Fix swig shadow warning + other linting issues

[dweindl]

Fixes swig warning

include/amici/simulation_parameters.h:71: Warning 509: Overloaded method amici::SimulationParameters::SimulationParameters(std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >) effectively ignored,
include/amici/simulation_parameters.h:54: Warning 509: as it is shadowed by amici::SimulationParameters::SimulationParameters(std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< int,std::allocator< int > >).

and some other linting warnings.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (a253b17) 76.46% compared to head (1aa2b8c) 76.54%.
Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2261      +/-   ##
===========================================
+ Coverage    76.46%   76.54%   +0.08%     
===========================================
  Files           92       92              
  Lines        14975    14974       -1     
===========================================
+ Hits         11450    11462      +12     
+ Misses        3525     3512      -13     

Flag	Coverage Δ
cpp	73.11% <100.00%> (-0.01%)	⬇️
cpp_python	37.09% <0.00%> (+<0.01%)	⬆️
petab	52.90% <ø> (ø)
python	78.13% <ø> (+0.23%)	⬆️
sbmlsuite	?

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

Files	Coverage Δ
include/amici/logging.h	100.00% <ø> (ø)
include/amici/model.h	61.11% <ø> (ø)
include/amici/simulation_parameters.h	66.66% <ø> (ø)
src/steadystateproblem.cpp	83.66% <100.00%> (-0.04%)	⬇️

... and 1 file with indirect coverage changes