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I've used on Anaconda with Python 3.x on Windows for years now. It has tons of features that out of the box that I use every day that cannot be easily installed on the bare-bones Python 2.7 that Linux Mint ships with.

I've installed Anaconda3 on previous Linux Mint systems using
Anaconda's docs for installing on Linux and it worked okay but I think that it might have screwed up those previous installations by letting Anaconda make Python 3 the default python on the path. Every now and when I would try to install basic applications through apt-get install they would fail and Python was sometimes be mentioned in the error messages. Also I've read that you can break the system by installing python 3 as path; here is one example.

So I noticed in the installation guide linked above that conda requires that Anaconda be pretended to the path;

The installer prompts “Do you wish the installer to prepend the Anaconda<2 or 3> install location to PATH in your /home//.bashrc ?” Enter Yes.

NOTE: If you enter “No”, you must manually add the path to Anaconda or conda will not work.

I don't know if that means Python 3 and Anaconda will be prepended to the path or just Anaconda?

Long story short what are the best practices for installing Anaconda3 on a Linux system?

UPDATE: I still haven't found an answer to this question but I was able to find some relevent information on this question from askubuntu.

There one user says to install with caution because:

Anaconda seems to install their own version of moc (for building Qt
apps), which may conflict with the system libraries if you compile
when /home/USER/anaconda3/bin is in your path.

In my experience one should not install Anaconda on linux mint using the method recommended by their website. I've noticed problems installing and using other unrelated software after installing Anaconda3 system-wide.