are you referring to 

extra_docker_shell_

scrip

t

Correct

the thing is that this runs before you create the virtual environment, so then in the new environment those settings are no longer there

Actually that is better, because this is what we need to setup the pip before it is used. So instead of passing --trusted-host just do:
extra_docker_shell_script: ["echo \"[global] \n trusted-host = pypi.python.org pypi.org files.pythonhosted.org YOUR_SERVER_HERE\" >> /etc/pip.conf", ]