Fix incorrect initialization for non-constant initial assignments

[dweindl]

Fixes a bug where targets of initial assignments are not initialized correctly if the initial assignment expression is implicitly time-dependent. Fixes #2936.

• eliminate state variables from x0 after replacing rate-of expressions
• implement supposed-to-be static expressions that have non-constant entities in their initial condition as state variables instead of expressions.

[codecov]

Codecov Report

❌ Patch coverage is 95.83333% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 79.02%. Comparing base (032c21a) to head (6996b7e).
⚠️ Report is 110 commits behind head on main.

Files with missing lines	Patch %	Lines
python/sdist/amici/sbml_import.py	92.30%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2939      +/-   ##
==========================================
- Coverage   79.60%   79.02%   -0.59%     
==========================================
  Files         362      362              
  Lines       23157    23175      +18     
  Branches     1588     1588              
==========================================
- Hits        18435    18314     -121     
- Misses       4710     4849     +139     
  Partials       12       12              

Flag	Coverage Δ
cpp	74.96% <95.83%> (-0.02%)	⬇️
cpp_python	33.15% <66.66%> (+0.02%)	⬆️
petab	38.80% <58.33%> (+0.01%)	⬆️
python	73.82% <95.83%> (-0.02%)	⬇️
sbmlsuite-jax	?

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Files with missing lines	Coverage Δ
python/sdist/amici/de_model.py	92.51% <100.00%> (-0.36%)	⬇️
python/sdist/amici/sbml_import.py	80.16% <92.30%> (-11.88%)	⬇️

... and 6 files with indirect coverage changes

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[FFroehlich]

Only apply this to new above?

[FFroehlich]

I think this has to be done in a loop as dict(zip(self._syms["w"], self.eq("w"), strict=True)) subs may introduce new self.sym("x_rdata") variables.

[dweindl]

w should not depend on x_rdata:

AMICI/python/sdist/amici/_codegen/cxx_functions.py

Lines 313 to 319 in e38afde

	"w": _FunctionInfo(
	"realtype *w, const realtype t, const realtype *x, "
	"const realtype *p, const realtype *k, "
	"const realtype *h, const realtype *tcl, const realtype *spl, "
	"bool include_static",
	assume_pow_positivity=True,
	),

Unless the respective substitutions in w are only made later, but I don't think that is the case - the rateOf processing should happen last.