Can't Open Consoles in Spyder 2.3.3

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Chris

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Mar 27, 2015, 3:01:59 AM3/27/15
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Hi,

I have just installed Spyder 2.3.3 on my IMac running OS X 10.10.2. Spyder was downloaded as the file:///Users/cbhe/Downloads/spyder-2.3.3-py2.7-2.dmg from https://bitbucket.org/spyder-ide/spyderlib/downloads and was copied into the Applications folder.

Prior to the installation I removed the three Spyder (V2.3.2) directories in /Library/Python/2.7/site-packages in an attempt to uninstall Spyder. As far as I can tell there is no Uninstall program for Spyder.

The version of Python running is Python 2.7.9rc1 (v2.7.9rc1:40eada278702, Nov 25 2014, 17:25:50)

I am now unable to open a Python or IPython console in Spyder but get the message when trying to open a console:

Traceback (most recent call last):
cannot import name multiarray
cannot import name multiarray  File "/usr/local/lib/python2.7/site-packages/py2app/apptemplate/lib/site.py", line 122, in <module>
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/spyderlib/widgets/externalshell/sitecustomize.py", line 406, in <module>
    class SpyderPdb(pdb.Pdb):
AttributeError: 'module' object has no attribute 'Pdb'

Does anyone have a suggestion as to how I might get Spyder working again? I am now at a stand again as far as actually doing anything useful.

Thanks.


Adrian Klaver

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Mar 27, 2015, 9:36:49 AM3/27/15
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On 03/27/2015 12:01 AM, Chris wrote:
> Hi,
>
> I have just installed Spyder 2.3.3 on my IMac running OS X 10.10.2.
> Spyder was downloaded as the
> file:///Users/cbhe/Downloads/spyder-2.3.3-py2.7-2.dmg from
> https://bitbucket.org/spyder-ide/spyderlib/downloads and was copied into
> the Applications folder.

Is this the same machine as the one we where working with previously?

>
> Prior to the installation I removed the three Spyder (V2.3.2)
> directories in /Library/Python/2.7/site-packages in an attempt to
> uninstall Spyder. As far as I can tell there is no Uninstall program for
> Spyder.

How did you install the previous versions of Spyder?

If you used a dmg, AFAIK there is no uninstall program for *.dmg, you
either drag the drive or the app into Trash and that is it.

>
> The version of Python running is Python 2.7.9rc1
> (v2.7.9rc1:40eada278702, Nov 25 2014, 17:25:50)
>
> I am now unable to open a Python or IPython console in Spyder but get
> the message when trying to open a console:
>
> Traceback (most recent call last):
> cannot import name multiarray
> cannot import name multiarray File
> "/usr/local/lib/python2.7/site-packages/py2app/apptemplate/lib/site.py",
> line 122, in <module>
> File
> "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/spyderlib/widgets/externalshell/sitecustomize.py",
> line 406, in <module>
> class SpyderPdb(pdb.Pdb):
> AttributeError: 'module' object has no attribute 'Pdb'

Looks to me that there is another module in the path named pdb that is
not the official pdb module. In other words it does not include the Pdb
class.

>
> Does anyone have a suggestion as to how I might get Spyder working
> again? I am now at a stand again as far as actually doing anything useful.

What is the version of Spyder you have open as shown in the About menu?

>
> Thanks.
>
>
> --
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--
Adrian Klaver
adrian...@aklaver.com

Chris

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Mar 28, 2015, 7:30:01 AM3/28/15
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Adrian,

Yes same machine and same learner driver. Everything was going well with Metis and Networkx until I tried to install the visualisation packages Pygraphviz and Graphviz. I was unable to get them to work and so (misguidedly) I thought I would try a later version of Spyder.

Previous version of Spyder was 2.3.2. It was installed from the .dmg file by dragging the Spyder icon onto the Applications folder. It was awhile ago and I can't remember any more details.

The current version of Spyder is 2.3.3 and was installed by pip 'pip install spyder'. The  About Spyder menu result is below:

Spyder 2.3.3 
The Scientific PYthon Development EnviRonment 
Copyright © 2009-2012 Pierre Raybaut 
Copyright © 2010-2015 The Spyder Development Team 
Licensed under the terms of the MIT License 
Created by Pierre Raybaut 
Developed and maintained by the Spyder Development Team 
Many thanks to all the Spyder beta-testers and regular users. 
Most of the icons come from the Crystal Project (© 2006-2007 Everaldo Coelho). Other icons by Yusuke Kamiyamane (all rights reserved) and by The Oxygen icon theme. 
For bug reports and feature requests, please go to our Github website. For discussions around the project, please go to our Google Group 
This project is part of a larger effort to promote and facilitate the use of Python for scientific and engineering software development. The popular Python distributions Anaconda, WinPython and Python(x,y) also contribute to this plan. 
Python 2.7.8 64bits, Qt 4.8.6, PyQt4 (API v2) 4.11.1 on Darwin

The error message from the IPython console is

An error ocurred while starting the kernel
Traceback (most recent call last):
cannot import name multiarray
cannot import name multiarray
cannot import name multiarray
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/spyderlib/widgets/externalshell/start_ipython_kernel.py", line 182, in 
from IPython.kernel.zmq.kernelapp import IPKernelApp
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/__init__.py", line 48, in 
from .core.application import Application
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/application.py", line 24, in 
from IPython.core import release, crashhandler
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/crashhandler.py", line 28, in 
from IPython.core import ultratb
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/ultratb.py", line 110, in 
from IPython.core import debugger
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/debugger.py", line 59, in 
from pdb import Pdb as OldPdb
ImportError: cannot import name Pdb

The /Library/Python/2.7/site-packages directory contains

Fl1cker:~ cbhe$ cd /Library/Python/2.7/site-packages;la

/Library/Python/2.7/site-packages

total 120

 0 drwxr-xr-x  10 root  wheel    340 27 Mar 16:24 Babel-1.3-py2.7.egg-info

 0 drwxr-xr-x  10 root  wheel    340 27 Mar 16:24 Jinja2-2.7.3-py2.7.egg-info

 0 drwxr-xr-x   8 root  wheel    272 27 Mar 16:24 MarkupSafe-0.23-py2.7.egg-info

 0 drwxr-xr-x   8 root  wheel    272 26 Mar 16:39 MeshPy-2014.1-py2.7.egg-info

 0 drwxr-xr-x   7 root  wheel    238 26 Mar 16:19 PyMetis-2014.1-py2.7.egg-info

 0 drwxr-xr-x   7 root  wheel    238 27 Mar 15:07 PyVTK-0.4.85-py2.7.egg-info

 0 drwxr-xr-x   9 root  wheel    306 27 Mar 16:24 Pygments-2.0.2.dist-info

 0 -rw-r--r--   1 root  wheel    119 10 Sep  2014 README

 0 drwxr-xr-x   9 root  wheel    306 27 Mar 16:24 Sphinx-1.3.1.dist-info

 0 drwxr-xr-x  55 root  wheel   1870 27 Mar 15:29 _pytest

 0 drwxr-xr-x  14 root  wheel    476 27 Mar 16:24 alabaster

 0 drwxr-xr-x   8 root  wheel    272 27 Mar 16:24 alabaster-0.7.3-py2.7.egg-info

 0 drwxr-xr-x   8 root  wheel    272 26 Mar 16:33 appdirs-1.4.0.dist-info

48 -rw-r--r--   1 root  wheel  22374 26 Mar 16:33 appdirs.py

48 -rw-r--r--   1 root  wheel  20617 26 Mar 16:33 appdirs.pyc

 0 drwxr-xr-x  24 root  wheel    816 27 Mar 16:24 babel

 0 drwxr-xr-x   5 root  wheel    170 10 Mar 22:11 decorator-3.4.0-py2.7.egg

 0 drwxr-xr-x  24 root  wheel    816 27 Mar 16:24 docutils

 0 drwxr-xr-x   7 root  wheel    238 27 Mar 16:24 docutils-0.12-py2.7.egg-info

 8 -rw-r--r--   1 root  wheel    309 10 Mar 22:47 easy-install.pth

 0 drwxr-xr-x  14 root  wheel    476 27 Mar 12:43 graphviz

 0 drwxr-xr-x   8 root  wheel    272 27 Mar 12:43 graphviz-0.4.3.dist-info

 0 drwxr-xr-x  49 root  wheel   1666 27 Mar 16:24 jinja2

 0 drwxr-xr-x  14 root  wheel    476 27 Mar 16:24 markupsafe

 0 drwxr-xr-x  24 root  wheel    816 26 Mar 16:39 meshpy

 0 drwxr-xr-x   5 root  wheel    170 10 Mar 22:11 networkx-1.9.1-py2.7.egg

 0 drwxr-xr-x  34 root  wheel   1156 16 Mar 22:10 pip

 0 drwxr-xr-x  10 root  wheel    340 16 Mar 22:10 pip-6.0.8.dist-info

 0 drwxr-xr-x  25 root  wheel    850 26 Mar 16:33 py

 0 drwxr-xr-x   8 root  wheel    272 26 Mar 16:33 py-1.4.26-py2.7.egg-info

 0 drwxr-xr-x  36 root  wheel   1224 27 Mar 16:24 pygments

 0 drwxr-xr-x   5 root  wheel    170 26 Mar 16:19 pymetis

 0 drwxr-xr-x  10 root  wheel    340 27 Mar 15:29 pytest-2.7.0-py2.7.egg-info

 8 -rw-r--r--   1 root  wheel    498 27 Mar 15:29 pytest.py

 8 -rw-r--r--   1 root  wheel    540 27 Mar 15:29 pytest.pyc

 0 drwxr-xr-x  40 root  wheel   1360 26 Mar 16:33 pytools

 0 drwxr-xr-x   8 root  wheel    272 26 Mar 16:33 pytools-2014.3.5-py2.7.egg-info

 0 drwxr-xr-x  42 root  wheel   1428 27 Mar 15:07 pyvtk

 0 drwxr-xr-x  40 root  wheel   1360 27 Mar 16:24 snowballstemmer

 0 drwxr-xr-x   7 root  wheel    238 27 Mar 16:24 snowballstemmer-1.2.0-py2.7.egg-info

 0 drwxr-xr-x  52 root  wheel   1768 27 Mar 16:24 sphinx

 0 drwxr-xr-x  13 root  wheel    442 27 Mar 16:24 sphinx_rtd_theme

 0 drwxr-xr-x   8 root  wheel    272 27 Mar 16:24 sphinx_rtd_theme-0.1.7.dist-info

 0 drwxr-xr-x   7 root  wheel    238 27 Mar 20:51 spyder-2.3.4-py2.7.egg-info

 0 drwxr-xr-x  48 root  wheel   1632 27 Mar 20:51 spyderlib

 0 drwxr-xr-x  17 root  wheel    578 27 Mar 20:51 spyderplugins

/Library/Python/2.7/site-packages

Fl1cker:site-packages cbhe$ 


I now notice that pip has installed version 2.3.4. I am not sure how this happened, but guess that it is the source of the problem!

So what to do to get out from under??


Adrian Klaver

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Mar 28, 2015, 9:55:50 AM3/28/15
to spyd...@googlegroups.com
On 03/28/2015 04:30 AM, Chris wrote:
>
>
> On Friday, March 27, 2015 at 6:01:59 PM UTC+11, Chris wrote:

> Adrian,
>
> Yes same machine and same learner driver. Everything was going well with
> Metis and Networkx until I tried to install the visualisation packages
> Pygraphviz and Graphviz. I was unable to get them to work and so
> (misguidedly) I thought I would try a later version of Spyder.

Troubleshooting is not made easier by introducing more variables.

>
> Previous version of Spyder was 2.3.2. It was installed from the .dmg
> file by dragging the Spyder icon onto the Applications folder. It was
> awhile ago and I can't remember any more details.

From what I understand the way to uninstall it is to drag the Spyder
icon out of Applications into Trash.

>
> The current version of Spyder is 2.3.3 and was installed by pip 'pip
> install spyder'. The About Spyder menu result is below:
>
> Spyder 2.3.3
> The Scientific PYthon Development EnviRonment
> Copyright © 2009-2012 Pierre Raybaut
> Copyright © 2010-2015 The Spyder Development Team
> Licensed under the terms of the MIT License
> Created by Pierre Raybaut
> Developed and maintained by the Spyder Development Team
> Many thanks to all the Spyder beta-testers and regular users.
> Most of the icons come from the Crystal Project (© 2006-2007 Everaldo
> Coelho). Other icons by Yusuke Kamiyamane (all rights reserved) and by
> The Oxygen icon theme.
> For bug reports and feature requests, please go to our Github website.
> For discussions around the project, please go to our Google Group
> This project is part of a larger effort to promote and facilitate the
> use of Python for scientific and engineering software development. The
> popular Python distributions Anaconda, WinPython and Python(x,y) also
> contribute to this plan.
> Python 2.7.8 64bits, Qt 4.8.6, PyQt4 (API v2) 4.11.1 on Darwin
>

>
> I now notice that pip has installed version 2.3.4. I am not sure how
> this happened, but guess that it is the source of the problem!

So how did you start the 2.3.3 version above?

>
> So what to do to get out from under??

pip uninstall spyder

>
>
> --



--
Adrian Klaver
adrian...@aklaver.com

Chris

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Mar 29, 2015, 12:17:08 AM3/29/15
to spyd...@googlegroups.com


On Friday, March 27, 2015 at 6:01:59 PM UTC+11, Chris wrote:
Adrian,

I uninstalled V2.3.4 with pip and removed Spyder from the Applications folder by dragging it to Trash. I also moved spyderlib to spyderlib.old in the /Library/Python/2.7/site-packages folder. As far as I could tell Spyder was not present.

I then opened the Spyder 2.3.3 .dmg file in the Downloads folder and dragged the Spyder icon to the Applications folder. When I opened Spyder I got the same error message as before. I repeated the process using the Spyder 2.3.2 .dmg but got the same result.

So again I moved spyderlib to spyderlib.old and ran 'pip uninstall spyder'. The contents of the site-packages folder and the result of rerunning 'pip uninstall spyder'  are below.

 sh-3.2# cd /Library/Python/2.7/site-packages;ls -l
total 120
drwxr-xr-x  10 root  wheel    340 27 Mar 16:24 Babel-1.3-py2.7.egg-info
drwxr-xr-x  10 root  wheel    340 27 Mar 16:24 Jinja2-2.7.3-py2.7.egg-info
drwxr-xr-x   8 root  wheel    272 27 Mar 16:24 MarkupSafe-0.23-py2.7.egg-info
drwxr-xr-x   8 root  wheel    272 26 Mar 16:39 MeshPy-2014.1-py2.7.egg-info
drwxr-xr-x   7 root  wheel    238 26 Mar 16:19 PyMetis-2014.1-py2.7.egg-info
drwxr-xr-x   7 root  wheel    238 27 Mar 15:07 PyVTK-0.4.85-py2.7.egg-info
drwxr-xr-x   9 root  wheel    306 27 Mar 16:24 Pygments-2.0.2.dist-info
-rw-r--r--   1 root  wheel    119 10 Sep  2014 README
drwxr-xr-x   9 root  wheel    306 27 Mar 16:24 Sphinx-1.3.1.dist-info
drwxr-xr-x  55 root  wheel   1870 27 Mar 15:29 _pytest
drwxr-xr-x  14 root  wheel    476 27 Mar 16:24 alabaster
drwxr-xr-x   8 root  wheel    272 27 Mar 16:24 alabaster-0.7.3-py2.7.egg-info
drwxr-xr-x   8 root  wheel    272 26 Mar 16:33 appdirs-1.4.0.dist-info
-rw-r--r--   1 root  wheel  22374 26 Mar 16:33 appdirs.py
-rw-r--r--   1 root  wheel  20617 26 Mar 16:33 appdirs.pyc
drwxr-xr-x  24 root  wheel    816 27 Mar 16:24 babel
drwxr-xr-x   5 root  wheel    170 10 Mar 22:11 decorator-3.4.0-py2.7.egg
drwxr-xr-x  24 root  wheel    816 27 Mar 16:24 docutils
drwxr-xr-x   7 root  wheel    238 27 Mar 16:24 docutils-0.12-py2.7.egg-info
-rw-r--r--   1 root  wheel    309 10 Mar 22:47 easy-install.pth
drwxr-xr-x  14 root  wheel    476 27 Mar 12:43 graphviz
drwxr-xr-x   8 root  wheel    272 27 Mar 12:43 graphviz-0.4.3.dist-info
drwxr-xr-x  49 root  wheel   1666 27 Mar 16:24 jinja2
drwxr-xr-x  14 root  wheel    476 27 Mar 16:24 markupsafe
drwxr-xr-x  24 root  wheel    816 26 Mar 16:39 meshpy
drwxr-xr-x   5 root  wheel    170 10 Mar 22:11 networkx-1.9.1-py2.7.egg
drwxr-xr-x  34 root  wheel   1156 16 Mar 22:10 pip
drwxr-xr-x  10 root  wheel    340 16 Mar 22:10 pip-6.0.8.dist-info
drwxr-xr-x  25 root  wheel    850 26 Mar 16:33 py
drwxr-xr-x   8 root  wheel    272 26 Mar 16:33 py-1.4.26-py2.7.egg-info
drwxr-xr-x  36 root  wheel   1224 27 Mar 16:24 pygments
drwxr-xr-x   5 root  wheel    170 26 Mar 16:19 pymetis
drwxr-xr-x  10 root  wheel    340 27 Mar 15:29 pytest-2.7.0-py2.7.egg-info
-rw-r--r--   1 root  wheel    498 27 Mar 15:29 pytest.py
-rw-r--r--   1 root  wheel    540 27 Mar 15:29 pytest.pyc
drwxr-xr-x  40 root  wheel   1360 26 Mar 16:33 pytools
drwxr-xr-x   8 root  wheel    272 26 Mar 16:33 pytools-2014.3.5-py2.7.egg-info
drwxr-xr-x  42 root  wheel   1428 27 Mar 15:07 pyvtk
drwxr-xr-x  40 root  wheel   1360 27 Mar 16:24 snowballstemmer
drwxr-xr-x   7 root  wheel    238 27 Mar 16:24 snowballstemmer-1.2.0-py2.7.egg-info
drwxr-xr-x  52 root  wheel   1768 27 Mar 16:24 sphinx
drwxr-xr-x  13 root  wheel    442 27 Mar 16:24 sphinx_rtd_theme
drwxr-xr-x   8 root  wheel    272 27 Mar 16:24 sphinx_rtd_theme-0.1.7.dist-info
drwxr-xr-x   3 root  wheel    102 29 Mar 13:56 spyderlib.old
sh-3.2# pip uninstall spyder
Cannot uninstall requirement spyder, not installed
sh-3.2#

At this point (as far as I can tell) there is no Spyder application on my system.

What do you recommend I try next to get a working copy of Spyder installed??

Adrian Klaver

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Mar 29, 2015, 10:42:56 AM3/29/15
to spyd...@googlegroups.com
I am not sure which before we are talking about so, which error message
would that be?

>
> So again I moved spyderlib to spyderlib.old and ran 'pip uninstall
> spyder'. The contents of the site-packages folder and the result of
> rerunning 'pip uninstall spyder' are below.
>

> At this point (as far as I can tell) there is no Spyder application on
> my system.
>
> What do you recommend I try next to get a working copy of Spyder installed??

Get the 2.3.4 dmg from here:

https://github.com/spyder-ide/spyder/releases

Install it into Applications and try it. Report back errors. Please do
not do anything else until we have had a chance to look at the errors if
they exist.

Chris

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Mar 29, 2015, 8:46:54 PM3/29/15
to spyd...@googlegroups.com


On Friday, March 27, 2015 at 6:01:59 PM UTC+11, Chris wrote:
Adrian

OK, I downloaded the 2.3.4  dmg as requested, dragged Spyder to the Applications folder, double clicked the icon and Syder opened with the following error messages from the Python and IPython consoles respectively:

cannot import name multiarray
cannot import name multiarray
cannot import name multiarray
Traceback (most recent call last):
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/spyderlib/widgets/externalshell/start_ipython_kernel.py", line 161, in <module>
    from IPython.kernel.zmq.kernelapp import IPKernelApp
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/IPython/__init__.py", line 48, in <module>
    from .core.application import Application
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/IPython/core/application.py", line 24, in <module>
    from IPython.core import release, crashhandler
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/IPython/core/crashhandler.py", line 28, in <module>
    from IPython.core import ultratb
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/IPython/core/ultratb.py", line 110, in <module>
    from IPython.core import debugger
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/IPython/core/debugger.py", line 59, in <module>
    from pdb import Pdb as OldPdb
ImportError: cannot import name Pdb
An error ocurred while starting the kernel
cannot import name multiarray
cannot import name multiarray
cannot import name multiarray

Traceback (most recent call last):
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/spyderlib/widgets/externalshell/start_ipython_kernel.py", line 161, in 

from IPython.kernel.zmq.kernelapp import IPKernelApp
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/__init__.py", line 48, in 
from .core.application import Application
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/application.py", line 24, in 
from IPython.core import release, crashhandler
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/crashhandler.py", line 28, in 
from IPython.core import ultratb
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/ultratb.py", line 110, in 
from IPython.core import debugger
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/debugger.py", line 59, in 
from pdb import Pdb as OldPdb
ImportError: cannot import name Pdb

The About Spyder is:
---------------------------------------------------------------------------------
Spyder 2.3.4 

The Scientific PYthon Development EnviRonment

Copyright © 2009 - 2015 Pierre Raybaut
Copyright © 2010 - 2015 The Spyder Development Team

Licensed under the terms of the MIT License

Created by Pierre Raybaut
Developed and maintained by the Spyder Development Team
Many thanks to all the Spyder beta-testers and regular users.

Most of the icons come from the Crystal Project (© 2006-2007 Everaldo Coelho). Other icons by Yusuke Kamiyamane (all rights reserved) and by The Oxygen icon theme.

For bug reports and feature requests, please go to our Github website. For discussions around the project, please go to our Google Group

This project is part of a larger effort to promote and facilitate the use of Python for scientific and engineering software development. The popular Python distributions Anaconda, WinPython and Python(x,y) also contribute to this plan.

Python 2.7.8 64bits, Qt 4.8.6, PyQt4 (API v2) 4.11.1 on Darwin

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


The directory /Library/Python/2.7/site-packages contains:

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

0 drwxr-xr-x  14 root  wheel    476 27 Mar 12:43 graphviz

 0 drwxr-xr-x   8 root  wheel    272 27 Mar 12:43 graphviz-0.4.3.dist-info

 0 drwxr-xr-x  49 root  wheel   1666 27 Mar 16:24 jinja2

 0 drwxr-xr-x  14 root  wheel    476 27 Mar 16:24 markupsafe

 0 drwxr-xr-x  24 root  wheel    816 26 Mar 16:39 meshpy

 0 drwxr-xr-x   5 root  wheel    170 10 Mar 22:11 networkx-1.9.1-py2.7.egg

 0 drwxr-xr-x  34 root  wheel   1156 16 Mar 22:10 pip

 0 drwxr-xr-x  10 root  wheel    340 16 Mar 22:10 pip-6.0.8.dist-info

 0 drwxr-xr-x  25 root  wheel    850 26 Mar 16:33 py

 0 drwxr-xr-x   8 root  wheel    272 26 Mar 16:33 py-1.4.26-py2.7.egg-info

 0 drwxr-xr-x  36 root  wheel   1224 27 Mar 16:24 pygments

 0 drwxr-xr-x   5 root  wheel    170 26 Mar 16:19 pymetis

 0 drwxr-xr-x  10 root  wheel    340 27 Mar 15:29 pytest-2.7.0-py2.7.egg-info

 8 -rw-r--r--   1 root  wheel    498 27 Mar 15:29 pytest.py

 8 -rw-r--r--   1 root  wheel    540 27 Mar 15:29 pytest.pyc

 0 drwxr-xr-x  40 root  wheel   1360 26 Mar 16:33 pytools

 0 drwxr-xr-x   8 root  wheel    272 26 Mar 16:33 pytools-2014.3.5-py2.7.egg-info

 0 drwxr-xr-x  42 root  wheel   1428 27 Mar 15:07 pyvtk

 0 drwxr-xr-x  40 root  wheel   1360 27 Mar 16:24 snowballstemmer

 0 drwxr-xr-x   7 root  wheel    238 27 Mar 16:24 snowballstemmer-1.2.0-py2.7.egg-info

 0 drwxr-xr-x  52 root  wheel   1768 27 Mar 16:24 sphinx

 0 drwxr-xr-x  13 root  wheel    442 27 Mar 16:24 sphinx_rtd_theme

 0 drwxr-xr-x   8 root  wheel    272 27 Mar 16:24 sphinx_rtd_theme-0.1.7.dist-info

 0 drwxr-xr-x   3 root  wheel    102 29 Mar 13:56 spyderlib.old

/Library/Python/2.7/site-packages

Fl1cker:site-packages cbhe$ exit

logout

[Process completed]

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

I have made no other changes apart from closing the application.

Hope this helps.








Chris

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Apr 9, 2015, 5:22:35 AM4/9/15
to spyd...@googlegroups.com
Adrian,

I was wondering if you had any further thoughts about my problem. In the interim I have tried several clean installs of Yosemite in the hope that I could start again with a clean operating system, but using the Migration Assistant merely copied over all the non OS X files and the result was the same. I then tried to a clean install without the Migration Assistant and it all got too hard, so I reverted to the last backup and am back where I started!

Can you suggest a strategy for me to try to get Spyder working again?


On Friday, March 27, 2015 at 6:01:59 PM UTC+11, Chris wrote:

Adrian Klaver

unread,
Apr 9, 2015, 10:03:55 AM4/9/15
to spyd...@googlegroups.com
On 04/09/2015 02:22 AM, Chris wrote:
> Adrian,
>
> I was wondering if you had any further thoughts about my problem. In the
> interim I have tried several clean installs of Yosemite in the hope that
> I could start again with a clean operating system, but using the
> Migration Assistant merely copied over all the non OS X files and the
> result was the same. I then tried to a clean install without the
> Migration Assistant and it all got too hard, so I reverted to the last
> backup and am back where I started!
>
> Can you suggest a strategy for me to try to get Spyder working again?
>

Hmm. I missed your previous post somewhere along the line. Just went
back to the archives to look at it. Right now I do not have any ideas, I
will need to do some thinking on this.


--
Adrian Klaver
adrian...@aklaver.com

Adrian Klaver

unread,
Apr 10, 2015, 10:19:51 AM4/10/15
to spyd...@googlegroups.com
On 04/09/2015 02:22 AM, Chris wrote:
> Adrian,
>
> I was wondering if you had any further thoughts about my problem. In the
> interim I have tried several clean installs of Yosemite in the hope that
> I could start again with a clean operating system, but using the
> Migration Assistant merely copied over all the non OS X files and the
> result was the same. I then tried to a clean install without the
> Migration Assistant and it all got too hard, so I reverted to the last
> backup and am back where I started!
>
> Can you suggest a strategy for me to try to get Spyder working again?

Looks to me like Spyder cannot find pdb. Not sure why that is?

So does Spyder load the editor portion?

Where do the errors you see show up?

Chris

unread,
Apr 15, 2015, 6:34:10 AM4/15/15
to spyd...@googlegroups.com
Adrian,

Sorry about the delayed response, I have been on the road.

So, I opened Spyder 2.3.3 again and went to Run/Configure and clicked on Run. The attached .pdf of the Run window shows the detail. The result was the appearance of a Python console. So far so good.

I then ran a test file (test_python.py) with the following response.

------------------------------------------------------------
Python 2.7.8 (default, Aug 15 2014, 13:43:01) 
[GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.61)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> runfile('/Users/cbhe/scripts/test_python.py', wdir='/Users/cbhe/scripts')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'runfile' is not defined
>>> 
----------------------------------------------------------

I then opened an IPython console which opened with the following (no prompting from myself)

----------------------------------------
An error ocurred while starting the kernel
Traceback (most recent call last):
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/spyderlib/widgets/externalshell/start_ipython_kernel.py", line 161, in 
from IPython.kernel.zmq.kernelapp import IPKernelApp
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/__init__.py", line 48, in 
from .core.application import Application
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/application.py", line 24, in 
from IPython.core import release, crashhandler
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/crashhandler.py", line 28, in 
from IPython.core import ultratb
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/ultratb.py", line 110, in 
from IPython.core import debugger
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/debugger.py", line 59, in 
from pdb import Pdb as OldPdb
File "/Library/Python/2.7/site‑packages/_pytest/pdb.py", line 6, in 
import pytest
ImportError: No module named pytest
-------------------------------------------
 
Not sure what the above implies, except possibly that I have managed to mangle the installation (I simply opened the .dmg file and clicked on the Spyder icon) in some way.

If this does not help in diagnosing my problem are you able to suggest how I might go about deleting all the files associated with Spyder so I can start again with a clean slate?




On Friday, March 27, 2015 at 6:01:59 PM UTC+11, Chris wrote:
Screen Shot 2015-04-15 at 8.08.21 pm.pdf

Adrian Klaver

unread,
Apr 15, 2015, 10:04:18 AM4/15/15
to spyd...@googlegroups.com
On 04/15/2015 03:34 AM, Chris wrote:
> Adrian,
>
> Sorry about the delayed response, I have been on the road.
>
> So, I opened Spyder 2.3.3 again and went to Run/Configure and clicked on
> Run. The attached .pdf of the Run window shows the detail. The result
> was the appearance of a Python console. So far so good.
>
> I then ran a test file (test_python.py) with the following response.
>
> ------------------------------------------------------------
> Python 2.7.8 (default, Aug 15 2014, 13:43:01)
> [GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.61)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> runfile('/Users/cbhe/scripts/test_python.py',
> wdir='/Users/cbhe/scripts')
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> NameError: name 'runfile' is not defined
> >>>
> ----------------------------------------------------------

So the problem is not that you cannot open a Console it is that a file
will not run it.

So:

1) What happens if you do Consoles --> Open a Python console?

2) If it opens what happens if you do import os?

3) What happens if you Run the file, but leave the Working Directory
unchecked?

4) Under Preferences --> Console --> Advanced Settings, what is the
Python interpreter set to?

>
> I then opened an IPython console which opened with the following (no
> prompting from myself)

How did you open the IPython console?
Not sure why pytest is being called? Also it looks like it jumped from
the Spyder app libraries to the system libraries. Will get to that
problem later.
>
> If this does not help in diagnosing my problem are you able to suggest
> how I might go about deleting all the files associated with Spyder so I
> can start again with a clean slate?

No, that has been done before to no effect. Lets work with what you have.
>
>
>
>



--
Adrian Klaver
adrian...@aklaver.com

Chris Edwards

unread,
Apr 19, 2015, 6:23:36 AM4/19/15
to spyd...@googlegroups.com
Adrian,

I open Spyder, click on  ‘Consoles' and click on 'Open a Python console' and a 'Python 1’ console showing the following:
——————————————————————————————
Python 2.7.8 (default, Aug 15 2014, 13:43:01) 
[GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.61)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> 
—————————————————————————————

I then type 'import os' and get the following:
———————————————————————————
Python 2.7.8 (default, Aug 15 2014, 13:43:01) 
[GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.61)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import os
>>> 
————————————————————————————————

With Global Working Directory unchecked (see attached .pdf) I run a file (test_python.py) and get:
——————————————————————————————
Python 2.7.8 (default, Aug 15 2014, 13:43:01) 
[GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.61)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import os
>>> runfile('/Users/cbhe/scripts/test_python.py', wdir='/Users/cbhe/scripts')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'runfile' is not defined
>>> 
—————————————————————————————————

When I click on ‘Preferences' I get the following:
——————————————————————————————————
Spyder Internal Console

This console is used to report application
internal errors and to inspect Spyder
internals with the following commands:
  spy.app, spy.window, dir(spy)

Please don't use it to run your code

>>> Traceback (most recent call last):
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/spyderlib/spyder.py", line 2048, in edit_preferences
    widget = plugin.create_configwidget(dlg)
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/spyderlib/plugins/__init__.py", line 275, in create_configwidget
    configwidget.initialize()
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/spyderlib/plugins/configdialog.py", line 59, in initialize
    self.setup_page()
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/spyderlib/plugins/ipythonconsole.py", line 410, in setup_page
    sympy_present = programs.is_module_installed("sympy")
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/spyderlib/utils/programs.py", line 284, in is_module_installed
    actver = get_module_version(module_name)
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/spyderlib/utils/programs.py", line 230, in get_module_version
    mod = __import__(module_name)
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/sympy/__init__.py", line 37, in <module>
    from .core import *
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/sympy/core/__init__.py", line 8, in <module>
    from .expr import Expr, AtomicExpr
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/sympy/core/expr.py", line 7, in <module>
    from .evalf import EvalfMixin, pure_complex
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/sympy/core/evalf.py", line 9, in <module>
    import sympy.mpmath.libmp as libmp
AttributeError: 'module' object has no attribute ‘mpmath’
——————————————————————————————————————

When I click on Consoles and then click on Open an IPython cosole I get an IP Kernel and an Ipython Console 1/A showing respectively:
———————————————————————————————
Traceback (most recent call last):
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/spyderlib/widgets/externalshell/start_ipython_kernel.py", line 161, in <module>
    from IPython.kernel.zmq.kernelapp import IPKernelApp
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/IPython/__init__.py", line 48, in <module>
    from .core.application import Application
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/IPython/core/application.py", line 24, in <module>
    from IPython.core import release, crashhandler
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/IPython/core/crashhandler.py", line 28, in <module>
    from IPython.core import ultratb
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/IPython/core/ultratb.py", line 110, in <module>
    from IPython.core import debugger
  File "/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/IPython/core/debugger.py", line 59, in <module>
    from pdb import Pdb as OldPdb
  File "/Library/Python/2.7/site-packages/_pytest/pdb.py", line 6, in <module>
    import pytest
ImportError: No module named pytest


An error ocurred while starting the kernel
Traceback (most recent call last):
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/spyderlib/widgets/externalshell/start_ipython_kernel.py", line 161, in 
from IPython.kernel.zmq.kernelapp import IPKernelApp
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/__init__.py", line 48, in 
from .core.application import Application
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/application.py", line 24, in 
from IPython.core import release, crashhandler
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/crashhandler.py", line 28, in 
from IPython.core import ultratb
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/ultratb.py", line 110, in 
from IPython.core import debugger
File "/Applications/Spyder‑Py2.app/Contents/Resources/lib/python2.7/IPython/core/debugger.py", line 59, in 
from pdb import Pdb as OldPdb
File "/Library/Python/2.7/site‑packages/_pytest/pdb.py", line 6, in 
import pytest
ImportError: No module named pytest
—————————————————————————————————

When I run spy.app, spy.window and dir(spy) from the Spyder Internal Console I get:
———————————————————————————————
<spyderlib.utils.qthelpers.MacApplication object at 0x108457f28>

>>> spy.window
<spyderlib.spyder.MainWindow object at 0x1140538a0>

>>> dir(spy)
['app', 'versions', 'window']
——————————————————————————————

I really hope this helps.

Regards

Chris





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Screen Shot 2015-04-19 at 7.46.28 pm.pdf

Adrian Klaver

unread,
Apr 19, 2015, 4:15:18 PM4/19/15
to spyd...@googlegroups.com
On 04/19/2015 03:23 AM, Chris Edwards wrote:
> Adrian,
>
> I open Spyder, click on ‘Consoles' and click on 'Open a Python console'
> and a 'Python 1’ console showing the following:
> ——————————————————————————————
> Python 2.7.8 (default, Aug 15 2014, 13:43:01)
> [GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.61)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>>
> —————————————————————————————
>
> I then type 'import os' and get the following:
> ———————————————————————————
> Python 2.7.8 (default, Aug 15 2014, 13:43:01)
> [GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.61)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import os
> >>>
> ————————————————————————————————
>
> With Global Working Directory unchecked (see attached .pdf) I run a file
> (test_python.py) and get:

Wrong check box. Look for the one in Run --> Configure

Unchecking Global Working Directory just removes the Working Directory
toolbar from the application.

> ——————————————————————————————
> <http://programs.is>_module_installed("sympy")
I have no idea what is going on. Someone who understand the mess that is
OS X will need to help you with this.

>
> I really hope this helps.
>
> Regards
>
> Chris
>
>
>
>
>
>> On 16 Apr 2015, at 12:04 am, Adrian Klaver <adrian...@aklaver.com
>> adrian...@aklaver.com <mailto:adrian...@aklaver.com>
>>
>> --
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>
>
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--
Adrian Klaver
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Chris Edwards

unread,
Apr 19, 2015, 9:50:54 PM4/19/15
to spyd...@googlegroups.com
Adrian,

I unchecked the Run —> Configure Working Directory (see attached .pdf file) as requested.

I then ran the test file and got the following:

Python 2.7.8 (default, Aug 15 2014, 13:43:01)
[GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.61)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> runfile('/Users/cbhe/scripts/test_python.py')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
NameError: name 'runfile' is not defined
>>>

I also found an IDL 'Python 2.7.9rc1 Shell’ window on the desktop showing:

Python 2.7.9rc1 (v2.7.9rc1:40eada278702, Nov 25 2014, 17:25:50)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "copyright", "credits" or "license()" for more information.
>>> WARNING: The version of Tcl/Tk (8.5.9) in use may be unstable.
Visit http://www.python.org/download/mac/tcltk/ for current information.

I tried to replicate this but was unable to get the IDL window again.

Perhaps the ‘unstable’ warning is a clue?

Chris



Screen Shot 2015-04-20 at 11.36.57 am.pdf

Adrian Klaver

unread,
Apr 20, 2015, 10:05:41 AM4/20/15
to spyd...@googlegroups.com
The clue is that you have two different versions of Python on your
machine, 2.7.8 which looks to be the version that comes with the Spyder
dmg and 2.7.9rc1 which looks to be the system(OS X) version. The only
thing I have left is:

Go to Preferences --> Console --> Advanced Settings and see what the
Python executable is set to. If 'Use the following Python executable' is
not checked and set to the OS X version of Python, then change it to the
OS X Python and check it.

>
> Chris
>
>
>


--
Adrian Klaver
adrian...@aklaver.com

Chris

unread,
Apr 24, 2015, 9:17:04 AM4/24/15
to spyd...@googlegroups.com
I went to Preferences as you suggested and could not get any further as I got the kernel error again.
I tried tried for a clean install of Spyder. I uninstalled it using pip and then downloaded the DMG file again and reinstalled. But I did not get a clean install because the reinstalled Spyder found my old PATH and script files and it behaved exactly the same when I tried to go to Preferences.
Clearly uninstalling it with pip does not remove all the associated files.
So the question is how to uninstall Spyder so that I can get a clean install and start over?


On Friday, March 27, 2015 at 6:01:59 PM UTC+11, Chris wrote:

Adrian Klaver

unread,
Apr 24, 2015, 10:42:49 AM4/24/15
to spyd...@googlegroups.com
On 04/24/2015 06:17 AM, Chris wrote:
> I went to Preferences as you suggested and could not get any further as
> I got the kernel error again.
> I tried tried for a clean install of Spyder. I uninstalled it using pip
> and then downloaded the DMG file again and reinstalled. But I did not
> get a clean install because the reinstalled Spyder found my old PATH and
> script files and it behaved exactly the same when I tried to go to
> Preferences.
> Clearly uninstalling it with pip does not remove all the associated files.
> So the question is how to uninstall Spyder so that I can get a clean
> install and start over?

Well I am pretty sure pip is not going to uninstall the dmg version of
Spyder. It will only uninstall any system version.

You need to remember a dmg is short for disk image

http://en.wikipedia.org/wiki/Apple_Disk_Image

It is a self contained unit that creates a virtual disk on your machine.
To uninstall it see here:

https://gigaom.com/2008/04/22/beginning-mac-application-installuninstall/

Chris

unread,
Apr 25, 2015, 4:07:04 AM4/25/15
to spyd...@googlegroups.com
Adrian,

I tried several likely uninstallers but no joy. It seemed that there was always a file not found.

Finally Carlos provided the 'silver bullet' answer on another forum. This was the single command line

rm -Rf ~/.spyder2


I can now run both the OS X 10.10.3 and Windows 7 instances of Spyder. I am left wondering why such a great product like Spyder does not provide the ability to reset back to a clean installation.

So, this closes the thread and I am now back to solving the Graphviz problem that started this Odyssey.

Thank you for your patience with this dummy user.


On Friday, March 27, 2015 at 6:01:59 PM UTC+11, Chris wrote:
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