PyGithub is a library for interacting with the GitHub API; it will not let you clone your repository or otherwise interact with a local git repository.

GitPython is a Python interface to git and can be used to clone a remote repository. In fact, there's an example of exactly that at the beginning of the tutorial to which you have linked.

That said, it's not clear from your question exactly what you hope to accomplish -- learning the git commandline interface is an important skill if you're going to be working with GitHub (or git in general). While you can probably perform many of the same tasks with GitPython, you are arguably going to be spending much of your time duplicating the existing functionality of the commandline tools.

While this question was asked a while ago and I don't know the state of the libraries at that point, it is worth mentioning for searchers that GitPython does a good job of abstracting the command line tools so that you don't need to use subprocess. There are some useful built in abstractions that you can use, but for everything else you can do things like:

import git
repo = git.Repo( '/home/me/repodir' )
print repo.git.status()
# checkout and track a remote branch
print repo.git.checkout( 'origin/somebranch', b='somebranch' )
# add a file
print repo.git.add( 'somefile' )
# commit
print repo.git.commit( m='my commit message' )
# now we are one commit ahead
print repo.git.status()

Everything else in GitPython just makes it easier to navigate. I'm fairly well satisfied with this library and appreciate that it is a wrapper on the underlying git tools.

UPDATE: I've switched to using the sh module for not just git but most commandline utilities I need in python. To replicate the above I would do this instead:

import sh
git = sh.git.bake(_cwd='/home/me/repodir')
print git.status()
# checkout and track a remote branch
print git.checkout('-b', 'somebranch')
# add a file
print git.add('somefile')
# commit
print git.commit(m='my commit message')
# now we are one commit ahead
print git.status()

Since you mentioned you are a beginner python programmer, I would suggest you to try to use the JSON API without any Github library first. It really isn't that difficult and it will help you a lot later in your programming life since same approach can be applied to any JSON API. Especially if it seems that trying out libraries will take days.

I'm not saying that some library isn't easier to use, I'm just saying the small extra effort to use the API directly might be worth it in the long run. At least it will help you understand why some of those libraries seem "unintuitive" (as you said).

Simple example to fetch creation time of django repository:

import requests
import json
r = requests.get('https://api.github.com/repos/django/django')
if(r.ok):
    repoItem = json.loads(r.text or r.content)
    print "Django repository created: " + repoItem['created_at']

This is using the popular requests library. In your code you'll naturally need to handle the error cases too.

If you need access with authentication it will be a bit more complex.