Issues

• Hierarchical: scaling * (...) + 1 passes validation, then the inner solver fits scaling * ((...) + 1)

  bug
  ICB-DCM/pyPESTO#1785 · Filter by author FFroehlich opened on Oct 10, 2026

• PEtab v2: no way to estimate parameters on a log scale

  enhancementPEtab
  ICB-DCM/pyPESTO#1781 · Filter by author FFroehlich opened on Oct 7, 2026

• Hierarchical PEtab v2 problems can't be unpickled after the objective was evaluated

  AMICIbugfixed but not releasedhierarchicalPEtab
  ICB-DCM/pyPESTO#1771 · Filter by author FFroehlich opened on Sep 28, 2026
  2

  

• Hierarchical optimization silently assumes Gaussian noise for PEtab v1 problems

  bughierarchicalPEtab
  ICB-DCM/pyPESTO#1764 · Filter by author FFroehlich opened on Sep 28, 2026

• Remove Hessian from Result per defalt

  question
  ICB-DCM/pyPESTO#1723 · Filter by author Doresic opened on Jun 16, 2026
  1

• Make Fides default

  optimization
  ICB-DCM/pyPESTO#1715 · Filter by author Doresic opened on May 25, 2026
  2

• Add deprecation function

  enhancement
  Feature

  ICB-DCM/pyPESTO#1710 · Filter by author Doresic opened on May 7, 2026

• Julia Tests Failing

  CI
  Task

  ICB-DCM/pyPESTO#1701 · Filter by author PaulJonasJost opened on Mar 18, 2026
  2

• Ensembles with noisy realizations

  enhancement
  Feature

  ICB-DCM/pyPESTO#1699 · Filter by author arrjon opened on Mar 17, 2026
  2

• PymcSampler and fixed parameters

  bugsampling
  ICB-DCM/pyPESTO#1681 · Filter by author dweindl opened on Feb 12, 2026
  4

• Replace Problem.x_guesses?

  ICB-DCM/pyPESTO#1678 · Filter by author dweindl opened on Feb 9, 2026
  3

  

• [Docs] IpoptOptimizer issues when using MPI on Ubuntu 25.04 / 25.10

  documentationoptimization
  ICB-DCM/pyPESTO#1675 · Filter by author stephanmg opened on Jan 23, 2026

• Hard to swap between hierarchical and standard because of sigma

  hierarchicaloptimizationPEtab
  ICB-DCM/pyPESTO#1653 · Filter by author Doresic opened on Dec 4, 2025
  5

• Profiles do not show if dropoff due to bound hitting

  enhancementprofilingvisualization
  ICB-DCM/pyPESTO#1651 · Filter by author Doresic opened on Dec 2, 2025
  2

• Unified Interface: Absolute Tolerance

  enhancementoptimization
  ICB-DCM/pyPESTO#1646 · Filter by author PaulJonasJost opened on Nov 28, 2025
  

• Inconsistent types in get_prediction_dataset

  ICB-DCM/pyPESTO#1625 · Filter by author devoncallan opened on Oct 16, 2025
  3

• Renaming in profiling

  profilingquestion
  ICB-DCM/pyPESTO#1624 · Filter by author plakrisenko opened on Oct 15, 2025
  1

• FAILED test/base/test_roadrunner.py::test_petab_case[0018-sbml-v1.0.0]

  CIPEtab
  ICB-DCM/pyPESTO#1597 · Filter by author dweindl opened on Aug 20, 2025
  3

  

• Fix test/petab/test_petabSimulator.py::test_petab_case[0020-sbml-v1.0.0]

  bugPEtab
  ICB-DCM/pyPESTO#1583 · Filter by author dweindl opened on Jun 24, 2025
  2

• Select: use termination flag from PEtab Select to end model selection

  bug
  ICB-DCM/pyPESTO#1576 · Filter by author dilpath opened on May 13, 2025
  

• Sampling fails due to degenerate covariance matrix in parameter proposal step.

  bugsampling
  ICB-DCM/pyPESTO#1575 · Filter by author vwiela opened on May 13, 2025
  1

• Using parameter_profile with a specific start point

  profiling
  ICB-DCM/pyPESTO#1565 · Filter by author sumiya11 opened on Apr 2, 2025
  3

• Update example/petab_import.ipynb

  documentationPEtab
  ICB-DCM/pyPESTO#1562 · Filter by author dweindl opened on Mar 28, 2025
  1

• Common interface for common optimizer options

  enhancementoptimization
  ICB-DCM/pyPESTO#1553 · Filter by author dweindl opened on Mar 4, 2025
  

• Inconsistent fval calculation in gradient check

  ICB-DCM/pyPESTO#1547 · Filter by author m-philipps opened on Jan 21, 2025
  1