Workaround for PEtab problems with state-dependent noise models

[dweindl]

PEtab does currently not allow observables in noiseFormula and AMICI cannot handle states in sigma expressions. Therefore, where possible, replace species occurring in the error model definition by observableIds.

See also #1788

[codecov]

Codecov Report

Merging #1791 (de392f4) into develop (a6f9894) will increase coverage by 0.05%.
The diff coverage is 0.00%.

❗ Current head de392f4 differs from pull request most recent head b6167e5. Consider uploading reports for the commit b6167e5 to get more accurate results

@@             Coverage Diff             @@
##           develop    #1791      +/-   ##
===========================================
+ Coverage    72.95%   73.00%   +0.05%     
===========================================
  Files           71       71              
  Lines        12237    12238       +1     
===========================================
+ Hits          8927     8934       +7     
+ Misses        3310     3304       -6     

Flag	Coverage Δ
cpp	74.36% <ø> (+0.08%)	⬆️
python	68.19% <0.00%> (-0.02%)	⬇️

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

Impacted Files	Coverage Δ
python/amici/petab_import.py	0.00% <0.00%> (ø)
src/solver_cvodes.cpp	70.52% <0.00%> (+0.16%)	⬆️
src/sundials_matrix_wrapper.cpp	81.83% <0.00%> (+0.83%)	⬆️
src/exception.cpp	81.08% <0.00%> (+5.40%)	⬆️

[FFroehlich]

test with Raia_CancerResearch2011 bechmark model? if gradients don't match for that model just ignore?

[FFroehlich]

test with Raia_CancerResearch2011 bechmark model? if gradients don't match for that model just ignore failure?

[FFroehlich]

test with Raia_CancerResearch2011 bechmark model? if llh value doesn't match just ignore for that model?

[dweindl]

test with Raia_CancerResearch2011 bechmark model? if gradients don't match for that model just ignore?

In its current form, that one uses observables in noiseFormula, not states. So not a good test case (yet).

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

0.0% Coverage
0.0% Duplication