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 63.26531% with 18 lines in your changes missing coverage. Please review.

Project coverage is 31.75%. Comparing base (bbdeaf3) to head (613244a).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #372      +/-   ##
==========================================
- Coverage   31.80%   31.75%   -0.06%     
==========================================
  Files          90       90              
  Lines       10750    10752       +2     
  Branches     1423     1423              
==========================================
- Hits         3419     3414       -5     
- Misses       7216     7223       +7     
  Partials      115      115              

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[tieneupin]

Looks good!