How to run python scripts from shell file without messing up directory paths

Question

I have a python script that loads data files using relative paths. I then have a shell script from a parent directory that runs the python script like so

automate.sh contents:

python3 /path/to/python/file/file.py

file.py contents:

import numpy as np
np.loadtxt(./data/data2load.txt)

The problem is when I run this python script from the shell script, the relative path is broken. It tries to find the file to load in /path/to/shell/script/data/data2load.txt. Is there a robust way to fix this without using absolute paths?

The fix I currently have is in my automate.sh, I instead write:

cd /path/to/python/file
python3 file.py
cd ../../../..

But this is obviuosly really tedious

Selcuk · Accepted Answer · 2020-05-19 07:17:59Z

1

You should be able to do the following:

import os

BASE_DIR = os.path.dirname(os.path.realpath(__file__))
DATA_PATH = os.path.join(BASE_DIR, "data/data2load.txt")

the value of DATA_PATH will now be /path/to/python/file/data/data2load.txt, so:

np.loadtxt(DATA_PATH)

should always load the correct file.

answered May 19, 2020 at 7:17

Selcuk

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2 Comments

24n8 Over a year ago

Thanks. Just to confirm, is BASE_DIR set to the directory that' calling the python script? In this case it's the directory of the shell script?

Selcuk Over a year ago

Yes, __file__ is always set to the full path of the script itself therefore BASE_DIR will be the parent directory of the .py file.

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