From: Rob Clewley <rhc28@co...>  20070712 02:52:28

Hi, There are lots of minor improvements and fixes in this version, but a major feature is the support for userdefined functions for continuation using PyCont. Also added: some basic phaseplane 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 userdefined 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 normbased 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) 