IPython problems on Ubuntu 12.04

[ceball]

$ cat /etc/issue
Ubuntu 12.04.3 LTS \n \l

I followed the instructions for installing dependencies on Ubuntu (http://topographica.org/Downloads/index.html#quick-recipe-for-ubuntu-linux). I then cloned the repository. When I ran ./topographica, I got:

INFO:root:Time: 000000.00 CommandLine: Creating /home/ceball/Documents/Topographica
INFO:root:Time: 000000.00 OpenMP: Using 2 threads on a machine with 2 detected CPUs
Output path: /home/ceball/Documents/Topographica

Welcome to Topographica!

Type help() for interactive help with python, help(topo) for general
information about Topographica, help(commandname) for info on a
specific command, or topo.about() for info on this release, including
licensing information.

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/home/ceball/uoe/topographica/topographica in <module>()
     35 # Process the command-line arguments

     36 from topo.misc.commandline import process_argv
---> 37 process_argv(argv[1:])

/home/ceball/uoe/topographica/topo/misc/commandline.py in process_argv(argv)
    663
    664             # Load Topographica IPython extension in embedded shell

--> 665             ipshell.extension_manager.load_extension('topo.misc.ipython')
    666             ipshell()
    667             sys.exit()

/usr/lib/python2.7/dist-packages/IPython/core/extensions.pyc in load_extension(self, module_str)
     85         if module_str not in sys.modules:
     86             with prepended_to_syspath(self.ipython_extension_dir):
---> 87                 __import__(module_str)
     88         mod = sys.modules[module_str]
     89         return self._call_load_ipython_extension(mod)

/home/ceball/uoe/topographica/topo/misc/ipython.py in <module>()
     17     from IPython.display import HTML, Javascript, display
     18 except:
---> 19     from nose.plugins.skip import SkipTest
     20     raise SkipTest("IPython extension requires IPython >= 0.12")
     21

ImportError: No module named nose.plugins.skip
>>> 

I then did 'apt-get install python-nose', which changed the error to:

---------------------------------------------------------------------------
SkipTest                                  Traceback (most recent call last)
/home/ceball/uoe/topographica/topographica in <module>()
     35 # Process the command-line arguments

     36 from topo.misc.commandline import process_argv
---> 37 process_argv(argv[1:])

/home/ceball/uoe/topographica/topo/misc/commandline.pyc in process_argv(argv)
    663
    664             # Load Topographica IPython extension in embedded shell

--> 665             ipshell.extension_manager.load_extension('topo.misc.ipython')
    666             ipshell()
    667             sys.exit()

/usr/lib/python2.7/dist-packages/IPython/core/extensions.pyc in load_extension(self, module_str)
     85         if module_str not in sys.modules:
     86             with prepended_to_syspath(self.ipython_extension_dir):
---> 87                 __import__(module_str)
     88         mod = sys.modules[module_str]
     89         return self._call_load_ipython_extension(mod)

/home/ceball/uoe/topographica/topo/misc/ipython.py in <module>()
     18 except:
     19     from nose.plugins.skip import SkipTest
---> 20     raise SkipTest("IPython extension requires IPython >= 0.12")
     21
     22

SkipTest: IPython extension requires IPython >= 0.12
>>> 

Based on "IPython.core.display or IPython.display ?" (http://python.6.x6.nabble.com/IPython-core-display-or-IPython-display-td5023256.html), I made a change that solved the problem for me:

$ git diff
diff --git a/topo/misc/ipython.py b/topo/misc/ipython.py
index c8edbff..315670b 100644
--- a/topo/misc/ipython.py
+++ b/topo/misc/ipython.py
@@ -14,7 +14,7 @@ from matplotlib import pyplot as plt

 try:
     from IPython.core.pylabtools import print_figure
-    from IPython.display import HTML, Javascript, display
+    from IPython.core.display import HTML, Javascript, display
 except:
     from nose.plugins.skip import SkipTest
     raise SkipTest("IPython extension requires IPython >= 0.12")

[ceball]

The version of IPython:

topo_t000000.00_c1>>> import IPython
topo_t000000.00_c2>>> IPython.__version__
               Out[2]:'0.12.1'

[jbednar]

That's odd, since doozy is running Ubuntu 12.04 and tests pass there. Jean-Luc would want us to have a newer IPython (it's now at 1.1, I think!), but we do still need to make sure it runs on Ubuntu 12.04, which is not all that old and is a "Long-Term Stable" release.

[ceball]

Maybe doozy's version of ipython has been upgraded independently of apt? Note /usr/local below:

ceball@doozy:~/topographica$ ./topographica 
INFO:root:Time: 000000.00 CommandLine: Creating /home/ceball/Documents/Topographica
INFO:root:Time: 000000.00 OpenMP: Using 2 threads on a machine with 2 detected CPUs
Output path: /home/ceball/Documents/Topographica

Welcome to Topographica!

Type help() for interactive help with python, help(topo) for general
information about Topographica, help(commandname) for info on a
specific command, or topo.about() for info on this release, including
licensing information.

topo_t000000.00_c1>>> import IPython

topo_t000000.00_c2>>> IPython.__version__
               Out[2]:'0.13.1'

topo_t000000.00_c3>>> IPython.__file__
               Out[3]:'/usr/local/lib/python2.7/dist-packages/ipython-0.13.1-py2.7.egg/IPython/__init__.pyc'

[ceball]

I've just updated (87f64b58c777721d148752c025b3b2820947b5e1), and now I get a different error (sorry, haven't made any attempt to investigate):

$ cat /etc/issue
Ubuntu 12.04.4 LTS \n \l
$ ./topographica -i
Output path: /home/ceball/Documents/Topographica

Welcome to Topographica!

Type help() for interactive help with python, help(topo) for general
information about Topographica, help(commandname) for info on a
specific command, or topo.about() for info on this release, including
licensing information.

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/home/ceball/uoe/topographica/topographica in <module>()
     39 # Process the command-line arguments

     40 from topo.misc.commandline import process_argv
---> 41 process_argv(argv[1:])

/home/ceball/uoe/topographica/topo/misc/commandline.pyc in process_argv(argv)
    767
    768             # Load Topographica IPython extension in embedded shell

--> 769             ipshell.extension_manager.load_extension('topo.misc.ipython')
    770             ipshell()
    771

/usr/lib/python2.7/dist-packages/IPython/core/extensions.pyc in load_extension(self, module_str)
     85         if module_str not in sys.modules:
     86             with prepended_to_syspath(self.ipython_extension_dir):
---> 87                 __import__(module_str)
     88         mod = sys.modules[module_str]
     89         return self._call_load_ipython_extension(mod)

/home/ceball/uoe/topographica/topo/misc/ipython.py in <module>()
    169 #===============#

    170
--> 171 from dataviews.ipython import load_ipython_extension as load_imagen_extension
    172 from dataviews.ipython import stack_display, view_display
    173

/home/ceball/uoe/topographica/external/imagen/dataviews/ipython.py in <module>()
      5 from IPython.core.pylabtools import print_figure
      6 from IPython.core import page
----> 7 from IPython.core.magic import Magics, magics_class, line_magic
      8
      9 import param

ImportError: cannot import name Magics

[jbednar]

That's still related to having a too-old version of IPython; the Magics support changed in a later version. I've asked Jean-Luc to make sure that things still run (even if some features have to be disabled) in older IPythons, until the newer versions become more widely installed.

[jlstevens]

I would hope this has been fixed now!

I'll close this issue now but if there is still a problem I'll reopen it again.