Pypesto

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- **Breaking Changes**
- Remove Aesara support (1453, 1455)
- General
- CI improvements (1436, 1437, 1438, 1439, 1440, 1443, 1473, 1484, 1486, 1490, 1485)
- Update references/documentation (1404, 1456, 1474, 1479, 1483, 1470, 1498)
- Profile
- Improve Profiling Code (1447)
- Visualize
- allow log and/or linear scale for visualization (1435)
- More informative error message for start indices. (1472)
- Optimization
- SacessOptimizer: Fix acceptance threshold for objective improvement (1457)
- SacessOptimizer: expose more hyperparameters + minor fixes (1459, 1476)
- SacessOptimizer, ESSOptimizer: Bound-normalize parameters for proximity check (1462)
- ESSOptimizer: Fix bug in recombination and go-beyond (1477, 1480)
- Objective
- FD-objective correctly working with fixed parameters (1446)
- Petab Importer reforge (1442, 1502)
- Use cloudpickle for serializing NegLogParameterPriors (1467)
- Update PEtab.jl integration to match version 3.X (1489)
- Sampling
- Bayes Factor Tutorial (1444)
- Ensemble
- Added HPD calculation to ensemble (1431)

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* General
* Notebook on history usage and comparison of multiple results. (1389)
* GHA/test improvements (1423, 1408, 1430)
* Numpy 2.0 compatibility (1420, 1433)
* PEtab
* Issue a warning if a fixed parameter has a prior defined (1413)
* Update to libpetab 0.4.0 (1422)
* Optimize
* Added a Result object with lazy hdf5 loading (1421)
* RoadRunner
* Roadrunner handling of petab issue 0019 (1419)
* Disentangle amici and roadrunner (1429)
* Amici
* Require `return_dict` in `ObjectiveBase.call_unprocessed` (fixes AMICI posterior RData) (1424)
* Hierarchical
* Visualize: visualization of estimated observable mapping (1409)
* Hierarchical: avoid recomputing inner parameters if simulation failed (1426)
* Visualization
* Fixing Aggregated Objective Visualisations (1411)

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* **New Feature**: Variational inference with PyMC (1306)
* PEtab
* Import of petab independent of amici (1355)
* Problem
* Added option to sample startpoints for a problem, from the problem directly. (1364)
* More detailed defaults for problem.get_full_vector (1393)
* Save pypesto and python version to the problem. (1382)
* Objective
* Fix calling priors in sampling with fixed parameters (1378)
* Fix JaxObjective (1400)
* Optimize
* ESS optimizers: suppress divide-by-zero warnings; report n_eval (1380)
* SacessOptimizer: collect worker stats (1381)
* Add load method to Hdf5AmiciHistory (1370)
* Hierarchical
* Relative: fix log of zero for default 0 sigma values (1377)
* Sample
* Fix pypesto.sample.geweke_test.spectrum for nfft<=3 (1388)
* Visualize
* Handle correlation plot with nans (1365)
* General
* Remove scipy requirement from pypesto[pymc] (1376)
* Require and test python >=3.10 according to NEP 29 (1379)
* Fix various warnings (1384)
* Small changes to GHA actions and tests (1386, 1387, 1402, 1385)
* Improve Documentation (1394, 1391, 1399, 1292, 1390)

..........

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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)