Merge pull request #2781 from dweindl/release_0.33.0

Release 0.33.0

Author: dweindl

.github/workflows/test_pypi.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
         os: [ubuntu-24.04, macos-latest]
 
     runs-on: ${{ matrix.os }}

.github/workflows/test_python_ver_matrix.yml

@@ -26,8 +26,6 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - python-version: '3.10'
-            experimental: false
           - python-version: '3.11'
             experimental: false
           - python-version: '3.12'

.gitignore

@@ -9,15 +9,9 @@ tests/cpp/build_xcode/*
 tests/cpp/Testing/*
 
 doc-venv/*
-doc/*
 fonts/*
 images/*
 stylesheets/*
-documentation/_build/*
-documentation/_exhale_cpp_api/*
-documentation/_exhale_matlab_api/*
-documentation/_doxyoutput_amici_cpp/*
-documentation/_doxyoutput_amici_matlab/*
 sed-ml/*
 
 models/*
@@ -191,8 +185,6 @@ ThirdParty/swig-*
 ThirdParty/ragel-*.tar.gz
 _untracked/
 
-documentation/generated/*
-
 # vim
 *.swp
 tests/performance/CS_Signalling_ERBB_RAS_AKT/

CHANGELOG.md

@@ -4,6 +4,56 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+### v0.33.0 (2025-06-11)
+
+Note that this release requires Python >= 3.11.
+
+**Fixes**
+
+* Fixed an issue in SBML AlgebraicRule processing leading to import failure if
+  a species occurred in multiple AlgebraicRules
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2744
+
+* Fixed a potential segfault when running forward sensitivity analysis for
+  models without state variables
+
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2749
+
+* Fixed a dimension bug for presimulation parameters in ExpDataView
+
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2746
+
+* Fixed incorrect initialization for initial assignments with explicit time
+  dependence
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2779
+
+**Features**
+
+* AMICI now supports SBML events with `use_values_from_trigger_time=true`
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2741
+
+* AMICI now supports SBML events with constant priorities
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2730
+
+**Other changes**
+
+* doc: Added a caveats section listing some known issues and potentially
+  unexpected behavior in AMICI
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2735
+
+* Added warnings for presimulation and steady state simulation with events.
+  So far, events were not fully supported in these modes. This is subject to
+  change.
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2755
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.32.0...v0.33.0
+
 ### v0.32.0 (2025-05-15)
 
 **Breaking changes**

doc/.gitignore

@@ -0,0 +1,8 @@
+_build/
+_doxyoutput_amici_cpp/
+_doxyoutput_amici_matlab/
+_exhale_cpp_api/
+_exhale_matlab_api/
+examples/example_presimulation/model_presimulation/
+generated/
+build_doxygen/

doc/MATLAB_.md

@@ -191,7 +191,7 @@ from within Matlab. This not quite comfortable yet, but it is possible.
 Here for proof of concept:
 
 * Install the python package as described in the documentation
-* Ensure `pyversion` shows the correct python version (>= 3.10)
+* Ensure `pyversion` shows the correct python version (>= 3.11)
 * Then, from within the AMICI `matlab/` directory:
 
     ```

doc/PYTHON.rst

@@ -8,5 +8,6 @@ Python interface
    Installation <python_installation>
    Examples <python_examples>
    Usage <python_interface>
+   Caveats <python_caveats>
    FAQ <python_faq>
    API reference <python_modules>

doc/examples/example_petab/petab.ipynb

@@ -50,7 +50,7 @@
    "source": [
     "model_name = \"Boehm_JProteomeRes2014\"\n",
     "# local path or URL to the yaml file for the PEtab problem\n",
-    "petab_yaml = f\"https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/{model_name}/{model_name}.yaml\"\n",
+    "petab_yaml = f\"https://benchmarking-initiative.github.io/Benchmark-Models-PEtab/tree/Benchmark-Models/{model_name}/{model_name}.yaml\"\n",
     "# load the problem using the PEtab library\n",
     "petab_problem = petab.Problem.from_yaml(petab_yaml)"
    ]