Are you saying that parts of the figure are drawn outside the bounding box when you include the PGF code in LaTeX? Are you having any trouble with PDF produced by the PGF backend? Can you post some example code that illustrates the problem you are having?

I just tried savefig() sending it to a pdf file and it has the same issue. The bounding box looks to be positioned correctly though. Incidentally, if I run this in ipython notebook, the pdf works although the notebook might be using a different backend for pdf, although I'm not sure.

import numpy as np
import matplotlib as mpl
mpl.use('pgf')
import matplotlib.pyplot as plt

fig = plt.figure(1)
ax1 = fig.add_subplot(121)
ax2 = fig.add_subplot(122)

plt.tight_layout()
extent1 = ax1.get_window_extent().transformed(fig.dpi_scale_trans.inverted())
fig.savefig('test.pgf', bbox_inches=extent1)
fig.savefig('test.pdf', bbox_inches=extent1)
plt.show()

Sorry about closed/open I'm new to github

Hm, I think the actual problem is that I never implemented support for user defined extents in bbox_inches :). I did some changes for making bbox_inches='tight' work, but that seems to be a completely different mechanism.

Actually, the output isn't completely wrong. As you said, the size of the bounding box is right, the point of origin seems to be good, it appears to be some problem with the scaling. I had some problems with hardcoded dpi values in matplotlib earlier, maybe this is yet another of these cases.

Yep, set fig.savefig('test.pdf', bbox_inches=extent1, dpi=72.) as a workaround when working with the pgf backend. I'll try to find the hardcoded dpi value.

Yup, that worked for the pdf, but not the pgf as you mentioned.

If the first call of
\pgfusepath{use as bounding box}%
is changed to
\pgfusepath{use as bounding box, clip}%
then the pgf file works in my latex document. Looks like this happens at line 794 of backend_pgf.py

Ah ok, so in addition to the scaling error, "use as bounding box" doesn't seem to prevent pgf from drawing outside the boundaries. I'll include this in the fix for this issue.