Logarithmic y-axis bins in python

try

plt.yscale('log', nonposy='clip')

http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.yscale

The issue is with the bottom of bars being at y=0 and the default is to mask out in-valid points (log(0) -> undefined) when doing the log transformation (there was discussion of changing this, but I don't remember which way it went) so when it tries to draw the rectangles for you bar plot, the bottom edge is masked out -> no rectangles.

np.logspace returns bins in [1-10], logarithmically spaced - in my case xx is a npvector >0 so the following code does the trick

logbins=np.max(xx)*(np.logspace(0, 1, num=1000) - 1)/9
hh,ee=np.histogram(xx, density=True, bins=logbins)