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You can install your pip packages for specific python versions. From the docs:
On Linux, Mac OS X, and other POSIX systems, use the versioned Python commands in combination with the -m switch to run the appropriate copy of pip:
# default Python 2
python2 -m pip install SomePackage
# specifically Python 2.7
python2.7 -m pip install SomePackage
# default Python 3
python3 -m pip install SomePackage
# specifically Python 3.4
python3.4 -m pip install SomePackage
https://docs.python.org/3/installing/index.html