Question

I have to make graphs from several files with data. I already found a way to run a simple command

xmgrace -batch batch.bfile -nosafe -hardcopy

in which batch.bfile is a text file with grace commands to print the graph I want. I already tried it manually and it works perfectly. To do this with several files I just have to edit one parameter inside batch.bfile and run the same command every time I make a change.

I have already written a python code which edits batch.bfile and goes through all the data files with a for cycle. In each cycle step I want to run the mentioned command directly in the command line.

After searching a bit I found two solutions, one with os.system() and another with subprocess.Popen() and I could only make subprocess.Popen() work without giving any errors by writing:

subprocess.Popen("xmgrace -batch batch.bfile -nosafe -hardcopy", shell=True)

Problem is, this doesn’t do anything in practice, i.e., it just isn’t the same as running the command directly in the command line. I already tried writing the full directory for the batch.bfile but nothing changed.

I am using Python 2.7 and Mac OS 10.7

Answer 1

Have you checked running xmgrace from the command line using sh? (i.e. invoke /bin/sh, then run xmgrace… which should be the same shell that Popen is using when you set shell=true).

Another solution would be to create a shell script (create a file like myscript.sh, and run chmod +x from the terminal). In the script call xmgrace:

#!/bin/bash
xmgrace -batch batch.bfile -nosafe -hardcopy

You could then test that myscript.sh works, which ought to pick up any environment variables that might be in your profile that might differ from python. If this works, you could call the script from python’s subprocess.Popen(‘myscript.sh’). You can check what the environment variables are set in python for subprocess by running:

import os
os.environ