snake_case

[dweindl]

The previous mix of snake_case and camelCase was a mess. Convert everything to snake_case.

More could be done to make the API more consistent, but I'd rather get this merged asap, to avoid merge hell.

Related to #887.

Also includes:

• some minor documentation fixes
• replacement of public data members by corresponding getters and, where relevant, setters
• swig ignores

[codecov]

Codecov Report

❌ Patch coverage is 82.20742% with 187 lines in your changes missing coverage. Please review.
✅ Project coverage is 75.79%. Comparing base (f005fac) to head (7816454).
⚠️ Report is 117 commits behind head on main.

Files with missing lines	Patch %	Lines
models/model_calvetti_py/main.cpp	0.00%	12 Missing ⚠️
models/model_dirac_py/main.cpp	0.00%	12 Missing ⚠️
models/model_events_py/main.cpp	0.00%	12 Missing ⚠️
models/model_jakstat_adjoint_py/main.cpp	0.00%	12 Missing ⚠️
models/model_nested_events_py/main.cpp	0.00%	12 Missing ⚠️
models/model_neuron_py/main.cpp	0.00%	12 Missing ⚠️
models/model_robertson_py/main.cpp	0.00%	12 Missing ⚠️
models/model_steadystate_py/main.cpp	0.00%	12 Missing ⚠️
src/edata.cpp	91.45%	10 Missing ⚠️
src/forwardproblem.cpp	94.79%	9 Missing ⚠️
... and 19 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2969      +/-   ##
==========================================
- Coverage   77.29%   75.79%   -1.50%     
==========================================
  Files         307      307              
  Lines       19938    19991      +53     
  Branches     1502     1499       -3     
==========================================
- Hits        15411    15153     -258     
- Misses       4514     4825     +311     
  Partials       13       13              

Flag	Coverage Δ
cpp	71.96% <80.17%> (-0.82%)	⬇️
cpp_python	38.21% <34.48%> (-0.07%)	⬇️
petab	39.25% <45.63%> (-0.08%)	⬇️
python	69.53% <78.23%> (-0.81%)	⬇️
sbmlsuite-jax	?

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

Files with missing lines	Coverage Δ
include/amici/abstract_model.h	100.00% <ø> (ø)
include/amici/backwardproblem.h	95.45% <100.00%> (ø)
include/amici/edata.h	100.00% <ø> (ø)
include/amici/forwardproblem.h	97.39% <100.00%> (ø)
include/amici/misc.h	91.30% <100.00%> (ø)
include/amici/model_ode.h	100.00% <ø> (ø)
include/amici/model_state.h	97.11% <100.00%> (ø)
include/amici/newton_solver.h	100.00% <ø> (ø)
include/amici/rdata.h	100.00% <100.00%> (ø)
include/amici/simulation_parameters.h	100.00% <100.00%> (ø)
... and 76 more

... and 6 files with indirect coverage changes

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