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Release v0.5.4#1468

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PaulJonasJost merged 37 commits intomainICB-DCM/pyPESTO:mainfrom developICB-DCM/pyPESTO:developCopy head branch name to clipboardOct 31, 2024

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Commits on Aug 1, 2024

• Bump actions/checkout from 3 to 4 (#1436)

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• Bump actions/setup-python from 4 to 5 (#1437)

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• Bump codecov/codecov-action from 3 to 4 (#1438)

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• Bump julia-actions/cache from 1 to 2 (#1439)

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• Bump julia-actions/setup-julia from 1 to 2 (#1440)

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Commits on Aug 5, 2024

• Bump actions/cache from 3 to 4 (#1443)

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Commits on Aug 13, 2024

• Visualize: allow for log scale of hierarchical parameters for visualization (#1435)

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Commits on Sep 4, 2024

• Removing Aesara from readthedocs (#1453)

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Commits on Sep 5, 2024

• FD objective with fixed parameters (#1446)

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Commits on Sep 9, 2024

• Update references (#1404)

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Commits on Sep 11, 2024

• Removed aesara as supported objective. (#1455)

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Commits on Sep 12, 2024

• Bayes factor Tutorial (#1444)

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Commits on Sep 13, 2024

• Doc: fix formatting (#1456)

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Commits on Sep 15, 2024

• SacessOptimizer: Fix acceptance threshold for objective improvement (#1457)

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Commits on Sep 16, 2024

• SacessOptimizer: expose more hyperparameters + minor fixes (#1459)

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• SacessOptimizer, ESSOptimizer: Bound-normalize parameters for proximity check (#1462)

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Commits on Sep 23, 2024

• More informative info message for start indices. (#1472)

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Commits on Sep 24, 2024

• Petab Importer reforge (#1442)

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Commits on Sep 25, 2024

• Pypesto features in Readme.md updated (#1474)

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Commits on Sep 26, 2024

• Fix #1461: test for bridge sampling (#1473)

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• Use cloudpickle for serializing NegLogParameterPriors (#1467)

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Commits on Sep 30, 2024

• Added HPD calculation to ensemble (#1431)

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Commits on Oct 2, 2024

• Update Python requirement in INSTALL.rst (#1479)

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• ESSOptimizer: Fix recombination bug (#1477)

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Commits on Oct 8, 2024

• ESSOptimizer: Fix bug in go-beyond (#1480)

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• Fix sphinx config (#1483)

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• GHA: trigger CI workflow on merge_group event (#1484)

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• Updating the notebooks (#1470)

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Commits on Oct 10, 2024

• Changes to codeowners discussed at retreat (#1485)

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Commits on Oct 17, 2024

• SacessOptimizer fixes (#1476)

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• GHA: Fix pysb installation failures (#1490)

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Commits on Oct 18, 2024

• Clean up sampling tests (#1486)

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Commits on Oct 22, 2024

• update preprint to article (#1498)

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Commits on Oct 23, 2024

• Profile: improve profiling code (#1447)

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• Updated PEtab.jl to work with version 3.x (#1489)

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Commits on Oct 30, 2024

• Added a deprecated version of create_model (#1502)

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• prepare release v0.5.4 (#1469)

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