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Add support for complex noise formulae in roadrunner #1363

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merged 5 commits into from
Apr 12, 2024

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PaulJonasJost
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This currently assumes two things:

  • The noise formula for one observable is always the same
  • There is no time dependent changes in the parameters of the formula

I think both assumptions are things we make implicitly in PEtab/pyPESTO?

@PaulJonasJost PaulJonasJost self-assigned this Apr 9, 2024
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codecov-commenter commented Apr 9, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.39%. Comparing base (45edfd2) to head (761eb3e).

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Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #1363      +/-   ##
===========================================
- Coverage    84.44%   84.39%   -0.06%     
===========================================
  Files          157      157              
  Lines        12899    12914      +15     
===========================================
+ Hits         10893    10899       +6     
- Misses        2006     2015       +9     

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Looks good!

pypesto/objective/roadrunner/petab_importer_roadrunner.py Outdated Show resolved Hide resolved
@PaulJonasJost PaulJonasJost merged commit 0830e95 into develop Apr 12, 2024
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@PaulJonasJost PaulJonasJost deleted the roadrunner_complexsigma branch April 12, 2024 09:19
@PaulJonasJost PaulJonasJost mentioned this pull request Apr 12, 2024
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dweindl commented Apr 15, 2024

  • There is no time dependent changes in the parameters of the formula

I think both assumptions are things we make implicitly in PEtab/pyPESTO?

I don't think pypesto should assume that without verification.
For PEtab/amici it's just a limitation of amici.

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4 participants