[dweindl]

Fix the compilation of models with noise formulas that refer to model expressions (e.g., targets of assignment rules).

sigmay and sigmaz are evaluated without the expressions w, so the generated code referred to undeclared variables. The expressions are now substituted in DEModel._compute_equation (only for noise formulas that contain any), before the existing check for state-dependent noise formulas. That check replaces states by the matching observable; the expressions are now also substituted in the observable formula before solving for the state. Otherwise, expressions that depend on the states (e.g., readout := A in #3384) were rejected at import.

Adds test_noise_formula_with_expression, which checks sigmay, ssigmay and sigmaz for time-resolved and event noise formulas that refer to an expression, including a state-dependent one for sigmay. On main, the model does not compile.

Still not supported: noise formulas that depend on piecewise functions or events (sigmay/sigmaz have no Heaviside argument) or on splines, and state-dependent event noise formulas (also without expressions, e.g., sigma="x * p", since sigmaz has no z argument).

ssigmaz is not checked, since it is never filled in ReturnData (#3380).

Fixes #3377.
Fixes #3384.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79.89%. Comparing base (8181384) to head (4924189).
⚠️ Report is 8 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3379      +/-   ##
==========================================
+ Coverage   79.54%   79.89%   +0.34%     
==========================================
  Files         320      320              
  Lines       22466    22593     +127     
  Branches     1507     1516       +9     
==========================================
+ Hits        17870    18050     +180     
+ Misses       4588     4535      -53     
  Partials        8        8              

Flag	Coverage Δ
cpp	73.97% <100.00%> (+0.39%)	⬆️
cpp_python	35.15% <50.00%> (-0.03%)	⬇️
petab	48.70% <100.00%> (-0.19%)	⬇️
petab_sciml	16.98% <100.00%> (-0.05%)	⬇️
petab_sciml_benchmarks	15.55% <100.00%> (-0.04%)	⬇️
python	72.14% <100.00%> (+0.34%)	⬆️
sbmlsuite	50.98% <ø> (+0.37%)	⬆️

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Files with missing lines	Coverage Δ
python/sdist/amici/_symbolic/de_model.py	93.54% <100.00%> (+0.88%)	⬆️

... and 17 files with indirect coverage changes

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[dweindl]

Superseded by #3388.