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Merge pull request #2554 from dweindl/release_0.27.0
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Release 0.27.0
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dweindl authored Oct 21, 2024
2 parents e89a1de + 8e9f93a commit 638c3ee
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2 changes: 1 addition & 1 deletion .github/workflows/test_petab_test_suite.yml
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Expand Up @@ -79,7 +79,7 @@ jobs:
source ./venv/bin/activate \
&& python3 -m pip uninstall -y petab \
&& python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \
&& python3 -m pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching \
&& python3 -m pip install git+https://github.com/pysb/pysb@master \
&& python3 -m pip install sympy>=1.12.1
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5 changes: 5 additions & 0 deletions .github/workflows/test_python_cplusplus.yml
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Expand Up @@ -38,6 +38,11 @@ jobs:
- name: Set up AMICI C++ libraries
uses: ./.github/actions/setup-amici-cpp

- name: Install libsuitesparse-dev
# We don't need libsuitesparse-dev, but let's have it installed,
# to ensure that its presence does not break the build
run: sudo apt-get install -y libsuitesparse-dev

- name: C++ tests
run: scripts/run-cpp-tests.sh

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18 changes: 10 additions & 8 deletions .github/workflows/test_python_ver_matrix.yml
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Expand Up @@ -25,8 +25,15 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ['3.10', '3.11', '3.12']
experimental: [false]
include:
- python-version: '3.10'
experimental: false
- python-version: '3.11'
experimental: false
- python-version: '3.12'
experimental: false
- python-version: '3.13'
experimental: true

steps:
- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
Expand All @@ -53,12 +60,7 @@ jobs:
# install pysb before sympy to allow for sympy>=1.12 (https://github.com/pysb/pysb/commit/e83937cb8c74afc9b2fa96595b68464946745f33)
- run: source venv/bin/activate && pip3 install git+https://github.com/pysb/pysb

# until sympy>1.12 is released
- run: source venv/bin/activate && pip3 install git+https://github.com/sympy/sympy.git@master
if: matrix.python-version == '3.12'

- run: source venv/bin/activate && pip3 install "sympy>=1.12.1"
if: matrix.python-version != '3.12'
- run: source venv/bin/activate && pip3 install "sympy>1.12"

- name: Get Pooch Cache Directory
id: get-pooch-cache
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35 changes: 35 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -4,6 +4,41 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni

## v0.X Series

### v0.27.0 (2024-10-21)

This release comes with an **updated version of the SUNDIALS package (7.1.1)** (https://github.com/AMICI-dev/AMICI/pull/2513).
For C++ users of some of AMICI's internal RAII classes, this may include some
breaking changes. The Python API is not affected.

*Note regarding **editable** installations (`pip install -e ...`):*
Due to the SUNDIALS update, it will be necessary to clean out some temporary
build directories (at least `ThirdParty/sundials/build/`,
`python/sdist/build/`) before rebuilding the package.

**Fixes**

* Fixed a bug that led to program termination if a root-after-reinitialization
error (potentially also others) occurred at an output timepoint

by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2555

* CMake: Fixes compilation errors for models named `model`

by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2547

* Updated CMake export config, making it easier to use AMICI in CMake projects
and fixing some potential issues with interferring packages

by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2540

* CMake: Set policies for CMake 3.31

by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2539

* Documentation fixes by @FFroehlich, @ChocolateCharlie, @dweindl

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.26.3...v0.27.0


### v0.26.3 (2024-10-03)

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17 changes: 8 additions & 9 deletions CMakeLists.txt
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Expand Up @@ -4,7 +4,7 @@
cmake_minimum_required(VERSION 3.22)
# When updating the policy version, please also update it in
# src/CMakeLists.template.cmake
cmake_policy(VERSION 3.22...3.30)
cmake_policy(VERSION 3.22...3.31)

project(amici)

Expand Down Expand Up @@ -265,28 +265,27 @@ target_compile_definitions(

target_link_libraries(
${PROJECT_NAME}
PUBLIC SUNDIALS::generic_static
SUNDIALS::nvecserial_static
PUBLIC SUNDIALS::nvecserial_static
SUNDIALS::sunmatrixband_static
SUNDIALS::sunmatrixdense_static
SUNDIALS::sunmatrixsparse_static
SUNDIALS::sunlinsolband_static
SUNDIALS::sunlinsoldense_static
SUNDIALS::sunlinsolpcg_static
SUNDIALS::sunlinsolspbcgs_static
SUNDIALS::sunlinsolspfgmr_static
SUNDIALS::sunlinsolspgmr_static
SUNDIALS::sunlinsolsptfqmr_static
SUNDIALS::sunlinsolklu_static
SUNDIALS::sunnonlinsolnewton_static
SUNDIALS::sunnonlinsolfixedpoint_static
SUNDIALS::cvodes_static
SUNDIALS::idas_static
$<$<BOOL:${Boost_CHRONO_FOUND}>:Boost::chrono>
$<$<BOOL:${OpenMP_FOUND}>:OpenMP::OpenMP_CXX>
${CMAKE_DL_LIBS}
PRIVATE
BLAS::BLAS
SUNDIALS::sunnonlinsolnewton_static
SUNDIALS::sunnonlinsolfixedpoint_static
SUNDIALS::sunlinsolklu_static
SUNDIALS::sunlinsolband_static
SUNDIALS::sunlinsoldense_static
SUNDIALS::sunlinsolpcg_static
$<$<BOOL:${SUNDIALS_SUPERLUMT_ENABLE}>:SUNDIALS::sundials_sunlinsolsuperlumt>
)

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119 changes: 119 additions & 0 deletions ThirdParty/sundials/CITATIONS.md
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@@ -0,0 +1,119 @@
# Citing SUNDIALS

We ask users of SUNDIALS to cite the following papers in any publications
reporting work done with SUNDIALS:

```bibtex
@article{gardner2022sundials,
title = {Enabling new flexibility in the {SUNDIALS} suite of nonlinear and differential/algebraic equation solvers},
author = {Gardner, David J and Reynolds, Daniel R and Woodward, Carol S and Balos, Cody J},
journal = {ACM Transactions on Mathematical Software (TOMS)},
publisher = {ACM},
volume = {48},
number = {3},
pages = {1--24},
year = {2022},
doi = {10.1145/3539801}
}
```

```bibtex
@article{hindmarsh2005sundials,
title = {{SUNDIALS}: Suite of nonlinear and differential/algebraic equation solvers},
author = {Hindmarsh, Alan C and Brown, Peter N and Grant, Keith E and Lee, Steven L and Serban, Radu and Shumaker, Dan E and Woodward, Carol S},
journal = {ACM Transactions on Mathematical Software (TOMS)},
publisher = {ACM},
volume = {31},
number = {3},
pages = {363--396},
year = {2005},
doi = {10.1145/1089014.1089020}
}
```

If any GPU features of SUNDIALS were utilized, please also cite:

```bibtex
@article{balos2021enabling,
title = {{Enabling GPU accelerated computing in the SUNDIALS time integration library}},
author = {Balos, Cody J and Gardner, David J and Woodward, Carol S and Reynolds, Daniel R},
journal = {Parallel Computing},
publisher = {Elsevier},
volume = {108},
pages = {102836},
year = {2021},
doi = {10.1016/j.parco.2021.102836}
}
```

When using the ARKODE package from SUNDIALS, please also cite:

```bibtex
@article{reynolds2023arkode,
title = {{ARKODE: A flexible IVP solver infrastructure for one-step methods}},
author = {Reynolds, Daniel R and Gardner, David J and Woodward, Carol S and Chinomona, Rujeko},
journal = {ACM Transactions on Mathematical Software},
volume = {49},
number = {2},
pages = {1--26},
year = {2023},
doi = {10.1145/3594632}
}
```

We also ask that users cite the documentation for the package and version that
they are using rather than the combined SUNDIALS online guide:

```bibtex
@Misc{arkodeDocumentation,
author = {Daniel R. Reynolds and David J. Gardner and Carol S. Woodward and Cody J. Balos},
title = {User Documentation for ARKODE},
year = {2024},
note = {v6.1.1}
}
```

```bibtex
@Misc{cvodeDocumentation,
author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
title = {User Documentation for CVODE},
year = {2024},
note = {v7.1.1}
}
```

```bibtex
@Misc{cvodesDocumentation,
author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
title = {User Documentation for CVODES},
year = {2024},
note = {v7.1.1}
}
```

```bibtex
@Misc{idaDocumentation,
author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
title = {User Documentation for IDA},
year = {2024},
note = {v7.1.1}
}
```

```bibtex
@Misc{idasDocumentation,
author = {Radu Serban and Cosmin Petra and Alan C. Hindmarsh and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
title = {User Documentation for IDAS},
year = {2024},
note = {v6.1.1}
}
```

```bibtex
@Misc{kinsolDocumentation,
author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
title = {User Documentation for KINSOL},
year = {2024},
note = {v7.1.1}
}
```
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