[PaulJonasJost]

• Only to be released after merging in Fix CI with amici 1.2.0 and petab 0.10.0 #1804 and Update the required python to 3.12 #1797
• Bumped up amici version to most recent

CHANGELOG

• Breaking changes
  • Remove deprecated PetabImporterRR; use PetabImporter(..., simulator_type="roadrunner") (Remove the deprecated PetabImporterRR #1793)
  • Raise minimum versions of numpy, scipy, pandas, matplotlib, amici (>=1.2) and other optional extras (Update the required python to 3.12 #1797)
  • Gradients of parameters without sensitivities are NaN instead of 0 (Return NaN gradients for parameters without sensitivities #1776)
• PEtab v2 (experimental)
  • Hierarchical optimization for PEtab v2 problems (Hierarchical optimization for the PEtab v2 importer #1740, Hierarchical: validate PEtab v2 problems with relative data #1744)
  • parameter_scales argument for log-scale estimation (Support parameter scales for PEtab v2 problems #1782)
• Hierarchical optimization
  • Fix wrong results for observables with constant offset terms (Support constant unscaled terms in hierarchical observable formulas #1786)
  • Respect noise models of data without inner parameters (Hierarchical: honour noise models of data without inner parameters #1778, Reject non-normal noise with inner parameters in the v1 hierarchical importer #1779)
  • Fix NumericalInnerSolver stopping early for small sigmas (Optimize inner sigmas on log scale in NumericalInnerSolver #1788)
  • Plot observable mappings of offset-only relative observables (Plot observable mappings of offset-only relative observables #1787)
• Other smaller Bugfixes (Avoid deprecated inplace keyword (pandas 3.1) #1798, Fix CI with amici 1.2.0 and petab 0.10.0 #1804, Fix IndexError when mixing user and automatic reference point colors #1759, Fix spurious pairing errors in hierarchical validation on pandas 3 #1768)

[codecov-commenter]

⚠️ Please install the to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 87.02%. Comparing base (3c2a450) to head (748c93c).
❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1805      +/-   ##
==========================================
- Coverage   87.05%   87.02%   -0.03%     
==========================================
  Files         160      160              
  Lines       14383    14383              
==========================================
- Hits        12521    12517       -4     
- Misses       1862     1866       +4     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Doresic]

Looks good! just a couple of adjustments

[Doresic]

I would rename this, it's more that it rejects non-normal noise models for observables with inner parameters (previously silently accepted them)

[Doresic]

add "requires Python>=3.12”?

[PaulJonasJost]

we had this already in the previous release, it was just never enforced.