Can't import matplotlib.pyplot in Sage 6.2

[Jim Clark]

Hello,

A script that I wrote in April under Sage 6.1.1 stopped working; attempting to import matplotlib.pyplot produces an error:

Jims-computer:HW2 jim$ sage

┌────────────────────────────────────────────────────────────────────┐

│ Sage Version 6.2, Release Date: 2014-05-06                         │

│ Type "notebook()" for the browser-based notebook interface.        │

│ Type "help()" for help.                                            │

└────────────────────────────────────────────────────────────────────┘

sage: import matplotlib.pyplot as mpl

---------------------------------------------------------------------------

ImportError                               Traceback (most recent call last)

<ipython-input-1-0309ea03fddd> in <module>()

----> 1 import matplotlib.pyplot as mpl

/Applications/sage/local/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-macosx-10.9-x86_64.egg/matplotlib/pyplot.py in <module>()

     96 

     97 from matplotlib.backends import pylab_setup

---> 98 _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()

     99 

    100 

/Applications/sage/local/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-macosx-10.9-x86_64.egg/matplotlib/backends/__init__.pyc in pylab_setup()

     26     # imports. 0 means only perform absolute imports.

     27     backend_mod = __import__(backend_name,

---> 28                              globals(),locals(),[backend_name],0)

     29 

     30     # Things we pull in from all backends

/Applications/sage/local/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-macosx-10.9-x86_64.egg/matplotlib/backends/backend_tkagg.py in <module>()

      9 

     10 # Paint image to Tk photo blitter extension

---> 11 import matplotlib.backends.tkagg as tkagg

     12 

     13 from matplotlib.backends.backend_agg import FigureCanvasAgg

/Applications/sage/local/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-macosx-10.9-x86_64.egg/matplotlib/backends/tkagg.py in <module>()

      1 from __future__ import print_function

----> 2 from matplotlib.backends import _tkagg

      3 import Tkinter as Tk

      4 

      5 def blit(photoimage, aggimage, bbox=None, colormode=1):

ImportError: cannot import name _tkagg

sage: 

Downloaded and installed the Sage 6.2 binary on OSX 10.9.3.

Seems like a regression error, but I don’t know how to fix it…

Please help.

Thank you,

Jim Clark

[kcrisman]

Hi!  Is it possible that some locations changed in your installation?  Here is an old post that has a very similar error:

https://groups.google.com/forum/#!topic/sage-support/fV2VNL-5UuY

Otherwise, perhaps the problem may be the one described here:

http://ask.sagemath.org/question/626/sage-python-import-matplotlib-no-module-named

in which case the binary was probably compiled without tkagg support, which is normal.  You could Compile Sage from scratch, perhaps could redo matplotlib.  See also http://ask.sagemath.org/question/3962/gui-backend-matplotlib-in-sage

Now, we did upgrade matplotlib in http://trac.sagemath.org/ticket/14993 so I wouldn't be surprised if that did cause some problems (there were several tickets fixed) but it is a little surprising that this is the one, since we have this same line in the documentation at 

http://www.sagemath.org/doc/reference/plotting/sage/plot/plot.html#sage.plot.plot.SelectiveFormatter

I hope that ONE of these things helps, but I'm sorry if not - in that event, any other platform details would be very helpful for us.

[Jim Clark]

Thank you for the response, kcrisman (sorry I don’t know your first name).

Configuration: Apple MacBook pro running OSX 10.9.3

Downloaded and installed vanilla sage-6.2-x86_64-Darwin-OSX_10.9_x86_64.dmg

I have set export SAGE_MATPLOTLIB_GUI=no in my .bash_profile (due to a similar situation in the past. I only want to use matplotlib to save to .png files, not to view interactively.) I am happy with Sage being built without tkagg support.

(I also have python, scipy, matplotlib, etc. installed via macports, but Sage has always worked as a stand-alone environment, which pleases me. I work in the two environments independently. macports stuff is up-to-date.)

Has anyone else experienced this problem? The test is exceedingly simple:

sage: import matplotlib.pyplot as plt

I actually found the same reports you suggest via Google before submitting this question to sage-support.

What I have attempted:

1. Acting on http://ask.sagemath.org/question/626/sage-python-import-matplotlib-no-module-named, I edited 

/Applications/sage/local/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-macosx-10.9-x86_64.egg/matplotlib/backends/tkagg.py

changed import _tkagg

to import backend_tkagg as _tkagg

which then caused the error

ImportError: cannot import name backend_tkagg

2. Acting on http://ask.sagemath.org/question/3962/gui-backend-matplotlib-in-sage, I rebuilt matplotlib via sage -f matplotlib

That failed, probably for the reason explained in that report, so I reinstalled vanilla Sage 6.2

If I am the only person experiencing this problem, then it must be something in my configuration,

but I’d really like to know if this is a problem in the Sage 6.2 distribution, so it can get fixed.

Thanks to all,

Jim

On May 27, 2014, at 9:33 AM, kcrisman <kcri...@gmail.com> wrote:

[kcrisman]

Thank you for the response, kcrisman (sorry I don’t know your first name).

No problem - very long ago I just chose this handle.

 

Thanks for your config info - I don't see why any of this should affect it, thankfully, though I'm sorry you have had such trouble!  Glad you found the other references; this is puzzling, I agree.  It can't be universal or the doctest I mentioned earlier would be failing.

In fact, one test you could do is to test that one file.  You'd have to cd into the actual Sage-6.2-... directory and then do

./sage -t src/sage/plot/plot.py

 

I think so, at least - the syntax seems to have changed somewhat with the change in the directory layout.

Has anyone else experienced this problem? The test is exceedingly simple:

sage: import matplotlib.pyplot as plt

This is working for me, on 10.7 built from scratch, though; I haven't tried the binary.

Can someone who has access to 10.9 Mavericks download the binary and see if this is a problem?  My suspicion is that something went wrong in the compilation of the binary, though I can't say what.

- kcrisman

[Jim Clark]

On May 28, 2014, at 5:11 AM, kcrisman <kcri...@gmail.com> wrote:

In fact, one test you could do is to test that one file.  You'd have to cd into the actual Sage-6.2-... directory and then do

./sage -t src/sage/plot/plot.py

 

Fails the test (same error: cannot import name _tkagg):

Jims-computer:sage jim$ ./sage -t src/sage/plot/plot.py

init.sage does not exist ... creating

Running doctests with ID 2014-05-28-09-13-04-3aafce8a.

Doctesting 1 file.

sage -t src/sage/plot/plot.py

**********************************************************************

File "src/sage/plot/plot.py", line 262, in sage.plot.plot

Failed example:

    from pylab import *

… (skipping)

        from matplotlib.backends import _tkagg

    ImportError: cannot import name _tkagg

… (skipping much more)

3 items had failures:

  11 of  77 in sage.plot.plot

   7 of  12 in sage.plot.plot.SelectiveFormatter

   7 of  12 in sage.plot.plot.SelectiveFormatter.None._SelectiveFormatterClass.__init__

    [374 tests, 25 failures, 93.39 s]

----------------------------------------------------------------------

sage -t src/sage/plot/plot.py  # 25 doctests failed

----------------------------------------------------------------------

Total time for all tests: 93.8 seconds

    cpu time: 70.3 seconds

    cumulative wall time: 93.4 seconds

I captured the entire output into a log file that I could send, if that would help.

Still the question remains: does anyone else experience the failure on Mac OSX 10.9 when you do:

sage: import matplotlib.pyplot as plt

Again, thanks,

Jim

[John H Palmieri]

Try this: start a new Sage session and do

    sage: import matplotlib
    sage: matplotlib.get_backend()

What does it return? If it returns 'TkAgg', try

    sage: matplotlib.use('agg')

    sage: import matplotlib.pyplot as plt

Let us know what happens.

--
John

[John H Palmieri]

Oh, and to answer your other question: I just downloaded the Sage binary on an OS X Mavericks 10.9.3 machine and was unable to replicate the problem. I wonder if the presence of the macports stuff is interfering somehow. Have you set any environment variables related to matplotllib (other than SAGE_MATPLOTLIB_GUI)?

--
John

[Jim Clark]

On May 28, 2014, at 10:15 AM, John H Palmieri <jhpalm...@gmail.com> wrote:

Try this: start a new Sage session and do

    sage: import matplotlib
    sage: matplotlib.get_backend()

What does it return? If it returns 'TkAgg', try

    sage: matplotlib.use('agg')
    sage: import matplotlib.pyplot as plt

Let us know what happens.

ims-computer:~ jim$ sage

┌────────────────────────────────────────────────────────────────────┐

│ Sage Version 6.2, Release Date: 2014-05-06                         │

│ Type "notebook()" for the browser-based notebook interface.        │

│ Type "help()" for help.                                            │

└────────────────────────────────────────────────────────────────────┘

sage: import matplotlib

sage: matplotlib.get_backend()

'TkAgg'

sage: matplotlib.use('agg')

sage: import matplotlib.pyplot as plt

sage: 

Success! A work-around (albeit an obscure one…)

Jim

[Jim Clark]

On May 28, 2014, at 10:21 AM, John H Palmieri <jhpalm...@gmail.com> wrote:

Oh, and to answer your other question: I just downloaded the Sage binary on an OS X Mavericks 10.9.3 machine and was unable to replicate the problem. I wonder if the presence of the macports stuff is interfering somehow. Have you set any environment variables related to matplotllib (other than SAGE_MATPLOTLIB_GUI)?

Short answer: no.  Could be PATH or PYTHONPATH ?

Jims-computer:~ jim$ env

TERM_PROGRAM=Apple_Terminal

SHELL=/bin/bash

TERM=xterm-256color

TMPDIR=/var/folders/7f/87pw4jw1691785kvc9kw2lkr0000gv/T/

Apple_PubSub_Socket_Render=/tmp/launch-rgHVzO/Render

TERM_PROGRAM_VERSION=326

TERM_SESSION_ID=3E9FF6BD-7ADF-42F9-A763-BF3EC2E001B2

USER=jim

SAGE_BROWSER=open -a "/Applications/Google Chrome.app"

SSH_AUTH_SOCK=/tmp/launch-9nUl4C/Listeners

__CF_USER_TEXT_ENCODING=0x1FB:0:0

PATH=/opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Applications/sage:/usr/local/cuda/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/texbin:/usr/local/bin

__CHECKFIX1436934=1

PWD=/Users/jim

EDITOR=/usr/bin/edit

LANG=en_US.UTF-8

SHLVL=1

HOME=/Users/jim

DYLD_LIBRARY_PATH=/usr/local/cuda/lib:

PYTHONPATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages:

LOGNAME=jim

SAGE_MATPLOTLIB_GUI=no

SECURITYSESSIONID=186a5

_=/usr/bin/env

Also…

~/.matplotlib/matplotlibrc contains

backend:  TkAgg

I’ll try moving this out of the way…

Jim

[Jim Clark]

On May 28, 2014, at 10:42 AM, Jim Clark <jimfort...@earthlink.net> wrote:

Also…

~/.matplotlib/matplotlibrc contains

backend:  TkAgg

I’ll try moving this out of the way…

Found the culprit! Renamed matplotlibrc to matplotlibrc.bak,

started a fresh terminal window and restarted Sage

and now import matplotlib.pyplot as plt works.

Thanks, John Palmieri — your suggestion led me to the source of the problem.

Perhaps I need to find a better way to insulate macports from Sage…

Jim

[John H Palmieri]

It looks like the actual problem is a bug in Sage (which has been fixed in the beta releases of Sage 6.3). Namely, when Sage runs, it is supposed to use ~/.sage/matplotlib-1.3.1 rather than ~/.matplotlib for matplotlib configuration (just for your sort of situation), but this doesn't work right in Sage 6.2. This is fixed at http://trac.sagemath.org/ticket/16305, in case you want to make the change to your copy of Sage 6.2.

--
John

[Jim Clark]

On May 28, 2014, at 11:26 AM, John H Palmieri <jhpalm...@gmail.com> wrote:

It looks like the actual problem is a bug in Sage (which has been fixed in the beta releases of Sage 6.3). Namely, when Sage runs, it is supposed to use ~/.sage/matplotlib-1.3.1 rather than ~/.matplotlib for matplotlib configuration (just for your sort of situation), but this doesn't work right in Sage 6.2. This is fixed athttp://trac.sagemath.org/ticket/16305, in case you want to make the change to your copy of Sage 6.2.

Ahh, so it is a bug.. I’m glad it’s been found and fixed. I’ll wait for Sage 6.3, since I now have a workaround.

Thanks again for your help.

Jim

[kcrisman]

It looks like the actual problem is a bug in Sage (which has been fixed in the beta releases of Sage 6.3). Namely, when Sage runs, it is supposed to use ~/.sage/matplotlib-1.3.1 rather than ~/.matplotlib for matplotlib configuration (just for your sort of situation), but this doesn't work right in Sage 6.2. This is fixed athttp://trac.sagemath.org/ticket/16305, in case you want to make the change to your copy of Sage 6.2.

Ahh, so it is a bug.. I’m glad it’s been found and fixed. I’ll wait for Sage 6.3, since I now have a workaround.

Thanks again for your help.

Jim

Awesome resolution.  Thanks for helping on this, John.  I don't know why the rc file didn't occur to me, that often has been a problem in the past, as you say.

- kcrisman