Prepare release v0.4.2

[PaulJonasJost]

0.4.2 (2024-01-30)

• 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)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files

```diff @@ 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 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

[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?