Code

Jax export#1861

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FFroehlich merged 94 commits intodevelopAMICI-dev/AMICI:developfrom jax_exportAMICI-dev/AMICI:jax_exportCopy head branch name to clipboardNov 19, 2024

+2,829-55

Commits

Commits on Aug 25, 2022

• basic prototype

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Commits on Aug 26, 2022

• Merge branch 'develop' into jax_export

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• add dimerization example, add second order code, refactor jit

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• remove equinox dependency, list dependencies

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• make jax optional

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• Merge branch 'develop' into jax_export

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  c3a77f7

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• support conservation laws

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  7cd8553

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• fixup

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• fix jit nesting

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• use vmap for vectorization

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• fixups

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• add multithreaded simulation runner

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• fix my

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Commits on Sep 9, 2022

• Merge branch 'develop' into jax_export

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Commits on Sep 13, 2022

• fixes

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Commits on Apr 10, 2024

• merge

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  51812d6

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• fixup merge

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• fix install

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• actually generate code

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• fix

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• fix

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• add better default coefficients, fix jax

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• ignore fujita in jax

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• ignore smith

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Commits on Apr 11, 2024

• optimize & fix bachmann

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• fix import/wokflow

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Commits on Apr 12, 2024

• Update __init__.template.py

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• fix jax imports

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• Update setup.cfg

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• add preequilibration support

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  1ec591c

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Commits on Apr 13, 2024

• fix jax tests

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Commits on Apr 14, 2024

• add filterwarning

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  4125c51

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• fix parameter transformation

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Commits on Oct 19, 2024

• Merge branch 'develop' into jax_export

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  781bb3b

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• reenable ruff format

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• post merge cleanup

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  c01f707

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• "fix" splines

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• Update .pre-commit-config.yaml

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• Merge branch 'develop' into jax_export

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Commits on Oct 21, 2024

• force optimistix 0.0.9

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• Merge branch 'jax_export' of https://github.com/AMICI-dev/AMICI into jax_export

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  d6c5bcd

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• add support for heavyside functions

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  7faae32

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• cleanup & actually run tests

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Commits on Oct 22, 2024

• simply tests + add support for non-dynamic simulation in jax

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Commits on Oct 23, 2024

• Merge branch 'develop' into jax_export

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  7c3aef9

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Commits on Oct 24, 2024

• fix for NONCONST_CLS

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• fix petab path

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• Merge branch 'develop' into jax_export

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• Merge branch 'develop' into jax_export

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  37b9329

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• fixup merge

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Commits on Oct 25, 2024

• support postequilibration

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  2f3834d

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• fixup

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  5366632

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• fix

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• fix gradients

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• fix hessian

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• Update test_petab_benchmark.py

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Commits on Oct 27, 2024

• Merge branch 'develop' into jax_export

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• skip smith in jax

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• exclude more models

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Commits on Nov 9, 2024

• refactor: remove use of edatas

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• update template

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• Update .pre-commit-config.yaml

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Commits on Nov 11, 2024

• Merge branch 'develop' into jax_export

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  4a5e7d2

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Commits on Nov 12, 2024

• fix python jax tests

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  f745be0

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• simplify petab interface

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• add parameter values to model class

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  7292451

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• refactor parameter mapping

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• refactor & simplify

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Commits on Nov 16, 2024

• refsctor

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• update template

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• Update .pre-commit-config.yaml

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  eaae778

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• refactor fix test

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• Update petab.py

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Commits on Nov 17, 2024

• fixups

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  b129c86

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• fixup

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  9b6a62b

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• add documentation and typing

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• add runtime typechecks to jax tests

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• add coverage from benchmark tests

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• add api versioning and reenable jit compilation

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Commits on Nov 18, 2024

• review comments

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• use temporary directories

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• fix doc

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• Update test_jax.py

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• don't generate code if jax/diffrax not available

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• Merge branch 'develop' into jax_export

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Commits on Nov 19, 2024

• add example

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  f7c2c10

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• fix doc

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• fix notebook symlink

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• update notebook

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• Update ExampleJaxPEtab.ipynb

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• Update ExampleJaxPEtab.ipynb

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• fix compilation issue

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• Merge branch 'develop' into jax_export

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• fix

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