prepare release v0.5.0

[PaulJonasJost]

Best look at #1342 to check whether everything is included.

• General
  • Include pymc in the documentation. (Include pymc in the documentation. #1305)
  • Ruff Codechecks (Ruff codechecks #1307)
  • Support RoadRunner as simulator for PEtab problems (Roadrunner as simulator #1336, Added deepcpy functionality and small test for roadrunner. #1347)
• Hierarchical
  • Semiquant: Fix spline knot initialization (Semiquant: Fix spline inner parameter initial values #1313, Semiquantitative: Repeat change of #1313 #1323)
  • Semiquant: Add spline knots to the optimization result (Semiquant: Add spline knots to the optimization result #1314)
  • Semiquant: fix inner opt tolerance (Semiquantitative: fix inner opt tolerance  #1330)
  • Relative: Fix return of relative calculator if sim fails (Relative: Fix return of relative calculator if sim fails #1315)
  • Relative: Hierarchical optimization: fix unnecessary simulation (Hierarchical optimization: fix unnecessary simulation #1327)
  • Relative: Fix return of inner parameters on objective call (Relative: Fix return of inner parameters on objective call #1333)
• Optimize
  • Support ipopt with gradient approximation (Support ipopt with gradient approximation #1310)
  • Deprecate CmaesOptimizer in favor of CmaOptimizer (Fix CMAES installation hint #1311)
  • ESSOptimizer: Respect local_n2 in case of failed initial local search (ESSOptimizer: Respect local_n2 in case of failed initial local search #1328)
  • Remove CESSOptimizer (Remove CESSOptimizer #1320)
  • SacessOptimizer: use 'spawn' start method for multiprocessing (SacessOptimizer: use 'spawn' start method #1353)
• PEtab
  • Fix unwanted amici model recompilation in PEtab importer (Fix unwanted amici model recompilation #1319)
• Sample
  • Adding Thermodynamic Integration (Adding Thermodynamic Integration #1326, Fix Chain Burn-in Calculation in Thermodynamic Integration #1361)
  • Dynesty warnings added (Dynesty warnings added #1324)
  • Dynesty: method to save raw results (dynesty: new method to save only the raw dynesty sample results #1331)
• Ensembles
  • Ensembles: don't expect OptimizerResult.id to be convertible to int (Ensembles: don't expect OptimizerResult.id to be convertible to int #1351)
• Misc
  • Updated Code to match dependency updates (Removed amici DeprecationWarnings #1316, Fixed some leftover amici depractions. #1344, fix jax deprecations #1346, Remove some warnings #1345)
  • Ignore code formatting in git blame (ignore git blame for code reformatting #1317)
  • Updated deployment method (Changed to use API token for deployment #1341)
  • add pyupgrade to codechecks (pre-commit: pyupgrade #1352)
  • Temporarily require scipy<1.13.0 for pypesto[pymc] (Require scipy<1.13.0 for pypesto[pymc] #1360)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.38%. Comparing base (0830e95) to head (c823b67).

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Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1366      +/-   ##
===========================================
- Coverage    84.45%   84.38%   -0.08%     
===========================================
  Files          157      157              
  Lines        12914    12914              
===========================================
- Hits         10907    10897      -10     
- Misses        2007     2017      +10     

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[FFroehlich]

would be nice to have #1346 in the next release :)

[PaulJonasJost]

would be nice to have #1346 in the next release :)

@FFroehlich, it is in there (Misc first point), but can move it to an explicit bulletpoint :)

[FFroehlich]

would be nice to have #1346 in the next release :)

@FFroehlich, it is in there (Misc first point), but can move it to an explicit bulletpoint :)

ah, sorry missed that :)

[Doresic]

Looks good! Everything seems to be there.