Isolating Python Environments with pyenv, virtualenv, and virtualenvwrapper

March 2018 · 9 minutes

This guide provides the motivation behind isolating Python environments and the means by which multiple Python versions and Python package versions can be managed effortlessly. Instead of installing all dependencies to, say, /usr/lib/python2.7/site-packages (or wherever your platform’s standard location is), pyenv, virtualenv, and virtualenvwrapper can be used to give each application is own, virtual environment.

Technology

First, a brief overview of the technology that we will be using:

Homebrew

pyenv

virtualenvwrapper

virtualenv

Of note is the order in which the above tools are listed. You can think of each as a shell encasing the tools below it. virtualenv is our core technology, which enables the creation of separate Python package version environments. virtualenvwrapper simplifies the capabilities of virtualenv and consolidates environments into a single location. pyenv allows the Python version install to be changed effortlessly. Homebrew is used to manage our global (or system-level) installation of Python and Python packages.

Installation

Install Python2 and Python3:

This section has been changed to reflect how Homebrew now handles Python installations. For more information, read this article created by the Homebrew developers.

First, let’s update brew:

$ brew update

then install Python 2 and Python 3:

$ brew install python2 python3

Confirm install:

$ python2 -V
Python 2.7.15
$ which python2
/usr/local/bin/python2

$ python3 -V
Python 3.7.2
$ which python3
/usr/local/bin/python3

Note: Your versions may vary from those listed above. This is fine.

Note: Homebrew installs packages to their own directory and then symlinks their files into /usr/local/bin. macOS comes pre-packaged with Python which is located at /usr/bin/python. We will not be using this installation of Python at all in this setup. Our Homebrew installation of Python 2 and Python 3 will serve as our global installation.

Install pip

As of Homebrew (1.2.4), python2 and python3 install pip2 and pip3, respectively. I prefer to use these installations to install Python packages in order to keep the global install space uncluttered. This allows the Homebrew Python 2 and Python 3 installations to be the global authority. However, if you wish to use a global pip installation tied to your default Python installation—which is pre-installed on your Mac—execute sudo easy_install pip to install pip globally.

Confirm install:

$ pip -V
pip 19.0.2 from /usr/local/lib/python2.7/site-packages/pip (python 2.7)
$ which pip
/usr/local/bin/pip

$ pip2 -V
pip 19.0.2 from /usr/local/lib/python2.7/site-packages/pip (python 2.7)
$ which pip2
/usr/local/bin/pip2

$ pip3 -V
pip 19.0.2 from /usr/local/lib/python3.7/site-packages/pip (python 3.7)
$ which pip3
/usr/local/bin/pip3

Any pip packages will be installed to /usr/local/lib/python2.7/site-packages and /usr/local/lib/python3.6/site-packages respectively depending on the Python version.

Our installation of pip2 and pip3 will serve as our global installation.

Note: pip and pip2 are, for all intents and purposed, the same binary and can be used interchangeably. Going forward, we will use pip.

Install virtualenv and virtualenvwrapper

$ pip install virtualenv virtualenvwrapper

Confirm install:

$ pip list --format freeze | grep virtualenv
virtualenv==16.4.0
virtualenv-clone==0.5.1
virtualenvwrapper==4.8.4

Configure virtualenv

Create a directory in your $HOME directory for virtual environments:

$ mkdir ~/.virtualenvs

Add the following lines to your .bashrc, .zshrc, or .bash_profile per your preference and shell:

export WORKON_HOME=$HOME/.virtualenvs
export VIRTUALENVWRAPPER_PYTHON=/usr/local/bin/python2
export VIRTUALENVWRAPPER_VIRTUALENV=/usr/local/bin/virtualenv
source /usr/local/bin/virtualenvwrapper.sh

Note: This will tell virtualenvwrapper to use the Homebrew installation of Python 2 and virtualenv. If you do not specify VIRTUALENVWRAPPER_PYTHON and VIRTUALENVWRAPPER_VIRTUALENV, you will need to install virtualenv and virtualenvwrapper in each environment you plan to invoke virtualenvwrapper commands (e.g. mkvirtualenv).

Restart your shell (in this case I am using zsh):

$ exec zsh

Alternatively, you can use exec bash if you are using a bash shell.

Note: You should see output from the virtualenvwrapper.sh script similar to the following:

$ exec zsh
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/premkproject
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/postmkproject
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/initialize
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/premkvirtualenv
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/postmkvirtualenv
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/prermvirtualenv
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/postrmvirtualenv
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/predeactivate
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/postdeactivate
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/preactivate
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/postactivate
virtualenvwrapper.user_scripts creating /Users/<username>/.virtualenvs/get_env_details

Create a virtual environment

Use the mkvirtualenv to create a new virtual environment:

$ mkvirtualenv myenv
New python executable in /Users/<username>/.virtualenvs/myenv/bin/python2.7
Also creating executable in /Users/<username>/.virtualenvs/myenv/bin/python
Installing setuptools, pip, wheel...
done.
$ (myenv)

To switch between virtual environments:

$ workon <virtual_environment>
$ (virtual_environment)

To exit a virtual environment:

$ deactivate
$

Now when a virtualenv is activated all the Python packages that you install without using sudo will be installed inside the virtualenv site-packages directory in ~/.virtualenvs.

Congratulations! You are now well on your way to developing with virtual environments. However, we still need to install pyenv in order to quickly switch between Python versions similar to how we have done with virtualenv and virtualenvwrapper.

Install pyenv and pyenv-virtualenvwrapper

$ brew install pyenv pyenv-virtualenvwrapper

Confirm install:

$ pyenv --version
pyenv 1.2.9

$ pyenv-virtualenvwrapper --version
pyenv-virtualenvwrapper 20140609 (virtualenvwrapper 4.8.4)

Configure pyenv

Install the Python versions you wish to use:

$ pyenv install 2.7.8
$ pyenv install 2.7.15
$ pyenv install 3.7.2

Note: This may take a few minutes.

Note: For work, I need to use Python 2.7.8. This version is completely optional, however Python 2.7.15 and 3.7.2 are the most up-to-date Python installations at the time of this writing and it is nice to have these versions at your disposal.

If you received the following error:

ERROR: The Python ssl extension was not compiled. Missing the OpenSSL lib?

You may need to tell the compiler where the openssl package is located:

CFLAGS="-I$(brew --prefix openssl)/include" \
LDFLAGS="-L$(brew --prefix openssl)/lib" \
pyenv install -v 2.7.8

Check out the pyenv Wiki for common build problems.

Note: When running Mojave or higher (10.14+) you will also need to install the additional SDK headers. You can also check under /Library/Developer/CommandLineTools/Packages/ as some versions of macOS will have the .pkg already installed.

sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /

Next, add the following lines to your .bashrc, .zshrc, or .bash_profile per your preference and shell:

# set up pyenv
eval "$(pyenv init -)"

python2.latest() {
  pyenv shell 2.7.15
  pyenv virtualenvwrapper
}

python3.latest() {
  pyenv shell 3.7.2
  pyenv virtualenvwrapper
}

# default to Python 2.7.15
python2.latest

Restart your shell (in this case I am using zsh):

$ exec zsh

Alternatively, you can use exec bash if you are using a bash shell.

Understanding shims

Notice, you are now using a version of Python provided by pyenv through the use of shims:

$ which python
/Users/<username>/.pyenv/shims/python

pyenv works by inserting a directory of shims at the front of your PATH environment variable:

$(pyenv root)/shims:/usr/local/bin:/usr/bin:/bin

In this way, you can switch between Python installations using the following commands:

$ python2.latest
$ python -V
Python 2.7.15

$ python3.latest
$ python -V
Python 3.7.2

Now, let’s reiterate what we just did. First, we installed python2 and python3 using Homebrew to take the place of our global Python installation. Next, we allowed for isolated Python package environments using virtualenv and virtualenvwrapper. Finally, we diverted our system-wide Python installation to specific Python versions using pyenv. Now that we have our system set up, let’s test it.

Note: Removing eval "$(pyenv init -)" and subsequent lines from your zsh or bash configuration file should revert your system back to the system-wide installation of Python installed via Homebrew.

Test your virtual environment configuration

If you comment out the # set up pyenv section of your zsh or bash configuration file, you should revert your system back to the system-wide installation of Python installed via Homebrew.

# set up pyenv
# eval "$(pyenv init -)"
#
# python2.latest() {
#   pyenv shell 2.7.15
#   pyenv virtualenvwrapper
# }
#
# python3.latest() {
#   pyenv shell 3.7.2
#   pyenv virtualenvwrapper
# }
#
# default to Python 2.7.15
# python2.latest
exec zsh
# global Python install of version 2.7.15 via Homebrew
$ python2 -V
Python 2.7.15
$ which python2
/usr/local/bin/python2

# global Python install of version 3.7.2 via Homebrew
$ python3 -V
Python 3.7.2
$ which python3
/usr/local/bin/python3

Now, let’s reapply our pyenv configuration and restart our shell.

Uncomment the # set up pyenv section of your zsh or bash configuration file:

# set up pyenv
eval "$(pyenv init -)"

python2.latest() {
  pyenv shell 2.7.15
  pyenv virtualenvwrapper
}

python3.latest() {
  pyenv shell 3.7.2
  pyenv virtualenvwrapper
}

# default to Python 2.7.15
python2.latest
$ exec zsh
# apply the Python 2.7.15 pyenv shell
$ python2.latest
$ python -V
Python 2.7.15
$ which python
/Users/nkraus/.pyenv/shims/python

# apply the Python 3.7.2 pyenv shell
$ python3.latest
$ python -V
Python 3.7.2
$ which python
/Users/nkraus/.pyenv/shims/python

We find that our Python installations are pinned to the installations installed via pyenv. We can now create virtual environments using each of these Python installations:

$ python2.latest
$ mkvirtualenv python2
...
$ python -V
Python 2.7.15

$ deactivate

$ python3.latest
$ mkvirtualenv python3
...
$ python -V
Python 3.7.2

$ deactivate

Done! You have successfully configured your development environment using pyenv, virtualenv, and virtualenvwrapper in order to isolate Python environments.

Update - 2018-11-08

Hitting this error?

mkvirtualenv:78: /usr/local/bin/virtualenv: bad interpreter: /usr/local/opt/python/bin/python2.7: no such file or directory

This error is due to the fact that virtualenv uses the absolute path of the Python 2 installation (#!/usr/local/opt/python/bin/python2.7). As of March 1st, 2018, Homebrew updated the python formula to use Python 3:

On 1st March 2018 the python formula will be upgraded to Python 3.x and a python@2 formula will be added for installing Python 2.7 (although this will be keg-only so neither python nor python2 will be added to the PATH by default without a manual brew link --force). We will maintain python2, python3 and python@3 aliases. Any formulae that use depends_on “python” outside Homebrew/core will need to be updated at this point if they wish to keep using Python 2. Note: macOS has provided Python 2.7 since OS X Lion (10.7) so you can update formulae that need Python 2 today by removing depends_on “python” so they use the system Python instead.

To remedy this change, virtualenv changed the path of the Python 2 installation to use the python@2 formula (#!/usr/local/opt/python@2/bin/python2.7).

To remedy this issue, upgrade the virtualenv and virtualenvwrapper Python packages for the Python 2 installation installed via Homebrew:

$ which python
/usr/local/bin/python
$ pip install --upgrade virtualenv virtualenvwrapper