Drop MATLAB-interface

CHANGELOG.md

@@ -2,6 +2,15 @@
 
 See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioning_policy.html).
 
+## v1.X Series
+
+### v1.0.0 (unreleased)
+
+BREAKING CHANGES
+
+* The MATLAB interface has been removed.
+
+
 ## v0.X Series
 
 ### v0.34.1 (2025-08-25)

CMakeLists.txt

@@ -172,7 +172,6 @@ set(AMICI_SRC_LIST
     src/edata.cpp
     src/exception.cpp
     src/simulation_parameters.cpp
-    src/spline.cpp
     src/solver.cpp
     src/solver_cvodes.cpp
     src/solver_idas.cpp
@@ -213,7 +212,6 @@ set(AMICI_SRC_LIST
     include/amici/solver_cvodes.h
     include/amici/solver.h
     include/amici/solver_idas.h
-    include/amici/spline.h
     include/amici/splinefunctions.h
     include/amici/steadystateproblem.h
     include/amici/sundials_linsol_wrapper.h
@@ -309,35 +307,6 @@ if(AMICI_PYTHON_BUILD_EXT_ONLY)
 endif()
 
 # Create targets to make the sources show up in IDEs for convenience
-
-# For matlab interface
-if(NOT AMICI_PYTHON_BUILD_EXT_ONLY)
-
-  set(MATLAB_SOURCES
-      src/interface_matlab.cpp src/returndata_matlab.cpp
-      include/amici/interface_matlab.h include/amici/returndata_matlab.h)
-  find_package(Matlab)
-  # In case we can find Matlab, we create a respective library to compile the
-  # extension from cmake. Otherwise we just create a dummy target for the files
-  # to show up inside IDEs. (Set the Matlab_ROOT_DIR cmake variable if CMake
-  # cannot find your Matlab installation)
-  if(${Matlab_FOUND})
-    add_library(matlabInterface ${MATLAB_SOURCES})
-    set_target_properties(matlabInterface PROPERTIES INCLUDE_DIRECTORIES
-                                                     "${Matlab_INCLUDE_DIRS}")
-    target_link_libraries(matlabInterface PUBLIC amici)
-  else()
-    add_custom_target(
-      matlabInterface
-      SOURCES ${MATLAB_SOURCES}
-      COMMENT "Dummy target for MATLAB interface files")
-  endif()
-  set_property(
-    TARGET matlabInterface
-    APPEND
-    PROPERTY INCLUDE_DIRECTORIES "${CMAKE_CURRENT_SOURCE_DIR}/include/")
-endif()
-
 # For template files
 add_custom_target(
   fileTemplates

LICENSE.md

@@ -32,9 +32,3 @@ The AMICI logo is released under the Creative Commons CC0 1.0 Universal
   terms given in `ThirdParty/SuiteSparse/LICENSE.txt`
 * *gsl-lite* is redistributed under the MIT License (MIT) with the terms given
   in `ThirdParty/gsl/gsl/gsl-lite.hpp`
-* *xml2struct* and *struct2xml* are redistributed under the BSD 2-Clause
-  License (BSD-2-Clause) with terms given in
-  `matlab/auxiliary/xml2struct/license.txt` and
-  `matlab/auxiliary/struct2xml/license.txt`
-* *CalcMD5* is redistributed under the BSD 2-Clause License (BSD-2-Clause)
-  with terms given in `matlab/auxiliary/CalcMD5/license.txt`

README.md

@@ -4,21 +4,20 @@
 
 ## About
 
-AMICI provides a multi-language (Python, C++, Matlab) interface for the
+AMICI provides a Python and C++ interface for the
 [SUNDIALS](https://computing.llnl.gov/projects/sundials/) solvers
 [CVODES](https://computing.llnl.gov/projects/sundials/cvodes)
 (for ordinary differential equations) and
 [IDAS](https://computing.llnl.gov/projects/sundials/idas)
 (for algebraic differential equations). AMICI allows the user to read
 differential equation models specified as [SBML](http://sbml.org/)
 or [PySB](http://pysb.org/)
-and automatically compiles such models into Python modules, C++ libraries or
-Matlab `.mex` simulation files.
+and automatically compiles such models into Python modules or C++ libraries.
 The generated model expressions along with the corresponding sensitivity
 equations are transformed into native C++ code which allows for a significantly
 faster simulation.
 
-**NOTE: The MATLAB interface is no longer supported and will be removed soon.**
+**NOTE: The former MATLAB interface has been removed in AMICI 1.0.**
 
 Beyond forward integration, the compiled simulation file also allows for
 forward sensitivity analysis, steady state sensitivity analysis and
@@ -53,7 +52,7 @@ constrained optimization problems.
 * Generation of C++ code for model simulation and sensitivity
   computation
 * Access to and high customizability of CVODES and IDAS solver
-* Python, C++, Matlab interface
+* Python and C++ interface
 * Sensitivity analysis
   * forward
   * steady state
@@ -66,11 +65,10 @@ constrained optimization problems.
 ## Interfaces & workflow
 
 The AMICI workflow starts with importing a model from either
-[SBML](http://sbml.org/) (Matlab, Python), [PySB](http://pysb.org/) (Python),
-or a Matlab definition of the model (Matlab-only). From this input,
-all equations for model simulation
+[SBML](http://sbml.org/) (Python) or [PySB](http://pysb.org/) (Python).
+From this input, all equations for model simulation
 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
+compiled into a plain C++ library or a Python module, and
 is then used for model simulation.
 
 ![AMICI workflow](https://raw.githubusercontent.com/AMICI-dev/AMICI/main/doc/gfx/amici_workflow.png)
@@ -79,19 +77,15 @@ is then used for model simulation.
 
 The AMICI source code is available at https://github.com/AMICI-dev/AMICI/.
 To install AMICI, first read the installation instructions for
-[Python](https://amici.readthedocs.io/en/latest/python_installation.html),
-[C++](https://amici.readthedocs.io/en/latest/cpp_installation.html) or
-[Matlab](https://amici.readthedocs.io/en/latest/matlab_installation.html).
+[Python](https://amici.readthedocs.io/en/latest/python_installation.html) or
+[C++](https://amici.readthedocs.io/en/latest/cpp_installation.html).
 There are also instructions for using AMICI inside
 [containers](https://github.com/AMICI-dev/AMICI/tree/main/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/main/doc/examples/getting_started/GettingStarted.ipynb)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AMICI-dev/AMICI/main?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/main/matlab/examples).
-
 Comprehensive documentation is available at
 [https://amici.readthedocs.io/en/latest/](https://amici.readthedocs.io/en/latest/).
 

doc/AGENTS.md

@@ -4,14 +4,13 @@ This Agents.md file provides comprehensive guidance for OpenAI Codex and other A
 
 ## Project Structure for OpenAI Codex Navigation
 
-AMICI is a python package that uses SWIG to generate python bindings to C++ code. There are also a deprecated matlab interface to the C++ code, which will be removed at some point in the future.
+AMICI is a python package that uses SWIG to generate python bindings to C++ code.
 
 - `/binder`: binder configuration
 - `/cmake`: various cmake utility functions
 - `/container`: docker configuration
 - `/doc`: high level documentation, all API documentation is automatically generated using doxygen/sphinx
 - `/include`: C++ header files
-- `/matlab`: matlab interface
 - `/models`: pre-generated c++ models for testing
 - `/python`: python source code
   - `/benchmark`: helper scripts for benchmarking

doc/CI.md

@@ -49,12 +49,6 @@ To run the SBML Test Suite test cases, the easiest way is:
    Once the test cases are available locally, for debugging it might be easier
    to directly use `pytest` with `tests/sbml/testSBMLSuite.py`.
 
-
-## Matlab tests (not included in CI pipeline)
-
-To execute the Matlab test suite, run `tests/testModels.m`.
-
-
 ## Model simulation integration tests
 
 Many of our integration tests are model simulations. The simulation results
@@ -69,17 +63,7 @@ This code is to be updated whenever `amici::Model` changes.
 
 ### Regenerating C++ code of the test models
 
-Regeneration of the model code has to be done whenever `amici::Model` or
-the Matlab model import routines change.
-
-This is done with
-
-    tests/cpp/wrapTestModels.m
-
-**Note:** This is currently only possible from Matlab < R2018a. This should
-change as soon as 1) all second-order sensitivity code is ported to C++/Python,
-2) a non-SBML import exists for Python and 3) support for events has been added
-for Python.
+*To be updated*
 
 
 ### Regenerating expected results

matlab/mtoc/config/Doxyfile.template → doc/Doxyfile.template

@@ -947,10 +947,8 @@ WARN_LOGFILE           =
 
 INPUT                  = "_SourceDir_/README.md" \
                          "_SourceDir_/LICENSE.md" \
-                         "_SourceDir_/doc/MATLAB_.md" \
                          "_SourceDir_/doc/CPP_.md" \
-                         "_SourceDir_/include" \
-                         "_SourceDir_/matlab"
+                         "_SourceDir_/include"
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1040,11 +1038,6 @@ EXCLUDE_PATTERNS       = "_SourceDir_/models/*" \
                          "_SourceDir_/tests/*" \
                          "_SourceDir_/scripts/*" \
                          "_SourceDir_/ThirdParty/*" \
-                         "_SourceDir_/matlab/examples/*" \
-                         "_SourceDir_/matlab/mtoc/*" \
-                         "_SourceDir_/matlab/auxiliary/*" \
-                         "_SourceDir_/matlab/SBMLimporter/*" \
-                         "_SourceDir_/matlab/tests/*" \
                          "_SourceDir_/python/tests/*" \
                          "_SourceDir_/python/sdist/*" \
                          "_SourceDir_/python/examples/example_*/model_*" \
@@ -1127,7 +1120,7 @@ INPUT_FILTER           =
 # need to set EXTENSION_MAPPING for the extension otherwise the files are not
 # properly processed by doxygen.
 
-FILTER_PATTERNS        = "*.m=_MTOCFILTER_"
+# FILTER_PATTERNS        = "*.m=_MTOCFILTER_"
 
 # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
 # INPUT_FILTER) will also be used to filter the input files that are used for
@@ -1330,7 +1323,7 @@ HTML_FOOTER            =
 # obsolete.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_STYLESHEET        = _ConfDir_/customdoxygen.css
+# HTML_STYLESHEET        = _ConfDir_/customdoxygen.css
 
 # The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
 # cascading style sheets that are included after the standard style sheets
@@ -1971,7 +1964,7 @@ PAPER_TYPE             = a4
 # If left blank no extra packages will be included.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-EXTRA_PACKAGES         = "_LatexExtras_"
+# EXTRA_PACKAGES         = "_LatexExtras_"
 
 # The LATEX_HEADER tag can be used to specify a user-defined LaTeX header for
 # the generated LaTeX document. The header should contain everything until the