prepare release 0.5.2

[PaulJonasJost]

• New Feature: Variational inference with PyMC (Variational inference with PyMC #1306)
• PEtab
  • Import of petab independent of amici (Move petab imports for PetabImporter #1355)
• Problem
  • Added option to sample startpoints of a problem, from the problem directly. (Added option to sample startpoints of a problem, from the problem directly #1364)
  • More detailed defaults for problem.get_full_vector (More detailed defaults for problem.get_full_vector #1393)
  • Save pypesto and python version to the problem. (Saves pypesto and python version to the problem. #1382)
• Objective
  • Fix calling priors in sampling with fixed parameters (Calling prior in sampling with fixed parameters does not work #1378)
• Optimize
  • ESS optimizers: suppress divide-by-zero warnings; report n_eval (ESS optimizers: suppress divide-by-zero warnings; report n_eval #1380)
  • SacessOptimizer: collect worker stats (SacessOptimizer: collect worker stats #1381)
  • Add load method to Hdf5AmiciHistory (add load method to Hdf5AmiciHistory #1370)
• Hierarchical
  • Relative: fix log of zero for default 0 sigma values (Relative: fix log of zero for default 0 sigma values #1377)
• Sample
  • Fix pypesto.sample.geweke_test.spectrum for nfft<=3 (Fix pypesto.sample.geweke_test.spectrum for nfft<=3 #1388)
• Visualize
  • Handle correlation plot with nans (Correlation plot with nans #1365)
• General
  • Remove scipy requirement from pypesto[pymc] (Require scipy<1.13.0 for pypesto[pymc] only for python3.9 (#1360) #1376)
  • Require and test python >=3.10 according to NEP 29 (Require and test python>=3.10 #1379)
  • Fix various warnings (Update deprecated amici imports #1384)
  • Small changes to GHA actions and tests (GHA: use macos-12 runner #1386, GHA: Test macos-14 #1387, fix #1401 #1402, Update test_thermodynamic_integration #1385)
  • Improve Documentation (Correct header for roadrunner example #1394, remove random.seed in favor of np.random.seed #1391, update readme links #1399, Doc: Update references #1292, Fix in doc of visualise.optimization_stats #1390)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.93%. Comparing base (0b8417f) to head (c4e7fd5).

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Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1407      +/-   ##
===========================================
- Coverage    83.98%   83.93%   -0.06%     
===========================================
  Files          160      160              
  Lines        13065    13061       -4     
===========================================
- Hits         10973    10963      -10     
- Misses        2092     2098       +6     

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[m-philipps]

Nice, thanks for preparing.

[FFroehlich]

can we please add (#1400) in this release aswell? I already reviewed but since I also added some test code another maintainer might want to have a second look.

[Doresic]

Looks good! Thanks