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PyCharm
In PyCharm external tools are created in the External Tools section of the Settings dialog. Open that dialog by activating the File\Settings... menu command
In the Settings dialog click the green + button to add a new command. The Create Tool dialog will be displayed.
In the Name box enter a name for the tool
In the Program box either use the ... button to browse to MXSPyCOM.exe or enter the full path to the program. e.g. C:\Program Files\MXSPyCOM\MXSPyCOM.exe
In the Arguments box enter either -s or -f, a space, and then the PyCharm variable for the currently loaded file,
The external tool will be available in PyCharm's Tools\External Tools menu list.
More information on external tools in PyCharm can be found here.