Remove deprecated functionality

[dweindl]

Removed all deprecated functionality in v1.0.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 76.44%. Comparing base (6d0402a) to head (35fc9a3).
⚠️ Report is 127 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2960      +/-   ##
==========================================
- Coverage   77.13%   76.44%   -0.70%     
==========================================
  Files         307      307              
  Lines       19955    19929      -26     
  Branches     1508     1502       -6     
==========================================
- Hits        15393    15235     -158     
- Misses       4549     4681     +132     
  Partials       13       13              

Flag	Coverage Δ
cpp	72.60% <ø> (-0.03%)	⬇️
cpp_python	38.25% <ø> (+0.06%)	⬆️
petab	39.46% <ø> (+0.05%)	⬆️
python	70.35% <ø> (-0.02%)	⬇️
sbmlsuite-jax	?

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Files with missing lines	Coverage Δ
python/sdist/amici/petab/petab_import.py	100.00% <ø> (ø)
python/sdist/amici/petab/simulations.py	94.89% <ø> (ø)
python/sdist/amici/sbml_import.py	80.14% <ø> (-12.05%)	⬇️

... and 9 files with indirect coverage changes

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