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Release v0.5.5#1545

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PaulJonasJost merged 36 commits intomainICB-DCM/pyPESTO:mainfrom developICB-DCM/pyPESTO:developCopy head branch name to clipboardJan 13, 2025

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Commits on Nov 5, 2024

• ESSOptimizer: Fix priority for local search startpoints (#1503)

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Commits on Nov 8, 2024

• AmiciObjective/PEtab import: Fix plist (#1493)

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Commits on Nov 11, 2024

• Select: support user-provided calibration results (#1338)

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Commits on Nov 12, 2024

• Hierarchical: fix no error if inner observable parameter in noise formula & viceversa (#1504)

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• Hierarchical: remove inner datas from relative calculator (#1505)

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• Select: problem-specific minimize method for SaCeSS (#1339)

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Commits on Nov 19, 2024

• Fix ESSOptimizer min of empty sequence (#1510)

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• PEtab: Fix warning from fill_in_parameters with fixed parameters (#1509)

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• Doc: extend scatter search documentation (#1506)

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Commits on Nov 20, 2024

• Fix handling of PEtab fixed parameters (#1514)

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Commits on Nov 26, 2024

• Exclude nlopt==2.9.0 (#1519)

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• Fix test_deepcopy_objective, test_preeq_guesses (#1521)

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• Update references (#1491)

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Commits on Nov 27, 2024

• Fix NLoptOptimizer.__repr__ (#1518)

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• Improve exception-handling in SacessOptimizer (#1517)

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• CI: don't cache amici; pytest ignore amici_models; passenv BNGPATH (#1523)

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• Update CODEOWNERS (#1516)

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• Don't modify sys.path for amici model imports (#1522)

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Commits on Nov 28, 2024

• Previously, only writing Result was supported. (#1528)

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• Set OptimizerResult.optimizer in Optimizer.minimize (#1525)

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• Push latest pyPESTO (develop) build as image with tag latest to docker.io (#1083)

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Commits on Dec 2, 2024

• Bump actions/checkout from 2 to 4 (#1532)

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• Visualize: fix flatten of observable mapping with one observable (#1515)

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Commits on Dec 9, 2024

• Pin petab-select (#1536)

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Commits on Dec 10, 2024

• SacessOptimizer: More efficient saving of intermediate results (#1529)

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• Fix get_parameter_prior_dict docstring (#1537)

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• Bump codecov/codecov-action from 4 to 5 (#1508)

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Commits on Dec 18, 2024

• Update publish_dockerhub.yml (#1538)

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Commits on Jan 8, 2025

• Merge branch 'main' into develop

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• SciPy 1.15 compatibility (#1544)

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• Doc: IpoptOptimizer (#1543)

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• Bump docker/login-action from 2 to 3 (#1531)

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• Update parameters.py (#1542)

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• Fix not scaling inner pars when applying to rdatas (#1534)

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Commits on Jan 11, 2025

• Select: use the new "standardized" petab_select classes (#1530)

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Commits on Jan 13, 2025

• Prepare release 0.5.5 (#1546)

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