Update to work with current versions of the packages and make everything work

[oxinabox]

This PR does a few things:

• Updates to use new version of everything. I didn't try too hard to keep old versions compatible
  • main changes is to Makie
• Run shapes tests to the main tests file
• adds examples to the tests just to make sure they do not error
• Fix it so the convex hull test don't error (but only one passes, idk why)
• Lighting being set on plots is removed: how to set it has changed and makie defaults seem fine,
• makes docs build per the steps on docs CI script
• Adds tests to CI