Filtering pytng reader warnings (resolves #3986)

[ooprathamm]

Fixes #3986

Changes made in this Pull Request:

• added filter for repeated warning in test_tng.py

PR Checklist

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

[github-actions]

Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our Code of Conduct and that first time contributors introduce themselves on the developer mailing list so we can get to know you. You can learn more about participating here. Please also add yourself to package/AUTHORS as part of this PR.

[codecov]

Codecov Report

Base: 93.52% // Head: 93.52% // No change to project coverage 👍

Coverage data is based on head (940bef4) compared to base (096f799).
Patch has no changes to coverable lines.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #4010   +/-   ##
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  Coverage    93.52%   93.52%           
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  Files          190      190           
  Lines        25028    25028           
  Branches      3542     3542           
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  Hits         23407    23407           
  Misses        1100     1100           
  Partials       521      521           

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[ooprathamm]

@IAlibay I hope this is what you meant. The filter has been applied specifically for test_tng.py

Current captured warnings -

[orbeckst]

@ooprathamm could you please edit your original PR comment at the top to include the issue number that you're fixing as Fixes #3986 ? This links your PR to the issue and is an important part of organizing work on the project. Thanks.

[hmacdope]

@ooprathamm just double checking do you have pytng installed? Otherwise the tests will be skipped.

[hmacdope]

I verified on my own setup that warnings down from ~900 to ~80 so seems to work

[hmacdope]

LGTM!

[hmacdope]

After some discussion @IAlibay and myself have decided we want to eliminate all the warnings.
Try adding the same filter to more test fixture classes until the warning count gets to 0 for the "Stride of block" warnings.

[ooprathamm]

I verified on my own setup that warnings down from ~900 to ~80 so seems to work

@hmacdope the difference in warnings seems to be from other optional dependencies in your system (for mine and as stated in #3986 ~600 to ~7 warnings)

is there list of optional dependencies that I need to install other than pytng

[hmacdope]

No just pytng should be fine! Try and get the last 7 gone and then we should be good to go.

[ooprathamm]

@hmacdope filtered all the warnings in test_tng also removed deprecation warning thrown for xdrlib in topology package

[IAlibay]

Just the one thing, also please add yourself to AUTHORS and your name to the top of the changelog (a changelog entry is not required). We also would ask if you could introduce yourself on the mailing list if you haven't done so (please include your github handle).

[IAlibay]

Just the one thing from me.

[hmacdope]

Looks good to me, I think you have already introduced yourself on the Mailing list, so good to go from me.

[IAlibay]

lgtm, thanks!