PyDSTool

To run the internal test suite, you must have pytest and mock installed. You can install them via pip or your system package manager, then execute the tests using setup.py.

# Install testing dependencies
sudo pip install py.test mock

# Run tests
python setup.py test

To generate an HTML coverage report, install pytest-cov and run py.test with the appropriate coverage flags. The resulting report can be viewed by opening htmlcov/index.html in a web browser.

# Install coverage tool
sudo pip install pytest-cov

# Run coverage
py.test --cov PyDSTool --cov-report html --cov-config .coveragerc

Examples are located in the examples directory. Some examples require an external compiler (like gcc or gfortran). You can run all examples in the correct order using the run_all_tests.py script.

If you do not have a working C/Fortran compiler, you may need to edit run_all_tests.py to disable external compiler tests.

Note on Matplotlib errors: On some platforms, you might see a Fatal Python error: PyEval_RestoreThread: NULL tstate when the script attempts to close matplotlib windows. This error can be safely ignored; you may simply need to close the plot windows manually.

cd examples
python run_all_tests.py

To install PyDSTool on Debian or Ubuntu systems, first install the required system dependencies including gfortran, swig, numpy, scipy, and matplotlib. Then, install the package using setup.py.

Note: You can install for the local user only by running without sudo and adding the --user flag.

# Install system dependencies
sudo apt-get update
sudo apt-get install -qq gfortran swig
sudo apt-get install -qq python-numpy python-scipy python-matplotlib

# Install PyDSTool
sudo python setup.py install
# OR for development mode
sudo python setup.py develop
# OR for local user only
python setup.py install --user