Pycharm environment different than command line

by

.bash_profile is being read by bash (your command line interpreter) only.
However if you want to preserve bash environment for PyCharm there is one
true Linux way.

Run PyCharm from your command line (from bash).
Thus environment variables will be inherited from bash to pycharm.
Read $man environ for information on linux environment inheritance process.
So all you need is just launch ${PATH_TO_PYCHARM}/bin/pycharm.sh from command line.
Or create launcher which invokes bash for PyCharm launching.

Thats it ! Hope that works for you.

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