diff --git a/cmake/AmiciFindBLAS.cmake b/cmake/AmiciFindBLAS.cmake index 22460ec1aa..37bb4c287e 100644 --- a/cmake/AmiciFindBLAS.cmake +++ b/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. diff --git a/doc/.gitignore b/doc/.gitignore index 82ef00f6bd..2bfdff2d64 100644 --- a/doc/.gitignore +++ b/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/ diff --git a/doc/README.md b/doc/README.md index f844bc4ea1..15db6b89e1 100644 --- a/doc/README.md +++ b/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 diff --git a/python/sdist/amici/__init__.py b/python/sdist/amici/__init__.py index b83b06ff3f..ebab7efd22 100644 --- a/python/sdist/amici/__init__.py +++ b/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 diff --git a/python/sdist/amici/de_export.py b/python/sdist/amici/de_export.py index 34c1cb0bbc..d2d67cfaec 100644 --- a/python/sdist/amici/de_export.py +++ b/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 diff --git a/python/sdist/amici/sbml_import.py b/python/sdist/amici/sbml_import.py index a04e133b06..5139f830cc 100644 --- a/python/sdist/amici/sbml_import.py +++ b/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 diff --git a/python/tests/test_pregenerated_models.py b/python/tests/test_pregenerated_models.py index 0c03fa66a9..2acdff19c4 100755 --- a/python/tests/test_pregenerated_models.py +++ b/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