jorgehatccrma / pydstool

PyDSTool main development repo

PyDSTool v0.88

April 2014. This is a beta release version.

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Requirements

• Python 2.6+ or 3.3+;
• numpy > 1.6;
• scipy > 0.9.

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 PyDSTool:

  sudo python setup.py install

  or

  sudo python setup.py develop

  Run without sudo and add flag --user 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.

Full API documentation can be found locally here. It is auto-generated from the source code using Epydoc and is meant as a reference for functions and classes only.

Tests and examples

Running examples

Examples can be found in the examples directory. Some examples can only be run once, others have produced their output, for instance HH_loaded.py, HH_loaded_dopri.py. 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 'run_all_tests.py':

cd examples
python run_all_tests.py

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 gcc and gfortran 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 py.test and mock, using pip:

sudo pip install py.test mock

or package manager:

sudo apt-get install python-pytest python-mock

Then run:

python setup.py test

Getting coverage report

• install pytest-cov

  sudo pip install pytest-cov

• run py.test

  py.test --cov PyDSTool --cov-report html --cov-config .coveragerc

• open file htmlcov/index.html in your browser

Change histories

Older (pre-git) version change histories appear in the bzr repository browser, and some older information is in the headers of each source file. An overview of the changes in a new release can be found in the SourceForge release notes.

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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.)