Can you specify a command to run after you embed into IPython?

The document stated that IPython.start_ipython reads the configuration file, while IPython.embed does not. With that in mind, let's use the former:

import IPython

c = IPython.Config()
c.InteractiveShellApp.exec_lines = [
    '%pylab qt4',
    "print 'System Ready!'",
]

IPython.start_ipython(config=c)

Update

I am not sure what you meant by to keep the current namespace. If you meant local/global variables:

IPython.start_ipython(config=c, user_ns=locals())   # Pass in local variables
IPython.start_ipython(config=c, user_ns=globals())  # Pass in global variables

The IPython.config package has been deprecated since IPython 4.0. You should import from traitlets.config instead.

import IPython
from pkg_resources import parse_version # installed with setuptools

if parse_version(IPython.release.version) >= parse_version('4.0.0'):
    from traitlets.config import Config
else:
    import IPython.config
    from IPython.config import Config

c = Config()
c.InteractiveShellApp.exec_lines = [
    '%pylab qt4'
    "print('System Ready!')",
]
IPython.start_ipython(config=c)