pyPESTO v0.4.0

• General
  • Documentation (#1140, #1146, #1152, #1149, #1192)
  • Updated Jupyter Notebooks (#1141)
  • Update code to avoid deprecations/warnings (#1158, #1184)
  • Updated maintainers and codeownership (#1171, #1170)
  • Improve tests and GHA (#1178, #1185, #1188, #1190, #1193, #1199, #1198, #1197, #1208)
• Profile:
  • Fix problem overwrite of profiling (#1153)
  • Add warning, trying to profile fixed parameter (#1155)
  • ProfileOptions: add some basic integrity checking (#1163)
  • Fix pypesto.profile.parameter_profile incorrectly assuming symmetric bounds (#1166)
  • Improve pypesto/profile/profile_next_guess.py (#1167)
  • Parameter profile: retry optimization in case of failure (#1168)
  • Fix incorrect types in pypesto.result.profile.ProfilerResult (#1210)
• Problem:
  • Add/forward startpoint_kwargs in PetabImporter.create_problem (#1135)
  • Support valid AMICI noise distributions that are invalid in PEtab (#1157)
  • Fix startpoint sampling for PEtab-derived problems with fixed parameters (#1169)
• Optimize
  • Log traceback in case of exceptions during optimizations (#1156)
  • Saccess optimizer improvements (#1177, #1187, #1194, #1195, #1201, #1202, #1204)
  • ESS optimizer improvements (#1176, #1181, #1182)
  • Fix check for allow_failed_starts (#1180)
  • Handle message and exitflag in histories (#1203)
  • Fix indexing error for 0-dimensional HDF5 datasets (#1206)
• Hierarchical:
  • Fix HierarchicalAmiciCalculator.__call__ not setting 'hess' in result (#1161)
• Visualization:
  • Fix legend argument checking for waterfall/parameter/history plots (#1139)
  • Fix waterfall start indices for multiple results (#1200)