Bash cell magic in IPython script

Question

This is my first post on SO, so please let me know if the problem is not well defined. I have a script process.ipy in which I am trying to implement a cell magic as follows,

#!/usr/bin/env ipython

%%bash
ls

When I run this on the command line (Ubuntu and zsh shell), I get the following error,

$ ipython process.ipy                                                                                                 
File "<ipython-input-1-f108be8d32f2>", line 3
  %%bash
  ^
SyntaxError: invalid syntax

However, I can run this in the ipython session without a problem,

In [1]: %%bash
   ...: ls
   ...: 
process.ipy

More confusing, is that the single line version works in the script,

#!/usr/bin/env ipython

!ls

What am I doing wrong? Is something not setup correctly?

score 5 · Answer 1 · edited May 23 '17 at 12:16

5

Short Answer: magic commands are understood only in an IPython interactive session, not in scripts.

Longer Answer: they can be called in scripts, but only using a library call, not the %% notation as described in How to run an IPython magic from a script (or timing a Python script). Note that the mechanism is IPython version dependent.

edited May 23 '17 at 12:16

Community

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answered Jan 14 '15 at 20:06

msw

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I guess I didn't read that post well enough. Will keep this in mind. gmk's suggestion seems to work. – pacificprince Jan 14 '15 at 20:15

score 3 · Accepted Answer · answered Jan 14 '15 at 19:52

3

You do not need the #!/usr/bin/env ipython line at the top. The error :

%%bash
ls

answered Jan 14 '15 at 19:52

magic-sudo

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Thanks, what made it work is the newline between the `%%bash` magic to the actual command(s). – Yinon Ehrlich Mar 28 '23 at 12:58

score 1 · Answer 3 · answered Jan 14 '15 at 19:51

1

You do not need the #!/usr/bin/env ipython line at the top. The cell magic should be first line in the cell.

just try the following and it should work

%%bash
ls

answered Jan 14 '15 at 19:51

Amit

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Bash cell magic in IPython script

3 Answers3