Vector bugfix

[scohenjanes5]

This fixes a bug for still images of pbc systems with both axes and custom vectors requested where neither or only one was shown.

I made additional changes to treat these two vector sources the same by combining the sources of vectors early, so a consistent set of transformations can be applied without duplicating work.

I also unified the scattered means by which rotation is applied so it is the same scheme for vectors, the lattice box and all tests.

[codecov-commenter]

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Codecov Report

❌ Patch coverage is 71.11111% with 13 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/xyzrender/api.py	71.42%	5 Missing and 3 partials ⚠️
src/xyzrender/utils.py	33.33%	4 Missing ⚠️
src/xyzrender/viewer.py	83.33%	0 Missing and 1 partial ⚠️

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[aligfellow]

Thanks for your work on this!

I made a couple of changes. Running something like this scaled all vectors, including the crystallographic axes. I added an "is_axis" flag to the VectorArrow, which lets us control the vector annotation scale separate from the axes.

xyzrender examples/structures/caffeine_cell.xyz --cell --vectors examples/strucutres/ethanol_dip.json --vector-scale 10 

Stylistically, the --vectors flag was plural, and other vector_scale was singluar. I changed the vector flag to be singular (sorry if thats annoying), but I've updated the docs/readme to fit that. This now fits stylistically with label.