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LAMMPS continuous check in chain trajectory #4170

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merged 25 commits into from
Jun 26, 2023

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jaclark5
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@jaclark5 jaclark5 commented Jun 15, 2023

Fixes #3546

This is an alternative to PR #3849

Changes made in this Pull Request:

  • Add definition for ts.data['time'] in LAMMPSDumpReader

PR Checklist

  • Tests?
  • [NA] Docs?
  • CHANGELOG updated?
  • Issue raised/referenced?

📚 Documentation preview 📚: https://mdanalysis--4170.org.readthedocs.build/en/4170/

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github-actions bot commented Jun 15, 2023

Linter Bot Results:

Hi @jaclark5! 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 ⚠️ Possible failure

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/5378722463/jobs/9758913675


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

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codecov bot commented Jun 15, 2023

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (3bd407c) 93.61% compared to head (8c1bc38) 93.61%.

Additional details and impacted files
@@           Coverage Diff            @@
##           develop    #4170   +/-   ##
========================================
  Coverage    93.61%   93.61%           
========================================
  Files          193      193           
  Lines        25169    25170    +1     
  Branches      4059     4059           
========================================
+ Hits         23561    23562    +1     
  Misses        1092     1092           
  Partials       516      516           
Impacted Files Coverage Δ
package/MDAnalysis/coordinates/LAMMPS.py 95.04% <100.00%> (+0.01%) ⬆️
package/MDAnalysis/coordinates/chain.py 86.69% <100.00%> (ø)

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.

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@hmacdope hmacdope left a comment

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Thanks @jaclark5 see my comments.

testsuite/MDAnalysisTests/datafiles.py Outdated Show resolved Hide resolved
package/MDAnalysis/coordinates/chain.py Outdated Show resolved Hide resolved
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@jaclark5 if you can resolve conflicts I can re-review ASAP. :)

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One last thing then should be good to go.

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Thanks @jaclark5!

@hmacdope hmacdope merged commit b943ca0 into MDAnalysis:develop Jun 26, 2023
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continuous chain reader support for LAMMPS trajectories
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