O guia do spyder indica o comando %matplotlib qt para ter o gráfico em 
janela própria. Como devo fazer isso no script. Como exemplo abaixo 
apresento meu script que roda no Ipython:

import numpy
import pylab as pl
pl.plot([0,1,2,3], [0,1,2,3], 'b-.', label='line 1', linewidth=2)
pl.plot([0,1,2,3], [0,3,4,9], 'r-',  label='line 2',linewidth=2)
pl.axis([0, 3.5, 0, 10])
pl.legend()
pl.title('Earthquake Magnitude in Japan from 3/9-3/12')
pl.xlabel('Time')
pl.ylabel('Magnitude')

obrigado Antonio

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