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I'm trying to get a least at a basic understanding of how to install the codelucas/newspaper app (I don't know if this is called an app or a package...I have only worked with WordPress and old HTML sites before, so the terminology is just totally messing with me. I would have though that I should be able to connect github desktop to the source code directory of the web app area and upload..

I am reading what I can but then come across terms like flask and pip and django, etc.... any suggestions on what might give me a clearer understanding of how this all works?

Github Desktop is for interacting with github. Once you have files on github, you can use git to get them to your PythonAnywhere account. See the github section here: http://help.pythonanywhere.com/pages/UploadingAndDownloadingFiles/