minrk / singlecell Goto Github PK

$ git clone https://github.com/minrk/singlecell.git .
$ python singlecell.py 
Traceback (most recent call last):
  File "singlecell.py", line 54, in <module>
    from IPython.html.services.kernels.handlers import (
ImportError: cannot import name 'IOPubHandler'
$ ipython --version
3.1.0

Is my version of IPython supported?

╭─lwm@lwm-Latitude-D620 ~/repos/singlecell ‹master›
╰─$ python singlecell.py 1 ↵
Traceback (most recent call last):
File "singlecell.py", line 39, in
from IPython.kernel.multikernelmanager import MultiKernelManager
File "/usr/lib/python2.7/dist-packages/IPython/kernel/init.py", line 10, in
raise ImportError(doc)
ImportError: IPython.kernel has been replaced by IPython.parallel.

The previous version of IPython's parallel library was located at this
location (IPython.kernel). It has been moved to the IPython.parallel
subpackage and has been refactored to use zeromq/pyzmq instead of twisted.

Please see INSERT URL for further details.

╭─lwm@lwm-Latitude-D620 ~/repos/singlecell ‹master›
╰─$ python --version 1 ↵
Python 2.7.4

╭─lwm@lwm-Latitude-D620 ~/repos/singlecell ‹master›
╰─$ cat /proc/version
Linux version 3.8.0-31-generic (buildd@aatxe) (gcc version 4.7.3 (Ubuntu/Linaro 4.7.3-1ubuntu1) ) #46-Ubuntu SMP Tue Sep 10 19:56:49 UTC 2013

Hi,
I work with Shreyas Cholia and Matt Henderson at LBL, and just tried to run the singlecell example against the current 1.0-dev branch of IPython (up to commit 6c864917746d41814534986080b3e1d4e21ee254 ) and even after a few rounds of changing the import statements for what seems to be refactoring of the module namespace, it still won't run. Here's the current error:

Traceback (most recent call last):
File "singlecell.py", line 46, in
from IPython.frontend.html.notebook.notebookapp import (
ImportError: cannot import name _kernel_action_regex

Before I wander too much further down this rabbit hole, am I just doing something wrong, or has the 1.0-dev basically made this example obsolete?

Thanks,
Steve