Add combination of bonds primitive and trust radius optimiser

[shoubhikraj]

(1) Adds a linear combination of bonds as a primitive
(2) Trust radius quasi-Newton optimiser

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Checklist

• The changes include an associated explanation of how/why
• Test pass
• Documentation has been updated
• Changelog has been updated

[codecov]

Codecov Report

Attention: Patch coverage is 98.45758% with 6 lines in your changes missing coverage. Please review.

Project coverage is 97.43%. Comparing base (76398fc) to head (fb4328b).

Files	Patch %	Lines
autode/opt/optimisers/qa.py	92.53%	5 Missing ⚠️
autode/opt/optimisers/crfo.py	98.91%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           v1.4.4     #345      +/-   ##
==========================================
+ Coverage   97.39%   97.43%   +0.04%     
==========================================
  Files         202      204       +2     
  Lines       23278    23626     +348     
==========================================
+ Hits        22672    23021     +349     
+ Misses        606      605       -1     

Flag	Coverage Δ
unittests	97.43% <98.45%> (+0.04%)	⬆️

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[t-young31]

Looks great – left some small suggestions 🚀

[shoubhikraj]

@t-young31 Hi, do you know why the tests are failing with a RecursionError on a numpy allclose call? I have no idea how this error is happening.

[t-young31]

looks like a major numpy update (https://github.com/duartegroup/autodE/actions/runs/9922667636/job/27421474592?pr=345#step:5:148) – will have a look for a solution.

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edit: Looks like we're hitting:

https://github.com/numpy/numpy/blob/7bff2754f64cb855c39b59cf6d0b7bc51fe49a61/numpy/_core/numeric.py#L2419

autodE/autode/values.py

Line 622 in 2f3af32

and np.allclose(self, other)

♻️

[shoubhikraj]

@t-young31 Could you have one last check before merge please?

[t-young31]

🚀