Prepare release 0.5.5

[PaulJonasJost]

• General
  • Exclude nlopt==2.9.0 from setup (Exclude nlopt==2.9.0 #1519)
  • Improve CI (Fix test_deepcopy_objective, test_preeq_guesses #1521, CI: don't cache amici; pytest ignore amici_models; passenv BNGPATH #1523, Bump actions/checkout from 2 to 4 #1532, Pin petab-select #1536, Bump codecov/codecov-action from 4 to 5 #1508)
  • Update references/documentation (Doc: extend scatter search documentation #1506, Update references #1491, Update CODEOWNERS #1516)
  • Docker Image (Push latest pyPESTO (develop) build as image with tag latest to docker.io #1083, Update publish_dockerhub.yml #1538)
• Hierarchical
  • Fix no error if inner observable parameter in noise formula & viceversa (Hierarchical: fix no error if inner observable parameter in noise formula & viceversa #1504)
  • Remove inner datas from relative calculator (Hierarchical: remove inner datas from relative calculator #1505)
• Optimization
  • ESSOptimizer: Fix priority for local search startpoints (ESSOptimizer: Fix priority for local search startpoints #1503)
  • Fix NLoptOptimizer.repr (Fix NLoptOptimizer.__repr__ #1518)
  • Improve exception-handling in SacessOptimizer (Improve exception-handling in SacessOptimizer #1517)
  • Fix ESSOptimizer min of empty sequence (Fix ESSOptimizer min of empty sequence #1510)
  • Don't modify sys.path for amici model imports (Don't modify sys.path for amici model imports #1522)
  • Set OptimizerResult.optimizer in Optimizer.minimize (Set OptimizerResult.optimizer in Optimizer.minimize #1525)
  • SacessOptimizer: More efficient saving of intermediate results (SacessOptimizer: More efficient saving of intermediate results #1529)
• Objective
  • AmiciObjective/PEtab import: Fix plist (AmiciObjective/PEtab import: Fix plist #1493)
  • PEtab: Fix warning from fill_in_parameters with fixed parameters (PEtab: Fix warning from fill_in_parameters with fixed parameters #1509)
  • Amici: Fix handling of PEtab fixed parameters (Fix handling of PEtab fixed parameters #1514)
  • Fix get_parameter_prior_dict docstring (Fix get_parameter_prior_dict docstring #1537)
• Select
  • Support user-provided calibration results (Select: support user-provided calibration results #1338)
  • Problem-specific minimize method for SaCeSS (Select: problem-specific minimize method for SaCeSS #1339)
• Storage
  • Enable writing Optimize(r)Result directly in Writer (More flexible OptimizationResultHDF5Writer #1528)
• Visualize
  • Fix flatten of observable mapping with one observable (Visualize: fix flatten of observable mapping with one observable #1515)

[codecov-commenter]

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.35%. Comparing base (e31852b) to head (528fac9).
Report is 2 commits behind head on develop.

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Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1546      +/-   ##
===========================================
- Coverage    84.36%   84.35%   -0.02%     
===========================================
  Files          163      163              
  Lines        14034    14034              
===========================================
- Hits         11840    11838       -2     
- Misses        2194     2196       +2     

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[Doresic]

I think #1542 missing. It was just recently pushed.
Do you want to wait for #1497 and #1534? The latter is already in the queue.

[vwiela]

I would add #1542 and #1534.

PR #1497 is a nice add-on to examples and documentation, but if you don't want to wait, fine for me to leave it for the next release.

[dilpath]

Is including #1530 possible? Otherwise pyPESTO will not be compatible with the latest PEtab Select version