Add stacklevel to warnings

[dweindl]

Make it easier to find out where warnings originate from.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 77.60%. Comparing base (6b05ddd) to head (7bdeb07).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2421      +/-   ##
===========================================
- Coverage    77.63%   77.60%   -0.03%     
===========================================
  Files          324      324              
  Lines        20913    20913              
  Branches      1464     1464              
===========================================
- Hits         16236    16230       -6     
- Misses        4674     4680       +6     
  Partials         3        3              

Flag	Coverage Δ
cpp	73.38% <ø> (-0.03%)	⬇️
cpp_python	34.12% <ø> (ø)
petab	36.70% <ø> (ø)
python	72.14% <ø> (-0.03%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
python/sdist/amici/logging.py	79.16% <ø> (ø)
python/sdist/amici/parameter_mapping.py	0.00% <ø> (ø)
python/sdist/amici/petab/conditions.py	97.43% <ø> (ø)
python/sdist/amici/petab_objective.py	0.00% <ø> (ø)
python/sdist/amici/petab_simulate.py	0.00% <ø> (ø)
python/sdist/amici/petab_util.py	0.00% <ø> (ø)
python/sdist/amici/sbml_import.py	78.77% <ø> (ø)
python/sdist/amici/swig_wrappers.py	92.42% <ø> (ø)

... and 2 files with indirect coverage changes

[FFroehlich]

Hmm, is it not possible to manage this using a context manager? Seems rather difficult to keep stack levels cohesive throughout the package.

[dweindl]

Hmm, is it not possible to manage this using a context manager? Seems rather difficult to keep stack levels cohesive throughout the package.

Finding the precise frame / code location where some deprecated argument is introduced is overkill in my opinion.

For the module-level deprecation warnings, stacklevel=2 always makes sense, because this will show the location of the deprecated import statement.

[FFroehlich]

Hmm, is it not possible to manage this using a context manager? Seems rather difficult to keep stack levels cohesive throughout the package.

Finding the precise frame / code location where some deprecated argument is introduced is overkill in my opinion.

For the module-level deprecation warnings, stacklevel=2 always makes sense, because this will show the location of the deprecated import statement.

Yes, my concern is more that the next time we add a warning, we will forget to add the stacklevel=2 argument.

[dweindl]

my concern is more that the next time we add a warning, we will forget to add the stacklevel=2 argument.

Oh, no worries, I'm happy to add a reminder: https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/