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I get clipping errors when I use fill_between(), set ylim such that not all of the graph is inside the plotting area, and export to PGF. See code below:
Python:
import numpy as np
from matplotlib import pyplot as plt
np.random.seed(3)
n = 100
m = np.random.random(n)
M = m + np.random.random(n)
M[80] = 3
plt.fill_between(np.arange(n), m, M)
plt.ylim(0,2.1)
plt.savefig('test.pgf')