Update NCDF Reader to read .ncrst Restart Files

[jeremyleung521]

Fixes #5030

Changes made in this Pull Request:

• Updated NCDF Reader to read Amber .ncrst restart files
• Added tests to verify that the ncrst file is readed correctly. The test file I used is created from a .nc file already present in MDAnalysisTest
• Noticed @jpkrowe did not add himself to the changelog, so also added him here.

PR Checklist

• Issue raised/referenced?
• Tests updated/added?
• Documentation updated/added?
• package/CHANGELOG file updated?
• Is your name in package/AUTHORS? (If it is not, add it!)

Developers Certificate of Origin

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

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📚 Documentation preview 📚: https://mdanalysis--5031.org.readthedocs.build/en/5031/

[github-actions]

Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our Code of Conduct and that first time contributors introduce themselves on GitHub Discussions so we can get to know you. You can learn more about participating here. Please also add yourself to package/AUTHORS as part of this PR.

[jeremyleung521]

Turning this PR into a draft for now, because there is a wide-affecting bug with the SingleFrameReaderBase's n_atoms attribute, which is causing things to fail. (#5052) Will wait for that to fix itself before moving forward, as that needs to be fixed for this to be implemented properly.

[orbeckst]

Now that #5052 has been fixed, would it be worthwhile to rebase the PR and see if can continue?

[jeremyleung521]

Regarding the status of this PR:

• The MDAnalysis building failure and the n_atoms variable are both fixed. Those commits are merged in.
• The main code should be done, the old tests from [WIP] Add NCRestart reader #3942 is ported as well
• I need to fix/re-integrate the tests in test_netcdf.py I wrote for the previous code back into the newer version. Will do this in the next couple weeks.
• All tests currently passes

[orbeckst]

Ok, thanks for the explanation.

[yuxuanzhuang]

Thanks lgtm!

[IAlibay]

Sorry I completely lapsed on reviewing this.

I'm unfortunately going to have to put a pause on this so that it doesn't get eagerly merged into the upcoming release. There's a few things I had in my notes I needed to check before we merged this - mostly AMBER format things.