Merge pull request #2690 from AMICI-dev/release_0.31.2

Release 0.31.2

Author: dweindl

.github/workflows/test_valgrind.yml

@@ -14,6 +14,9 @@ on:
 jobs:
   valgrind_cpp:
     name: Valgrind C++
+    # don't run cron job on forks
+    if: github.repository == 'AMICI-dev/AMICI'
+
     runs-on: ubuntu-24.04
 
     strategy:
@@ -61,6 +64,8 @@ jobs:
 
   valgrind_python:
     name: Valgrind Python
+    # don't run cron job on forks
+    if: github.repository == 'AMICI-dev/AMICI'
 
     runs-on: ubuntu-24.04
 

.github/workflows/test_windows.yml

@@ -18,7 +18,7 @@ jobs:
 
     env:
       AMICI_SKIP_CMAKE_TESTS: "TRUE"
-      openBLAS_version: "0.3.19"
+      openBLAS_version: "0.3.29"
       AMICI_DLL_DIRS: "C:\\BLAS\\OpenBLAS\\bin"
       LIB: "C:/BLAS/OpenBLAS/lib"
       CFLAGS: "-nologo"

CHANGELOG.md

@@ -4,6 +4,24 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+### v0.31.2 (2025-04-23)
+
+Bugfix-only release.
+
+* SBML import: Handle unsolvable event triggers
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2686
+* Fixed a clang compiler warning related to variable length arrays
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2688
+* Temporarily require interpax<=0.3.6
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2678
+* Update OpenBLAS installation script to work with CMake>=4
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2679
+* GHA: Don't run cron jobs on forks by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2669
+* Fixed Matlab documentation build with CMake 4.0
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2676
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.31.1...v0.31.2
+
 ### v0.31.1 (2025-03-21)
 
 Bugfix-only release.

README.md

@@ -128,23 +128,25 @@ There is a list of [publications using AMICI](https://amici.readthedocs.io/en/la
 If you used AMICI in your work, we are happy to include
 your project, please let us know via a GitHub issue.
 
-When using AMICI in your project, please cite
+When using AMICI in your project, please cite:
+
 * Fröhlich, F., Weindl, D., Schälte, Y., Pathirana, D., Paszkowski, Ł., Lines, G.T., Stapor, P. and Hasenauer, J., 2021.
   AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models. Bioinformatics, btab227,
   [DOI:10.1093/bioinformatics/btab227](https://doi.org/10.1093/bioinformatics/btab227).
-```
-@article{frohlich2020amici,
-  title={AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models},
-  author={Fr{\"o}hlich, Fabian and Weindl, Daniel and Sch{\"a}lte, Yannik and Pathirana, Dilan and Paszkowski, {\L}ukasz and Lines, Glenn Terje and Stapor, Paul and Hasenauer, Jan},
-  journal = {Bioinformatics},
-  year = {2021},
-  month = {04},
-  issn = {1367-4803},
-  doi = {10.1093/bioinformatics/btab227},
-  note = {btab227},
-  eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab227/36866220/btab227.pdf},
-}
-```
+
+  ```bibtex
+  @article{frohlich2020amici,
+    title={AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models},
+    author={Fr{\"o}hlich, Fabian and Weindl, Daniel and Sch{\"a}lte, Yannik and Pathirana, Dilan and Paszkowski, {\L}ukasz and Lines, Glenn Terje and Stapor, Paul and Hasenauer, Jan},
+    journal = {Bioinformatics},
+    year = {2021},
+    month = {04},
+    issn = {1367-4803},
+    doi = {10.1093/bioinformatics/btab227},
+    note = {btab227},
+    eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab227/36866220/btab227.pdf},
+  }
+  ```
 
 When presenting work that employs AMICI, feel free to use one of the icons in
 [doc/gfx/](https://github.com/AMICI-dev/AMICI/tree/master/doc/gfx),

doc/background.rst

@@ -52,13 +52,13 @@ publications:
 .. note::
 
    Implementation details of the latest AMICI versions may differ from the ones
-   given in the references manuscripts.
+   given in the referenced manuscripts.
 
 
 Third-Party numerical algorithms used by AMICI
 ----------------------------------------------
 
-AMICI uses the following packages from SUNDIALS:
+AMICI uses the following packages from `SUNDIALS <https://computing.llnl.gov/projects/sundials>`__:
 
 * CVODES:
 
@@ -70,7 +70,7 @@ AMICI uses the following packages from SUNDIALS:
 
 * IDAS
 
-AMICI uses the following packages from SuiteSparse:
+AMICI uses the following packages from `SuiteSparse <https://github.com/DrTimothyAldenDavis/SuiteSparse>`__:
 
 * Algorithm 907: **KLU** A Direct Sparse Solver for Circuit Simulation
   Problems. Timothy A. Davis, Ekanathan Palamadai Natarajan,

doc/development.rst

@@ -109,28 +109,10 @@ Python
 
 -  We use Python `type
    hints <https://docs.python.org/3/library/typing.html>`__ for all
-   functions (but not for class attributes, since they are not supported
-   by the current Python doxygen filter). In Python code, type hints
-   should be used instead of doxygen ``@type``.
+   functions and attributes. We do not include any other redundant
+   type annotation in docstrings.
 
-   For function docstrings, follow this format:
-
-   ::
-
-      """One-line description.
-
-      Possible a more detailed description
-
-      Arguments:
-          Argument1: This needs to start on the same line, otherwise the current
-              doxygen filter will fail.
-
-          Returns:
-              Return value
-
-          Raises:
-              SomeError in case of some error.
-      """
+-  We use the `sphinx docstring-style <https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html>`__ for new code.
 
 C++
 ^^^

doc/how_to_cite.rst

@@ -32,12 +32,12 @@ When using AMICI in your project, please cite
      }
 
 When presenting work that employs AMICI, feel free to use one of the icons in
-`documentation/gfx/ <https://github.com/AMICI-dev/AMICI/tree/master/documentation/gfx>`_,
+`documentation/gfx/ <https://github.com/AMICI-dev/AMICI/tree/master/doc/gfx>`_,
 which are available under a
-`CC0 <https://github.com/AMICI-dev/AMICI/tree/master/documentation/gfx/LICENSE.md>`_
+`CC0 <https://github.com/AMICI-dev/AMICI/tree/master/doc/gfx/LICENSE.md>`_
 license:
 
-.. image:: https://raw.githubusercontent.com/AMICI-dev/AMICI/master/documentation/gfx/logo_text.png
-   :target: https://raw.githubusercontent.com/AMICI-dev/AMICI/master/documentation/gfx/logo_text.png
+.. image:: https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/logo_text.png
+   :target: https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/logo_text.png
    :height: 75
    :alt: AMICI LOGO

pytest.ini

@@ -11,7 +11,7 @@ filterwarnings =
     ignore:Conservation laws for non-constant species in models with RateRules are currently not supported and will be turned off.:UserWarning
     ignore:Conservation laws for non-constant species in models with Species-AssignmentRules are currently not supported and will be turned off.:UserWarning
     ignore:Conservation laws for non-constant species in combination with parameterized stoichiometric coefficients are not currently supported and will be turned off.:UserWarning
-    ignore:Support for PEtab2.0 is experimental!:UserWarning
+    ignore:Support for PEtab2.0.*experimental:UserWarning
     ignore:The JAX module is experimental and the API may change in the future.:ImportWarning
     # hundreds of SBML <=5.17 warnings
     ignore:.*inspect.getargspec\(\) is deprecated.*:DeprecationWarning

python/sdist/amici/de_export.py

@@ -407,6 +407,7 @@ def _write_index_files(self, name: str) -> None:
         filename = os.path.join(self.model_path, f"{name}.h")
         with open(filename, "w") as fileout:
             fileout.write("\n".join(lines))
+            fileout.write("\n")
 
     def _write_function_file(self, function: str) -> None:
         """