pyPESTO v0.5.0

• General
  • Include pymc in the documentation. (#1305)
  • Ruff Codechecks (#1307)
  • Support RoadRunner as simulator for PEtab problems (#1336, #1347, #1348, #1363)
• Hierarchical
  • Semiquant: Fix spline knot initialization (#1313, #1323)
  • Semiquant: Add spline knots to the optimization result (#1314)
  • Semiquant: fix inner opt tolerance (#1330)
  • Relative: Fix return of relative calculator if sim fails (#1315)
  • Relative: Hierarchical optimization: fix unnecessary simulation (#1327)
  • Relative: Fix return of inner parameters on objective call (#1333)
• Optimize
  • Support ipopt with gradient approximation (#1310)
  • Deprecate CmaesOptimizer in favor of CmaOptimizer (#1311)
  • ESSOptimizer: Respect local_n2 in case of failed initial local search (#1328)
  • Remove CESSOptimizer (#1320)
  • SacessOptimizer: use 'spawn' start method for multiprocessing (#1353)
• PEtab
  • Fix unwanted amici model recompilation in PEtab importer (#1319)
• Sample
  • Adding Thermodynamic Integration (#1326, #1361)
  • Dynesty warnings added (#1324)
  • Dynesty: method to save raw results (#1331)
• Ensembles
  • Ensembles: don't expect OptimizerResult.id to be convertible to int (#1351)
• Misc
  • Updated Code to match dependency updates (#1316, #1344, #1346, #1345)
  • Ignore code formatting in git blame (#1317)
  • Updated deployment method (#1341, #1371, #1373)
  • add pyupgrade to codechecks (#1352)
  • Temporarily require scipy<1.13.0 for pypesto[pymc] (#1360)