Pypesto

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* 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)

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* General
* Stabilize tests (1240, 1254, 1300, 1302, 1303)
* Update type annotations and documentations (1239, 1248, 1255, 1258, 1251, 1268, 1275)
* GHA/Codeowner changes (1260, 1261, 1259, 1262, 1285)
* Update utility functions (1243)
* Refactor progress bars (1272)
* Clear Notebook output(1246, 1277, 1274, 1271, 1276, 1278)
* Optimize
* (Sac)ESSOptimizer: History of best objective values (1212)
* Fix missing fixed parameters in scatter search results (1265)
* Fix TypeError in pypesto.result.optimize.OptimizerResult.summary if x0 is None (1266)
* ESSOptimizer: Include results for local searches in OptimizeResult (1270)
* **New Feature**: Spline Approximation (1222)
* Select
* Allow for hierarchical problems (1241)
* custom minimize method (1264)
* Set estimated parameters in petab_select.Models (1287)
* Hierarchical
* Log space startpoint sampling (1242)
* Support for box constraints on offset and scaling parameters (1238)
* restructuring and add relative to InnerCalculatorCollector (1245)
* Semiquantitative: Robust regularization calculation (1297)
* History
* Support pathlib.Path for result/history files (1247)
* Extended Amici history (1263)
* Visualize
* Fix time trajectories for hierarchical problems (1213)
* Fix hierarchical parameter plotting for all optimizers (1244)
* Sacess history plot (1250)
* Objective
* Fix PEtab.jl version to before 2.5.0 (temporarily) (1256)
* PEtab
* Enable Importer passing verbose to create_model (1269)
* PetabImporter: version-specific amici model directories (1283)
* Problem
* Problem: add inner problem names, bounds and hierarchical flag (1282)
* Use warnings.warn instead of logging.warn when loading Problem from HDF5 without an Objective (1253)
* Ensemble
* EnsemblePrediction: remove "no predictor" warning (1293)

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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)