Prepare release v0.4.2

[PaulJonasJost]

0.4.2 (2024-01-30)

• General
  • Stabilize tests (Select: reduce test failure frequency #1240, Fix test.util.load_amici_objective / AmiciVersionError #1254)
  • Update type annotations and documentations (Doc: Update/add/fix type annotations in ensemble+predict #1239, Doc: Fix links, typos, grammer, punctuation in doc/example/amici.ipynb #1248, Doc: Prettify petab.select docs #1255, Doc: Update SacessOptimizer #1258, Doc: enable linking to matplotlib & petab-select docs #1251, Doc: Update sphinx/rtd config to enable re-executing notebooks #1268, Doc: Clear amici and conversion reaction notebook output #1275)
  • GHA/Codeowner changes (GHA: Clear PR cache after merge #1260, GHA: Reduce cache size #1261, GHA: Set mpl backend #1259, GHA: Fix install_deps.sh #1262, Set only active maintainers as default codeowners #1285)
  • Update utility functions (delete_nan_inf can handle list input type #1243)
  • Refactor progress bars (Refactor progress bars #1272)
  • Clear Notebook output(Execute all notebooks / clear notebook output #1246, Doc: Use clang on RTD #1277, Doc: Clear hierarchical optimization notebook output #1274, Doc: Clear petab notebook output #1271, Doc: Clear getting-started notebook output #1276, Doc: Clear notebook output (fixed parameters, prior definition, store) #1278,)
• Optimize
  • (Sac)ESSOptimizer: History of best objective values ( (Sac)ESSOptimizer: Create history of best objective values #1212)
  • Fix missing fixed parameters in scatter search results (Fix missing fixed parameters in scatter search results #1265)
  • Fix TypeError in pypesto.result.optimize.OptimizerResult.summary if x0 is None (Fix potential TypeError in pypesto.result.optimize.OptimizerResult.summary if x0 is None #1266)
  • ESSOptimizer: Include results for local searches in OptimizeResult (ESSOptimizer: Include results for local searches in OptimizeResult #1270)
• New Feature: Spline Approximation (Feature spline regularization #1222)
• Select
  • Allow for hierarchical problems (Add option for hierarchical models #1241)
  • custom minimize method (Select: custom minimize method #1264)
• Hierarchical
  • Log space startpoint sampling (Hierarchical log space startpoint sampling #1242)
  • Support for box constraints on offset and scaling parameters (Hierarchical optimization: Support for box constraints on offset and scaling parameters #1238)
  • restructuring and add relative to InnerCalculatorCollector (Hierarchical: restructuring and add relative to InnerCalculatorCollector #1245)
• History
  • Support pathlib.Path for result/history files (Support pathlib.Path for result/history files #1247)
  • Extended Amici history (Extended Amici history #1263)
• Visualize
  • Fix time trajectories for hierarchical problems (Fix time trajectory simulation for hierarchical solver #1213)
  • Fix hierarchical parameter plotting for all optimizers (Fix hierarchical parameter plotting for all optimizers #1244)
  • Sacess history plot (Vis: Sacess history plot #1250)
• Objective
  • Fix PEtab.jl version to before 2.5.0 (temporarily) (PEtab.jl makes problems since 2.5.1 #1256)
• PEtab
  • Enable Importer passing verbose to create_model (petab: Enable Importer passing verbose to create_model #1269)
  • PetabImporter: version-specific amici model directories (PetabImporter: version-specific amici model directories #1283)
• Problem
  • Problem: add inner problem names, bounds and hierarchical flag (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 (Use warnings.warn instead of logging.warn when loading Problem from H… #1253)
• Ensemble
  • EnsemblePrediction: remove "no predictor" warning (EnsemblePrediction: remove "no predictor" warning #1293)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (97af270) 84.42% compared to head (e300789) 84.37%.

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Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1299      +/-   ##
===========================================
- Coverage    84.42%   84.37%   -0.05%     
===========================================
  Files          153      153              
  Lines        12455    12455              
===========================================
- Hits         10515    10509       -6     
- Misses        1940     1946       +6     

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[Doresic]

I noticed this quality check fail on my other PR as well. Not sure where it comes from, as it was correct till now. Did the nbqa-black formatter change in any way?

[Doresic]

Looks good, thank you!
We can (or should) also add #1300 and #1297 as those can be already merged.