(Spyder maintainer here) This code both clears the console and removes all variables present on the namespace at the same time:
try:
from IPython import get_ipython
get_ipython().magic('clear')
get_ipython().magic('reset -f')
except:
pass
It also has the advantage that it works inside and outside Spyder.
Note: Right now this approach generates an error in the console after it's run. We'll fix that error in the next Spyder version (3.3.4), to be released in March/2019.
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