I've already expalined 
here https://github.com/sagemath/sage-windows/issues/12 that PyCharm 
doesn't support Cygwin Python,
and thus it's not going to be trivial to fix. The reason that we must use 
Cygwin Python is that a number of essential Sage components (i.e. Python 
extensions you need) e.g. GAP, won't work natively on Windows, as they use 
fork() and other Unix/Posix specific system functions.  

On Saturday, December 16, 2017 at 12:19:56 PM UTC, PHPirate wrote:
>
> Thanks, it sounds reasonable. But do you mean the Jupyter notebook 
> included with Sage, which you can start with 
> sage --notebook ipython
> from the Sage shell? I do not like notebooks such as this one and 
> Mathematica because they do not go well with a VCS. Is it then possible to 
> use this Jupyter to edit and run Sage files saved in a better way, like 
> python files?
>

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