Remove matlab leftovers

.github/ISSUE_TEMPLATE/bug_report.md

@@ -17,9 +17,11 @@ assignees: ''
 
 **AMICI version and system environment**
  - OS and version: [e.g. Ubuntu, iOS, Windows]
- - AMICI interface: [e.g. Python, Matlab, C++]
+ - AMICI interface: [e.g. Python, C++]
+ - Simulator type: [e.g. SUNDIALS, diffrax]
  - AMICI version:
- - Additional information: Compiler name and version used, Python/Matlab version, ...
+ - Additional information:
+   Compiler name and version used, Python version, ...
 
 **How to fix**
 Do you know how to resolve the problem?

doc/development.rst

@@ -50,9 +50,12 @@ process described below:
 
    -  Run ``scripts/buildAll.sh && scripts/run-cpp-tests.sh``.
 
-   -  If you made changes to the Matlab or C++ code and have a Matlab
-      license, please also run ``tests/cpp/wrapTestModels.m`` and
-      ``tests/testModels.m``
+   -  If you made changes related to code generation or version number, run
+
+      .. code-block:: shell
+
+         python -c "from amici.testing.models import import_test_models; import_test_models()"
+
 
    -  If you made changes to the Python or C++ code, run
       ``make python-tests`` in ``build``
@@ -149,9 +152,9 @@ To create a new release, please follow these steps:
 
 4. Regenerate the test models by running
 
-    ```shell
-    python -c "from amici.testing.models import import_test_models; import_test_models()"
-    ```
+   .. code-block:: shell
+
+      python -c "from amici.testing.models import import_test_models; import_test_models()"
 
     This ensures that the models can be imported with the new version.
 

include/amici/model_state.h

@@ -277,13 +277,14 @@ struct ModelStateDerived {
     SUNMatrixWrapper dtotal_cldx_rdata;
 
     /**
-     * Temporary storage of `dxdotdp` data across functions, Matlab only
+     * Temporary storage of `dxdotdp` data across functions
      * (dimension: `nplist` x `nx_solver` , row-major)
      */
     AmiVectorArray dxdotdp;
 
-    /** Sparse observable derivative of data likelihood, only used if
-     * `pythonGenerated` == `true` (dimension `nytrue`, `nJ` x `ny`, row-major)
+    /**
+     * Sparse observable derivative of data likelihood
+     * (dimension `nytrue`, `nJ` x `ny`, row-major)
      */
     std::vector<SUNMatrixWrapper> dJydy_;
 

python/sdist/amici/_symbolic/de_model.py

@@ -1358,8 +1358,9 @@ def _compute_equation(self, name: str) -> None:
         :param name:
             name of the symbolic variable
         """
-        # replacement ensures that we don't have to adapt name in abstract
-        # model and keep backwards compatibility with matlab
+        # replacement ensures that we don't have to adapt name in
+        # amici::AbstractModel and keep backwards compatibility with matlab
+        # TODO(cleanup): Change in amici::AbstractModel and remove
         match_deriv = DERIVATIVE_PATTERN.match(
             re.sub(r"dJ(y|z|rz)dsigma", r"dJ\1dsigma\1", name)
             .replace("sigmarz", "sigmaz")

tox.ini

@@ -19,5 +19,5 @@ change_dir = doc/
 allowlist_externals =
     rm
 commands =
-    rm -rf amici_models/ _doxyoutput_amici_cpp/ _exhale_cpp_api/ _exhale_matlab_api/ generated/ _build/
+    rm -rf amici_models/ _doxyoutput_amici_cpp/ _exhale_cpp_api/ generated/ _build/
     sphinx-build -T -E -W --keep-going -b html -d _build/doctrees-readthedocs -D language=en . _build/html