Code

State reinitialisation in JAX#2619

Code

Merged

FFroehlich merged 29 commits intodevelopAMICI-dev/AMICI:developfrom jax_reinitialisationAMICI-dev/AMICI:jax_reinitialisationCopy head branch name to clipboardDec 8, 2024

+470-124

Commits

Commits on Dec 4, 2024

• disentangle sim & preeq

  FFroehlich

  committed
  14c9d22

• disentangle sim & preeq

  FFroehlich

  committed
  42d4767

Commits on Dec 5, 2024

• run preequilibration once

  FFroehlich

  committed
  f53d4a0

• fix symlink

  FFroehlich

  committed
  019efd6

• separate default dirs for jax/cpp, honour model dir/name

  FFroehlich

  committed
  1613aa2

• fix notebook

  FFroehlich

  committed
  513ca2a

• fix path SNAFU

  FFroehlich

  committed
  69f2fa4

• fix models without preequilibration

  FFroehlich

  committed
  ba37d0b

• fix tests

  FFroehlich

  committed
  1f0af69

• fixup

  FFroehlich

  committed
  08afd8b

• fix doc typehints

  FFroehlich

  committed
  7a780ad

• fix notebook

  FFroehlich

  committed
  9d82a6c

• implement jax-based reinitialisation

  FFroehlich

  committed
  ee84559

• add more defaults & doc

  FFroehlich

  committed
  c6affff

• fix state ids

  FFroehlich

  committed
  757ffa1

• Merge branch 'develop' into jax_reinitialisation

  FFroehlich

  authored
  01e12fc

• fix template

  FFroehlich

  committed
  cf93155

Commits on Dec 6, 2024

• Update model.py

  FFroehlich

  committed
  a946ef3

• breaking jax release

  FFroehlich

  committed
  8fcfc72

• add jax runner to petab testsuite & fix

  FFroehlich

  committed
  2562371

• fix notebook

  FFroehlich

  committed
  8c19f42

• refactor petab test cases

  FFroehlich

  committed
  2be3ef6

• fix parameter unscaling

  FFroehlich

  committed
  7b5383c

• fixups

  FFroehlich

  committed
  4eb18d9

Commits on Dec 7, 2024

• refactor & simplify

  FFroehlich

  committed
  61ab683

• fixup

  FFroehlich

  committed
  01cd6bb

• fix notebook

  FFroehlich

  committed
  17e2ef2

• fixup

  FFroehlich

  committed
  73e5034

• Update petab.py

  FFroehlich

  committed
  c6b9cae