From the jupyter qtconsole you can use the %save magic to save your work. It's more cumbersome than I would like because you have to specify which input cells you want to save, but still quite handy.
For example, to save input cells 2 through 7 to a file called MyCommands.py, you simply type
%save MyCommands.py 2-7
Which will save the file in your current working directory. It'll even warn you and ask for confirmation if the file already exists.
For more information, use jupyter's extremely useful built-in help functionality by adding a question mark after the item you want help with.
%save?
Which prints the docstring
Docstring: Save a set of lines or a macro to a given filename.
Usage: %save [options] filename n1-n2 n3-n4 ... n5 .. n6 ...
Options:
-r: use 'raw' input. By default, the 'processed' history is used,
so that magics are loaded in their transformed version to valid
Python. If this option is given, the raw input as typed as the
command line is used instead.
-f: force overwrite. If file exists, %save will prompt for overwrite unless -f is given.
-a: append to the file instead of overwriting it.
This function uses the same syntax as %history for input ranges, then
saves the lines to the filename you specify.
It adds a '.py' extension to the file if you don't do so yourself, and
it asks for confirmation before overwriting existing files.
If -r option is used, the default extension is .ipy. File:
~/anaconda3/lib/python3.5/site-packages/IPython/core/magics/code.py
Note that you can use the question mark to investigate any function or object with a docstring (i.e. enumerate?, range?).
