Refactor types to check with pyright

[jenshnielsen]

Over Christmas I spent a bit of time experimenting with getting types to check with pyright in addition to mypy
This is mainly motivated by having typechecking inline in vscode
There are a number of differences.

• Pyright is somewhat less flexible if a parameter defined within a branch and later used within another branch with the same condition.
• Pyright does not allow inline operations such as - (minus) on numpy arrays unless the dtype is known (could be string etc)
• pyright is less flexible with type narrowing when unknown types are used
• pyright checks code even if the function is not typed at all, so exlude a bunch of stuff that is not typed
• pyright has a way of generation stubs automatically so I have generated stubs to check agains for some of our packages

[codecov]

Codecov Report

Merging #4894 (d115000) into master (56b8a0c) will decrease coverage by 0.91%.
The diff coverage is 58.94%.

@@            Coverage Diff             @@
##           master    #4894      +/-   ##
==========================================
- Coverage   68.32%   67.40%   -0.92%     
==========================================
  Files         340      340              
  Lines       32157    32236      +79     
==========================================
- Hits        21970    21729     -241     
- Misses      10187    10507     +320     

[astafan8]

looks nice! some of the found things are indeed well-found bugs!

[jenshnielsen]

Ipython became typed in #4897 so those stubs should be removed