Add optimal_geometry method

[sofroniewn]

This PR closes #10 by adding an optimal_geometry method to the properties API. It also adds a make_copy method to the Mol and Sol systems. It adds basic tests to cover the make_copy and optimal_geometry.

Overall I tried to match the code, naming, and commenting style of the repo as best I could - feel free to change or request changes on anything you don't like.

One thing I am wondering is if you still like the optimal_geometry name and function descriptions. Alternatives could emphasize that it is a position that is a local minimum of the energy. I don't really mind.

[mfkasim1]

Thank you for your PR! I have several comments, mostly minor and should be easily addressed. Overall, it looks good!

[codecov-commenter]

Codecov Report

Merging #11 (a678f31) into master (864fbe4) will increase coverage by 0.08%.
The diff coverage is 96.72%.

@@            Coverage Diff             @@
##           master      #11      +/-   ##
==========================================
+ Coverage   92.00%   92.09%   +0.08%     
==========================================
  Files          72       72              
  Lines        7505     7564      +59     
==========================================
+ Hits         6905     6966      +61     
+ Misses        600      598       -2     

Flag	Coverage Δ
unittests	92.09% <96.72%> (+0.08%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
dqc/system/base_system.py	71.66% <50.00%> (-0.27%)	⬇️
dqc/api/properties.py	98.94% <100.00%> (+0.09%)	⬆️
dqc/system/mol.py	85.85% <100.00%> (+0.36%)	⬆️
dqc/system/sol.py	93.12% <100.00%> (+2.00%)	⬆️
dqc/test/test_properties.py	100.00% <100.00%> (ø)
dqc/test/test_system.py	98.85% <100.00%> (+0.12%)	⬆️
dqc/utils/datastruct.py	96.42% <0.00%> (+1.19%)	⬆️

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[sofroniewn]

I have pushed what I think are all the requested changes - please let me know if you have any more or if there is anything else you'd like to see changed before merge.

[mfkasim1]

Thanks for the changes. I have several minor comments on the changes like before.
Another thing is the mypy test fails (you can see the red cross next to typestyle test). Can you fix this in this PR? If not, I can fix it after this being merged.
To test it locally, you can just execute in terminal mypy in the same directory as the file mypy.ini.

[mfkasim1]

Please use **kwargs here instead of kwargs to differentiate between method(kwargs) and method(**kwargs)

[sofroniewn]

done

[sofroniewn]

Thanks for the changes. I have several minor comments on the changes like before.

I have now fixed all of those, please let me know if there is anything else or if you want things fixed in a different way.

Another thing is the mypy test fails (you can see the red cross next to typestyle test). Can you fix this in this PR? If not, I can fix it after this being merged.
To test it locally, you can just execute in terminal mypy in the same directory as the file mypy.ini.

I think it might be best if you fix the mypy errors if you can. I'm not so familiar with mypy and the best way to fix them. It looks like there are three

• one around Too many arguments for "BaseQCCalc", which looks like it can be solved by adding an init method to the class (see stackoverflow) but it might be easier if you do that if you like that solution
• two around passing a dict to Mol and Sol respectively. It wasn't clear to me how to do that.

I have allowed edits from maintainers so feel free to directly push to this PR too

[mfkasim1]

Great, thanks for the PR! It looks good to me, so I will merge it once the ci tests are passed. I can do the mypy correction later.