Executing bash profile aliases from python script

Question

I am aware that many similar questions have been posted here but none of them seems to work in my case. I have a few commands in my bash profile like below

export HEADAS=/Users/heasoft/x86_64-apple-darwin18.7.0
alias heainit=". $HEADAS/headas-init.sh"
. $HEADAS/headas-init.sh

export SAS_DIR=/Users/sas-Darwin-16.7.0-64/xmmsas
alias sas=". $SAS_DIR/setsas.sh"

sit='source ~/.bash_profile'

in which I created an alias to run them consecutively: alias prep1='sit; heainit; sas. This works just fine when I execute it in the command line. But I want to insert in a python script and run it from there. I am running Python (v 3.7.4). So, as suggested in here, I tried

import subprocess

command = "prep1"
process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None, shell=True)
output = process.communicate()   
print(output[0].decode())

But I get an error saying command not found. I tried to export it in bash profile but got an error stating -bash: export: prep1: not a function

I also tried the method suggested in here, but still nothing. Related to this, I couldn't even run a shell command like below in python

epatplot set=evli.FTZ plotfile="pn_filtered_pat.ps" 2>&1 | tee pn_filtered_pat.txt

Here is my Python script attempt

command = "epatplot set=evli.FTZ plotfile="pn_filtered_pat.ps" 2>&1 | tee pn_filtered_pat.txt"
process = subprocess.Popen(command.split(), stdout=subprocess.PIPE)
output, error = process.communicate()

I get SyntaxError: invalid syntax. I know where this syntax error is rising from but don't know how to fix.

I am a beginner in python so I appreciate any help/guidance.

You can create a bash child processes, which reads your alias-commands, but what are you then going to do with this? You can not evern execute them in the very same subprocess (unless you explicitly turn on alias processing for non-interactive shells), and of course their definition is gone in every other subprocess you are creating later. — user1934428
– user1934428, Commented Jun 29, 2020 at 10:54

Mike Organek · Accepted Answer · 2020-06-28 13:26:58Z

3

Please see this answer: https://askubuntu.com/a/98791/1100014

The recommendation is to convert your aliases to bash functions and then export them with -f to be available in subshells.

When you call Popen, execute "bash -c <functionname>".

As for your last script attempt, you have a conflict in quotation marks. Replace the outer quotes with single quotes like this:

command = 'epatplot set=evli.FTZ plotfile="pn_filtered_pat.ps" 2>&1 | tee pn_filtered_pat.txt'
process = subprocess.Popen(command.split(), stdout=subprocess.PIPE)
output, error = process.communicate()

answered Jun 28, 2020 at 13:26

Mike Organek

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1 Comment

tngn Over a year ago

in macOS (Ventura 13.2) bash functions defined without the "function" keyword would cause error: syntax error near unexpected token `('. A definition with the keyword (cf. linuxize.com/post/bash-functions) would execute just fine.

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