[pydstool-users] PyDSTool 0.85 released

[Rob C. <rh...@co...>]

Hi,

There are lots of minor improvements and fixes in this version, but a
major feature is the support for user-defined functions for
continuation using PyCont.

Also added: some basic phase-plane tools, calculation of phase
response curves for oscillators and support for some special math
functions. A summary of changes is below.

Thanks!
Rob, Erik, and Drew.


Summary of changes
-----------------------------

 * PyCont can now perform continuation according to the zeros of user-defined
    functions or bounds (see example tests/PyCont_vanDerPol.py and
    PyCont_Hopfield.py)
 * Support for scipy.special functions in Generator definitions (Python targets
    only. C targets with a more limited range of functions will be
supported soon)
 * A few phase plane analysis tools have been added to Toolbox/phaseplane.py
    -- in particular, the finding of fixed points, nullclines,
    and some simple code to compute saddle manifolds in planar systems
 * Phase response curves can now be calculated for limit cycles using
the adjoint
    method (see tests/ML_adjointPRC.py and HH_adjointPRC.py for examples)
 * Generators now include auxiliary variable data in recorded event data
 * Pointset comparisons using arithmetic operators now consistent with the
     norm-based comparisons used by Points
 * Time mesh points for external inputs to integrators now forced to
be integration
     mesh points for greater numerical accuracy and stability
 * VODE now supports 'use_special' for forcing values of output trajectory mesh
 * Improved support for numpy float and int types alongside standard
python types
 * Improved numerical first derivative computed by central finite
differences and
    Ridders' method
 * Added a multilinear regression auxiliary function builder
    (common.py/makeMultilinearRegrFn)
 * Support for parameter estimation using least squares using
qualitative features
    such as positions of extrema (see wiki page ParamEst)
 * Moved ParamEst.py into PyDSTool/Toolbox, a more logical home, and removed its
    default import in PyDSTool
 * Added Toolbox/ModelHelper.py for additional model building utilities (esp.
    for neural modelling)
 * Minor bug fixes and improvements (see Trac wiki site for full change log)