Use IDs and names from ReturnData

[dweindl]

• Remove the remainder of the old monkey-patching to store model entity names and IDs on ReturnData for RDataReporting::full.
• Update/simplify plotting functions accordingly
• Update getting-started notebook and documentation

Related to #3107.

[codecov]

Codecov Report

❌ Patch coverage is 30.00000% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.56%. Comparing base (505a137) to head (929c856).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
python/sdist/amici/sim/sundials/plotting.py	0.00%	13 Missing ⚠️
python/sdist/amici/sim/sundials/_numpy.py	85.71%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3112      +/-   ##
==========================================
- Coverage   78.26%   77.56%   -0.70%     
==========================================
  Files         315      315              
  Lines       20487    20482       -5     
  Branches     1484     1484              
==========================================
- Hits        16034    15887     -147     
- Misses       4445     4587     +142     
  Partials        8        8              

Flag	Coverage Δ
cpp	71.69% <30.00%> (-0.04%)	⬇️
cpp_python	37.85% <0.00%> (+<0.01%)	⬆️
petab	46.56% <0.00%> (+0.01%)	⬆️
petab_sciml	13.93% <0.00%> (+<0.01%)	⬆️
python	70.35% <30.00%> (-0.03%)	⬇️
sbmlsuite-jax	?

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

Files with missing lines	Coverage Δ
python/sdist/amici/sim/sundials/_numpy.py	88.46% <85.71%> (+1.04%)	⬆️
python/sdist/amici/sim/sundials/plotting.py	0.00% <0.00%> (ø)

... and 7 files with indirect coverage changes

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[FFroehlich]

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