcprot.pyx	100.00% <100.00%> (ø)
package/MDAnalysis/lib/mdamath.py	100.00% <0.00%> (ø)
package/MDAnalysis/lib/pkdtree.py	83.83% <0.00%> (ø)
package/MDAnalysis/lib/distances.py	97.62% <0.00%> (ø)
package/MDAnalysis/visualization/streamlines_3D.py	70.49% <0.00%> (ø)
... and 4 more

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

☔ View full report at Codecov.
📢 Do you have feedback about the report comment? Let us know in this issue.

[Hakarishirenai]

@hmacdope does this look good ?

[hmacdope]

Thanks for fixing the tests! Great job. Would you mind running the benchmarks to see if we have any regressions?

I only ask because it is possible to select different versions of a function or datatype silently when using import numpy as np AND cimport numpy as np, which is no longer the case with your changes.

The command you want is probably something like

asv continuous  [commit from develop] [commit from your branch]

The readme on running the benchmarks is at https://github.com/MDAnalysis/mdanalysis/tree/develop/benchmarks

[hmacdope]

Benchmark block

[Hakarishirenai]

Sure, will give it a try

[orbeckst]

@hmacdope you blocked the PR. Did anything change that would allow us to move forward? Or should we close the PR??

[hmacdope]

@orbeckst Waiting for a benchmark run by @Hakarishirenai to certify no cython Numpy functions are being alaiesed back to Python level. I suppose I should probably just run them myself off this branch.

[hmacdope]

@Hakarishirenai are you able to run the benchmarks? I havn't had a chance Otherwise I will mark this PR as stale in a few days.

[IAlibay]

I'm closing this PR as stale (due to lack of activity), please reopen if necessary.