Migrate to pydantic version 2

[stephen-riggs]

This implements the changes needed for pydantic 2.

In doing this, we also upgrade to sqlalchemy 2, so one change has also been made for that.

Also this removes the procrunner dependency in favour of directly calling subprocess.

Before merging this we need to be able to run MSYS2 or a similar rust-compatible terminal on the microscopes.

Closes #315

[codecov]

Codecov Report

Attention: Patch coverage is 63.01370% with 27 lines in your changes missing coverage. Please review.

Project coverage is 28.33%. Comparing base (b7114c6) to head (e0b0411).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #372      +/-   ##
==========================================
- Coverage   28.34%   28.33%   -0.02%     
==========================================
  Files          71       71              
  Lines        9602     9610       +8     
  Branches     1284     1288       +4     
==========================================
+ Hits         2722     2723       +1     
- Misses       6786     6795       +9     
+ Partials       94       92       -2     

[tieneupin]

Looks good!