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mark analysis.pca.PCA as not parallelizable #4684

Merged
merged 2 commits into from
Aug 26, 2024
Merged

mark analysis.pca.PCA as not parallelizable #4684

merged 2 commits into from
Aug 26, 2024

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orbeckst
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@orbeckst orbeckst commented Aug 23, 2024 •
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Fixes #4680

Changes made in this Pull Request:

  • PCA explicitly marked as not parallelizable (at least not with simple split-apply-combine)

PR Checklist

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

Developers certificate of origin

📚 Documentation preview 📚: https://mdanalysis--4684.org.readthedocs.build/en/4684/

@orbeckst
mark analysis.pca.PCA as not parallelizable
4db6f27 
- fix #4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
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pep8speaks commented Aug 23, 2024 •
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Hello @orbeckst! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

Line 389:1: E302 expected 2 blank lines, found 1
Line 407:1: W391 blank line at end of file

Comment last updated at 2024-08-26 01:24:16 UTC

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github-actions bot commented Aug 23, 2024 •
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Linter Bot Results:

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

Some issues were found with the formatting of your code.

Code Location Outcome
main package ⚠️ Possible failure
testsuite ⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/10551888204/job/29229933588

Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

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codecov bot commented Aug 23, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.60%. Comparing base (94b1b79) to head (aa31e52).
Report is 38 commits behind head on develop.

Additional details and impacted files 
@@             Coverage Diff             @@
##           develop    #4684      +/-   ##
===========================================
- Coverage    93.62%   93.60%   -0.03%     
===========================================
  Files          173      185      +12     
  Lines        21418    22485    +1067     
  Branches      3978     3978              
===========================================
+ Hits         20052    21046     +994     
- Misses         903      976      +73     
  Partials       463      463

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hmacdope
hmacdope requested changes Aug 24, 2024
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package/CHANGELOG
@@ -55,6 +55,7 @@ Fixes
Enhancements
* Introduce parallelization API to `AnalysisBase` and to `analysis.rms.RMSD` class
(Issue #4158, PR #4304)
* explicitly mark `analysis.pca.PCA` as not parallelizable (Issue #4680)
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I know... but may I respectfully disagree here and suggest that we add anything regarding parallelization underneath the parent entry (Issue #4158)? It makes a lot more sense when you read the CHANGELOG.

If it's too confusing to break our convention here, I am happy to switch, of course.

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No worries

@orbeckst orbeckst self-assigned this Aug 26, 2024
@orbeckst orbeckst merged commit d73995a into develop Aug 26, 2024
22 of 23 checks passed
@orbeckst orbeckst deleted the pca-no-parallel branch August 26, 2024 10:07
yuxuanzhuang pushed a commit to yuxuanzhuang/mdanalysis that referenced this pull request Sep 9, 2024
@orbeckst @yuxuanzhuang
mark analysis.pca.PCA as not parallelizable (MDAnalysis#4684)
dc9654e 
- fix MDAnalysis#4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
- add tests
- update CHANGELOG
hmacdope pushed a commit that referenced this pull request Sep 10, 2024
@yuxuanzhuang @MattTDavies
@IAlibay @orbeckst
Remove GSD from optional test dependencies (#4707)
319b667 
* Fixed high dimensional GroupBase indexing.

* fixed pep8 issues

* Removed sanitisation

* Fix #4687 -- rdkit values in azure CI (#4688)

* Investigate rdkit issue

* Update azure-pipelines.yml

* fix numpy 2.0 import block

* fix imports

* mark analysis.pca.PCA as not parallelizable (#4684)

- fix #4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
- add tests
- update CHANGELOG

* disable gsd

* disable gsd in azure

* reduce timeout and set logical

* fix azure

* restore timeout to 200

---------

Co-authored-by: Matthew Davies <128810112+MattTDavies@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
RMeli pushed a commit to RMeli/mdanalysis that referenced this pull request Oct 3, 2024
@orbeckst @RMeli
mark analysis.pca.PCA as not parallelizable (MDAnalysis#4684)
3a30fa5 
- fix MDAnalysis#4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
- add tests
- update CHANGELOG
RMeli pushed a commit to RMeli/mdanalysis that referenced this pull request Oct 3, 2024
@yuxuanzhuang @MattTDavies
@IAlibay @orbeckst @RMeli
Remove GSD from optional test dependencies (MDAnalysis#4707)
007b211 
* Fixed high dimensional GroupBase indexing.

* fixed pep8 issues

* Removed sanitisation

* Fix MDAnalysis#4687 -- rdkit values in azure CI (MDAnalysis#4688)

* Investigate rdkit issue

* Update azure-pipelines.yml

* fix numpy 2.0 import block

* fix imports

* mark analysis.pca.PCA as not parallelizable (MDAnalysis#4684)

- fix MDAnalysis#4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
- add tests
- update CHANGELOG

* disable gsd

* disable gsd in azure

* reduce timeout and set logical

* fix azure

* restore timeout to 200

---------

Co-authored-by: Matthew Davies <128810112+MattTDavies@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
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MDAnalysis.analysis.pca: Implement parallelization or mark as unparallelizable
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@orbeckst @pep8speaks @hmacdope