lammps.py errors

[nataliyah123]

Partially Fixes #3925

Changes made in this Pull Request:

• added essential imports
• added missing files
• added missing variable

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.

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📚 Documentation preview 📚: https://mdanalysis--4458.org.readthedocs.build/en/4458/

[pep8speaks]

Hello @nataliyah123! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file package/MDAnalysis/coordinates/LAMMPS.py:

Line 84:70: W291 trailing whitespace

Comment last updated at 2024-03-31 11:45:59 UTC

[github-actions[bot]]

Linter Bot Results:

Hi @nataliyah123! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	⚠️ Possible failure
testsuite	✅ Passed

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/8497918894/job/23277037993

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Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 93.64%. Comparing base (e189a90) to head (1980350). Report is 20 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4458      +/-   ##
===========================================
+ Coverage    93.37%   93.64%   +0.26%     
===========================================
  Files          171      180       +9     
  Lines        21736    22327     +591     
  Branches      4012     3917      -95     
===========================================
+ Hits         20297    20908     +611     
- Misses         952      961       +9     
+ Partials       487      458      -29     

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

[nataliyah123]

is there any file named lammps.data?

[nataliyah123]

if take_this_frame not necessary I can shorten the code by directly assigning ts.frame a frame number

[nataliyah123]

@yuxuanzhuang I have tested the code on my system and both doctest and html are fine below is the screen shot

Document: documentation_pages/coordinates/LAMMPS

1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed.

but I think changes are not reflected on github. please check

[orbeckst]

@yuxuanzhuang I assigned the PR to you, if this is too much please say something. Thanks!

[orbeckst]

@yuxuanzhuang please squash merge when you're happy. Condense the commit message into something like

* partially addresses #3925
* fixes doctests in analysis.align

If CHANGELOG or AUTHORS were updated also mention that. See recent commit messages as examples.

Thanks!

[yuxuanzhuang]

Thanks!!! @nataliyah123