Python program in startup folder does not execute on startup

I have a file startup.ipy placed in /home/jovyan/.ipython/profile_default/startup/ on my docker image (scipy-notebook). startup.ipy contains the following command `% run /home/jovyan/work/sql-wrapper.ipy`

On opening a Python 3 notebook, I do not see the sql-wrapper.ipy being executed. However, running them manually inside a cell or exueting `% run /home/jovyan/work/sql-wrapper.ipy` works.

I using JupyterHub (0.7.2) and scipy-notebook from docker-stacks as my single user server docker image. I have also stripped the installation of Python 2 environment from the image as its not really required.

Reproduce the issue with startup.ipy in /home/jovyan/.ipython/profile_default/startup/ and sql-wrapper.ipy in /home/jovyan/work/ using the scipy-notebook image. Compare opening a Python 3 notebook with manually running %run, then trace the notebook startup entry point to determine why the startup command is skipped. Done means the file executes when a notebook opens.

Written by the indexing model from the issue text.