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changed dihedral atom group selection strings in test_dihedral.py #218

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merged 4 commits into from
Nov 17, 2022

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cadeduckworth
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changed selection string format for dihedral atom groups:

  • old format ('name *# or name *# ... ')
  • new format ('name *#', 'name *#', ... )
  • ensures that the atom group is not reordered alphanumerically
  • the dihedral atom group will be analyzed properly in the order that is specified with this format

@cadeduckworth cadeduckworth linked an issue Nov 4, 2022 that may be closed by this pull request
… pytest locally

* selection string format updated, final, correct, and consistent with original intended selection order
* updated values calculated for circmean, circvar for use in test_results_recursive2()
* changed order for arguments in assert_almost_equal() for use in test_results_recursive2() to align with format in numpy.testing docs, (actual, desired) for readability, does not affect accuracy or testing purposes
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codecov bot commented Nov 12, 2022

Codecov Report

Merging #218 (ab6a8be) into develop (ada0691) will increase coverage by 0.24%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           develop     #218      +/-   ##
===========================================
+ Coverage    78.52%   78.76%   +0.24%     
===========================================
  Files           11       11              
  Lines         1676     1691      +15     
  Branches       255      255              
===========================================
+ Hits          1316     1332      +16     
  Misses         276      276              
+ Partials        84       83       -1     
Impacted Files Coverage Δ
mdpow/analysis/dihedral.py 100.00% <0.00%> (ø)
mdpow/fep.py 69.06% <0.00%> (+0.11%) ⬆️
mdpow/equil.py 80.45% <0.00%> (+0.22%) ⬆️
mdpow/analysis/ensemble.py 97.15% <0.00%> (+0.48%) ⬆️
mdpow/restart.py 73.10% <0.00%> (+1.93%) ⬆️

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@orbeckst orbeckst left a comment

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Looking good, just skip the troublesome test for Python < 3.8

EDIT: add entry to CHANGES

mdpow/tests/test_dihedral.py Show resolved Hide resolved
…) to skip test in python<3.8 due to scipy version conflicts when calculating circvar
cadeduckworth added a commit that referenced this pull request Nov 17, 2022
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@orbeckst orbeckst left a comment

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Thanks, looking all good.

I had asked for an update to CHANGES but I realized that your PR only addresses tests, which are internal and not user-facing, so we do not need a CHANGES entry.

@orbeckst orbeckst merged commit 39fd002 into develop Nov 17, 2022
@orbeckst orbeckst deleted the 214_dihedralanalysis-test-issues branch November 17, 2022 16:06
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Well done, thank you @cadeduckworth !

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DihedralAnalysis test_results_recursive2 fails most of the time
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