Make compatible with numpy>=2

[AdeelH]

Overview

This PR makes a couple of small fixes to make the codebase compatible with numpy>=2. However, it does not update the required numpy version because of #2283. This means that docker images will still be built with numpy 1 for now, but users installing via pip will be able to install it alongside numpy>=2.

Testing Instructions

This was tested by updating to numpy==2.1.3 inside the docker container and then checking that unit and integration tests succeed.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.25%. Comparing base (fb3b199) to head (1b8c4a6).
Report is 4 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2282      +/-   ##
==========================================
- Coverage   90.31%   90.25%   -0.07%     
==========================================
  Files         199      199              
  Lines        9925     9925              
==========================================
- Hits         8964     8958       -6     
- Misses        961      967       +6     

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