From 9e310132153d5ee5a8771b72828a480263b6e786 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Wed, 26 Jun 2024 11:47:33 +0200 Subject: [PATCH 1/2] Require sympy>=1.12.1 for numpy>=2.0 compatibility (#2462) So far, sympy was restricted to 1.11 via pysb, but sympy 1.11 is incompatible with numpy>=2.0 --- python/sdist/pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/sdist/pyproject.toml b/python/sdist/pyproject.toml index f93d0c7e1b..e24bf6811a 100644 --- a/python/sdist/pyproject.toml +++ b/python/sdist/pyproject.toml @@ -16,7 +16,7 @@ description = "Advanced multi-language Interface to CVODES and IDAS" requires-python = ">=3.10" dependencies = [ "cmake-build-extension==0.6.0", - "sympy>=1.9", + "sympy>=1.12.1", "numpy>=1.19.3; python_version=='3.9'", "numpy>=1.21.4; python_version>='3.10'", "numpy>=1.23.2; python_version=='3.11'", From 474b473b33eab4c92b03aca59577e8333aedc2fb Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Wed, 26 Jun 2024 11:48:19 +0200 Subject: [PATCH 2/2] Update AMICI papers (#2466) --- documentation/background.rst | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/documentation/background.rst b/documentation/background.rst index 2a2e748672..f47c077d46 100644 --- a/documentation/background.rst +++ b/documentation/background.rst @@ -32,14 +32,22 @@ publications: * Lakrisenko, Polina, Paul Stapor, Stephan Grein, Łukasz Paszkowski, Dilan Pathirana, Fabian Fröhlich, Glenn Terje Lines, Daniel Weindl, - and Jan Hasenauer. 2022. + and Jan Hasenauer. 2023. **Efficient Computation of Adjoint Sensitivities at Steady-State in ODE Models - of Biochemical Reaction Networks.** *bioRxiv* 2022.08.08.503176. - DOI: `10.1101/2022.08.08.503176 `_. + of Biochemical Reaction Networks.** *PLoS Comput Biol* 19(1): e1010783. + DOI: `10.1371/journal.pcbi.1010783 `_. + +* L. Contento, P. Stapor, D. Weindl, and J. Hasenauer. 2023. + **A more expressive spline representation for SBML models improves code generation performance in AMICI**, + In: Pang, J., Niehren, J. (eds) Computational Methods in Systems Biology. + CMSB 2023. *Lecture Notes in Computer Science*, vol 14137. Springer, Cham. + DOI: `10.1007/978-3-031-42697-1_3 `_. + Preprint available at `bioRxiv `_. + +* Lakrisenko, Polina, Dilan Pathirana, Daniel Weindl, and Jan Hasenauer. 2024. + **Exploration of methods for computing sensitivities in ODE models at dynamic and steady states.** *arXiv:2405.16524 [q-bio.QM]*. + DOI: `10.48550/arXiv.2405.16524 `_. -* L. Contento, P. Stapor, D. Weindl, and J. Hasenauer, "A more expressive spline - representation for SBML models improves code generation performance in AMICI," - bioRxiv, 2023, DOI: `10.1101/2023.06.29.547120 `_. .. note::