Dask timeseries prototype

[ljwoods2]

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

• [x] 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.

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

[pep8speaks]

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

• In the file package/MDAnalysis/coordinates/H5MD.py:

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

[github-actions[bot]]

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

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

[codecov[bot]]

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 114 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/analysis/dasktimeseries.py	0.00%	35 Missing :warning:
package/MDAnalysis/coordinates/H5MD.py	12.12%	29 Missing :warning:

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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