Pipe Ipython magic output to a variable?

Question

I want to run a bash script in my ipython Notebook and save the output as a string in a python variable for further manipulation. Basically I want to pipe the output of the bash magic to a variable, For example the output of something like this:

%%bash
some_command [options] foo bar

Solution 1

What about using this:

myvar = !some_command --option1 --option2 foo bar

instead of the %%bash magic? Using the ! symbol runs the following command as a shell command, and the results are all stored in myvar. For running multiple commands and collecting the output of all of them, just put together a quick shell script.

Solution 2

For completeness, if you would still like to use the %%bash cell magic, you can pass the --out and --err flags to redirect the outputs from the stdout and stderr to a variable of your choice.

From the doucumentation:

%%bash --out output --err error
echo "hi, stdout"
echo "hello, stderr" >&2

will store the outputs in the variables output and error so that:

print(error)
print(output)

will print to the python console:

hello, stderr
hi, stdout

Solution 3

Notice the difference in the variable type between @MattDMo (SList) and @oLas (str) answers:

In [1]: output = !whoami

In [2]: type(output)
Out[2]: IPython.utils.text.SList

In [3]: %%bash --out output
   ...: whoami

In [4]: type(output)
Out[4]: str