Continuous integration (CI) and tests

AMICI uses a continuous integration pipeline running via This includes the following steps:

  • Checking existence and format of documentation

  • Static code analysis (

  • Unit and integration tests

  • Memory leak detection

More details are provided in the sections below.

The CI scripts and tests can be found in tests/ and scripts/. Some of the tests are integrated with CMake, see make help in the build directory.

C++ unit and integration tests

To run C++ tests, build AMICI with make or scripts/, then run scripts/

Python unit and integration tests

To run Python tests, run ../scripts/ from anywhere (assumes build directory is build/) or run make python-tests in your build directory.

SBML Test Suite

We test Python-AMICI SBML support using the test cases from the semantic SBML Test Suite. When making changes to the model import functions, make sure to run these tests.

To run the SBML Test Suite test cases, the easiest way is:

  1. Running scripts/ which creates a virtual Python environment and performs a development installation of AMICI from the current repository. (This needs to be run only once or after AMICI model generation or C++ changes).

  2. Running scripts/ This will download the test cases if necessary and run them all. A subset of test cases can be selected with an optional argument (e.g. scripts/ 1,3-6,8, to run cases 1, 3, 4, 5, 6 and 8).

    Once the test cases are available locally, for debugging it might be easier to directly use pytest with tests/

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 obtained from the Python and C++ are compared to results saved in an HDF5 file (tests/cpputest/expectedResults.h5). Settings and data for the test simulations are also specified in this file.

Note: The C++ code for the models is included in the repository under models/. 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


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.

Regenerating expected results

To update test results, run make test in the build directory, replace tests/cpputest/expectedResults.h5 by tests/cpputest/writeResults.h5.bak [ONLY DO THIS AFTER TRIPLE CHECKING CORRECTNESS OF RESULTS] Before replacing the test results, confirm that only expected datasets have changed, e.g. using

h5diff -v --relative 1e-8 tests/cpputest/expectedResults.h5 tests/cpputest/writeResults.h5.bak | less

Adding/Updating tests

To add new tests add a new corresponding python script (see, e.g., ./tests/generateTestConfig/ and add it to and run tests/ Then regenerate the expected test results (see above).