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Potential fix for flaky PyEMMA tests in 2.7#997

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dwhswenson merged 2 commits into
openpathsampling:masterfrom
dwhswenson:fix-flaky-pyemma
Mar 25, 2021
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Potential fix for flaky PyEMMA tests in 2.7#997
dwhswenson merged 2 commits into
openpathsampling:masterfrom
dwhswenson:fix-flaky-pyemma

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@dwhswenson

@dwhswenson dwhswenson commented Mar 24, 2021

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I've been having problems with PyEMMA tests being flaky in Py2.7 ever since #987. It seems like there's something that sometimes shows up in stderr, which ipynbtest didn't check but apparently nbval does. The error I get is:

Notebook cell execution failed
Cell 8: Cell outputs differ

Input:
cv(storage.trajectories[0]);

Traceback:
Unexpected output fields from running code: set([u'stderr'])

This PR adds ignores to that cell and another near it that also may cause problems.

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codecov Bot commented Mar 24, 2021 •
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Codecov Report

Merging #997 (3a2729d) into master (5ca0e40) will not change coverage.
The diff coverage is n/a.

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@@           Coverage Diff           @@
##           master     #997   +/-   ##
=======================================
  Coverage   80.58%   80.58%           
=======================================
  Files         138      138           
  Lines       14671    14671           
=======================================
  Hits        11823    11823           
  Misses       2848     2848

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@dwhswenson

dwhswenson commented Mar 24, 2021

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This is ready for review and comment. I will leave it open for at least 24 hours, merging no earlier than Thu 25 Mar 09:00 GMT (10:00 local).

@sroet

sroet commented Mar 24, 2021

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Do you mind adding a label/milestone indicating that this is fix for just python 2.7 and should probably be cleaned/reverted as soon as python 2.7 is dropped? LGTM otherwise

@dwhswenson

dwhswenson commented Mar 24, 2021

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Do you mind adding a label/milestone indicating that this is fix for just python 2.7 and should probably be cleaned/reverted as soon as python 2.7 is dropped?

I agree with the principle, but no need in this case. This notebook is about old-style CVs and netcdfplus, both of which will be replaced in 2.0, when we also drop 2.7. So the whole notebook will be removed then. (I'll probably use some of the current notebook as a guide to write tests for SimStore-based PyEMMAFeaturizerCVs.)

@dwhswenson dwhswenson merged commit 01382f1 into openpathsampling:master Mar 25, 2021
@dwhswenson dwhswenson deleted the fix-flaky-pyemma branch March 25, 2021 10:31
@dwhswenson dwhswenson mentioned this pull request Jul 5, 2021
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