Merge pull request #2667 from dweindl/release_0.31.1

Release 0.31.1

Author: dweindl

.github/workflows/deploy_branch.yml

@@ -5,7 +5,7 @@ jobs:
   sdist:
     name: Deploy Python Source Distribution
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.github/workflows/deploy_protected.yml

@@ -32,7 +32,7 @@ jobs:
     name: Deploy Docker Hub
     needs: [check-secret]
     if: needs.check-secret.outputs.secrets-defined == 'true'
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.github/workflows/deploy_release.yml

@@ -8,7 +8,7 @@ jobs:
   pypi:
     name: Deploy PyPI
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
@@ -47,7 +47,7 @@ jobs:
   bioSimulatorsUpdateCliAndDockerImage:
     name: Release to BioSimulators
     needs: pypi
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     env:
       # Owner/repository-id for the GitHub repository for the downstream command-line interface and Docker image
       DOWNSTREAM_REPOSITORY: biosimulators/Biosimulators_AMICI
@@ -72,7 +72,7 @@ jobs:
 
   dockerhub:
     name: Release to Docker Hub
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
     - name: Set up Python

.github/workflows/test_benchmark_collection_models.yml

@@ -17,7 +17,7 @@ jobs:
   build:
     name: Benchmark Collection
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       fail-fast: false
@@ -77,7 +77,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: coverage_py.xml
+        files: coverage_py.xml
         flags: python
         fail_ci_if_error: true
         verbose: true

.github/workflows/test_doc.yml

@@ -39,7 +39,7 @@ jobs:
 
   sphinx:
     name: Test Sphinx
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.github/workflows/test_install.yml

@@ -5,7 +5,7 @@ jobs:
   archive:
     name: Archive Install
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
@@ -46,7 +46,7 @@ jobs:
   sdist_ubuntu:
     name: sdist Install Ubuntu
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.github/workflows/test_matlab.yml

@@ -12,7 +12,7 @@ jobs:
   matlab:
     name: Matlab
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/test_performance.yml

@@ -19,7 +19,7 @@ jobs:
   build:
     name: Performance Test
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.github/workflows/test_petab_test_suite.yml

@@ -104,6 +104,6 @@ jobs:
         uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          file: coverage.xml
+          files: coverage.xml
           flags: petab
           fail_ci_if_error: true

.github/workflows/test_pypi.yml

@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
-        os: [ubuntu-22.04, macos-latest]
+        os: [ubuntu-24.04, macos-latest]
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/test_python_cplusplus.yml

@@ -11,7 +11,7 @@ on:
 jobs:
   ubuntu-cpp-python-tests:
     name: C++/Python tests Ubuntu
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
@@ -82,7 +82,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: build/coverage_py.xml
+        files: build/coverage_py.xml
         flags: python
         fail_ci_if_error: true
         verbose: true
@@ -102,7 +102,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: coverage.info
+        files: coverage.info
         flags: cpp
         fail_ci_if_error: true
 
@@ -118,7 +118,7 @@ jobs:
 
   ubuntu-python-tests:
     name: Python tests Ubuntu
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
@@ -164,7 +164,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: build/coverage_py.xml
+        files: build/coverage_py.xml
         flags: python
         fail_ci_if_error: true
         verbose: true
@@ -184,7 +184,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: coverage.info
+        files: coverage.info
         flags: cpp_python
         fail_ci_if_error: true
 
@@ -201,7 +201,7 @@ jobs:
 
   ubuntu-notebook-tests:
     name: Notebook tests Ubuntu
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.github/workflows/test_python_ver_matrix.yml

@@ -16,7 +16,7 @@ jobs:
   build:
     name: Python Version Matrix
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     continue-on-error: ${{ matrix.experimental }}
     env:
       AMICI_SKIP_CMAKE_TESTS: "TRUE"

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -22,7 +22,7 @@ on:
 jobs:
   build:
     name: SBML Semantic Test Suite
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       fail-fast: false

.github/workflows/test_valgrind.yml

@@ -14,7 +14,7 @@ on:
 jobs:
   valgrind_cpp:
     name: Valgrind C++
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
@@ -29,7 +29,16 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - name: Checkout code (scheduled)
+      if: github.event_name == 'schedule'
+      uses: actions/checkout@v4
+      with:
+        ref: develop
+
+    - name: Checkout code (manual, push, pull request)
+      if: github.event_name != 'schedule'
+      uses: actions/checkout@v4
+
     - run: git fetch --prune --unshallow
 
     - name: Install apt dependencies
@@ -53,7 +62,7 @@ jobs:
   valgrind_python:
     name: Valgrind Python
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.readthedocs.yml

@@ -8,17 +8,17 @@ version: 2
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   builder: html
-  configuration: documentation/conf.py
+  configuration: doc/conf.py
   fail_on_warning: True
 
 formats:
   - pdf
 
 python:
   install:
-    - requirements: documentation/rtd_requirements.txt
+    - requirements: doc/rtd_requirements.txt
 build:
-  os: "ubuntu-22.04"
+  os: "ubuntu-24.04"
   apt_packages:
     - libatlas-base-dev
     - libhdf5-serial-dev

CHANGELOG.md

@@ -4,6 +4,15 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+### v0.31.1 (2025-03-21)
+
+Bugfix-only release.
+
+* Handle relational operators in SBML import
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2652
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.31.0...v0.31.1
+
 ### v0.31.0 (2025-02-18)
 
 * Added `RDataReporting::observables_likelihood` for computing observables,

README.md

@@ -1,4 +1,4 @@
-<img src="https://raw.githubusercontent.com/AMICI-dev/AMICI/master/documentation/gfx/banner.png" height="60" align="left" alt="AMICI logo">
+<img src="https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/banner.png" height="60" align="left" alt="AMICI logo">
 
 ## Advanced Multilanguage Interface for CVODES and IDAS
 
@@ -73,7 +73,7 @@ are derived symbolically and C++ code is generated. This code is then
 compiled into a C++ library, a Python module, or a Matlab `.mex` file and
 is then used for model simulation.
 
-![AMICI workflow](https://raw.githubusercontent.com/AMICI-dev/AMICI/master/documentation/gfx/amici_workflow.png)
+![AMICI workflow](https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/amici_workflow.png)
 
 ## Getting started
 
@@ -86,8 +86,8 @@ There are also instructions for using AMICI inside
 [containers](https://github.com/AMICI-dev/AMICI/tree/master/container).
 
 To get you started with Python-AMICI, the best way might be checking out this
-[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/master/documentation/GettingStarted.ipynb)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AMICI-dev/AMICI/develop?labpath=documentation%2FGettingStarted.ipynb).
+[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/master/doc/examples/getting_started/GettingStarted.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AMICI-dev/AMICI/develop?labpath=doc%2Fexamples%2Fgetting_started%2FGettingStarted.ipynb).
 
 To get started with Matlab-AMICI, various examples are available
 in [matlab/examples/](https://github.com/AMICI-dev/AMICI/tree/master/matlab/examples).
@@ -147,11 +147,11 @@ 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),
+[doc/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:
 
 <p align="center">
-  <img src="https://raw.githubusercontent.com/AMICI-dev/AMICI/master/documentation/gfx/logo_text.png" height="75" alt="AMICI Logo">
+  <img src="https://raw.githubusercontent.com/AMICI-dev/AMICI/master/doc/gfx/logo_text.png" height="75" alt="AMICI Logo">
 </p>

binder/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 
 # install dependencies
 

binder/overview.ipynb

@@ -8,39 +8,39 @@
    "source": [
     "# AMICI example notebooks\n",
     "\n",
-    "* [Getting started](../documentation/GettingStarted.ipynb)\n",
+    "* [Getting started](../doc/examples/getting_started/GettingStarted.ipynb)\n",
     "\n",
     "  Brief intro to AMICI for first-time users.\n",
     "\n",
-    "* [SBML import, observation model, sensitivity analysis, data export and visualization](../python/examples/example_steadystate/ExampleSteadystate.ipynb)\n",
+    "* [SBML import, observation model, sensitivity analysis, data export and visualization](../doc/examples/getting_started_extended/GettingStartedExtended.ipynb)\n",
     "\n",
     "  A more detailed introduction to the AMICI interface, demonstrating sensitivity analysis, various options, finite difference checks, ...\n",
     "\n",
-    "* [PEtab import / simulation](../python/examples/example_petab/petab.ipynb)\n",
+    "* [PEtab import / simulation](../doc/examples/example_petab/petab.ipynb)\n",
     "\n",
     "  How to import and simulate PEtab problems.\n",
     "\n",
-    "* [Experimental conditions](../python/examples/example_presimulation/ExampleExperimentalConditions.ipynb)\n",
+    "* [Experimental conditions](../doc/examples/example_presimulation/ExampleExperimentalConditions.ipynb)\n",
     "\n",
     "  How to represent different experimental conditions in AMICI and how to use preequilibration.\n",
     "\n",
-    "* [Steadystate (sensitivities)](../python/examples/example_constant_species/ExampleEquilibrationLogic.ipynb)\n",
+    "* [Steadystate (sensitivities)](../doc/examples/example_steady_states/ExampleEquilibrationLogic.ipynb)\n",
     "\n",
     "  Describes and demonstrates the various algorithms for computing steady states and steady-state sensitivities.\n",
     "\n",
-    "* [Simulation errors](../python/examples/example_errors.ipynb)\n",
+    "* [Simulation errors](../doc/examples/example_errors.ipynb)\n",
     "\n",
     "  Demonstrates common simulation failures and gives some hints for interpreting, debugging, and fixing them.\n",
     "\n",
-    "* [Interfacing JAX](../python/examples/example_jax/ExampleJax.ipynb)\n",
+    "* [Interfacing JAX](../doc/examples/example_jax/ExampleJax.ipynb)\n",
     "\n",
     "  Provides guidance on how to combine AMICI with differential programming frameworks such as JAX.\n",
     "\n",
-    "* [Efficient spline interpolation](../python/examples/example_splines/ExampleSplines.ipynb)\n",
+    "* [Efficient spline interpolation](../doc/examples/example_splines/ExampleSplines.ipynb)\n",
     "\n",
-    "  Shows how to add annotated spline formulas to existing SBML models in order to speed up AMICI's model import.\n",
+    "  Shows how to add annotated spline formulas to existing SBML models to speed up AMICI's model import.\n",
     "\n",
-    "* [A real-world application of splines](../python/examples/example_splines_swameye/ExampleSplinesSwameye2003.ipynb)\n",
+    "* [A real-world application of splines](../doc/examples/example_splines_swameye/ExampleSplinesSwameye2003.ipynb)\n",
     "\n",
     "  An illustration of how to apply AMICI's spline functionalities to parameter estimation for a reaction network.\n"
    ]

documentation/CI.md renamed to doc/CI.md

@@ -191,11 +191,11 @@ 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 (3.6 or 3.7)
+* Ensure `pyversion` shows the correct python version (>= 3.10)
 * Then, from within the AMICI `matlab/` directory:
 
     ```
-    sbml_importer = py.amici.SbmlImporter('../python/examples/example_steadystate/model_steadystate_scaled.xml')
+    sbml_importer = py.amici.SbmlImporter('../doc/examples/getting_started/model_steadystate_scaled.xml')
     sbml_importer.sbml2amici('steadystate', 'steadystate_example_from_python')
     model = py.steadystate.getModel()
     solver = model.getSolver()