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I am a newbie to Ubuntu. I have just installed conda with python3 and python2 environments. I also see people say "sudo apt-get upgrade" will upgrade all packages installed. My concern is that will it upgrade the python2 package in the second env? If so, wouldn't this line of command very destructive?

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No not, If you use conda it is on their environment which conda mantain. Python 2 will be upgraded to latest python 2 version and not deleted and upgraded to python 3 because some apps still runs on it. apt upgrade will upgrade your conda not the environment you setup.

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