Virtual Environments For Software Development
Overview
Teaching: 30 min
Exercises: 0 minQuestions
What are virtual environments in software development and why you should use them?
How can we manage Python virtual environments and external (third-party) libraries?
Objectives
Set up a Python virtual environment for our software project using
venv
andpip
.Run our software from the command line.
Introduction
So far we have cloned our software project from GitHub and inspected its contents and architecture a bit. We now want to run our code to see what it does - let’s do that from the command line. For the most part of the course we will run our code and interact with Git from the command line. While we will develop and debug our code using the PyCharm IDE and it is possible to use Git from PyCharm too, typing commands in the command line allows you to familiarise yourself and learn it well. A bonus is that this knowledge is transferable to running code in other programming languages and is independent from any IDE you may use in the future.
If you have a little peek into our code
(e.g. run cat inflammation/views.py
from the project root),
you will see the following two lines somewhere at the top.
from matplotlib import pyplot as plt
import numpy as np
This means that our code requires two external libraries
(also called third-party packages or dependencies) -
numpy
and matplotlib
.
Python applications often use external libraries that don’t come as part of the standard Python distribution.
This means that you will have to use a package manager tool to install them on your system.
Applications will also sometimes need a
specific version of an external library
(e.g. because they were written to work with feature, class,
or function that may have been updated in more recent versions),
or a specific version of Python interpreter.
This means that each Python application you work with may require a different setup
and a set of dependencies so it is useful to be able to keep these configurations
separate to avoid confusion between projects.
The solution for this problem is to create a self-contained
virtual environment per project,
which contains a particular version of Python installation
plus a number of additional external libraries.
Virtual environments are not just a feature of Python - most modern programming languages use them to isolate libraries for a specific project and make it easier to develop, run, test and share code with others. Even languages that don’t explicitly have virtual environments have other mechanisms that promote per-project library collections. In this episode, we learn how to set up a virtual environment to develop our code and manage our external dependencies.
Virtual Environments
So what exactly are virtual environments, and why use them?
A Python virtual environment helps us create an isolated working copy of a software project that uses a specific version of Python interpreter together with specific versions of a number of external libraries installed into that virtual environment. Python virtual environments are implemented as directories with a particular structure within software projects, containing links to specified dependencies allowing isolation from other software projects on your machine that may require different versions of Python or external libraries.
As more external libraries are added to your Python project over time, you can add them to its specific virtual environment and avoid a great deal of confusion by having separate (smaller) virtual environments for each project rather than one huge global environment with potential package version clashes. Another big motivator for using virtual environments is that they make sharing your code with others much easier (as we will see shortly). Here are some typical scenarios where the use of virtual environments is highly recommended (almost unavoidable):
- You have an older project that only works under Python 2. You do not have the time to migrate the project to Python 3 or it may not even be possible as some of the third party dependencies are not available under Python 3. You have to start another project under Python 3. The best way to do this on a single machine is to set up two separate Python virtual environments.
- One of your Python 3 projects is locked to use a particular older version of a third party dependency. You cannot use the latest version of the dependency as it breaks things in your project. In a separate branch of your project, you want to try and fix problems introduced by the new version of the dependency without affecting the working version of your project. You need to set up a separate virtual environment for your branch to ‘isolate’ your code while testing the new feature.
You do not have to worry too much about specific versions of external libraries that your project depends on most of the time. Virtual environments also enable you to always use the latest available version without specifying it explicitly. They also enable you to use a specific older version of a package for your project, should you need to.
A Specific Python or Package Version is Only Ever Installed Once
Note that you will not have a separate Python or package installations for each of your projects - they will only ever be installed once on your system but will be referenced from different virtual environments.
Managing Python Virtual Environments
There are several commonly used command line tools for managing Python virtual environments:
venv
, available by default from the standardPython
distribution fromPython 3.3+
virtualenv
, needs to be installed separately but supports bothPython 2.7+
andPython 3.3+
versionspipenv
, created to fix certain shortcomings ofvirtualenv
conda
, package and environment management system (also included as part of the Anaconda Python distribution often used by the scientific community)poetry
, a modern Python packaging tool which handles virtual environments automatically
While there are pros and cons for using each of the above,
all will do the job of managing Python virtual environments for you
and it may be a matter of personal preference which one you go for.
In this course, we will use venv
to create and manage our virtual environment
(which is the preferred way for Python 3.3+).
The upside is that venv
virtual environments created from the command line are
also recognised and picked up automatically by PyCharm IDE,
as we will see in the next episode.
Managing External Packages
Part of managing your (virtual) working environment involves
installing, updating and removing external packages on your system.
The Python package manager tool pip
is most commonly used for this -
it interacts and obtains the packages from the central repository called
Python Package Index (PyPI).
pip
can now be used with all Python distributions (including Anaconda).
A Note on Anaconda and
conda
Anaconda is an open source Python distribution commonly used for scientific programming - it conveniently installs Python, package and environment management
conda
, and a number of commonly used scientific computing packages so you do not have to obtain them separately.conda
is an independent command line tool (available separately from the Anaconda distribution too) with dual functionality: (1) it is a package manager that helps you find Python packages from remote package repositories and install them on your system, and (2) it is also a virtual environment manager. So, you can useconda
for both tasks instead of usingvenv
andpip
.
Many Tools for the Job
Installing and managing Python distributions,
external libraries and virtual environments is, well, complex.
There is an abundance of tools for each task,
each with its advantages and disadvantages,
and there are different ways to achieve the same effect
(and even different ways to install the same tool!).
Note that each Python distribution comes with its own version of pip
-
and if you have several Python versions installed you have to be extra careful to
use the correct pip
to manage external packages for that Python version.
venv
and pip
are considered the de facto standards for virtual environment
and package management for Python 3.
However, the advantages of using Anaconda and conda
are that
you get (most of the) packages needed for scientific code development included with the distribution.
If you are only collaborating with others who are also using Anaconda,
you may find that conda
satisfies all your needs.
It is good, however, to be aware of all these tools, and use them accordingly.
As you become more familiar with them you will realise that
equivalent tools work in a similar way even though the command syntax may be different
(and that there are equivalent tools for other programming languages too
to which your knowledge can be ported).
Python Environment Hell
From XKCD (Creative Commons Attribution-NonCommercial 2.5 License)
Let us have a look at how we can create and manage virtual environments from the command line
using venv
and manage packages using pip
.
Creating Virtual Environments Using venv
Creating a virtual environment with venv
is done by executing the following command:
$ python3 -m venv /path/to/new/virtual/environment
where /path/to/new/virtual/environment
is a path to a directory where you want to place it -
conventionally within your software project so they are co-located.
This will create the target directory for the virtual environment
(and any parent directories that don’t exist already).
For our project let’s create a virtual environment called “venv”. First, ensure you are within the project root directory, then:
$ python3 -m venv venv
If you list the contents of the newly created directory “venv”, on a Mac or Linux system (slightly different on Windows as explained below) you should see something like:
$ ls -l venv
total 8
drwxr-xr-x 12 alex staff 384 5 Oct 11:47 bin
drwxr-xr-x 2 alex staff 64 5 Oct 11:47 include
drwxr-xr-x 3 alex staff 96 5 Oct 11:47 lib
-rw-r--r-- 1 alex staff 90 5 Oct 11:47 pyvenv.cfg
So, running the python3 -m venv venv
command created the target directory called “venv”
containing:
pyvenv.cfg
configuration file with a home key pointing to the Python installation from which the command was run,bin
subdirectory (calledScripts
on Windows) containing a symlink of the Python interpreter binary used to create the environment and the standard Python library,lib/pythonX.Y/site-packages
subdirectory (calledLib\site-packages
on Windows) to contain its own independent set of installed Python packages isolated from other projects,- various other configuration and supporting files and subdirectories.
Naming Virtual Environments
What is a good name to use for a virtual environment? Using “venv” or “.venv” as the name for an environment and storing it within the project’s directory seems to be the recommended way - this way when you come across such a subdirectory within a software project, by convention you know it contains its virtual environment details. A slight downside is that all different virtual environments on your machine then use the same name and the current one is determined by the context of the path you are currently located in. A (non-conventional) alternative is to use your project name for the name of the virtual environment, with the downside that there is nothing to indicate that such a directory contains a virtual environment. In our case, we have settled to use the name “venv” instead of “.venv” since it is not a hidden directory and we want it to be displayed by the command line when listing directory contents (the “.” in its name that would, by convention, make it hidden). In the future, you will decide what naming convention works best for you. Here are some references for each of the naming conventions:
- The Hitchhiker’s Guide to Python notes that “venv” is the general convention used globally
- The Python Documentation indicates that “.venv” is common
- “venv” vs “.venv” discussion
Once you’ve created a virtual environment, you will need to activate it.
On Mac or Linux, it is done as:
$ source venv/bin/activate
(venv) $
On Windows, recall that we have Scripts
directory instead of bin
and activating a virtual environment is done as:
$ source venv/Scripts/activate
(venv) $
Activating the virtual environment will change your command line’s prompt to show what virtual environment you are currently using (indicated by its name in round brackets at the start of the prompt), and modify the environment so that running Python will get you the particular version of Python configured in your virtual environment.
You can verify you are using your virtual environment’s version of Python
by checking the path using the command which
:
(venv) $ which python3
/home/alex/python-intermediate-inflammation/venv/bin/python3
When you’re done working on your project, you can exit the environment with:
(venv) $ deactivate
If you’ve just done the deactivate
,
ensure you reactivate the environment ready for the next part:
$ source venv/bin/activate
(venv) $
Python Within A Virtual Environment
Within a virtual environment, commands
python
andpip
will refer to the version of Python you created the environment with. If you create a virtual environment withpython3 -m venv venv
,python
will refer topython3
andpip
will refer topip3
.On some machines with Python 2 installed,
python
command may refer to the copy of Python 2 installed outside of the virtual environment instead, which can cause confusion. You can always check which version of Python you are using in your virtual environment with the commandwhich python
to be absolutely sure. We continue usingpython3
andpip3
in this material to avoid confusion for those users, but commandspython
andpip
may work for you as expected.
Note that, since our software project is being tracked by Git, the newly created virtual environment will show up in version control - we will see how to handle it using Git in one of the subsequent episodes.
Installing External Packages Using pip
We noticed earlier that our code depends on two external packages/libraries -
numpy
and matplotlib
.
In order for the code to run on your machine,
you need to install these two dependencies into your virtual environment.
To install the latest version of a package with pip
you use pip’s install
command and specify the package’s name, e.g.:
(venv) $ pip3 install numpy
(venv) $ pip3 install matplotlib
or like this to install multiple packages at once for short:
(venv) $ pip3 install numpy matplotlib
How About
python3 -m pip install
?Why are we not using
pip
as an argument topython3
command, in the same way we did withvenv
(i.e.python3 -m venv
)?python3 -m pip install
should be used according to the official Pip documentation; other official documentation still seems to have a mixture of usages. Core Python developer Brett Cannon offers a more detailed explanation of edge cases when the two options may produce different results and recommendspython3 -m pip install
. We kept the old-style command (pip3 install
) as it seems more prevalent among developers at the moment - but it may be a convention that will soon change and certainly something you should consider.
If you run the pip3 install
command on a package that is already installed,
pip
will notice this and do nothing.
To install a specific version of a Python package
give the package name followed by ==
and the version number,
e.g. pip3 install numpy==1.21.1
.
To specify a minimum version of a Python package,
you can do pip3 install numpy>=1.20
.
To upgrade a package to the latest version, e.g. pip3 install --upgrade numpy
.
To display information about a particular installed package do:
(venv) $ pip3 show numpy
Name: numpy
Version: 1.21.2
Summary: NumPy is the fundamental package for array computing with Python.
Home-page: https://www.numpy.org
Author: Travis E. Oliphant et al.
Author-email: None
License: BSD
Location: /Users/alex/work/SSI/Carpentries/python-intermediate-inflammation/inflammation/lib/python3.9/site-packages
Requires:
Required-by: matplotlib
To list all packages installed with pip
(in your current virtual environment):
(venv) $ pip3 list
Package Version
--------------- -------
cycler 0.11.0
fonttools 4.28.1
kiwisolver 1.3.2
matplotlib 3.5.0
numpy 1.21.4
packaging 21.2
Pillow 8.4.0
pip 21.1.3
pyparsing 2.4.7
python-dateutil 2.8.2
setuptools 57.0.0
setuptools-scm 6.3.2
six 1.16.0
tomli 1.2.2
To uninstall a package installed in the virtual environment do: pip3 uninstall package-name
.
You can also supply a list of packages to uninstall at the same time.
Exporting/Importing Virtual Environments Using pip
You are collaborating on a project with a team so, naturally,
you will want to share your environment with your collaborators
so they can easily ‘clone’ your software project with all of its dependencies
and everyone can replicate equivalent virtual environments on their machines.
pip
has a handy way of exporting, saving and sharing virtual environments.
To export your active environment -
use pip3 freeze
command to produce a list of packages installed in the virtual environment.
A common convention is to put this list in a requirements.txt
file:
(venv) $ pip3 freeze > requirements.txt
(venv) $ cat requirements.txt
cycler==0.11.0
fonttools==4.28.1
kiwisolver==1.3.2
matplotlib==3.5.0
numpy==1.21.4
packaging==21.2
Pillow==8.4.0
pyparsing==2.4.7
python-dateutil==2.8.2
setuptools-scm==6.3.2
six==1.16.0
tomli==1.2.2
The first of the above commands will create a requirements.txt
file in your current directory.
Yours may look a little different,
depending on the version of the packages you have installed,
as well as any differences in the packages that they themselves use.
The requirements.txt
file can then be committed to a version control system
(we will see how to do this using Git in one of the following episodes)
and get shipped as part of your software and shared with collaborators and/or users.
They can then replicate your environment
and install all the necessary packages from the project root as follows:
(venv) $ pip3 install -r requirements.txt
As your project grows - you may need to update your environment for a variety of reasons.
For example, one of your project’s dependencies has just released a new version
(dependency version number update),
you need an additional package for data analysis (adding a new dependency)
or you have found a better package and no longer need the older package
(adding a new and removing an old dependency).
What you need to do in this case
(apart from installing the new and removing the packages that are no longer needed
from your virtual environment)
is update the contents of the requirements.txt
file accordingly
by re-issuing pip freeze
command
and propagate the updated requirements.txt
file to your collaborators
via your code sharing platform (e.g. GitHub).
Official Documentation
For a full list of options and commands, consult the official
venv
documentation and the Installing Python Modules withpip
guide. Also check out the guide “Installing packages usingpip
and virtual environments”.
Running Python Scripts From Command Line
Congratulations!
Your environment is now activated and set up
to run our inflammation-analysis.py
script from the command line.
You should already be located in the root of the python-intermediate-inflammation
directory
(if not, please navigate to it from the command line now).
To run the script, type the following command:
(venv) $ python3 inflammation-analysis.py
usage: inflammation-analysis.py [-h] infiles [infiles ...]
inflammation-analysis.py: error: the following arguments are required: infiles
In the above command, we tell the command line two things:
- to find a Python interpreter (in this case, the one that was configured via the virtual environment), and
- to use it to run our script
inflammation-analysis.py
, which resides in the current directory.
As we can see, the Python interpreter ran our script, which threw an error -
inflammation-analysis.py: error: the following arguments are required: infiles
.
It looks like the script expects a list of input files to process,
so this is expected behaviour since we don’t supply any.
We will fix this error in a moment.
Key Points
Virtual environments keep Python versions and dependencies required by different projects separate.
A virtual environment is itself a directory structure.
Use
venv
to create and manage Python virtual environments.Use
pip
to install and manage Python external (third-party) libraries.
pip
allows you to declare all dependencies for a project in a separate file (by convention calledrequirements.txt
) which can be shared with collaborators/users and used to replicate a virtual environment.Use
pip3 freeze > requirements.txt
to take snapshot of your project’s dependencies.Use
pip3 install -r requirements.txt
to replicate someone else’s virtual environment on your machine from therequirements.txt
file.