Python matplotlib ValueError for logit scale axis label

Question

I'm getting what looks like a label positioning error when setting a label for a logit scale axis using matplotlib, here's my example:

import matplotlib.pyplot as plt;
from matplotlib.ticker import FormatStrFormatter;

x = [1,2,3,4,5];
y = [0.1,0.2,0.3,0.4,0.5];

fig,ax = plt.subplots();

ax.set_ylim([0.005,0.99]);
ax.set_yscale('logit');
ax.yaxis.set_minor_formatter(FormatStrFormatter(""));   

ax.set_xlabel("X axis");
ax.set_ylabel("Y axis"); #set y axis label (logit scale)

ax.plot(x,y);
plt.show();
plt.close();

Here's the trace:

Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/matplotlib/backends/backend_macosx.py", line 136, in _draw
    self.figure.draw(renderer)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/matplotlib/artist.py", line 63, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/matplotlib/figure.py", line 1143, in draw
    renderer, self, dsu, self.suppressComposite)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/matplotlib/image.py", line 139, in _draw_list_compositing_images
    a.draw(renderer)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/matplotlib/artist.py", line 63, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/matplotlib/axes/_base.py", line 2409, in draw
    mimage._draw_list_compositing_images(renderer, self, dsu)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/matplotlib/image.py", line 139, in _draw_list_compositing_images
    a.draw(renderer)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/matplotlib/artist.py", line 63, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/matplotlib/axis.py", line 1150, in draw
    self.label.draw(renderer)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/matplotlib/artist.py", line 63, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/matplotlib/text.py", line 762, in draw
    raise ValueError("posx and posy should be finite values")
ValueError: posx and posy should be finite values

Works great when I omit

ax.set_ylabel("Y axis"); #set y axis label (logit scale)

It doesn't seem to matter of the label is set before or after the axis scale. Anyone know how to work around this?

Answer 1

There is a bug in the way the text label is set, which results in a non-numeric bounding box for logit scales, see this issue on GitHub.

The solution is to add

ax.spines['left']._adjust_location()

(where 'left' can be replaced by 'right', 'top', 'bottom' depending on the axis one is interested in) in the code.

Complete example:

import matplotlib.pyplot as plt

x = [1,2,3,4,5]
y = [0.05,0.2,0.3,0.4,0.95]

fig,ax = plt.subplots()

ax.set_yscale('logit')

ax.set_xlabel("X axis")
ax.set_ylabel("Y axis")
ax.spines['left']._adjust_location()

ax.plot(x,y)
plt.show()