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This is a beta release version.

PyDSTool is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems).

PyDSTool is platform independent, written primarily in Python with some underlying C and Fortran legacy code for fast solving. It makes extensive use of the numpy and scipy libraries. PyDSTool supports symbolic math, optimization, phase plane analysis, continuation and bifurcation analysis, data analysis, and other tools for modeling -- particularly for biological applications.

The project is fully open source with a BSD license, and welcomes contributions from the community.

See more at 

Requirements ~~~~~~~~~~~~

  • Python 
    __ 3.6+;
  • numpy 
  • scipy 

Dopri/Radau and AUTO interface requirements ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • swig 
    __ > 2.0;
  • C compiler (e.g, gcc or clang);
  • GNU Fortran compiler (Radau only).

Optional requirements ^^^^^^^^^^^^^^^^^^^^^

  • matplotlib 
    __ Matplotlib is needed for plotting functionality and running many of the examples.

Recommended ^^^^^^^^^^^

  • ipython 

Installation ~~~~~~~~~~~~

Debian/Ubuntu ^^^^^^^^^^^^^

  • install necessary packages:


       sudo apt-get update
       sudo apt-get install -qq gfortran swig
       sudo apt-get install -qq python-numpy python-scipy python-matplotlib
  • install


       sudo python install



       sudo python develop

Run without

and add flag
to install for local user only.

Getting started and documentation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

See the

online documentation 
__, particularly the GettingStarted and Tutorials pages! Please report bugs and suggestions using the user forum linked to there.

Tests and examples ~~~~~~~~~~~~~~~~~~

Running examples ^^^^^^^^^^^^^^^^

Examples can be found in the

directory. Some examples can only be run once, others have produced their output, for instance, Several of the examples require an external compiler. An easy way to run all the examples in an appropriate order is to run the script '':


    cd examples

There is a simple option in that file that you may need to edit in order to select whether the external compiler tests should be run (in case you do not have

working on your system).

Note that on some platforms you will see an error report when the script tries to automatically close matplotlib graph windows, to the effect of:


"Fatal Python error: PyEval_RestoreThread: NULL tstate"

This error can be ignored. You may also have to close the plot windows yourself before the script can continue. This will depend on your platform and settings.

Running test suite ^^^^^^^^^^^^^^^^^^

To run test suite, install

__ and
__, using


    sudo pip install py.test mock

or package manager:


    sudo apt-get install python-pytest python-mock

Then run:


    python test

Getting coverage report ^^^^^^^^^^^^^^^^^^^^^^^

  • install


       sudo pip install pytest-cov
  • run


       py.test --cov PyDSTool --cov-report html --cov-config .coveragerc
  • open file
    in your browser

Credits ~~~~~~~

Coding and design by Robert Clewley, Erik Sherwood, Drew LaMar, Vladimir Zakharov, and John Guckenheimer, except where otherwise stated in the code or documentation. (Several other open source codes have been redistributed here under the compatible licenses.)

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