Sensitivities for AlgebraicRule models

[dweindl]

Support for AlgebraicRules was added in #2017. Sensitivity analysis is not yet supported.

This implements the missing Model_DAE::fdxdotdp and Model_DAE::fsxdot, and imports all SBML test suite models with sensitivity code.

Fixes #2102.

[codecov]

Codecov Report

❌ Patch coverage is 14.81481% with 23 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.66%. Comparing base (e728c2a) to head (0240f7f).
⚠️ Report is 63 commits behind head on main.

Files with missing lines	Patch %	Lines
src/model_dae.cpp	16.00%	21 Missing ⚠️
src/solver_idas.cpp	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2101      +/-   ##
==========================================
- Coverage   80.31%   79.66%   -0.65%     
==========================================
  Files         330      330              
  Lines       22641    22660      +19     
  Branches     1532     1533       +1     
==========================================
- Hits        18184    18052     -132     
- Misses       4447     4598     +151     
  Partials       10       10              

Flag	Coverage Δ
cpp	75.44% <14.81%> (-0.07%)	⬇️
cpp_python	33.76% <0.00%> (-0.03%)	⬇️
petab	39.16% <0.00%> (-0.05%)	⬇️
python	74.42% <14.81%> (-0.07%)	⬇️
sbmlsuite-jax	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
include/amici/model_state.h	97.19% <ø> (ø)
src/amici.cpp	74.48% <ø> (ø)
src/solver_idas.cpp	38.71% <0.00%> (ø)
src/model_dae.cpp	31.32% <16.00%> (-2.59%)	⬇️

... and 6 files with indirect coverage changes

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[dweindl]

Current state:

[idas_ic:IDAICFailFlag:-13] The linesearch algorithm failed: step too small or too many backtracks.
[OTHER] AMICI simulation failed: IDA routine IDACalcIC failed with error code -13. 

[FFroehlich]

Current state:

[idas_ic:IDAICFailFlag:-13] The linesearch algorithm failed: step too small or too many backtracks.
[OTHER] AMICI simulation failed: IDA routine IDACalcIC failed with error code -13. 

I remember that we had issues with IC calculation for models where there shouldn't have been problems, even for simulation only.

[dweindl]

I remember that we had issues with IC calculation for models where there shouldn't have been problems, even for simulation only.

After a closer look:

For simulation-only, we are fine for all currently tested models.

For forward sensitivities, we have a variety of issues:

• sundials/src/idas/idas_ic.c:1415: Newton/Linesearch algorithm failed to converge. (-4)
  For the Python-imported Calvetti example (works with the old MATLAB example) if p1 is a parameter
• [idas_ic:IDAICFailFlag:-13] The linesearch algorithm failed: step too small or too many backtracks.
  For SBML test cases 00039, 00040, 00182, 00184, and many more
• [idas:IDASolve:ILL_INPUT] At t = 0.000405875, , mxstep steps taken before reaching tout.
  For SBML test case 00575 and others. (Increasing mxsteps is probably not the solution here.)
• Undeclared dx identifiers d{some x}dt in stau for DAE models with events (potentially related to sympy.matrices.common.ShapeError when importing SBML models with AlgebraicRule and Event #2106)
  For SBML test case 00661 and others. -> Fix dx-dependency of fstau #2897

[dweindl]

• [idas_ic:IDAICFailFlag:-13] The linesearch algorithm failed: step too small or too many backtracks.
  For SBML test cases 00039, 00040, 00182, 00184, and many more

• [idas:IDASolve:ILL_INPUT] At t = 0.000405875, , mxstep steps taken before reaching tout.
  For SBML test case 00575 and others. (Increasing mxsteps is probably not the solution here.)

For future reference: The problem was using the wrong mass matrix. In matlab-imported models, only M_ is initialized, in Python-imported models only MSparse_. Model_DAE::fsxdot was incorrectly using the all-zero M_, resulting in the above failures during IDACalcIC with FSA enabled.

[sonarqubecloud]

Quality Gate failed

Failed conditions
11.9% Duplication on New Code (required ≤ 3%)

See analysis details on SonarQube Cloud