Different environment variables loaded into the terminal and Pycharm

Question

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?

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
– chepner, Commented Feb 8, 2021 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
– Philipp, Commented Feb 8, 2021 at 19:03
This answer (stackoverflow.com/questions/27553576/…) says, that the .bashrc is loaded into os.environ on login. Evidently that cannot be true. — Philipp
– Philipp, Commented Feb 8, 2021 at 19:09
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
– chepner, Commented Feb 8, 2021 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
– Philipp, Commented Feb 8, 2021 at 19:25

Dharman · Accepted Answer · 2021-02-08 20:37:48Z

Your thing works for me. What I did was:

I edited my .bashrc with export PATH=/THIS/IS/TEST/PATH:$PATH in the last line.
Exited the terminal and created a new one to refresh my instance.
Checked if path is properly loaded with /THIS/IS/TEST/PATH using echo $PATH.
Opened up pycharm from current terminal using charm command.
Copy+Pasted your code

import os print(os.environ["PATH"])

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,

in the ~/.bashrc file, put this in the last line:

echo "$PATH" > ~/bash_path.txt

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.

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 stackoverflow.com/questions/42708389/…)
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).

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