0

I want to call an app from its bash command using Python. I added the path to the app to the PATH environment variable, so that this work in the terminal. However, when doing this in Pycharm, it does not work. I discovered, that is because apparently the environment variables are not all loaded in, when I call the app in Pycharm.

This is what I do in the terminal:

(save) philipp@philipp-Blade-15-Advanced-Model-Early-2020:~$ python
Python 3.8.2 (default, Mar 25 2020, 17:03:02) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import os
>>> os.environ["PATH"]
'/home/philipp/anaconda3/envs/save/bin:/home/philipp/anaconda3/condabin:/home/philipp/sumo/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin'

When I run the same command in Pycharm, I get this output:

'/home/philipp/anaconda3/envs/save/bin:/home/philipp/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin'

The output from Pycharm is missing /home/philipp/sumo/bin which is where I installed my app and where I need to call it from. I looked into this a lot, but could not figure out what the issue would be... I am using the same Anaconda environment in both cases. Can you point out the issue?

Philipp
  • 652
  • 2
  • 10
  • 28
  • 1
    It appears that the first two directories are added by your virtual environment, while `/home/philipp/sumo/bin` is added by your shell's configuration files. PyCharm isn't being started by your login shell, and so doesn't inherit a path containing `sumo/bin`. – chepner Feb 08 '21 at 18:32
  • @chepner Yes, I am adding `/home/philipp/sumo/bin` to `PATH` in the .bashrc file. Can you tell me, how I can use the same shell which the terminal uses in PyCharm as well? Also, in Windows this was working by default, I only came across the problem in Linux. – Philipp Feb 08 '21 at 19:03
  • This answer (https://stackoverflow.com/questions/27553576/load-environment-variables-of-bashrc-into-python) says, that the `.bashrc` is loaded into `os.environ` on login. Evidently that cannot be true. – Philipp Feb 08 '21 at 19:09
  • 1
    More or less, `.bashrc` is sourced when your *shell* starts. But PyCharm doesn't have your shell as the parent; it basically gets executed *for* you by another process, so it doesn't inherit from your login shell. – chepner Feb 08 '21 at 19:15
  • @chepner Ok, thanks. Then how do I insert the environment variables from bashrc when PyCharm starts a new shell? Also is there a Platform Independent method? Can you write an answer, so that I can upvote it? – Philipp Feb 08 '21 at 19:25
  • I don't know; I don't use PyCharm, so I don't know what mechanism it has for configuring the environment. I just know it's not inheriting it from your shell. – chepner Feb 08 '21 at 19:32
  • Alright, but this is enough information, so that I can google for a solution. Thanks! – Philipp Feb 08 '21 at 19:40

1 Answers1

1

Your thing works for me. What I did was:

  1. I edited my .bashrc with export PATH=/THIS/IS/TEST/PATH:$PATH in the last line.
  2. Exited the terminal and created a new one to refresh my instance.
  3. Checked if path is properly loaded with /THIS/IS/TEST/PATH using echo $PATH.
  4. Opened up pycharm from current terminal using charm command.
  5. Copy+Pasted your code
import os
print(os.environ["PATH"])
  1. Checked the printed output and I found the /THIS/IS/TEST/PATH.

Im running from a single terminal and using anaconda as well

Are you running pycharm from the terminal ?

(Alternative solution)

If it still doesn't work for you, why not just create a txt file that holds the PATH variable and refreshes whenever ~/.bashrc was called.

for example,

  1. in the ~/.bashrc file, put this in the last line:
echo "$PATH" > ~/bash_path.txt
  1. then just read the content as a variable in your python code
PATH = open('/absolute/path/to/bash_path.txt', 'r').read()
print(PATH)

which should have the same output as with the os.environ command.

Dharman
  • 30,962
  • 25
  • 85
  • 135
Kurt Rojas
  • 319
  • 2
  • 12
  • The first solution works for me. I did not know running PyCharm from the terminal was possible and that is would initialize the PATH env variable from the `.bashrc`. I also found, that one can input environment variables, which PyCharm then uses on startup (see here https://stackoverflow.com/questions/42708389/how-to-set-environment-variables-in-pycharm) – Philipp Feb 09 '21 at 09:04
  • That's good to know! I think the 2nd solution can be used in tandem with the pycharm environment setup you suggested. From what I saw from the link you sent, it still needs an env file (which is what the 2nd solution creates). – Kurt Rojas Feb 09 '21 at 10:41