Fix issues 231 and 232

[lohedges]

This PR closes #231 and closes #232 and also updates the copyright range in the source.

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have permission to release this code under the GPL3 license: [y]

Suggested reviewers:

@chryswoods

[lohedges]

I keep seeing failures in the CI for checks of the the atom indices involved in the restraints. (In particular, backbone restraints.) This seems to occur for certain Python variants on Linux, e.g. 3.10 and 3.11 above, but doesn't occur locally. It is also not reproducible from run-to-run on the CI.

I can only assume that this has somethng to do with the nucleic residue search added by @fjclark, although the logic looks completely sound. @chryswoods: Can you think of any reason why the search might give inconsistent results. I'm wondering if certain parts are done separately and the result is joined at the end, e.g. perhaps part is overwritten depending on the order of completion. The logic for the backbone search is here.

I saw this error when making the 2023.5.0 release. In that case it only happened with one out of the three Python variants for Linux and went away with a re-run.

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In particular, when failing, it's missing this atom:

In [1]: import BioSimSpace as BSS

In [2]: s = BSS.IO.readMolecules("demo/amber/ala/*")

In [3]: s[0].getAtoms()[s.getRestraintAtoms("backbone")[-1]]
Out[3]: <BioSimSpace.Atom: name='N', molecule=20, index=16>

[lohedges]

As expected, everything passed when re-running the CI. I think I'll merge these fixes for now so that people can take advantage of them, then try to work out what's going on in a separate fix branch.