I have written a module (a file my_mod.py file residing in the folder my_module).
Currently, I am working in the file cool_script.py that resides in the folder cur_proj. I have opened the folder in PyCharm using File — open (and I assume, hence, it is a PyCharm project).

In ProjectView (CMD-7), I can see my project cur_proj (in red) and under “External Libraries” I do see my_module. In cool_script.py, I can write

from my_module import my_mod as mm

and PyCharm even makes suggestion for my_mod. So far so good.

However, when I try to run cool_script.py, PyCharm tells me
“No module named my_module”

This seems strange to me, because

A) in the terminal (OS 10.10.2), in python, I can import the module no problem — there is a corresponding entry in the PYTHONPATH in .bashrc

B) in PyCharm — Settings — Project cur_proj — Project Interpreter — CogWheel next to python interpreter — more — show paths for selected interpreter icon, the paths from PYTHONPATH do appear (as I think they should)

Hence, why do I get the error when I try to run cool_script.py? — What am I missing?

Notes:

• I am not declaring a different / special python version at the top of cool_script.py
• I made sure that the path to my_module is correct
• I put __init__.py files (empty files) both in my_module and in cur_proj
• I am not using virtualenv

Addendum 2015-Feb-25

When I go in PyCharm to Run — Edit Configurations, for my current project, there are two options that are selected with a check mark: “Add content roots to PYTHONPATH” and “Add source roots to PYTHONPATH“. When I have both unchecked, I can load my module.

So it works now — but why?

Further questions emerged:

• What are “content roots” and what are “source roots”? And why does adding something to the PYTHONPATH make it somehow break?
• should I uncheck both of those options all the time (so also in the defaults, not only the project specific configurations (left panel of the Run/Debug Configurations dialog)?