Skip to content

Potential fix for flaky PyEMMA tests in 2.7 #997

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
merged 2 commits into from
Mar 25, 2021
Merged

Potential fix for flaky PyEMMA tests in 2.7 #997

merged 2 commits into from
Mar 25, 2021

Conversation

@dwhswenson
Copy link
Member

@dwhswenson dwhswenson commented Mar 24, 2021

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.

@codecov
Copy link

codecov bot commented Mar 24, 2021 •
edited
Loading

Codecov Report

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

Impacted file tree graph

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

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 5ca0e40...3a2729d. Read the comment docs.

@dwhswenson
Copy link
Member Author

dwhswenson commented Mar 24, 2021

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
Copy link
Member

sroet commented Mar 24, 2021

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
Copy link
Member Author

dwhswenson commented Mar 24, 2021

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
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@sroet sroet sroet approved these changes

Assignees

No one assigned

Labels

misc PR

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@dwhswenson @sroet