PySB import: Replace all PySB objects by plain sympy objects when cre…

[dweindl]

…ating the DEModel

Ensure that DEModel only contains plain sympy.Symbols, no pysb.Compmenents.

Also, consistently use symbol_with_assumptions.

Closes #3035.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.10%. Comparing base (e4374d8) to head (014aed1).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3072      +/-   ##
==========================================
- Coverage   77.74%   77.10%   -0.64%     
==========================================
  Files         313      313              
  Lines       20670    20678       +8     
  Branches     1500     1500              
==========================================
- Hits        16069    15943     -126     
- Misses       4592     4726     +134     
  Partials        9        9              

Flag	Coverage Δ
cpp	71.19% <94.11%> (+0.01%)	⬆️
cpp_python	37.26% <94.11%> (+0.02%)	⬆️
petab	45.90% <88.23%> (+0.04%)	⬆️
petab_sciml	13.83% <5.88%> (-0.01%)	⬇️
python	69.84% <94.11%> (+0.01%)	⬆️
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/_symbolic/de_model.py	91.86% <ø> (ø)
python/sdist/amici/importers/pysb/__init__.py	94.62% <100.00%> (+0.08%)	⬆️
python/sdist/amici/importers/utils.py	83.33% <100.00%> (-2.52%)	⬇️

... and 4 files with indirect coverage changes

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