Fix: Pca.py doctest error

[HeetVekariya]

Partially address #3925

Changes made in this Pull Request:

• Doctest for pca.py (package/MDAnalysis/analysis/pca.py) file contains two error (at two places: 1 and 2 ) due to wrong output in Expected:
  • 0.38147609331128324
  • 0.17478244043688052
• Corrected expected output according to the generated output as below:
  • 0.3814760933112831
  • 0.17478244043688054

PR Checklist

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

Developers certificate of origin

• I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

---

📚 Documentation preview 📚: https://mdanalysis--4377.org.readthedocs.build/en/4377/

[HeetVekariya]

I will update the change log when reviewed by maintainers.

[github-actions]

Linter Bot Results:

Hi @HeetVekariya! Thanks for making this PR. We linted your code and found the following:

There are currently no issues detected! 🎉

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.64%. Comparing base (93630da) to head (ea69941).

❗ Current head ea69941 differs from pull request most recent head de83fd1. Consider uploading reports for the commit de83fd1 to get more accurate results

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4377      +/-   ##
===========================================
- Coverage    93.66%   93.64%   -0.03%     
===========================================
  Files          168      180      +12     
  Lines        21248    22327    +1079     
  Branches      3917     3917              
===========================================
+ Hits         19902    20908    +1006     
- Misses         888      961      +73     
  Partials       458      458              

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[orbeckst]

@lilyminium could please handle this PR? I think rmsip was your code, wasn't it?

[lilyminium]

Thanks for opening this PR, @HeetVekariya -- however, I'm not sure that changing the output is the best solution to the failing doctest. The differences are somewhere around the ~15th decimal place, which seems to me to simply arise from precision error. IMO a more permanent solution to this issue might be to change it into a format that only prints out maybe the first 6 decimal places, using something like string formatting (with print) or rounding -- what do you think?

[HeetVekariya]

@lilyminium

• At the start i am thinking about the rounding, but thought that it is meant to have upto 17 decimals.
• But if you allow i can do round off upto 6 decimals.

[lilyminium]

Yes sure please do, rounding seems like the best solution here.

[lilyminium]

This LGTM but I'm confused why CI is failing -- restarting now.

[lilyminium]

/azp run

[azure-pipelines]

Azure Pipelines successfully started running 1 pipeline(s).

[lilyminium]

Sorry for the delay -- thanks for fixing this @HeetVekariya! Could you please update the CHANGELOG?

[HeetVekariya]

@lilyminium sorry for late response, I have updated the change log.

[orbeckst]

@lilyminium could you please check in on this PR? You approved it a while back but it hasn't been merged. Thanks!

[lilyminium]

Thanks @HeetVekariya -- merging now!

[HeetVekariya]

Thank you for merging 🙏