Release 0.27.0

.github/workflows/test_petab_test_suite.yml

@@ -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
 
 

.github/workflows/test_python_cplusplus.yml

@@ -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
 

.github/workflows/test_python_ver_matrix.yml

@@ -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
@@ -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

CHANGELOG.md

@@ -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)
 

CMakeLists.txt

@@ -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)
 
@@ -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>
 )
 

ThirdParty/sundials/CITATIONS.md

@@ -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}
+}
+```