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]

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.

[jeremyleung521]

@IAlibay Since it's been a while, I'll ping you again for review :) It's one of the features that our lab really, really needs and it would be nice if it could be implemented. Thanks!

[IAlibay]

@IAlibay Since it's been a while, I'll ping you again for review :) It's one of the features that our lab really, really needs and it would be nice if it could be implemented. Thanks!

I'm so sorry @jeremyleung521 - it's been very hard to find time to review this. I'm unfortunately OOO for the next couple of weeks, but I will put it at the top of my todo list at the start of March.

Again apologies, I know this has been dragging for a long while.