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 73.80952% with 11 lines in your changes missing coverage. Please review.

Project coverage is 27.18%. Comparing base (dd8f649) to head (846f7b5).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #372      +/-   ##
==========================================
- Coverage   27.32%   27.18%   -0.14%     
==========================================
  Files          78       78              
  Lines       10172    10244      +72     
  Branches     1354     1380      +26     
==========================================
+ Hits         2779     2785       +6     
- Misses       7298     7361      +63     
- Partials       95       98       +3     

[tieneupin]

Looks good!