Just to clarify this point, while modifying /etc/pip.conf should work, there are a number of benefits to using our recommended installation method for Stretch instead of continuing to use certbot-auto which I wanted to explain for people here.
When you run certbot-auto on Raspbian, it has to compile packages from source (on every update) because precompiled packages are not available for some of our dependencies on ARM systems. This process is slow and can completely fail on smaller systems with less memory. Additionally, certbot-auto installations take significantly more disk space than installations from OS packages because for stability, certbot-auto pulls in exact versions of most of our dependencies rather than reusing the versions already installed on your OS.
Installing Certbot through your package manager avoids both of these problems and come with the additional benefits of having automatic renewal preconfigured to make sure your certificates stay valid and having DNS plugins available for popular DNS providers.