IPython error executing system commands

Question

If I execute any system commend in ipython2/3 on my Ubuntu 16.04 machine, I get permission denied error as follows:

In [1]: ls
--------------------------------------------------------------------------
PermissionError                           Traceback (most recent call last)
<ipython-input-1-5b21b94dda0e> in <module>()
----> 1 get_ipython().magic('ls ')

I did not need to do anything special in Ubuntu 14.04. I have installed ipython2 and ipython3 with

pip2 install ipython --user
pip3 install ipython --user

I also tried installing it system-wide with sudo as

sudo pip2 install ipython
sudo pip3 install ipython

But the problem still persists. I do not get this problem in jupyter notebook.

How can I use system commands in IPython?

Answer 1

As written in ipython docs - You should prefix the command with !

e.g. for ls you should execute !ls

String lists (IPython.utils.text.SList) are handy way to process output from system commands. They are produced by var = !cmd syntax.

First, we acquire the output of ‘ls -l’:

[Q:doc/examples]|2> lines = !ls -l
 ==
['total 23',
 '-rw-rw-rw- 1 ville None 1163 Sep 30  2006 example-demo.py',
 '-rw-rw-rw- 1 ville None 1927 Sep 30  2006 example-embed-short.py',
 '-rwxrwxrwx 1 ville None 4606 Sep  1 17:15 example-embed.py',
 '-rwxrwxrwx 1 ville None 1017 Sep 30  2006 example-gnuplot.py',
 '-rwxrwxrwx 1 ville None  339 Jun 11 18:01 extension.py',
 '-rwxrwxrwx 1 ville None  113 Dec 20  2006 seteditor.py',
 '-rwxrwxrwx 1 ville None  245 Dec 12  2006 seteditor.pyc']

Answer 2

When I was setting up my machine, I created a dummy rootUser as the first admin user. Later on, I created another user with the same name, uid and gid as my workplace and added it to sudo. This some how causes permission problems which is really strange. Though I do not know the actual cause of the problem but I did reproduce it with the above steps. I solved this problem by creating the first user with the name same as my workplace. Later i changed the uid and gid and file/directly permissions accordingly. This solved the problem and I can now use ipython2/3 normally.