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eppy can read a "weather.ddy" file. (The design days are in the *.ddy file). You can do:

# assuming you have already opened an E+ file called `idf`
ddyidf = IDF("weather.ddy")
designdays = ddyidf.idfobjects["SizingPeriod:DesignDay".upper()]
designday = designdays[0]
print designday # check to see if it happened

# copy a design day into your idf file
idf.copyidfobject(designday)
idf.printidf() # check if it actually copied it in.

Using this, every time you switch the weather file, you can write some code that will insert the Design Days from the corresponding ddy file