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This is my first post on SO, so please tell me if I am doing something wrong.

I am interested in using different programming languages in ipython, similar to babel/literal programming in emacs org mode. What I like about emacs org mode is that one can have multiple "cells" connecting to the same R/bash session. This allows me to re-use variables/functions created in an earlier part of the document, even if I do something else in between.

I have found that this is possible in ipython with the Rmagic. As an example

In [1]: %load_ext rpy2.ipython

In [2]: %%R
        a <- 3
        a
Out [2]: 3

In [3]: something_in_python = 'I am doing something unrelated now'

In [4]: %%R
        cat('My variable a is still here, its value is: ', a) # a is still here!

Out [4]: My variable is still here, its value is: 3

I would very much like to be able to do something similar in bash. However, no matter whether I use "%%script bash" or %%sx, variables are not persistent. Here is what I am trying to do:

In [1]: %%script bash
        var1="hello"
        echo $var1

Out[1]: hello

In [2]: %%script bash
        echo $var1 # I need $var1 to be present in this cell too - but its gone!

Out[62]:

Is there anyway to have the same base session in multiple cells? Or at least to somehow pass on variables. Of course, I could play around with passing variables into python and then back into the next bash cell, but I have a feeling that there must be a better way. Thank you for your help!

PS: I looked for a solution, but I didn't find anything either here or through googling. There is some stuff like this: IPython Notebook previous cell content, but it doesn't seem to be helpful for my case.

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sjk
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  • No, the `%%script` and `%%sx` magics run each block in a new subprocess, so they can't share state. There is a [bash kernel](https://github.com/takluyver/bash_kernel/) which can store state between cells. If you want to do that with magics, you could use some of that machinery and define your own magic that will send code to a persistent bash process. – Thomas K May 13 '15 at 18:20
  • Hi Thomas, thanks a lot for your help! I will look into it as soon as I can and post what I have done if I can get it to work for me. For now it is already very helpful to know that it is not going to work with some simple solution I have overlooked so far. Thanks again! – sjk May 15 '15 at 07:19

1 Answers1

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One option, though limited, allows the stdout and stderr variables to be set. This gives you the availability of setting and passing two variables in between cells. For example:

In [1]:%%bash --out var1 --err var2
       echo "Hello"
       echo "Hi" >&2

In [2]:print(var1)
       print(var2)
# Resulting in:
       Hello

       Hi

In [3]:%%bash -s "$var1" "$var2"
       echo "arg1 takes on var1 = $1"
       echo "arg2 takes on var2 = $2"
# Resulting in:
       arg1 takes on var1 = Hello

       arg2 takes on var2 = Hi

Note that the eol character seems to make its way into the variable. You can use echo -n instead of echo to prevent the newline character from being added to the variable.

For details on using stdout and stderr see http://nbviewer.ipython.org/github/ipython/ipython/blob/master/examples/IPython%20Kernel/Script%20Magics.ipynb

For details on passing variables back in see Can I access python variables within a `%%bash` or `%%script` ipython notebook cell?

Fritz
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Bill
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  • Sorry that I didn't react for so long, just came back from vacation. Of course this is not exactly what I was looking for, but it is a starting point and no one seems to have a better solution, so I'll accept this as an answer. Thank you! – sjk Aug 02 '15 at 16:00
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    You can use `echo -n` instead of `echo` to prevent the newline character from being added to the variable. – PoolloverNathan Oct 31 '22 at 12:54