How To Manage Multiple Versions of Python on a Mac

Summary

It’s easy to install multiple versions of python on a Mac computer using installers from python.org, Homebrew, Conda, or other sources. This could create conflicts if a user wants to run one version of python but bash calls a different version instead.

This is guide will show you how to:

  • modify your bash profile to change which version of python is called by bash first.
  • use virtual environments to specify a version of python that will run a project.
  • uninstall specific versions of python.

Warnings


Mac OS needs python

DO NOT remove any versions of Python found in the following folders:

  • /usr/bin
  • system/Library

These versions of Python—which should be Python 2.7—are installed by Apple and used by Mac OS and other software to perform some functions. Deleting Python from these directories will break Mac OS and force you to reinstall it on your computer.

Other projects may need specific versions of python

You may have a python project or you may use python packages that require particular versions of Python. Uninstalling those versions would prevent those projects or packages from working until that version of python is reinstalled. For example, Python 3 is a dependency of Numpy; if you uninstalled Python 3, then Numpy wouldn’t work until you reinstalled Python 3.


Installation

Three common methods of installing python can be found here:

python.org

The python.org (python.org) installer can be found here.


Homebrew

First install Homebrew. The instructions are here, or enter the following command:

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"


To install Python 3:

brew install python

To install Python 2:

brew install python@2


Anaconda

Anaconda is generally used for scientific and machine learning applications.

For Ananconda follow installation instructions here.


Miniconda is a stripped down version of Anaconda.

For Miniconda follow installation instructions here.



PATH and .bash_profile

PATH

The path is a list of directories that your shell will look through when you execute a command. You can display the path on your computer using the echo $PATH command:

$ echo $PATH

/Library/Frameworks/Python.framework/Versions/3.7/bin:/Users/username/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/username/miniconda2/bin:/Users/username/miniconda3/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/X11/bin:/usr/local/git/bin

The directories above are separated by a colon, this is what they look like displayed in sequence:

  • /Library/Frameworks/Python.framework/Versions/3.7/bin
  • /Users/username/anaconda3/bin
  • /Library/Frameworks/Python.framework/Versions/2.7/bin
  • /Users/username/miniconda2/bin
  • /Users/username/miniconda3/bin
  • /Library/Frameworks/Python.framework/Versions/3.6/bin
  • /usr/local/bin
  • /usr/bin
  • /bin
  • /usr/sbin
  • /sbin
  • /usr/texbin
  • /opt/X11/bin
  • /usr/X11/bin
  • /usr/local/git/bin

When you ask your shell to run a particular command or run an interpreter, python for example, the shell looks through the different directories listed in the PATH in order they’re presented above. When the shell finds that command, it stops and calls it even if there is another version of the same command, with the same name, further down in the list.

.bash_profile

The bash profile is a set of instructions that are run by the shell when the user logs in to bash. You can add a variety of preferences to the bash profile, including modifications to the PATH. When anaconda, miniconda or other versions of python are installed they automatically add paths to their respective versions of python to the top of the bash profile.

Bash reads the bash profile in sequential order — from top to bottom — and adds those paths to the PATH in the order that they’re read. This means that the last path at the bottom of the bash profile will end up as the first path in the PATH. This means that if you have Python 3.6 installed on your computer, and then decide to add python 3.7, but keep 3.6, the installer will add Python 3.7 to the top of the bash profile but it will end up after python 3.6 in the PATH. Entering python3 in bash will call python 3.6, not 3.7.

If that was confusing compare the order that the python paths are added to my bash profile below to the PATH listed above. You’ll notice that their respective orders are opposite from each other.


Enter the following command to open the bash profile in TextEdit:

$ open ~/.bash_profile

My .bash_profile currently looks like this:

# Setting PATH for Python 3.6
# The original version is saved in .bash_profile.pysave
PATH="/Library/Frameworks/Python.framework/Versions/3.6/bin:${PATH}"
export PATH

# added by Miniconda3 installer
export PATH="/Users/username/miniconda3/bin:$PATH"

# added by Miniconda2 installer
export PATH="/Users/username/miniconda2/bin:$PATH"

# Setting PATH for Python 2.7
# The original version is saved in .bash_profile.pysave
PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"
export PATH

# added by Anaconda3 installer
export PATH="/Users/username/anaconda3/bin:$PATH"

# Setting PATH for Python 3.7
# The original version is saved in .bash_profile.pysave
PATH="/Library/Frameworks/Python.framework/Versions/3.7/bin:${PATH}"
export PATH

If you want to keep all of your installed versions of python, but want bash to open a different version first, just copy and paste it to the bottom of the bash profile. If you don’t want bash to run a particular version of python then delete it from bash profile and uninstall that version by following the instructions further down.

Don’t forget to save the bash profile before closing TextEdit. You also have to reload the bash profile in bash before any changes take effect. Just enter one of the following commands:

  • source ~/.bash_profile
  • . ~/.bash_profile

Homebrew - pyenv

Pyenv is a Homebrew package that allows a user to install multiple versions of python in Homebrew and specify which version of python they’d like to run.

Install pyenv:

$ brew install pyenv

Install different versions of python:

$ pyenv install 3.5.0
$ pyenv install 3.6.0

Show which versions of python are installed:

$ pyenv versions

* system (set by /Users/username/Programming/python/.python-version)
  3.5.0
  3.6.0

The asterisk indicates that the system version of python is active, but 3.5.0 and 3.6.0 are also installed.


Pyenv Local

Create a folder called PythonLocalProject, then display the version of python called by bash by entering python -V:

$ python -V
Python 3.6.5 :: Anaconda, Inc.

Now enter:

$ pyenv local 3.5.0

This creates a .python-version file which tells pyenv which version of python to run in that directory.

Entering ls -la shows us that file:

$ ls -la
total 8
drwxr-xr-x  3 username  staff   96 Aug  3 11:52 .
drwxr-xr-x  4 username  staff  128 Aug  3 11:56 ..
-rw-r--r--  1 username  staff    6 Aug  3 12:03 .python-version

Now enter pyenv versions:

$ pyenv versions
  system
* 3.5.0 (set by /Users/username/Programming/python/pythonproject/.python-version)
  3.6.0

And running this command shows which version of python is called by pyenv:

$ python -V
Python 3.5.0

To change pyenv to the system version of version 3.6.0 enter:

$ pyenv local system
$ pyenv local 3.6.0

This procedure is fine, you can set a version of python to run in a particular folder. But what if you want to use pyenv to set a global version of python.


Pyenv Global

Pyenv gives these instructions when you enter pyenv init in bash:

$ pyenv init

# Load pyenv automatically by appending
# the following to ~/.bash_profile:

eval "$(pyenv init -)"


Open the bash profile:

  • open ~/.bash_profile

Add this text to the bottom of the file:

  • eval "$(pyenv init -)"

Save the file and then enter:

  • source ~/.bash_profile


Entering echo $PATH will show that a pyenv shim has been added to the beginnning of the path:

  • /Users/username/.pyenv/shims:

And which python will return:

  • /Users/username/.pyenv/shims/python

This means that bash will run the version of python set by pyenv.


Navigate to a folder that doesn’t have a .python-version file and enter:

$ pyenv global 3.6.0
Python 3.6.0

This shows us that the global version of python is 3.6.0 and it is set by pyenv.

So this shows that bash will run whichever version of python that is set in pyenv.


If you navigate back to the PythonLocalProject folder with the .python-version file and run python -V you will notice that it doesn’t run the global version of python, it runs whichever version was last set with the pyenv local command.


Locate Python


We can use the which command to identify where specific versions of python are located:

$ which -a python
/Users/username/.pyenv/shims/python
/Users/username/anaconda3/bin/python
/Library/Frameworks/Python.framework/Versions/2.7/bin/python
/Users/username/miniconda2/bin/python
/Users/username/miniconda3/bin/python
/usr/local/bin/python
/usr/bin/python


$ which -a python3
/Users/username/.pyenv/shims/python3
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3
/Users/username/anaconda3/bin/python3
/Users/username/miniconda3/bin/python3
/Library/Frameworks/Python.framework/Versions/3.6/bin/python3
/usr/local/bin/python3

This shows some overlap as some versions of python appear in both searches.

The locations of the anaconda and miniconda versions of python are self explanatory, so are the pyenv installs, the python.org installer places python in the /Library/Frameworks/Python.framework/ directory. Homebrew installs all packages, including python, in /usr/local/Cellar, then Homebrew adds a symlink to /usr/local/binso that it’s version of python can be found in the path. Finally, Apple installs python in /usr/bin. Remember, don’t delete that version.


Uninstall python


Follow these instructions if you want to remove particular versions of python.

python.org

The python.org installer places all it’s installed files in the following folders:

  • The system applications folder, /Applications
  • /Library/Frameworks/Python.framework
  • /usr/local/bin

To delete all versions of python that were installed using the python.org installer, enter these commands in terminal:

sudo rm -rf '/Applications/Python X.Y' #replace X.Y with the version number on the folder
sudo rm -rf /Library/Frameworks/Python.framework
sudo rm -rf /usr/local/bin/python
sudo rm -rf /usr/local/bin/python3

To remove particular versions of python, you have to refer to the particular framework. The frameworks are installed in /Library/Frameworks/Python.framework and particular versions are found in /Library/Frameworks/Python.framework/Versions/X.Y. So for example if you wanted to uninstall only version 3.5 but leave other versions you would enter the following commands in bash:

sudo rm -rf /Library/Frameworks/Python.framework/Versions/3.5
sudo rm -rf '/Applications/Python 3.5'
sudo rm -rf /usr/local/bin/python3


Homebrew

To uninstall python that was installed using homebrew you need to identify what versions of python have been installed by Homebrew:

Enter:

$ brew list | grep 'python'

Currently brew refers to python3 as python and python 2 is called python@2.

To uninstall both python2 and python3 enter the following:

$ brew uninstall -f python python@2 

Homebrew will refuse to uninstall python if it has dependencies, just uninstall python and ignore the dependencies:

brew uninstall --ignore-dependencies python python@2

Or, add the dependencies to the list of items to be uninstalled:

$ brew uninstall -f python python@2 gdal geos libspatialite libxml2 numpy


Troubleshooting

It’s possible to have Homebrew’s Python directory at the beginning of the $PATH but calling python will still start the Apple installed version of Python or some other version. If that’s the case it’s possible that Homebrew’s Python install has become unlinked. This command will unlink and relink Python in Homebrew:

brew unlink python python@2 && brew link python python@2

Uninstall Python from Pyenv

To list versions of python installed using pyenv enter:

$ pyenv versions
* system (set by /Applications/.python-version)
  3.5.0
  3.6.0

To uninstall versions of python installed using pyenv enter:

$ pyenv uninstall 3.5.0
$ pyenv uninstall 3.6.0

Anaconda

The official removal instructions are found here, but deleting anaconda and miniconda is easy.

Anaconda and miniconda are installed in the users home directory: ~/miniconda2, ~/miniconda3,~/anaconda2, or ~/anaconda3

Depending on which version or versions you have, just enter the following commands:

rm -rf ~/anaconda2
rm -rf ~/anaconda3
rm -rf ~/miniconda2
rm -rf ~/miniconda3

Anaconda and miniconda also use several invisible files. Delete them by entering this command:

rm -rf ~/.condarc ~/.conda ~/.continuum


XKCD

And now for something completely different.

The Python Environment