Updates from BOUT++ 3D metric PR

[ZedThree]

https://github.com/boutproject/BOUT-dev/pull/2025

I've applied black formatting to this already

This branch was created with the following commands:

git checkout -b coords3d
git reset --hard 2718fabc3
git remote add --fetch bout git@github.com:boutproject/BOUT-dev.git
git cherry-pick -Xsubtree=tools/pylib \
  $(git log --reverse --pretty=format:"%h" --follow 32f402c53..bout/coord3d_merged2 -- tools/pylib/zoidberg)

This is the second attempt -- the first attempt, I used bout/next..bout/coord3d_merged2, but this resulted in some hairy conflicts.