Pypesto

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* General
* Documentation (1214, 1227, 1223, 1230, 1229)
* Update code to avoid deprecations and warnings (1217, 1219)
* Updated codeownership (1232, 1233)
* Update Citation (1221)
* Improved Testing (1218, 1216, 1231)
* History:
* Enable converting MemoryHistory to Hdf5History (1211)
* Profile:
* Code simplification and other clean up (1225)
* Fix incorrect indexing in `pypesto.profile.profile_next_guess.get_reg_polynomial` (1226)
* Optimize
* Warnings for scipy together with laplace prior (1228)
* Visualization:
* Skip the history trace, if trace is empty. Occurs for infinite initial values. (1234)
* Ensemble
* Fix Ensemble.from_optimization_endpoints (1237)

..........

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* 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)

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* Visualize:
* Get optimization result by id (1116)
* Storage:
* allow "{id}" in history storage filename (1118)
* Objective:
* adjusted PEtab.jl syntax to new release (1128, 1131)
* Documentation on PEtab importer updated (1126)
* Ensembles
* Additional option for cutoff calculation (1124)
* Ensembles from optimization endpoints now only takes free parameters (1130)
* General
* Added How to Cite (1125)
* Additional summary option (1134)
* Speed up base tests (1127)

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* Visualize:
* Restrict fval magnitude in waterfall with order_by_id (1090)
* Hierarchical parameter plot fix (1106)
* Fix y-limits on waterfall (1109)
* Sampling:
* Use cloudpickle for pickling dynesty sampler (1094)
* Optimize
* Small fix on hierarchical initialise (1095)
* Fix startpoint sampling for hierarchical optimization (1105)
* SacessOptimizer: retry reading, delay deleting (1110)
* SacessOptimizer: Fix logging with multiprocessing (1112)
* SacessOptimizer: tmpdir option (1115)
* Storage:
* fix storage (1099)
* Examples
* Notebook on differences (1098)
* Problem
* Add startpoint_method to Problem (1093)
* General
* Added new entry to bib (1100)
* PetabJL integration (1089)
* Other platform tests (1113)
* Dokumentation fixes (1120)
* Updated CODEOWNER (1123)

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* Visualize:
* Parameter plot w/ hier. pars, noise estimation for splines (1061)
* Sampling:
* AdaptiveMetropolis failure fix for bounded priors (1065)
* Ensembles
* Speed up Ensemble from History (1063)
* PEtab support:
* Support for petab 0.2.x (1073)
* Remove PetabImporterPysb 1082)
* Objective
* AggregatedObjective: objective-specific kwargs for call_unprocessed (1068)
* Select
* Use predecessor stored in file (1059)
* support petab-select version 0.1.8 (1070)
* Examples
* Synthetic data: update for libpetab-python v0.2.0 (1060)
* Fix error in sampling_diagnostics which led to test failure(1092)
* General
* Test fixes (1064)
* Fix numpy DeprecationWarnings (1076)
* GHA: Fix deprecation warnings (1075)
* Fixed bug on existing file and no overwrite (1046)
* Fix error in bound checking (1081)