doc: Fix formatting, update names, fix swig-ignores

[dweindl]

Fix formatting, update object names, fix swig-ignores

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 76.72%. Comparing base (ca04e25) to head (d491ccb).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3156      +/-   ##
==========================================
- Coverage   77.36%   76.72%   -0.64%     
==========================================
  Files         317      317              
  Lines       20629    20629              
  Branches     1483     1483              
==========================================
- Hits        15959    15827     -132     
- Misses       4662     4794     +132     
  Partials        8        8              

Flag	Coverage Δ
cpp	70.44% <ø> (ø)
cpp_python	37.14% <ø> (ø)
petab	47.16% <ø> (ø)
python	68.90% <ø> (ø)
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/model_dimensions.h	100.00% <ø> (ø)
include/amici/solver.h	100.00% <ø> (ø)
python/sdist/amici/sim/sundials/petab/_v2.py	93.20% <ø> (ø)

... and 4 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[FFroehlich]

👍