snake_case (#2969)

The previous mix of snake_case and camelCase was a mess. Convert everything to snake_case.

Related to #887.

Also includes:
* some minor documentation fixes
* replacement of public data members by corresponding getters and, where relevant, setters
* swig ignores

Author: dweindl

.github/workflows/test_benchmark_collection_models.yml

@@ -53,7 +53,7 @@ jobs:
       run: |
         python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@main \
         &&  python3 -m pip install -U sympy \
-        &&  python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git
+        &&  python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git@amici100
 
     - name: Download benchmark collection
       run: |
@@ -129,7 +129,7 @@ jobs:
       run: |
         python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@main \
         &&  python3 -m pip install -U sympy \
-        &&  python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git
+        &&  python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git@amici100
 
     - run: pip uninstall -y diffrax && pip install git+https://github.com/patrick-kidger/diffrax@dev # TODO FIXME https://github.com/patrick-kidger/diffrax/issues/654 + event dirs
 

.github/workflows/test_python_cplusplus.yml

@@ -53,7 +53,7 @@ jobs:
       run: scripts/installAmiciSource.sh
 
     - name: Check OpenMP support
-      run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+      run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiled_with_openmp())"
 
     - name: Python tests (part 1)
       run: |
@@ -273,7 +273,7 @@ jobs:
       run: scripts/installAmiciSource.sh
 
     - name: Check OpenMP support
-      run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+      run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiled_with_openmp())"
 
     - name: cppcheck
       run: scripts/run-cppcheck.sh
@@ -333,7 +333,7 @@ jobs:
         scripts/installAmiciSource.sh
 
     - name: Check OpenMP support
-      run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+      run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiled_with_openmp())"
 
     - name: Get BioNetGen
       run: scripts/buildBNGL.sh

CHANGELOG.md

@@ -31,6 +31,9 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 * `amici.petab.petab_import.import_model` has been removed.
   Use `amici.petab.petab_import.import_model_sbml` instead.
   (The former was just an alias for the latter.)
+* For a more consistent API, all function names are now snake_case instead of
+  camelCase.
+* `Model.getSolver` has been renamed to `Model.create_solver`.
 * The following deprecated functionality has been removed:
   * The complete MATLAB interface has been removed.
   * `NonlinearSolverIteration::functional` has been removed,

doc/cpp_interface.rst

@@ -56,7 +56,7 @@ The former provides some functions for reading and writing
 All model-specific functions are defined in the namespace ``model_$modelname``.
 
 The main function for running an AMICI simulation is
-:cpp:func:`amici::runAmiciSimulation`. This function requires
+:cpp:func:`amici::run_simulation`. This function requires
 
 * an instance of a :cpp:class:`amici::Model` subclass as generated during model
   import. For the example `model_steadystate` the respective class is provided
@@ -65,7 +65,7 @@ The main function for running an AMICI simulation is
 
 * a :cpp:class:`amici::Solver` instance. This solver instance needs to match
   the requirements of the model and can be obtained from
-  :cpp:func:`amici::AbstractModel::getSolver`.
+  :cpp:func:`amici::AbstractModel::create_solver`.
 
 * optionally an :cpp:class:`amici::ExpData` instance, which contains any
   experimental data (e.g. measurements, noise model parameters or model inputs)
@@ -76,7 +76,7 @@ all simulation results.
 
 For running simulations for multiple experimental conditions
 (multiple :cpp:class:`amici::ExpData` instances),
-:cpp:func:`amici::runAmiciSimulations`
+:cpp:func:`amici::run_simulations`
 provides an alternative entry point. If AMICI (and your application)
 have been compiled with OpenMP support (see installation guide), this allows
 for running those simulations in parallel.
@@ -97,7 +97,7 @@ model, which can be inconvenient in some cases.
 
 When working with a single model, the ``wrapfunctions.h`` file generated during
 model import can be used to avoid specifying model names explicitly. It defines
-a function ``amici::generic_model::getModel()``, that returns an instance of
+a function ``amici::generic_model::get_model()``, that returns an instance of
 the model class by a generic name.
 
 .. note::
@@ -121,7 +121,7 @@ and link the following libraries:
 * optionally HDF5 (C, HL, and CXX components)
   set CMake option ``ENABLE_HDF5`` to ``OFF`` to build without HDF5-support
 * optionally OpenMP (for parallel simulation of multiple conditions, see
-  :cpp:func:`amici::runAmiciSimulations`)
+  :cpp:func:`amici::run_simulations`)
 * optionally boost (only when using serialization of AMICI object)
 
 The simplest and recommended way is using the provide CMake files which take