Code

release 0.5.2#1406

Code

Merged

PaulJonasJost merged 29 commits intomainICB-DCM/pyPESTO:mainfrom developICB-DCM/pyPESTO:developCopy head branch name to clipboardMay 31, 2024

+1,153-322

Commits

Commits on Apr 17, 2024

• Fix lagging version number -> 0.5.1

  dweindl

  committed
  2d05621

  Copy full SHA for 2d05621

• move petab imports outside of try/except (#1355)

  Show description for d178070
  

  m-philipps

  and

  dweindl

  authored
  d178070

  Copy full SHA for d178070

Commits on Apr 18, 2024

• Require scipy<1.13.0 for pypesto[pymc] only for python3.9 (#1360) (#1376)

  Show description for ac03f47
  dweindl

  authored
  ac03f47

  Copy full SHA for ac03f47

• Added option to sample startpoints of a problem, from the problem directly. (#1364)

  Show description for 3b1a12f
  

  PaulJonasJost

  and

  m-philipps

  authored
  3b1a12f

  Copy full SHA for 3b1a12f

Commits on Apr 19, 2024

• Relative: fix log of zero for default 0 sigma values (#1377)

  Show description for 3edf785
  

  Doresic

  and

  arrjon

  authored
  3edf785

  Copy full SHA for 3edf785

Commits on May 2, 2024

• Correlation plot with nans (#1365)

  Show description for b95f422
  

  PaulJonasJost

  and

  m-philipps

  authored
  b95f422

  Copy full SHA for b95f422

• ESS optimizers: suppress divide-by-zero warnings; report n_eval (#1380)

  Show description for e197a8b
  dweindl

  authored
  e197a8b

  Copy full SHA for e197a8b

Commits on May 3, 2024

• Require and test python >=3.10 according to NEP 29 (#1379)

  Show description for fc7b615
  

  3 peopleauthored
  fc7b615

  Copy full SHA for fc7b615

• Update deprecated amici imports (#1384)

  dweindl

  authored
  4d81428

  Copy full SHA for 4d81428

• Remove obsolete pymc scipy requirement

  dweindl

  committed
  fbfae2a

  Copy full SHA for fbfae2a

• GHA: use macos-12 runner (#1386)

  Show description for 4f778cc
  dweindl

  authored
  4f778cc

  Copy full SHA for 4f778cc

• SacessOptimizer: collect worker stats (#1381)

  Show description for e4b15be
  dweindl

  authored
  e4b15be

  Copy full SHA for e4b15be

Commits on May 4, 2024

• Fix pypesto.sample.geweke_test.spectrum for nfft<=3 (#1388)

  Show description for cacd525
  dweindl

  authored
  cacd525

  Copy full SHA for cacd525

Commits on May 5, 2024

• GHA: Test macos-14 (#1387)

  Show description for ccc7f72
  dweindl

  authored
  ccc7f72

  Copy full SHA for ccc7f72

Commits on May 6, 2024

• add load method to Hdf5AmiciHistory (#1370)

  Show description for d9aa042
  plakrisenko

  authored
  d9aa042

  Copy full SHA for d9aa042

• Correct header for roadrunner example (#1394)

  Show description for 80ae7fa
  PaulJonasJost

  authored
  80ae7fa

  Copy full SHA for 80ae7fa

Commits on May 7, 2024

• remove random.seed in favor of np.random.seed (#1391)

  Show description for cf3cbc5
  PaulJonasJost

  authored
  cf3cbc5

  Copy full SHA for cf3cbc5

Commits on May 8, 2024

• update readme links (#1399)

  Show description for 18be6e3
  

  m-philipps

  and

  Doresic

  authored
  18be6e3

  Copy full SHA for 18be6e3

Commits on May 14, 2024

• More detailed defaults for problem.get_full_vector (#1393)

  Show description for 9d5c13b
  

  PaulJonasJost

  and

  m-philipps

  authored
  9d5c13b

  Copy full SHA for 9d5c13b

• Doc: Update references (#1292)

  Show description for 1206dc0
  dweindl

  authored
  1206dc0

  Copy full SHA for 1206dc0

Commits on May 15, 2024

• fix #1401 (#1402)

  Show description for 63c5662
  PaulJonasJost

  authored
  63c5662

  Copy full SHA for 63c5662

• Fix in doc of visualise.optimization_stats (#1390)

  Show description for 049493c
  PaulJonasJost

  authored
  049493c

  Copy full SHA for 049493c

Commits on May 16, 2024

• Calling prior in sampling with fixed parameters does not work (#1378)

  Show description for d5fde03
  arrjon

  authored
  d5fde03

  Copy full SHA for d5fde03

• Update test_thermodynamic_integration (#1385)

  Show description for 7fe40ba
  

  3 peopleauthored
  7fe40ba

  Copy full SHA for 7fe40ba

Commits on May 21, 2024

• Variational inference with PyMC (#1306)

  Show description for fefefd5
  arrjon

  authored
  fefefd5

  Copy full SHA for fefefd5

Commits on May 26, 2024

• Saves pypesto and python version to the problem. (#1382)

  Show description for 4222672
  

  PaulJonasJost

  and

  dweindl

  authored
  4222672

  Copy full SHA for 4222672

Commits on May 29, 2024

• Fix JaxObjective (#1400)

  Show description for 0b8417f
  

  3 peopleauthored
  0b8417f

  Copy full SHA for 0b8417f

Commits on May 31, 2024

• prepare release v0.5.2 (#1407)

  Show description for e9c9949
  

  3 peopleauthored
  e9c9949

  Copy full SHA for e9c9949

• Merge branch 'main' into develop

  PaulJonasJost

  authored
  c966568

  Copy full SHA for c966568