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Beginner's Guide: creating clean Python development environments

Introduction

Code interacts with its environment. For example, you can only run a Python script if you have Python installed on the system. Furthermore, a Python script will only run without raising ImportError exceptions if all the required packages are installed.

It therefore becomes important for you as a developer / computational scientist to understand and control the environment in which your code operates.

In this post I will illustrate a work flow for creating clean Python development environments.

Example: developing a Python package

In the previous post I illustrated how you could use a static code generator (cookiecutter) to create a basic template to develop a Python package.

Now suppose that we wanted to develop a Python package named “awesome”. Let us use a GitHub hosted Cookiecutter template to create a basic project layout.

$ cookiecutter gh:tjelvar-olsson/cookiecutter-pypackage
Cloning into 'cookiecutter-pypackage'...
remote: Counting objects: 48, done.
remote: Compressing objects: 100% (37/37), done.
remote: Total 48 (delta 13), reused 37 (delta 8), pack-reused 0
Unpacking objects: 100% (48/48), done.
Checking connectivity... done.
repo_name (default is "mypackage")? awesome
version (default is "0.0.1")? 
authors (default is "Tjelvar Olsson")?

This creates the directory awesome.

$ cd awesome/

With a number of files and directories in it.

$ tree
.
├── README.rst
├── awesome
│   └── __init__.py
├── docs
│   ├── Makefile
│   ├── make.bat
│   └── source
│       ├── README.rst
│       ├── conf.py
│       └── index.rst
├── setup.cfg
├── setup.py
└── tests
    ├── __init__.py
    └── tests.py

4 directories, 11 files

You may notice that there are some tests included by default. Let us try to run them.

$ python tests/tests.py
EE
======================================================================
ERROR: test_can_import_package (__main__.UnitTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "tests/tests.py", line 15, in test_can_import_package
    import awesome
ImportError: No module named awesome

======================================================================
ERROR: test_package_has_version_string (__main__.UnitTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "tests/tests.py", line 18, in test_package_has_version_string
    import awesome
ImportError: No module named awesome

----------------------------------------------------------------------
Ran 2 tests in 0.001s

FAILED (errors=2)

That’s not very good! What is going on? It seems that we cannot import the awesome module.

Depending on your level of familiarity with Python the problem may be obvious to you. However, when I started out with Python this caused me a lot of confusion. I clearly could import the awesome module!

$ python -c "import awesome; print(awesome.__version__)"
0.0.1

One of the places where Python looks for modules is within the directory of the calling script, which is why the command above works. However, when we run the tests/tests.py script there is no awesome package to be found within the tests directory, illustrated below.

$ cd tests/
$ python -c "import awesome; print(awesome.__version__)"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named awesome
$ cd ../

At this point one could start manually configuring the PYTHONPATH environment variable. However, let us look at a more elegant solution.

Making use of setuptools

In the previous post we started building up a basic setup.py file, which made use of the setuptools module.

You are probably already familiar with setuptools from installing other Python packages using the command python setup.py install. This installs the package of interest into your Python distribution’s site-packages directory.

However, this is not what we want to do because the package would be copied there and any changes that we made to our local development files would not take effect until we reinstalled the package. We want to be able to edit our local development files and see the effects take place immediately.

The solution to this problem is to use python setup.py develop which creates an .egg-link to our local development directory in the site-packages directory.

$ sudo python setup.py develop
Password:
running develop
...
Processing dependencies for awesome==0.0.1
Finished processing dependencies for awesome==0.0.1

Let us re-run the tests now that site-packages contains an awesome.egg-link.

$ python tests/tests.py 
..
----------------------------------------------------------------------
Ran 2 tests in 0.000s

OK

Great, we have a working development environment!

Before continuing let us square the circle by removing the development package we just installed.

$ sudo python setup.py develop --uninstall
Password:
running develop
...
Removing awesome 0.0.1 from easy-install.pth file

So far so good, but there are two issues with what we are currently doing. First of all we need to have root permissions to run python setup.py develop and python setup.py develop --uninstall when using the system’s Python. Secondly, when using the system’s Python we are using a (potentially) polluted environment.

Let me expand on the second issue. Suppose that you had the PyYAML package installed in your system’s Python. It is a very useful package, but it is not part of Python’s standard library. Suppose further that your package needed to be able to parse YAML files. You therefore start using PyYAML. Some time later you want to share your code with your friend Alice. You run your tests, of course you are writing tests as you go along, and they all pass. You feel happy and send the package Alice. However, Alice has not yet installed the PyYAML package and consequently her first experience of your code is an ImportError.

This ImportError could have been avoided by adding pyyaml as a requirement to our setup.py file. For more details see the “Specifying Dependencies” section in Scott Torborg’s How To Package Your Python Code.

However, the question is how could we have detected this issue before sending our code to Alice?

Creating a virtual Python development environment

There is a way to avoid making use of the system’s “polluted” Python, which also lets us work without requiring root privileges. When I first heard about this it sounded like magic.

The solution is to make use of virtualenv. From the virtualenv website:

virtualenv is a tool for creating isolated Python environments.

Let us install virtualenv using pip.

$ pip install virtualenv

Now we can create a virtual environment for our project. However, before we do that let me give you a tip: create a separate directory for storing all your virtual environments and give each virtual environment a descriptive name.

$ mkdir ~/virtualenvs

If you are anything like me you will end up having at least one virtual environment for each project you are working on.

$ virtualenv ~/virtualenvs/awesome
New python executable in /home/tjelvar/virtualenvs/awesome/bin/python
Installing setuptools, pip...done.

Note that this creates a directory named awesome in the ~/virtualenvs directory. You could have named it anything, but I like to use the same name as the project for which I intend to use the virtual environment. The ~/virtualenvs/awesome directory contains the virtual environment.

To make use of a virtual environment we need to “activate” it. This is done by sourcing the activate script in the bin directory of the virtual environment.

To get a feel for the effect of activating the virtual environment let us use which to find the path to python before and after we activate the virtual environment.

$ which python
/usr/bin/python

Now let us activate the virtual environment we just created.

$ source ~/virtualenvs/awesome/bin/activate
(awesome)$ which python
/home/tjelvar/virtualenvs/awesome/bin/python

When we source the activate script above it basically alters the PATH and PS1 environment variables. It also defines a deactivate function that one can use to reset the environment variables to their original state.

(awesome)$ deactivate
$ which python
/usr/bin/python

Tying it all together

That was a lot of pre-amble to be able to show a simple and effective work flow for setting up clean Python development environments.

Generate a new Python project template.

$ cookiecutter gh:tjelvar-olsson/cookiecutter-pypackage
...
repo_name (default is "mypackage")? awesome
...
$ cd awesome

Create a virtual environment for the project.

$ virtualenv ~/virtualenvs/awesome

Activate the virtual environment and use setuptools to create a development environment.

$ source ~/virtualenvs/awesome/bin/activate
(awesome)$ python setup.py develop

Run the tests!

Tests are great, they let us know that things are working as intended. Let us make sure that our setup is sound.

(awesome)$ python tests/tests.py
..
----------------------------------------------------------------------
Ran 2 tests in 0.000s

OK

Discussion

In this post I have shown you how to use setuptools and virtualenv to create reproducible, clean and isolated Python development environments.

However, the work flow is not limited to development environments. It is just as applicable to production environments and it is extensively used in the Python web development community. In fact, having the same work flow for setting up your development and production environments is a great bonus as it gives you more confidence in the end product.