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Deprecate nucleicacids pair distances results in favour of results.pair_distances [Issue 3744] #3958

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merged 7 commits into from
Dec 16, 2022

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@IAlibay IAlibay commented Dec 15, 2022

Fixes #3744

A bit of a hack on Results, but thankfully we were only deprecating the one thing.

Changes made in this Pull Request:

  • Directly indexing results is deprecated in favor of results.pair_distances. To be removed in v2.5.0
  • (being a bit eager on the 2.5.0 removal, can shift to 3.0.0 if it's really needed)

PR Checklist

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

@IAlibay IAlibay added this to the 2.4.0 milestone Dec 15, 2022
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IAlibay commented Dec 15, 2022

@MDAnalysis/coredevs - last one on the todo list for 2.4.0

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codecov bot commented Dec 15, 2022

Codecov Report

Base: 94.41% // Head: 94.44% // Increases project coverage by +0.03% 🎉

Coverage data is based on head (a6fb3a0) compared to base (1f48778).
Patch coverage: 95.83% of modified lines in pull request are covered.

Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #3958      +/-   ##
===========================================
+ Coverage    94.41%   94.44%   +0.03%     
===========================================
  Files          195      195              
  Lines        25423    25438      +15     
  Branches      3526     3527       +1     
===========================================
+ Hits         24003    24026      +23     
+ Misses        1376     1368       -8     
  Partials        44       44              
Impacted Files Coverage Δ
package/MDAnalysis/analysis/nucleicacids.py 95.38% <95.83%> (-0.62%) ⬇️
package/MDAnalysis/coordinates/DCD.py 100.00% <0.00%> (ø)
package/MDAnalysis/due.py 76.66% <0.00%> (+29.99%) ⬆️

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lgtm, thanks for the hack

package/MDAnalysis/analysis/nucleicacids.py Show resolved Hide resolved
testsuite/MDAnalysisTests/analysis/test_nucleicacids.py Outdated Show resolved Hide resolved
@IAlibay IAlibay mentioned this pull request Dec 15, 2022
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sorry, times should not be in results, I think

There's also low test coverage but I let this go because we remove it soon.

package/MDAnalysis/analysis/nucleicacids.py Show resolved Hide resolved
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IAlibay commented Dec 16, 2022

There's also low test coverage but I let this go because we remove it soon.

Always good to ask for more tests, turns out there were 3 cases I had overlooked!

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lgtm, thanks for the updates

package/MDAnalysis/analysis/nucleicacids.py Show resolved Hide resolved
self.results['times'] = np.array(self._times)
for i in range(self._n_sel):
self.results[i] = np.array(self._res_dict[i])
self.results['times'] = np.array(self.times)
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To be removed in 2.5.0

@IAlibay IAlibay merged commit 5e4dea3 into develop Dec 16, 2022
@IAlibay IAlibay deleted the issue-3744 branch December 16, 2022 01:05
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change nucleicacids results dict
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