Fix future warning from GSDReader, go cutting edge

[richardjgowers]

Fixes #4152

Changes made in this Pull Request:

PR Checklist

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

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📚 Documentation preview 📚: https://mdanalysis--4153.org.readthedocs.build/en/4153/

[IAlibay]

What's the regression like here? i.e. what minimum version of gsd will work here?

[codecov]

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (b943ca0) 93.61% compared to head (2fc3b58) 93.61%.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #4153   +/-   ##
========================================
  Coverage    93.61%   93.61%           
========================================
  Files          193      193           
  Lines        25170    25170           
  Branches      4059     4059           
========================================
  Hits         23562    23562           
  Misses        1092     1092           
  Partials       516      516           

Impacted Files	Coverage Δ
package/MDAnalysis/coordinates/GSD.py	91.89% <100.00%> (ø)
package/MDAnalysis/topology/GSDParser.py	92.85% <100.00%> (ø)

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[IAlibay]

The minimum numpy failure highlights the issue here, we can't make this change within the current NEP29 window.

[IAlibay]

Next NEP29 window is June 23 - let's try this after 2.5 gets released

[IAlibay]

So the 'r' writing mode was only introduced in the very latest version of GSD (released like 2 weeks ago). I don't know what the best approach is here - do we force folks to install the latest GSD, or do we leave it for now and accept that we are going to get a futurewarning for some cases? Or we support both the old and new version of gsd and switch between the two modes as necessary.

[IAlibay]

@richardjgowers I'mk going to use this PR as the place to test GSD 3.0.1. My view here is that now that it's not a core dependency we can just go cutting edge (if CI works)?

[github-actions]

Linter Bot Results:

Hi @richardjgowers! 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/5387612556/jobs/9779169252

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

[IAlibay]

Of course, NEP29...

can't self approve

[orbeckst]

Generally ok with the approach.

If we normally announce version bumps in deps then we should add a note to CHANGELOG but I leave this to you.

[orbeckst]

Failures such as

E       AttributeError: module 'gsd' has no attribute '__version__'

I am going to revoke my unconditional "approve" until these issues are addressed.

[orbeckst]

I am cool with gsd > 3.0.0 but the test failures need to be fixed first.