Fixed! Thanks both for your help and thank you Matthias for teaching me to 
fish. ;)

On 28 May 2017, 1:20 PM +1000, Matthias Bussonnier 
<[email protected]>, wrote:
> M is right, you can use --TerminalIPythonApp.matplotlib that should
> apply only to the terminal frontend. --IPKernelApp.matplotlib would
> apply only to the kernel.
>
> Usually when I have a question like that, I use the following (replace
> matplotlib by whatever option you need) to see all the options
> available.
>
> $ python -m ipykernel --help-all | grep matplotlib | grep '\-\-' and
> $ ipython --help-all | grep matplotlib | grep '\-\-'
>
> all the --UpperCase.lowercase are command line flags with equivalent
> c.UpperCase.lowercase you can use in config files.
> Obviously the one that appear in both of the above command affect
> Terminal and notebook (technically ipykernel) at the same time, those
> that appear only in one affect only said command.
>
> --
> M (the other one).
>
> On Sat, May 27, 2017 at 6:26 PM, Mike Pacer <[email protected]> wrote:
> > I'm guessing you can probably set it at a more specific level, but I'm not
> > sure off the top of my head.
> >
> > But I can suggest an alternative solution. Use matplotlib 2+ and it's
> > matplotlib.pyplot.ion() function. Doing that should not require you to
> > specify any particular backend. It also makes your notebooks easier to
> > export to a valid script.
> >
> > Cheers,
> > M
> >
> >
> > On Sat, May 27, 2017 at 18:13 Juan Nunez-Iglesias <[email protected]
> > wrote:
> > >
> > > Hi,
> > >
> > > I mostly use the IPython terminal when doing exploratory data analysis
> > > with Python. I used to call `ipython --matplotlib` each time until I found
> > > the `c.InteractiveShellApp.matplotlib = 'auto'` setting in
> > > ipython_config.py. However, now when I run a Jupyter notebook, if I try to
> > > use %matplotlib notebook, I get the error message:
> > >
> > > Warning: Cannot change to a different GUI toolkit: notebook. Using osx
> > > instead.
> > >
> > > Is there a way to specify that I only want the 'auto' setting for the
> > > IPython terminal, *not* for Jupyter kernels?
> > >
> > > Thanks!
> > >
> > > Juan.
> > >
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