pyPESTO v0.5.5

• Breaking Changes

  • PETab select: There are some deprecated features that will show up as warnings. In addition:

    • The plotting methods ignore some arguments. You will need to reimplement these with the newer approach, which uses
      plotting methods from the PEtab Select library instead. See the model selection notebook for examples.

    • All objects containing multiple models (e.g., dictionaries or lists) are now replaced by petab_select.Models,
      which supports dictionary and list methods.

      To convert your old list of models:

      petab_select.Models(list_of_Model)

• General
  • Exclude nlopt==2.9.0 from setup (#1519)
  • Improve CI (#1521, #1523, #1532, #1536, #1508, #1544, #1531)
  • Update references/documentation (#1506, #1491, #1516, #1543)
  • Docker Image (#1083, #1538)
• Hierarchical
  • Fix no error if inner observable parameter in noise formula & viceversa (#1504)
  • Remove inner datas from relative calculator (#1505)
  • Fix not scaling inner pars when applying to rdatas (#1534)
• Optimization
  • ESSOptimizer: Fix priority for local search startpoints (#1503)
  • Fix NLoptOptimizer.repr (#1518)
  • Improve exception-handling in SacessOptimizer (#1517)
  • Fix ESSOptimizer min of empty sequence (#1510)
  • Don't modify sys.path for amici model imports (#1522)
  • Set OptimizerResult.optimizer in Optimizer.minimize (#1525)
  • SacessOptimizer: More efficient saving of intermediate results (#1529)
• Objective
  • AmiciObjective/PEtab import: Fix plist (#1493)
  • PEtab: Fix warning from fill_in_parameters with fixed parameters (#1509)
  • Amici: Fix handling of PEtab fixed parameters (#1514)
  • Fix get_parameter_prior_dict docstring (#1537)
• Select
  • Support user-provided calibration results (#1338)
  • Problem-specific minimize method for SaCeSS (#1339)
  • Update for the latest PEtab Select version; see example notebook or the PEtab Select repo (#1530)
• Storage
  • Enable writing Optimize(r)Result directly in Writer (#1528)
  • Update parameter scale storage (#1542
• Visualize
  • Fix flatten of observable mapping with one observable (#1515)

pyPESTO v0.5.4

• 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)

pyPESTO v0.5.3

• 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)

pyPESTO v0.5.2

• 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)

pyPESTO v0.5.1

Re-release to fix pypi issues.

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)

pyPESTO v0.4.2

• General
  • Stabilize tests (#1240, #1254)
  • 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)
• Hierarchical
  • Log space startpoint sampling (#1242)
  • Support for box constraints on offset and scaling parameters (#1238)
  • restructuring and add relative to InnerCalculatorCollector (#1245)
• 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)

pyPESTO v0.4.1

• General
  • Documentation (#1214, #1227, #1223, #1230, #1229)
  • Update code to avoid deprecations and warnings (#1217, #1219)
  • Updated codeownership (#1232)
  • 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)

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)

pyPESTO v0.3.3

• 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)