Clean up warning capture

[brynpickering]

Fixes reduced coverage reported in #574 (I hope).

It turns out that the warning formatter wasn't being called, maybe some change in Python warnings (but couldn't see anything in the changelog). I've also updated how we capture warnings with our logging module, so it actually pipes warnings to the logger.

Reviewer checklist:

• Test(s) added to cover contribution
• Documentation updated
• Changelog updated
• Coverage maintained or improved

[codecov]

Codecov Report

Attention: Patch coverage is 88.88889% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 95.83%. Comparing base (872978d) to head (e8ec00b).
Report is 5 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #577      +/-   ##
==========================================
- Coverage   95.85%   95.83%   -0.02%     
==========================================
  Files          24       24              
  Lines        3619     3628       +9     
  Branches      788      724      -64     
==========================================
+ Hits         3469     3477       +8     
  Misses         86       86              
- Partials       64       65       +1     

Files	Coverage Δ
src/calliope/model.py	93.62% <100.00%> (-0.03%)	⬇️
src/calliope/preprocess/load.py	92.20% <ø> (ø)
src/calliope/util/logging.py	94.33% <100.00%> (+0.46%)	⬆️
src/calliope/exceptions.py	97.14% <66.66%> (-2.86%)	⬇️