Move petab v1 simulation code to amici.sim...

[dweindl]

Related to #3041.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.42%. Comparing base (a8dfd6e) to head (58df9dd).
⚠️ Report is 57 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3086      +/-   ##
==========================================
- Coverage   78.10%   77.42%   -0.69%     
==========================================
  Files         312      313       +1     
  Lines       20496    20497       +1     
  Branches     1500     1500              
==========================================
- Hits        16008    15869     -139     
- Misses       4479     4619     +140     
  Partials        9        9              

Flag	Coverage Δ
cpp	71.56% <100.00%> (+0.06%)	⬆️
cpp_python	37.61% <100.00%> (+0.09%)	⬆️
petab	46.29% <100.00%> (+<0.01%)	⬆️
petab_sciml	13.72% <0.00%> (-0.16%)	⬇️
python	70.20% <100.00%> (+0.06%)	⬆️
sbmlsuite-jax	?

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Files with missing lines	Coverage Δ
python/sdist/amici/adapters/fiddy.py	78.51% <ø> (ø)
...hon/sdist/amici/importers/petab/_petab_importer.py	89.69% <ø> (ø)
python/sdist/amici/importers/petab/v1/__init__.py	100.00% <ø> (ø)
...thon/sdist/amici/sim/sundials/petab/v1/__init__.py	100.00% <100.00%> (ø)
...n/sdist/amici/sim/sundials/petab/v1/_conditions.py	98.33% <ø> (ø)
...dist/amici/sim/sundials/petab/v1/_petab_problem.py	89.23% <ø> (ø)
.../sdist/amici/sim/sundials/petab/v1/_simulations.py	94.73% <ø> (ø)
...on/sdist/amici/sim/sundials/petab/v1/_simulator.py	96.66% <ø> (ø)
python/tests/petab_/test_petab_problem.py	100.00% <ø> (ø)
python/tests/test_petab_objective.py	100.00% <ø> (ø)
... and 1 more

... and 7 files with indirect coverage changes

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