Compatibility with Zarr Trajectory format [WIP]

[ljwoods2]

Changes made in this Pull Request:

• Modified the ChainedReader's _format_hint to not catch Zarr groups

This is just one way I am proposing to allow future compatibility with the zarrtraj format (https://github.com/Becksteinlab/zarrtraj) that I'm developing in Oliver's lab (and potentially GSOC). Since the zarrtraj format is still in the prototyping phase, there is no urgency to merge this or an alternate solution and I'm open to different ways of approaching it.

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--4557.org.readthedocs.build/en/4557/

[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/8531807262/job/23372008184

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[codecov[bot]]

Codecov Report

Attention: Patch coverage is 83.33333% with 1 line in your changes missing coverage. Please review.

Project coverage is 93.64%. Comparing base (73acc9b) to head (ee09673). Report is 28 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/coordinates/chain.py	83.33%	1 Missing :warning:

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4557      +/-   ##
===========================================
- Coverage    93.66%   93.64%   -0.03%     
===========================================
  Files          168      180      +12     
  Lines        21248    22333    +1085     
  Branches      3917     3917              
===========================================
+ Hits         19902    20913    +1011     
- Misses         888      962      +74     
  Partials       458      458              

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[hmacdope]

@ljwoods2 as I think you know, this will have to be held, until the zarrtraj stuff is more mature. Is there a general case though that this PR solves? E.G chainreader cannot handle objects that are not XX or YY?

[ljwoods2]

@hmacdope Yes, Oliver mentioned this issue: https://github.com/MDAnalysis/mdanalysis/issues/2884. I can come up with a better solution which in general allows object-based trajectory formats being passed in to not be caught by the ChainReader _format_hint

[ljwoods2]

Maybe it's as simple as iterating through all _format_hint() methods except for chainreader before checking chainreader

[orbeckst]

@ljwoods2 instead of "WIP" in the title you can also "convert to draft" to make the state extra clear (and really properly tagged in GH instead using a convention). It also has the advantage that you then only need a click (instead of a title change) when you're ready.

[ljwoods2]

Closing this because zarrtraj accepts filename strings instead of zarr.Group objects now, so no change to format_hint is needed