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Dask timeseries prototype #4714

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@ljwoods2 ljwoods2 commented Sep 23, 2024

Fixes #4713

Changes made in this Pull Request:

  • Added a minimal example "DaskTimeseriesAnalysisBase`
  • Modified the H5MDReader to expose a dasktimeseries method
  • Created example notebook

PR Checklist

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

Developers certificate of origin


📚 Documentation preview 📚: https://mdanalysis--4714.org.readthedocs.build/en/4714/

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pep8speaks commented Sep 23, 2024

Hello @ljwoods2! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

Line 815:58: E252 missing whitespace around parameter equals
Line 815:59: E252 missing whitespace around parameter equals
Line 816:20: E128 continuation line under-indented for visual indent
Line 816:52: E252 missing whitespace around parameter equals
Line 816:53: E252 missing whitespace around parameter equals
Line 817:20: E128 continuation line under-indented for visual indent
Line 817:40: E252 missing whitespace around parameter equals
Line 817:41: E252 missing whitespace around parameter equals
Line 817:66: E252 missing whitespace around parameter equals
Line 817:67: E252 missing whitespace around parameter equals
Line 818:20: E128 continuation line under-indented for visual indent
Line 818:39: E252 missing whitespace around parameter equals
Line 818:40: E252 missing whitespace around parameter equals
Line 819:20: E128 continuation line under-indented for visual indent
Line 819:40: E252 missing whitespace around parameter equals
Line 819:41: E252 missing whitespace around parameter equals
Line 826:80: E501 line too long (81 > 79 characters)
Line 841:80: E501 line too long (113 > 79 characters)
Line 858:1: W293 blank line contains whitespace
Line 862:1: W293 blank line contains whitespace

Comment last updated at 2024-10-02 22:17:36 UTC

@ljwoods2 ljwoods2 marked this pull request as draft September 23, 2024 02:22
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github-actions bot commented Sep 23, 2024

Linter Bot Results:

Hi @ljwoods2! 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 ✅ Passed

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/11152430432/job/30998029972


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 Sep 23, 2024

Codecov Report

Attention: Patch coverage is 5.88235% with 64 lines in your changes missing coverage. Please review.

Project coverage is 92.92%. Comparing base (4fafd51) to head (9d12872).
Report is 6 commits behind head on develop.

Files with missing lines Patch % Lines
package/MDAnalysis/analysis/dasktimeseries.py 0.00% 35 Missing ⚠️
package/MDAnalysis/coordinates/H5MD.py 12.12% 29 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #4714      +/-   ##
===========================================
- Coverage    93.54%   92.92%   -0.63%     
===========================================
  Files          173      174       +1     
  Lines        21434    21519      +85     
  Branches      3981     3991      +10     
===========================================
- Hits         20051    19997      -54     
- Misses         929     1059     +130     
- Partials       454      463       +9     

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Expose Dask "lazy timeseries" from compatible readers for full parallelism in analysis
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