Matplotlib issue on OS X ("ImportError: cannot import name _thread")

Question

At some point in the last few days, Matplotlib stopped working for me on OS X. Here's the error I get when trying to import matplotlib:

Traceback (most recent call last):
  File "/my/path/to/script/my_script.py", line 15, in <module>
    import matplotlib.pyplot as plt
  File "/Library/Python/2.7/site-packages/matplotlib/pyplot.py", line 34, in <module>
    from matplotlib.figure import Figure, figaspect
  File "/Library/Python/2.7/site-packages/matplotlib/figure.py", line 40, in <module>
    from matplotlib.axes import Axes, SubplotBase, subplot_class_factory
  File "/Library/Python/2.7/site-packages/matplotlib/axes/__init__.py", line 4, in <module>
    from ._subplots import *
  File "/Library/Python/2.7/site-packages/matplotlib/axes/_subplots.py", line 10, in <module>
    from matplotlib.axes._axes import Axes
  File "/Library/Python/2.7/site-packages/matplotlib/axes/_axes.py", line 22, in <module>
    import matplotlib.dates as _  # <-registers a date unit converter
  File "/Library/Python/2.7/site-packages/matplotlib/dates.py", line 126, in <module>
    from dateutil.rrule import (rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY,
  File "/Library/Python/2.7/site-packages/dateutil/rrule.py", line 14, in <module>
    from six.moves import _thread
ImportError: cannot import name _thread

The only system change I can think of was the Apple-forced NTP update and maybe some permission changes I did in /usr/local to get Brew working again.

I tried reinstalling both Matplotlib and Python-dateutil via Pip, but this did not help. Also tried a reboot. I'm running Python 2.7.6, which is located in /usr/bin/python. I'm running Yosemite (OS X 10.10.1).

Answer 1

sudo pip uninstall python-dateutil
sudo pip install python-dateutil==2.2

I had the same error message this afternoon as well, although I did recently upgrade to Yosemite. I'm not totally sure I understand why reverting dateutil to a previous version works for me, but since running the above I'm having no trouble (I generally use pyplot inline in an ipython notebook).

Answer 2

This problem is fixed in the latest six and dateutil versions. However, in OS X, even if you update your six to the latest version, you might not actually update it correctly. This is what happened to me:

After doing a pip2 install six -U, the new six module was installed in /Library/Python/2.7/site-packages/. However, when I loaded six in a python 2.7 terminal, and checked its path, this is what I got:

import six
print six.__file__
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/six.pyc

So, python was using an old version of six, which I removed by typing:

rm -rf /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/six.*

This fixed this issue for me.

Answer 3

Installing the python-dateutil==2.2 did not work for me.

But a quick-and-dirty workaround did work! I replace six.py in python 2.7 with the six.py from python 3.4 (virtualenv). Since, I have the problem in 2.7 but not 3.4.

UPDATE

I had the same problem again after reinstalling python (and after upgrading to El Capitan). Un-obvious thing is that this error occurs only in the IPython shell and notebook (when I do import matplotlib.pyplot as plt) but works fine from a Python shell.

So a better solution (that did work in my case) without a dirty work-around is to force install both six and ipython. Here is what I did to have this fixed :

$ pip install --ignore-installed six
$ pip install --ignore-installed ipython

Answer 4

It is possible that you have a perfectly installed version of any packages you have installed, but the version used by default is not the one you want. You can see the list of paths that python search from in order to find its packages as follows:

>>> import sys
>>> sys.path

In order to let python search first the most updated version of certain package, instead of removing the system version, what can be done is to set the system variable PYTHONPATH in the ~/.bash_profile (or ~/.bashrc if linux) config file to the path where the new packages are installed:

export PYTHONPATH=/Library/Python/2.7/site-packages

An alternative is to modify the python path inside your python script by adding the path at the beginning of the path list:

import sys
sys.path.insert(1,'/Library/Python/2.7/site-packages')

This needs to be done for every script you need a certain package version. You might want for some reason use an older version that you have installed. BTW all my installations with easy_install, or pip, or from sources go to /Library/Python/2.7/site-packages This worked en EL Capitan, and now also in macOS Sierra (10.12.2)