deprecate hydrogen bond analysis in water bridge analysis to master by xiki-tempula · Pull Request #3111 · MDAnalysis/mdanalysis

xiki-tempula · 2021-01-28T09:56:38Z

deprecate hydrogen bond analysis in water bridge analysis.
The hydrogen bond analysis is not used in the original water bridge analysis and I have cleared some reference to the hydrogen bond analysis in the doc sections.
Move water bridge analysis from hbonds to hydorgenbonds

Related to #2913, #2739 and #2746

PR Checklist

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

pep8speaks · 2021-01-28T09:56:42Z

Hello @xiki-tempula! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-03-13 17:09:43 UTC

codecov · 2021-01-28T10:46:59Z

Codecov Report

Merging #3111 (1eecb1a) into master (232b4dc) will increase coverage by 0.84%.
The diff coverage is 97.46%.

@@            Coverage Diff             @@
##           master    #3111      +/-   ##
==========================================
+ Coverage   90.96%   91.81%   +0.84%     
==========================================
  Files         161      167       +6     
  Lines       22181    22699     +518     
  Branches     3198     3198              
==========================================
+ Hits        20177    20841     +664     
- Misses       1381     1774     +393     
+ Partials      623       84     -539

Impacted Files	Coverage Δ
...nalysis/analysis/hydrogenbonds/wbridge_analysis.py	`97.43% <97.43%> (ø)`
...age/MDAnalysis/analysis/hbonds/wbridge_analysis.py	`100.00% <100.00%> (+7.10%)`	⬆️
...kage/MDAnalysis/analysis/hydrogenbonds/__init__.py	`100.00% <100.00%> (ø)`
package/MDAnalysis/topology/tpr/obj.py	`96.82% <0.00%> (-3.18%)`	⬇️
...onality_reduction/DimensionalityReductionMethod.py	`97.14% <0.00%> (-2.86%)`	⬇️
package/MDAnalysis/tests/__init__.py	`100.00% <0.00%> (ø)`
package/MDAnalysis/tests/datafiles.py	`31.25% <0.00%> (ø)`
package/MDAnalysis/analysis/legacy/x3dna.py	`0.00% <0.00%> (ø)`
package/MDAnalysis/due.py	`56.09% <0.00%> (ø)`
... and 88 more

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IAlibay · 2021-01-28T15:22:30Z

Couple of things maintenance things:

I've made this a target for 1.0.2, the code freeze is currently on for 1.0.1, so please don't merge until we release.
I've restarted the failed Travis job, hopefully that'll complete this time.

Quick question @xiki-tempula, did you make any changes to the moved waterbridge analysis code (or it is just a standard move)? Github has done the really annoying thing of doing +1.5k -1.5k so it's pseudo-impossible to review anything from the diff.

xiki-tempula · 2021-01-28T15:24:34Z

@IAlibay Nothing has changed in waterbridge analysis code. Just PEP8 changes.

orbeckst

Looks good (for 1.0.2). Thank you, @xiki-tempula !

* Move water bridge analysis from hbonds to hydrogenbonds (PR #2913) * part of #2739 * deprecate hydrogen bond analysis in water bridge in PR #3111 * Update CHANGELOG Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

orbeckst · 2021-02-17T17:25:35Z

@IAlibay you will merge this PR when 1.0.1 is out, right?

IAlibay · 2021-02-17T18:09:03Z

@IAlibay you will merge this PR when 1.0.1 is out, right?

Yup, I've placed it as a 1.0.2 milestone so we don't forget about it.

IAlibay · 2021-03-13T00:05:50Z

@xiki-tempula if you can update against the current master (probably will need to move the changelog entry to 1.0.2), I think we're at a point where we can merge this.

xiki-tempula · 2021-03-13T11:42:04Z

@IAlibay So I have merged the master and updated the changelog.
It seems that the test failed for py27 importlib.reload is introduced from py33.
I wonder if the master branch still needs to support py27?

IAlibay · 2021-03-13T12:34:21Z

@IAlibay So I have merged the master and updated the changelog.
It seems that the test failed for py27 importlib.reload is introduced from py33.
I wonder if the master branch still needs to support py27?

Yes unfortunately it does. I think you should be able to use reload_module from six.moves instead?

xiki-tempula · 2021-03-13T14:58:08Z

@IAlibay I think everything is fixed now.

IAlibay

Just some thoughts on py2 backward compatibility, and then one changelog addition.

IAlibay · 2021-03-13T16:55:01Z

package/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py

+      of a water bridge existence.
+
+"""
+from __future__ import division


to ensure proper backwards compatibility we'll need six.move's range and zip too (worth having a look for other deprecated py2 things, but I think that's it?).

Probably worth adding absolute_import here too.

I have added them but given that tests have all passed so I think should be fine.

Cheers. Yeah, it's really just for the sake of "correctness".

package/CHANGELOG

IAlibay

Thanks @xiki-tempula I'll merge once CI returns green.

…s#2913) * Move water bridge analysis from hbonds to hydrogenbonds (PR MDAnalysis#2913) * part of MDAnalysis#2739 * deprecate hydrogen bond analysis in water bridge in PR MDAnalysis#3111 * Update CHANGELOG Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

add deprecation

42dafa1

xiki-tempula added 2 commits January 28, 2021 09:58

PEP8

a6194f6

fix warning

e58f623

xiki-tempula marked this pull request as draft January 28, 2021 10:06

xiki-tempula added 2 commits January 28, 2021 10:15

fix doc

d48985e

fix test

5d8521c

xiki-tempula marked this pull request as ready for review January 28, 2021 10:51

xiki-tempula mentioned this pull request Jan 28, 2021

deprecate hydrogen bond analysis in water bridge analysis #2913

Merged

4 tasks

IAlibay added this to the 1.0.2 milestone Jan 28, 2021

IAlibay added the deprecation Deprecated functionality to give advance warning for API changes. label Jan 28, 2021

orbeckst approved these changes Feb 5, 2021

View reviewed changes

orbeckst assigned IAlibay Feb 5, 2021

xiki-tempula added 2 commits March 13, 2021 11:09

Merge remote-tracking branch 'upstream/master' into wb_master

c1f9a7d

Update CHANGELOG

53783c2

xiki-tempula added 2 commits March 13, 2021 11:49

fix py27 issue

f7187b3

rearrange the test

744f277

xiki-tempula added 4 commits March 13, 2021 13:23

py2 compatibkle

20f9af0

check if it is reload related error

7f05f55

from future import division

51ed243

fix pep8

7c600d6

fix doc

1a87df2

IAlibay requested changes Mar 13, 2021

View reviewed changes

for backward compatibility

1eecb1a

IAlibay approved these changes Mar 13, 2021

View reviewed changes

IAlibay merged commit 7ed893d into MDAnalysis:master Mar 13, 2021

xiki-tempula deleted the wb_master branch March 13, 2021 19:50

fiona-naughton added maintainability Component-Analysis labels Sep 26, 2023

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