This directory contains a number of build, installation, and CI scripts.

• buildAll.sh

  Build AMICI along with dependencies and test suite

• buildAmici.sh

  Build AMICI library and test models

• buildBNGL.sh

  Download and build BioNetGen (required for some tests)

• buildSuiteSparse.sh

  Build SuiteSparse included in this repository

• buildSundials.sh

  Build Sundials included in this repository

• buildSuperLUMT.sh

  Download and build the SuperLU-MT solver. Required to build CVODES/AMICI with SuperLU-MT support.

• buildValgrind.sh

  Download and build Valgrind. This is used if Valgrind versions provided by homebrew or apt are buggy.

• buildXcode.sh

  Build AMICI and C++ test models and test with XCode

• downloadAndBuildSwig.sh

  Download and build SWIG

• installAmiciArchive.sh

  Create a Python virtual environment and do an AMICI development installation

• installAmiciSource.sh

  Create a Python virtual environment and do a regular AMICI installation

• run-codecov.sh

  Script for Python test code coverage analysis

• run-cppcheck.sh

  Run static code analysis

• run-cpp-tests.sh

  Run C++ unit and integration tests

• run-doxygen.sh

  Run doxygen to create AMICI documentation

• runNotebook.sh

  Script for running Jupyter notebooks from the command line. Used for CI to ensure functioning notebooks.

• run-python-tests.sh

  Run the AMICI Python test suite

• run-SBMLTestsuite.sh

  Download and run the semantic SBML Test Suite

• run-valgrind.sh

  Run memory leak check using valgrind for all unit and integration tests. Assumes they have been built before in the default location.