PyGithub has 107 files in folder /github at the time of writing, but only 51 files are covered in codecov.io report.
Compare: https://codecov.io/gh/PyGithub/PyGithub/tree/master/github

This seems to be an issue on codecov.io, since the coverage report contains all 107 classes after the test.
Compare: https://codecov.io/api/gh/PyGithub/PyGithub/download/build?path=v4/raw/2020-12-24/F473F251CFE431584CB1C976534196B2/34d097ce473601624722b90fc5d0396011dd3acb/bc973103-0c9d-4aab-9009-458491840c75.txt

Can you please either open a support request with codecov for your project, or apply a manual workaround?
I can provide a PR which was reflecting all files based on manually applying the path fixes needed to match the codecov.io conventions...