Boxplot appears to reset the x-axis limits and ticks. For example, the following code

import matplotlib.pyplot as plt
import numpy as np

fig = plt.figure()
ax = plt.subplot()
ax.set_xlim(0, 4)
ax.set_xticks([0, 0.5, 1, 2, 3.5, 4])
ax.set_xticklabels(['a','b','c', '2', '3.5', '4']) 
ax.set_ylim(0, 8)
ax.set_yticks([0, 0.5, 1, 2, 3.5, 4, 8])
plt.savefig('before_boxplot.png')

produces this plot

But when I execute this code next

y1 = np.random.normal(10, 3, 20)
y2 = np.random.normal(3, 1, 20)
ax.boxplot([y1, y2], positions = [1,2])
plt.savefig('after_boxplot.png')

the plot changes to

Three things changed:

1. The x-axis limits used to be 0 to 4. They are now roughly 0.5 to 2.5.
2. The tick marks used to be at [0, 0.5, 1, 2, 3.5, 4]. They are now at [1, 2].
3. The tick mark labels used to be ['a','b','c', '2', '3.5', '4']. They are now ['a', 'b']. Based on the changes in (1) and (2) I would have expected the tick mark labels to be ['c', '2'].

The obvious work around is to set these parameters after you have called axes.boxplot(). However, reseting the axes is not consistent with axes.plot(), axes.bar(), axes.imshow(), or any other plotting method I have used. Other methods respect the user specified x limits and tick marks. This behavior also is not consistent with the y-axis behavior in boxplot. Boxplot respected the user specified y limits and tick marks.

I am working with Matplotlib 1.3.0.