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.

I have created a small set of code for this. And it worked. Sharing it here, so others can get benefit from it.

Sample code:

This code will upload a file/replace the existing file.

Local file path: /tmp/file.txt

Github folder name: folder1/

from github import Github
g = Github("username", "password")

repo = g.get_user().get_repo(GITHUB_REPO)
all_files = []
contents = repo.get_contents("")
while contents:
    file_content = contents.pop(0)
    if file_content.type == "dir":
        contents.extend(repo.get_contents(file_content.path))
    else:
        file = file_content
        all_files.append(str(file).replace('ContentFile(path="','').replace('")',''))

with open('/tmp/file.txt', 'r') as file:
    content = file.read()

# Upload to github
git_prefix = 'folder1/'
git_file = git_prefix + 'file.txt'
if git_file in all_files:
    contents = repo.get_contents(git_file)
    repo.update_file(contents.path, "committing files", content, contents.sha, branch="master")
    print(git_file + ' UPDATED')
else:
    repo.create_file(git_file, "committing files", content, branch="master")
    print(git_file + ' CREATED')

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