Added unwrap/wrap transformations

[davidercruz]

Adds a wrap transformation based on atoms.wrap and a unwrap transformation based on @richardjgowers 's _cutil.make_whole
Replaces PR #2020

PR Checklist

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

[jbarnoud]

There may have been a solution to save the previous PR, but this is much easier.

2 comments:

• the test for the compound argument does not test that the behavior is different from one value to the other;
• the linter is unhappy: https://travis-ci.com/MDAnalysis/mdanalysis/jobs/139284717#L645

Except for that, it looks good to me.

[codecov]

Codecov Report

Merging #2038 into develop will increase coverage by <.01%.
The diff coverage is 100%.

@@             Coverage Diff             @@
##           develop    #2038      +/-   ##
===========================================
+ Coverage    89.98%   89.99%   +<.01%     
===========================================
  Files          176      177       +1     
  Lines        22055    22075      +20     
  Branches      2896     2897       +1     
===========================================
+ Hits         19846    19866      +20     
  Misses        1612     1612              
  Partials       597      597

Impacted Files	Coverage Δ
package/MDAnalysis/transformations/wrap.py	100% <100%> (ø)
package/MDAnalysis/transformations/__init__.py	100% <100%> (ø)	⬆️
transformations/__init__.py	100% <0%> (ø)	⬆️

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[orbeckst]

If there are any more changes on this branch you will need to merge or rebase against develop because #2066 was "fixed".

[orbeckst]

@jbarnoud can you please make your comments #2038 (comment) a formal review so that the PR gets a chance to get merged?

[orbeckst]

@davidercruz (and @jbarnoud ?) could you please summarize what needs to be done to get this PR done?

I am not looking for a promise that this gets done over the next weekend/holidays but something that will help to get the work done. This is an open source project so I understand that everyone is short on time and priorities shift but it would be a real shame if this didn't make it into MDAnalysis. It is always possible that someone else might find the energy to finish it (e.g., @ianmkenney in my group has recently been playing with the OTFT) but in this case one should make it easy for others to pick up the work, especially if one has not been able to finish things.

[richardjgowers]

@orbeckst I’m happy to try and help Ian get up to speed after Xmas

…

On Fri, Dec 14, 2018 at 2:39 PM, Oliver Beckstein ***@***.***> wrote: @davidercruz <https://github.com/davidercruz> (and @jbarnoud <https://github.com/jbarnoud> ?) could you please summarize what needs to be done to get this PR done? I am not looking for a promise that this gets done over the next weekend/holidays but something that will help to get the work done. This is an open source project so I understand that everyone is short on time and priorities shift but it would be a real shame if this didn't make it into MDAnalysis. It is always possible that someone else might find the energy to finish it (e.g., @ianmkenney <https://github.com/ianmkenney> in my group has recently been playing with the OTFT) but in this case one should make it easy for others to pick up the work, especially if one has not been able to finish things. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2038 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AI0jByD7_WWXh0arJFIRLfNhnUNF_3gHks5u5AyGgaJpZM4V31eh> .

[davidercruz]

Hi all, the PR is failing due to taking too long on travis. It's probably caused by the tests that use the GRO and TPR systems used in the test_wrap_with_compounds in the test module. This function tests the compound flag for the wrap transformation, and thus requires a test system where the flags group, residues, segments and fragments are applicable.

The transformation themselves are very simple, as they act as a caller for the wrap and unwrap functions of the Atomgroup. I just need someone to review the code and I'll make the changes during the holidays.

Merry Christmas

[orbeckst]

@jbarnoud @richardjgowers @davidercruz any chance that this gets into 0.20.0 #2240 (as we had promised in the 0.19.x blog post)?

[orbeckst]

I merged develop into this branch and updated the CHANGELOG entry (has to go into 0.21).

[orbeckst]

I rewrote the history and rebased against develop.

Merge this branch (don't rebase).

[orbeckst]

I give this a preliminary LGTM. I will approve once CI looks good.

@davidercruz @jbarnoud @richardjgowers and last minute reasons why this should not get merged for 0.21?

[orbeckst]

All tests pass and the basics look sensible, so I give it an "let's run with it".

[orbeckst]

So – this is finally done! Thank you @davidercruz and @jbarnoud !

(Now it just needs to be fast... but that's a different story, starting with #2376.)