Motivation:
The start of a new year is a good (albeit, relatively arbitrary) time to reassess aspects of your workflow.
I, like many people, taught myself Python by jumping into different projects. The consequence of this ad-hoc learning was that I did not learn some of the fundamentals until much later in my project development.
At the end of the Fall ’23 semester, I found myself spending a lot of time cleaning up repositories and modules that I had constructed in the preceding months. I ended up restructuring and reorganizing significant portions of the code base, implementing organizational practices that I had learned after it’s conception.
This post is intended to save the reader from making the same mistake. Here, I present a recommended structure for new Python projects, and discuss the main components. This is largely targeted at Python users who have not had a formal Python training, or who are working with their first significantly sized project.
I provide an example_python_project, hosted on GitHub, as a demonstration and to serve as a template for beginners.
Content:
- Recommended structure
- Example project repository
- Project components (with example project)
- Modules, packages, __init__.py
- Executable
- README
- Documentation
- Tests
- Requirements
- LICENSE
- Conclusion
Recommended project structure
I’ll begin by presenting a recommended project structure. Further down, I provide some explanation and justification for this structure.
My example_python_project follows recommendations from Kenneth Reitz, co-author of The Hitchhiker’s Guide to Pythton (1), while also drawing from a similar demo-project, samplemod, by Navdeep Gill (2).
The project folder follows this structure:
example_python_project/
├── sample_package/
│ ├── subpackage/
│ │ ├── __init__.py
│ │ └── subpackage_module.py
│ ├── __init__.py
│ ├── helpers.py
│ └── module.py
├── docs/
│ └── documentation.md
├── tests/
│ ├── __init__.py
│ └── basic_test.py
├── main.py
├── README.md
├── requirements.txt
└── LICENSE
If you are just starting a project, it may seem unnecessary complex to begin with so much modularity. It may seem easier to open a .py file and start freewheeling. Here, I am trying to highlight the several reasons why it is important to take care when initially constructing a Python project. Some of these reasons include:
- Maintenance: A well-structured project makes it easier to understand the code, fix bugs, and add new features. This is especially important as the project grows in size and complexity.
- Collaboration: When working on a project with multiple developers, a clear structure makes it easier for everyone to understand how the code is organized and how different components interact with each other.
- Scalability: A well-structured project allows to scale up the codebase, adding new features and sub-components, without making the codebase hard to understand or maintain.
- Testing: A well-structured project makes it easier to write automated tests for the code. This helps to ensure that changes to the code do not break existing functionality.
- Distribution: A well-structured project makes it easier to distribute the code as a package. This allows others to easily install and use the code in their own projects.
Overall, taking the time to structure a Python project when starting can save a lot of time and heartache in the long run, by making the project easier to understand, maintain, and expand.
Example Project Repository
The repository containing this example project is available on GitHub here: example_python_project.
The project follows the recommended project structure above, and is designed to use modular functions from the module, helpers, and subpackage_module. It is intended to be a skeleton upon which you can build-up your own project.
If you would like to experiment with your own copy of the code, you can fork a copy of the repository, or Download a ZIP version.
Project overview
The project is a silly riddle program with no real usefulness other than forming the structure of the project. The bulk of the work is done in the main_module_function() which first prints a riddle on the screen, then iteratively uses the helper_function() and subpackage_function() to try and “solve” the riddle. Both of these functions simply return a random True/False, and are repeatedly called until the riddle is solved (when status == True).
Below is a visual representation of how the different functions are interacting. The green-box functions are contained within the main sample_package, while the blue-box function is stored in the subpackage.
The program can then be executed from a command line using the main.py executable:
C:\<your-local-directory>\example_python_project> python main.py
The output will first print out the riddle, then print statements indicating which functions are being used to “solve” the riddle. This is simply a means of demonstrating how the different functions are being activated, and not necessarily a recommended “Best Practice”.
A normal output should resemble something similar to the below, although there may be more or less print statements depending upon how many times it takes the random generator to produce a “True” solution:
Here is a riddle, maybe `sample_package` can help solve it:
What runs but has no feet, roars but has no mouth?
Lets see if the helper can solve the riddle.
The helper_function is helping!
The helper could not solve it.
Maybe the subpackage_module can help.
The subpackage_function is being used now.
The subpackage solved it, the answer is "A River"!
Project components
Modules, packages, __init__.py, oh my!
Before going any further, I want to take time to clarify some vocabulary which is helpful for understanding component interactions.
Module:
A module is simply a file ending in.py, which contains functions and or variables.Package:
A package is a collection of modules (.pyfiles) which relate to one another, and which contains an__init__.pyfile.
__init__.py
Inclusion of a__init__.pyfile (pronounced “dunder in-it”) within a folder will indicate to Python that the folder is a package. Often, the__init__module is empty, however it can be used to import other modules, or functions which will then be stored in namespace, making it available for use later.
For example, in my sample_package/__init__.py, I import all contents of the module.py and subpackage_module.py:
# Import the all functions from main and sub modules
from .module import *
from .subpackage.subpackage_module import *
This allows all of the functions stored within module to be callable from the primary sample_package directly, rather than specifying the various sub-structures needed to access various functions. For example, by including from .subpackage.subpackage_module import *, I able to run:
# IF __init__ imports all content from main and sub modules then you can do this:
import sample_package
sample_package.subpackage_module_function()
Rather than requiring the following fully-nested call, which is necessary when the __init__.py is empty:
# IF __init__ is EMPTY, then you need to do this:
import sample_package
sample_package.subpackage.subpackage_module.subpackage_module_function()
Notably, an __init__.py is not necessary to use modules and functions within a folder… however, customizing the imports present in the packages __init__.py will provide increased customization to your projects use. As the project increases in complexity, strategic usage of imports within the __init__ can keep your main executable functions cleaner.
Executables
So, you’ve crafted a Python project with a sleek, modular package design. The next step is to setup a single file which will execute the package.
Inclusion of a single executable has the benefit of providing a single-entry point for other users who want to run the program without getting lost in the project.
In the example_python_project, this is done with main.py:
# Import the main package
import sample_package
def run():
solved = sample_package.main_module_function()
return solved
# Run the function if this is the main file executed
if __name__ == "__main__":
run()
The program then can then be executed from a command line:
C:\<your-local-directory\example_python_project> python run_program.py
README
The README.md file is typically someone’s first encounter with your project. This is particularly true if the project is hosted on GitHub, where the README.md is used as the home-page of a repository.
A README.md file should include, at minimum, a brief description of the project, it’s purpose, and clear instructions on how to use the code.
Often, README files are written in Markdown, which includes simple text-formatting options. You can find a basic Markdown Cheat Sheet here. Although reStructuredText is often used, and even .txt files may be suitable.
Documentation
Great code requires great documentation. Initializing a new project with a dedicated docs/ folder may help hold you accountable for documenting the code along the way.
For information on how to use Sphinx and reStructuredText to create clean webpage-based documentation, you can see Rohini Gupta’s post on Using Python, Sphinx, and reStructuredText to Create a Book (and Introducing our eBook: Addressing Uncertainty in Multisector Dynamics Research!).
Tests
Bugs aren’t fun. They are even less fun when a code was bug-free yesterday but contains bugs today. Implementing automated tests in your project can help verify functionality throughout the development process and catch bugs when they may arise.
It is recommended to implement Unit Tests which verify individual components of the project. These tests should assert that function output properties align with expectations. As you develop your project in a modular way, you can go in and progressively add consecutive tests, then run all of the tests before sharing or pushing the project to others.
A standard Python instillation comes with the unittest package, which is intended to provide a framework for these tests. I provide an example test below, but deeper-dive into the unittest framework may require a dedicated future posts.
In the example_python_project, I include the basic_test.py to verify that the solution generated by main_module_function() is True using the unittest package:
import sample_package
import unittest
# Define a test suite targeting specific functionality
class BasicTestSuite(unittest.TestCase):
"""Basic test cases."""
def test_that_riddle_is_solved(self):
solved = sample_package.module.main_module_function()
self.assertTrue(solved)
if __name__ == '__main__':
unittest.main()
Running the basic_test module from the command line produce an “OK” if everything runs smoothly, otherwise will provide information regarding which tests are failing.
----------------------------------------------------------------------
Ran 1 test in 0.004s
OK
Currently, the example_python_project requires the basic_test module to be executed manually. To learn more about automating this process, you can see Andrew Dirck’s 2020 post: Automate unit testing with Github Actions for research codes.
Requirements
The requirements.txt is a simple text file which lists the dependencies, or necessary packages that are required to run the code.
This can be particularly important if your code requires a specific version of a package, since the package verison can be specified in the requirements.txt. Specifying a particular package version (e.g., numpy==1.24.1) can improve the reliability of your code, since different versions of these packages may operate in different ways in the future.
Here is an example of what might be inside a requirements.txt, if the numpy and random packages are necessary:
numpy==1.24.1
random==3.11.1
Users can easily install all the packages listed in requirements.txt using the command:
pip install -r requirements.txt
License
I’ll keep this section brief, since I am far from legally qualified to comment much on Licensing. However, general advice seems to suggest that if you are sharing code publicly, safest to include a license of some sort.
Inclusion of an open-source license allows other users to comfortably use and modify your code for their own purposes, allowing you to contribute and benefit the broader community. At the same time, protecting the original author from future liabilities associated with its use by others.
The GNU General Public License is the most common open-source license, however if you would like to know more about the different options, you can find some guidance here: https://choosealicense.com/
Conclusions
If you are an experienced Python user, there may not be anything new for you here but at the least I hope it serves as a reminder to take care in your project design this year.
Additionally, this is likely to be one part in a multi-part Introduction to Python series that I will be writing for future members of our research group. With that in mind, check back here later this spring for the subsequent parts if that interests you.
Best of luck!
References
(1) Reitz, K., & Schlusser, T. (2016). The Hitchhiker’s guide to Python: best practices for development. ” O’Reilly Media, Inc.”.
(2) Navdeep Gill. 2019. samplemod. https://github.com/navdeep-G/samplemod. (2023).
Source: 
Water Programming: A Collaborative Research Blog 