ModuleNotFoundError in a local repository

Question

I have cloned a git repo, and it is now local on my machine. Inside the path Pipes/Filtering there is a script called filter_pileup_by_site_list.py which I am trying to use, it's a docopt CLI so i'm going to the directory I have mentioned above and type the following in the terminal : python filter_pileup_by_site_list.py Filter_pileup_by_site <parameters>
The script imports a class from another directory in the repo which its path is: Pipes/Utility.
The command I have written above fails and returns the following error:

  File "filter_pileup_by_site_list.py", line 16, in <module>
    from Utility.Pileup_class import Pileup_line
ModuleNotFoundError: No module named 'Utility'

All the solutions I came across were related to PYTHONPATH so I edited it, now when I type in the terminal echo $PYTHONPATH i get /Pipes:/Pipes/Utility:/Pipes/Filtering:/Pipes/:/Bigdata/bioinf/Pipes3:/Bigdata/bioinf/Pipes:/Bigdata/users/eliran/Pipes
And it still returns the exact backtrace I had before.

If it does matter somehow, I'm using linux mint.

Can you share the import statements for the script you’re trying to execute? — Logan Elandt, May 26 '20 at 12:20
It appears in the backtrace. There ```from Utility.Pileup_class import Pileup_line``` — Eliran Turgeman, May 26 '20 at 12:26
Related question: https://stackoverflow.com/q/6134146/1216776 — stark, May 26 '20 at 12:32
The script is working fine on a linux server, the import itself is ok. — Eliran Turgeman, May 26 '20 at 12:56

score 0 · Accepted Answer · answered May 27 '20 at 08:31

Solution that worked for:

add these lines at the top of the script:

import sys  
sys.path.insert(1, 'path/to/another/directory')

The following works because as default python looks for files only in the local folder so I had to add the above line to tell it to search in the previous folder so it can find Utility folder.

ModuleNotFoundError in a local repository

1 Answers1