aliased Linux commands are not recognized from python (commands.getoutput)

Question

I'm working on Ubuntu 12.4 and I have matlab installed. Typically, in order to invoke matlab from terminal I have to type in '~/MATLAB/bin/matlab'. Obviously this is a bit annoying so I aliased this command by adding

alias matlab='sh ~/MATLAB/bin/matlab'

to .bashrc. Now everything is golden and typing 'matlab' in the terminal (bash) works from any directory.

The problem arises when I'm trying to invoke Matlab from a python script. having a statement like this:

>>> commands.getoutput('matlab')
'sh: 1: matlab: not found'

as it seems the alias is not being recognized. Just to make sure:

>>> commands.getoutput('~/MATLAB/bin/matlab')

works like a charm, and

>>> commands.getoutput('echo $SHELL')
'/bin/bash'

indeed verifies that python is trying to execute the cmd in bash...

Any idea what's happening here? why isn't the alias being recognized? how/can it be fixed?

Thanks!

`commands` is deprecated. Consider using subprocess ( http://docs.python.org/library/subprocess.html#module-subprocess ) instead. — mgilson, Aug 01 '12 at 14:25
Quick question -- what happens if you put your alias in `.bash_profile` also? — mgilson, Aug 01 '12 at 14:28
For background info see http://stackoverflow.com/questions/5971312/how-to-set-environmental-variables-in-python — Anton, Aug 01 '12 at 14:36
adding to .bash_profile doesn't help. I think ubuntu doesn't look there by default. — ScienceFriction, Aug 01 '12 at 14:40

aayoubi · Accepted Answer · 2012-08-01T17:02:02.850

5

Add the matlab binary path to your PATH environment variable.

PATH=~/MATLAB/bin/:$PATH
export PATH

Then python would find matlab:

>>> commands.getoutput('matlab')

I think commands doesn't know of your shell's current aliases. However environment variables such as PATH persist.

edited Aug 01 '12 at 17:02

answered Aug 01 '12 at 14:28

aayoubi

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You'll have to use "export PATH=..." or else python will not pick up the PATH value. – Anton Aug 01 '12 at 14:29
changing PATH might add unnecessary commands from `~/MATLAB/bin`. `ln -s ~/MATLAB/bin/matlab matlab` in a directory that is already in PATH might be more suitable here – jfs Aug 01 '12 at 14:36
thanks for the answer. Setting PATH and exporting ('export PATH= ...' added to .bashrc) solved the problem. – ScienceFriction Aug 01 '12 at 14:55
Thanks! i forgot the `export` keyword :) – aayoubi Aug 01 '12 at 17:01

score 4 · Answer 2 · answered Aug 01 '12 at 14:28

bash only evaluates ~/.bashrc if it's started as an interactive shell. If you have aliases in /.bashrc that you want bash to evaluate when it's run non-interactively, you could try setting the BASH_ENV environment variable from your Python script to point to ~/.bashrc.

The Bash Reference Manual gives some more detail on interactive versus non-interactive shells and on how to use BASH-ENV.

aliased Linux commands are not recognized from python (commands.getoutput)

2 Answers2