Prepare release v0.5.3

[PaulJonasJost]

• General
  • Notebook on history usage and comparison of multiple results. (Notebook on history usage and comparison of multiple results. #1389)
  • GHA/test improvements (GHA: Enable dependabot for action upgrades #1423, Added test for multiprocessing of roadrunner. #1408, Fixing some warnings #1430)
  • Numpy 2.0 compatibility (Numpy 2.0 compatibility #1420, Handle numpy 2.0 with older packages #1433)
• PEtab
  • Issue a warning if a fixed parameter has a prior defined (NegLogParameterPriors does not evaluate prior density at fixed params #1413)
  • Update to libpetab 0.4.0 (Update to libpetab 0.4.0 #1422)
• Optimize
  • Added a Result object with lazy hdf5 loading (Added a lazy result object. #1421)
• RoadRunner
  • Roadrunner handling of petab issue 0019 (Roadrunner handling of petab issue 0019 #1419)
  • Disentangle amici and roadrunner (Disentangle amici and roadrunner #1429)
• Amici
  • Require return_dict in ObjectiveBase.call_unprocessed (fixes AMICI posterior RData) (Fix return_dict when an AmiciObjective is inside AggregatedObjective #1424)
• Hierarchical
  • Visualize: visualization of estimated observable mapping (Visualize: visualization of estimated observable mapping #1409)
  • Hierarchical: avoid recomputing inner parameters if simulation failed (Hierarchical: avoid recomputing inner parameters if simulation failed #1426)
• Visualization
  • Fixing Aggregated Objective Visualisations (Fixing Aggregated Objective Visualisations #1411)

[codecov-commenter]

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.24%. Comparing base (cda1cca) to head (6cce7f3).

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Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1434      +/-   ##
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- Coverage    83.24%   83.24%   -0.01%     
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  Files          161      161              
  Lines        13396    13396              
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- Hits         11152    11151       -1     
- Misses        2244     2245       +1     

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[Doresic]

Looks good! Everything seems to be there