Remove MATLAB leftovers (#2961)

Related to #2727.

Author: dweindl

cmake/AmiciFindBLAS.cmake

@@ -1,7 +1,6 @@
 # Find a BLAS
 #
-# AMICI requires BLAS, currently Intel MKL, CBLAS or MATLAB BLAS can be used.
-# The latter is not supported via CMake yet.
+# AMICI requires BLAS, currently at least Intel MKL, CBLAS can be used.
 #
 # This module defines the BLAS::BLAS IMPORTED target.
 

doc/.gitignore

@@ -1,8 +1,6 @@
 _build/
 _doxyoutput_amici_cpp/
-_doxyoutput_amici_matlab/
 _exhale_cpp_api/
-_exhale_matlab_api/
 examples/example_presimulation/model_presimulation/
 generated/
 build_doxygen/

doc/README.md

@@ -22,13 +22,12 @@ The documentation comprises:
 * Python API documentation of Python generated via SWIG (doxygen-style comments
   translated to docstrings by SWIG)
 * C++ API documentation (doxygen -> exhale -> breathe -> sphinx)
-* Matlab API documentation (mtocpp -> doxygen -> exhale -> breathe -> sphinx)
 
 ### Doxygen-only (legacy)
 
 (Parts of the) AMICI documentation can also be directly created using
 [doxygen](http://www.doxygen.nl/) directly. It combines Markdown files from
-`doc/` and in-source documentation from the C++ and Matlab source files.
+`doc/` and in-source documentation from the C++ source files.
 
 The documentation is generated by running
 
@@ -40,15 +39,8 @@ The resulting HTML and PDF documentation will be created in
 
 #### Doxygen configuration
 
-The main doxygen configuration file is located in
-`matlab/mtoc/config/Doxyfile.template`. Edit this file for inclusion or
-exclusion of additional files.
-
-#### Matlab documentation
-
-Matlab documentation is processed by
-[mtoc++](https://www.morepas.org/software/mtocpp/docs/tools.html).
-This is configured in `matlab/mtoc/config`.
+The main doxygen configuration file is located in `doc/Doxyfile.template`.
+Edit this file for inclusion or exclusion of additional files.
 
 ## Writing documentation
 
@@ -62,13 +54,13 @@ Graphics for documentation are kept in `doc/gfx/`.
 ### When using Markdown
 
 * Note that there are some incompatibilities of GitHub Markdown and Doxygen
-  Markdown. Ideally documentation should be written in a format compatible with
+  Markdown. Ideally, documentation should be written in a format compatible with
   both.
-  This affects for example images links which currently cause trouble in
+  This affects, for example, image links which currently cause trouble in
   Doxygen.
 
 * Where possible, relative links are preferred over absolute links. However,
-  they should work with both Github and Doxygen and ideally with local files
+  they should work with both GitHub and Doxygen and ideally with local files
   for offline use.
 
 * Please stick to the limit of 80 characters per line for readability of raw

python/sdist/amici/__init__.py

@@ -239,13 +239,13 @@ def import_model_module(
 
     module_path = Path(model_root, module_name, "__init__.py")
 
-    # We may want to import a matlab-generated model where the extension
+    # We may want to import an externally compiled model where the extension
     #  is in a different directory. This is not a regular use case. It's only
     #  used in the amici tests and can be removed at any time.
     #  The models (currently) use the default swig-import and require
     #  modifying sys.path.
-    module_path_matlab = Path(model_root, f"{module_name}.py")
-    if not module_path.is_file() and module_path_matlab.is_file():
+    module_path_external = Path(model_root, f"{module_name}.py")
+    if not module_path.is_file() and module_path_external.is_file():
         with set_path(model_root):
             # prevent segfaults under pytest
             #  see also:
@@ -257,7 +257,7 @@ def import_model_module(
                     category=DeprecationWarning,
                     message="builtin type .* has no __module__ attribute",
                 )
-                return _module_from_path(module_name, module_path_matlab)
+                return _module_from_path(module_name, module_path_external)
 
     module = _module_from_path(module_name, module_path)
     module._self = module

python/sdist/amici/de_export.py

@@ -240,8 +240,7 @@ def __init__(
     @log_execution_time("generating cpp code", logger)
     def generate_model_code(self) -> None:
         """
-        Generates the native C++ code for the loaded model and a Matlab
-        script that can be run to compile a mex file from the C++ code
+        Generates the model code (Python package + C++ extension).
         """
         with _monkeypatched(
             sp.Pow, "_eval_derivative", _custom_pow_eval_derivative

python/sdist/amici/sbml_import.py

@@ -301,8 +301,8 @@ def sbml2amici(
         constructor.
 
         The resulting model can be imported as a regular Python module (if
-        `compile=True`), or used from Matlab or C++ as described in the
-        documentation of the respective AMICI interface.
+        `compile=True`), or used from C++ as described in the documentation of
+        AMICI's C++ interface.
 
         Note that this generates model ODEs for changes in concentrations, not
         amounts unless the `hasOnlySubstanceUnits` attribute has been

python/tests/test_pregenerated_models.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-"""Run simulations with Matlab-AMICI pre-generated models and verify using
+"""Run simulations with pre-generated models and verify using
 saved expectations."""
 
 import os