add 3d viz to ligandatommapping

[atravitz]

resolves OpenFreeEnergy/openfe#1498

copied over from openfe and named LigandAtomMapping.view_3d()

the plan is to deprecate openfe.utils.visualization_3d.view_mapping_3d

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[codecov]

Codecov Report

❌ Patch coverage is 90.24390% with 8 lines in your changes missing coverage. Please review.
✅ Project coverage is 98.76%. Comparing base (ce63dc3) to head (c0052af).
⚠️ Report is 18 commits behind head on main.

Files with missing lines	Patch %	Lines
gufe/utils.py	75.00%	4 Missing ⚠️
gufe/mapping/ligandatommapping.py	89.28%	3 Missing ⚠️
gufe/visualization/mapping_visualization.py	97.36%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #646      +/-   ##
==========================================
- Coverage   99.05%   98.76%   -0.29%     
==========================================
  Files          40       40              
  Lines        2430     2510      +80     
==========================================
+ Hits         2407     2479      +72     
- Misses         23       31       +8     

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[atravitz]

opinions on view_3d vs view_3D?

[IAlibay]

I like the spirit / implementation of this approach.

The only thing I would bikeshed on is the name of the method, but purely on a "we might need to unify with draw at some point into a single keyword" - although as I say, not a hill I am that invested in.

[IAlibay]

opinions on view_3d vs view_3D?

I prefer D but only very mildly - I'd go with what you prefer, as long as we're consistent.

[mikemhenry]

I think that using this decorator will actually only raise an issue with py3Dmol missing when you actually use the function.

[mikemhenry]

good idea! we will need to update the branch rules after we merge this PR in. I am happy with it for now, but it might be better to call it something like "min deps" so we can keep adding things to the install step. We can wait until the next optional dep we add to do this.