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Dynamical systems simulation in python

Trying out PyDSTools [webpage, download]
These guys look professional - they have a test suite that you can run to check everything out.
  1. You need to put a file called PyDSTool.pth [read this]
    Play close attention to the trick about subdirectories - you have to repeat it for each level, not just the root level. I have my install in c:\programs\PyDSTool and my file has
  2. I have scipy version 0.6.0 but PyDSTool doesn't detect that properly. I commented out the relevant lines in PyDSTool's root
    #if vernums[1] != 5:
    # raise RuntimeError("SciPy v0.5.1 or above is required")

    and it continued with the tests.
Things seem to work OK, only one thing was declared broken:
PyCont: appears to be broken on your system

But, there were periodic errors of the nature:

***** Testing script ****************************

Gnuplot not available
------- Examples of implicit function as variable
1D example: a half-circle using newton's method (secant method for estimating de
Change sign of 'y' initial condition to solve for other half-circle
Gen defined? => False
traj1 = testimp.compute('traj1')
Error in supplied functional specification code
Traceback (most recent call last):
File "", line 54, in
traj1 = testimp.compute('traj1')
File "C:\Programs\PyDSTool\Generator\", line 294, in compute
exec tempspec[0] in globals()
File "string", line 1
def _specfn_imptest_316e-006(ds, t, x, parsinps):
SyntaxError: invalid syntax

***** Testing passed on test file

Which I can't understand


  1. Hi -- that's an odd platform specific problem you have with time.clock(). The easy fix is to change the return line in the function PyDSTool.common.timestamp to be the following:

    return c.replace(".","").replace("-","")[:tdigits+1]

    (obviously without the newline that this comment box forces on me!)


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