lammps.py errors #4458
lammps.py errors #4458
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Hello @nataliyah123! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2024-03-31 11:45:59 UTC |
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.
Please have a look at the Please note: The |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #4458 +/- ##
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+ Coverage 93.37% 93.64% +0.26%
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Files 171 180 +9
Lines 21736 22327 +591
Branches 4012 3917 -95
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+ Hits 20297 20908 +611
- Misses 952 961 +9
+ Partials 487 458 -29 ☔ View full report in Codecov by Sentry. |
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is there any file named lammps.data? |
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if take_this_frame not necessary I can shorten the code by directly assigning ts.frame a frame number |
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Please check the documentation preview https://mdanalysis--4458.org.readthedocs.build/en/4458/documentation_pages/coordinates/LAMMPS.html#module-MDAnalysis.coordinates.LAMMPS to make sure the code blocks visually look nice.
I don't think it's necessary to add .. doctest::. If it's problematic to add them, just remove them.
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| :class:`~MDAnalysis.topology.LAMMPSParser.DATAParser`) together with a | |||
| LAMMPS DCD with "*real*" provide the keyword *format="LAMMPS*":: | |||
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| >>> u = MDAnalysis.Universe("lammps.data", "lammps_real.dcd", format="LAMMPS") | |||
| ..testsetup:: | |||
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This code block should be placed right after the title level Example: Loading xxx
| >>> import MDAnalysis | ||
| >>> from MDAnalysis.tests.datafiles import LAMMPSdata2, LAMMPSdcd2 | ||
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| ..doctest:: |
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| ..doctest:: | |
| .. doctest:: |
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| ..doctest:: | ||
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| >>> u = MDAnalysis.Universe(LAMMPSdata2, LAMMPSdcd2, format="LAMMPS") | ||
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| If the trajectory uses *units nano* then use :: |
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| If the trajectory uses *units nano* then use :: | |
| If the trajectory uses *units nano* then use |
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@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/LAMMPS1 items passed all tests: but I think changes are not reflected on github. please check |
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| Example: Loading a LAMMPS simulation | |||
| ------------------------------------ | |||
| .. testsetup:: | |||
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You can just remove this, what testsetup does is that the code right below it runs without showing it in the documentation.
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@yuxuanzhuang I assigned the PR to you, if this is too much please say something. Thanks! |
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@yuxuanzhuang please squash merge when you're happy. Condense the commit message into something like If CHANGELOG or AUTHORS were updated also mention that. See recent commit messages as examples. Thanks! |
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Thanks!!! @nataliyah123 |
Partially addresses #3925
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📚 Documentation preview 📚: https://mdanalysis--4458.org.readthedocs.build/en/4458/