I just encountered very unpleasant error with Pycharm when trying to push or pull to my private repository:
Git Pull Failed: fatal: Could not read from remote repository.
The problem and solution is as follows. I use SSH key for login into GitHub and Pycharm needs to know about it. Unfortunately, Pycharm supposes that your key to GitHub is exactly in
~/.ssh/id_rsa.pub. So solution is to create symlinks:
cd ~/.ssh ln -s github_key_name id_rsa ln -s github_key_name.pub id_rsa.pub
Everything should work now.