%run magic and script containing Matplotlib FuncAnimation

[insearcho...@gmail.com]

I have a bit of a strange issue. 

I have a Matplotlib FuncAnimation that runs correctly in a standalone script in IPython. It also runs correctly if I copy the entire script into a notebook cell and run it after the following magic

    %matplotlib notebook

However, if I use the following two magics

    %matplotlib notebook

    %run myscript.py

the animation does not run correctly. 

I'd prefer to use $run so that I can pass command line arguments to the script.

Any ideas why using the two magics approach would not work, but pasting the entire script into a cell does?

[Thomas Kluyver]

Are you using the two magics in one cell, or over two cells? Some of the effects of the %matplotlib magic may not take effect until the next cell.

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[insearchof answers]

I tried it both ways and got the same results. 

In my cell where I pasted the entire script, I have the %matplotlib notebook at the top of that same cell and the script runs correctly. It also runs correctly if I move the  %matplotlib notebook into a cell by itself. 

The only time the script does not work correctly is with %run. It appears that my plt.cla() call (which I need for my particular animation) in each frame is being ignored (or not working correctly) in this case, but it works fine in the cell that contains the entire script. 

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