This is a matplotlib question, and you can get around this by using a backend that doesn't display to the user, e.g. 'Agg':
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
plt.plot([1,2,3])
plt.savefig('/tmp/test.png')
EDIT: If you don't want to lose the ability to display plots, turn off Interactive Mode, and only call plt.show() when you are ready to display the plots:
import matplotlib.pyplot as plt
# Turn interactive plotting off
plt.ioff()
# Create a new figure, plot into it, then close it so it never gets displayed
fig = plt.figure()
plt.plot([1,2,3])
plt.savefig('/tmp/test0.png')
plt.close(fig)
# Create a new figure, plot into it, then don't close it so it does get displayed
plt.figure()
plt.plot([1,3,2])
plt.savefig('/tmp/test1.png')
# Display all "open" (non-closed) figures
plt.show()