'MDAnalysis.analysis.nucleicacids' parallelization #4727

talagayev · 2024-10-07T20:48:30Z

Fixes #4670 attempt

Changes made in this Pull Request:

added backends and aggregators to NucPairDist in analysis.nucleicacids
added the client_NucPairDist in conftest.py
added client_NucPairDist in run() in test_nucleicacids.py

Here the Error:

AttributeError: 'WatsonCrickDist' object has no attribute '_res_array' appears for all of the tests where the client_NucPairDist is used, same goes not only for WatsonCrickDist, but also for MinorPairDist and MajorPairDist.

I am a little bit stuck, since I am not sure if I need to modify the analysis.nucleicacids to fix this error, thus I made this PR as a draft to get more input and ideas how to fix this issue :)

PR Checklist

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

Developers certificate of origin

I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

📚 Documentation preview 📚: https://mdanalysis--4727.org.readthedocs.build/en/4727/

added backend and aggregators

added NucPairDist to the conftest.py

added client_NucPairDist to the tests

github-actions · 2024-10-07T20:50:43Z

Linter Bot Results:

Hi @talagayev! Thanks for making this PR. We linted your code and found the following:

There are currently no issues detected! 🎉

pep8speaks · 2024-10-10T00:59:02Z

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

In the file package/MDAnalysis/analysis/nucleicacids.py:

Line 178:1: W293 blank line contains whitespace

Comment last updated at 2024-12-14 22:05:51 UTC

codecov · 2024-10-10T01:12:04Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.63%. Comparing base (c6bfa09) to head (482c6c9).
Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4727      +/-   ##
===========================================
- Coverage    93.65%   93.63%   -0.03%     
===========================================
  Files          177      189      +12     
  Lines        21763    22833    +1070     
  Branches      3065     3065              
===========================================
+ Hits         20382    21379     +997     
- Misses         929     1002      +73     
  Partials       452      452

☔ View full report in Codecov by Sentry.
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yuxuanzhuang

Looking good! Could you also help fix the pep8?

package/MDAnalysis/analysis/nucleicacids.py

talagayev · 2024-10-14T17:27:35Z

Looking good! Could you also help fix the pep8?

Yes, I have now access again to a PC, although with slow internet, so I will adjust it for pep8 and also add the additional stuff that is missing (changelog etc.).

I would also create an additional PR draft for analysis.align, since there I am not sure if it can be parallelized :)

fixing PEP

added versionchanged for addition of parallelization

Added Parallelization of nucleicacids.py and fixed lettering

Addition of mention of modification to self.results.distances

yuxuanzhuang

lgtm!

package/MDAnalysis/analysis/nucleicacids.py

removed _res_dict

moved back _res_dict

removed _res_sel

remove unecessary ,

orbeckst · 2024-10-22T16:25:15Z

@yuxuanzhuang thanks for the review. Could you please shepherd the PR to completion?

(I think we're in feature-freeze for 2.8.0 #4733 but check the issue for updates.)

package/MDAnalysis/analysis/nucleicacids.py

talagayev · 2024-11-26T21:32:26Z

@yuxuanzhuang for this one, since it is also approved it can be merged, but now with the new release the CHANGELOG also changes. should I modify it?

If yes would it be then 2.9.0

IAlibay

Please don't modify the changelog @talagayev - I'm in the process of finalizing the release. Once I've merged in the changelog update for 2.9.0 then folks can merge more things.

talagayev · 2024-11-26T21:48:23Z

Hey @IAlibay, perfect sounds good 😸

IAlibay

Alright you're good to go @talagayev - just update against develop and it should be ok (I'm approving as "unblock" I didn't actually read the contents of this PR sorry).

talagayev · 2024-11-26T23:13:09Z

Alright you're good to go @talagayev - just update against develop and it should be ok (I'm approving as "unblock" I didn't actually read the contents of this PR sorry).

Updated it, should be ready :) All good, was mainly the parallelization implementation similar to some other PR request that I did, with @yuxuanzhuang looking at them

talagayev · 2024-11-26T23:20:04Z

Ah need to move it to 2.9.0 in the CHANGELOG, will do it now

moved to 2.9.0

orbeckst · 2024-12-13T15:59:43Z

@yuxuanzhuang I think this one is good to go but please have a last look over.

package/MDAnalysis/analysis/nucleicacids.py

package/CHANGELOG

yuxuanzhuang · 2024-12-14T23:06:34Z

@talagayev Thanks for your contribution!

talagayev · 2024-12-14T23:08:58Z

@talagayev Thanks for your contribution!

Happy to help :) and thanks to you too, for helping with the PR :)

talagayev added 3 commits October 7, 2024 22:34

Update nucleicacids.py

b00d502

added backend and aggregators

Update conftest.py

dc03a02

added NucPairDist to the conftest.py

Update test_nucleicacids.py

39612c8

added client_NucPairDist to the tests

yuxuanzhuang self-requested a review October 10, 2024 00:08

fix nucl parallel

8feb071

yuxuanzhuang requested changes Oct 14, 2024

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talagayev added 7 commits October 14, 2024 20:10

Update nucleicacids.py

b2d81b0

fixing PEP

Update nucleicacids.py

e30716b

Update nucleicacids.py

883eb1e

added versionchanged for addition of parallelization

Update nucleicacids.py

701ed01

Update conftest.py

82a89f9

Update CHANGELOG

886832e

Added Parallelization of nucleicacids.py and fixed lettering

Update nucleicacids.py

c722ac4

Addition of mention of modification to self.results.distances

talagayev marked this pull request as ready for review October 14, 2024 19:09

yuxuanzhuang approved these changes Oct 18, 2024

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talagayev added 4 commits October 18, 2024 20:18

Update nucleicacids.py

d08347f

removed _res_dict

Update nucleicacids.py

f471ad6

moved back _res_dict

Update nucleicacids.py

140366c

removed _res_sel

Update nucleicacids.py

5a119db

remove unecessary ,

tylerjereddy added Component-Analysis parallelization labels Oct 19, 2024

orbeckst assigned yuxuanzhuang Oct 22, 2024

orbeckst reviewed Oct 23, 2024

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Update package/MDAnalysis/analysis/nucleicacids.py

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IAlibay requested changes Nov 26, 2024

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IAlibay approved these changes Nov 26, 2024

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Merge branch 'MDAnalysis:develop' into nucleic_parallel

7ba976e

talagayev and others added 2 commits November 27, 2024 00:21

Update CHANGELOG

00cb335

moved to 2.9.0

Merge branch 'develop' into nucleic_parallel

0b60c1f

orbeckst reviewed Dec 13, 2024

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orbeckst and others added 2 commits December 13, 2024 09:03

Apply suggestions from code review

047bd8c

Merge remote-tracking branch 'upstream/develop' into nucleic_parallel

482c6c9

RMeli approved these changes Dec 14, 2024

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yuxuanzhuang merged commit 7f686ca into MDAnalysis:develop Dec 14, 2024
23 of 24 checks passed

talagayev deleted the nucleic_parallel branch December 14, 2024 23:09

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'MDAnalysis.analysis.nucleicacids' parallelization #4727

'MDAnalysis.analysis.nucleicacids' parallelization #4727

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'MDAnalysis.analysis.nucleicacids' parallelization #4727

'MDAnalysis.analysis.nucleicacids' parallelization #4727

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