Installation instructions

Install the dependencies for the test suite

First, install the following dependencies of the test suite:

Install the optional dependencies for the test suite

To check that Docker image for simulation tools can be converted into Singularity images, also install Singularity. Installation instructions are available at https://sylabs.io/docs/.

The following packages are also required to test simulation tools that execute models encoded in several specific languages:

  • Java: required to test simulation tools that execute models encoded in NeuroML/LEMS.

  • Perl: required to test simulation tools that execute models encoded in BioNetGen.

  • XPP: required to test simulation tools that execute models encoded in XPP.

Install the test suite

After installing the dependencies outlined above, run the command below to install the BioSimulators test suite.

Note, although the test suite is available from PyPI, test suite should be installed from the Git repository because the package in PyPI does not include the example COMBINE archives needed for most of the tests.

Note, the test suite should generally by installed with the logging option, which installs capturer to collect the standard output and standard error generated by each test case. capturer is optional because it doesn’t support Windows. In addition, some Mac OS users have reported issues with capturer.

git clone --branch deploy https://github.com/biosimulators/Biosimulators_test_suite.git
pip install -e Biosimulators_test_suite[logging]