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Changes encore.hes() details output #2484

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merged 15 commits into from
Feb 18, 2020
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mtiberti
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Fixes #2465

Changes made in this Pull Request:

  • Removed arrayfication of encore.hes details
  • I'm also changing the condition for which details are returned - they are now always returned without the need to use the details flag. This is more consistent with the behaviour of ces and dres. Previously, None was returned instead if the details flag was False.
  • Changed docs accordingly

PR Checklist

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

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codecov bot commented Jan 31, 2020

Codecov Report

Merging #2484 into develop will increase coverage by 0.11%.
The diff coverage is n/a.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    #2484      +/-   ##
===========================================
+ Coverage    90.56%   90.68%   +0.11%     
===========================================
  Files          170      170              
  Lines        22830    22828       -2     
  Branches      2944     2943       -1     
===========================================
+ Hits         20677    20701      +24     
+ Misses        1559     1540      -19     
+ Partials       594      587       -7     
Impacted Files Coverage Δ
...age/MDAnalysis/analysis/hbonds/hbond_autocorrel.py 87.50% <0.00%> (-0.56%) ⬇️
package/MDAnalysis/core/groups.py 98.38% <0.00%> (+0.09%) ⬆️
package/MDAnalysis/analysis/waterdynamics.py 90.64% <0.00%> (+0.23%) ⬆️
package/MDAnalysis/core/topologyobjects.py 97.87% <0.00%> (+0.35%) ⬆️
package/MDAnalysis/lib/formats/libdcd.pyx 78.96% <0.00%> (+0.64%) ⬆️
package/MDAnalysis/analysis/gnm.py 96.06% <0.00%> (+0.78%) ⬆️
package/MDAnalysis/lib/util.py 88.26% <0.00%> (+0.87%) ⬆️
package/MDAnalysis/analysis/lineardensity.py 83.11% <0.00%> (+1.29%) ⬆️
package/MDAnalysis/coordinates/TRZ.py 83.83% <0.00%> (+1.50%) ⬆️
package/MDAnalysis/analysis/base.py 98.94% <0.00%> (+4.21%) ⬆️

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@orbeckst
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orbeckst commented Feb 3, 2020

@lilyminium would you mind having a quick look and comment if this PR fixes your original issue?

Please feel free to ping me when you need a final review for merge. Thanks.

@lilyminium
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Looks good to me, thanks @mtiberti!

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@lilyminium thanks for the review.

@mtiberti can you please fix the documentation and CHANGELOG – see my comments. Thank you!

@@ -19,6 +19,7 @@ mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira
* 0.21.0

Fixes
* encore.hes() returns non-array details (Issue #2465)
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This is not a fix but a Change because for a user who wants to process the output something changes – please move to Change section.

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Also add to Changes that hes() does not take the details keyword argument anymore.

@@ -48,6 +49,7 @@ Fixes
* Added parmed to setup.py

Enhancements
* encore.hes() always returns details, consistently with ces and dres (Issue #2465)
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Are these really two different things that the PR does? To me it looks like a single entry under Changes.

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orbeckst commented Feb 4, 2020

Can you please also resolve the conflict on CHANGELOG so that it can be merged cleanly?

@lilyminium lilyminium mentioned this pull request Feb 7, 2020
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@mtiberti
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sorry - I hadn't realised the build was failing because of wrong spacing in the docstring. It should be fixed now.

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orbeckst commented Feb 17, 2020

@lilyminium , does this look good to you now? (I don't want to squash-merge without giving you a chance to look, given that @richardjgowers asked for your opinion.)

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Looks great, thank you @mtiberti

(array([[ 0. , 38279683.95892926],
[ 38279683.95892926, 0. ]]), None)
>>> HES, details = encore.hes([ens1, ens2])
>>> print HES
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Could you please just change this to print(HES) for python 3 users?

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Many thanks @lilyminium

@orbeckst orbeckst self-assigned this Feb 18, 2020
@orbeckst orbeckst merged commit 156ca53 into develop Feb 18, 2020
@orbeckst orbeckst deleted the fix_2365_encore_hes_return branch February 18, 2020 07:33
@mtiberti
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Thank you both!

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encore.hes returns an numpy array of a dict
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