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I just bought a MacBook Pro and the preinstalled version of python is 2.7.x and I was attempting to install biopython but that requires python 3.6 and higher.
I then downloaded the latest python which is 3.8.5.
When I run terminal to install biopython I get an error saying that biopython requires version above 3.6 to run and that version 2.7 is downloaded.
How can I make it so it recognizes version 3.8.5 or any version above 3.6?

Harshit Ruwali
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Chris
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3 Answers3

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For your terminal to run python 3.x run

python3 <your command>

and similarly for pip

pip3 install <package name>

Or you can just make a virtual environment. Ref here.

Harshit Ruwali
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2

Symlink python to python3 in /usr/bin. If you ever need to access python 2.7 run python2.7.

brew install python3
brew link
sudo mv /usr/bin/python /usr/bin/python2.7 # skip this step if /usr/bin/python2.7 already exists
ln -s /usr/local/bin/python $(which python3) # note /usr/local/bin instead of /usr/bin

Note:

Use brew (ubiquitous open source MacOS package manager) to install python3. This will make maintaining package installs, versions and updates a lot simpler.

References:

Brew: https://brew.sh

pygeek
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    Here he have already installed python3.x. And so what he have to is update the path for python3. – Harshit Ruwali Sep 18 '20 at 19:34
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    @HarshitRuwali You installed python, but there's no easy way to update it and other packages that you install in the future without using a package manager. But yes, you need to update the symlink in /usr/bin to point to python3. – pygeek Sep 18 '20 at 19:37
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I've checked docs for biopython https://biopython.org/wiki/Download and they ask you to run

pip install biopython

So what you have to ensure is that your pip uses Python 3+ like here

> pip -V
pip 20.2.2 from /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pip (python 3.7)
Łukasz
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    you can't run a pip command like that on MacOS without being in a virtual environment. You have to use the `python3 -m pip install ` or you can use the outdated pip3 wrapper. – monsieuralfonse64 Sep 18 '20 at 21:20